Build branch add-agat-convert-spgff2tsv with version add-agat-convert-spgff2tsv (fa5ed70)

Build pipeline: viash-hub.biobox.add-agat-convert-spgff2tsv-t5ds2 Source commit: fa5ed706e5 Source message: add tests
2024-07-31 07:42:13 +00:00
commit 90a16ac646
519 changed files with 303450 additions and 0 deletions
--- a/.gitignore
+++ b/.gitignore
@@ -0,0 +1,18 @@
+*.DS_Store
+*__pycache__
+
+# IDE ignores
+.idea/
+.vscode/
+
+# R specific ignores
+.Rhistory
+.Rproj.user
+*.Rproj
+
+# viash specific ignores
+target/
+
+# nextflow specific ignores
+.nextflow*
+work
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -0,0 +1,135 @@
+# biobox x.x.x
+
+## BREAKING CHANGES
+
+* `star/star_align_reads`: Change all arguments from `--camelCase` to `--snake_case` (PR #62).
+
+* `star/star_genome_generate`: Change all arguments from `--camelCase` to `--snake_case` (PR #62).
+
+## NEW FUNCTIONALITY
+
+* `star/star_align_reads`: Add star solo related arguments (PR #62).
+
+* `bd_rhapsody/bd_rhapsody_make_reference`: Create a reference for the BD Rhapsody pipeline (PR #75).
+
+* `umitools/umitools_dedup`: Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read (PR #54).
+
+* `seqtk`:
+  - `seqtk/seqtk_sample`: Subsamples sequences from FASTA/Q files (PR #68).
+  - `seqtk/seqtk_subseq`: Extract the sequences (complete or subsequence) from the FASTA/FASTQ files
+                based on a provided sequence IDs or region coordinates file (PR #85).
+
+* `agat/agat_convert_sp_gff2gtf`: convert any GTF/GFF file into a proper GTF file (PR #76).
+
+## MINOR CHANGES
+
+* `busco` components: update BUSCO to `5.7.1` (PR #72).
+
+* Update CI to reusable workflow in `viash-io/viash-actions` (PR #86).
+
+## DOCUMENTATION
+
+* Extend the contributing guidelines (PR #82):
+
+  - Update format to Viash 0.9.
+
+  - Descriptions should be formatted in markdown.
+
+  - Add defaults to descriptions, not as a default of the argument.
+
+  - Explain parameter expansion.
+
+  - Mention that the contents of the output of components in tests should be checked.
+
+* Add authorship to existing components (PR #88).
+
+## BUG FIXES
+
+* `pear`: fix component not exiting with the correct exitcode when PEAR fails (PR #70).
+
+* `cutadapt`: fix `--par_quality_cutoff_r2` argument (PR #69).
+
+* `cutadapt`: demultiplexing is now disabled by default. It can be re-enabled by using `demultiplex_mode` (PR #69).
+
+* `multiqc`: update multiple separator to `;` (PR #81).
+
+
+# biobox 0.1.0
+
+## NEW FEATURES
+
+* `arriba`: Detect gene fusions from RNA-seq data (PR #1).
+
+* `fastp`: An ultra-fast all-in-one FASTQ preprocessor (PR #3).
+
+* `busco`: 
+    - `busco/busco_run`: Assess genome assembly and annotation completeness with single copy orthologs (PR #6).
+    - `busco/busco_list_datasets`: Lists available busco datasets (PR #18).
+    - `busco/busco_download_datasets`: Download busco datasets (PR #19).
+
+* `cutadapt`: Remove adapter sequences from high-throughput sequencing reads (PR #7).
+
+* `featurecounts`: Assign sequence reads to genomic features (PR #11).
+
+* `bgzip`: Add bgzip functionality to compress and decompress files (PR #13).
+
+* `pear`: Paired-end read merger (PR #10).
+
+* `lofreq/call`: Call variants from a BAM file (PR #17).
+
+* `lofreq/indelqual`: Insert indel qualities into BAM file (PR #17).
+
+* `multiqc`: Aggregate results from bioinformatics analyses across many samples into a single report (PR #42).
+
+* `star`:
+    - `star/star_align_reads`: Align reads to a reference genome (PR #22).
+    - `star/star_genome_generate`: Generate a genome index for STAR alignment (PR #58).
+
+* `gffread`: Validate, filter, convert and perform other operations on GFF files (PR #29).  
+
+* `salmon`:
+    - `salmon/salmon_index`: Create a salmon index for the transcriptome to use Salmon in the mapping-based mode (PR #24).
+    - `salmon/salmon_quant`: Transcript quantification from RNA-seq data (PR #24).
+
+* `samtools`:
+    - `samtools/samtools_flagstat`: Counts the number of alignments in SAM/BAM/CRAM files for each FLAG type (PR #31).
+    - `samtools/samtools_idxstats`: Reports alignment summary statistics for a SAM/BAM/CRAM file (PR #32).
+    - `samtools/samtools_index`: Index SAM/BAM/CRAM files (PR #35).
+    - `samtools/samtools_sort`: Sort SAM/BAM/CRAM files (PR #36).
+    - `samtools/samtools_stats`: Reports alignment summary statistics for a BAM file (PR #39).
+    - `samtools/samtools_faidx`: Indexes FASTA files to enable random access to fasta and fastq files (PR #41).
+    - `samtools/samtools_collate`: Shuffles and groups reads in SAM/BAM/CRAM files together by their names (PR #42).
+    - `samtools/samtools_view`: Views and converts SAM/BAM/CRAM files (PR #48).
+    - `samtools/samtools_fastq`: Converts a SAM/BAM/CRAM file to FASTQ (PR #52).
+    - `samtools/samtools_fastq`: Converts a SAM/BAM/CRAM file to FASTA (PR #53).
+
+* `umi_tools`:
+    -`umi_tools/umi_tools_extract`: Flexible removal of UMI sequences from fastq reads (PR #71).
+
+* `falco`: A C++ drop-in replacement of FastQC to assess the quality of sequence read data (PR #43).
+
+* `bedtools`:
+    - `bedtools_getfasta`: extract sequences from a FASTA file for each of the
+                           intervals defined in a BED/GFF/VCF file (PR #59).
+
+## MINOR CHANGES
+
+* Uniformize component metadata (PR #23).
+
+* Update to Viash 0.8.5 (PR #25).
+
+* Update to Viash 0.9.0-RC3 (PR #51).
+
+* Update to Viash 0.9.0-RC6 (PR #63).
+
+* Switch to viash-hub/toolbox actions (PR #64).
+
+## DOCUMENTATION
+
+* Update README (PR #64).
+
+## BUG FIXES
+
+* Add escaping character before leading hashtag in the description field of the config file (PR #50).
+
+* Format URL in biobase/bcl_convert description (PR #55).
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -0,0 +1,414 @@
+
+# Contributing guidelines
+
+We encourage contributions from the community. To contribute:
+
+1. **Fork the Repository**: Start by forking this repository to your account.
+2. **Develop Your Component**: Create your Viash component, ensuring it aligns with our best practices (detailed below).
+3. **Submit a Pull Request**: After testing your component, submit a pull request for review.
+
+## Procedure of adding a component
+
+### Step 1: Find a component to contribute
+
+* Find a tool to contribute to this repo.
+
+* Check whether it is already in the [Project board](https://github.com/orgs/viash-hub/projects/1).
+
+* Check whether there is a corresponding [Snakemake wrapper](https://github.com/snakemake/snakemake-wrappers/blob/master/bio) or [nf-core module](https://github.com/nf-core/modules/tree/master/modules/nf-core) which we can use as inspiration.
+
+* Create an issue to show that you are working on this component.
+
+
+### Step 2: Add config template
+
+Change all occurrences of `xxx` to the name of the component.
+
+Create a file at `src/xxx/config.vsh.yaml` with contents:
+
+```yaml
+name: xxx
+description: xxx
+keywords: [tag1, tag2]
+links:
+  homepage: yyy
+  documentation: yyy
+  issue_tracker: yyy
+  repository: yyy
+references: 
+  doi: 12345/12345678.yz
+license: MIT/Apache-2.0/GPL-3.0/...
+argument_groups:
+  - name: Inputs
+    arguments: <...>
+  - name: Outputs
+    arguments: <...>
+  - name: Arguments
+    arguments: <...>
+resources:
+  - type: bash_script
+    path: script.sh
+test_resources:
+  - type: bash_script
+    path: test.sh
+  - type: file
+    path: test_data
+engines:
+  - <...>
+runners:
+  - type: executable
+  - type: nextflow
+```
+
+### Step 3: Fill in the metadata
+
+Fill in the relevant metadata fields in the config. Here is an example of the metadata of an existing component.
+
+```yaml
+name: arriba
+description: Detect gene fusions from RNA-Seq data
+keywords: [Gene fusion, RNA-Seq]
+links:
+  homepage: https://arriba.readthedocs.io/en/latest/
+  documentation: https://arriba.readthedocs.io/en/latest/
+  repository: https://github.com/suhrig/arriba
+  issue_tracker: https://github.com/suhrig/arriba/issues
+references:
+  doi: 10.1101/gr.257246.119
+  bibtex: |
+    @article{
+      ... a bibtex entry in case the doi is not available ...
+    }
+license: MIT
+```
+
+### Step 4: Find a suitable container
+
+Google `biocontainer <name of component>` and find the container that is most suitable. Typically the link will be `https://quay.io/repository/biocontainers/xxx?tab=tags`.
+
+If no such container is found, you can create a custom container in the next step. 
+
+
+### Step 5: Create help file
+
+To help develop the component, we store the `--help` output of the tool in a file at `src/xxx/help.txt`.
+
+````bash
+cat <<EOF > src/xxx/help.txt
+```sh
+xxx --help
+```
+EOF
+
+docker run quay.io/biocontainers/xxx:tag xxx --help >> src/xxx/help.txt
+````
+
+Notes:
+
+* This help file has no functional purpose, but it is useful for the developer to see the help output of the tool.
+
+* Some tools might not have a `--help` argument but instead have a `-h` argument. For example, for `arriba`, the help message is obtained by running `arriba -h`:
+  
+  ```bash
+  docker run quay.io/biocontainers/arriba:2.4.0--h0033a41_2 arriba -h
+  ```
+
+
+### Step 6: Create or fetch test data
+
+To help develop the component, it's interesting to have some test data available. In most cases, we can use the test data from the Snakemake wrappers. 
+
+To make sure we can reproduce the test data in the future, we store the command to fetch the test data in a file at `src/xxx/test_data/script.sh`.
+
+```bash
+cat <<EOF > src/xxx/test_data/script.sh
+
+# clone repo
+if [ ! -d /tmp/snakemake-wrappers ]; then
+  git clone --depth 1 --single-branch --branch master https://github.com/snakemake/snakemake-wrappers /tmp/snakemake-wrappers
+fi
+
+# copy test data
+cp -r /tmp/snakemake-wrappers/bio/xxx/test/* src/xxx/test_data
+EOF
+```
+
+The test data should be suitable for testing this component. Ensure that the test data is small enough: ideally <1KB, preferably <10KB, if need be <100KB.
+
+### Step 7: Add arguments for the input files
+
+By looking at the help file, we add the input arguments to the config file. Here is an example of the input arguments of an existing component.
+
+For instance, in the [arriba help file](src/arriba/help.txt), we see the following:
+
+    Usage: arriba [-c Chimeric.out.sam] -x Aligned.out.bam \
+                  -g annotation.gtf -a assembly.fa [-b blacklists.tsv] [-k known_fusions.tsv] \
+                  [-t tags.tsv] [-p protein_domains.gff3] [-d structural_variants_from_WGS.tsv] \
+                  -o fusions.tsv [-O fusions.discarded.tsv] \
+                  [OPTIONS]
+
+    -x FILE  File in SAM/BAM/CRAM format with main alignments as generated by STAR 
+              (Aligned.out.sam). Arriba extracts candidate reads from this file. 
+
+Based on this information, we can add the following input arguments to the config file.
+
+```yaml
+argument_groups:
+  - name: Inputs
+    arguments:
+    - name: --bam
+      alternatives: -x
+      type: file
+      description: |
+        File in SAM/BAM/CRAM format with main alignments as generated by STAR
+        (`Aligned.out.sam`). Arriba extracts candidate reads from this file.
+      required: true
+      example: Aligned.out.bam
+```
+
+Check the [documentation](https://viash.io/reference/config/functionality/arguments) for more information on the format of input arguments.
+
+Several notes:
+
+* Argument names should be formatted in `--snake_case`. This means arguments like `--foo-bar` should be formatted as `--foo_bar`, and short arguments like `-f` should receive a longer name like `--foo`.
+
+* Input arguments can have `multiple: true` to allow the user to specify multiple files.
+
+* The description should be formatted in markdown.
+
+### Step 8: Add arguments for the output files
+
+By looking at the help file, we now also add output arguments to the config file.
+
+For example, in the [arriba help file](src/arriba/help.txt), we see the following:
+
+
+    Usage: arriba [-c Chimeric.out.sam] -x Aligned.out.bam \
+                  -g annotation.gtf -a assembly.fa [-b blacklists.tsv] [-k known_fusions.tsv] \
+                  [-t tags.tsv] [-p protein_domains.gff3] [-d structural_variants_from_WGS.tsv] \
+                  -o fusions.tsv [-O fusions.discarded.tsv] \
+                  [OPTIONS]
+
+     -o FILE  Output file with fusions that have passed all filters. 
+
+     -O FILE  Output file with fusions that were discarded due to filtering. 
+
+Based on this information, we can add the following output arguments to the config file.
+
+```yaml
+argument_groups:
+  - name: Outputs
+    arguments:
+      - name: --fusions
+        alternatives: -o
+        type: file
+        direction: output
+        description: |
+          Output file with fusions that have passed all filters.
+        required: true
+        example: fusions.tsv
+      - name: --fusions_discarded
+        alternatives: -O
+        type: file
+        direction: output
+        description: |
+          Output file with fusions that were discarded due to filtering. 
+        required: false
+        example: fusions.discarded.tsv
+```
+
+Note: 
+
+* Preferably, these outputs should not be directories but files. For example, if a tool outputs a directory `foo/` containing files `foo/bar.txt` and `foo/baz.txt`, there should be two output arguments `--bar` and `--baz` (as opposed to one output argument which outputs the whole `foo/` directory).
+
+### Step 9: Add arguments for the other arguments
+
+Finally, add all other arguments to the config file. There are a few exceptions:
+
+* Arguments related to specifying CPU and memory requirements are handled separately and should not be added to the config file.
+
+* Arguments related to printing the information such as printing the version (`-v`, `--version`) or printing the help (`-h`, `--help`) should not be added to the config file.
+
+* If the help lists defaults, do not add them as defaults but to the description. Example: `description: <Explanation of parameter>. Default: 10.`
+
+
+### Step 10: Add a Docker engine
+
+To ensure reproducibility of components, we require that all components are run in a Docker container. 
+
+```yaml
+engines:
+  - type: docker
+    image: quay.io/biocontainers/xxx:0.1.0--py_0
+```
+
+The container should have your tool installed, as well as `ps`.
+
+If you didn't find a suitable container in the previous step, you can create a custom container. For example:
+
+```yaml
+engines:
+  - type: docker
+    image: python:3.10
+    setup:
+      - type: python
+        packages: numpy
+```
+
+For more information on how to do this, see the [documentation](https://viash.io/guide/component/add-dependencies.html#steps-for-creating-a-custom-docker-platform).
+
+Here is a list of base containers we can recommend:
+
+* Bash: [`bash`](https://hub.docker.com/_/bash), [`ubuntu`](https://hub.docker.com/_/ubuntu)
+* C#: [`ghcr.io/data-intuitive/dotnet-script`](https://github.com/data-intuitive/ghcr-dotnet-script/pkgs/container/dotnet-script)
+* JavaScript: [`node`](https://hub.docker.com/_/node)
+* Python: [`python`](https://hub.docker.com/_/python), [`nvcr.io/nvidia/pytorch`](https://catalog.ngc.nvidia.com/orgs/nvidia/containers/pytorch)
+* R: [`eddelbuettel/r2u`](https://hub.docker.com/r/eddelbuettel/r2u), [`rocker/tidyverse`](https://hub.docker.com/r/rocker/tidyverse)
+* Scala: [`sbtscala/scala-sbt`](https://hub.docker.com/r/sbtscala/scala-sbt)
+
+### Step 11: Write a runner script
+
+Next, we need to write a runner script that runs the tool with the input arguments. Create a Bash script named `src/xxx/script.sh` which runs the tool with the input arguments.
+
+```bash
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+# unset flags
+[[ "$par_option" == "false" ]] && unset par_option
+
+xxx \
+  --input "$par_input" \
+  --output "$par_output" \
+  ${par_option:+--option}
+```
+
+When building a Viash component, Viash will automatically replace the `## VIASH START` and `## VIASH END` lines (and anything in between) with environment variables based on the arguments specified in the config.
+
+As an example, this is what the Bash script for the `arriba` component looks like:
+
+```bash
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+# unset flags
+[[ "$par_skip_duplicate_marking" == "false" ]] && unset par_skip_duplicate_marking
+[[ "$par_extra_information" == "false" ]] && unset par_extra_information
+[[ "$par_fill_gaps" == "false" ]] && unset par_fill_gaps
+
+arriba \
+  -x "$par_bam" \
+  -a "$par_genome" \
+  -g "$par_gene_annotation" \
+  -o "$par_fusions" \
+  ${par_known_fusions:+-k "${par_known_fusions}"} \
+  ${par_blacklist:+-b "${par_blacklist}"} \
+  # ...
+  ${par_extra_information:+-X} \
+  ${par_fill_gaps:+-I}
+```
+
+Notes:
+
+* If your arguments can contain special variables (e.g. `$`), you can use quoting (need to find a documentation page for this) to make sure you can use the string as input. Example: `-x ${par_bam@Q}`.
+
+* Optional arguments can be passed to the command conditionally using Bash [parameter expansion](https://www.gnu.org/software/bash/manual/html_node/Shell-Parameter-Expansion.html). For example: `${par_known_fusions:+-k ${par_known_fusions@Q}}`
+
+* If your tool allows for multiple inputs using a separator other than `;` (which is the default Viash multiple separator), you can substitute these values with a command like: `par_disable_filters=$(echo $par_disable_filters | tr ';' ',')`.
+
+
+### Step 12: Create test script
+
+If the unit test requires test resources, these should be provided in the `test_resources` section of the component. 
+
+```yaml
+test_resources:
+  - type: bash_script
+    path: test.sh
+  - type: file
+    path: test_data
+```
+
+Create a test script at `src/xxx/test.sh` that runs the component with the test data. This script should run the component (available with `$meta_executable`) with the test data and check if the output is as expected. The script should exit with a non-zero exit code if the output is not as expected. For example:
+
+```bash
+#!/bin/bash
+
+set -e
+
+## VIASH START
+## VIASH END
+
+#############################################
+# helper functions
+assert_file_exists() {
+  [ -f "$1" ] || { echo "File '$1' does not exist" && exit 1; }
+}
+assert_file_doesnt_exist() {
+  [ ! -f "$1" ] || { echo "File '$1' exists but shouldn't" && exit 1; }
+}
+assert_file_empty() {
+  [ ! -s "$1" ] || { echo "File '$1' is not empty but should be" && exit 1; }
+}
+assert_file_not_empty() {
+  [ -s "$1" ] || { echo "File '$1' is empty but shouldn't be" && exit 1; }
+}
+assert_file_contains() {
+  grep -q "$2" "$1" || { echo "File '$1' does not contain '$2'" && exit 1; }
+}
+assert_file_not_contains() {
+  grep -q "$2" "$1" && { echo "File '$1' contains '$2' but shouldn't" && exit 1; }
+}
+assert_file_contains_regex() {
+  grep -q -E "$2" "$1" || { echo "File '$1' does not contain '$2'" && exit 1; }
+}
+assert_file_not_contains_regex() {
+  grep -q -E "$2" "$1" && { echo "File '$1' contains '$2' but shouldn't" && exit 1; }
+}
+#############################################
+
+echo "> Run $meta_name with test data"
+"$meta_executable" \
+  --input "$meta_resources_dir/test_data/reads_R1.fastq" \
+  --output "output.txt" \
+  --option
+
+echo ">> Check if output exists"
+assert_file_exists "output.txt"
+
+echo ">> Check if output is empty"
+assert_file_not_empty "output.txt"
+
+echo ">> Check if output is correct"
+assert_file_contains "output.txt" "some expected output"
+
+echo "> All tests succeeded!"
+```
+
+Notes:
+
+* Do always check the contents of the output file. If the output is not deterministic, you can use regular expressions to check the output.
+
+* If possible, generate your own test data instead of copying it from an external resource.
+
+### Step 13: Create a `/var/software_versions.txt` file
+
+For the sake of transparency and reproducibility, we require that the versions of the software used in the component are documented.
+
+For now, this is managed by creating a file `/var/software_versions.txt` in the `setup` section of the Docker engine.
+
+```yaml
+engines:
+  - type: docker
+    image: quay.io/biocontainers/xxx:0.1.0--py_0
+    setup:
+      - type: docker
+        # note: /var/software_versions.txt should contain:
+        #   arriba: "2.4.0"
+        run: |
+          echo "xxx: \"0.1.0\"" > /var/software_versions.txt
+```
--- a/21
+++ b/21
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Data Intuitive
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
--- a/README.md
+++ b/README.md
@@ -0,0 +1,72 @@
+
+
+# 🌱📦 biobox
+
+[![ViashHub](https://img.shields.io/badge/ViashHub-biobox-7a4baa.png)](https://web.viash-hub.com/packages/biobox)
+[![GitHub](https://img.shields.io/badge/GitHub-viash--hub%2Fbiobox-blue.png)](https://github.com/viash-hub/biobox)
+[![GitHub
+License](https://img.shields.io/github/license/viash-hub/biobox.png)](https://github.com/viash-hub/biobox/blob/main/LICENSE)
+[![GitHub
+Issues](https://img.shields.io/github/issues/viash-hub/biobox.png)](https://github.com/viash-hub/biobox/issues)
+[![Viash
+version](https://img.shields.io/badge/Viash-v0.9.0--RC6-blue)](https://viash.io)
+
+A collection of bioinformatics tools for working with sequence data.
+
+## Objectives
+
+- **Reusability**: Facilitating the use of components across various
+  projects and contexts.
+- **Reproducibility**: Ensuring that components are reproducible and can
+  be easily shared.
+- **Best Practices**: Adhering to established standards in software
+  development and bioinformatics.
+
+## Contributing
+
+We encourage contributions from the community. To contribute:
+
+1.  **Fork the Repository**: Start by forking this repository to your
+    account.
+2.  **Develop Your Component**: Create your Viash component, ensuring it
+    aligns with our best practices (detailed below).
+3.  **Submit a Pull Request**: After testing your component, submit a
+    pull request for review.
+
+## Contribution Guidelines
+
+The contribution guidelines describes which steps you should follow to
+contribute a component to this repository.
+
+1.  Find a component to contribute
+2.  Add config template
+3.  Fill in the metadata
+4.  Find a suitable container
+5.  Create help file
+6.  Create or fetch test data
+7.  Add arguments for the input files
+8.  Add arguments for the output files
+9.  Add arguments for the other arguments
+10. Add a Docker engine
+11. Write a runner script
+12. Create test script
+13. Create a `/var/software_versions.txt` file
+
+See the
+[CONTRIBUTING](https://github.com/viash-hub/biobox/blob/main/CONTRIBUTING.md)
+file for more details.
+
+## Support and Community
+
+For support, questions, or to join our community:
+
+- **Issues**: Submit questions or issues via the [GitHub issue
+  tracker](https://github.com/viash-hub/biobox/issues).
+- **Discussions**: Join our discussions via [GitHub
+  Discussions](https://github.com/viash-hub/biobox/discussions).
+
+## License
+
+This repository is licensed under an MIT license. See the
+[LICENSE](https://github.com/viash-hub/biobox/blob/main/LICENSE) file
+for details.
--- a/README.qmd
+++ b/README.qmd
@@ -0,0 +1,62 @@
+---
+format: gfm
+---
+```{r setup, include=FALSE}
+project <- yaml::read_yaml("_viash.yaml")
+license <- paste0(project$links$repository, "/blob/main/LICENSE")
+contributing <- paste0(project$links$repository, "/blob/main/CONTRIBUTING.md")
+```
+# 🌱📦 `r project$name`
+
+[![ViashHub](https://img.shields.io/badge/ViashHub-`r project$name`-7a4baa)](https://web.viash-hub.com/packages/`r project$name`) 
+[![GitHub](https://img.shields.io/badge/GitHub-viash--hub%2F`r project$name`-blue)](`r project$links$repository`) 
+[![GitHub License](https://img.shields.io/github/license/viash-hub/`r project$name`)](`r license`) 
+[![GitHub Issues](https://img.shields.io/github/issues/viash-hub/`r project$name`)](`r project$links$issue_tracker`) 
+[![Viash version](https://img.shields.io/badge/Viash-v`r gsub("-", "--", project$viash_version)`-blue)](https://viash.io)
+
+`r project$description`
+
+## Objectives
+
+- **Reusability**: Facilitating the use of components across various projects and contexts.
+- **Reproducibility**: Ensuring that components are reproducible and can be easily shared.
+- **Best Practices**: Adhering to established standards in software development and bioinformatics.
+
+## Contributing
+
+We encourage contributions from the community. To contribute:
+
+1. **Fork the Repository**: Start by forking this repository to your account.
+2. **Develop Your Component**: Create your Viash component, ensuring it aligns with our best practices (detailed below).
+3. **Submit a Pull Request**: After testing your component, submit a pull request for review.
+
+## Contribution Guidelines
+
+The contribution guidelines describes which steps you should follow to contribute a component to this repository.
+
+```{r echo=FALSE}
+lines <- readr::read_lines("CONTRIBUTING.md")
+
+index_start <- grep("^### Step [0-9]*:", lines)
+
+index_end <- c(index_start[-1] - 1, length(lines))
+
+name <- gsub("^### Step [0-9]*: *", "", lines[index_start])
+
+knitr::asis_output(
+  paste(paste0(" 1. ", name, "\n"), collapse = "")
+)
+```
+
+See the [CONTRIBUTING](`r contributing`) file for more details.
+
+
+## Support and Community
+
+For support, questions, or to join our community:
+
+- **Issues**: Submit questions or issues via the [GitHub issue tracker](`r project$links$issue_tracker`).
+- **Discussions**: Join our discussions via [GitHub Discussions](`r project$links$repository`/discussions).
+
+## License
+This repository is licensed under an MIT license. See the [LICENSE](`r license`) file for details.
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -0,0 +1,13 @@
+name: biobox
+description: |
+  A collection of bioinformatics tools for working with sequence data.
+license: MIT
+keywords: [bioinformatics, modules, sequencing]
+links:
+  issue_tracker: https://github.com/viash-hub/biobox/issues
+  repository: https://github.com/viash-hub/biobox
+
+viash_version: 0.9.0-RC6
+
+config_mods: |
+  .requirements.commands := ['ps']
--- a/main.nf
+++ b/main.nf
@@ -0,0 +1,3 @@
+workflow {
+print("This is a dummy placeholder for pipeline execution. Please use the corresponding nf files for running pipelines.")
+}
--- a/nextflow.config
+++ b/nextflow.config
@@ -0,0 +1,6 @@
+manifest {
+  name = "biobox"
+  version = "add-agat-convert-spgff2tsv"
+  defaultBranch = "main"
+  nextflowVersion = "!>=20.12.1-edge"
+}
--- a/src/_authors/angela_o_pisco.yaml
+++ b/src/_authors/angela_o_pisco.yaml
@@ -0,0 +1,14 @@
+name: Angela Oliveira Pisco
+info:
+  role: Contributor
+  links:
+    github: aopisco
+    orcid: "0000-0003-0142-2355"
+    linkedin: aopisco
+  organizations:
+    - name: Insitro
+      href: https://insitro.com
+      role: Director of Computational Biology
+    - name: Open Problems
+      href: https://openproblems.bio
+      role: Core Member
--- a/src/_authors/dorien_roosen.yaml
+++ b/src/_authors/dorien_roosen.yaml
@@ -0,0 +1,10 @@
+name: Dorien Roosen
+info:
+  links:
+    email: dorien@data-intuitive.com
+    github: dorien-er
+    linkedin: dorien-roosen
+  organizations:
+    - name: Data Intuitive
+      href: https://www.data-intuitive.com
+      role: Data Scientist
--- a/src/_authors/dries_schaumont.yaml
+++ b/src/_authors/dries_schaumont.yaml
@@ -0,0 +1,11 @@
+name: Dries Schaumont
+info:
+  links:
+    email: dries@data-intuitive.com
+    github: DriesSchaumont
+    orcid: "0000-0002-4389-0440"
+    linkedin: dries-schaumont
+  organizations:
+    - name: Data Intuitive
+      href: https://www.data-intuitive.com
+      role: Data Scientist
--- a/src/_authors/emma_rousseau.yaml
+++ b/src/_authors/emma_rousseau.yaml
@@ -0,0 +1,10 @@
+name: Emma Rousseau
+info:
+  links:
+    email: emma@data-intuitive.com
+    github: emmarousseau
+    linkedin: emmarousseau1
+  organizations:
+    - name: Data Intuitive
+      href: https://www.data-intuitive.com
+      role: Bioinformatician
--- a/src/_authors/jakub_majercik.yaml
+++ b/src/_authors/jakub_majercik.yaml
@@ -0,0 +1,10 @@
+name: Jakub Majercik
+info:
+  links:
+    email: jakub@data-intuitive.com
+    github: jakubmajercik
+    linkedin: jakubmajercik
+  organizations:
+    - name: Data Intuitive
+      href: https://www.data-intuitive.com
+      role: Bioinformatics Engineer
--- a/src/_authors/kai_waldrant.yaml
+++ b/src/_authors/kai_waldrant.yaml
@@ -0,0 +1,14 @@
+name: Kai Waldrant
+info:
+  links:
+    email: kai@data-intuitive.com
+    github: KaiWaldrant
+    orcid: "0009-0003-8555-1361"
+    linkedin: kaiwaldrant
+  organizations:
+    - name: Data Intuitive
+      href: https://www.data-intuitive.com
+      role: Bioinformatician
+    - name: Open Problems
+      href: https://openproblems.bio
+      role: Contributor
--- a/src/_authors/leila_paquay.yaml
+++ b/src/_authors/leila_paquay.yaml
@@ -0,0 +1,10 @@
+name: Leïla Paquay
+info:
+  links:
+    email: leila@data-intuitive.com
+    github: Leila011
+    linkedin: leilapaquay
+  organizations:
+    - name: Data Intuitive
+      href: https://www.data-intuitive.com
+      role: Software Developer
--- a/src/_authors/robrecht_cannoodt.yaml
+++ b/src/_authors/robrecht_cannoodt.yaml
@@ -0,0 +1,14 @@
+name: Robrecht Cannoodt
+info:
+  links:
+    email: robrecht@data-intuitive.com
+    github: rcannood
+    orcid: "0000-0003-3641-729X"
+    linkedin: robrechtcannoodt
+  organizations:
+    - name: Data Intuitive
+      href: https://www.data-intuitive.com
+      role: Data Science Engineer
+    - name: Open Problems
+      href: https://openproblems.bio
+      role: Core Member
--- a/src/_authors/sai_nirmayi_yasa.yaml
+++ b/src/_authors/sai_nirmayi_yasa.yaml
@@ -0,0 +1,10 @@
+name: Sai Nirmayi Yasa
+info:
+  links:
+    email: nirmayi@data-intuitive.com
+    github: sainirmayi
+    linkedin: sai-nirmayi-yasa
+  organizations:
+    - name: Data Intuitive
+      href: https://www.data-intuitive.com
+      role: Junior Bioinformatics Researcher
--- a/src/_authors/theodoro_gasperin.yaml
+++ b/src/_authors/theodoro_gasperin.yaml
@@ -0,0 +1,10 @@
+name: Theodoro Gasperin Terra Camargo
+info:
+  links:
+    email: theodorogtc@gmail.com
+    github: tgaspe
+    linkedin: theodoro-gasperin-terra-camargo
+  organizations:
+    - name: Data Intuitive
+      href: https://www.data-intuitive.com
+      role: Bioinformatician
--- a/src/_authors/toni_verbeiren.yaml
+++ b/src/_authors/toni_verbeiren.yaml
@@ -0,0 +1,9 @@
+name: Toni Verbeiren
+info:
+  links:
+    github: tverbeiren
+    linkedin: verbeiren
+  organizations:
+  - name: Data Intuitive
+    href: https://www.data-intuitive.com
+    role: Data Scientist and CEO
--- a/src/_authors/weiwei_schultz.yaml
+++ b/src/_authors/weiwei_schultz.yaml
@@ -0,0 +1,5 @@
+name: Weiwei Schultz
+info:
+  organizations:
+    - name: Janssen R&D US
+      role: Associate Director Data Sciences
--- a/src/agat/agat_convert_sp_gff2gtf/config.vsh.yaml
+++ b/src/agat/agat_convert_sp_gff2gtf/config.vsh.yaml
@@ -0,0 +1,94 @@
+name: agat_convert_sp_gff2gtf
+namespace: agat
+description: |
+  The script aims to convert any GTF/GFF file into a proper GTF file. Full
+  information about the format can be found here:
+  https://agat.readthedocs.io/en/latest/gxf.html You can choose among 7
+  different GTF types (1, 2, 2.1, 2.2, 2.5, 3 or relax). Depending the
+  version selected the script will filter out the features that are not
+  accepted. For GTF2.5 and 3, every level1 feature (e.g nc_gene
+  pseudogene) will be converted into gene feature and every level2 feature
+  (e.g mRNA ncRNA) will be converted into transcript feature. Using the
+  "relax" option you will produce a GTF-like output keeping all original
+  feature types (3rd column). No modification will occur e.g. mRNA to
+  transcript.
+
+  To be fully GTF compliant all feature have a gene_id and a transcript_id
+  attribute. The gene_id is unique identifier for the genomic source of
+  the transcript, which is used to group transcripts into genes. The
+  transcript_id is a unique identifier for the predicted transcript, which
+  is used to group features into transcripts.
+keywords: [gene annotations, GTF conversion]
+links:
+  homepage: https://github.com/NBISweden/AGAT
+  documentation: https://agat.readthedocs.io/
+  issue_tracker: https://github.com/NBISweden/AGAT/issues
+  repository: https://github.com/NBISweden/AGAT
+references: 
+  doi: 10.5281/zenodo.3552717
+license: GPL-3.0
+authors:
+  - __merge__: /src/_authors/leila_paquay.yaml
+    roles: [ author, maintainer ]
+
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: --gff
+        alternatives: [-i]
+        description: Input GFF/GTF file that will be read
+        type: file
+        required: true
+        direction: input
+        example: input.gff
+  - name: Outputs
+    arguments:       
+      - name: --output
+        alternatives: [-o, --out, --outfile, --gtf]
+        description: Output GTF file. If no output file is specified, the output will be written to STDOUT.
+        type: file
+        direction: output
+        required: true
+        example: output.gtf
+  - name: Arguments
+    arguments:
+      - name: --gtf_version
+        description: |
+          Version of the GTF output (1,2,2.1,2.2,2.5,3 or relax). Default value from AGAT config file (relax for the default config). The script option has the higher priority.  
+          
+            * relax: all feature types are accepted.  
+            * GTF3 (9 feature types accepted): gene, transcript, exon, CDS, Selenocysteine, start_codon, stop_codon, three_prime_utr and five_prime_utr.  
+            * GTF2.5 (8 feature types accepted): gene, transcript, exon, CDS, UTR, start_codon, stop_codon, Selenocysteine.  
+            * GTF2.2 (9 feature types accepted): CDS, start_codon, stop_codon, 5UTR, 3UTR, inter, inter_CNS, intron_CNS and exon.  
+            * GTF2.1 (6 feature types accepted): CDS, start_codon, stop_codon, exon, 5UTR, 3UTR.  
+            * GTF2 (4 feature types accepted): CDS, start_codon, stop_codon, exon.  
+            * GTF1 (5 feature types accepted): CDS, start_codon, stop_codon, exon, intron.  
+        type: string
+        choices: [relax, "1", "2", "2.1", "2.2", "2.5", "3"]
+        required: false
+        example: "3"
+      - name: --config
+        alternatives: [-c]
+        description: |
+          Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
+        type: file
+        required: false
+        example: custom_agat_config.yaml
+resources:
+  - type: bash_script
+    path: script.sh
+test_resources:
+  - type: bash_script
+    path: test.sh
+  - type: file
+    path: test_data
+engines:
+  - type: docker
+    image: quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0
+    setup:
+      - type: docker
+        run: |
+          agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.txt
+runners:
+  - type: executable
+  - type: nextflow
--- a/src/agat/agat_convert_sp_gff2gtf/help.txt
+++ b/src/agat/agat_convert_sp_gff2gtf/help.txt
@@ -0,0 +1,102 @@
+```sh
+agat_convert_sp_gff2gtf.pl --help
+```
+ ------------------------------------------------------------------------------
+|   Another GFF Analysis Toolkit (AGAT) - Version: v1.4.0                      |
+|   https://github.com/NBISweden/AGAT                                          |
+|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
+ ------------------------------------------------------------------------------
+
+
+Name:
+    agat_convert_sp_gff2gtf.pl
+
+Description:
+    The script aims to convert any GTF/GFF file into a proper GTF file. Full
+    information about the format can be found here:
+    https://agat.readthedocs.io/en/latest/gxf.html You can choose among 7
+    different GTF types (1, 2, 2.1, 2.2, 2.5, 3 or relax). Depending the
+    version selected the script will filter out the features that are not
+    accepted. For GTF2.5 and 3, every level1 feature (e.g nc_gene
+    pseudogene) will be converted into gene feature and every level2 feature
+    (e.g mRNA ncRNA) will be converted into transcript feature. Using the
+    "relax" option you will produce a GTF-like output keeping all original
+    feature types (3rd column). No modification will occur e.g. mRNA to
+    transcript.
+
+    To be fully GTF compliant all feature have a gene_id and a transcript_id
+    attribute. The gene_id is unique identifier for the genomic source of
+    the transcript, which is used to group transcripts into genes. The
+    transcript_id is a unique identifier for the predicted transcript, which
+    is used to group features into transcripts.
+
+Usage:
+        agat_convert_sp_gff2gtf.pl --gff infile.gff [ -o outfile ]
+        agat_convert_sp_gff2gtf -h
+
+Options:
+    --gff, --gtf or -i
+            Input GFF/GTF file that will be read
+
+    --gtf_version version of the GTF output (1,2,2.1,2.2,2.5,3 or relax).
+    Default value from AGAT config file (relax for the default config). The
+    script option has the higher priority.
+            relax: all feature types are accepted.
+
+            GTF3 (9 feature types accepted): gene, transcript, exon, CDS,
+            Selenocysteine, start_codon, stop_codon, three_prime_utr and
+            five_prime_utr
+
+            GTF2.5 (8 feature types accepted): gene, transcript, exon, CDS,
+            UTR, start_codon, stop_codon, Selenocysteine
+
+            GTF2.2 (9 feature types accepted): CDS, start_codon, stop_codon,
+            5UTR, 3UTR, inter, inter_CNS, intron_CNS and exon
+
+            GTF2.1 (6 feature types accepted): CDS, start_codon, stop_codon,
+            exon, 5UTR, 3UTR
+
+            GTF2 (4 feature types accepted): CDS, start_codon, stop_codon,
+            exon
+
+            GTF1 (5 feature types accepted): CDS, start_codon, stop_codon,
+            exon, intron
+
+    -o , --output , --out , --outfile or --gtf
+            Output GTF file. If no output file is specified, the output will
+            be written to STDOUT.
+
+    -c or --config
+            String - Input agat config file. By default AGAT takes as input
+            agat_config.yaml file from the working directory if any,
+            otherwise it takes the orignal agat_config.yaml shipped with
+            AGAT. To get the agat_config.yaml locally type: "agat config
+            --expose". The --config option gives you the possibility to use
+            your own AGAT config file (located elsewhere or named
+            differently).
+
+    -h or --help
+            Display this helpful text.
+
+Feedback:
+  Did you find a bug?:
+    Do not hesitate to report bugs to help us keep track of the bugs and
+    their resolution. Please use the GitHub issue tracking system available
+    at this address:
+
+                https://github.com/NBISweden/AGAT/issues
+
+     Ensure that the bug was not already reported by searching under Issues.
+     If you're unable to find an (open) issue addressing the problem, open a new one.
+     Try as much as possible to include in the issue when relevant:
+     - a clear description,
+     - as much relevant information as possible,
+     - the command used,
+     - a data sample,
+     - an explanation of the expected behaviour that is not occurring.
+
+  Do you want to contribute?:
+    You are very welcome, visit this address for the Contributing
+    guidelines:
+    https://github.com/NBISweden/AGAT/blob/master/CONTRIBUTING.md
+
--- a/src/agat/agat_convert_sp_gff2gtf/script.sh
+++ b/src/agat/agat_convert_sp_gff2gtf/script.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+agat_convert_sp_gff2gtf.pl \
+  -i "$par_gff" \
+  -o "$par_output" \
+  ${par_gtf_version:+--gtf_version "${par_gtf_version}"} \
+  ${par_config:+--config "${par_config}"}
--- a/src/agat/agat_convert_sp_gff2gtf/test.sh
+++ b/src/agat/agat_convert_sp_gff2gtf/test.sh
@@ -0,0 +1,37 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+test_dir="${meta_resources_dir}/test_data"
+
+echo "> Run $meta_name with test data"
+"$meta_executable" \
+  --gff "$test_dir/0_test.gff" \
+  --output "output.gtf" 
+
+echo ">> Checking output"
+[ ! -f "output.gtf" ] && echo "Output file output.gtf does not exist" && exit 1
+
+echo ">> Check if output is empty"
+[ ! -s "output.gtf" ] && echo "Output file output.gtf is empty" && exit 1
+
+echo ">> Check if the conversion resulted in the right GTF format"
+idGFF=$(head -n 2 "$test_dir/0_test.gff" | grep -o 'ID=[^;]*' | cut -d '=' -f 2-)
+expectedGTF="gene_id \"$idGFF\"; ID \"$idGFF\";"
+extractedGTF=$(head -n 3 "output.gtf" | grep -o 'gene_id "[^"]*"; ID "[^"]*";')
+[ "$extractedGTF" != "$expectedGTF" ] && echo "Output file output.gtf does not have the right format" && exit 1
+
+rm output.gtf
+
+echo "> Run $meta_name with test data and GTF version 2.5"
+"$meta_executable" \
+  --gff "$test_dir/0_test.gff" \
+  --output "output.gtf" \
+  --gtf_version "2.5"
+
+echo ">> Check if the output file header display the right GTF version"
+grep -q "##gtf-version 2.5" "output.gtf"
+[ $? -ne 0 ] && echo "Output file output.gtf header does not display the right GTF version" && exit 1
+
+echo "> Test successful"
--- a/src/agat/agat_convert_sp_gff2gtf/test_data/0_test.gff
+++ b/src/agat/agat_convert_sp_gff2gtf/test_data/0_test.gff
@@ -0,0 +1,36 @@
+##gff-version 3
+scaffold625	maker	gene	337818	343277	.	+	.	ID=CLUHARG00000005458;Name=TUBB3_2
+scaffold625	maker	mRNA	337818	343277	.	+	.	ID=CLUHART00000008717;Parent=CLUHARG00000005458
+scaffold625	maker	exon	337818	337971	.	+	.	ID=CLUHART00000008717:exon:1404;Parent=CLUHART00000008717
+scaffold625	maker	exon	340733	340841	.	+	.	ID=CLUHART00000008717:exon:1405;Parent=CLUHART00000008717
+scaffold625	maker	exon	341518	341628	.	+	.	ID=CLUHART00000008717:exon:1406;Parent=CLUHART00000008717
+scaffold625	maker	exon	341964	343277	.	+	.	ID=CLUHART00000008717:exon:1407;Parent=CLUHART00000008717
+scaffold625	maker	CDS	337915	337971	.	+	0	ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
+scaffold625	maker	CDS	340733	340841	.	+	0	ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
+scaffold625	maker	CDS	341518	341628	.	+	2	ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
+scaffold625	maker	CDS	341964	343033	.	+	2	ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
+scaffold625	maker	five_prime_UTR	337818	337914	.	+	.	ID=CLUHART00000008717:five_prime_utr;Parent=CLUHART00000008717
+scaffold625	maker	three_prime_UTR	343034	343277	.	+	.	ID=CLUHART00000008717:three_prime_utr;Parent=CLUHART00000008717
+scaffold789	maker	gene	558184	564780	.	+	.	ID=CLUHARG00000003852;Name=PF11_0240
+scaffold789	maker	mRNA	558184	564780	.	+	.	ID=CLUHART00000006146;Parent=CLUHARG00000003852
+scaffold789	maker	exon	558184	560123	.	+	.	ID=CLUHART00000006146:exon:995;Parent=CLUHART00000006146
+scaffold789	maker	exon	561401	561519	.	+	.	ID=CLUHART00000006146:exon:996;Parent=CLUHART00000006146
+scaffold789	maker	exon	564171	564235	.	+	.	ID=CLUHART00000006146:exon:997;Parent=CLUHART00000006146
+scaffold789	maker	exon	564372	564780	.	+	.	ID=CLUHART00000006146:exon:998;Parent=CLUHART00000006146
+scaffold789	maker	CDS	558191	560123	.	+	0	ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
+scaffold789	maker	CDS	561401	561519	.	+	2	ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
+scaffold789	maker	CDS	564171	564235	.	+	0	ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
+scaffold789	maker	CDS	564372	564588	.	+	1	ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
+scaffold789	maker	five_prime_UTR	558184	558190	.	+	.	ID=CLUHART00000006146:five_prime_utr;Parent=CLUHART00000006146
+scaffold789	maker	three_prime_UTR	564589	564780	.	+	.	ID=CLUHART00000006146:three_prime_utr;Parent=CLUHART00000006146
+scaffold789	maker	mRNA	558184	564780	.	+	.	ID=CLUHART00000006147;Parent=CLUHARG00000003852
+scaffold789	maker	exon	558184	560123	.	+	.	ID=CLUHART00000006147:exon:997;Parent=CLUHART00000006147
+scaffold789	maker	exon	561401	561519	.	+	.	ID=CLUHART00000006147:exon:998;Parent=CLUHART00000006147
+scaffold789	maker	exon	562057	562121	.	+	.	ID=CLUHART00000006147:exon:999;Parent=CLUHART00000006147
+scaffold789	maker	exon	564372	564780	.	+	.	ID=CLUHART00000006147:exon:1000;Parent=CLUHART00000006147
+scaffold789	maker	CDS	558191	560123	.	+	0	ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
+scaffold789	maker	CDS	561401	561519	.	+	2	ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
+scaffold789	maker	CDS	562057	562121	.	+	0	ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
+scaffold789	maker	CDS	564372	564588	.	+	1	ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
+scaffold789	maker	five_prime_UTR	558184	558190	.	+	.	ID=CLUHART00000006147:five_prime_utr;Parent=CLUHART00000006147
+scaffold789	maker	three_prime_UTR	564589	564780	.	+	.	ID=CLUHART00000006147:three_prime_utr;Parent=CLUHART00000006147
--- a/src/agat/agat_convert_sp_gff2gtf/test_data/script.sh
+++ b/src/agat/agat_convert_sp_gff2gtf/test_data/script.sh
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+# clone repo
+if [ ! -d /tmp/agat_source ]; then
+  git clone --depth 1 --single-branch --branch master https://github.com/NBISweden/AGAT /tmp/agat_source
+fi
+
+# copy test data
+cp -r /tmp/agat_source/t/gff_syntax/in/0_test.gff src/agat/agat_convert_sp_gff2gtf/test_data
--- a/src/agat/agat_convert_sp_gff2tsv/config.vsh.yaml
+++ b/src/agat/agat_convert_sp_gff2tsv/config.vsh.yaml
@@ -0,0 +1,70 @@
+name: agat_convert_sp_gff2tsv
+namespace: agat
+description: |
+    The script aims to convert gtf/gff file into tabulated file. Attribute's
+    tags from the 9th column become column titles.
+keywords: [gene annotations, GFF conversion]
+links:
+  homepage: https://github.com/NBISweden/AGAT
+  documentation: https://agat.readthedocs.io/en/latest/tools/agat_convert_sp_gff2tsv.html
+  issue_tracker: https://github.com/NBISweden/AGAT/issues
+  repository: https://github.com/NBISweden/AGAT
+references: 
+  doi: 10.5281/zenodo.3552717
+license: GPL-3.0
+authors:
+  - __merge__: /src/_authors/leila_paquay.yaml
+    roles: [ author, maintainer ]
+
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: --gff
+        alternatives: [-f]
+        description: Input GTF/GFF file.
+        type: file
+        required: true
+        direction: input
+        example: input.gff
+  - name: Outputs
+    arguments:       
+      - name: --output
+        alternatives: [-o, --out, --outfile]
+        description: Output GFF file. If no output file is specified, the output will be written to STDOUT.
+        type: file
+        direction: output
+        required: true
+        example: output.gff
+  - name: Arguments
+    arguments:
+      - name: --config
+        alternatives: [-c]
+        description: |
+          String - Input agat config file. By default AGAT takes as input
+          agat_config.yaml file from the working directory if any,
+          otherwise it takes the orignal agat_config.yaml shipped with
+          AGAT. To get the agat_config.yaml locally type: "agat config
+          --expose". The --config option gives you the possibility to use
+          your own AGAT config file (located elsewhere or named
+          differently).        
+        type: file
+        required: false
+        example: custom_agat_config.yaml
+resources:
+  - type: bash_script
+    path: script.sh
+test_resources:
+  - type: bash_script
+    path: test.sh
+  - type: file
+    path: test_data
+engines:
+  - type: docker
+    image: quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0
+    setup:
+      - type: docker
+        run: |
+          agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.txt
+runners:
+  - type: executable
+  - type: nextflow
--- a/src/agat/agat_convert_sp_gff2tsv/help.txt
+++ b/src/agat/agat_convert_sp_gff2tsv/help.txt
@@ -0,0 +1,63 @@
+```sh
+agat_convert_sp_gff2tsv.pl --help
+```
+
+ ------------------------------------------------------------------------------
+|   Another GFF Analysis Toolkit (AGAT) - Version: v1.4.0                      |
+|   https://github.com/NBISweden/AGAT                                          |
+|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
+ ------------------------------------------------------------------------------
+
+
+Name:
+    agat_convert_sp_gff2tsv.pl
+
+Description:
+    The script aims to convert gtf/gff file into tabulated file. Attribute's
+    tags from the 9th column become column titles.
+
+Usage:
+        agat_convert_sp_gff2tsv.pl -gff file.gff [ -o outfile ]
+        agat_convert_sp_gff2tsv.pl --help
+
+Options:
+    --gff or -f
+            Input GTF/GFF file.
+
+    -o , --output , --out or --outfile
+            Output GFF file. If no output file is specified, the output will
+            be written to STDOUT.
+
+    -c or --config
+            String - Input agat config file. By default AGAT takes as input
+            agat_config.yaml file from the working directory if any,
+            otherwise it takes the orignal agat_config.yaml shipped with
+            AGAT. To get the agat_config.yaml locally type: "agat config
+            --expose". The --config option gives you the possibility to use
+            your own AGAT config file (located elsewhere or named
+            differently).
+
+    -h or --help
+            Display this helpful text.
+
+Feedback:
+  Did you find a bug?:
+    Do not hesitate to report bugs to help us keep track of the bugs and
+    their resolution. Please use the GitHub issue tracking system available
+    at this address:
+
+                https://github.com/NBISweden/AGAT/issues
+
+     Ensure that the bug was not already reported by searching under Issues.
+     If you're unable to find an (open) issue addressing the problem, open a new one.
+     Try as much as possible to include in the issue when relevant:
+     - a clear description,
+     - as much relevant information as possible,
+     - the command used,
+     - a data sample,
+     - an explanation of the expected behaviour that is not occurring.
+
+  Do you want to contribute?:
+    You are very welcome, visit this address for the Contributing
+    guidelines:
+    https://github.com/NBISweden/AGAT/blob/master/CONTRIBUTING.md
--- a/src/agat/agat_convert_sp_gff2tsv/script.sh
+++ b/src/agat/agat_convert_sp_gff2tsv/script.sh
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+agat_convert_sp_gff2tsv.pl \
+  -f "$par_gff" \
+  -o "$par_output" \
+  ${par_config:+--config "${par_config}"}
--- a/src/agat/agat_convert_sp_gff2tsv/test.sh
+++ b/src/agat/agat_convert_sp_gff2tsv/test.sh
@@ -0,0 +1,27 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+test_dir="${meta_resources_dir}/test_data"
+out_dir="${meta_resources_dir}/out_data"
+
+echo "> Run $meta_name with test data"
+"$meta_executable" \
+  --gff "$test_dir/1.gff" \
+  --output "$out_dir/output.gff" 
+
+echo ">> Checking output"
+[ ! -f "$out_dir/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
+
+echo ">> Check if output is empty"
+[ ! -s "$out_dir/output.gff" ] && echo "Output file output.gff is empty" && exit 1
+
+echo ">> Check if output matches expected output"
+diff "$out_dir/output.gff" "$test_dir/agat_convert_sp_gff2tsv_1.tsv"
+if [ $? -ne 0 ]; then
+  echo "Output file output.gff does not match expected output"
+  exit 1
+fi
+
+echo "> Test successful"
--- a/src/agat/agat_convert_sp_gff2tsv/test_data/1.gff
+++ b/src/agat/agat_convert_sp_gff2tsv/test_data/1.gff
@@ -0,0 +1,942 @@
+##gff-version 3
+##sequence-region   1 1 43270923
+#!genome-build RAP-DB IRGSP-1.0
+#!genome-version IRGSP-1.0
+#!genome-date 2015-10
+#!genome-build-accession GCA_001433935.1
+1	RAP-DB	chromosome	1	43270923	.	.	.	ID=chromosome:1;Alias=Chr1,AP014957.1,NC_029256.1
+###
+1	irgsp	repeat_region	2000	2100	.	+	.	ID=fakeRepeat1
+###
+1	irgsp	gene	2983	10815	.	+	.	ID=gene:Os01g0100100;biotype=protein_coding;description=RabGAP/TBC domain containing protein. (Os01t0100100-01);gene_id=Os01g0100100;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	2983	10815	.	+	.	ID=transcript:Os01t0100100-01;Parent=gene:Os01g0100100;biotype=protein_coding;transcript_id=Os01t0100100-01
+1	irgsp	exon	2983	3268	.	+	.	Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100100-01.exon1;rank=1
+1	irgsp	five_prime_UTR	2983	3268	.	+	.	Parent=transcript:Os01t0100100-01
+1	irgsp	five_prime_UTR	3354	3448	.	+	.	Parent=transcript:Os01t0100100-01
+1	irgsp	exon	3354	3616	.	+	.	Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0100100-01.exon2;rank=2
+1	irgsp	CDS	3449	3616	.	+	0	ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
+1	irgsp	exon	4357	4455	.	+	.	Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100100-01.exon3;rank=3
+1	irgsp	CDS	4357	4455	.	+	0	ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
+1	irgsp	exon	5457	5560	.	+	.	Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon4;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0100100-01.exon4;rank=4
+1	irgsp	CDS	5457	5560	.	+	0	ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
+1	irgsp	exon	7136	7944	.	+	.	Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon5;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=Os01t0100100-01.exon5;rank=5
+1	irgsp	CDS	7136	7944	.	+	1	ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
+1	irgsp	exon	8028	8150	.	+	.	Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon6;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=Os01t0100100-01.exon6;rank=6
+1	irgsp	CDS	8028	8150	.	+	2	ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
+1	irgsp	exon	8232	8320	.	+	.	Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon7;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100100-01.exon7;rank=7
+1	irgsp	CDS	8232	8320	.	+	2	ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
+1	irgsp	exon	8408	8608	.	+	.	Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon8;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100100-01.exon8;rank=8
+1	irgsp	CDS	8408	8608	.	+	0	ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
+1	irgsp	exon	9210	9615	.	+	.	Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon9;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0100100-01.exon9;rank=9
+1	irgsp	CDS	9210	9615	.	+	0	ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
+1	irgsp	exon	10102	10187	.	+	.	Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon10;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100100-01.exon10;rank=10
+1	irgsp	CDS	10102	10187	.	+	2	ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
+1	irgsp	CDS	10274	10297	.	+	0	ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
+1	irgsp	exon	10274	10430	.	+	.	Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon11;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0100100-01.exon11;rank=11
+1	irgsp	three_prime_UTR	10298	10430	.	+	.	Parent=transcript:Os01t0100100-01
+1	irgsp	exon	10504	10815	.	+	.	Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon12;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100100-01.exon12;rank=12
+1	irgsp	three_prime_UTR	10504	10815	.	+	.	Parent=transcript:Os01t0100100-01
+###
+1	irgsp	gene	11218	12435	.	+	.	ID=gene:Os01g0100200;biotype=protein_coding;description=Conserved hypothetical protein. (Os01t0100200-01);gene_id=Os01g0100200;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	11218	12435	.	+	.	ID=transcript:Os01t0100200-01;Parent=gene:Os01g0100200;biotype=protein_coding;transcript_id=Os01t0100200-01
+1	irgsp	five_prime_UTR	11218	11797	.	+	.	Parent=transcript:Os01t0100200-01
+1	irgsp	exon	11218	12060	.	+	.	Parent=transcript:Os01t0100200-01;Name=Os01t0100200-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0100200-01.exon1;rank=1
+1	irgsp	CDS	11798	12060	.	+	0	ID=CDS:Os01t0100200-01;Parent=transcript:Os01t0100200-01;protein_id=Os01t0100200-01
+1	irgsp	CDS	12152	12317	.	+	1	ID=CDS:Os01t0100200-01;Parent=transcript:Os01t0100200-01;protein_id=Os01t0100200-01
+1	irgsp	exon	12152	12435	.	+	.	Parent=transcript:Os01t0100200-01;Name=Os01t0100200-01.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0100200-01.exon2;rank=2
+1	irgsp	three_prime_UTR	12318	12435	.	+	.	Parent=transcript:Os01t0100200-01
+###
+1	irgsp	gene	11372	12284	.	-	.	ID=gene:Os01g0100300;biotype=protein_coding;description=Cytochrome P450 domain containing protein. (Os01t0100300-00);gene_id=Os01g0100300;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	11372	12284	.	-	.	ID=transcript:Os01t0100300-00;Parent=gene:Os01g0100300;biotype=protein_coding;transcript_id=Os01t0100300-00
+1	irgsp	exon	11372	12042	.	-	.	Parent=transcript:Os01t0100300-00;Name=Os01t0100300-00.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100300-00.exon2;rank=2
+1	irgsp	CDS	11372	12042	.	-	2	ID=CDS:Os01t0100300-00;Parent=transcript:Os01t0100300-00;protein_id=Os01t0100300-00
+1	irgsp	exon	12146	12284	.	-	.	Parent=transcript:Os01t0100300-00;Name=Os01t0100300-00.exon1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0100300-00.exon1;rank=1
+1	irgsp	CDS	12146	12284	.	-	0	ID=CDS:Os01t0100300-00;Parent=transcript:Os01t0100300-00;protein_id=Os01t0100300-00
+###
+1	irgsp	gene	12721	15685	.	+	.	ID=gene:Os01g0100400;biotype=protein_coding;description=Similar to Pectinesterase-like protein. (Os01t0100400-01);gene_id=Os01g0100400;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	12721	15685	.	+	.	ID=transcript:Os01t0100400-01;Parent=gene:Os01g0100400;biotype=protein_coding;transcript_id=Os01t0100400-01
+1	irgsp	five_prime_UTR	12721	12773	.	+	.	Parent=transcript:Os01t0100400-01
+1	irgsp	exon	12721	13813	.	+	.	Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0100400-01.exon1;rank=1
+1	irgsp	CDS	12774	13813	.	+	0	ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
+1	irgsp	exon	13906	14271	.	+	.	Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0100400-01.exon2;rank=2
+1	irgsp	CDS	13906	14271	.	+	1	ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
+1	irgsp	exon	14359	14437	.	+	.	Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0100400-01.exon3;rank=3
+1	irgsp	CDS	14359	14437	.	+	1	ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
+1	irgsp	exon	14969	15171	.	+	.	Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon4;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0100400-01.exon4;rank=4
+1	irgsp	CDS	14969	15171	.	+	0	ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
+1	irgsp	CDS	15266	15359	.	+	1	ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
+1	irgsp	exon	15266	15685	.	+	.	Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon5;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0100400-01.exon5;rank=5
+1	irgsp	three_prime_UTR	15360	15685	.	+	.	Parent=transcript:Os01t0100400-01
+###
+1	irgsp	gene	12808	13978	.	-	.	ID=gene:Os01g0100466;biotype=protein_coding;description=Hypothetical protein. (Os01t0100466-00);gene_id=Os01g0100466;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	12808	13978	.	-	.	ID=transcript:Os01t0100466-00;Parent=gene:Os01g0100466;biotype=protein_coding;transcript_id=Os01t0100466-00
+1	irgsp	three_prime_UTR	12808	12868	.	-	.	Parent=transcript:Os01t0100466-00
+1	irgsp	exon	12808	13782	.	-	.	Parent=transcript:Os01t0100466-00;Name=Os01t0100466-00.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100466-00.exon2;rank=2
+1	irgsp	CDS	12869	13102	.	-	0	ID=CDS:Os01t0100466-00;Parent=transcript:Os01t0100466-00;protein_id=Os01t0100466-00
+1	irgsp	five_prime_UTR	13103	13782	.	-	.	Parent=transcript:Os01t0100466-00
+1	irgsp	exon	13880	13978	.	-	.	Parent=transcript:Os01t0100466-00;Name=Os01t0100466-00.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100466-00.exon1;rank=1
+1	irgsp	five_prime_UTR	13880	13978	.	-	.	Parent=transcript:Os01t0100466-00
+###
+1	irgsp	gene	16399	20144	.	+	.	ID=gene:Os01g0100500;biotype=protein_coding;description=Immunoglobulin-like domain containing protein. (Os01t0100500-01);gene_id=Os01g0100500;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	16399	20144	.	+	.	ID=transcript:Os01t0100500-01;Parent=gene:Os01g0100500;biotype=protein_coding;transcript_id=Os01t0100500-01
+1	irgsp	five_prime_UTR	16399	16598	.	+	.	Parent=transcript:Os01t0100500-01
+1	irgsp	exon	16399	16976	.	+	.	Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0100500-01.exon1;rank=1
+1	irgsp	CDS	16599	16976	.	+	0	ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
+1	irgsp	exon	17383	17474	.	+	.	Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0100500-01.exon2;rank=2
+1	irgsp	CDS	17383	17474	.	+	0	ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
+1	irgsp	exon	17558	18258	.	+	.	Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon3;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=Os01t0100500-01.exon3;rank=3
+1	irgsp	CDS	17558	18258	.	+	1	ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
+1	irgsp	exon	18501	18571	.	+	.	Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon4;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100500-01.exon4;rank=4
+1	irgsp	CDS	18501	18571	.	+	2	ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
+1	irgsp	exon	18968	19057	.	+	.	Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon5;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100500-01.exon5;rank=5
+1	irgsp	CDS	18968	19057	.	+	0	ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
+1	irgsp	exon	19142	19321	.	+	.	Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon6;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100500-01.exon6;rank=6
+1	irgsp	CDS	19142	19321	.	+	0	ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
+1	irgsp	CDS	19531	19593	.	+	0	ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
+1	irgsp	exon	19531	19629	.	+	.	Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon7;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0100500-01.exon7;rank=7
+1	irgsp	three_prime_UTR	19594	19629	.	+	.	Parent=transcript:Os01t0100500-01
+1	irgsp	exon	19734	20144	.	+	.	Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon8;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100500-01.exon8;rank=8
+1	irgsp	three_prime_UTR	19734	20144	.	+	.	Parent=transcript:Os01t0100500-01
+###
+1	irgsp	gene	22841	26892	.	+	.	ID=gene:Os01g0100600;biotype=protein_coding;description=Single-stranded nucleic acid binding R3H domain containing protein. (Os01t0100600-01);gene_id=Os01g0100600;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	22841	26892	.	+	.	ID=transcript:Os01t0100600-01;Parent=gene:Os01g0100600;biotype=protein_coding;transcript_id=Os01t0100600-01
+1	irgsp	five_prime_UTR	22841	23231	.	+	.	Parent=transcript:Os01t0100600-01
+1	irgsp	exon	22841	23281	.	+	.	Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0100600-01.exon1;rank=1
+1	irgsp	CDS	23232	23281	.	+	0	ID=CDS:Os01t0100600-01;Parent=transcript:Os01t0100600-01;protein_id=Os01t0100600-01
+1	irgsp	exon	23572	23847	.	+	.	Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0100600-01.exon2;rank=2
+1	irgsp	CDS	23572	23847	.	+	1	ID=CDS:Os01t0100600-01;Parent=transcript:Os01t0100600-01;protein_id=Os01t0100600-01
+1	irgsp	exon	23962	24033	.	+	.	Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon3;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0100600-01.exon3;rank=3
+1	irgsp	CDS	23962	24033	.	+	1	ID=CDS:Os01t0100600-01;Parent=transcript:Os01t0100600-01;protein_id=Os01t0100600-01
+1	irgsp	exon	24492	24577	.	+	.	Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon4;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=Os01t0100600-01.exon4;rank=4
+1	irgsp	CDS	24492	24577	.	+	1	ID=CDS:Os01t0100600-01;Parent=transcript:Os01t0100600-01;protein_id=Os01t0100600-01
+1	irgsp	exon	25445	25519	.	+	.	Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon5;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=Os01t0100600-01.exon5;rank=5
+1	irgsp	CDS	25445	25519	.	+	2	ID=CDS:Os01t0100600-01;Parent=transcript:Os01t0100600-01;protein_id=Os01t0100600-01
+1	irgsp	CDS	25883	26391	.	+	2	ID=CDS:Os01t0100600-01;Parent=transcript:Os01t0100600-01;protein_id=Os01t0100600-01
+1	irgsp	exon	25883	26892	.	+	.	Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon6;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0100600-01.exon6;rank=6
+1	irgsp	three_prime_UTR	26392	26892	.	+	.	Parent=transcript:Os01t0100600-01
+###
+1	irgsp	gene	25861	26424	.	-	.	ID=gene:Os01g0100650;biotype=protein_coding;description=Hypothetical gene. (Os01t0100650-00);gene_id=Os01g0100650;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	25861	26424	.	-	.	ID=transcript:Os01t0100650-00;Parent=gene:Os01g0100650;biotype=protein_coding;transcript_id=Os01t0100650-00
+1	irgsp	three_prime_UTR	25861	26039	.	-	.	Parent=transcript:Os01t0100650-00
+1	irgsp	exon	25861	26424	.	-	.	Parent=transcript:Os01t0100650-00;Name=Os01t0100650-00.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100650-00.exon1;rank=1
+1	irgsp	CDS	26040	26423	.	-	0	ID=CDS:Os01t0100650-00;Parent=transcript:Os01t0100650-00;protein_id=Os01t0100650-00
+1	irgsp	five_prime_UTR	26424	26424	.	-	.	Parent=transcript:Os01t0100650-00
+###
+1	irgsp	gene	27143	28644	.	+	.	ID=gene:Os01g0100700;biotype=protein_coding;description=Similar to 40S ribosomal protein S5-1. (Os01t0100700-01);gene_id=Os01g0100700;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	27143	28644	.	+	.	ID=transcript:Os01t0100700-01;Parent=gene:Os01g0100700;biotype=protein_coding;transcript_id=Os01t0100700-01
+1	irgsp	five_prime_UTR	27143	27220	.	+	.	Parent=transcript:Os01t0100700-01
+1	irgsp	exon	27143	27292	.	+	.	Parent=transcript:Os01t0100700-01;Name=Os01t0100700-01.exon1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0100700-01.exon1;rank=1
+1	irgsp	CDS	27221	27292	.	+	0	ID=CDS:Os01t0100700-01;Parent=transcript:Os01t0100700-01;protein_id=Os01t0100700-01
+1	irgsp	exon	27370	27641	.	+	.	Parent=transcript:Os01t0100700-01;Name=Os01t0100700-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0100700-01.exon2;rank=2
+1	irgsp	CDS	27370	27641	.	+	0	ID=CDS:Os01t0100700-01;Parent=transcript:Os01t0100700-01;protein_id=Os01t0100700-01
+1	irgsp	exon	28090	28293	.	+	.	Parent=transcript:Os01t0100700-01;Name=Os01t0100700-01.exon3;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0100700-01.exon3;rank=3
+1	irgsp	CDS	28090	28293	.	+	1	ID=CDS:Os01t0100700-01;Parent=transcript:Os01t0100700-01;protein_id=Os01t0100700-01
+1	irgsp	CDS	28365	28419	.	+	1	ID=CDS:Os01t0100700-01;Parent=transcript:Os01t0100700-01;protein_id=Os01t0100700-01
+1	irgsp	exon	28365	28644	.	+	.	Parent=transcript:Os01t0100700-01;Name=Os01t0100700-01.exon4;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0100700-01.exon4;rank=4
+1	irgsp	three_prime_UTR	28420	28644	.	+	.	Parent=transcript:Os01t0100700-01
+###
+1	irgsp	gene	29818	34453	.	+	.	ID=gene:Os01g0100800;biotype=protein_coding;description=Protein of unknown function DUF1664 family protein. (Os01t0100800-01);gene_id=Os01g0100800;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	29818	34453	.	+	.	ID=transcript:Os01t0100800-01;Parent=gene:Os01g0100800;biotype=protein_coding;transcript_id=Os01t0100800-01
+1	irgsp	five_prime_UTR	29818	29939	.	+	.	Parent=transcript:Os01t0100800-01
+1	irgsp	exon	29818	29976	.	+	.	Parent=transcript:Os01t0100800-01;Name=Os01t0100800-01.exon1;constitutive=1;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Os01t0100800-01.exon1;rank=1
+1	irgsp	CDS	29940	29976	.	+	0	ID=CDS:Os01t0100800-01;Parent=transcript:Os01t0100800-01;protein_id=Os01t0100800-01
+1	irgsp	exon	30146	30228	.	+	.	Parent=transcript:Os01t0100800-01;Name=Os01t0100800-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100800-01.exon2;rank=2
+1	irgsp	CDS	30146	30228	.	+	2	ID=CDS:Os01t0100800-01;Parent=transcript:Os01t0100800-01;protein_id=Os01t0100800-01
+1	irgsp	exon	30735	30806	.	+	.	Parent=transcript:Os01t0100800-01;Name=Os01t0100800-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100800-01.exon3;rank=3
+1	irgsp	CDS	30735	30806	.	+	0	ID=CDS:Os01t0100800-01;Parent=transcript:Os01t0100800-01;protein_id=Os01t0100800-01
+1	irgsp	exon	30885	30963	.	+	.	Parent=transcript:Os01t0100800-01;Name=Os01t0100800-01.exon4;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0100800-01.exon4;rank=4
+1	irgsp	CDS	30885	30963	.	+	0	ID=CDS:Os01t0100800-01;Parent=transcript:Os01t0100800-01;protein_id=Os01t0100800-01
+1	irgsp	exon	31258	31325	.	+	.	Parent=transcript:Os01t0100800-01;Name=Os01t0100800-01.exon5;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100800-01.exon5;rank=5
+1	irgsp	CDS	31258	31325	.	+	2	ID=CDS:Os01t0100800-01;Parent=transcript:Os01t0100800-01;protein_id=Os01t0100800-01
+1	irgsp	exon	31505	31606	.	+	.	Parent=transcript:Os01t0100800-01;Name=Os01t0100800-01.exon6;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100800-01.exon6;rank=6
+1	irgsp	CDS	31505	31606	.	+	0	ID=CDS:Os01t0100800-01;Parent=transcript:Os01t0100800-01;protein_id=Os01t0100800-01
+1	irgsp	exon	32377	32466	.	+	.	Parent=transcript:Os01t0100800-01;Name=Os01t0100800-01.exon7;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100800-01.exon7;rank=7
+1	irgsp	CDS	32377	32466	.	+	0	ID=CDS:Os01t0100800-01;Parent=transcript:Os01t0100800-01;protein_id=Os01t0100800-01
+1	irgsp	exon	32542	32616	.	+	.	Parent=transcript:Os01t0100800-01;Name=Os01t0100800-01.exon8;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100800-01.exon8;rank=8
+1	irgsp	CDS	32542	32616	.	+	0	ID=CDS:Os01t0100800-01;Parent=transcript:Os01t0100800-01;protein_id=Os01t0100800-01
+1	irgsp	exon	32712	32744	.	+	.	Parent=transcript:Os01t0100800-01;Name=Os01t0100800-01.exon9;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100800-01.exon9;rank=9
+1	irgsp	CDS	32712	32744	.	+	0	ID=CDS:Os01t0100800-01;Parent=transcript:Os01t0100800-01;protein_id=Os01t0100800-01
+1	irgsp	exon	32828	32905	.	+	.	Parent=transcript:Os01t0100800-01;Name=Os01t0100800-01.exon10;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100800-01.exon10;rank=10
+1	irgsp	CDS	32828	32905	.	+	0	ID=CDS:Os01t0100800-01;Parent=transcript:Os01t0100800-01;protein_id=Os01t0100800-01
+1	irgsp	exon	33274	33330	.	+	.	Parent=transcript:Os01t0100800-01;Name=Os01t0100800-01.exon11;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100800-01.exon11;rank=11
+1	irgsp	CDS	33274	33330	.	+	0	ID=CDS:Os01t0100800-01;Parent=transcript:Os01t0100800-01;protein_id=Os01t0100800-01
+1	irgsp	exon	33400	33471	.	+	.	Parent=transcript:Os01t0100800-01;Name=Os01t0100800-01.exon12;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100800-01.exon12;rank=12
+1	irgsp	CDS	33400	33471	.	+	0	ID=CDS:Os01t0100800-01;Parent=transcript:Os01t0100800-01;protein_id=Os01t0100800-01
+1	irgsp	exon	33543	33617	.	+	.	Parent=transcript:Os01t0100800-01;Name=Os01t0100800-01.exon13;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100800-01.exon13;rank=13
+1	irgsp	CDS	33543	33617	.	+	0	ID=CDS:Os01t0100800-01;Parent=transcript:Os01t0100800-01;protein_id=Os01t0100800-01
+1	irgsp	CDS	33975	34124	.	+	0	ID=CDS:Os01t0100800-01;Parent=transcript:Os01t0100800-01;protein_id=Os01t0100800-01
+1	irgsp	exon	33975	34453	.	+	.	Parent=transcript:Os01t0100800-01;Name=Os01t0100800-01.exon14;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0100800-01.exon14;rank=14
+1	irgsp	three_prime_UTR	34125	34453	.	+	.	Parent=transcript:Os01t0100800-01
+###
+1	irgsp	gene	35623	41136	.	+	.	ID=gene:Os01g0100900;Name=SPHINGOSINE-1-PHOSPHATE LYASE 1%2C Sphingosine-1-Phoshpate Lyase 1;biotype=protein_coding;description=Sphingosine-1-phosphate lyase%2C Disease resistance response (Os01t0100900-01);gene_id=Os01g0100900;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	35623	41136	.	+	.	ID=transcript:Os01t0100900-01;Parent=gene:Os01g0100900;biotype=protein_coding;transcript_id=Os01t0100900-01
+1	irgsp	five_prime_UTR	35623	35742	.	+	.	Parent=transcript:Os01t0100900-01
+1	irgsp	exon	35623	35939	.	+	.	Parent=transcript:Os01t0100900-01;Name=Os01t0100900-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0100900-01.exon1;rank=1
+1	irgsp	CDS	35743	35939	.	+	0	ID=CDS:Os01t0100900-01;Parent=transcript:Os01t0100900-01;protein_id=Os01t0100900-01
+1	irgsp	exon	36027	36072	.	+	.	Parent=transcript:Os01t0100900-01;Name=Os01t0100900-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0100900-01.exon2;rank=2
+1	irgsp	CDS	36027	36072	.	+	1	ID=CDS:Os01t0100900-01;Parent=transcript:Os01t0100900-01;protein_id=Os01t0100900-01
+1	irgsp	exon	36517	36668	.	+	.	Parent=transcript:Os01t0100900-01;Name=Os01t0100900-01.exon3;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0100900-01.exon3;rank=3
+1	irgsp	CDS	36517	36668	.	+	0	ID=CDS:Os01t0100900-01;Parent=transcript:Os01t0100900-01;protein_id=Os01t0100900-01
+1	irgsp	exon	36818	36877	.	+	.	Parent=transcript:Os01t0100900-01;Name=Os01t0100900-01.exon4;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0100900-01.exon4;rank=4
+1	irgsp	CDS	36818	36877	.	+	1	ID=CDS:Os01t0100900-01;Parent=transcript:Os01t0100900-01;protein_id=Os01t0100900-01
+1	irgsp	exon	37594	37818	.	+	.	Parent=transcript:Os01t0100900-01;Name=Os01t0100900-01.exon5;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0100900-01.exon5;rank=5
+1	irgsp	CDS	37594	37818	.	+	1	ID=CDS:Os01t0100900-01;Parent=transcript:Os01t0100900-01;protein_id=Os01t0100900-01
+1	irgsp	exon	37892	38033	.	+	.	Parent=transcript:Os01t0100900-01;Name=Os01t0100900-01.exon6;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0100900-01.exon6;rank=6
+1	irgsp	CDS	37892	38033	.	+	1	ID=CDS:Os01t0100900-01;Parent=transcript:Os01t0100900-01;protein_id=Os01t0100900-01
+1	irgsp	exon	38276	38326	.	+	.	Parent=transcript:Os01t0100900-01;Name=Os01t0100900-01.exon7;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100900-01.exon7;rank=7
+1	irgsp	CDS	38276	38326	.	+	0	ID=CDS:Os01t0100900-01;Parent=transcript:Os01t0100900-01;protein_id=Os01t0100900-01
+1	irgsp	exon	38434	38525	.	+	.	Parent=transcript:Os01t0100900-01;Name=Os01t0100900-01.exon8;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0100900-01.exon8;rank=8
+1	irgsp	CDS	38434	38525	.	+	0	ID=CDS:Os01t0100900-01;Parent=transcript:Os01t0100900-01;protein_id=Os01t0100900-01
+1	irgsp	exon	39319	39445	.	+	.	Parent=transcript:Os01t0100900-01;Name=Os01t0100900-01.exon9;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0100900-01.exon9;rank=9
+1	irgsp	CDS	39319	39445	.	+	1	ID=CDS:Os01t0100900-01;Parent=transcript:Os01t0100900-01;protein_id=Os01t0100900-01
+1	irgsp	exon	39553	39568	.	+	.	Parent=transcript:Os01t0100900-01;Name=Os01t0100900-01.exon10;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0100900-01.exon10;rank=10
+1	irgsp	CDS	39553	39568	.	+	0	ID=CDS:Os01t0100900-01;Parent=transcript:Os01t0100900-01;protein_id=Os01t0100900-01
+1	irgsp	exon	39939	40046	.	+	.	Parent=transcript:Os01t0100900-01;Name=Os01t0100900-01.exon11;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=Os01t0100900-01.exon11;rank=11
+1	irgsp	CDS	39939	40046	.	+	2	ID=CDS:Os01t0100900-01;Parent=transcript:Os01t0100900-01;protein_id=Os01t0100900-01
+1	irgsp	exon	40135	40189	.	+	.	Parent=transcript:Os01t0100900-01;Name=Os01t0100900-01.exon12;constitutive=1;ensembl_end_phase=2;ensembl_phase=1;exon_id=Os01t0100900-01.exon12;rank=12
+1	irgsp	CDS	40135	40189	.	+	2	ID=CDS:Os01t0100900-01;Parent=transcript:Os01t0100900-01;protein_id=Os01t0100900-01
+1	irgsp	exon	40456	40602	.	+	.	Parent=transcript:Os01t0100900-01;Name=Os01t0100900-01.exon13;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0100900-01.exon13;rank=13
+1	irgsp	CDS	40456	40602	.	+	1	ID=CDS:Os01t0100900-01;Parent=transcript:Os01t0100900-01;protein_id=Os01t0100900-01
+1	irgsp	exon	40703	40781	.	+	.	Parent=transcript:Os01t0100900-01;Name=Os01t0100900-01.exon14;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0100900-01.exon14;rank=14
+1	irgsp	CDS	40703	40781	.	+	1	ID=CDS:Os01t0100900-01;Parent=transcript:Os01t0100900-01;protein_id=Os01t0100900-01
+1	irgsp	CDS	40885	41007	.	+	0	ID=CDS:Os01t0100900-01;Parent=transcript:Os01t0100900-01;protein_id=Os01t0100900-01
+1	irgsp	exon	40885	41136	.	+	.	Parent=transcript:Os01t0100900-01;Name=Os01t0100900-01.exon15;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0100900-01.exon15;rank=15
+1	irgsp	three_prime_UTR	41008	41136	.	+	.	Parent=transcript:Os01t0100900-01
+###
+1	irgsp	gene	58658	61090	.	+	.	ID=gene:Os01g0101150;biotype=protein_coding;description=Hypothetical conserved gene. (Os01t0101150-00);gene_id=Os01g0101150;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	58658	61090	.	+	.	ID=transcript:Os01t0101150-00;Parent=gene:Os01g0101150;biotype=protein_coding;transcript_id=Os01t0101150-00
+1	irgsp	exon	58658	61090	.	+	.	Parent=transcript:Os01t0101150-00;Name=Os01t0101150-00.exon1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0101150-00.exon1;rank=1
+1	irgsp	CDS	58658	61090	.	+	0	ID=CDS:Os01t0101150-00;Parent=transcript:Os01t0101150-00;protein_id=Os01t0101150-00
+###
+1	irgsp	gene	62060	65537	.	+	.	ID=gene:Os01g0101200;biotype=protein_coding;description=2%2C3-diketo-5-methylthio-1-phosphopentane phosphatase domain containing protein. (Os01t0101200-01)%3B2%2C3-diketo-5-methylthio-1-phosphopentane phosphatase domain containing protein. (Os01t0101200-02);gene_id=Os01g0101200;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	62060	63576	.	+	.	ID=transcript:Os01t0101200-01;Parent=gene:Os01g0101200;biotype=protein_coding;transcript_id=Os01t0101200-01
+1	irgsp	five_prime_UTR	62060	62103	.	+	.	Parent=transcript:Os01t0101200-01
+1	irgsp	exon	62060	62295	.	+	.	Parent=transcript:Os01t0101200-01;Name=Os01t0101200-01.exon1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0101200-01.exon1;rank=1
+1	irgsp	CDS	62104	62295	.	+	0	ID=CDS:Os01t0101200-01;Parent=transcript:Os01t0101200-01;protein_id=Os01t0101200-01
+1	irgsp	exon	62385	62905	.	+	.	Parent=transcript:Os01t0101200-01;Name=Os01t0101200-02.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0101200-02.exon2;rank=2
+1	irgsp	CDS	62385	62905	.	+	0	ID=CDS:Os01t0101200-01;Parent=transcript:Os01t0101200-01;protein_id=Os01t0101200-01
+1	irgsp	exon	62996	63114	.	+	.	Parent=transcript:Os01t0101200-01;Name=Os01t0101200-02.exon3;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=Os01t0101200-02.exon3;rank=3
+1	irgsp	CDS	62996	63114	.	+	1	ID=CDS:Os01t0101200-01;Parent=transcript:Os01t0101200-01;protein_id=Os01t0101200-01
+1	irgsp	CDS	63248	63345	.	+	2	ID=CDS:Os01t0101200-01;Parent=transcript:Os01t0101200-01;protein_id=Os01t0101200-01
+1	irgsp	exon	63248	63576	.	+	.	Parent=transcript:Os01t0101200-01;Name=Os01t0101200-01.exon4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0101200-01.exon4;rank=4
+1	irgsp	three_prime_UTR	63346	63576	.	+	.	Parent=transcript:Os01t0101200-01
+1	irgsp	mRNA	62112	65537	.	+	.	ID=transcript:Os01t0101200-02;Parent=gene:Os01g0101200;biotype=protein_coding;transcript_id=Os01t0101200-02
+1	irgsp	five_prime_UTR	62112	62112	.	+	.	Parent=transcript:Os01t0101200-02
+1	irgsp	exon	62112	62295	.	+	.	Parent=transcript:Os01t0101200-02;Name=Os01t0101200-02.exon1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0101200-02.exon1;rank=1
+1	irgsp	CDS	62113	62295	.	+	0	ID=CDS:Os01t0101200-02;Parent=transcript:Os01t0101200-02;protein_id=Os01t0101200-02
+1	irgsp	exon	62385	62905	.	+	.	Parent=transcript:Os01t0101200-02;Name=Os01t0101200-02.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0101200-02.exon2;rank=2
+1	irgsp	CDS	62385	62905	.	+	0	ID=CDS:Os01t0101200-02;Parent=transcript:Os01t0101200-02;protein_id=Os01t0101200-02
+1	irgsp	exon	62996	63114	.	+	.	Parent=transcript:Os01t0101200-02;Name=Os01t0101200-02.exon3;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=Os01t0101200-02.exon3;rank=3
+1	irgsp	CDS	62996	63114	.	+	1	ID=CDS:Os01t0101200-02;Parent=transcript:Os01t0101200-02;protein_id=Os01t0101200-02
+1	irgsp	CDS	63248	63345	.	+	2	ID=CDS:Os01t0101200-02;Parent=transcript:Os01t0101200-02;protein_id=Os01t0101200-02
+1	irgsp	exon	63248	65537	.	+	.	Parent=transcript:Os01t0101200-02;Name=Os01t0101200-02.exon4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0101200-02.exon4;rank=4
+1	irgsp	three_prime_UTR	63346	65537	.	+	.	Parent=transcript:Os01t0101200-02
+###
+1	irgsp	gene	63350	66302	.	-	.	ID=gene:Os01g0101300;biotype=protein_coding;description=Similar to MRNA%2C partial cds%2C clone: RAFL22-26-L17. (Fragment). (Os01t0101300-01);gene_id=Os01g0101300;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	63350	66302	.	-	.	ID=transcript:Os01t0101300-01;Parent=gene:Os01g0101300;biotype=protein_coding;transcript_id=Os01t0101300-01
+1	irgsp	three_prime_UTR	63350	63669	.	-	.	Parent=transcript:Os01t0101300-01
+1	irgsp	exon	63350	63783	.	-	.	Parent=transcript:Os01t0101300-01;Name=Os01t0101300-01.exon7;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0101300-01.exon7;rank=7
+1	irgsp	CDS	63670	63783	.	-	0	ID=CDS:Os01t0101300-01;Parent=transcript:Os01t0101300-01;protein_id=Os01t0101300-01
+1	irgsp	exon	63877	64020	.	-	.	Parent=transcript:Os01t0101300-01;Name=Os01t0101300-01.exon6;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0101300-01.exon6;rank=6
+1	irgsp	CDS	63877	64020	.	-	0	ID=CDS:Os01t0101300-01;Parent=transcript:Os01t0101300-01;protein_id=Os01t0101300-01
+1	irgsp	exon	64339	64431	.	-	.	Parent=transcript:Os01t0101300-01;Name=Os01t0101300-01.exon5;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0101300-01.exon5;rank=5
+1	irgsp	CDS	64339	64431	.	-	0	ID=CDS:Os01t0101300-01;Parent=transcript:Os01t0101300-01;protein_id=Os01t0101300-01
+1	irgsp	exon	64665	64779	.	-	.	Parent=transcript:Os01t0101300-01;Name=Os01t0101300-01.exon4;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0101300-01.exon4;rank=4
+1	irgsp	CDS	64665	64779	.	-	1	ID=CDS:Os01t0101300-01;Parent=transcript:Os01t0101300-01;protein_id=Os01t0101300-01
+1	irgsp	exon	64902	65152	.	-	.	Parent=transcript:Os01t0101300-01;Name=Os01t0101300-01.exon3;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0101300-01.exon3;rank=3
+1	irgsp	CDS	64902	65152	.	-	0	ID=CDS:Os01t0101300-01;Parent=transcript:Os01t0101300-01;protein_id=Os01t0101300-01
+1	irgsp	exon	65248	65431	.	-	.	Parent=transcript:Os01t0101300-01;Name=Os01t0101300-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0101300-01.exon2;rank=2
+1	irgsp	CDS	65248	65431	.	-	1	ID=CDS:Os01t0101300-01;Parent=transcript:Os01t0101300-01;protein_id=Os01t0101300-01
+1	irgsp	CDS	65628	65950	.	-	0	ID=CDS:Os01t0101300-01;Parent=transcript:Os01t0101300-01;protein_id=Os01t0101300-01
+1	irgsp	exon	65628	66302	.	-	.	Parent=transcript:Os01t0101300-01;Name=Os01t0101300-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0101300-01.exon1;rank=1
+1	irgsp	five_prime_UTR	65951	66302	.	-	.	Parent=transcript:Os01t0101300-01
+###
+1	irgsp	gene	72816	78349	.	+	.	ID=gene:Os01g0101600;biotype=protein_coding;description=Immunoglobulin-like fold domain containing protein. (Os01t0101600-01)%3BImmunoglobulin-like fold domain containing protein. (Os01t0101600-02)%3BHypothetical conserved gene. (Os01t0101600-03);gene_id=Os01g0101600;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	72816	78349	.	+	.	ID=transcript:Os01t0101600-01;Parent=gene:Os01g0101600;biotype=protein_coding;transcript_id=Os01t0101600-01
+1	irgsp	five_prime_UTR	72816	72902	.	+	.	Parent=transcript:Os01t0101600-01
+1	irgsp	exon	72816	73935	.	+	.	Parent=transcript:Os01t0101600-01;Name=Os01t0101600-01.exon1;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Os01t0101600-01.exon1;rank=1
+1	irgsp	CDS	72903	73935	.	+	0	ID=CDS:Os01t0101600-01;Parent=transcript:Os01t0101600-01;protein_id=Os01t0101600-01
+1	irgsp	exon	74468	74981	.	+	.	Parent=transcript:Os01t0101600-01;Name=Os01t0101600-02.exon2;constitutive=0;ensembl_end_phase=2;ensembl_phase=1;exon_id=Os01t0101600-02.exon2;rank=2
+1	irgsp	CDS	74468	74981	.	+	2	ID=CDS:Os01t0101600-01;Parent=transcript:Os01t0101600-01;protein_id=Os01t0101600-01
+1	irgsp	CDS	75619	77008	.	+	1	ID=CDS:Os01t0101600-01;Parent=transcript:Os01t0101600-01;protein_id=Os01t0101600-01
+1	irgsp	exon	75619	77205	.	+	.	Parent=transcript:Os01t0101600-01;Name=Os01t0101600-01.exon3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0101600-01.exon3;rank=3
+1	irgsp	three_prime_UTR	77009	77205	.	+	.	Parent=transcript:Os01t0101600-01
+1	irgsp	exon	77333	78349	.	+	.	Parent=transcript:Os01t0101600-01;Name=Os01t0101600-01.exon4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0101600-01.exon4;rank=4
+1	irgsp	three_prime_UTR	77333	78349	.	+	.	Parent=transcript:Os01t0101600-01
+1	irgsp	mRNA	72823	77699	.	+	.	ID=transcript:Os01t0101600-02;Parent=gene:Os01g0101600;biotype=protein_coding;transcript_id=Os01t0101600-02
+1	irgsp	five_prime_UTR	72823	72902	.	+	.	Parent=transcript:Os01t0101600-02
+1	irgsp	exon	72823	73935	.	+	.	Parent=transcript:Os01t0101600-02;Name=Os01t0101600-02.exon1;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Os01t0101600-02.exon1;rank=1
+1	irgsp	CDS	72903	73935	.	+	0	ID=CDS:Os01t0101600-02;Parent=transcript:Os01t0101600-02;protein_id=Os01t0101600-02
+1	irgsp	exon	74468	74981	.	+	.	Parent=transcript:Os01t0101600-02;Name=Os01t0101600-02.exon2;constitutive=0;ensembl_end_phase=2;ensembl_phase=1;exon_id=Os01t0101600-02.exon2;rank=2
+1	irgsp	CDS	74468	74981	.	+	2	ID=CDS:Os01t0101600-02;Parent=transcript:Os01t0101600-02;protein_id=Os01t0101600-02
+1	irgsp	CDS	75619	77008	.	+	1	ID=CDS:Os01t0101600-02;Parent=transcript:Os01t0101600-02;protein_id=Os01t0101600-02
+1	irgsp	exon	75619	77699	.	+	.	Parent=transcript:Os01t0101600-02;Name=Os01t0101600-02.exon3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0101600-02.exon3;rank=3
+1	irgsp	three_prime_UTR	77009	77699	.	+	.	Parent=transcript:Os01t0101600-02
+1	irgsp	mRNA	75942	77699	.	+	.	ID=transcript:Os01t0101600-03;Parent=gene:Os01g0101600;biotype=protein_coding;transcript_id=Os01t0101600-03
+1	irgsp	five_prime_UTR	75942	75943	.	+	.	Parent=transcript:Os01t0101600-03
+1	irgsp	exon	75942	77699	.	+	.	Parent=transcript:Os01t0101600-03;Name=Os01t0101600-03.exon1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0101600-03.exon1;rank=1
+1	irgsp	CDS	75944	77008	.	+	0	ID=CDS:Os01t0101600-03;Parent=transcript:Os01t0101600-03;protein_id=Os01t0101600-03
+1	irgsp	three_prime_UTR	77009	77699	.	+	.	Parent=transcript:Os01t0101600-03
+###
+1	irgsp	gene	82426	84095	.	+	.	ID=gene:Os01g0101700;Name=DnaJ domain protein C1%2C rice DJC26 homolog;biotype=protein_coding;description=Similar to chaperone protein dnaJ 20. (Os01t0101700-00);gene_id=Os01g0101700;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	82426	84095	.	+	.	ID=transcript:Os01t0101700-00;Parent=gene:Os01g0101700;biotype=protein_coding;transcript_id=Os01t0101700-00
+1	irgsp	five_prime_UTR	82426	82506	.	+	.	Parent=transcript:Os01t0101700-00
+1	irgsp	exon	82426	82932	.	+	.	Parent=transcript:Os01t0101700-00;Name=Os01t0101700-00.exon1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0101700-00.exon1;rank=1
+1	irgsp	CDS	82507	82932	.	+	0	ID=CDS:Os01t0101700-00;Parent=transcript:Os01t0101700-00;protein_id=Os01t0101700-00
+1	irgsp	CDS	83724	83864	.	+	0	ID=CDS:Os01t0101700-00;Parent=transcript:Os01t0101700-00;protein_id=Os01t0101700-00
+1	irgsp	exon	83724	84095	.	+	.	Parent=transcript:Os01t0101700-00;Name=Os01t0101700-00.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0101700-00.exon2;rank=2
+1	irgsp	three_prime_UTR	83865	84095	.	+	.	Parent=transcript:Os01t0101700-00
+###
+1	irgsp	gene	85337	88844	.	+	.	ID=gene:Os01g0101800;biotype=protein_coding;description=Conserved hypothetical protein. (Os01t0101800-01);gene_id=Os01g0101800;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	85337	88844	.	+	.	ID=transcript:Os01t0101800-01;Parent=gene:Os01g0101800;biotype=protein_coding;transcript_id=Os01t0101800-01
+1	irgsp	five_prime_UTR	85337	85378	.	+	.	Parent=transcript:Os01t0101800-01
+1	irgsp	exon	85337	85600	.	+	.	Parent=transcript:Os01t0101800-01;Name=Os01t0101800-01.exon1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0101800-01.exon1;rank=1
+1	irgsp	CDS	85379	85600	.	+	0	ID=CDS:Os01t0101800-01;Parent=transcript:Os01t0101800-01;protein_id=Os01t0101800-01
+1	irgsp	exon	85737	85830	.	+	.	Parent=transcript:Os01t0101800-01;Name=Os01t0101800-01.exon2;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0101800-01.exon2;rank=2
+1	irgsp	CDS	85737	85830	.	+	0	ID=CDS:Os01t0101800-01;Parent=transcript:Os01t0101800-01;protein_id=Os01t0101800-01
+1	irgsp	exon	85935	86086	.	+	.	Parent=transcript:Os01t0101800-01;Name=Os01t0101800-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0101800-01.exon3;rank=3
+1	irgsp	CDS	85935	86086	.	+	2	ID=CDS:Os01t0101800-01;Parent=transcript:Os01t0101800-01;protein_id=Os01t0101800-01
+1	irgsp	exon	86212	86299	.	+	.	Parent=transcript:Os01t0101800-01;Name=Os01t0101800-01.exon4;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0101800-01.exon4;rank=4
+1	irgsp	CDS	86212	86299	.	+	0	ID=CDS:Os01t0101800-01;Parent=transcript:Os01t0101800-01;protein_id=Os01t0101800-01
+1	irgsp	exon	86399	87681	.	+	.	Parent=transcript:Os01t0101800-01;Name=Os01t0101800-01.exon5;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0101800-01.exon5;rank=5
+1	irgsp	CDS	86399	87681	.	+	2	ID=CDS:Os01t0101800-01;Parent=transcript:Os01t0101800-01;protein_id=Os01t0101800-01
+1	irgsp	exon	88291	88398	.	+	.	Parent=transcript:Os01t0101800-01;Name=Os01t0101800-01.exon6;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0101800-01.exon6;rank=6
+1	irgsp	CDS	88291	88398	.	+	0	ID=CDS:Os01t0101800-01;Parent=transcript:Os01t0101800-01;protein_id=Os01t0101800-01
+1	irgsp	CDS	88500	88583	.	+	0	ID=CDS:Os01t0101800-01;Parent=transcript:Os01t0101800-01;protein_id=Os01t0101800-01
+1	irgsp	exon	88500	88844	.	+	.	Parent=transcript:Os01t0101800-01;Name=Os01t0101800-01.exon7;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0101800-01.exon7;rank=7
+1	irgsp	three_prime_UTR	88584	88844	.	+	.	Parent=transcript:Os01t0101800-01
+###
+1	irgsp	gene	86211	88583	.	-	.	ID=gene:Os01g0101850;biotype=protein_coding;description=Hypothetical protein. (Os01t0101850-00);gene_id=Os01g0101850;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	86211	88583	.	-	.	ID=transcript:Os01t0101850-00;Parent=gene:Os01g0101850;biotype=protein_coding;transcript_id=Os01t0101850-00
+1	irgsp	exon	86211	86277	.	-	.	Parent=transcript:Os01t0101850-00;Name=Os01t0101850-00.exon4;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0101850-00.exon4;rank=4
+1	irgsp	three_prime_UTR	86211	86277	.	-	.	Parent=transcript:Os01t0101850-00
+1	irgsp	three_prime_UTR	86384	87326	.	-	.	Parent=transcript:Os01t0101850-00
+1	irgsp	exon	86384	87694	.	-	.	Parent=transcript:Os01t0101850-00;Name=Os01t0101850-00.exon3;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0101850-00.exon3;rank=3
+1	irgsp	CDS	87327	87662	.	-	0	ID=CDS:Os01t0101850-00;Parent=transcript:Os01t0101850-00;protein_id=Os01t0101850-00
+1	irgsp	five_prime_UTR	87663	87694	.	-	.	Parent=transcript:Os01t0101850-00
+1	irgsp	exon	88308	88396	.	-	.	Parent=transcript:Os01t0101850-00;Name=Os01t0101850-00.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0101850-00.exon2;rank=2
+1	irgsp	five_prime_UTR	88308	88396	.	-	.	Parent=transcript:Os01t0101850-00
+1	irgsp	exon	88496	88583	.	-	.	Parent=transcript:Os01t0101850-00;Name=Os01t0101850-00.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0101850-00.exon1;rank=1
+1	irgsp	five_prime_UTR	88496	88583	.	-	.	Parent=transcript:Os01t0101850-00
+###
+1	irgsp	gene	88883	89228	.	-	.	ID=gene:Os01g0101900;biotype=protein_coding;description=Similar to OSIGBa0075F02.3 protein. (Os01t0101900-00);gene_id=Os01g0101900;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	88883	89228	.	-	.	ID=transcript:Os01t0101900-00;Parent=gene:Os01g0101900;biotype=protein_coding;transcript_id=Os01t0101900-00
+1	irgsp	three_prime_UTR	88883	88985	.	-	.	Parent=transcript:Os01t0101900-00
+1	irgsp	exon	88883	89228	.	-	.	Parent=transcript:Os01t0101900-00;Name=Os01t0101900-00.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0101900-00.exon1;rank=1
+1	irgsp	CDS	88986	89204	.	-	0	ID=CDS:Os01t0101900-00;Parent=transcript:Os01t0101900-00;protein_id=Os01t0101900-00
+1	irgsp	five_prime_UTR	89205	89228	.	-	.	Parent=transcript:Os01t0101900-00
+###
+1	irgsp	gene	89763	91465	.	-	.	ID=gene:Os01g0102000;Name=NON-SPECIFIC PHOSPHOLIPASE C5;biotype=protein_coding;description=Phosphoesterase family protein. (Os01t0102000-01);gene_id=Os01g0102000;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	89763	91465	.	-	.	ID=transcript:Os01t0102000-01;Parent=gene:Os01g0102000;biotype=protein_coding;transcript_id=Os01t0102000-01
+1	irgsp	three_prime_UTR	89763	89824	.	-	.	Parent=transcript:Os01t0102000-01
+1	irgsp	exon	89763	91465	.	-	.	Parent=transcript:Os01t0102000-01;Name=Os01t0102000-01.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0102000-01.exon1;rank=1
+1	irgsp	CDS	89825	91411	.	-	0	ID=CDS:Os01t0102000-01;Parent=transcript:Os01t0102000-01;protein_id=Os01t0102000-01
+1	irgsp	five_prime_UTR	91412	91465	.	-	.	Parent=transcript:Os01t0102000-01
+###
+1	irgsp	gene	134300	135439	.	+	.	ID=gene:Os01g0102300;Name=OsTLP27;biotype=protein_coding;description=Thylakoid lumen protein%2C Photosynthesis and chloroplast development (Os01t0102300-01);gene_id=Os01g0102300;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	134300	135439	.	+	.	ID=transcript:Os01t0102300-01;Parent=gene:Os01g0102300;biotype=protein_coding;transcript_id=Os01t0102300-01
+1	irgsp	five_prime_UTR	134300	134310	.	+	.	Parent=transcript:Os01t0102300-01
+1	irgsp	exon	134300	134615	.	+	.	Parent=transcript:Os01t0102300-01;Name=Os01t0102300-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0102300-01.exon1;rank=1
+1	irgsp	CDS	134311	134615	.	+	0	ID=CDS:Os01t0102300-01;Parent=transcript:Os01t0102300-01;protein_id=Os01t0102300-01
+1	irgsp	exon	134698	134824	.	+	.	Parent=transcript:Os01t0102300-01;Name=Os01t0102300-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0102300-01.exon2;rank=2
+1	irgsp	CDS	134698	134824	.	+	1	ID=CDS:Os01t0102300-01;Parent=transcript:Os01t0102300-01;protein_id=Os01t0102300-01
+1	irgsp	CDS	134912	135253	.	+	0	ID=CDS:Os01t0102300-01;Parent=transcript:Os01t0102300-01;protein_id=Os01t0102300-01
+1	irgsp	exon	134912	135439	.	+	.	Parent=transcript:Os01t0102300-01;Name=Os01t0102300-01.exon3;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0102300-01.exon3;rank=3
+1	irgsp	three_prime_UTR	135254	135439	.	+	.	Parent=transcript:Os01t0102300-01
+###
+1	irgsp	gene	139826	141555	.	+	.	ID=gene:Os01g0102400;Name=HAP5H SUBUNIT OF CCAAT-BOX BINDING COMPLEX;biotype=protein_coding;description=Histone-fold domain containing protein. (Os01t0102400-01);gene_id=Os01g0102400;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	139826	141555	.	+	.	ID=transcript:Os01t0102400-01;Parent=gene:Os01g0102400;biotype=protein_coding;transcript_id=Os01t0102400-01
+1	irgsp	exon	139826	139906	.	+	.	Parent=transcript:Os01t0102400-01;Name=Os01t0102400-01.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0102400-01.exon1;rank=1
+1	irgsp	five_prime_UTR	139826	139906	.	+	.	Parent=transcript:Os01t0102400-01
+1	irgsp	five_prime_UTR	140120	140149	.	+	.	Parent=transcript:Os01t0102400-01
+1	irgsp	exon	140120	141555	.	+	.	Parent=transcript:Os01t0102400-01;Name=Os01t0102400-01.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0102400-01.exon2;rank=2
+1	irgsp	CDS	140150	141415	.	+	0	ID=CDS:Os01t0102400-01;Parent=transcript:Os01t0102400-01;protein_id=Os01t0102400-01
+1	irgsp	three_prime_UTR	141416	141555	.	+	.	Parent=transcript:Os01t0102400-01
+###
+1	irgsp	gene	141959	144554	.	+	.	ID=gene:Os01g0102500;biotype=protein_coding;description=Conserved hypothetical protein. (Os01t0102500-01);gene_id=Os01g0102500;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	141959	144554	.	+	.	ID=transcript:Os01t0102500-01;Parent=gene:Os01g0102500;biotype=protein_coding;transcript_id=Os01t0102500-01
+1	irgsp	five_prime_UTR	141959	142083	.	+	.	Parent=transcript:Os01t0102500-01
+1	irgsp	exon	141959	142631	.	+	.	Parent=transcript:Os01t0102500-01;Name=Os01t0102500-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0102500-01.exon1;rank=1
+1	irgsp	CDS	142084	142631	.	+	0	ID=CDS:Os01t0102500-01;Parent=transcript:Os01t0102500-01;protein_id=Os01t0102500-01
+1	irgsp	exon	143191	143431	.	+	.	Parent=transcript:Os01t0102500-01;Name=Os01t0102500-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0102500-01.exon2;rank=2
+1	irgsp	CDS	143191	143431	.	+	1	ID=CDS:Os01t0102500-01;Parent=transcript:Os01t0102500-01;protein_id=Os01t0102500-01
+1	irgsp	exon	143563	143680	.	+	.	Parent=transcript:Os01t0102500-01;Name=Os01t0102500-01.exon3;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0102500-01.exon3;rank=3
+1	irgsp	CDS	143563	143680	.	+	0	ID=CDS:Os01t0102500-01;Parent=transcript:Os01t0102500-01;protein_id=Os01t0102500-01
+1	irgsp	CDS	143817	143908	.	+	2	ID=CDS:Os01t0102500-01;Parent=transcript:Os01t0102500-01;protein_id=Os01t0102500-01
+1	irgsp	exon	143817	144554	.	+	.	Parent=transcript:Os01t0102500-01;Name=Os01t0102500-01.exon4;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0102500-01.exon4;rank=4
+1	irgsp	three_prime_UTR	143909	144554	.	+	.	Parent=transcript:Os01t0102500-01
+###
+1	irgsp	gene	145603	147847	.	+	.	ID=gene:Os01g0102600;Name=Shikimate kinase 4;biotype=protein_coding;description=Shikimate kinase domain containing protein. (Os01t0102600-01)%3BSimilar to shikimate kinase family protein. (Os01t0102600-02);gene_id=Os01g0102600;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	145603	147847	.	+	.	ID=transcript:Os01t0102600-01;Parent=gene:Os01g0102600;biotype=protein_coding;transcript_id=Os01t0102600-01
+1	irgsp	five_prime_UTR	145603	145644	.	+	.	Parent=transcript:Os01t0102600-01
+1	irgsp	exon	145603	145786	.	+	.	Parent=transcript:Os01t0102600-01;Name=Os01t0102600-01.exon1;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Os01t0102600-01.exon1;rank=1
+1	irgsp	CDS	145645	145786	.	+	0	ID=CDS:Os01t0102600-01;Parent=transcript:Os01t0102600-01;protein_id=Os01t0102600-01
+1	irgsp	exon	145905	145951	.	+	.	Parent=transcript:Os01t0102600-01;Name=Os01t0102600-01.exon2;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0102600-01.exon2;rank=2
+1	irgsp	CDS	145905	145951	.	+	2	ID=CDS:Os01t0102600-01;Parent=transcript:Os01t0102600-01;protein_id=Os01t0102600-01
+1	irgsp	exon	146028	146082	.	+	.	Parent=transcript:Os01t0102600-01;Name=Os01t0102600-01.exon3;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0102600-01.exon3;rank=3
+1	irgsp	CDS	146028	146082	.	+	0	ID=CDS:Os01t0102600-01;Parent=transcript:Os01t0102600-01;protein_id=Os01t0102600-01
+1	irgsp	exon	146179	146339	.	+	.	Parent=transcript:Os01t0102600-01;Name=Os01t0102600-01.exon4;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0102600-01.exon4;rank=4
+1	irgsp	CDS	146179	146339	.	+	2	ID=CDS:Os01t0102600-01;Parent=transcript:Os01t0102600-01;protein_id=Os01t0102600-01
+1	irgsp	exon	146450	146532	.	+	.	Parent=transcript:Os01t0102600-01;Name=Os01t0102600-01.exon5;constitutive=0;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0102600-01.exon5;rank=5
+1	irgsp	CDS	146450	146532	.	+	0	ID=CDS:Os01t0102600-01;Parent=transcript:Os01t0102600-01;protein_id=Os01t0102600-01
+1	irgsp	exon	146611	146719	.	+	.	Parent=transcript:Os01t0102600-01;Name=Os01t0102600-01.exon6;constitutive=0;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0102600-01.exon6;rank=6
+1	irgsp	CDS	146611	146719	.	+	1	ID=CDS:Os01t0102600-01;Parent=transcript:Os01t0102600-01;protein_id=Os01t0102600-01
+1	irgsp	exon	147106	147184	.	+	.	Parent=transcript:Os01t0102600-01;Name=Os01t0102600-01.exon7;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0102600-01.exon7;rank=7
+1	irgsp	CDS	147106	147184	.	+	0	ID=CDS:Os01t0102600-01;Parent=transcript:Os01t0102600-01;protein_id=Os01t0102600-01
+1	irgsp	exon	147311	147375	.	+	.	Parent=transcript:Os01t0102600-01;Name=Os01t0102600-02.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0102600-02.exon2;rank=8
+1	irgsp	CDS	147311	147375	.	+	2	ID=CDS:Os01t0102600-01;Parent=transcript:Os01t0102600-01;protein_id=Os01t0102600-01
+1	irgsp	CDS	147507	147575	.	+	0	ID=CDS:Os01t0102600-01;Parent=transcript:Os01t0102600-01;protein_id=Os01t0102600-01
+1	irgsp	exon	147507	147847	.	+	.	Parent=transcript:Os01t0102600-01;Name=Os01t0102600-01.exon9;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0102600-01.exon9;rank=9
+1	irgsp	three_prime_UTR	147576	147847	.	+	.	Parent=transcript:Os01t0102600-01
+1	irgsp	mRNA	147104	147805	.	+	.	ID=transcript:Os01t0102600-02;Parent=gene:Os01g0102600;biotype=protein_coding;transcript_id=Os01t0102600-02
+1	irgsp	five_prime_UTR	147104	147105	.	+	.	Parent=transcript:Os01t0102600-02
+1	irgsp	exon	147104	147184	.	+	.	Parent=transcript:Os01t0102600-02;Name=Os01t0102600-02.exon1;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Os01t0102600-02.exon1;rank=1
+1	irgsp	CDS	147106	147184	.	+	0	ID=CDS:Os01t0102600-02;Parent=transcript:Os01t0102600-02;protein_id=Os01t0102600-02
+1	irgsp	exon	147311	147375	.	+	.	Parent=transcript:Os01t0102600-02;Name=Os01t0102600-02.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0102600-02.exon2;rank=2
+1	irgsp	CDS	147311	147375	.	+	2	ID=CDS:Os01t0102600-02;Parent=transcript:Os01t0102600-02;protein_id=Os01t0102600-02
+1	irgsp	CDS	147507	147575	.	+	0	ID=CDS:Os01t0102600-02;Parent=transcript:Os01t0102600-02;protein_id=Os01t0102600-02
+1	irgsp	exon	147507	147805	.	+	.	Parent=transcript:Os01t0102600-02;Name=Os01t0102600-02.exon3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0102600-02.exon3;rank=3
+1	irgsp	three_prime_UTR	147576	147805	.	+	.	Parent=transcript:Os01t0102600-02
+###
+1	irgsp	gene	148085	150568	.	+	.	ID=gene:Os01g0102700;biotype=protein_coding;description=Translocon-associated beta family protein. (Os01t0102700-01);gene_id=Os01g0102700;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	148085	150568	.	+	.	ID=transcript:Os01t0102700-01;Parent=gene:Os01g0102700;biotype=protein_coding;transcript_id=Os01t0102700-01
+1	irgsp	five_prime_UTR	148085	148146	.	+	.	Parent=transcript:Os01t0102700-01
+1	irgsp	exon	148085	148313	.	+	.	Parent=transcript:Os01t0102700-01;Name=Os01t0102700-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0102700-01.exon1;rank=1
+1	irgsp	CDS	148147	148313	.	+	0	ID=CDS:Os01t0102700-01;Parent=transcript:Os01t0102700-01;protein_id=Os01t0102700-01
+1	irgsp	exon	149450	149548	.	+	.	Parent=transcript:Os01t0102700-01;Name=Os01t0102700-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0102700-01.exon2;rank=2
+1	irgsp	CDS	149450	149548	.	+	1	ID=CDS:Os01t0102700-01;Parent=transcript:Os01t0102700-01;protein_id=Os01t0102700-01
+1	irgsp	exon	149634	149742	.	+	.	Parent=transcript:Os01t0102700-01;Name=Os01t0102700-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0102700-01.exon3;rank=3
+1	irgsp	CDS	149634	149742	.	+	1	ID=CDS:Os01t0102700-01;Parent=transcript:Os01t0102700-01;protein_id=Os01t0102700-01
+1	irgsp	exon	149856	149931	.	+	.	Parent=transcript:Os01t0102700-01;Name=Os01t0102700-01.exon4;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0102700-01.exon4;rank=4
+1	irgsp	CDS	149856	149931	.	+	0	ID=CDS:Os01t0102700-01;Parent=transcript:Os01t0102700-01;protein_id=Os01t0102700-01
+1	irgsp	CDS	150152	150318	.	+	2	ID=CDS:Os01t0102700-01;Parent=transcript:Os01t0102700-01;protein_id=Os01t0102700-01
+1	irgsp	exon	150152	150568	.	+	.	Parent=transcript:Os01t0102700-01;Name=Os01t0102700-01.exon5;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0102700-01.exon5;rank=5
+1	irgsp	three_prime_UTR	150319	150568	.	+	.	Parent=transcript:Os01t0102700-01
+###
+1	irgsp	gene	152853	156449	.	+	.	ID=gene:Os01g0102800;Name=Cockayne syndrome WD-repeat protein;biotype=protein_coding;description=Similar to chromatin remodeling complex subunit. (Os01t0102800-01);gene_id=Os01g0102800;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	152853	156449	.	+	.	ID=transcript:Os01t0102800-01;Parent=gene:Os01g0102800;biotype=protein_coding;transcript_id=Os01t0102800-01
+1	irgsp	five_prime_UTR	152853	152853	.	+	.	Parent=transcript:Os01t0102800-01
+1	irgsp	exon	152853	153025	.	+	.	Parent=transcript:Os01t0102800-01;Name=Os01t0102800-01.exon1;constitutive=1;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Os01t0102800-01.exon1;rank=1
+1	irgsp	CDS	152854	153025	.	+	0	ID=CDS:Os01t0102800-01;Parent=transcript:Os01t0102800-01;protein_id=Os01t0102800-01
+1	irgsp	exon	153178	154646	.	+	.	Parent=transcript:Os01t0102800-01;Name=Os01t0102800-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0102800-01.exon2;rank=2
+1	irgsp	CDS	153178	154646	.	+	2	ID=CDS:Os01t0102800-01;Parent=transcript:Os01t0102800-01;protein_id=Os01t0102800-01
+1	irgsp	exon	155010	155450	.	+	.	Parent=transcript:Os01t0102800-01;Name=Os01t0102800-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0102800-01.exon3;rank=3
+1	irgsp	CDS	155010	155450	.	+	0	ID=CDS:Os01t0102800-01;Parent=transcript:Os01t0102800-01;protein_id=Os01t0102800-01
+1	irgsp	CDS	155543	156214	.	+	0	ID=CDS:Os01t0102800-01;Parent=transcript:Os01t0102800-01;protein_id=Os01t0102800-01
+1	irgsp	exon	155543	156449	.	+	.	Parent=transcript:Os01t0102800-01;Name=Os01t0102800-01.exon4;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0102800-01.exon4;rank=4
+1	irgsp	three_prime_UTR	156215	156449	.	+	.	Parent=transcript:Os01t0102800-01
+###
+1	irgsp	gene	164577	168921	.	+	.	ID=gene:Os01g0102850;biotype=protein_coding;description=Similar to nitrilase 2. (Os01t0102850-00);gene_id=Os01g0102850;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	164577	168921	.	+	.	ID=transcript:Os01t0102850-00;Parent=gene:Os01g0102850;biotype=protein_coding;transcript_id=Os01t0102850-00
+1	irgsp	exon	164577	164905	.	+	.	Parent=transcript:Os01t0102850-00;Name=Os01t0102850-00.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0102850-00.exon1;rank=1
+1	irgsp	five_prime_UTR	164577	164905	.	+	.	Parent=transcript:Os01t0102850-00
+1	irgsp	five_prime_UTR	168499	168804	.	+	.	Parent=transcript:Os01t0102850-00
+1	irgsp	exon	168499	168921	.	+	.	Parent=transcript:Os01t0102850-00;Name=Os01t0102850-00.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0102850-00.exon2;rank=2
+1	irgsp	CDS	168805	168921	.	+	0	ID=CDS:Os01t0102850-00;Parent=transcript:Os01t0102850-00;protein_id=Os01t0102850-00
+###
+1	irgsp	gene	169390	170316	.	-	.	ID=gene:Os01g0102900;Name=LIGHT-REGULATED GENE 1;biotype=protein_coding;description=Light-regulated protein%2C Regulation of light-dependent attachment of LEAF-TYPE FERREDOXIN-NADP+ OXIDOREDUCTASE (LFNR) to the thylakoid membrane (Os01t0102900-01);gene_id=Os01g0102900;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	169390	170316	.	-	.	ID=transcript:Os01t0102900-01;Parent=gene:Os01g0102900;biotype=protein_coding;transcript_id=Os01t0102900-01
+1	irgsp	three_prime_UTR	169390	169598	.	-	.	Parent=transcript:Os01t0102900-01
+1	irgsp	exon	169390	169656	.	-	.	Parent=transcript:Os01t0102900-01;Name=Os01t0102900-01.exon3;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0102900-01.exon3;rank=3
+1	irgsp	CDS	169599	169656	.	-	1	ID=CDS:Os01t0102900-01;Parent=transcript:Os01t0102900-01;protein_id=Os01t0102900-01
+1	irgsp	exon	169751	169909	.	-	.	Parent=transcript:Os01t0102900-01;Name=Os01t0102900-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0102900-01.exon2;rank=2
+1	irgsp	CDS	169751	169909	.	-	1	ID=CDS:Os01t0102900-01;Parent=transcript:Os01t0102900-01;protein_id=Os01t0102900-01
+1	irgsp	CDS	170091	170260	.	-	0	ID=CDS:Os01t0102900-01;Parent=transcript:Os01t0102900-01;protein_id=Os01t0102900-01
+1	irgsp	exon	170091	170316	.	-	.	Parent=transcript:Os01t0102900-01;Name=Os01t0102900-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0102900-01.exon1;rank=1
+1	irgsp	five_prime_UTR	170261	170316	.	-	.	Parent=transcript:Os01t0102900-01
+###
+1	irgsp	gene	170798	173144	.	-	.	ID=gene:Os01g0103000;biotype=protein_coding;description=Snf7 family protein. (Os01t0103000-01);gene_id=Os01g0103000;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	170798	173144	.	-	.	ID=transcript:Os01t0103000-01;Parent=gene:Os01g0103000;biotype=protein_coding;transcript_id=Os01t0103000-01
+1	irgsp	three_prime_UTR	170798	171044	.	-	.	Parent=transcript:Os01t0103000-01
+1	irgsp	exon	170798	171095	.	-	.	Parent=transcript:Os01t0103000-01;Name=Os01t0103000-01.exon7;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0103000-01.exon7;rank=7
+1	irgsp	CDS	171045	171095	.	-	0	ID=CDS:Os01t0103000-01;Parent=transcript:Os01t0103000-01;protein_id=Os01t0103000-01
+1	irgsp	exon	171406	171554	.	-	.	Parent=transcript:Os01t0103000-01;Name=Os01t0103000-01.exon6;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0103000-01.exon6;rank=6
+1	irgsp	CDS	171406	171554	.	-	2	ID=CDS:Os01t0103000-01;Parent=transcript:Os01t0103000-01;protein_id=Os01t0103000-01
+1	irgsp	exon	171764	171875	.	-	.	Parent=transcript:Os01t0103000-01;Name=Os01t0103000-01.exon5;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0103000-01.exon5;rank=5
+1	irgsp	CDS	171764	171875	.	-	0	ID=CDS:Os01t0103000-01;Parent=transcript:Os01t0103000-01;protein_id=Os01t0103000-01
+1	irgsp	exon	172398	172469	.	-	.	Parent=transcript:Os01t0103000-01;Name=Os01t0103000-01.exon4;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0103000-01.exon4;rank=4
+1	irgsp	CDS	172398	172469	.	-	0	ID=CDS:Os01t0103000-01;Parent=transcript:Os01t0103000-01;protein_id=Os01t0103000-01
+1	irgsp	exon	172578	172671	.	-	.	Parent=transcript:Os01t0103000-01;Name=Os01t0103000-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0103000-01.exon3;rank=3
+1	irgsp	CDS	172578	172671	.	-	1	ID=CDS:Os01t0103000-01;Parent=transcript:Os01t0103000-01;protein_id=Os01t0103000-01
+1	irgsp	exon	172770	172921	.	-	.	Parent=transcript:Os01t0103000-01;Name=Os01t0103000-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0103000-01.exon2;rank=2
+1	irgsp	CDS	172770	172921	.	-	0	ID=CDS:Os01t0103000-01;Parent=transcript:Os01t0103000-01;protein_id=Os01t0103000-01
+1	irgsp	CDS	173004	173072	.	-	0	ID=CDS:Os01t0103000-01;Parent=transcript:Os01t0103000-01;protein_id=Os01t0103000-01
+1	irgsp	exon	173004	173144	.	-	.	Parent=transcript:Os01t0103000-01;Name=Os01t0103000-01.exon1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0103000-01.exon1;rank=1
+1	irgsp	five_prime_UTR	173073	173144	.	-	.	Parent=transcript:Os01t0103000-01
+###
+1	irgsp	gene	178607	180575	.	+	.	ID=gene:Os01g0103100;biotype=protein_coding;description=TGF-beta receptor%2C type I/II extracellular region family protein. (Os01t0103100-01)%3BSimilar to predicted protein. (Os01t0103100-02);gene_id=Os01g0103100;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	178607	180548	.	+	.	ID=transcript:Os01t0103100-01;Parent=gene:Os01g0103100;biotype=protein_coding;transcript_id=Os01t0103100-01
+1	irgsp	five_prime_UTR	178607	178641	.	+	.	Parent=transcript:Os01t0103100-01
+1	irgsp	exon	178607	180548	.	+	.	Parent=transcript:Os01t0103100-01;Name=Os01t0103100-01.exon1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0103100-01.exon1;rank=1
+1	irgsp	CDS	178642	180462	.	+	0	ID=CDS:Os01t0103100-01;Parent=transcript:Os01t0103100-01;protein_id=Os01t0103100-01
+1	irgsp	three_prime_UTR	180463	180548	.	+	.	Parent=transcript:Os01t0103100-01
+1	irgsp	mRNA	178652	180575	.	+	.	ID=transcript:Os01t0103100-02;Parent=gene:Os01g0103100;biotype=protein_coding;transcript_id=Os01t0103100-02
+1	irgsp	five_prime_UTR	178652	178677	.	+	.	Parent=transcript:Os01t0103100-02
+1	irgsp	exon	178652	180575	.	+	.	Parent=transcript:Os01t0103100-02;Name=Os01t0103100-02.exon1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0103100-02.exon1;rank=1
+1	irgsp	CDS	178678	180462	.	+	0	ID=CDS:Os01t0103100-02;Parent=transcript:Os01t0103100-02;protein_id=Os01t0103100-02
+1	irgsp	three_prime_UTR	180463	180575	.	+	.	Parent=transcript:Os01t0103100-02
+###
+1	irgsp	gene	178815	180433	.	-	.	ID=gene:Os01g0103075;biotype=protein_coding;description=Hypothetical protein. (Os01t0103075-00);gene_id=Os01g0103075;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	178815	180433	.	-	.	ID=transcript:Os01t0103075-00;Parent=gene:Os01g0103075;biotype=protein_coding;transcript_id=Os01t0103075-00
+1	irgsp	three_prime_UTR	178815	179511	.	-	.	Parent=transcript:Os01t0103075-00
+1	irgsp	exon	178815	180433	.	-	.	Parent=transcript:Os01t0103075-00;Name=Os01t0103075-00.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0103075-00.exon1;rank=1
+1	irgsp	CDS	179512	180054	.	-	0	ID=CDS:Os01t0103075-00;Parent=transcript:Os01t0103075-00;protein_id=Os01t0103075-00
+1	irgsp	five_prime_UTR	180055	180433	.	-	.	Parent=transcript:Os01t0103075-00
+###
+1	Ensembl_Plants	ncRNA_gene	182074	182154	.	+	.	ID=gene:ENSRNA049442722;Name=tRNA-Leu;biotype=tRNA;description=tRNA-Leu for anticodon AAG;gene_id=ENSRNA049442722;logic_name=trnascan_gene
+1	Ensembl_Plants	tRNA	182074	182154	.	+	.	ID=transcript:ENSRNA049442722-T1;Parent=gene:ENSRNA049442722;biotype=tRNA;transcript_id=ENSRNA049442722-T1
+1	Ensembl_Plants	exon	182074	182154	.	+	.	Parent=transcript:ENSRNA049442722-T1;Name=ENSRNA049442722-E1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSRNA049442722-E1;rank=1
+###
+1	irgsp	gene	185189	185828	.	-	.	ID=gene:Os01g0103400;biotype=protein_coding;description=Hypothetical gene. (Os01t0103400-01);gene_id=Os01g0103400;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	185189	185828	.	-	.	ID=transcript:Os01t0103400-01;Parent=gene:Os01g0103400;biotype=protein_coding;transcript_id=Os01t0103400-01
+1	irgsp	three_prime_UTR	185189	185434	.	-	.	Parent=transcript:Os01t0103400-01
+1	irgsp	exon	185189	185828	.	-	.	Parent=transcript:Os01t0103400-01;Name=Os01t0103400-01.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0103400-01.exon1;rank=1
+1	irgsp	CDS	185435	185827	.	-	0	ID=CDS:Os01t0103400-01;Parent=transcript:Os01t0103400-01;protein_id=Os01t0103400-01
+1	irgsp	five_prime_UTR	185828	185828	.	-	.	Parent=transcript:Os01t0103400-01
+###
+1	irgsp	repeat_region	186000	186100	.	+	.	ID=fakeRepeat2
+###
+1	irgsp	gene	186250	190904	.	-	.	ID=gene:Os01g0103600;biotype=protein_coding;description=Similar to sterol-8%2C7-isomerase. (Os01t0103600-01)%3BEmopamil-binding family protein. (Os01t0103600-02);gene_id=Os01g0103600;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	186250	190262	.	-	.	ID=transcript:Os01t0103600-02;Parent=gene:Os01g0103600;biotype=protein_coding;transcript_id=Os01t0103600-02
+1	irgsp	three_prime_UTR	186250	186515	.	-	.	Parent=transcript:Os01t0103600-02
+1	irgsp	exon	186250	186771	.	-	.	Parent=transcript:Os01t0103600-02;Name=Os01t0103600-02.exon4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0103600-02.exon4;rank=4
+1	irgsp	CDS	186516	186771	.	-	1	ID=CDS:Os01t0103600-02;Parent=transcript:Os01t0103600-02;protein_id=Os01t0103600-02
+1	irgsp	exon	189607	189715	.	-	.	Parent=transcript:Os01t0103600-02;Name=Os01t0103600-02.exon3;constitutive=0;ensembl_end_phase=2;ensembl_phase=1;exon_id=Os01t0103600-02.exon3;rank=3
+1	irgsp	CDS	189607	189715	.	-	2	ID=CDS:Os01t0103600-02;Parent=transcript:Os01t0103600-02;protein_id=Os01t0103600-02
+1	irgsp	exon	189841	189990	.	-	.	Parent=transcript:Os01t0103600-02;Name=Os01t0103600-02.exon2;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=Os01t0103600-02.exon2;rank=2
+1	irgsp	CDS	189841	189990	.	-	2	ID=CDS:Os01t0103600-02;Parent=transcript:Os01t0103600-02;protein_id=Os01t0103600-02
+1	irgsp	CDS	190087	190231	.	-	0	ID=CDS:Os01t0103600-02;Parent=transcript:Os01t0103600-02;protein_id=Os01t0103600-02
+1	irgsp	exon	190087	190262	.	-	.	Parent=transcript:Os01t0103600-02;Name=Os01t0103600-02.exon1;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Os01t0103600-02.exon1;rank=1
+1	irgsp	five_prime_UTR	190232	190262	.	-	.	Parent=transcript:Os01t0103600-02
+1	irgsp	mRNA	187345	190904	.	-	.	ID=transcript:Os01t0103600-01;Parent=gene:Os01g0103600;biotype=protein_coding;transcript_id=Os01t0103600-01
+1	irgsp	three_prime_UTR	187345	189395	.	-	.	Parent=transcript:Os01t0103600-01
+1	irgsp	exon	187345	189715	.	-	.	Parent=transcript:Os01t0103600-01;Name=Os01t0103600-01.exon3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0103600-01.exon3;rank=3
+1	irgsp	CDS	189396	189715	.	-	2	ID=CDS:Os01t0103600-01;Parent=transcript:Os01t0103600-01;protein_id=Os01t0103600-01
+1	irgsp	exon	189841	189990	.	-	.	Parent=transcript:Os01t0103600-01;Name=Os01t0103600-02.exon2;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=Os01t0103600-02.exon2;rank=2
+1	irgsp	CDS	189841	189990	.	-	2	ID=CDS:Os01t0103600-01;Parent=transcript:Os01t0103600-01;protein_id=Os01t0103600-01
+1	irgsp	CDS	190087	190231	.	-	0	ID=CDS:Os01t0103600-01;Parent=transcript:Os01t0103600-01;protein_id=Os01t0103600-01
+1	irgsp	exon	190087	190904	.	-	.	Parent=transcript:Os01t0103600-01;Name=Os01t0103600-01.exon1;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Os01t0103600-01.exon1;rank=1
+1	irgsp	five_prime_UTR	190232	190904	.	-	.	Parent=transcript:Os01t0103600-01
+###
+1	irgsp	gene	187545	188586	.	+	.	ID=gene:Os01g0103650;biotype=protein_coding;description=Hypothetical gene. (Os01t0103650-00);gene_id=Os01g0103650;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	187545	188586	.	+	.	ID=transcript:Os01t0103650-00;Parent=gene:Os01g0103650;biotype=protein_coding;transcript_id=Os01t0103650-00
+1	irgsp	five_prime_UTR	187545	187546	.	+	.	Parent=transcript:Os01t0103650-00
+1	irgsp	exon	187545	188020	.	+	.	Parent=transcript:Os01t0103650-00;Name=Os01t0103650-00.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0103650-00.exon1;rank=1
+1	irgsp	CDS	187547	187768	.	+	0	ID=CDS:Os01t0103650-00;Parent=transcript:Os01t0103650-00;protein_id=Os01t0103650-00
+1	irgsp	three_prime_UTR	187769	188020	.	+	.	Parent=transcript:Os01t0103650-00
+1	irgsp	exon	188060	188385	.	+	.	Parent=transcript:Os01t0103650-00;Name=Os01t0103650-00.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0103650-00.exon2;rank=2
+1	irgsp	three_prime_UTR	188060	188385	.	+	.	Parent=transcript:Os01t0103650-00
+1	irgsp	exon	188455	188586	.	+	.	Parent=transcript:Os01t0103650-00;Name=Os01t0103650-00.exon3;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0103650-00.exon3;rank=3
+1	irgsp	three_prime_UTR	188455	188586	.	+	.	Parent=transcript:Os01t0103650-00
+###
+1	irgsp	gene	191037	196287	.	+	.	ID=gene:Os01g0103700;biotype=protein_coding;description=Conserved hypothetical protein. (Os01t0103700-01);gene_id=Os01g0103700;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	191037	196287	.	+	.	ID=transcript:Os01t0103700-01;Parent=gene:Os01g0103700;biotype=protein_coding;transcript_id=Os01t0103700-01
+1	irgsp	exon	191037	191161	.	+	.	Parent=transcript:Os01t0103700-01;Name=Os01t0103700-01.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0103700-01.exon1;rank=1
+1	irgsp	five_prime_UTR	191037	191161	.	+	.	Parent=transcript:Os01t0103700-01
+1	irgsp	five_prime_UTR	191625	191693	.	+	.	Parent=transcript:Os01t0103700-01
+1	irgsp	exon	191625	191705	.	+	.	Parent=transcript:Os01t0103700-01;Name=Os01t0103700-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0103700-01.exon2;rank=2
+1	irgsp	CDS	191694	191705	.	+	0	ID=CDS:Os01t0103700-01;Parent=transcript:Os01t0103700-01;protein_id=Os01t0103700-01
+1	irgsp	exon	192399	192506	.	+	.	Parent=transcript:Os01t0103700-01;Name=Os01t0103700-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0103700-01.exon3;rank=3
+1	irgsp	CDS	192399	192506	.	+	0	ID=CDS:Os01t0103700-01;Parent=transcript:Os01t0103700-01;protein_id=Os01t0103700-01
+1	irgsp	exon	192958	193161	.	+	.	Parent=transcript:Os01t0103700-01;Name=Os01t0103700-01.exon4;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0103700-01.exon4;rank=4
+1	irgsp	CDS	192958	193161	.	+	0	ID=CDS:Os01t0103700-01;Parent=transcript:Os01t0103700-01;protein_id=Os01t0103700-01
+1	irgsp	exon	193248	193356	.	+	.	Parent=transcript:Os01t0103700-01;Name=Os01t0103700-01.exon5;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0103700-01.exon5;rank=5
+1	irgsp	CDS	193248	193356	.	+	0	ID=CDS:Os01t0103700-01;Parent=transcript:Os01t0103700-01;protein_id=Os01t0103700-01
+1	irgsp	CDS	193434	193507	.	+	2	ID=CDS:Os01t0103700-01;Parent=transcript:Os01t0103700-01;protein_id=Os01t0103700-01
+1	irgsp	exon	193434	196287	.	+	.	Parent=transcript:Os01t0103700-01;Name=Os01t0103700-01.exon6;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0103700-01.exon6;rank=6
+1	irgsp	three_prime_UTR	193508	196287	.	+	.	Parent=transcript:Os01t0103700-01
+###
+1	irgsp	gene	197647	200803	.	+	.	ID=gene:Os01g0103800;Name=OsDW1-01g;biotype=protein_coding;description=Conserved hypothetical protein. (Os01t0103800-01);gene_id=Os01g0103800;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	197647	200803	.	+	.	ID=transcript:Os01t0103800-01;Parent=gene:Os01g0103800;biotype=protein_coding;transcript_id=Os01t0103800-01
+1	irgsp	exon	197647	197838	.	+	.	Parent=transcript:Os01t0103800-01;Name=Os01t0103800-01.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0103800-01.exon1;rank=1
+1	irgsp	five_prime_UTR	197647	197838	.	+	.	Parent=transcript:Os01t0103800-01
+1	irgsp	five_prime_UTR	198034	198129	.	+	.	Parent=transcript:Os01t0103800-01
+1	irgsp	exon	198034	198225	.	+	.	Parent=transcript:Os01t0103800-01;Name=Os01t0103800-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0103800-01.exon2;rank=2
+1	irgsp	CDS	198130	198225	.	+	0	ID=CDS:Os01t0103800-01;Parent=transcript:Os01t0103800-01;protein_id=Os01t0103800-01
+1	irgsp	exon	198830	200036	.	+	.	Parent=transcript:Os01t0103800-01;Name=Os01t0103800-01.exon3;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0103800-01.exon3;rank=3
+1	irgsp	CDS	198830	200036	.	+	0	ID=CDS:Os01t0103800-01;Parent=transcript:Os01t0103800-01;protein_id=Os01t0103800-01
+1	irgsp	CDS	200253	200479	.	+	2	ID=CDS:Os01t0103800-01;Parent=transcript:Os01t0103800-01;protein_id=Os01t0103800-01
+1	irgsp	exon	200253	200803	.	+	.	Parent=transcript:Os01t0103800-01;Name=Os01t0103800-01.exon4;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0103800-01.exon4;rank=4
+1	irgsp	three_prime_UTR	200480	200803	.	+	.	Parent=transcript:Os01t0103800-01
+###
+1	irgsp	gene	201944	206202	.	+	.	ID=gene:Os01g0103900;biotype=protein_coding;description=Polynucleotidyl transferase%2C Ribonuclease H fold domain containing protein. (Os01t0103900-01);gene_id=Os01g0103900;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	201944	206202	.	+	.	ID=transcript:Os01t0103900-01;Parent=gene:Os01g0103900;biotype=protein_coding;transcript_id=Os01t0103900-01
+1	irgsp	five_prime_UTR	201944	202041	.	+	.	Parent=transcript:Os01t0103900-01
+1	irgsp	exon	201944	202110	.	+	.	Parent=transcript:Os01t0103900-01;Name=Os01t0103900-01.exon1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0103900-01.exon1;rank=1
+1	irgsp	CDS	202042	202110	.	+	0	ID=CDS:Os01t0103900-01;Parent=transcript:Os01t0103900-01;protein_id=Os01t0103900-01
+1	irgsp	exon	202252	202359	.	+	.	Parent=transcript:Os01t0103900-01;Name=Os01t0103900-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0103900-01.exon2;rank=2
+1	irgsp	CDS	202252	202359	.	+	0	ID=CDS:Os01t0103900-01;Parent=transcript:Os01t0103900-01;protein_id=Os01t0103900-01
+1	irgsp	exon	203007	203127	.	+	.	Parent=transcript:Os01t0103900-01;Name=Os01t0103900-01.exon3;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0103900-01.exon3;rank=3
+1	irgsp	CDS	203007	203127	.	+	0	ID=CDS:Os01t0103900-01;Parent=transcript:Os01t0103900-01;protein_id=Os01t0103900-01
+1	irgsp	exon	203302	203429	.	+	.	Parent=transcript:Os01t0103900-01;Name=Os01t0103900-01.exon4;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0103900-01.exon4;rank=4
+1	irgsp	CDS	203302	203429	.	+	2	ID=CDS:Os01t0103900-01;Parent=transcript:Os01t0103900-01;protein_id=Os01t0103900-01
+1	irgsp	exon	203511	203658	.	+	.	Parent=transcript:Os01t0103900-01;Name=Os01t0103900-01.exon5;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0103900-01.exon5;rank=5
+1	irgsp	CDS	203511	203658	.	+	0	ID=CDS:Os01t0103900-01;Parent=transcript:Os01t0103900-01;protein_id=Os01t0103900-01
+1	irgsp	exon	203760	203938	.	+	.	Parent=transcript:Os01t0103900-01;Name=Os01t0103900-01.exon6;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0103900-01.exon6;rank=6
+1	irgsp	CDS	203760	203938	.	+	2	ID=CDS:Os01t0103900-01;Parent=transcript:Os01t0103900-01;protein_id=Os01t0103900-01
+1	irgsp	exon	204203	204440	.	+	.	Parent=transcript:Os01t0103900-01;Name=Os01t0103900-01.exon7;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0103900-01.exon7;rank=7
+1	irgsp	CDS	204203	204440	.	+	0	ID=CDS:Os01t0103900-01;Parent=transcript:Os01t0103900-01;protein_id=Os01t0103900-01
+1	irgsp	exon	204543	204635	.	+	.	Parent=transcript:Os01t0103900-01;Name=Os01t0103900-01.exon8;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=Os01t0103900-01.exon8;rank=8
+1	irgsp	CDS	204543	204635	.	+	2	ID=CDS:Os01t0103900-01;Parent=transcript:Os01t0103900-01;protein_id=Os01t0103900-01
+1	irgsp	exon	204730	204875	.	+	.	Parent=transcript:Os01t0103900-01;Name=Os01t0103900-01.exon9;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0103900-01.exon9;rank=9
+1	irgsp	CDS	204730	204875	.	+	2	ID=CDS:Os01t0103900-01;Parent=transcript:Os01t0103900-01;protein_id=Os01t0103900-01
+1	irgsp	exon	205042	205149	.	+	.	Parent=transcript:Os01t0103900-01;Name=Os01t0103900-01.exon10;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0103900-01.exon10;rank=10
+1	irgsp	CDS	205042	205149	.	+	0	ID=CDS:Os01t0103900-01;Parent=transcript:Os01t0103900-01;protein_id=Os01t0103900-01
+1	irgsp	exon	205290	205378	.	+	.	Parent=transcript:Os01t0103900-01;Name=Os01t0103900-01.exon11;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0103900-01.exon11;rank=11
+1	irgsp	CDS	205290	205378	.	+	0	ID=CDS:Os01t0103900-01;Parent=transcript:Os01t0103900-01;protein_id=Os01t0103900-01
+1	irgsp	CDS	205534	205543	.	+	1	ID=CDS:Os01t0103900-01;Parent=transcript:Os01t0103900-01;protein_id=Os01t0103900-01
+1	irgsp	exon	205534	206202	.	+	.	Parent=transcript:Os01t0103900-01;Name=Os01t0103900-01.exon12;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0103900-01.exon12;rank=12
+1	irgsp	three_prime_UTR	205544	206202	.	+	.	Parent=transcript:Os01t0103900-01
+###
+1	irgsp	gene	206131	209606	.	-	.	ID=gene:Os01g0104000;biotype=protein_coding;description=C-type lectin domain containing protein. (Os01t0104000-01)%3BSimilar to predicted protein. (Os01t0104000-02);gene_id=Os01g0104000;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	206131	209581	.	-	.	ID=transcript:Os01t0104000-02;Parent=gene:Os01g0104000;biotype=protein_coding;transcript_id=Os01t0104000-02
+1	irgsp	three_prime_UTR	206131	206449	.	-	.	Parent=transcript:Os01t0104000-02
+1	irgsp	exon	206131	207029	.	-	.	Parent=transcript:Os01t0104000-02;Name=Os01t0104000-02.exon4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0104000-02.exon4;rank=4
+1	irgsp	CDS	206450	207029	.	-	1	ID=CDS:Os01t0104000-02;Parent=transcript:Os01t0104000-02;protein_id=Os01t0104000-02
+1	irgsp	exon	207706	208273	.	-	.	Parent=transcript:Os01t0104000-02;Name=Os01t0104000-02.exon3;constitutive=0;ensembl_end_phase=2;ensembl_phase=1;exon_id=Os01t0104000-02.exon3;rank=3
+1	irgsp	CDS	207706	208273	.	-	2	ID=CDS:Os01t0104000-02;Parent=transcript:Os01t0104000-02;protein_id=Os01t0104000-02
+1	irgsp	exon	208408	208836	.	-	.	Parent=transcript:Os01t0104000-02;Name=Os01t0104000-01.exon2;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=Os01t0104000-01.exon2;rank=2
+1	irgsp	CDS	208408	208836	.	-	2	ID=CDS:Os01t0104000-02;Parent=transcript:Os01t0104000-02;protein_id=Os01t0104000-02
+1	irgsp	CDS	209438	209525	.	-	0	ID=CDS:Os01t0104000-02;Parent=transcript:Os01t0104000-02;protein_id=Os01t0104000-02
+1	irgsp	exon	209438	209581	.	-	.	Parent=transcript:Os01t0104000-02;Name=Os01t0104000-02.exon1;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Os01t0104000-02.exon1;rank=1
+1	irgsp	five_prime_UTR	209526	209581	.	-	.	Parent=transcript:Os01t0104000-02
+1	irgsp	mRNA	206134	209606	.	-	.	ID=transcript:Os01t0104000-01;Parent=gene:Os01g0104000;biotype=protein_coding;transcript_id=Os01t0104000-01
+1	irgsp	three_prime_UTR	206134	206449	.	-	.	Parent=transcript:Os01t0104000-01
+1	irgsp	exon	206134	207029	.	-	.	Parent=transcript:Os01t0104000-01;Name=Os01t0104000-01.exon4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0104000-01.exon4;rank=4
+1	irgsp	CDS	206450	207029	.	-	1	ID=CDS:Os01t0104000-01;Parent=transcript:Os01t0104000-01;protein_id=Os01t0104000-01
+1	irgsp	exon	207706	208276	.	-	.	Parent=transcript:Os01t0104000-01;Name=Os01t0104000-01.exon3;constitutive=0;ensembl_end_phase=2;ensembl_phase=1;exon_id=Os01t0104000-01.exon3;rank=3
+1	irgsp	CDS	207706	208276	.	-	2	ID=CDS:Os01t0104000-01;Parent=transcript:Os01t0104000-01;protein_id=Os01t0104000-01
+1	irgsp	exon	208408	208836	.	-	.	Parent=transcript:Os01t0104000-01;Name=Os01t0104000-01.exon2;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=Os01t0104000-01.exon2;rank=2
+1	irgsp	CDS	208408	208836	.	-	2	ID=CDS:Os01t0104000-01;Parent=transcript:Os01t0104000-01;protein_id=Os01t0104000-01
+1	irgsp	CDS	209438	209525	.	-	0	ID=CDS:Os01t0104000-01;Parent=transcript:Os01t0104000-01;protein_id=Os01t0104000-01
+1	irgsp	exon	209438	209606	.	-	.	Parent=transcript:Os01t0104000-01;Name=Os01t0104000-01.exon1;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Os01t0104000-01.exon1;rank=1
+1	irgsp	five_prime_UTR	209526	209606	.	-	.	Parent=transcript:Os01t0104000-01
+###
+1	irgsp	gene	209771	214173	.	+	.	ID=gene:Os01g0104100;Name=cold-inducible%2C cold-inducible zinc finger protein;biotype=protein_coding;description=Similar to protein binding / zinc ion binding. (Os01t0104100-01)%3BSimilar to protein binding / zinc ion binding. (Os01t0104100-02);gene_id=Os01g0104100;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	209771	214173	.	+	.	ID=transcript:Os01t0104100-01;Parent=gene:Os01g0104100;biotype=protein_coding;transcript_id=Os01t0104100-01
+1	irgsp	exon	209771	209896	.	+	.	Parent=transcript:Os01t0104100-01;Name=Os01t0104100-01.exon1;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104100-01.exon1;rank=1
+1	irgsp	CDS	209771	209896	.	+	0	ID=CDS:Os01t0104100-01;Parent=transcript:Os01t0104100-01;protein_id=Os01t0104100-01
+1	irgsp	exon	210244	210563	.	+	.	Parent=transcript:Os01t0104100-01;Name=Os01t0104100-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0104100-01.exon2;rank=2
+1	irgsp	CDS	210244	210563	.	+	0	ID=CDS:Os01t0104100-01;Parent=transcript:Os01t0104100-01;protein_id=Os01t0104100-01
+1	irgsp	exon	210659	210890	.	+	.	Parent=transcript:Os01t0104100-01;Name=Os01t0104100-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0104100-01.exon3;rank=3
+1	irgsp	CDS	210659	210890	.	+	1	ID=CDS:Os01t0104100-01;Parent=transcript:Os01t0104100-01;protein_id=Os01t0104100-01
+1	irgsp	exon	211015	211160	.	+	.	Parent=transcript:Os01t0104100-01;Name=Os01t0104100-01.exon4;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0104100-01.exon4;rank=4
+1	irgsp	CDS	211015	211160	.	+	0	ID=CDS:Os01t0104100-01;Parent=transcript:Os01t0104100-01;protein_id=Os01t0104100-01
+1	irgsp	exon	212265	212352	.	+	.	Parent=transcript:Os01t0104100-01;Name=Os01t0104100-01.exon5;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0104100-01.exon5;rank=5
+1	irgsp	CDS	212265	212352	.	+	1	ID=CDS:Os01t0104100-01;Parent=transcript:Os01t0104100-01;protein_id=Os01t0104100-01
+1	irgsp	exon	212433	212579	.	+	.	Parent=transcript:Os01t0104100-01;Name=Os01t0104100-01.exon6;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104100-01.exon6;rank=6
+1	irgsp	CDS	212433	212579	.	+	0	ID=CDS:Os01t0104100-01;Parent=transcript:Os01t0104100-01;protein_id=Os01t0104100-01
+1	irgsp	exon	213490	213639	.	+	.	Parent=transcript:Os01t0104100-01;Name=Os01t0104100-01.exon7;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104100-01.exon7;rank=7
+1	irgsp	CDS	213490	213639	.	+	0	ID=CDS:Os01t0104100-01;Parent=transcript:Os01t0104100-01;protein_id=Os01t0104100-01
+1	irgsp	CDS	213741	213788	.	+	0	ID=CDS:Os01t0104100-01;Parent=transcript:Os01t0104100-01;protein_id=Os01t0104100-01
+1	irgsp	exon	213741	214173	.	+	.	Parent=transcript:Os01t0104100-01;Name=Os01t0104100-01.exon8;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0104100-01.exon8;rank=8
+1	irgsp	three_prime_UTR	213789	214173	.	+	.	Parent=transcript:Os01t0104100-01
+1	irgsp	mRNA	209794	214147	.	+	.	ID=transcript:Os01t0104100-02;Parent=gene:Os01g0104100;biotype=protein_coding;transcript_id=Os01t0104100-02
+1	irgsp	five_prime_UTR	209794	209794	.	+	.	Parent=transcript:Os01t0104100-02
+1	irgsp	exon	209794	209896	.	+	.	Parent=transcript:Os01t0104100-02;Name=Os01t0104100-02.exon1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0104100-02.exon1;rank=1
+1	irgsp	CDS	209795	209896	.	+	0	ID=CDS:Os01t0104100-02;Parent=transcript:Os01t0104100-02;protein_id=Os01t0104100-02
+1	irgsp	exon	210244	210563	.	+	.	Parent=transcript:Os01t0104100-02;Name=Os01t0104100-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0104100-01.exon2;rank=2
+1	irgsp	CDS	210244	210563	.	+	0	ID=CDS:Os01t0104100-02;Parent=transcript:Os01t0104100-02;protein_id=Os01t0104100-02
+1	irgsp	exon	210659	210890	.	+	.	Parent=transcript:Os01t0104100-02;Name=Os01t0104100-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0104100-01.exon3;rank=3
+1	irgsp	CDS	210659	210890	.	+	1	ID=CDS:Os01t0104100-02;Parent=transcript:Os01t0104100-02;protein_id=Os01t0104100-02
+1	irgsp	exon	211015	211160	.	+	.	Parent=transcript:Os01t0104100-02;Name=Os01t0104100-01.exon4;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0104100-01.exon4;rank=4
+1	irgsp	CDS	211015	211160	.	+	0	ID=CDS:Os01t0104100-02;Parent=transcript:Os01t0104100-02;protein_id=Os01t0104100-02
+1	irgsp	exon	212265	212352	.	+	.	Parent=transcript:Os01t0104100-02;Name=Os01t0104100-01.exon5;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0104100-01.exon5;rank=5
+1	irgsp	CDS	212265	212352	.	+	1	ID=CDS:Os01t0104100-02;Parent=transcript:Os01t0104100-02;protein_id=Os01t0104100-02
+1	irgsp	exon	212433	212579	.	+	.	Parent=transcript:Os01t0104100-02;Name=Os01t0104100-01.exon6;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104100-01.exon6;rank=6
+1	irgsp	CDS	212433	212579	.	+	0	ID=CDS:Os01t0104100-02;Parent=transcript:Os01t0104100-02;protein_id=Os01t0104100-02
+1	irgsp	exon	213490	213639	.	+	.	Parent=transcript:Os01t0104100-02;Name=Os01t0104100-01.exon7;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104100-01.exon7;rank=7
+1	irgsp	CDS	213490	213639	.	+	0	ID=CDS:Os01t0104100-02;Parent=transcript:Os01t0104100-02;protein_id=Os01t0104100-02
+1	irgsp	CDS	213741	213788	.	+	0	ID=CDS:Os01t0104100-02;Parent=transcript:Os01t0104100-02;protein_id=Os01t0104100-02
+1	irgsp	exon	213741	214147	.	+	.	Parent=transcript:Os01t0104100-02;Name=Os01t0104100-02.exon8;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0104100-02.exon8;rank=8
+1	irgsp	three_prime_UTR	213789	214147	.	+	.	Parent=transcript:Os01t0104100-02
+###
+1	irgsp	gene	216212	217345	.	+	.	ID=gene:Os01g0104200;Name=NAC DOMAIN-CONTAINING PROTEIN 16;biotype=protein_coding;description=No apical meristem (NAM) protein domain containing protein. (Os01t0104200-00);gene_id=Os01g0104200;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	216212	217345	.	+	.	ID=transcript:Os01t0104200-00;Parent=gene:Os01g0104200;biotype=protein_coding;transcript_id=Os01t0104200-00
+1	irgsp	exon	216212	216769	.	+	.	Parent=transcript:Os01t0104200-00;Name=Os01t0104200-00.exon1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104200-00.exon1;rank=1
+1	irgsp	CDS	216212	216769	.	+	0	ID=CDS:Os01t0104200-00;Parent=transcript:Os01t0104200-00;protein_id=Os01t0104200-00
+1	irgsp	exon	216884	217345	.	+	.	Parent=transcript:Os01t0104200-00;Name=Os01t0104200-00.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104200-00.exon2;rank=2
+1	irgsp	CDS	216884	217345	.	+	0	ID=CDS:Os01t0104200-00;Parent=transcript:Os01t0104200-00;protein_id=Os01t0104200-00
+###
+1	irgsp	gene	226897	229301	.	+	.	ID=gene:Os01g0104400;biotype=protein_coding;description=Ricin B-related lectin domain containing protein. (Os01t0104400-01)%3BRicin B-related lectin domain containing protein. (Os01t0104400-02)%3BRicin B-related lectin domain containing protein. (Os01t0104400-03);gene_id=Os01g0104400;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	226897	229229	.	+	.	ID=transcript:Os01t0104400-01;Parent=gene:Os01g0104400;biotype=protein_coding;transcript_id=Os01t0104400-01
+1	irgsp	five_prime_UTR	226897	227181	.	+	.	Parent=transcript:Os01t0104400-01
+1	irgsp	exon	226897	227634	.	+	.	Parent=transcript:Os01t0104400-01;Name=Os01t0104400-01.exon1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0104400-01.exon1;rank=1
+1	irgsp	CDS	227182	227634	.	+	0	ID=CDS:Os01t0104400-01;Parent=transcript:Os01t0104400-01;protein_id=Os01t0104400-01
+1	irgsp	exon	227742	227864	.	+	.	Parent=transcript:Os01t0104400-01;Name=Os01t0104400-03.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104400-03.exon2;rank=2
+1	irgsp	CDS	227742	227864	.	+	0	ID=CDS:Os01t0104400-01;Parent=transcript:Os01t0104400-01;protein_id=Os01t0104400-01
+1	irgsp	exon	228557	228785	.	+	.	Parent=transcript:Os01t0104400-01;Name=Os01t0104400-03.exon3;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0104400-03.exon3;rank=3
+1	irgsp	CDS	228557	228785	.	+	0	ID=CDS:Os01t0104400-01;Parent=transcript:Os01t0104400-01;protein_id=Os01t0104400-01
+1	irgsp	CDS	228930	228931	.	+	2	ID=CDS:Os01t0104400-01;Parent=transcript:Os01t0104400-01;protein_id=Os01t0104400-01
+1	irgsp	exon	228930	229229	.	+	.	Parent=transcript:Os01t0104400-01;Name=Os01t0104400-01.exon4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0104400-01.exon4;rank=4
+1	irgsp	three_prime_UTR	228932	229229	.	+	.	Parent=transcript:Os01t0104400-01
+1	irgsp	mRNA	227139	229301	.	+	.	ID=transcript:Os01t0104400-02;Parent=gene:Os01g0104400;biotype=protein_coding;transcript_id=Os01t0104400-02
+1	irgsp	five_prime_UTR	227139	227181	.	+	.	Parent=transcript:Os01t0104400-02
+1	irgsp	exon	227139	227634	.	+	.	Parent=transcript:Os01t0104400-02;Name=Os01t0104400-02.exon1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0104400-02.exon1;rank=1
+1	irgsp	CDS	227182	227634	.	+	0	ID=CDS:Os01t0104400-02;Parent=transcript:Os01t0104400-02;protein_id=Os01t0104400-02
+1	irgsp	exon	227742	227864	.	+	.	Parent=transcript:Os01t0104400-02;Name=Os01t0104400-03.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104400-03.exon2;rank=2
+1	irgsp	CDS	227742	227864	.	+	0	ID=CDS:Os01t0104400-02;Parent=transcript:Os01t0104400-02;protein_id=Os01t0104400-02
+1	irgsp	exon	228557	228785	.	+	.	Parent=transcript:Os01t0104400-02;Name=Os01t0104400-03.exon3;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0104400-03.exon3;rank=3
+1	irgsp	CDS	228557	228785	.	+	0	ID=CDS:Os01t0104400-02;Parent=transcript:Os01t0104400-02;protein_id=Os01t0104400-02
+1	irgsp	CDS	228930	228931	.	+	2	ID=CDS:Os01t0104400-02;Parent=transcript:Os01t0104400-02;protein_id=Os01t0104400-02
+1	irgsp	exon	228930	229301	.	+	.	Parent=transcript:Os01t0104400-02;Name=Os01t0104400-02.exon4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0104400-02.exon4;rank=4
+1	irgsp	three_prime_UTR	228932	229301	.	+	.	Parent=transcript:Os01t0104400-02
+1	irgsp	mRNA	227179	229214	.	+	.	ID=transcript:Os01t0104400-03;Parent=gene:Os01g0104400;biotype=protein_coding;transcript_id=Os01t0104400-03
+1	irgsp	five_prime_UTR	227179	227181	.	+	.	Parent=transcript:Os01t0104400-03
+1	irgsp	exon	227179	227634	.	+	.	Parent=transcript:Os01t0104400-03;Name=Os01t0104400-03.exon1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0104400-03.exon1;rank=1
+1	irgsp	CDS	227182	227634	.	+	0	ID=CDS:Os01t0104400-03;Parent=transcript:Os01t0104400-03;protein_id=Os01t0104400-03
+1	irgsp	exon	227742	227864	.	+	.	Parent=transcript:Os01t0104400-03;Name=Os01t0104400-03.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104400-03.exon2;rank=2
+1	irgsp	CDS	227742	227864	.	+	0	ID=CDS:Os01t0104400-03;Parent=transcript:Os01t0104400-03;protein_id=Os01t0104400-03
+1	irgsp	exon	228557	228785	.	+	.	Parent=transcript:Os01t0104400-03;Name=Os01t0104400-03.exon3;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0104400-03.exon3;rank=3
+1	irgsp	CDS	228557	228785	.	+	0	ID=CDS:Os01t0104400-03;Parent=transcript:Os01t0104400-03;protein_id=Os01t0104400-03
+1	irgsp	CDS	228930	228931	.	+	2	ID=CDS:Os01t0104400-03;Parent=transcript:Os01t0104400-03;protein_id=Os01t0104400-03
+1	irgsp	exon	228930	229214	.	+	.	Parent=transcript:Os01t0104400-03;Name=Os01t0104400-03.exon4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0104400-03.exon4;rank=4
+1	irgsp	three_prime_UTR	228932	229214	.	+	.	Parent=transcript:Os01t0104400-03
+###
+1	irgsp	gene	241680	243440	.	+	.	ID=gene:Os01g0104500;Name=NAC DOMAIN-CONTAINING PROTEIN 20;biotype=protein_coding;description=No apical meristem (NAM) protein domain containing protein. (Os01t0104500-01);gene_id=Os01g0104500;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	241680	243440	.	+	.	ID=transcript:Os01t0104500-01;Parent=gene:Os01g0104500;biotype=protein_coding;transcript_id=Os01t0104500-01
+1	irgsp	exon	241680	241702	.	+	.	Parent=transcript:Os01t0104500-01;Name=Os01t0104500-01.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0104500-01.exon1;rank=1
+1	irgsp	five_prime_UTR	241680	241702	.	+	.	Parent=transcript:Os01t0104500-01
+1	irgsp	five_prime_UTR	241866	241907	.	+	.	Parent=transcript:Os01t0104500-01
+1	irgsp	exon	241866	242091	.	+	.	Parent=transcript:Os01t0104500-01;Name=Os01t0104500-01.exon2;constitutive=1;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Os01t0104500-01.exon2;rank=2
+1	irgsp	CDS	241908	242091	.	+	0	ID=CDS:Os01t0104500-01;Parent=transcript:Os01t0104500-01;protein_id=Os01t0104500-01
+1	irgsp	CDS	242199	242977	.	+	2	ID=CDS:Os01t0104500-01;Parent=transcript:Os01t0104500-01;protein_id=Os01t0104500-01
+1	irgsp	exon	242199	243440	.	+	.	Parent=transcript:Os01t0104500-01;Name=Os01t0104500-01.exon3;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0104500-01.exon3;rank=3
+1	irgsp	three_prime_UTR	242978	243440	.	+	.	Parent=transcript:Os01t0104500-01
+###
+1	irgsp	gene	248828	256872	.	-	.	ID=gene:Os01g0104600;Name=DE-ETIOLATED1;biotype=protein_coding;description=Homolog of Arabidopsis DE-ETIOLATED1 (DET1)%2C Modulation of the ABA signaling pathway and ABA biosynthesis%2C Regulation of chlorophyll content (Os01t0104600-01)%3BSimilar to Light-mediated development protein DET1 (Deetiolated1 homolog) (tDET1) (High pigmentation protein 2) (Protein dark green). (Os01t0104600-02);gene_id=Os01g0104600;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	248828	256571	.	-	.	ID=transcript:Os01t0104600-02;Parent=gene:Os01g0104600;biotype=protein_coding;transcript_id=Os01t0104600-02
+1	irgsp	three_prime_UTR	248828	248970	.	-	.	Parent=transcript:Os01t0104600-02
+1	irgsp	exon	248828	249107	.	-	.	Parent=transcript:Os01t0104600-02;Name=Os01t0104600-01.exon11;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0104600-01.exon11;rank=11
+1	irgsp	CDS	248971	249107	.	-	2	ID=CDS:Os01t0104600-02;Parent=transcript:Os01t0104600-02;protein_id=Os01t0104600-02
+1	irgsp	exon	249369	249468	.	-	.	Parent=transcript:Os01t0104600-02;Name=Os01t0104600-01.exon10;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0104600-01.exon10;rank=10
+1	irgsp	CDS	249369	249468	.	-	0	ID=CDS:Os01t0104600-02;Parent=transcript:Os01t0104600-02;protein_id=Os01t0104600-02
+1	irgsp	exon	249861	249956	.	-	.	Parent=transcript:Os01t0104600-02;Name=Os01t0104600-01.exon9;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104600-01.exon9;rank=9
+1	irgsp	CDS	249861	249956	.	-	0	ID=CDS:Os01t0104600-02;Parent=transcript:Os01t0104600-02;protein_id=Os01t0104600-02
+1	irgsp	exon	250617	250781	.	-	.	Parent=transcript:Os01t0104600-02;Name=Os01t0104600-01.exon8;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104600-01.exon8;rank=8
+1	irgsp	CDS	250617	250781	.	-	0	ID=CDS:Os01t0104600-02;Parent=transcript:Os01t0104600-02;protein_id=Os01t0104600-02
+1	irgsp	exon	250860	250940	.	-	.	Parent=transcript:Os01t0104600-02;Name=Os01t0104600-01.exon7;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104600-01.exon7;rank=7
+1	irgsp	CDS	250860	250940	.	-	0	ID=CDS:Os01t0104600-02;Parent=transcript:Os01t0104600-02;protein_id=Os01t0104600-02
+1	irgsp	exon	251026	251082	.	-	.	Parent=transcript:Os01t0104600-02;Name=Os01t0104600-01.exon6;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104600-01.exon6;rank=6
+1	irgsp	CDS	251026	251082	.	-	0	ID=CDS:Os01t0104600-02;Parent=transcript:Os01t0104600-02;protein_id=Os01t0104600-02
+1	irgsp	exon	251316	251384	.	-	.	Parent=transcript:Os01t0104600-02;Name=Os01t0104600-01.exon5;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104600-01.exon5;rank=5
+1	irgsp	CDS	251316	251384	.	-	0	ID=CDS:Os01t0104600-02;Parent=transcript:Os01t0104600-02;protein_id=Os01t0104600-02
+1	irgsp	exon	251695	251790	.	-	.	Parent=transcript:Os01t0104600-02;Name=Os01t0104600-01.exon4;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104600-01.exon4;rank=4
+1	irgsp	CDS	251695	251790	.	-	0	ID=CDS:Os01t0104600-02;Parent=transcript:Os01t0104600-02;protein_id=Os01t0104600-02
+1	irgsp	exon	255325	255553	.	-	.	Parent=transcript:Os01t0104600-02;Name=Os01t0104600-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0104600-01.exon3;rank=3
+1	irgsp	CDS	255325	255553	.	-	1	ID=CDS:Os01t0104600-02;Parent=transcript:Os01t0104600-02;protein_id=Os01t0104600-02
+1	irgsp	exon	255674	256098	.	-	.	Parent=transcript:Os01t0104600-02;Name=Os01t0104600-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0104600-01.exon2;rank=2
+1	irgsp	CDS	255674	256098	.	-	0	ID=CDS:Os01t0104600-02;Parent=transcript:Os01t0104600-02;protein_id=Os01t0104600-02
+1	irgsp	CDS	256361	256441	.	-	0	ID=CDS:Os01t0104600-02;Parent=transcript:Os01t0104600-02;protein_id=Os01t0104600-02
+1	irgsp	exon	256361	256571	.	-	.	Parent=transcript:Os01t0104600-02;Name=Os01t0104600-02.exon1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0104600-02.exon1;rank=1
+1	irgsp	five_prime_UTR	256442	256571	.	-	.	Parent=transcript:Os01t0104600-02
+1	irgsp	mRNA	248828	256872	.	-	.	ID=transcript:Os01t0104600-01;Parent=gene:Os01g0104600;biotype=protein_coding;transcript_id=Os01t0104600-01
+1	irgsp	three_prime_UTR	248828	248970	.	-	.	Parent=transcript:Os01t0104600-01
+1	irgsp	exon	248828	249107	.	-	.	Parent=transcript:Os01t0104600-01;Name=Os01t0104600-01.exon11;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0104600-01.exon11;rank=11
+1	irgsp	CDS	248971	249107	.	-	2	ID=CDS:Os01t0104600-01;Parent=transcript:Os01t0104600-01;protein_id=Os01t0104600-01
+1	irgsp	exon	249369	249468	.	-	.	Parent=transcript:Os01t0104600-01;Name=Os01t0104600-01.exon10;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0104600-01.exon10;rank=10
+1	irgsp	CDS	249369	249468	.	-	0	ID=CDS:Os01t0104600-01;Parent=transcript:Os01t0104600-01;protein_id=Os01t0104600-01
+1	irgsp	exon	249861	249956	.	-	.	Parent=transcript:Os01t0104600-01;Name=Os01t0104600-01.exon9;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104600-01.exon9;rank=9
+1	irgsp	CDS	249861	249956	.	-	0	ID=CDS:Os01t0104600-01;Parent=transcript:Os01t0104600-01;protein_id=Os01t0104600-01
+1	irgsp	exon	250617	250781	.	-	.	Parent=transcript:Os01t0104600-01;Name=Os01t0104600-01.exon8;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104600-01.exon8;rank=8
+1	irgsp	CDS	250617	250781	.	-	0	ID=CDS:Os01t0104600-01;Parent=transcript:Os01t0104600-01;protein_id=Os01t0104600-01
+1	irgsp	exon	250860	250940	.	-	.	Parent=transcript:Os01t0104600-01;Name=Os01t0104600-01.exon7;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104600-01.exon7;rank=7
+1	irgsp	CDS	250860	250940	.	-	0	ID=CDS:Os01t0104600-01;Parent=transcript:Os01t0104600-01;protein_id=Os01t0104600-01
+1	irgsp	exon	251026	251082	.	-	.	Parent=transcript:Os01t0104600-01;Name=Os01t0104600-01.exon6;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104600-01.exon6;rank=6
+1	irgsp	CDS	251026	251082	.	-	0	ID=CDS:Os01t0104600-01;Parent=transcript:Os01t0104600-01;protein_id=Os01t0104600-01
+1	irgsp	exon	251316	251384	.	-	.	Parent=transcript:Os01t0104600-01;Name=Os01t0104600-01.exon5;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104600-01.exon5;rank=5
+1	irgsp	CDS	251316	251384	.	-	0	ID=CDS:Os01t0104600-01;Parent=transcript:Os01t0104600-01;protein_id=Os01t0104600-01
+1	irgsp	exon	251695	251790	.	-	.	Parent=transcript:Os01t0104600-01;Name=Os01t0104600-01.exon4;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104600-01.exon4;rank=4
+1	irgsp	CDS	251695	251790	.	-	0	ID=CDS:Os01t0104600-01;Parent=transcript:Os01t0104600-01;protein_id=Os01t0104600-01
+1	irgsp	exon	255325	255553	.	-	.	Parent=transcript:Os01t0104600-01;Name=Os01t0104600-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0104600-01.exon3;rank=3
+1	irgsp	CDS	255325	255553	.	-	1	ID=CDS:Os01t0104600-01;Parent=transcript:Os01t0104600-01;protein_id=Os01t0104600-01
+1	irgsp	exon	255674	256098	.	-	.	Parent=transcript:Os01t0104600-01;Name=Os01t0104600-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0104600-01.exon2;rank=2
+1	irgsp	CDS	255674	256098	.	-	0	ID=CDS:Os01t0104600-01;Parent=transcript:Os01t0104600-01;protein_id=Os01t0104600-01
+1	irgsp	CDS	256361	256441	.	-	0	ID=CDS:Os01t0104600-01;Parent=transcript:Os01t0104600-01;protein_id=Os01t0104600-01
+1	irgsp	exon	256361	256872	.	-	.	Parent=transcript:Os01t0104600-01;Name=Os01t0104600-01.exon1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0104600-01.exon1;rank=1
+1	irgsp	five_prime_UTR	256442	256872	.	-	.	Parent=transcript:Os01t0104600-01
+###
+1	irgsp	gene	261530	268145	.	+	.	ID=gene:Os01g0104800;biotype=protein_coding;description=Sas10/Utp3 family protein. (Os01t0104800-01)%3BHypothetical conserved gene. (Os01t0104800-02);gene_id=Os01g0104800;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	261530	268145	.	+	.	ID=transcript:Os01t0104800-01;Parent=gene:Os01g0104800;biotype=protein_coding;transcript_id=Os01t0104800-01
+1	irgsp	five_prime_UTR	261530	261561	.	+	.	Parent=transcript:Os01t0104800-01
+1	irgsp	exon	261530	261661	.	+	.	Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon1;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Os01t0104800-01.exon1;rank=1
+1	irgsp	CDS	261562	261661	.	+	0	ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
+1	irgsp	exon	261767	261805	.	+	.	Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon2;constitutive=0;ensembl_end_phase=1;ensembl_phase=1;exon_id=Os01t0104800-01.exon2;rank=2
+1	irgsp	CDS	261767	261805	.	+	2	ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
+1	irgsp	exon	261895	261941	.	+	.	Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon3;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0104800-01.exon3;rank=3
+1	irgsp	CDS	261895	261941	.	+	2	ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
+1	irgsp	exon	262582	262681	.	+	.	Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon4;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0104800-01.exon4;rank=4
+1	irgsp	CDS	262582	262681	.	+	0	ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
+1	irgsp	exon	262925	263181	.	+	.	Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon5;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0104800-01.exon5;rank=5
+1	irgsp	CDS	262925	263181	.	+	2	ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
+1	irgsp	exon	263525	263640	.	+	.	Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon6;constitutive=0;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0104800-01.exon6;rank=6
+1	irgsp	CDS	263525	263640	.	+	0	ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
+1	irgsp	exon	264014	264098	.	+	.	Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon7;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0104800-01.exon7;rank=7
+1	irgsp	CDS	264014	264098	.	+	1	ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
+1	irgsp	exon	265236	265415	.	+	.	Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon8;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104800-01.exon8;rank=8
+1	irgsp	CDS	265236	265415	.	+	0	ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
+1	irgsp	exon	265506	265649	.	+	.	Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon9;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104800-01.exon9;rank=9
+1	irgsp	CDS	265506	265649	.	+	0	ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
+1	irgsp	exon	265740	265817	.	+	.	Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon10;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104800-01.exon10;rank=10
+1	irgsp	CDS	265740	265817	.	+	0	ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
+1	irgsp	exon	265909	266045	.	+	.	Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon11;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0104800-01.exon11;rank=11
+1	irgsp	CDS	265909	266045	.	+	0	ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
+1	irgsp	exon	266138	266246	.	+	.	Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon12;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0104800-01.exon12;rank=12
+1	irgsp	CDS	266138	266246	.	+	1	ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
+1	irgsp	exon	267237	267514	.	+	.	Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon13;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0104800-01.exon13;rank=13
+1	irgsp	CDS	267237	267514	.	+	0	ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
+1	irgsp	exon	267591	267657	.	+	.	Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon14;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0104800-01.exon14;rank=14
+1	irgsp	CDS	267591	267657	.	+	1	ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
+1	irgsp	exon	267734	267802	.	+	.	Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon15;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104800-01.exon15;rank=15
+1	irgsp	CDS	267734	267802	.	+	0	ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
+1	irgsp	CDS	267880	268011	.	+	0	ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
+1	irgsp	exon	267880	268145	.	+	.	Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon16;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0104800-01.exon16;rank=16
+1	irgsp	three_prime_UTR	268012	268145	.	+	.	Parent=transcript:Os01t0104800-01
+1	irgsp	mRNA	263523	268120	.	+	.	ID=transcript:Os01t0104800-02;Parent=gene:Os01g0104800;biotype=protein_coding;transcript_id=Os01t0104800-02
+1	irgsp	five_prime_UTR	263523	263524	.	+	.	Parent=transcript:Os01t0104800-02
+1	irgsp	exon	263523	263640	.	+	.	Parent=transcript:Os01t0104800-02;Name=Os01t0104800-02.exon1;constitutive=0;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0104800-02.exon1;rank=1
+1	irgsp	CDS	263525	263640	.	+	0	ID=CDS:Os01t0104800-02;Parent=transcript:Os01t0104800-02;protein_id=Os01t0104800-02
+1	irgsp	exon	264014	264098	.	+	.	Parent=transcript:Os01t0104800-02;Name=Os01t0104800-01.exon7;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0104800-01.exon7;rank=2
+1	irgsp	CDS	264014	264098	.	+	1	ID=CDS:Os01t0104800-02;Parent=transcript:Os01t0104800-02;protein_id=Os01t0104800-02
+1	irgsp	exon	265236	265415	.	+	.	Parent=transcript:Os01t0104800-02;Name=Os01t0104800-01.exon8;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104800-01.exon8;rank=3
+1	irgsp	CDS	265236	265415	.	+	0	ID=CDS:Os01t0104800-02;Parent=transcript:Os01t0104800-02;protein_id=Os01t0104800-02
+1	irgsp	exon	265506	265649	.	+	.	Parent=transcript:Os01t0104800-02;Name=Os01t0104800-01.exon9;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104800-01.exon9;rank=4
+1	irgsp	CDS	265506	265649	.	+	0	ID=CDS:Os01t0104800-02;Parent=transcript:Os01t0104800-02;protein_id=Os01t0104800-02
+1	irgsp	exon	265740	265817	.	+	.	Parent=transcript:Os01t0104800-02;Name=Os01t0104800-01.exon10;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104800-01.exon10;rank=5
+1	irgsp	CDS	265740	265817	.	+	0	ID=CDS:Os01t0104800-02;Parent=transcript:Os01t0104800-02;protein_id=Os01t0104800-02
+1	irgsp	exon	265909	266045	.	+	.	Parent=transcript:Os01t0104800-02;Name=Os01t0104800-01.exon11;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0104800-01.exon11;rank=6
+1	irgsp	CDS	265909	266045	.	+	0	ID=CDS:Os01t0104800-02;Parent=transcript:Os01t0104800-02;protein_id=Os01t0104800-02
+1	irgsp	exon	266138	266246	.	+	.	Parent=transcript:Os01t0104800-02;Name=Os01t0104800-01.exon12;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0104800-01.exon12;rank=7
+1	irgsp	CDS	266138	266246	.	+	1	ID=CDS:Os01t0104800-02;Parent=transcript:Os01t0104800-02;protein_id=Os01t0104800-02
+1	irgsp	exon	267237	267514	.	+	.	Parent=transcript:Os01t0104800-02;Name=Os01t0104800-01.exon13;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0104800-01.exon13;rank=8
+1	irgsp	CDS	267237	267514	.	+	0	ID=CDS:Os01t0104800-02;Parent=transcript:Os01t0104800-02;protein_id=Os01t0104800-02
+1	irgsp	exon	267591	267657	.	+	.	Parent=transcript:Os01t0104800-02;Name=Os01t0104800-01.exon14;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0104800-01.exon14;rank=9
+1	irgsp	CDS	267591	267657	.	+	1	ID=CDS:Os01t0104800-02;Parent=transcript:Os01t0104800-02;protein_id=Os01t0104800-02
+1	irgsp	exon	267734	267802	.	+	.	Parent=transcript:Os01t0104800-02;Name=Os01t0104800-01.exon15;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104800-01.exon15;rank=10
+1	irgsp	CDS	267734	267802	.	+	0	ID=CDS:Os01t0104800-02;Parent=transcript:Os01t0104800-02;protein_id=Os01t0104800-02
+1	irgsp	CDS	267880	268011	.	+	0	ID=CDS:Os01t0104800-02;Parent=transcript:Os01t0104800-02;protein_id=Os01t0104800-02
+1	irgsp	exon	267880	268120	.	+	.	Parent=transcript:Os01t0104800-02;Name=Os01t0104800-02.exon11;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0104800-02.exon11;rank=11
+1	irgsp	three_prime_UTR	268012	268120	.	+	.	Parent=transcript:Os01t0104800-02
+###
+1	irgsp	gene	270179	275084	.	-	.	ID=gene:Os01g0104900;biotype=protein_coding;description=Transferase family protein. (Os01t0104900-01)%3BHypothetical conserved gene. (Os01t0104900-02);gene_id=Os01g0104900;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	270179	275084	.	-	.	ID=transcript:Os01t0104900-01;Parent=gene:Os01g0104900;biotype=protein_coding;transcript_id=Os01t0104900-01
+1	irgsp	three_prime_UTR	270179	270355	.	-	.	Parent=transcript:Os01t0104900-01
+1	irgsp	exon	270179	271333	.	-	.	Parent=transcript:Os01t0104900-01;Name=Os01t0104900-01.exon2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0104900-01.exon2;rank=2
+1	irgsp	CDS	270356	271333	.	-	0	ID=CDS:Os01t0104900-01;Parent=transcript:Os01t0104900-01;protein_id=Os01t0104900-01
+1	irgsp	CDS	274529	274957	.	-	0	ID=CDS:Os01t0104900-01;Parent=transcript:Os01t0104900-01;protein_id=Os01t0104900-01
+1	irgsp	exon	274529	275084	.	-	.	Parent=transcript:Os01t0104900-01;Name=Os01t0104900-01.exon1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0104900-01.exon1;rank=1
+1	irgsp	five_prime_UTR	274958	275084	.	-	.	Parent=transcript:Os01t0104900-01
+1	irgsp	mRNA	270250	271518	.	-	.	ID=transcript:Os01t0104900-02;Parent=gene:Os01g0104900;biotype=protein_coding;transcript_id=Os01t0104900-02
+1	irgsp	three_prime_UTR	270250	270355	.	-	.	Parent=transcript:Os01t0104900-02
+1	irgsp	exon	270250	271333	.	-	.	Parent=transcript:Os01t0104900-02;Name=Os01t0104900-02.exon2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0104900-02.exon2;rank=2
+1	irgsp	CDS	270356	271309	.	-	0	ID=CDS:Os01t0104900-02;Parent=transcript:Os01t0104900-02;protein_id=Os01t0104900-02
+1	irgsp	five_prime_UTR	271310	271333	.	-	.	Parent=transcript:Os01t0104900-02
+1	irgsp	exon	271457	271518	.	-	.	Parent=transcript:Os01t0104900-02;Name=Os01t0104900-02.exon1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0104900-02.exon1;rank=1
+1	irgsp	five_prime_UTR	271457	271518	.	-	.	Parent=transcript:Os01t0104900-02
+###
+1	irgsp	gene	284762	291892	.	-	.	ID=gene:Os01g0105300;biotype=protein_coding;description=Similar to HAT family dimerisation domain containing protein%2C expressed. (Os01t0105300-01);gene_id=Os01g0105300;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	284762	291892	.	-	.	ID=transcript:Os01t0105300-01;Parent=gene:Os01g0105300;biotype=protein_coding;transcript_id=Os01t0105300-01
+1	irgsp	three_prime_UTR	284762	284930	.	-	.	Parent=transcript:Os01t0105300-01
+1	irgsp	exon	284762	287047	.	-	.	Parent=transcript:Os01t0105300-01;Name=Os01t0105300-01.exon5;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0105300-01.exon5;rank=5
+1	irgsp	CDS	284931	285020	.	-	0	ID=CDS:Os01t0105300-01;Parent=transcript:Os01t0105300-01;protein_id=Os01t0105300-01
+1	irgsp	five_prime_UTR	285021	287047	.	-	.	Parent=transcript:Os01t0105300-01
+1	irgsp	exon	291398	291436	.	-	.	Parent=transcript:Os01t0105300-01;Name=Os01t0105300-01.exon4;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0105300-01.exon4;rank=4
+1	irgsp	five_prime_UTR	291398	291436	.	-	.	Parent=transcript:Os01t0105300-01
+1	irgsp	exon	291520	291534	.	-	.	Parent=transcript:Os01t0105300-01;Name=Os01t0105300-01.exon3;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0105300-01.exon3;rank=3
+1	irgsp	five_prime_UTR	291520	291534	.	-	.	Parent=transcript:Os01t0105300-01
+1	irgsp	exon	291678	291738	.	-	.	Parent=transcript:Os01t0105300-01;Name=Os01t0105300-01.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0105300-01.exon2;rank=2
+1	irgsp	five_prime_UTR	291678	291738	.	-	.	Parent=transcript:Os01t0105300-01
+1	irgsp	exon	291838	291892	.	-	.	Parent=transcript:Os01t0105300-01;Name=Os01t0105300-01.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0105300-01.exon1;rank=1
+1	irgsp	five_prime_UTR	291838	291892	.	-	.	Parent=transcript:Os01t0105300-01
+###
+1	irgsp	gene	288372	292296	.	+	.	ID=gene:Os01g0105400;biotype=protein_coding;description=Similar to Kinesin heavy chain. (Os01t0105400-01);gene_id=Os01g0105400;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	288372	292296	.	+	.	ID=transcript:Os01t0105400-01;Parent=gene:Os01g0105400;biotype=protein_coding;transcript_id=Os01t0105400-01
+1	irgsp	exon	288372	288846	.	+	.	Parent=transcript:Os01t0105400-01;Name=Os01t0105400-01.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0105400-01.exon1;rank=1
+1	irgsp	five_prime_UTR	288372	288846	.	+	.	Parent=transcript:Os01t0105400-01
+1	irgsp	exon	288950	289116	.	+	.	Parent=transcript:Os01t0105400-01;Name=Os01t0105400-01.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0105400-01.exon2;rank=2
+1	irgsp	five_prime_UTR	288950	289116	.	+	.	Parent=transcript:Os01t0105400-01
+1	irgsp	exon	289202	289572	.	+	.	Parent=transcript:Os01t0105400-01;Name=Os01t0105400-01.exon3;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0105400-01.exon3;rank=3
+1	irgsp	five_prime_UTR	289202	289572	.	+	.	Parent=transcript:Os01t0105400-01
+1	irgsp	exon	289661	289830	.	+	.	Parent=transcript:Os01t0105400-01;Name=Os01t0105400-01.exon4;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0105400-01.exon4;rank=4
+1	irgsp	five_prime_UTR	289661	289830	.	+	.	Parent=transcript:Os01t0105400-01
+1	irgsp	five_prime_UTR	290395	290432	.	+	.	Parent=transcript:Os01t0105400-01
+1	irgsp	exon	290395	290512	.	+	.	Parent=transcript:Os01t0105400-01;Name=Os01t0105400-01.exon5;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0105400-01.exon5;rank=5
+1	irgsp	CDS	290433	290512	.	+	0	ID=CDS:Os01t0105400-01;Parent=transcript:Os01t0105400-01;protein_id=Os01t0105400-01
+1	irgsp	CDS	291372	291558	.	+	1	ID=CDS:Os01t0105400-01;Parent=transcript:Os01t0105400-01;protein_id=Os01t0105400-01
+1	irgsp	exon	291372	291574	.	+	.	Parent=transcript:Os01t0105400-01;Name=Os01t0105400-01.exon6;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0105400-01.exon6;rank=6
+1	irgsp	three_prime_UTR	291559	291574	.	+	.	Parent=transcript:Os01t0105400-01
+1	irgsp	exon	291648	291779	.	+	.	Parent=transcript:Os01t0105400-01;Name=Os01t0105400-01.exon7;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0105400-01.exon7;rank=7
+1	irgsp	three_prime_UTR	291648	291779	.	+	.	Parent=transcript:Os01t0105400-01
+1	irgsp	exon	291859	291948	.	+	.	Parent=transcript:Os01t0105400-01;Name=Os01t0105400-01.exon8;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0105400-01.exon8;rank=8
+1	irgsp	three_prime_UTR	291859	291948	.	+	.	Parent=transcript:Os01t0105400-01
+1	irgsp	exon	292073	292296	.	+	.	Parent=transcript:Os01t0105400-01;Name=Os01t0105400-01.exon9;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0105400-01.exon9;rank=9
+1	irgsp	three_prime_UTR	292073	292296	.	+	.	Parent=transcript:Os01t0105400-01
+###
+1	irgsp	gene	303233	306736	.	+	.	ID=gene:Os01g0105700;Name=basic helix-loop-helix protein 071;biotype=protein_coding;description=Basic helix-loop-helix dimerisation region bHLH domain containing protein. (Os01t0105700-01);gene_id=Os01g0105700;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	303233	306736	.	+	.	ID=transcript:Os01t0105700-01;Parent=gene:Os01g0105700;biotype=protein_coding;transcript_id=Os01t0105700-01
+1	irgsp	five_prime_UTR	303233	303328	.	+	.	Parent=transcript:Os01t0105700-01
+1	irgsp	exon	303233	303471	.	+	.	Parent=transcript:Os01t0105700-01;Name=Os01t0105700-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0105700-01.exon1;rank=1
+1	irgsp	CDS	303329	303471	.	+	0	ID=CDS:Os01t0105700-01;Parent=transcript:Os01t0105700-01;protein_id=Os01t0105700-01
+1	irgsp	exon	303981	304509	.	+	.	Parent=transcript:Os01t0105700-01;Name=Os01t0105700-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0105700-01.exon2;rank=2
+1	irgsp	CDS	303981	304509	.	+	1	ID=CDS:Os01t0105700-01;Parent=transcript:Os01t0105700-01;protein_id=Os01t0105700-01
+1	irgsp	exon	305572	305718	.	+	.	Parent=transcript:Os01t0105700-01;Name=Os01t0105700-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0105700-01.exon3;rank=3
+1	irgsp	CDS	305572	305718	.	+	0	ID=CDS:Os01t0105700-01;Parent=transcript:Os01t0105700-01;protein_id=Os01t0105700-01
+1	irgsp	exon	305834	305899	.	+	.	Parent=transcript:Os01t0105700-01;Name=Os01t0105700-01.exon4;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0105700-01.exon4;rank=4
+1	irgsp	CDS	305834	305899	.	+	0	ID=CDS:Os01t0105700-01;Parent=transcript:Os01t0105700-01;protein_id=Os01t0105700-01
+1	irgsp	exon	305993	306058	.	+	.	Parent=transcript:Os01t0105700-01;Name=Os01t0105700-01.exon5;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0105700-01.exon5;rank=5
+1	irgsp	CDS	305993	306058	.	+	0	ID=CDS:Os01t0105700-01;Parent=transcript:Os01t0105700-01;protein_id=Os01t0105700-01
+1	irgsp	exon	306171	306245	.	+	.	Parent=transcript:Os01t0105700-01;Name=Os01t0105700-01.exon6;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0105700-01.exon6;rank=6
+1	irgsp	CDS	306171	306245	.	+	0	ID=CDS:Os01t0105700-01;Parent=transcript:Os01t0105700-01;protein_id=Os01t0105700-01
+1	irgsp	CDS	306353	306493	.	+	0	ID=CDS:Os01t0105700-01;Parent=transcript:Os01t0105700-01;protein_id=Os01t0105700-01
+1	irgsp	exon	306353	306736	.	+	.	Parent=transcript:Os01t0105700-01;Name=Os01t0105700-01.exon7;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0105700-01.exon7;rank=7
+1	irgsp	three_prime_UTR	306494	306736	.	+	.	Parent=transcript:Os01t0105700-01
+###
+1	irgsp	gene	306871	308842	.	-	.	ID=gene:Os01g0105800;Name=IRON-SULFUR CLUSTER PROTEIN 9;biotype=protein_coding;description=Similar to Iron sulfur assembly protein 1. (Os01t0105800-01);gene_id=Os01g0105800;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	306871	308842	.	-	.	ID=transcript:Os01t0105800-01;Parent=gene:Os01g0105800;biotype=protein_coding;transcript_id=Os01t0105800-01
+1	irgsp	three_prime_UTR	306871	307123	.	-	.	Parent=transcript:Os01t0105800-01
+1	irgsp	exon	306871	307217	.	-	.	Parent=transcript:Os01t0105800-01;Name=Os01t0105800-01.exon4;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0105800-01.exon4;rank=4
+1	irgsp	CDS	307124	307217	.	-	1	ID=CDS:Os01t0105800-01;Parent=transcript:Os01t0105800-01;protein_id=Os01t0105800-01
+1	irgsp	exon	307296	307413	.	-	.	Parent=transcript:Os01t0105800-01;Name=Os01t0105800-01.exon3;constitutive=1;ensembl_end_phase=2;ensembl_phase=1;exon_id=Os01t0105800-01.exon3;rank=3
+1	irgsp	CDS	307296	307413	.	-	2	ID=CDS:Os01t0105800-01;Parent=transcript:Os01t0105800-01;protein_id=Os01t0105800-01
+1	irgsp	CDS	308397	308601	.	-	0	ID=CDS:Os01t0105800-01;Parent=transcript:Os01t0105800-01;protein_id=Os01t0105800-01
+1	irgsp	exon	308397	308626	.	-	.	Parent=transcript:Os01t0105800-01;Name=Os01t0105800-01.exon2;constitutive=1;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Os01t0105800-01.exon2;rank=2
+1	irgsp	five_prime_UTR	308602	308626	.	-	.	Parent=transcript:Os01t0105800-01
+1	irgsp	exon	308703	308842	.	-	.	Parent=transcript:Os01t0105800-01;Name=Os01t0105800-01.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0105800-01.exon1;rank=1
+1	irgsp	five_prime_UTR	308703	308842	.	-	.	Parent=transcript:Os01t0105800-01
+###
+1	irgsp	gene	309520	313170	.	-	.	ID=gene:Os01g0105900;biotype=protein_coding;description=Carbohydrate/purine kinase domain containing protein. (Os01t0105900-01);gene_id=Os01g0105900;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	309520	313170	.	-	.	ID=transcript:Os01t0105900-01;Parent=gene:Os01g0105900;biotype=protein_coding;transcript_id=Os01t0105900-01
+1	irgsp	three_prime_UTR	309520	309821	.	-	.	Parent=transcript:Os01t0105900-01
+1	irgsp	exon	309520	310070	.	-	.	Parent=transcript:Os01t0105900-01;Name=Os01t0105900-01.exon8;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0105900-01.exon8;rank=8
+1	irgsp	CDS	309822	310070	.	-	0	ID=CDS:Os01t0105900-01;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
+1	irgsp	exon	310256	310367	.	-	.	Parent=transcript:Os01t0105900-01;Name=Os01t0105900-01.exon7;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0105900-01.exon7;rank=7
+1	irgsp	CDS	310256	310367	.	-	1	ID=CDS:Os01t0105900-01;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
+1	irgsp	exon	310455	310552	.	-	.	Parent=transcript:Os01t0105900-01;Name=Os01t0105900-01.exon6;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0105900-01.exon6;rank=6
+1	irgsp	CDS	310455	310552	.	-	0	ID=CDS:Os01t0105900-01;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
+1	irgsp	exon	310632	310739	.	-	.	Parent=transcript:Os01t0105900-01;Name=Os01t0105900-01.exon5;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0105900-01.exon5;rank=5
+1	irgsp	CDS	310632	310739	.	-	0	ID=CDS:Os01t0105900-01;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
+1	irgsp	exon	310880	310918	.	-	.	Parent=transcript:Os01t0105900-01;Name=Os01t0105900-01.exon4;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0105900-01.exon4;rank=4
+1	irgsp	CDS	310880	310918	.	-	0	ID=CDS:Os01t0105900-01;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
+1	irgsp	exon	311002	311073	.	-	.	Parent=transcript:Os01t0105900-01;Name=Os01t0105900-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0105900-01.exon3;rank=3
+1	irgsp	CDS	311002	311073	.	-	0	ID=CDS:Os01t0105900-01;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
+1	irgsp	exon	311163	311426	.	-	.	Parent=transcript:Os01t0105900-01;Name=Os01t0105900-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0105900-01.exon2;rank=2
+1	irgsp	CDS	311163	311426	.	-	0	ID=CDS:Os01t0105900-01;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
+1	irgsp	CDS	312867	313064	.	-	0	ID=CDS:Os01t0105900-01;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
+1	irgsp	exon	312867	313170	.	-	.	Parent=transcript:Os01t0105900-01;Name=Os01t0105900-01.exon1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0105900-01.exon1;rank=1
+1	irgsp	five_prime_UTR	313065	313170	.	-	.	Parent=transcript:Os01t0105900-01
+###
+1	irgsp	gene	319754	322205	.	+	.	ID=gene:Os01g0106200;biotype=protein_coding;description=Similar to RER1A protein (AtRER1A). (Os01t0106200-01);gene_id=Os01g0106200;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	319754	322205	.	+	.	ID=transcript:Os01t0106200-01;Parent=gene:Os01g0106200;biotype=protein_coding;transcript_id=Os01t0106200-01
+1	irgsp	five_prime_UTR	319754	319874	.	+	.	Parent=transcript:Os01t0106200-01
+1	irgsp	exon	319754	320236	.	+	.	Parent=transcript:Os01t0106200-01;Name=Os01t0106200-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0106200-01.exon1;rank=1
+1	irgsp	CDS	319875	320236	.	+	0	ID=CDS:Os01t0106200-01;Parent=transcript:Os01t0106200-01;protein_id=Os01t0106200-01
+1	irgsp	exon	321468	321648	.	+	.	Parent=transcript:Os01t0106200-01;Name=Os01t0106200-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0106200-01.exon2;rank=2
+1	irgsp	CDS	321468	321648	.	+	1	ID=CDS:Os01t0106200-01;Parent=transcript:Os01t0106200-01;protein_id=Os01t0106200-01
+1	irgsp	CDS	321928	321975	.	+	0	ID=CDS:Os01t0106200-01;Parent=transcript:Os01t0106200-01;protein_id=Os01t0106200-01
+1	irgsp	exon	321928	322205	.	+	.	Parent=transcript:Os01t0106200-01;Name=Os01t0106200-01.exon3;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0106200-01.exon3;rank=3
+1	irgsp	three_prime_UTR	321976	322205	.	+	.	Parent=transcript:Os01t0106200-01
+###
+1	irgsp	gene	322591	323923	.	-	.	ID=gene:Os01g0106300;biotype=protein_coding;description=Similar to Isoflavone reductase homolog IRL (EC 1.3.1.-). (Os01t0106300-01);gene_id=Os01g0106300;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	322591	323923	.	-	.	ID=transcript:Os01t0106300-01;Parent=gene:Os01g0106300;biotype=protein_coding;transcript_id=Os01t0106300-01
+1	irgsp	three_prime_UTR	322591	322809	.	-	.	Parent=transcript:Os01t0106300-01
+1	irgsp	exon	322591	322973	.	-	.	Parent=transcript:Os01t0106300-01;Name=Os01t0106300-01.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0106300-01.exon2;rank=2
--- a/src/agat/agat_convert_sp_gff2tsv/test_data/agat_convert_sp_gff2tsv_1.tsv
+++ b/src/agat/agat_convert_sp_gff2tsv/test_data/agat_convert_sp_gff2tsv_1.tsv
@@ -0,0 +1,881 @@
+seq_id	source_tag	primary_tag	start	end	score	strand	frame	Alias	biotype	constitutive	description	ensembl_end_phase	ensembl_phase	exon_id	gene_id	ID	logic_name	Name	Parent	protein_id	rank	transcript_id
+1	irgsp	repeat_region	2000	2100	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	fakeRepeat1	N/A	N/A	N/A	N/A	N/A	N/A
+1	irgsp	gene	2983	10815	.	1	.	N/A	protein_coding	N/A	RabGAP/TBC domain containing protein. (Os01t0100100-01)	N/A	N/A	N/A	Os01g0100100	gene:Os01g0100100	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	2983	10815	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0100100-01	N/A	N/A	gene:Os01g0100100	N/A	N/A	Os01t0100100-01
+1	irgsp	exon	2983	3268	.	1	.	N/A	N/A	1	N/A	-1	-1	Os01t0100100-01.exon1	N/A	Os01t0100100-01.exon1	N/A	Os01t0100100-01.exon1	transcript:Os01t0100100-01	N/A	1	N/A
+1	irgsp	exon	3354	3616	.	1	.	N/A	N/A	1	N/A	0	-1	Os01t0100100-01.exon2	N/A	Os01t0100100-01.exon2	N/A	Os01t0100100-01.exon2	transcript:Os01t0100100-01	N/A	2	N/A
+1	irgsp	exon	4357	4455	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0100100-01.exon3	N/A	Os01t0100100-01.exon3	N/A	Os01t0100100-01.exon3	transcript:Os01t0100100-01	N/A	3	N/A
+1	irgsp	exon	5457	5560	.	1	.	N/A	N/A	1	N/A	2	0	Os01t0100100-01.exon4	N/A	Os01t0100100-01.exon4	N/A	Os01t0100100-01.exon4	transcript:Os01t0100100-01	N/A	4	N/A
+1	irgsp	exon	7136	7944	.	1	.	N/A	N/A	1	N/A	1	2	Os01t0100100-01.exon5	N/A	Os01t0100100-01.exon5	N/A	Os01t0100100-01.exon5	transcript:Os01t0100100-01	N/A	5	N/A
+1	irgsp	exon	8028	8150	.	1	.	N/A	N/A	1	N/A	1	1	Os01t0100100-01.exon6	N/A	Os01t0100100-01.exon6	N/A	Os01t0100100-01.exon6	transcript:Os01t0100100-01	N/A	6	N/A
+1	irgsp	exon	8232	8320	.	1	.	N/A	N/A	1	N/A	0	1	Os01t0100100-01.exon7	N/A	Os01t0100100-01.exon7	N/A	Os01t0100100-01.exon7	transcript:Os01t0100100-01	N/A	7	N/A
+1	irgsp	exon	8408	8608	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0100100-01.exon8	N/A	Os01t0100100-01.exon8	N/A	Os01t0100100-01.exon8	transcript:Os01t0100100-01	N/A	8	N/A
+1	irgsp	exon	9210	9615	.	1	.	N/A	N/A	1	N/A	1	0	Os01t0100100-01.exon9	N/A	Os01t0100100-01.exon9	N/A	Os01t0100100-01.exon9	transcript:Os01t0100100-01	N/A	9	N/A
+1	irgsp	exon	10102	10187	.	1	.	N/A	N/A	1	N/A	0	1	Os01t0100100-01.exon10	N/A	Os01t0100100-01.exon10	N/A	Os01t0100100-01.exon10	transcript:Os01t0100100-01	N/A	10	N/A
+1	irgsp	exon	10274	10430	.	1	.	N/A	N/A	1	N/A	-1	0	Os01t0100100-01.exon11	N/A	Os01t0100100-01.exon11	N/A	Os01t0100100-01.exon11	transcript:Os01t0100100-01	N/A	11	N/A
+1	irgsp	exon	10504	10815	.	1	.	N/A	N/A	1	N/A	-1	-1	Os01t0100100-01.exon12	N/A	Os01t0100100-01.exon12	N/A	Os01t0100100-01.exon12	transcript:Os01t0100100-01	N/A	12	N/A
+1	irgsp	CDS	3449	3616	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100100-01	N/A	N/A	transcript:Os01t0100100-01	Os01t0100100-01	N/A	N/A
+1	irgsp	CDS	4357	4455	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100100-01	N/A	N/A	transcript:Os01t0100100-01	Os01t0100100-01	N/A	N/A
+1	irgsp	CDS	5457	5560	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100100-01	N/A	N/A	transcript:Os01t0100100-01	Os01t0100100-01	N/A	N/A
+1	irgsp	CDS	7136	7944	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100100-01	N/A	N/A	transcript:Os01t0100100-01	Os01t0100100-01	N/A	N/A
+1	irgsp	CDS	8028	8150	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100100-01	N/A	N/A	transcript:Os01t0100100-01	Os01t0100100-01	N/A	N/A
+1	irgsp	CDS	8232	8320	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100100-01	N/A	N/A	transcript:Os01t0100100-01	Os01t0100100-01	N/A	N/A
+1	irgsp	CDS	8408	8608	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100100-01	N/A	N/A	transcript:Os01t0100100-01	Os01t0100100-01	N/A	N/A
+1	irgsp	CDS	9210	9615	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100100-01	N/A	N/A	transcript:Os01t0100100-01	Os01t0100100-01	N/A	N/A
+1	irgsp	CDS	10102	10187	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100100-01	N/A	N/A	transcript:Os01t0100100-01	Os01t0100100-01	N/A	N/A
+1	irgsp	CDS	10274	10297	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100100-01	N/A	N/A	transcript:Os01t0100100-01	Os01t0100100-01	N/A	N/A
+1	irgsp	five_prime_UTR	2983	3268	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-1	N/A	N/A	transcript:Os01t0100100-01	N/A	N/A	N/A
+1	irgsp	five_prime_UTR	3354	3448	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-2	N/A	N/A	transcript:Os01t0100100-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	10298	10430	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-1	N/A	N/A	transcript:Os01t0100100-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	10504	10815	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-2	N/A	N/A	transcript:Os01t0100100-01	N/A	N/A	N/A
+1	irgsp	gene	11218	12435	.	1	.	N/A	protein_coding	N/A	Conserved hypothetical protein. (Os01t0100200-01)	N/A	N/A	N/A	Os01g0100200	gene:Os01g0100200	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	11218	12435	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0100200-01	N/A	N/A	gene:Os01g0100200	N/A	N/A	Os01t0100200-01
+1	irgsp	exon	11218	12060	.	1	.	N/A	N/A	1	N/A	2	-1	Os01t0100200-01.exon1	N/A	Os01t0100200-01.exon1	N/A	Os01t0100200-01.exon1	transcript:Os01t0100200-01	N/A	1	N/A
+1	irgsp	exon	12152	12435	.	1	.	N/A	N/A	1	N/A	-1	2	Os01t0100200-01.exon2	N/A	Os01t0100200-01.exon2	N/A	Os01t0100200-01.exon2	transcript:Os01t0100200-01	N/A	2	N/A
+1	irgsp	CDS	11798	12060	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100200-01	N/A	N/A	transcript:Os01t0100200-01	Os01t0100200-01	N/A	N/A
+1	irgsp	CDS	12152	12317	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100200-01	N/A	N/A	transcript:Os01t0100200-01	Os01t0100200-01	N/A	N/A
+1	irgsp	five_prime_UTR	11218	11797	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-3	N/A	N/A	transcript:Os01t0100200-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	12318	12435	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-3	N/A	N/A	transcript:Os01t0100200-01	N/A	N/A	N/A
+1	irgsp	gene	11372	12284	.	-1	.	N/A	protein_coding	N/A	Cytochrome P450 domain containing protein. (Os01t0100300-00)	N/A	N/A	N/A	Os01g0100300	gene:Os01g0100300	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	11372	12284	.	-1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0100300-00	N/A	N/A	gene:Os01g0100300	N/A	N/A	Os01t0100300-00
+1	irgsp	exon	11372	12042	.	-1	.	N/A	N/A	1	N/A	0	1	Os01t0100300-00.exon2	N/A	Os01t0100300-00.exon2	N/A	Os01t0100300-00.exon2	transcript:Os01t0100300-00	N/A	2	N/A
+1	irgsp	exon	12146	12284	.	-1	.	N/A	N/A	1	N/A	1	0	Os01t0100300-00.exon1	N/A	Os01t0100300-00.exon1	N/A	Os01t0100300-00.exon1	transcript:Os01t0100300-00	N/A	1	N/A
+1	irgsp	CDS	11372	12042	.	-1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100300-00	N/A	N/A	transcript:Os01t0100300-00	Os01t0100300-00	N/A	N/A
+1	irgsp	CDS	12146	12284	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100300-00	N/A	N/A	transcript:Os01t0100300-00	Os01t0100300-00	N/A	N/A
+1	irgsp	gene	12721	15685	.	1	.	N/A	protein_coding	N/A	Similar to Pectinesterase-like protein. (Os01t0100400-01)	N/A	N/A	N/A	Os01g0100400	gene:Os01g0100400	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	12721	15685	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0100400-01	N/A	N/A	gene:Os01g0100400	N/A	N/A	Os01t0100400-01
+1	irgsp	exon	12721	13813	.	1	.	N/A	N/A	1	N/A	2	-1	Os01t0100400-01.exon1	N/A	Os01t0100400-01.exon1	N/A	Os01t0100400-01.exon1	transcript:Os01t0100400-01	N/A	1	N/A
+1	irgsp	exon	13906	14271	.	1	.	N/A	N/A	1	N/A	2	2	Os01t0100400-01.exon2	N/A	Os01t0100400-01.exon2	N/A	Os01t0100400-01.exon2	transcript:Os01t0100400-01	N/A	2	N/A
+1	irgsp	exon	14359	14437	.	1	.	N/A	N/A	1	N/A	0	2	Os01t0100400-01.exon3	N/A	Os01t0100400-01.exon3	N/A	Os01t0100400-01.exon3	transcript:Os01t0100400-01	N/A	3	N/A
+1	irgsp	exon	14969	15171	.	1	.	N/A	N/A	1	N/A	2	0	Os01t0100400-01.exon4	N/A	Os01t0100400-01.exon4	N/A	Os01t0100400-01.exon4	transcript:Os01t0100400-01	N/A	4	N/A
+1	irgsp	exon	15266	15685	.	1	.	N/A	N/A	1	N/A	-1	2	Os01t0100400-01.exon5	N/A	Os01t0100400-01.exon5	N/A	Os01t0100400-01.exon5	transcript:Os01t0100400-01	N/A	5	N/A
+1	irgsp	CDS	12774	13813	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100400-01	N/A	N/A	transcript:Os01t0100400-01	Os01t0100400-01	N/A	N/A
+1	irgsp	CDS	13906	14271	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100400-01	N/A	N/A	transcript:Os01t0100400-01	Os01t0100400-01	N/A	N/A
+1	irgsp	CDS	14359	14437	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100400-01	N/A	N/A	transcript:Os01t0100400-01	Os01t0100400-01	N/A	N/A
+1	irgsp	CDS	14969	15171	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100400-01	N/A	N/A	transcript:Os01t0100400-01	Os01t0100400-01	N/A	N/A
+1	irgsp	CDS	15266	15359	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100400-01	N/A	N/A	transcript:Os01t0100400-01	Os01t0100400-01	N/A	N/A
+1	irgsp	five_prime_UTR	12721	12773	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-4	N/A	N/A	transcript:Os01t0100400-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	15360	15685	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-4	N/A	N/A	transcript:Os01t0100400-01	N/A	N/A	N/A
+1	irgsp	gene	12808	13978	.	-1	.	N/A	protein_coding	N/A	Hypothetical protein. (Os01t0100466-00)	N/A	N/A	N/A	Os01g0100466	gene:Os01g0100466	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	12808	13978	.	-1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0100466-00	N/A	N/A	gene:Os01g0100466	N/A	N/A	Os01t0100466-00
+1	irgsp	exon	12808	13782	.	-1	.	N/A	N/A	1	N/A	-1	-1	Os01t0100466-00.exon2	N/A	Os01t0100466-00.exon2	N/A	Os01t0100466-00.exon2	transcript:Os01t0100466-00	N/A	2	N/A
+1	irgsp	exon	13880	13978	.	-1	.	N/A	N/A	1	N/A	-1	-1	Os01t0100466-00.exon1	N/A	Os01t0100466-00.exon1	N/A	Os01t0100466-00.exon1	transcript:Os01t0100466-00	N/A	1	N/A
+1	irgsp	CDS	12869	13102	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100466-00	N/A	N/A	transcript:Os01t0100466-00	Os01t0100466-00	N/A	N/A
+1	irgsp	five_prime_UTR	13103	13782	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-5	N/A	N/A	transcript:Os01t0100466-00	N/A	N/A	N/A
+1	irgsp	five_prime_UTR	13880	13978	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-6	N/A	N/A	transcript:Os01t0100466-00	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	12808	12868	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-5	N/A	N/A	transcript:Os01t0100466-00	N/A	N/A	N/A
+1	irgsp	gene	16399	20144	.	1	.	N/A	protein_coding	N/A	Immunoglobulin-like domain containing protein. (Os01t0100500-01)	N/A	N/A	N/A	Os01g0100500	gene:Os01g0100500	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	16399	20144	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0100500-01	N/A	N/A	gene:Os01g0100500	N/A	N/A	Os01t0100500-01
+1	irgsp	exon	16399	16976	.	1	.	N/A	N/A	1	N/A	0	-1	Os01t0100500-01.exon1	N/A	Os01t0100500-01.exon1	N/A	Os01t0100500-01.exon1	transcript:Os01t0100500-01	N/A	1	N/A
+1	irgsp	exon	17383	17474	.	1	.	N/A	N/A	1	N/A	2	0	Os01t0100500-01.exon2	N/A	Os01t0100500-01.exon2	N/A	Os01t0100500-01.exon2	transcript:Os01t0100500-01	N/A	2	N/A
+1	irgsp	exon	17558	18258	.	1	.	N/A	N/A	1	N/A	1	2	Os01t0100500-01.exon3	N/A	Os01t0100500-01.exon3	N/A	Os01t0100500-01.exon3	transcript:Os01t0100500-01	N/A	3	N/A
+1	irgsp	exon	18501	18571	.	1	.	N/A	N/A	1	N/A	0	1	Os01t0100500-01.exon4	N/A	Os01t0100500-01.exon4	N/A	Os01t0100500-01.exon4	transcript:Os01t0100500-01	N/A	4	N/A
+1	irgsp	exon	18968	19057	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0100500-01.exon5	N/A	Os01t0100500-01.exon5	N/A	Os01t0100500-01.exon5	transcript:Os01t0100500-01	N/A	5	N/A
+1	irgsp	exon	19142	19321	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0100500-01.exon6	N/A	Os01t0100500-01.exon6	N/A	Os01t0100500-01.exon6	transcript:Os01t0100500-01	N/A	6	N/A
+1	irgsp	exon	19531	19629	.	1	.	N/A	N/A	1	N/A	-1	0	Os01t0100500-01.exon7	N/A	Os01t0100500-01.exon7	N/A	Os01t0100500-01.exon7	transcript:Os01t0100500-01	N/A	7	N/A
+1	irgsp	exon	19734	20144	.	1	.	N/A	N/A	1	N/A	-1	-1	Os01t0100500-01.exon8	N/A	Os01t0100500-01.exon8	N/A	Os01t0100500-01.exon8	transcript:Os01t0100500-01	N/A	8	N/A
+1	irgsp	CDS	16599	16976	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100500-01	N/A	N/A	transcript:Os01t0100500-01	Os01t0100500-01	N/A	N/A
+1	irgsp	CDS	17383	17474	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100500-01	N/A	N/A	transcript:Os01t0100500-01	Os01t0100500-01	N/A	N/A
+1	irgsp	CDS	17558	18258	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100500-01	N/A	N/A	transcript:Os01t0100500-01	Os01t0100500-01	N/A	N/A
+1	irgsp	CDS	18501	18571	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100500-01	N/A	N/A	transcript:Os01t0100500-01	Os01t0100500-01	N/A	N/A
+1	irgsp	CDS	18968	19057	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100500-01	N/A	N/A	transcript:Os01t0100500-01	Os01t0100500-01	N/A	N/A
+1	irgsp	CDS	19142	19321	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100500-01	N/A	N/A	transcript:Os01t0100500-01	Os01t0100500-01	N/A	N/A
+1	irgsp	CDS	19531	19593	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100500-01	N/A	N/A	transcript:Os01t0100500-01	Os01t0100500-01	N/A	N/A
+1	irgsp	five_prime_UTR	16399	16598	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-7	N/A	N/A	transcript:Os01t0100500-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	19594	19629	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-6	N/A	N/A	transcript:Os01t0100500-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	19734	20144	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-7	N/A	N/A	transcript:Os01t0100500-01	N/A	N/A	N/A
+1	irgsp	gene	22841	26892	.	1	.	N/A	protein_coding	N/A	Single-stranded nucleic acid binding R3H domain containing protein. (Os01t0100600-01)	N/A	N/A	N/A	Os01g0100600	gene:Os01g0100600	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	22841	26892	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0100600-01	N/A	N/A	gene:Os01g0100600	N/A	N/A	Os01t0100600-01
+1	irgsp	exon	22841	23281	.	1	.	N/A	N/A	1	N/A	2	-1	Os01t0100600-01.exon1	N/A	Os01t0100600-01.exon1	N/A	Os01t0100600-01.exon1	transcript:Os01t0100600-01	N/A	1	N/A
+1	irgsp	exon	23572	23847	.	1	.	N/A	N/A	1	N/A	2	2	Os01t0100600-01.exon2	N/A	Os01t0100600-01.exon2	N/A	Os01t0100600-01.exon2	transcript:Os01t0100600-01	N/A	2	N/A
+1	irgsp	exon	23962	24033	.	1	.	N/A	N/A	1	N/A	2	2	Os01t0100600-01.exon3	N/A	Os01t0100600-01.exon3	N/A	Os01t0100600-01.exon3	transcript:Os01t0100600-01	N/A	3	N/A
+1	irgsp	exon	24492	24577	.	1	.	N/A	N/A	1	N/A	1	2	Os01t0100600-01.exon4	N/A	Os01t0100600-01.exon4	N/A	Os01t0100600-01.exon4	transcript:Os01t0100600-01	N/A	4	N/A
+1	irgsp	exon	25445	25519	.	1	.	N/A	N/A	1	N/A	1	1	Os01t0100600-01.exon5	N/A	Os01t0100600-01.exon5	N/A	Os01t0100600-01.exon5	transcript:Os01t0100600-01	N/A	5	N/A
+1	irgsp	exon	25883	26892	.	1	.	N/A	N/A	1	N/A	-1	1	Os01t0100600-01.exon6	N/A	Os01t0100600-01.exon6	N/A	Os01t0100600-01.exon6	transcript:Os01t0100600-01	N/A	6	N/A
+1	irgsp	CDS	23232	23281	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100600-01	N/A	N/A	transcript:Os01t0100600-01	Os01t0100600-01	N/A	N/A
+1	irgsp	CDS	23572	23847	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100600-01	N/A	N/A	transcript:Os01t0100600-01	Os01t0100600-01	N/A	N/A
+1	irgsp	CDS	23962	24033	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100600-01	N/A	N/A	transcript:Os01t0100600-01	Os01t0100600-01	N/A	N/A
+1	irgsp	CDS	24492	24577	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100600-01	N/A	N/A	transcript:Os01t0100600-01	Os01t0100600-01	N/A	N/A
+1	irgsp	CDS	25445	25519	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100600-01	N/A	N/A	transcript:Os01t0100600-01	Os01t0100600-01	N/A	N/A
+1	irgsp	CDS	25883	26391	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100600-01	N/A	N/A	transcript:Os01t0100600-01	Os01t0100600-01	N/A	N/A
+1	irgsp	five_prime_UTR	22841	23231	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-8	N/A	N/A	transcript:Os01t0100600-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	26392	26892	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-8	N/A	N/A	transcript:Os01t0100600-01	N/A	N/A	N/A
+1	irgsp	gene	25861	26424	.	-1	.	N/A	protein_coding	N/A	Hypothetical gene. (Os01t0100650-00)	N/A	N/A	N/A	Os01g0100650	gene:Os01g0100650	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	25861	26424	.	-1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0100650-00	N/A	N/A	gene:Os01g0100650	N/A	N/A	Os01t0100650-00
+1	irgsp	exon	25861	26424	.	-1	.	N/A	N/A	1	N/A	-1	-1	Os01t0100650-00.exon1	N/A	Os01t0100650-00.exon1	N/A	Os01t0100650-00.exon1	transcript:Os01t0100650-00	N/A	1	N/A
+1	irgsp	CDS	26040	26423	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100650-00	N/A	N/A	transcript:Os01t0100650-00	Os01t0100650-00	N/A	N/A
+1	irgsp	five_prime_UTR	26424	26424	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-9	N/A	N/A	transcript:Os01t0100650-00	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	25861	26039	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-9	N/A	N/A	transcript:Os01t0100650-00	N/A	N/A	N/A
+1	irgsp	gene	27143	28644	.	1	.	N/A	protein_coding	N/A	Similar to 40S ribosomal protein S5-1. (Os01t0100700-01)	N/A	N/A	N/A	Os01g0100700	gene:Os01g0100700	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	27143	28644	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0100700-01	N/A	N/A	gene:Os01g0100700	N/A	N/A	Os01t0100700-01
+1	irgsp	exon	27143	27292	.	1	.	N/A	N/A	1	N/A	0	-1	Os01t0100700-01.exon1	N/A	Os01t0100700-01.exon1	N/A	Os01t0100700-01.exon1	transcript:Os01t0100700-01	N/A	1	N/A
+1	irgsp	exon	27370	27641	.	1	.	N/A	N/A	1	N/A	2	0	Os01t0100700-01.exon2	N/A	Os01t0100700-01.exon2	N/A	Os01t0100700-01.exon2	transcript:Os01t0100700-01	N/A	2	N/A
+1	irgsp	exon	28090	28293	.	1	.	N/A	N/A	1	N/A	2	2	Os01t0100700-01.exon3	N/A	Os01t0100700-01.exon3	N/A	Os01t0100700-01.exon3	transcript:Os01t0100700-01	N/A	3	N/A
+1	irgsp	exon	28365	28644	.	1	.	N/A	N/A	1	N/A	-1	2	Os01t0100700-01.exon4	N/A	Os01t0100700-01.exon4	N/A	Os01t0100700-01.exon4	transcript:Os01t0100700-01	N/A	4	N/A
+1	irgsp	CDS	27221	27292	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100700-01	N/A	N/A	transcript:Os01t0100700-01	Os01t0100700-01	N/A	N/A
+1	irgsp	CDS	27370	27641	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100700-01	N/A	N/A	transcript:Os01t0100700-01	Os01t0100700-01	N/A	N/A
+1	irgsp	CDS	28090	28293	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100700-01	N/A	N/A	transcript:Os01t0100700-01	Os01t0100700-01	N/A	N/A
+1	irgsp	CDS	28365	28419	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100700-01	N/A	N/A	transcript:Os01t0100700-01	Os01t0100700-01	N/A	N/A
+1	irgsp	five_prime_UTR	27143	27220	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-10	N/A	N/A	transcript:Os01t0100700-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	28420	28644	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-10	N/A	N/A	transcript:Os01t0100700-01	N/A	N/A	N/A
+1	irgsp	gene	29818	34453	.	1	.	N/A	protein_coding	N/A	Protein of unknown function DUF1664 family protein. (Os01t0100800-01)	N/A	N/A	N/A	Os01g0100800	gene:Os01g0100800	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	29818	34453	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0100800-01	N/A	N/A	gene:Os01g0100800	N/A	N/A	Os01t0100800-01
+1	irgsp	exon	29818	29976	.	1	.	N/A	N/A	1	N/A	1	-1	Os01t0100800-01.exon1	N/A	Os01t0100800-01.exon1	N/A	Os01t0100800-01.exon1	transcript:Os01t0100800-01	N/A	1	N/A
+1	irgsp	exon	30146	30228	.	1	.	N/A	N/A	1	N/A	0	1	Os01t0100800-01.exon2	N/A	Os01t0100800-01.exon2	N/A	Os01t0100800-01.exon2	transcript:Os01t0100800-01	N/A	2	N/A
+1	irgsp	exon	30735	30806	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0100800-01.exon3	N/A	Os01t0100800-01.exon3	N/A	Os01t0100800-01.exon3	transcript:Os01t0100800-01	N/A	3	N/A
+1	irgsp	exon	30885	30963	.	1	.	N/A	N/A	1	N/A	1	0	Os01t0100800-01.exon4	N/A	Os01t0100800-01.exon4	N/A	Os01t0100800-01.exon4	transcript:Os01t0100800-01	N/A	4	N/A
+1	irgsp	exon	31258	31325	.	1	.	N/A	N/A	1	N/A	0	1	Os01t0100800-01.exon5	N/A	Os01t0100800-01.exon5	N/A	Os01t0100800-01.exon5	transcript:Os01t0100800-01	N/A	5	N/A
+1	irgsp	exon	31505	31606	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0100800-01.exon6	N/A	Os01t0100800-01.exon6	N/A	Os01t0100800-01.exon6	transcript:Os01t0100800-01	N/A	6	N/A
+1	irgsp	exon	32377	32466	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0100800-01.exon7	N/A	Os01t0100800-01.exon7	N/A	Os01t0100800-01.exon7	transcript:Os01t0100800-01	N/A	7	N/A
+1	irgsp	exon	32542	32616	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0100800-01.exon8	N/A	Os01t0100800-01.exon8	N/A	Os01t0100800-01.exon8	transcript:Os01t0100800-01	N/A	8	N/A
+1	irgsp	exon	32712	32744	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0100800-01.exon9	N/A	Os01t0100800-01.exon9	N/A	Os01t0100800-01.exon9	transcript:Os01t0100800-01	N/A	9	N/A
+1	irgsp	exon	32828	32905	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0100800-01.exon10	N/A	Os01t0100800-01.exon10	N/A	Os01t0100800-01.exon10	transcript:Os01t0100800-01	N/A	10	N/A
+1	irgsp	exon	33274	33330	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0100800-01.exon11	N/A	Os01t0100800-01.exon11	N/A	Os01t0100800-01.exon11	transcript:Os01t0100800-01	N/A	11	N/A
+1	irgsp	exon	33400	33471	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0100800-01.exon12	N/A	Os01t0100800-01.exon12	N/A	Os01t0100800-01.exon12	transcript:Os01t0100800-01	N/A	12	N/A
+1	irgsp	exon	33543	33617	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0100800-01.exon13	N/A	Os01t0100800-01.exon13	N/A	Os01t0100800-01.exon13	transcript:Os01t0100800-01	N/A	13	N/A
+1	irgsp	exon	33975	34453	.	1	.	N/A	N/A	1	N/A	-1	0	Os01t0100800-01.exon14	N/A	Os01t0100800-01.exon14	N/A	Os01t0100800-01.exon14	transcript:Os01t0100800-01	N/A	14	N/A
+1	irgsp	CDS	29940	29976	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100800-01	N/A	N/A	transcript:Os01t0100800-01	Os01t0100800-01	N/A	N/A
+1	irgsp	CDS	30146	30228	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100800-01	N/A	N/A	transcript:Os01t0100800-01	Os01t0100800-01	N/A	N/A
+1	irgsp	CDS	30735	30806	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100800-01	N/A	N/A	transcript:Os01t0100800-01	Os01t0100800-01	N/A	N/A
+1	irgsp	CDS	30885	30963	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100800-01	N/A	N/A	transcript:Os01t0100800-01	Os01t0100800-01	N/A	N/A
+1	irgsp	CDS	31258	31325	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100800-01	N/A	N/A	transcript:Os01t0100800-01	Os01t0100800-01	N/A	N/A
+1	irgsp	CDS	31505	31606	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100800-01	N/A	N/A	transcript:Os01t0100800-01	Os01t0100800-01	N/A	N/A
+1	irgsp	CDS	32377	32466	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100800-01	N/A	N/A	transcript:Os01t0100800-01	Os01t0100800-01	N/A	N/A
+1	irgsp	CDS	32542	32616	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100800-01	N/A	N/A	transcript:Os01t0100800-01	Os01t0100800-01	N/A	N/A
+1	irgsp	CDS	32712	32744	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100800-01	N/A	N/A	transcript:Os01t0100800-01	Os01t0100800-01	N/A	N/A
+1	irgsp	CDS	32828	32905	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100800-01	N/A	N/A	transcript:Os01t0100800-01	Os01t0100800-01	N/A	N/A
+1	irgsp	CDS	33274	33330	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100800-01	N/A	N/A	transcript:Os01t0100800-01	Os01t0100800-01	N/A	N/A
+1	irgsp	CDS	33400	33471	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100800-01	N/A	N/A	transcript:Os01t0100800-01	Os01t0100800-01	N/A	N/A
+1	irgsp	CDS	33543	33617	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100800-01	N/A	N/A	transcript:Os01t0100800-01	Os01t0100800-01	N/A	N/A
+1	irgsp	CDS	33975	34124	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100800-01	N/A	N/A	transcript:Os01t0100800-01	Os01t0100800-01	N/A	N/A
+1	irgsp	five_prime_UTR	29818	29939	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-11	N/A	N/A	transcript:Os01t0100800-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	34125	34453	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-11	N/A	N/A	transcript:Os01t0100800-01	N/A	N/A	N/A
+1	irgsp	gene	35623	41136	.	1	.	N/A	protein_coding	N/A	Sphingosine-1-phosphate lyase, Disease resistance response (Os01t0100900-01)	N/A	N/A	N/A	Os01g0100900	gene:Os01g0100900	irgspv1.0-20170804-genes	SPHINGOSINE-1-PHOSPHATE LYASE 1, Sphingosine-1-Phoshpate Lyase 1	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	35623	41136	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0100900-01	N/A	N/A	gene:Os01g0100900	N/A	N/A	Os01t0100900-01
+1	irgsp	exon	35623	35939	.	1	.	N/A	N/A	1	N/A	2	-1	Os01t0100900-01.exon1	N/A	Os01t0100900-01.exon1	N/A	Os01t0100900-01.exon1	transcript:Os01t0100900-01	N/A	1	N/A
+1	irgsp	exon	36027	36072	.	1	.	N/A	N/A	1	N/A	0	2	Os01t0100900-01.exon2	N/A	Os01t0100900-01.exon2	N/A	Os01t0100900-01.exon2	transcript:Os01t0100900-01	N/A	2	N/A
+1	irgsp	exon	36517	36668	.	1	.	N/A	N/A	1	N/A	2	0	Os01t0100900-01.exon3	N/A	Os01t0100900-01.exon3	N/A	Os01t0100900-01.exon3	transcript:Os01t0100900-01	N/A	3	N/A
+1	irgsp	exon	36818	36877	.	1	.	N/A	N/A	1	N/A	2	2	Os01t0100900-01.exon4	N/A	Os01t0100900-01.exon4	N/A	Os01t0100900-01.exon4	transcript:Os01t0100900-01	N/A	4	N/A
+1	irgsp	exon	37594	37818	.	1	.	N/A	N/A	1	N/A	2	2	Os01t0100900-01.exon5	N/A	Os01t0100900-01.exon5	N/A	Os01t0100900-01.exon5	transcript:Os01t0100900-01	N/A	5	N/A
+1	irgsp	exon	37892	38033	.	1	.	N/A	N/A	1	N/A	0	2	Os01t0100900-01.exon6	N/A	Os01t0100900-01.exon6	N/A	Os01t0100900-01.exon6	transcript:Os01t0100900-01	N/A	6	N/A
+1	irgsp	exon	38276	38326	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0100900-01.exon7	N/A	Os01t0100900-01.exon7	N/A	Os01t0100900-01.exon7	transcript:Os01t0100900-01	N/A	7	N/A
+1	irgsp	exon	38434	38525	.	1	.	N/A	N/A	1	N/A	2	0	Os01t0100900-01.exon8	N/A	Os01t0100900-01.exon8	N/A	Os01t0100900-01.exon8	transcript:Os01t0100900-01	N/A	8	N/A
+1	irgsp	exon	39319	39445	.	1	.	N/A	N/A	1	N/A	0	2	Os01t0100900-01.exon9	N/A	Os01t0100900-01.exon9	N/A	Os01t0100900-01.exon9	transcript:Os01t0100900-01	N/A	9	N/A
+1	irgsp	exon	39553	39568	.	1	.	N/A	N/A	1	N/A	1	0	Os01t0100900-01.exon10	N/A	Os01t0100900-01.exon10	N/A	Os01t0100900-01.exon10	transcript:Os01t0100900-01	N/A	10	N/A
+1	irgsp	exon	39939	40046	.	1	.	N/A	N/A	1	N/A	1	1	Os01t0100900-01.exon11	N/A	Os01t0100900-01.exon11	N/A	Os01t0100900-01.exon11	transcript:Os01t0100900-01	N/A	11	N/A
+1	irgsp	exon	40135	40189	.	1	.	N/A	N/A	1	N/A	2	1	Os01t0100900-01.exon12	N/A	Os01t0100900-01.exon12	N/A	Os01t0100900-01.exon12	transcript:Os01t0100900-01	N/A	12	N/A
+1	irgsp	exon	40456	40602	.	1	.	N/A	N/A	1	N/A	2	2	Os01t0100900-01.exon13	N/A	Os01t0100900-01.exon13	N/A	Os01t0100900-01.exon13	transcript:Os01t0100900-01	N/A	13	N/A
+1	irgsp	exon	40703	40781	.	1	.	N/A	N/A	1	N/A	0	2	Os01t0100900-01.exon14	N/A	Os01t0100900-01.exon14	N/A	Os01t0100900-01.exon14	transcript:Os01t0100900-01	N/A	14	N/A
+1	irgsp	exon	40885	41136	.	1	.	N/A	N/A	1	N/A	-1	0	Os01t0100900-01.exon15	N/A	Os01t0100900-01.exon15	N/A	Os01t0100900-01.exon15	transcript:Os01t0100900-01	N/A	15	N/A
+1	irgsp	CDS	35743	35939	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100900-01	N/A	N/A	transcript:Os01t0100900-01	Os01t0100900-01	N/A	N/A
+1	irgsp	CDS	36027	36072	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100900-01	N/A	N/A	transcript:Os01t0100900-01	Os01t0100900-01	N/A	N/A
+1	irgsp	CDS	36517	36668	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100900-01	N/A	N/A	transcript:Os01t0100900-01	Os01t0100900-01	N/A	N/A
+1	irgsp	CDS	36818	36877	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100900-01	N/A	N/A	transcript:Os01t0100900-01	Os01t0100900-01	N/A	N/A
+1	irgsp	CDS	37594	37818	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100900-01	N/A	N/A	transcript:Os01t0100900-01	Os01t0100900-01	N/A	N/A
+1	irgsp	CDS	37892	38033	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100900-01	N/A	N/A	transcript:Os01t0100900-01	Os01t0100900-01	N/A	N/A
+1	irgsp	CDS	38276	38326	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100900-01	N/A	N/A	transcript:Os01t0100900-01	Os01t0100900-01	N/A	N/A
+1	irgsp	CDS	38434	38525	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100900-01	N/A	N/A	transcript:Os01t0100900-01	Os01t0100900-01	N/A	N/A
+1	irgsp	CDS	39319	39445	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100900-01	N/A	N/A	transcript:Os01t0100900-01	Os01t0100900-01	N/A	N/A
+1	irgsp	CDS	39553	39568	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100900-01	N/A	N/A	transcript:Os01t0100900-01	Os01t0100900-01	N/A	N/A
+1	irgsp	CDS	39939	40046	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100900-01	N/A	N/A	transcript:Os01t0100900-01	Os01t0100900-01	N/A	N/A
+1	irgsp	CDS	40135	40189	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100900-01	N/A	N/A	transcript:Os01t0100900-01	Os01t0100900-01	N/A	N/A
+1	irgsp	CDS	40456	40602	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100900-01	N/A	N/A	transcript:Os01t0100900-01	Os01t0100900-01	N/A	N/A
+1	irgsp	CDS	40703	40781	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100900-01	N/A	N/A	transcript:Os01t0100900-01	Os01t0100900-01	N/A	N/A
+1	irgsp	CDS	40885	41007	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0100900-01	N/A	N/A	transcript:Os01t0100900-01	Os01t0100900-01	N/A	N/A
+1	irgsp	five_prime_UTR	35623	35742	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-12	N/A	N/A	transcript:Os01t0100900-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	41008	41136	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-12	N/A	N/A	transcript:Os01t0100900-01	N/A	N/A	N/A
+1	irgsp	gene	58658	61090	.	1	.	N/A	protein_coding	N/A	Hypothetical conserved gene. (Os01t0101150-00)	N/A	N/A	N/A	Os01g0101150	gene:Os01g0101150	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	58658	61090	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0101150-00	N/A	N/A	gene:Os01g0101150	N/A	N/A	Os01t0101150-00
+1	irgsp	exon	58658	61090	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0101150-00.exon1	N/A	Os01t0101150-00.exon1	N/A	Os01t0101150-00.exon1	transcript:Os01t0101150-00	N/A	1	N/A
+1	irgsp	CDS	58658	61090	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101150-00	N/A	N/A	transcript:Os01t0101150-00	Os01t0101150-00	N/A	N/A
+1	irgsp	gene	62060	65537	.	1	.	N/A	protein_coding	N/A	2,3-diketo-5-methylthio-1-phosphopentane phosphatase domain containing protein. (Os01t0101200-01);2,3-diketo-5-methylthio-1-phosphopentane phosphatase domain containing protein. (Os01t0101200-02)	N/A	N/A	N/A	Os01g0101200	gene:Os01g0101200	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	62060	63576	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0101200-01	N/A	N/A	gene:Os01g0101200	N/A	N/A	Os01t0101200-01
+1	irgsp	exon	62060	62295	.	1	.	N/A	N/A	0	N/A	0	-1	Os01t0101200-01.exon1	N/A	Os01t0101200-01.exon1	N/A	Os01t0101200-01.exon1	transcript:Os01t0101200-01	N/A	1	N/A
+1	irgsp	exon	62385	62905	.	1	.	N/A	N/A	1	N/A	2	0	Os01t0101200-02.exon2	N/A	Os01t0101200-02.exon2	N/A	Os01t0101200-02.exon2	transcript:Os01t0101200-01	N/A	2	N/A
+1	irgsp	exon	62996	63114	.	1	.	N/A	N/A	1	N/A	1	2	Os01t0101200-02.exon3	N/A	Os01t0101200-02.exon3	N/A	Os01t0101200-02.exon3	transcript:Os01t0101200-01	N/A	3	N/A
+1	irgsp	exon	63248	63576	.	1	.	N/A	N/A	0	N/A	-1	1	Os01t0101200-01.exon4	N/A	Os01t0101200-01.exon4	N/A	Os01t0101200-01.exon4	transcript:Os01t0101200-01	N/A	4	N/A
+1	irgsp	CDS	62104	62295	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101200-01	N/A	N/A	transcript:Os01t0101200-01	Os01t0101200-01	N/A	N/A
+1	irgsp	CDS	62385	62905	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101200-01	N/A	N/A	transcript:Os01t0101200-01	Os01t0101200-01	N/A	N/A
+1	irgsp	CDS	62996	63114	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101200-01	N/A	N/A	transcript:Os01t0101200-01	Os01t0101200-01	N/A	N/A
+1	irgsp	CDS	63248	63345	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101200-01	N/A	N/A	transcript:Os01t0101200-01	Os01t0101200-01	N/A	N/A
+1	irgsp	five_prime_UTR	62060	62103	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-13	N/A	N/A	transcript:Os01t0101200-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	63346	63576	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-13	N/A	N/A	transcript:Os01t0101200-01	N/A	N/A	N/A
+1	irgsp	mRNA	62112	65537	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0101200-02	N/A	N/A	gene:Os01g0101200	N/A	N/A	Os01t0101200-02
+1	irgsp	exon	62112	62295	.	1	.	N/A	N/A	0	N/A	0	-1	Os01t0101200-02.exon1	N/A	Os01t0101200-02.exon1	N/A	Os01t0101200-02.exon1	transcript:Os01t0101200-02	N/A	1	N/A
+1	irgsp	exon	62385	62905	.	1	.	N/A	N/A	1	N/A	2	0	Os01t0101200-02.exon2	N/A	agat-exon-1	N/A	Os01t0101200-02.exon2	transcript:Os01t0101200-02	N/A	2	N/A
+1	irgsp	exon	62996	63114	.	1	.	N/A	N/A	1	N/A	1	2	Os01t0101200-02.exon3	N/A	agat-exon-2	N/A	Os01t0101200-02.exon3	transcript:Os01t0101200-02	N/A	3	N/A
+1	irgsp	exon	63248	65537	.	1	.	N/A	N/A	0	N/A	-1	1	Os01t0101200-02.exon4	N/A	Os01t0101200-02.exon4	N/A	Os01t0101200-02.exon4	transcript:Os01t0101200-02	N/A	4	N/A
+1	irgsp	CDS	62113	62295	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101200-02	N/A	N/A	transcript:Os01t0101200-02	Os01t0101200-02	N/A	N/A
+1	irgsp	CDS	62385	62905	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101200-02	N/A	N/A	transcript:Os01t0101200-02	Os01t0101200-02	N/A	N/A
+1	irgsp	CDS	62996	63114	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101200-02	N/A	N/A	transcript:Os01t0101200-02	Os01t0101200-02	N/A	N/A
+1	irgsp	CDS	63248	63345	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101200-02	N/A	N/A	transcript:Os01t0101200-02	Os01t0101200-02	N/A	N/A
+1	irgsp	five_prime_UTR	62112	62112	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-14	N/A	N/A	transcript:Os01t0101200-02	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	63346	65537	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-14	N/A	N/A	transcript:Os01t0101200-02	N/A	N/A	N/A
+1	irgsp	gene	63350	66302	.	-1	.	N/A	protein_coding	N/A	Similar to MRNA, partial cds, clone: RAFL22-26-L17. (Fragment). (Os01t0101300-01)	N/A	N/A	N/A	Os01g0101300	gene:Os01g0101300	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	63350	66302	.	-1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0101300-01	N/A	N/A	gene:Os01g0101300	N/A	N/A	Os01t0101300-01
+1	irgsp	exon	63350	63783	.	-1	.	N/A	N/A	1	N/A	-1	0	Os01t0101300-01.exon7	N/A	Os01t0101300-01.exon7	N/A	Os01t0101300-01.exon7	transcript:Os01t0101300-01	N/A	7	N/A
+1	irgsp	exon	63877	64020	.	-1	.	N/A	N/A	1	N/A	0	0	Os01t0101300-01.exon6	N/A	Os01t0101300-01.exon6	N/A	Os01t0101300-01.exon6	transcript:Os01t0101300-01	N/A	6	N/A
+1	irgsp	exon	64339	64431	.	-1	.	N/A	N/A	1	N/A	0	0	Os01t0101300-01.exon5	N/A	Os01t0101300-01.exon5	N/A	Os01t0101300-01.exon5	transcript:Os01t0101300-01	N/A	5	N/A
+1	irgsp	exon	64665	64779	.	-1	.	N/A	N/A	1	N/A	0	2	Os01t0101300-01.exon4	N/A	Os01t0101300-01.exon4	N/A	Os01t0101300-01.exon4	transcript:Os01t0101300-01	N/A	4	N/A
+1	irgsp	exon	64902	65152	.	-1	.	N/A	N/A	1	N/A	2	0	Os01t0101300-01.exon3	N/A	Os01t0101300-01.exon3	N/A	Os01t0101300-01.exon3	transcript:Os01t0101300-01	N/A	3	N/A
+1	irgsp	exon	65248	65431	.	-1	.	N/A	N/A	1	N/A	0	2	Os01t0101300-01.exon2	N/A	Os01t0101300-01.exon2	N/A	Os01t0101300-01.exon2	transcript:Os01t0101300-01	N/A	2	N/A
+1	irgsp	exon	65628	66302	.	-1	.	N/A	N/A	1	N/A	2	-1	Os01t0101300-01.exon1	N/A	Os01t0101300-01.exon1	N/A	Os01t0101300-01.exon1	transcript:Os01t0101300-01	N/A	1	N/A
+1	irgsp	CDS	63670	63783	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101300-01	N/A	N/A	transcript:Os01t0101300-01	Os01t0101300-01	N/A	N/A
+1	irgsp	CDS	63877	64020	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101300-01	N/A	N/A	transcript:Os01t0101300-01	Os01t0101300-01	N/A	N/A
+1	irgsp	CDS	64339	64431	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101300-01	N/A	N/A	transcript:Os01t0101300-01	Os01t0101300-01	N/A	N/A
+1	irgsp	CDS	64665	64779	.	-1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101300-01	N/A	N/A	transcript:Os01t0101300-01	Os01t0101300-01	N/A	N/A
+1	irgsp	CDS	64902	65152	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101300-01	N/A	N/A	transcript:Os01t0101300-01	Os01t0101300-01	N/A	N/A
+1	irgsp	CDS	65248	65431	.	-1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101300-01	N/A	N/A	transcript:Os01t0101300-01	Os01t0101300-01	N/A	N/A
+1	irgsp	CDS	65628	65950	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101300-01	N/A	N/A	transcript:Os01t0101300-01	Os01t0101300-01	N/A	N/A
+1	irgsp	five_prime_UTR	65951	66302	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-15	N/A	N/A	transcript:Os01t0101300-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	63350	63669	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-15	N/A	N/A	transcript:Os01t0101300-01	N/A	N/A	N/A
+1	irgsp	gene	72816	78349	.	1	.	N/A	protein_coding	N/A	Immunoglobulin-like fold domain containing protein. (Os01t0101600-01);Immunoglobulin-like fold domain containing protein. (Os01t0101600-02);Hypothetical conserved gene. (Os01t0101600-03)	N/A	N/A	N/A	Os01g0101600	gene:Os01g0101600	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	72816	78349	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0101600-01	N/A	N/A	gene:Os01g0101600	N/A	N/A	Os01t0101600-01
+1	irgsp	exon	72816	73935	.	1	.	N/A	N/A	0	N/A	1	-1	Os01t0101600-01.exon1	N/A	Os01t0101600-01.exon1	N/A	Os01t0101600-01.exon1	transcript:Os01t0101600-01	N/A	1	N/A
+1	irgsp	exon	74468	74981	.	1	.	N/A	N/A	0	N/A	2	1	Os01t0101600-02.exon2	N/A	Os01t0101600-02.exon2	N/A	Os01t0101600-02.exon2	transcript:Os01t0101600-01	N/A	2	N/A
+1	irgsp	exon	75619	77205	.	1	.	N/A	N/A	0	N/A	-1	2	Os01t0101600-01.exon3	N/A	Os01t0101600-01.exon3	N/A	Os01t0101600-01.exon3	transcript:Os01t0101600-01	N/A	3	N/A
+1	irgsp	exon	77333	78349	.	1	.	N/A	N/A	0	N/A	-1	-1	Os01t0101600-01.exon4	N/A	Os01t0101600-01.exon4	N/A	Os01t0101600-01.exon4	transcript:Os01t0101600-01	N/A	4	N/A
+1	irgsp	CDS	72903	73935	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101600-01	N/A	N/A	transcript:Os01t0101600-01	Os01t0101600-01	N/A	N/A
+1	irgsp	CDS	74468	74981	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101600-01	N/A	N/A	transcript:Os01t0101600-01	Os01t0101600-01	N/A	N/A
+1	irgsp	CDS	75619	77008	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101600-01	N/A	N/A	transcript:Os01t0101600-01	Os01t0101600-01	N/A	N/A
+1	irgsp	five_prime_UTR	72816	72902	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-16	N/A	N/A	transcript:Os01t0101600-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	77009	77205	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-16	N/A	N/A	transcript:Os01t0101600-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	77333	78349	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-17	N/A	N/A	transcript:Os01t0101600-01	N/A	N/A	N/A
+1	irgsp	mRNA	72823	77699	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0101600-02	N/A	N/A	gene:Os01g0101600	N/A	N/A	Os01t0101600-02
+1	irgsp	exon	72823	73935	.	1	.	N/A	N/A	0	N/A	1	-1	Os01t0101600-02.exon1	N/A	Os01t0101600-02.exon1	N/A	Os01t0101600-02.exon1	transcript:Os01t0101600-02	N/A	1	N/A
+1	irgsp	exon	74468	74981	.	1	.	N/A	N/A	0	N/A	2	1	Os01t0101600-02.exon2	N/A	agat-exon-3	N/A	Os01t0101600-02.exon2	transcript:Os01t0101600-02	N/A	2	N/A
+1	irgsp	exon	75619	77699	.	1	.	N/A	N/A	0	N/A	-1	2	Os01t0101600-02.exon3	N/A	Os01t0101600-02.exon3	N/A	Os01t0101600-02.exon3	transcript:Os01t0101600-02	N/A	3	N/A
+1	irgsp	CDS	72903	73935	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101600-02	N/A	N/A	transcript:Os01t0101600-02	Os01t0101600-02	N/A	N/A
+1	irgsp	CDS	74468	74981	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101600-02	N/A	N/A	transcript:Os01t0101600-02	Os01t0101600-02	N/A	N/A
+1	irgsp	CDS	75619	77008	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101600-02	N/A	N/A	transcript:Os01t0101600-02	Os01t0101600-02	N/A	N/A
+1	irgsp	five_prime_UTR	72823	72902	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-17	N/A	N/A	transcript:Os01t0101600-02	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	77009	77699	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-18	N/A	N/A	transcript:Os01t0101600-02	N/A	N/A	N/A
+1	irgsp	mRNA	75942	77699	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0101600-03	N/A	N/A	gene:Os01g0101600	N/A	N/A	Os01t0101600-03
+1	irgsp	exon	75942	77699	.	1	.	N/A	N/A	0	N/A	-1	-1	Os01t0101600-03.exon1	N/A	Os01t0101600-03.exon1	N/A	Os01t0101600-03.exon1	transcript:Os01t0101600-03	N/A	1	N/A
+1	irgsp	CDS	75944	77008	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101600-03	N/A	N/A	transcript:Os01t0101600-03	Os01t0101600-03	N/A	N/A
+1	irgsp	five_prime_UTR	75942	75943	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-18	N/A	N/A	transcript:Os01t0101600-03	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	77009	77699	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-19	N/A	N/A	transcript:Os01t0101600-03	N/A	N/A	N/A
+1	irgsp	gene	82426	84095	.	1	.	N/A	protein_coding	N/A	Similar to chaperone protein dnaJ 20. (Os01t0101700-00)	N/A	N/A	N/A	Os01g0101700	gene:Os01g0101700	irgspv1.0-20170804-genes	DnaJ domain protein C1, rice DJC26 homolog	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	82426	84095	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0101700-00	N/A	N/A	gene:Os01g0101700	N/A	N/A	Os01t0101700-00
+1	irgsp	exon	82426	82932	.	1	.	N/A	N/A	1	N/A	0	-1	Os01t0101700-00.exon1	N/A	Os01t0101700-00.exon1	N/A	Os01t0101700-00.exon1	transcript:Os01t0101700-00	N/A	1	N/A
+1	irgsp	exon	83724	84095	.	1	.	N/A	N/A	1	N/A	-1	0	Os01t0101700-00.exon2	N/A	Os01t0101700-00.exon2	N/A	Os01t0101700-00.exon2	transcript:Os01t0101700-00	N/A	2	N/A
+1	irgsp	CDS	82507	82932	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101700-00	N/A	N/A	transcript:Os01t0101700-00	Os01t0101700-00	N/A	N/A
+1	irgsp	CDS	83724	83864	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101700-00	N/A	N/A	transcript:Os01t0101700-00	Os01t0101700-00	N/A	N/A
+1	irgsp	five_prime_UTR	82426	82506	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-19	N/A	N/A	transcript:Os01t0101700-00	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	83865	84095	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-20	N/A	N/A	transcript:Os01t0101700-00	N/A	N/A	N/A
+1	irgsp	gene	85337	88844	.	1	.	N/A	protein_coding	N/A	Conserved hypothetical protein. (Os01t0101800-01)	N/A	N/A	N/A	Os01g0101800	gene:Os01g0101800	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	85337	88844	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0101800-01	N/A	N/A	gene:Os01g0101800	N/A	N/A	Os01t0101800-01
+1	irgsp	exon	85337	85600	.	1	.	N/A	N/A	1	N/A	0	-1	Os01t0101800-01.exon1	N/A	Os01t0101800-01.exon1	N/A	Os01t0101800-01.exon1	transcript:Os01t0101800-01	N/A	1	N/A
+1	irgsp	exon	85737	85830	.	1	.	N/A	N/A	1	N/A	1	0	Os01t0101800-01.exon2	N/A	Os01t0101800-01.exon2	N/A	Os01t0101800-01.exon2	transcript:Os01t0101800-01	N/A	2	N/A
+1	irgsp	exon	85935	86086	.	1	.	N/A	N/A	1	N/A	0	1	Os01t0101800-01.exon3	N/A	Os01t0101800-01.exon3	N/A	Os01t0101800-01.exon3	transcript:Os01t0101800-01	N/A	3	N/A
+1	irgsp	exon	86212	86299	.	1	.	N/A	N/A	1	N/A	1	0	Os01t0101800-01.exon4	N/A	Os01t0101800-01.exon4	N/A	Os01t0101800-01.exon4	transcript:Os01t0101800-01	N/A	4	N/A
+1	irgsp	exon	86399	87681	.	1	.	N/A	N/A	1	N/A	0	1	Os01t0101800-01.exon5	N/A	Os01t0101800-01.exon5	N/A	Os01t0101800-01.exon5	transcript:Os01t0101800-01	N/A	5	N/A
+1	irgsp	exon	88291	88398	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0101800-01.exon6	N/A	Os01t0101800-01.exon6	N/A	Os01t0101800-01.exon6	transcript:Os01t0101800-01	N/A	6	N/A
+1	irgsp	exon	88500	88844	.	1	.	N/A	N/A	1	N/A	-1	0	Os01t0101800-01.exon7	N/A	Os01t0101800-01.exon7	N/A	Os01t0101800-01.exon7	transcript:Os01t0101800-01	N/A	7	N/A
+1	irgsp	CDS	85379	85600	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101800-01	N/A	N/A	transcript:Os01t0101800-01	Os01t0101800-01	N/A	N/A
+1	irgsp	CDS	85737	85830	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101800-01	N/A	N/A	transcript:Os01t0101800-01	Os01t0101800-01	N/A	N/A
+1	irgsp	CDS	85935	86086	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101800-01	N/A	N/A	transcript:Os01t0101800-01	Os01t0101800-01	N/A	N/A
+1	irgsp	CDS	86212	86299	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101800-01	N/A	N/A	transcript:Os01t0101800-01	Os01t0101800-01	N/A	N/A
+1	irgsp	CDS	86399	87681	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101800-01	N/A	N/A	transcript:Os01t0101800-01	Os01t0101800-01	N/A	N/A
+1	irgsp	CDS	88291	88398	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101800-01	N/A	N/A	transcript:Os01t0101800-01	Os01t0101800-01	N/A	N/A
+1	irgsp	CDS	88500	88583	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101800-01	N/A	N/A	transcript:Os01t0101800-01	Os01t0101800-01	N/A	N/A
+1	irgsp	five_prime_UTR	85337	85378	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-20	N/A	N/A	transcript:Os01t0101800-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	88584	88844	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-21	N/A	N/A	transcript:Os01t0101800-01	N/A	N/A	N/A
+1	irgsp	gene	86211	88583	.	-1	.	N/A	protein_coding	N/A	Hypothetical protein. (Os01t0101850-00)	N/A	N/A	N/A	Os01g0101850	gene:Os01g0101850	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	86211	88583	.	-1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0101850-00	N/A	N/A	gene:Os01g0101850	N/A	N/A	Os01t0101850-00
+1	irgsp	exon	86211	86277	.	-1	.	N/A	N/A	1	N/A	-1	-1	Os01t0101850-00.exon4	N/A	Os01t0101850-00.exon4	N/A	Os01t0101850-00.exon4	transcript:Os01t0101850-00	N/A	4	N/A
+1	irgsp	exon	86384	87694	.	-1	.	N/A	N/A	1	N/A	-1	-1	Os01t0101850-00.exon3	N/A	Os01t0101850-00.exon3	N/A	Os01t0101850-00.exon3	transcript:Os01t0101850-00	N/A	3	N/A
+1	irgsp	exon	88308	88396	.	-1	.	N/A	N/A	1	N/A	-1	-1	Os01t0101850-00.exon2	N/A	Os01t0101850-00.exon2	N/A	Os01t0101850-00.exon2	transcript:Os01t0101850-00	N/A	2	N/A
+1	irgsp	exon	88496	88583	.	-1	.	N/A	N/A	1	N/A	-1	-1	Os01t0101850-00.exon1	N/A	Os01t0101850-00.exon1	N/A	Os01t0101850-00.exon1	transcript:Os01t0101850-00	N/A	1	N/A
+1	irgsp	CDS	87327	87662	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101850-00	N/A	N/A	transcript:Os01t0101850-00	Os01t0101850-00	N/A	N/A
+1	irgsp	five_prime_UTR	87663	87694	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-21	N/A	N/A	transcript:Os01t0101850-00	N/A	N/A	N/A
+1	irgsp	five_prime_UTR	88308	88396	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-22	N/A	N/A	transcript:Os01t0101850-00	N/A	N/A	N/A
+1	irgsp	five_prime_UTR	88496	88583	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-23	N/A	N/A	transcript:Os01t0101850-00	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	86211	86277	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-22	N/A	N/A	transcript:Os01t0101850-00	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	86384	87326	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-23	N/A	N/A	transcript:Os01t0101850-00	N/A	N/A	N/A
+1	irgsp	gene	88883	89228	.	-1	.	N/A	protein_coding	N/A	Similar to OSIGBa0075F02.3 protein. (Os01t0101900-00)	N/A	N/A	N/A	Os01g0101900	gene:Os01g0101900	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	88883	89228	.	-1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0101900-00	N/A	N/A	gene:Os01g0101900	N/A	N/A	Os01t0101900-00
+1	irgsp	exon	88883	89228	.	-1	.	N/A	N/A	1	N/A	-1	-1	Os01t0101900-00.exon1	N/A	Os01t0101900-00.exon1	N/A	Os01t0101900-00.exon1	transcript:Os01t0101900-00	N/A	1	N/A
+1	irgsp	CDS	88986	89204	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0101900-00	N/A	N/A	transcript:Os01t0101900-00	Os01t0101900-00	N/A	N/A
+1	irgsp	five_prime_UTR	89205	89228	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-24	N/A	N/A	transcript:Os01t0101900-00	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	88883	88985	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-24	N/A	N/A	transcript:Os01t0101900-00	N/A	N/A	N/A
+1	irgsp	gene	89763	91465	.	-1	.	N/A	protein_coding	N/A	Phosphoesterase family protein. (Os01t0102000-01)	N/A	N/A	N/A	Os01g0102000	gene:Os01g0102000	irgspv1.0-20170804-genes	NON-SPECIFIC PHOSPHOLIPASE C5	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	89763	91465	.	-1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0102000-01	N/A	N/A	gene:Os01g0102000	N/A	N/A	Os01t0102000-01
+1	irgsp	exon	89763	91465	.	-1	.	N/A	N/A	1	N/A	-1	-1	Os01t0102000-01.exon1	N/A	Os01t0102000-01.exon1	N/A	Os01t0102000-01.exon1	transcript:Os01t0102000-01	N/A	1	N/A
+1	irgsp	CDS	89825	91411	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102000-01	N/A	N/A	transcript:Os01t0102000-01	Os01t0102000-01	N/A	N/A
+1	irgsp	five_prime_UTR	91412	91465	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-25	N/A	N/A	transcript:Os01t0102000-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	89763	89824	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-25	N/A	N/A	transcript:Os01t0102000-01	N/A	N/A	N/A
+1	irgsp	gene	134300	135439	.	1	.	N/A	protein_coding	N/A	Thylakoid lumen protein, Photosynthesis and chloroplast development (Os01t0102300-01)	N/A	N/A	N/A	Os01g0102300	gene:Os01g0102300	irgspv1.0-20170804-genes	OsTLP27	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	134300	135439	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0102300-01	N/A	N/A	gene:Os01g0102300	N/A	N/A	Os01t0102300-01
+1	irgsp	exon	134300	134615	.	1	.	N/A	N/A	1	N/A	2	-1	Os01t0102300-01.exon1	N/A	Os01t0102300-01.exon1	N/A	Os01t0102300-01.exon1	transcript:Os01t0102300-01	N/A	1	N/A
+1	irgsp	exon	134698	134824	.	1	.	N/A	N/A	1	N/A	0	2	Os01t0102300-01.exon2	N/A	Os01t0102300-01.exon2	N/A	Os01t0102300-01.exon2	transcript:Os01t0102300-01	N/A	2	N/A
+1	irgsp	exon	134912	135439	.	1	.	N/A	N/A	1	N/A	-1	0	Os01t0102300-01.exon3	N/A	Os01t0102300-01.exon3	N/A	Os01t0102300-01.exon3	transcript:Os01t0102300-01	N/A	3	N/A
+1	irgsp	CDS	134311	134615	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102300-01	N/A	N/A	transcript:Os01t0102300-01	Os01t0102300-01	N/A	N/A
+1	irgsp	CDS	134698	134824	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102300-01	N/A	N/A	transcript:Os01t0102300-01	Os01t0102300-01	N/A	N/A
+1	irgsp	CDS	134912	135253	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102300-01	N/A	N/A	transcript:Os01t0102300-01	Os01t0102300-01	N/A	N/A
+1	irgsp	five_prime_UTR	134300	134310	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-26	N/A	N/A	transcript:Os01t0102300-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	135254	135439	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-26	N/A	N/A	transcript:Os01t0102300-01	N/A	N/A	N/A
+1	irgsp	gene	139826	141555	.	1	.	N/A	protein_coding	N/A	Histone-fold domain containing protein. (Os01t0102400-01)	N/A	N/A	N/A	Os01g0102400	gene:Os01g0102400	irgspv1.0-20170804-genes	HAP5H SUBUNIT OF CCAAT-BOX BINDING COMPLEX	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	139826	141555	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0102400-01	N/A	N/A	gene:Os01g0102400	N/A	N/A	Os01t0102400-01
+1	irgsp	exon	139826	139906	.	1	.	N/A	N/A	1	N/A	-1	-1	Os01t0102400-01.exon1	N/A	Os01t0102400-01.exon1	N/A	Os01t0102400-01.exon1	transcript:Os01t0102400-01	N/A	1	N/A
+1	irgsp	exon	140120	141555	.	1	.	N/A	N/A	1	N/A	-1	-1	Os01t0102400-01.exon2	N/A	Os01t0102400-01.exon2	N/A	Os01t0102400-01.exon2	transcript:Os01t0102400-01	N/A	2	N/A
+1	irgsp	CDS	140150	141415	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102400-01	N/A	N/A	transcript:Os01t0102400-01	Os01t0102400-01	N/A	N/A
+1	irgsp	five_prime_UTR	139826	139906	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-27	N/A	N/A	transcript:Os01t0102400-01	N/A	N/A	N/A
+1	irgsp	five_prime_UTR	140120	140149	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-28	N/A	N/A	transcript:Os01t0102400-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	141416	141555	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-27	N/A	N/A	transcript:Os01t0102400-01	N/A	N/A	N/A
+1	irgsp	gene	141959	144554	.	1	.	N/A	protein_coding	N/A	Conserved hypothetical protein. (Os01t0102500-01)	N/A	N/A	N/A	Os01g0102500	gene:Os01g0102500	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	141959	144554	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0102500-01	N/A	N/A	gene:Os01g0102500	N/A	N/A	Os01t0102500-01
+1	irgsp	exon	141959	142631	.	1	.	N/A	N/A	1	N/A	2	-1	Os01t0102500-01.exon1	N/A	Os01t0102500-01.exon1	N/A	Os01t0102500-01.exon1	transcript:Os01t0102500-01	N/A	1	N/A
+1	irgsp	exon	143191	143431	.	1	.	N/A	N/A	1	N/A	0	2	Os01t0102500-01.exon2	N/A	Os01t0102500-01.exon2	N/A	Os01t0102500-01.exon2	transcript:Os01t0102500-01	N/A	2	N/A
+1	irgsp	exon	143563	143680	.	1	.	N/A	N/A	1	N/A	1	0	Os01t0102500-01.exon3	N/A	Os01t0102500-01.exon3	N/A	Os01t0102500-01.exon3	transcript:Os01t0102500-01	N/A	3	N/A
+1	irgsp	exon	143817	144554	.	1	.	N/A	N/A	1	N/A	-1	1	Os01t0102500-01.exon4	N/A	Os01t0102500-01.exon4	N/A	Os01t0102500-01.exon4	transcript:Os01t0102500-01	N/A	4	N/A
+1	irgsp	CDS	142084	142631	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102500-01	N/A	N/A	transcript:Os01t0102500-01	Os01t0102500-01	N/A	N/A
+1	irgsp	CDS	143191	143431	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102500-01	N/A	N/A	transcript:Os01t0102500-01	Os01t0102500-01	N/A	N/A
+1	irgsp	CDS	143563	143680	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102500-01	N/A	N/A	transcript:Os01t0102500-01	Os01t0102500-01	N/A	N/A
+1	irgsp	CDS	143817	143908	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102500-01	N/A	N/A	transcript:Os01t0102500-01	Os01t0102500-01	N/A	N/A
+1	irgsp	five_prime_UTR	141959	142083	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-29	N/A	N/A	transcript:Os01t0102500-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	143909	144554	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-28	N/A	N/A	transcript:Os01t0102500-01	N/A	N/A	N/A
+1	irgsp	gene	145603	147847	.	1	.	N/A	protein_coding	N/A	Shikimate kinase domain containing protein. (Os01t0102600-01);Similar to shikimate kinase family protein. (Os01t0102600-02)	N/A	N/A	N/A	Os01g0102600	gene:Os01g0102600	irgspv1.0-20170804-genes	Shikimate kinase 4	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	145603	147847	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0102600-01	N/A	N/A	gene:Os01g0102600	N/A	N/A	Os01t0102600-01
+1	irgsp	exon	145603	145786	.	1	.	N/A	N/A	0	N/A	1	-1	Os01t0102600-01.exon1	N/A	Os01t0102600-01.exon1	N/A	Os01t0102600-01.exon1	transcript:Os01t0102600-01	N/A	1	N/A
+1	irgsp	exon	145905	145951	.	1	.	N/A	N/A	0	N/A	0	1	Os01t0102600-01.exon2	N/A	Os01t0102600-01.exon2	N/A	Os01t0102600-01.exon2	transcript:Os01t0102600-01	N/A	2	N/A
+1	irgsp	exon	146028	146082	.	1	.	N/A	N/A	0	N/A	1	0	Os01t0102600-01.exon3	N/A	Os01t0102600-01.exon3	N/A	Os01t0102600-01.exon3	transcript:Os01t0102600-01	N/A	3	N/A
+1	irgsp	exon	146179	146339	.	1	.	N/A	N/A	0	N/A	0	1	Os01t0102600-01.exon4	N/A	Os01t0102600-01.exon4	N/A	Os01t0102600-01.exon4	transcript:Os01t0102600-01	N/A	4	N/A
+1	irgsp	exon	146450	146532	.	1	.	N/A	N/A	0	N/A	2	0	Os01t0102600-01.exon5	N/A	Os01t0102600-01.exon5	N/A	Os01t0102600-01.exon5	transcript:Os01t0102600-01	N/A	5	N/A
+1	irgsp	exon	146611	146719	.	1	.	N/A	N/A	0	N/A	0	2	Os01t0102600-01.exon6	N/A	Os01t0102600-01.exon6	N/A	Os01t0102600-01.exon6	transcript:Os01t0102600-01	N/A	6	N/A
+1	irgsp	exon	147106	147184	.	1	.	N/A	N/A	0	N/A	1	0	Os01t0102600-01.exon7	N/A	Os01t0102600-01.exon7	N/A	Os01t0102600-01.exon7	transcript:Os01t0102600-01	N/A	7	N/A
+1	irgsp	exon	147311	147375	.	1	.	N/A	N/A	1	N/A	0	1	Os01t0102600-02.exon2	N/A	Os01t0102600-02.exon2	N/A	Os01t0102600-02.exon2	transcript:Os01t0102600-01	N/A	8	N/A
+1	irgsp	exon	147507	147847	.	1	.	N/A	N/A	0	N/A	-1	0	Os01t0102600-01.exon9	N/A	Os01t0102600-01.exon9	N/A	Os01t0102600-01.exon9	transcript:Os01t0102600-01	N/A	9	N/A
+1	irgsp	CDS	145645	145786	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102600-01	N/A	N/A	transcript:Os01t0102600-01	Os01t0102600-01	N/A	N/A
+1	irgsp	CDS	145905	145951	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102600-01	N/A	N/A	transcript:Os01t0102600-01	Os01t0102600-01	N/A	N/A
+1	irgsp	CDS	146028	146082	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102600-01	N/A	N/A	transcript:Os01t0102600-01	Os01t0102600-01	N/A	N/A
+1	irgsp	CDS	146179	146339	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102600-01	N/A	N/A	transcript:Os01t0102600-01	Os01t0102600-01	N/A	N/A
+1	irgsp	CDS	146450	146532	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102600-01	N/A	N/A	transcript:Os01t0102600-01	Os01t0102600-01	N/A	N/A
+1	irgsp	CDS	146611	146719	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102600-01	N/A	N/A	transcript:Os01t0102600-01	Os01t0102600-01	N/A	N/A
+1	irgsp	CDS	147106	147184	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102600-01	N/A	N/A	transcript:Os01t0102600-01	Os01t0102600-01	N/A	N/A
+1	irgsp	CDS	147311	147375	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102600-01	N/A	N/A	transcript:Os01t0102600-01	Os01t0102600-01	N/A	N/A
+1	irgsp	CDS	147507	147575	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102600-01	N/A	N/A	transcript:Os01t0102600-01	Os01t0102600-01	N/A	N/A
+1	irgsp	five_prime_UTR	145603	145644	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-30	N/A	N/A	transcript:Os01t0102600-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	147576	147847	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-29	N/A	N/A	transcript:Os01t0102600-01	N/A	N/A	N/A
+1	irgsp	mRNA	147104	147805	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0102600-02	N/A	N/A	gene:Os01g0102600	N/A	N/A	Os01t0102600-02
+1	irgsp	exon	147104	147184	.	1	.	N/A	N/A	0	N/A	1	-1	Os01t0102600-02.exon1	N/A	Os01t0102600-02.exon1	N/A	Os01t0102600-02.exon1	transcript:Os01t0102600-02	N/A	1	N/A
+1	irgsp	exon	147311	147375	.	1	.	N/A	N/A	1	N/A	0	1	Os01t0102600-02.exon2	N/A	agat-exon-4	N/A	Os01t0102600-02.exon2	transcript:Os01t0102600-02	N/A	2	N/A
+1	irgsp	exon	147507	147805	.	1	.	N/A	N/A	0	N/A	-1	0	Os01t0102600-02.exon3	N/A	Os01t0102600-02.exon3	N/A	Os01t0102600-02.exon3	transcript:Os01t0102600-02	N/A	3	N/A
+1	irgsp	CDS	147106	147184	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102600-02	N/A	N/A	transcript:Os01t0102600-02	Os01t0102600-02	N/A	N/A
+1	irgsp	CDS	147311	147375	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102600-02	N/A	N/A	transcript:Os01t0102600-02	Os01t0102600-02	N/A	N/A
+1	irgsp	CDS	147507	147575	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102600-02	N/A	N/A	transcript:Os01t0102600-02	Os01t0102600-02	N/A	N/A
+1	irgsp	five_prime_UTR	147104	147105	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-31	N/A	N/A	transcript:Os01t0102600-02	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	147576	147805	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-30	N/A	N/A	transcript:Os01t0102600-02	N/A	N/A	N/A
+1	irgsp	gene	148085	150568	.	1	.	N/A	protein_coding	N/A	Translocon-associated beta family protein. (Os01t0102700-01)	N/A	N/A	N/A	Os01g0102700	gene:Os01g0102700	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	148085	150568	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0102700-01	N/A	N/A	gene:Os01g0102700	N/A	N/A	Os01t0102700-01
+1	irgsp	exon	148085	148313	.	1	.	N/A	N/A	1	N/A	2	-1	Os01t0102700-01.exon1	N/A	Os01t0102700-01.exon1	N/A	Os01t0102700-01.exon1	transcript:Os01t0102700-01	N/A	1	N/A
+1	irgsp	exon	149450	149548	.	1	.	N/A	N/A	1	N/A	2	2	Os01t0102700-01.exon2	N/A	Os01t0102700-01.exon2	N/A	Os01t0102700-01.exon2	transcript:Os01t0102700-01	N/A	2	N/A
+1	irgsp	exon	149634	149742	.	1	.	N/A	N/A	1	N/A	0	2	Os01t0102700-01.exon3	N/A	Os01t0102700-01.exon3	N/A	Os01t0102700-01.exon3	transcript:Os01t0102700-01	N/A	3	N/A
+1	irgsp	exon	149856	149931	.	1	.	N/A	N/A	1	N/A	1	0	Os01t0102700-01.exon4	N/A	Os01t0102700-01.exon4	N/A	Os01t0102700-01.exon4	transcript:Os01t0102700-01	N/A	4	N/A
+1	irgsp	exon	150152	150568	.	1	.	N/A	N/A	1	N/A	-1	1	Os01t0102700-01.exon5	N/A	Os01t0102700-01.exon5	N/A	Os01t0102700-01.exon5	transcript:Os01t0102700-01	N/A	5	N/A
+1	irgsp	CDS	148147	148313	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102700-01	N/A	N/A	transcript:Os01t0102700-01	Os01t0102700-01	N/A	N/A
+1	irgsp	CDS	149450	149548	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102700-01	N/A	N/A	transcript:Os01t0102700-01	Os01t0102700-01	N/A	N/A
+1	irgsp	CDS	149634	149742	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102700-01	N/A	N/A	transcript:Os01t0102700-01	Os01t0102700-01	N/A	N/A
+1	irgsp	CDS	149856	149931	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102700-01	N/A	N/A	transcript:Os01t0102700-01	Os01t0102700-01	N/A	N/A
+1	irgsp	CDS	150152	150318	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102700-01	N/A	N/A	transcript:Os01t0102700-01	Os01t0102700-01	N/A	N/A
+1	irgsp	five_prime_UTR	148085	148146	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-32	N/A	N/A	transcript:Os01t0102700-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	150319	150568	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-31	N/A	N/A	transcript:Os01t0102700-01	N/A	N/A	N/A
+1	irgsp	gene	152853	156449	.	1	.	N/A	protein_coding	N/A	Similar to chromatin remodeling complex subunit. (Os01t0102800-01)	N/A	N/A	N/A	Os01g0102800	gene:Os01g0102800	irgspv1.0-20170804-genes	Cockayne syndrome WD-repeat protein	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	152853	156449	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0102800-01	N/A	N/A	gene:Os01g0102800	N/A	N/A	Os01t0102800-01
+1	irgsp	exon	152853	153025	.	1	.	N/A	N/A	1	N/A	1	-1	Os01t0102800-01.exon1	N/A	Os01t0102800-01.exon1	N/A	Os01t0102800-01.exon1	transcript:Os01t0102800-01	N/A	1	N/A
+1	irgsp	exon	153178	154646	.	1	.	N/A	N/A	1	N/A	0	1	Os01t0102800-01.exon2	N/A	Os01t0102800-01.exon2	N/A	Os01t0102800-01.exon2	transcript:Os01t0102800-01	N/A	2	N/A
+1	irgsp	exon	155010	155450	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0102800-01.exon3	N/A	Os01t0102800-01.exon3	N/A	Os01t0102800-01.exon3	transcript:Os01t0102800-01	N/A	3	N/A
+1	irgsp	exon	155543	156449	.	1	.	N/A	N/A	1	N/A	-1	0	Os01t0102800-01.exon4	N/A	Os01t0102800-01.exon4	N/A	Os01t0102800-01.exon4	transcript:Os01t0102800-01	N/A	4	N/A
+1	irgsp	CDS	152854	153025	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102800-01	N/A	N/A	transcript:Os01t0102800-01	Os01t0102800-01	N/A	N/A
+1	irgsp	CDS	153178	154646	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102800-01	N/A	N/A	transcript:Os01t0102800-01	Os01t0102800-01	N/A	N/A
+1	irgsp	CDS	155010	155450	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102800-01	N/A	N/A	transcript:Os01t0102800-01	Os01t0102800-01	N/A	N/A
+1	irgsp	CDS	155543	156214	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102800-01	N/A	N/A	transcript:Os01t0102800-01	Os01t0102800-01	N/A	N/A
+1	irgsp	five_prime_UTR	152853	152853	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-33	N/A	N/A	transcript:Os01t0102800-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	156215	156449	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-32	N/A	N/A	transcript:Os01t0102800-01	N/A	N/A	N/A
+1	irgsp	gene	164577	168921	.	1	.	N/A	protein_coding	N/A	Similar to nitrilase 2. (Os01t0102850-00)	N/A	N/A	N/A	Os01g0102850	gene:Os01g0102850	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	164577	168921	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0102850-00	N/A	N/A	gene:Os01g0102850	N/A	N/A	Os01t0102850-00
+1	irgsp	exon	164577	164905	.	1	.	N/A	N/A	1	N/A	-1	-1	Os01t0102850-00.exon1	N/A	Os01t0102850-00.exon1	N/A	Os01t0102850-00.exon1	transcript:Os01t0102850-00	N/A	1	N/A
+1	irgsp	exon	168499	168921	.	1	.	N/A	N/A	1	N/A	0	-1	Os01t0102850-00.exon2	N/A	Os01t0102850-00.exon2	N/A	Os01t0102850-00.exon2	transcript:Os01t0102850-00	N/A	2	N/A
+1	irgsp	CDS	168805	168921	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102850-00	N/A	N/A	transcript:Os01t0102850-00	Os01t0102850-00	N/A	N/A
+1	irgsp	five_prime_UTR	164577	164905	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-34	N/A	N/A	transcript:Os01t0102850-00	N/A	N/A	N/A
+1	irgsp	five_prime_UTR	168499	168804	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-35	N/A	N/A	transcript:Os01t0102850-00	N/A	N/A	N/A
+1	irgsp	gene	169390	170316	.	-1	.	N/A	protein_coding	N/A	Light-regulated protein, Regulation of light-dependent attachment of LEAF-TYPE FERREDOXIN-NADP+ OXIDOREDUCTASE (LFNR) to the thylakoid membrane (Os01t0102900-01)	N/A	N/A	N/A	Os01g0102900	gene:Os01g0102900	irgspv1.0-20170804-genes	LIGHT-REGULATED GENE 1	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	169390	170316	.	-1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0102900-01	N/A	N/A	gene:Os01g0102900	N/A	N/A	Os01t0102900-01
+1	irgsp	exon	169390	169656	.	-1	.	N/A	N/A	1	N/A	-1	2	Os01t0102900-01.exon3	N/A	Os01t0102900-01.exon3	N/A	Os01t0102900-01.exon3	transcript:Os01t0102900-01	N/A	3	N/A
+1	irgsp	exon	169751	169909	.	-1	.	N/A	N/A	1	N/A	2	2	Os01t0102900-01.exon2	N/A	Os01t0102900-01.exon2	N/A	Os01t0102900-01.exon2	transcript:Os01t0102900-01	N/A	2	N/A
+1	irgsp	exon	170091	170316	.	-1	.	N/A	N/A	1	N/A	2	-1	Os01t0102900-01.exon1	N/A	Os01t0102900-01.exon1	N/A	Os01t0102900-01.exon1	transcript:Os01t0102900-01	N/A	1	N/A
+1	irgsp	CDS	169599	169656	.	-1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102900-01	N/A	N/A	transcript:Os01t0102900-01	Os01t0102900-01	N/A	N/A
+1	irgsp	CDS	169751	169909	.	-1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102900-01	N/A	N/A	transcript:Os01t0102900-01	Os01t0102900-01	N/A	N/A
+1	irgsp	CDS	170091	170260	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0102900-01	N/A	N/A	transcript:Os01t0102900-01	Os01t0102900-01	N/A	N/A
+1	irgsp	five_prime_UTR	170261	170316	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-36	N/A	N/A	transcript:Os01t0102900-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	169390	169598	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-33	N/A	N/A	transcript:Os01t0102900-01	N/A	N/A	N/A
+1	irgsp	gene	170798	173144	.	-1	.	N/A	protein_coding	N/A	Snf7 family protein. (Os01t0103000-01)	N/A	N/A	N/A	Os01g0103000	gene:Os01g0103000	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	170798	173144	.	-1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0103000-01	N/A	N/A	gene:Os01g0103000	N/A	N/A	Os01t0103000-01
+1	irgsp	exon	170798	171095	.	-1	.	N/A	N/A	1	N/A	-1	0	Os01t0103000-01.exon7	N/A	Os01t0103000-01.exon7	N/A	Os01t0103000-01.exon7	transcript:Os01t0103000-01	N/A	7	N/A
+1	irgsp	exon	171406	171554	.	-1	.	N/A	N/A	1	N/A	0	1	Os01t0103000-01.exon6	N/A	Os01t0103000-01.exon6	N/A	Os01t0103000-01.exon6	transcript:Os01t0103000-01	N/A	6	N/A
+1	irgsp	exon	171764	171875	.	-1	.	N/A	N/A	1	N/A	1	0	Os01t0103000-01.exon5	N/A	Os01t0103000-01.exon5	N/A	Os01t0103000-01.exon5	transcript:Os01t0103000-01	N/A	5	N/A
+1	irgsp	exon	172398	172469	.	-1	.	N/A	N/A	1	N/A	0	0	Os01t0103000-01.exon4	N/A	Os01t0103000-01.exon4	N/A	Os01t0103000-01.exon4	transcript:Os01t0103000-01	N/A	4	N/A
+1	irgsp	exon	172578	172671	.	-1	.	N/A	N/A	1	N/A	0	2	Os01t0103000-01.exon3	N/A	Os01t0103000-01.exon3	N/A	Os01t0103000-01.exon3	transcript:Os01t0103000-01	N/A	3	N/A
+1	irgsp	exon	172770	172921	.	-1	.	N/A	N/A	1	N/A	2	0	Os01t0103000-01.exon2	N/A	Os01t0103000-01.exon2	N/A	Os01t0103000-01.exon2	transcript:Os01t0103000-01	N/A	2	N/A
+1	irgsp	exon	173004	173144	.	-1	.	N/A	N/A	1	N/A	0	-1	Os01t0103000-01.exon1	N/A	Os01t0103000-01.exon1	N/A	Os01t0103000-01.exon1	transcript:Os01t0103000-01	N/A	1	N/A
+1	irgsp	CDS	171045	171095	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103000-01	N/A	N/A	transcript:Os01t0103000-01	Os01t0103000-01	N/A	N/A
+1	irgsp	CDS	171406	171554	.	-1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103000-01	N/A	N/A	transcript:Os01t0103000-01	Os01t0103000-01	N/A	N/A
+1	irgsp	CDS	171764	171875	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103000-01	N/A	N/A	transcript:Os01t0103000-01	Os01t0103000-01	N/A	N/A
+1	irgsp	CDS	172398	172469	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103000-01	N/A	N/A	transcript:Os01t0103000-01	Os01t0103000-01	N/A	N/A
+1	irgsp	CDS	172578	172671	.	-1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103000-01	N/A	N/A	transcript:Os01t0103000-01	Os01t0103000-01	N/A	N/A
+1	irgsp	CDS	172770	172921	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103000-01	N/A	N/A	transcript:Os01t0103000-01	Os01t0103000-01	N/A	N/A
+1	irgsp	CDS	173004	173072	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103000-01	N/A	N/A	transcript:Os01t0103000-01	Os01t0103000-01	N/A	N/A
+1	irgsp	five_prime_UTR	173073	173144	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-37	N/A	N/A	transcript:Os01t0103000-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	170798	171044	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-34	N/A	N/A	transcript:Os01t0103000-01	N/A	N/A	N/A
+1	irgsp	gene	178607	180575	.	1	.	N/A	protein_coding	N/A	TGF-beta receptor, type I/II extracellular region family protein. (Os01t0103100-01);Similar to predicted protein. (Os01t0103100-02)	N/A	N/A	N/A	Os01g0103100	gene:Os01g0103100	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	178607	180548	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0103100-01	N/A	N/A	gene:Os01g0103100	N/A	N/A	Os01t0103100-01
+1	irgsp	exon	178607	180548	.	1	.	N/A	N/A	0	N/A	-1	-1	Os01t0103100-01.exon1	N/A	Os01t0103100-01.exon1	N/A	Os01t0103100-01.exon1	transcript:Os01t0103100-01	N/A	1	N/A
+1	irgsp	CDS	178642	180462	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103100-01	N/A	N/A	transcript:Os01t0103100-01	Os01t0103100-01	N/A	N/A
+1	irgsp	five_prime_UTR	178607	178641	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-38	N/A	N/A	transcript:Os01t0103100-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	180463	180548	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-35	N/A	N/A	transcript:Os01t0103100-01	N/A	N/A	N/A
+1	irgsp	mRNA	178652	180575	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0103100-02	N/A	N/A	gene:Os01g0103100	N/A	N/A	Os01t0103100-02
+1	irgsp	exon	178652	180575	.	1	.	N/A	N/A	0	N/A	-1	-1	Os01t0103100-02.exon1	N/A	Os01t0103100-02.exon1	N/A	Os01t0103100-02.exon1	transcript:Os01t0103100-02	N/A	1	N/A
+1	irgsp	CDS	178678	180462	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103100-02	N/A	N/A	transcript:Os01t0103100-02	Os01t0103100-02	N/A	N/A
+1	irgsp	five_prime_UTR	178652	178677	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-39	N/A	N/A	transcript:Os01t0103100-02	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	180463	180575	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-36	N/A	N/A	transcript:Os01t0103100-02	N/A	N/A	N/A
+1	irgsp	gene	178815	180433	.	-1	.	N/A	protein_coding	N/A	Hypothetical protein. (Os01t0103075-00)	N/A	N/A	N/A	Os01g0103075	gene:Os01g0103075	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	178815	180433	.	-1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0103075-00	N/A	N/A	gene:Os01g0103075	N/A	N/A	Os01t0103075-00
+1	irgsp	exon	178815	180433	.	-1	.	N/A	N/A	1	N/A	-1	-1	Os01t0103075-00.exon1	N/A	Os01t0103075-00.exon1	N/A	Os01t0103075-00.exon1	transcript:Os01t0103075-00	N/A	1	N/A
+1	irgsp	CDS	179512	180054	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103075-00	N/A	N/A	transcript:Os01t0103075-00	Os01t0103075-00	N/A	N/A
+1	irgsp	five_prime_UTR	180055	180433	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-40	N/A	N/A	transcript:Os01t0103075-00	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	178815	179511	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-37	N/A	N/A	transcript:Os01t0103075-00	N/A	N/A	N/A
+1	Ensembl_Plants	ncRNA_gene	182074	182154	.	1	.	N/A	tRNA	N/A	tRNA-Leu for anticodon AAG	N/A	N/A	N/A	ENSRNA049442722	gene:ENSRNA049442722	trnascan_gene	tRNA-Leu	N/A	N/A	N/A	N/A
+1	Ensembl_Plants	tRNA	182074	182154	.	1	.	N/A	tRNA	N/A	N/A	N/A	N/A	N/A	N/A	transcript:ENSRNA049442722-T1	N/A	N/A	gene:ENSRNA049442722	N/A	N/A	ENSRNA049442722-T1
+1	Ensembl_Plants	exon	182074	182154	.	1	.	N/A	N/A	1	N/A	-1	-1	ENSRNA049442722-E1	N/A	ENSRNA049442722-E1	N/A	ENSRNA049442722-E1	transcript:ENSRNA049442722-T1	N/A	1	N/A
+1	irgsp	gene	185189	185828	.	-1	.	N/A	protein_coding	N/A	Hypothetical gene. (Os01t0103400-01)	N/A	N/A	N/A	Os01g0103400	gene:Os01g0103400	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	185189	185828	.	-1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0103400-01	N/A	N/A	gene:Os01g0103400	N/A	N/A	Os01t0103400-01
+1	irgsp	exon	185189	185828	.	-1	.	N/A	N/A	1	N/A	-1	-1	Os01t0103400-01.exon1	N/A	Os01t0103400-01.exon1	N/A	Os01t0103400-01.exon1	transcript:Os01t0103400-01	N/A	1	N/A
+1	irgsp	CDS	185435	185827	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103400-01	N/A	N/A	transcript:Os01t0103400-01	Os01t0103400-01	N/A	N/A
+1	irgsp	five_prime_UTR	185828	185828	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-41	N/A	N/A	transcript:Os01t0103400-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	185189	185434	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-38	N/A	N/A	transcript:Os01t0103400-01	N/A	N/A	N/A
+1	irgsp	repeat_region	186000	186100	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	fakeRepeat2	N/A	N/A	N/A	N/A	N/A	N/A
+1	irgsp	gene	186250	190904	.	-1	.	N/A	protein_coding	N/A	Similar to sterol-8,7-isomerase. (Os01t0103600-01);Emopamil-binding family protein. (Os01t0103600-02)	N/A	N/A	N/A	Os01g0103600	gene:Os01g0103600	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	186250	190262	.	-1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0103600-02	N/A	N/A	gene:Os01g0103600	N/A	N/A	Os01t0103600-02
+1	irgsp	exon	186250	186771	.	-1	.	N/A	N/A	0	N/A	-1	2	Os01t0103600-02.exon4	N/A	Os01t0103600-02.exon4	N/A	Os01t0103600-02.exon4	transcript:Os01t0103600-02	N/A	4	N/A
+1	irgsp	exon	189607	189715	.	-1	.	N/A	N/A	0	N/A	2	1	Os01t0103600-02.exon3	N/A	Os01t0103600-02.exon3	N/A	Os01t0103600-02.exon3	transcript:Os01t0103600-02	N/A	3	N/A
+1	irgsp	exon	189841	189990	.	-1	.	N/A	N/A	1	N/A	1	1	Os01t0103600-02.exon2	N/A	Os01t0103600-02.exon2	N/A	Os01t0103600-02.exon2	transcript:Os01t0103600-02	N/A	2	N/A
+1	irgsp	exon	190087	190262	.	-1	.	N/A	N/A	0	N/A	1	-1	Os01t0103600-02.exon1	N/A	Os01t0103600-02.exon1	N/A	Os01t0103600-02.exon1	transcript:Os01t0103600-02	N/A	1	N/A
+1	irgsp	CDS	186516	186771	.	-1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103600-02	N/A	N/A	transcript:Os01t0103600-02	Os01t0103600-02	N/A	N/A
+1	irgsp	CDS	189607	189715	.	-1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103600-02	N/A	N/A	transcript:Os01t0103600-02	Os01t0103600-02	N/A	N/A
+1	irgsp	CDS	189841	189990	.	-1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103600-02	N/A	N/A	transcript:Os01t0103600-02	Os01t0103600-02	N/A	N/A
+1	irgsp	CDS	190087	190231	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103600-02	N/A	N/A	transcript:Os01t0103600-02	Os01t0103600-02	N/A	N/A
+1	irgsp	five_prime_UTR	190232	190262	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-42	N/A	N/A	transcript:Os01t0103600-02	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	186250	186515	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-39	N/A	N/A	transcript:Os01t0103600-02	N/A	N/A	N/A
+1	irgsp	mRNA	187345	190904	.	-1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0103600-01	N/A	N/A	gene:Os01g0103600	N/A	N/A	Os01t0103600-01
+1	irgsp	exon	187345	189715	.	-1	.	N/A	N/A	0	N/A	-1	1	Os01t0103600-01.exon3	N/A	Os01t0103600-01.exon3	N/A	Os01t0103600-01.exon3	transcript:Os01t0103600-01	N/A	3	N/A
+1	irgsp	exon	189841	189990	.	-1	.	N/A	N/A	1	N/A	1	1	Os01t0103600-02.exon2	N/A	agat-exon-5	N/A	Os01t0103600-02.exon2	transcript:Os01t0103600-01	N/A	2	N/A
+1	irgsp	exon	190087	190904	.	-1	.	N/A	N/A	0	N/A	1	-1	Os01t0103600-01.exon1	N/A	Os01t0103600-01.exon1	N/A	Os01t0103600-01.exon1	transcript:Os01t0103600-01	N/A	1	N/A
+1	irgsp	CDS	189396	189715	.	-1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103600-01	N/A	N/A	transcript:Os01t0103600-01	Os01t0103600-01	N/A	N/A
+1	irgsp	CDS	189841	189990	.	-1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103600-01	N/A	N/A	transcript:Os01t0103600-01	Os01t0103600-01	N/A	N/A
+1	irgsp	CDS	190087	190231	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103600-01	N/A	N/A	transcript:Os01t0103600-01	Os01t0103600-01	N/A	N/A
+1	irgsp	five_prime_UTR	190232	190904	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-43	N/A	N/A	transcript:Os01t0103600-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	187345	189395	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-40	N/A	N/A	transcript:Os01t0103600-01	N/A	N/A	N/A
+1	irgsp	gene	187545	188586	.	1	.	N/A	protein_coding	N/A	Hypothetical gene. (Os01t0103650-00)	N/A	N/A	N/A	Os01g0103650	gene:Os01g0103650	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	187545	188586	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0103650-00	N/A	N/A	gene:Os01g0103650	N/A	N/A	Os01t0103650-00
+1	irgsp	exon	187545	188020	.	1	.	N/A	N/A	1	N/A	-1	-1	Os01t0103650-00.exon1	N/A	Os01t0103650-00.exon1	N/A	Os01t0103650-00.exon1	transcript:Os01t0103650-00	N/A	1	N/A
+1	irgsp	exon	188060	188385	.	1	.	N/A	N/A	1	N/A	-1	-1	Os01t0103650-00.exon2	N/A	Os01t0103650-00.exon2	N/A	Os01t0103650-00.exon2	transcript:Os01t0103650-00	N/A	2	N/A
+1	irgsp	exon	188455	188586	.	1	.	N/A	N/A	1	N/A	-1	-1	Os01t0103650-00.exon3	N/A	Os01t0103650-00.exon3	N/A	Os01t0103650-00.exon3	transcript:Os01t0103650-00	N/A	3	N/A
+1	irgsp	CDS	187547	187768	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103650-00	N/A	N/A	transcript:Os01t0103650-00	Os01t0103650-00	N/A	N/A
+1	irgsp	five_prime_UTR	187545	187546	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-44	N/A	N/A	transcript:Os01t0103650-00	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	187769	188020	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-41	N/A	N/A	transcript:Os01t0103650-00	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	188060	188385	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-42	N/A	N/A	transcript:Os01t0103650-00	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	188455	188586	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-43	N/A	N/A	transcript:Os01t0103650-00	N/A	N/A	N/A
+1	irgsp	gene	191037	196287	.	1	.	N/A	protein_coding	N/A	Conserved hypothetical protein. (Os01t0103700-01)	N/A	N/A	N/A	Os01g0103700	gene:Os01g0103700	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	191037	196287	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0103700-01	N/A	N/A	gene:Os01g0103700	N/A	N/A	Os01t0103700-01
+1	irgsp	exon	191037	191161	.	1	.	N/A	N/A	1	N/A	-1	-1	Os01t0103700-01.exon1	N/A	Os01t0103700-01.exon1	N/A	Os01t0103700-01.exon1	transcript:Os01t0103700-01	N/A	1	N/A
+1	irgsp	exon	191625	191705	.	1	.	N/A	N/A	1	N/A	0	-1	Os01t0103700-01.exon2	N/A	Os01t0103700-01.exon2	N/A	Os01t0103700-01.exon2	transcript:Os01t0103700-01	N/A	2	N/A
+1	irgsp	exon	192399	192506	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0103700-01.exon3	N/A	Os01t0103700-01.exon3	N/A	Os01t0103700-01.exon3	transcript:Os01t0103700-01	N/A	3	N/A
+1	irgsp	exon	192958	193161	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0103700-01.exon4	N/A	Os01t0103700-01.exon4	N/A	Os01t0103700-01.exon4	transcript:Os01t0103700-01	N/A	4	N/A
+1	irgsp	exon	193248	193356	.	1	.	N/A	N/A	1	N/A	1	0	Os01t0103700-01.exon5	N/A	Os01t0103700-01.exon5	N/A	Os01t0103700-01.exon5	transcript:Os01t0103700-01	N/A	5	N/A
+1	irgsp	exon	193434	196287	.	1	.	N/A	N/A	1	N/A	-1	1	Os01t0103700-01.exon6	N/A	Os01t0103700-01.exon6	N/A	Os01t0103700-01.exon6	transcript:Os01t0103700-01	N/A	6	N/A
+1	irgsp	CDS	191694	191705	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103700-01	N/A	N/A	transcript:Os01t0103700-01	Os01t0103700-01	N/A	N/A
+1	irgsp	CDS	192399	192506	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103700-01	N/A	N/A	transcript:Os01t0103700-01	Os01t0103700-01	N/A	N/A
+1	irgsp	CDS	192958	193161	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103700-01	N/A	N/A	transcript:Os01t0103700-01	Os01t0103700-01	N/A	N/A
+1	irgsp	CDS	193248	193356	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103700-01	N/A	N/A	transcript:Os01t0103700-01	Os01t0103700-01	N/A	N/A
+1	irgsp	CDS	193434	193507	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103700-01	N/A	N/A	transcript:Os01t0103700-01	Os01t0103700-01	N/A	N/A
+1	irgsp	five_prime_UTR	191037	191161	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-45	N/A	N/A	transcript:Os01t0103700-01	N/A	N/A	N/A
+1	irgsp	five_prime_UTR	191625	191693	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-46	N/A	N/A	transcript:Os01t0103700-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	193508	196287	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-44	N/A	N/A	transcript:Os01t0103700-01	N/A	N/A	N/A
+1	irgsp	gene	197647	200803	.	1	.	N/A	protein_coding	N/A	Conserved hypothetical protein. (Os01t0103800-01)	N/A	N/A	N/A	Os01g0103800	gene:Os01g0103800	irgspv1.0-20170804-genes	OsDW1-01g	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	197647	200803	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0103800-01	N/A	N/A	gene:Os01g0103800	N/A	N/A	Os01t0103800-01
+1	irgsp	exon	197647	197838	.	1	.	N/A	N/A	1	N/A	-1	-1	Os01t0103800-01.exon1	N/A	Os01t0103800-01.exon1	N/A	Os01t0103800-01.exon1	transcript:Os01t0103800-01	N/A	1	N/A
+1	irgsp	exon	198034	198225	.	1	.	N/A	N/A	1	N/A	0	-1	Os01t0103800-01.exon2	N/A	Os01t0103800-01.exon2	N/A	Os01t0103800-01.exon2	transcript:Os01t0103800-01	N/A	2	N/A
+1	irgsp	exon	198830	200036	.	1	.	N/A	N/A	1	N/A	1	0	Os01t0103800-01.exon3	N/A	Os01t0103800-01.exon3	N/A	Os01t0103800-01.exon3	transcript:Os01t0103800-01	N/A	3	N/A
+1	irgsp	exon	200253	200803	.	1	.	N/A	N/A	1	N/A	-1	1	Os01t0103800-01.exon4	N/A	Os01t0103800-01.exon4	N/A	Os01t0103800-01.exon4	transcript:Os01t0103800-01	N/A	4	N/A
+1	irgsp	CDS	198130	198225	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103800-01	N/A	N/A	transcript:Os01t0103800-01	Os01t0103800-01	N/A	N/A
+1	irgsp	CDS	198830	200036	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103800-01	N/A	N/A	transcript:Os01t0103800-01	Os01t0103800-01	N/A	N/A
+1	irgsp	CDS	200253	200479	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103800-01	N/A	N/A	transcript:Os01t0103800-01	Os01t0103800-01	N/A	N/A
+1	irgsp	five_prime_UTR	197647	197838	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-47	N/A	N/A	transcript:Os01t0103800-01	N/A	N/A	N/A
+1	irgsp	five_prime_UTR	198034	198129	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-48	N/A	N/A	transcript:Os01t0103800-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	200480	200803	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-45	N/A	N/A	transcript:Os01t0103800-01	N/A	N/A	N/A
+1	irgsp	gene	201944	206202	.	1	.	N/A	protein_coding	N/A	Polynucleotidyl transferase, Ribonuclease H fold domain containing protein. (Os01t0103900-01)	N/A	N/A	N/A	Os01g0103900	gene:Os01g0103900	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	201944	206202	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0103900-01	N/A	N/A	gene:Os01g0103900	N/A	N/A	Os01t0103900-01
+1	irgsp	exon	201944	202110	.	1	.	N/A	N/A	1	N/A	0	-1	Os01t0103900-01.exon1	N/A	Os01t0103900-01.exon1	N/A	Os01t0103900-01.exon1	transcript:Os01t0103900-01	N/A	1	N/A
+1	irgsp	exon	202252	202359	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0103900-01.exon2	N/A	Os01t0103900-01.exon2	N/A	Os01t0103900-01.exon2	transcript:Os01t0103900-01	N/A	2	N/A
+1	irgsp	exon	203007	203127	.	1	.	N/A	N/A	1	N/A	1	0	Os01t0103900-01.exon3	N/A	Os01t0103900-01.exon3	N/A	Os01t0103900-01.exon3	transcript:Os01t0103900-01	N/A	3	N/A
+1	irgsp	exon	203302	203429	.	1	.	N/A	N/A	1	N/A	0	1	Os01t0103900-01.exon4	N/A	Os01t0103900-01.exon4	N/A	Os01t0103900-01.exon4	transcript:Os01t0103900-01	N/A	4	N/A
+1	irgsp	exon	203511	203658	.	1	.	N/A	N/A	1	N/A	1	0	Os01t0103900-01.exon5	N/A	Os01t0103900-01.exon5	N/A	Os01t0103900-01.exon5	transcript:Os01t0103900-01	N/A	5	N/A
+1	irgsp	exon	203760	203938	.	1	.	N/A	N/A	1	N/A	0	1	Os01t0103900-01.exon6	N/A	Os01t0103900-01.exon6	N/A	Os01t0103900-01.exon6	transcript:Os01t0103900-01	N/A	6	N/A
+1	irgsp	exon	204203	204440	.	1	.	N/A	N/A	1	N/A	1	0	Os01t0103900-01.exon7	N/A	Os01t0103900-01.exon7	N/A	Os01t0103900-01.exon7	transcript:Os01t0103900-01	N/A	7	N/A
+1	irgsp	exon	204543	204635	.	1	.	N/A	N/A	1	N/A	1	1	Os01t0103900-01.exon8	N/A	Os01t0103900-01.exon8	N/A	Os01t0103900-01.exon8	transcript:Os01t0103900-01	N/A	8	N/A
+1	irgsp	exon	204730	204875	.	1	.	N/A	N/A	1	N/A	0	1	Os01t0103900-01.exon9	N/A	Os01t0103900-01.exon9	N/A	Os01t0103900-01.exon9	transcript:Os01t0103900-01	N/A	9	N/A
+1	irgsp	exon	205042	205149	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0103900-01.exon10	N/A	Os01t0103900-01.exon10	N/A	Os01t0103900-01.exon10	transcript:Os01t0103900-01	N/A	10	N/A
+1	irgsp	exon	205290	205378	.	1	.	N/A	N/A	1	N/A	2	0	Os01t0103900-01.exon11	N/A	Os01t0103900-01.exon11	N/A	Os01t0103900-01.exon11	transcript:Os01t0103900-01	N/A	11	N/A
+1	irgsp	exon	205534	206202	.	1	.	N/A	N/A	1	N/A	-1	2	Os01t0103900-01.exon12	N/A	Os01t0103900-01.exon12	N/A	Os01t0103900-01.exon12	transcript:Os01t0103900-01	N/A	12	N/A
+1	irgsp	CDS	202042	202110	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103900-01	N/A	N/A	transcript:Os01t0103900-01	Os01t0103900-01	N/A	N/A
+1	irgsp	CDS	202252	202359	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103900-01	N/A	N/A	transcript:Os01t0103900-01	Os01t0103900-01	N/A	N/A
+1	irgsp	CDS	203007	203127	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103900-01	N/A	N/A	transcript:Os01t0103900-01	Os01t0103900-01	N/A	N/A
+1	irgsp	CDS	203302	203429	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103900-01	N/A	N/A	transcript:Os01t0103900-01	Os01t0103900-01	N/A	N/A
+1	irgsp	CDS	203511	203658	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103900-01	N/A	N/A	transcript:Os01t0103900-01	Os01t0103900-01	N/A	N/A
+1	irgsp	CDS	203760	203938	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103900-01	N/A	N/A	transcript:Os01t0103900-01	Os01t0103900-01	N/A	N/A
+1	irgsp	CDS	204203	204440	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103900-01	N/A	N/A	transcript:Os01t0103900-01	Os01t0103900-01	N/A	N/A
+1	irgsp	CDS	204543	204635	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103900-01	N/A	N/A	transcript:Os01t0103900-01	Os01t0103900-01	N/A	N/A
+1	irgsp	CDS	204730	204875	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103900-01	N/A	N/A	transcript:Os01t0103900-01	Os01t0103900-01	N/A	N/A
+1	irgsp	CDS	205042	205149	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103900-01	N/A	N/A	transcript:Os01t0103900-01	Os01t0103900-01	N/A	N/A
+1	irgsp	CDS	205290	205378	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103900-01	N/A	N/A	transcript:Os01t0103900-01	Os01t0103900-01	N/A	N/A
+1	irgsp	CDS	205534	205543	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0103900-01	N/A	N/A	transcript:Os01t0103900-01	Os01t0103900-01	N/A	N/A
+1	irgsp	five_prime_UTR	201944	202041	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-49	N/A	N/A	transcript:Os01t0103900-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	205544	206202	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-46	N/A	N/A	transcript:Os01t0103900-01	N/A	N/A	N/A
+1	irgsp	gene	206131	209606	.	-1	.	N/A	protein_coding	N/A	C-type lectin domain containing protein. (Os01t0104000-01);Similar to predicted protein. (Os01t0104000-02)	N/A	N/A	N/A	Os01g0104000	gene:Os01g0104000	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	206131	209581	.	-1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0104000-02	N/A	N/A	gene:Os01g0104000	N/A	N/A	Os01t0104000-02
+1	irgsp	exon	206131	207029	.	-1	.	N/A	N/A	0	N/A	-1	2	Os01t0104000-02.exon4	N/A	Os01t0104000-02.exon4	N/A	Os01t0104000-02.exon4	transcript:Os01t0104000-02	N/A	4	N/A
+1	irgsp	exon	207706	208273	.	-1	.	N/A	N/A	0	N/A	2	1	Os01t0104000-02.exon3	N/A	Os01t0104000-02.exon3	N/A	Os01t0104000-02.exon3	transcript:Os01t0104000-02	N/A	3	N/A
+1	irgsp	exon	208408	208836	.	-1	.	N/A	N/A	1	N/A	1	1	Os01t0104000-01.exon2	N/A	Os01t0104000-01.exon2	N/A	Os01t0104000-01.exon2	transcript:Os01t0104000-02	N/A	2	N/A
+1	irgsp	exon	209438	209581	.	-1	.	N/A	N/A	0	N/A	1	-1	Os01t0104000-02.exon1	N/A	Os01t0104000-02.exon1	N/A	Os01t0104000-02.exon1	transcript:Os01t0104000-02	N/A	1	N/A
+1	irgsp	CDS	206450	207029	.	-1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104000-02	N/A	N/A	transcript:Os01t0104000-02	Os01t0104000-02	N/A	N/A
+1	irgsp	CDS	207706	208273	.	-1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104000-02	N/A	N/A	transcript:Os01t0104000-02	Os01t0104000-02	N/A	N/A
+1	irgsp	CDS	208408	208836	.	-1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104000-02	N/A	N/A	transcript:Os01t0104000-02	Os01t0104000-02	N/A	N/A
+1	irgsp	CDS	209438	209525	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104000-02	N/A	N/A	transcript:Os01t0104000-02	Os01t0104000-02	N/A	N/A
+1	irgsp	five_prime_UTR	209526	209581	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-50	N/A	N/A	transcript:Os01t0104000-02	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	206131	206449	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-47	N/A	N/A	transcript:Os01t0104000-02	N/A	N/A	N/A
+1	irgsp	mRNA	206134	209606	.	-1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0104000-01	N/A	N/A	gene:Os01g0104000	N/A	N/A	Os01t0104000-01
+1	irgsp	exon	206134	207029	.	-1	.	N/A	N/A	0	N/A	-1	2	Os01t0104000-01.exon4	N/A	Os01t0104000-01.exon4	N/A	Os01t0104000-01.exon4	transcript:Os01t0104000-01	N/A	4	N/A
+1	irgsp	exon	207706	208276	.	-1	.	N/A	N/A	0	N/A	2	1	Os01t0104000-01.exon3	N/A	Os01t0104000-01.exon3	N/A	Os01t0104000-01.exon3	transcript:Os01t0104000-01	N/A	3	N/A
+1	irgsp	exon	208408	208836	.	-1	.	N/A	N/A	1	N/A	1	1	Os01t0104000-01.exon2	N/A	agat-exon-6	N/A	Os01t0104000-01.exon2	transcript:Os01t0104000-01	N/A	2	N/A
+1	irgsp	exon	209438	209606	.	-1	.	N/A	N/A	0	N/A	1	-1	Os01t0104000-01.exon1	N/A	Os01t0104000-01.exon1	N/A	Os01t0104000-01.exon1	transcript:Os01t0104000-01	N/A	1	N/A
+1	irgsp	CDS	206450	207029	.	-1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104000-01	N/A	N/A	transcript:Os01t0104000-01	Os01t0104000-01	N/A	N/A
+1	irgsp	CDS	207706	208276	.	-1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104000-01	N/A	N/A	transcript:Os01t0104000-01	Os01t0104000-01	N/A	N/A
+1	irgsp	CDS	208408	208836	.	-1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104000-01	N/A	N/A	transcript:Os01t0104000-01	Os01t0104000-01	N/A	N/A
+1	irgsp	CDS	209438	209525	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104000-01	N/A	N/A	transcript:Os01t0104000-01	Os01t0104000-01	N/A	N/A
+1	irgsp	five_prime_UTR	209526	209606	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-51	N/A	N/A	transcript:Os01t0104000-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	206134	206449	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-48	N/A	N/A	transcript:Os01t0104000-01	N/A	N/A	N/A
+1	irgsp	gene	209771	214173	.	1	.	N/A	protein_coding	N/A	Similar to protein binding / zinc ion binding. (Os01t0104100-01);Similar to protein binding / zinc ion binding. (Os01t0104100-02)	N/A	N/A	N/A	Os01g0104100	gene:Os01g0104100	irgspv1.0-20170804-genes	cold-inducible, cold-inducible zinc finger protein	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	209771	214173	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0104100-01	N/A	N/A	gene:Os01g0104100	N/A	N/A	Os01t0104100-01
+1	irgsp	exon	209771	209896	.	1	.	N/A	N/A	0	N/A	0	0	Os01t0104100-01.exon1	N/A	Os01t0104100-01.exon1	N/A	Os01t0104100-01.exon1	transcript:Os01t0104100-01	N/A	1	N/A
+1	irgsp	exon	210244	210563	.	1	.	N/A	N/A	1	N/A	2	0	Os01t0104100-01.exon2	N/A	Os01t0104100-01.exon2	N/A	Os01t0104100-01.exon2	transcript:Os01t0104100-01	N/A	2	N/A
+1	irgsp	exon	210659	210890	.	1	.	N/A	N/A	1	N/A	0	2	Os01t0104100-01.exon3	N/A	Os01t0104100-01.exon3	N/A	Os01t0104100-01.exon3	transcript:Os01t0104100-01	N/A	3	N/A
+1	irgsp	exon	211015	211160	.	1	.	N/A	N/A	1	N/A	2	0	Os01t0104100-01.exon4	N/A	Os01t0104100-01.exon4	N/A	Os01t0104100-01.exon4	transcript:Os01t0104100-01	N/A	4	N/A
+1	irgsp	exon	212265	212352	.	1	.	N/A	N/A	1	N/A	0	2	Os01t0104100-01.exon5	N/A	Os01t0104100-01.exon5	N/A	Os01t0104100-01.exon5	transcript:Os01t0104100-01	N/A	5	N/A
+1	irgsp	exon	212433	212579	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0104100-01.exon6	N/A	Os01t0104100-01.exon6	N/A	Os01t0104100-01.exon6	transcript:Os01t0104100-01	N/A	6	N/A
+1	irgsp	exon	213490	213639	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0104100-01.exon7	N/A	Os01t0104100-01.exon7	N/A	Os01t0104100-01.exon7	transcript:Os01t0104100-01	N/A	7	N/A
+1	irgsp	exon	213741	214173	.	1	.	N/A	N/A	0	N/A	-1	0	Os01t0104100-01.exon8	N/A	Os01t0104100-01.exon8	N/A	Os01t0104100-01.exon8	transcript:Os01t0104100-01	N/A	8	N/A
+1	irgsp	CDS	209771	209896	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104100-01	N/A	N/A	transcript:Os01t0104100-01	Os01t0104100-01	N/A	N/A
+1	irgsp	CDS	210244	210563	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104100-01	N/A	N/A	transcript:Os01t0104100-01	Os01t0104100-01	N/A	N/A
+1	irgsp	CDS	210659	210890	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104100-01	N/A	N/A	transcript:Os01t0104100-01	Os01t0104100-01	N/A	N/A
+1	irgsp	CDS	211015	211160	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104100-01	N/A	N/A	transcript:Os01t0104100-01	Os01t0104100-01	N/A	N/A
+1	irgsp	CDS	212265	212352	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104100-01	N/A	N/A	transcript:Os01t0104100-01	Os01t0104100-01	N/A	N/A
+1	irgsp	CDS	212433	212579	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104100-01	N/A	N/A	transcript:Os01t0104100-01	Os01t0104100-01	N/A	N/A
+1	irgsp	CDS	213490	213639	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104100-01	N/A	N/A	transcript:Os01t0104100-01	Os01t0104100-01	N/A	N/A
+1	irgsp	CDS	213741	213788	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104100-01	N/A	N/A	transcript:Os01t0104100-01	Os01t0104100-01	N/A	N/A
+1	irgsp	three_prime_UTR	213789	214173	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-49	N/A	N/A	transcript:Os01t0104100-01	N/A	N/A	N/A
+1	irgsp	mRNA	209794	214147	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0104100-02	N/A	N/A	gene:Os01g0104100	N/A	N/A	Os01t0104100-02
+1	irgsp	exon	209794	209896	.	1	.	N/A	N/A	0	N/A	0	-1	Os01t0104100-02.exon1	N/A	Os01t0104100-02.exon1	N/A	Os01t0104100-02.exon1	transcript:Os01t0104100-02	N/A	1	N/A
+1	irgsp	exon	210244	210563	.	1	.	N/A	N/A	1	N/A	2	0	Os01t0104100-01.exon2	N/A	agat-exon-7	N/A	Os01t0104100-01.exon2	transcript:Os01t0104100-02	N/A	2	N/A
+1	irgsp	exon	210659	210890	.	1	.	N/A	N/A	1	N/A	0	2	Os01t0104100-01.exon3	N/A	agat-exon-8	N/A	Os01t0104100-01.exon3	transcript:Os01t0104100-02	N/A	3	N/A
+1	irgsp	exon	211015	211160	.	1	.	N/A	N/A	1	N/A	2	0	Os01t0104100-01.exon4	N/A	agat-exon-9	N/A	Os01t0104100-01.exon4	transcript:Os01t0104100-02	N/A	4	N/A
+1	irgsp	exon	212265	212352	.	1	.	N/A	N/A	1	N/A	0	2	Os01t0104100-01.exon5	N/A	agat-exon-10	N/A	Os01t0104100-01.exon5	transcript:Os01t0104100-02	N/A	5	N/A
+1	irgsp	exon	212433	212579	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0104100-01.exon6	N/A	agat-exon-11	N/A	Os01t0104100-01.exon6	transcript:Os01t0104100-02	N/A	6	N/A
+1	irgsp	exon	213490	213639	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0104100-01.exon7	N/A	agat-exon-12	N/A	Os01t0104100-01.exon7	transcript:Os01t0104100-02	N/A	7	N/A
+1	irgsp	exon	213741	214147	.	1	.	N/A	N/A	0	N/A	-1	0	Os01t0104100-02.exon8	N/A	Os01t0104100-02.exon8	N/A	Os01t0104100-02.exon8	transcript:Os01t0104100-02	N/A	8	N/A
+1	irgsp	CDS	209795	209896	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104100-02	N/A	N/A	transcript:Os01t0104100-02	Os01t0104100-02	N/A	N/A
+1	irgsp	CDS	210244	210563	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104100-02	N/A	N/A	transcript:Os01t0104100-02	Os01t0104100-02	N/A	N/A
+1	irgsp	CDS	210659	210890	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104100-02	N/A	N/A	transcript:Os01t0104100-02	Os01t0104100-02	N/A	N/A
+1	irgsp	CDS	211015	211160	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104100-02	N/A	N/A	transcript:Os01t0104100-02	Os01t0104100-02	N/A	N/A
+1	irgsp	CDS	212265	212352	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104100-02	N/A	N/A	transcript:Os01t0104100-02	Os01t0104100-02	N/A	N/A
+1	irgsp	CDS	212433	212579	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104100-02	N/A	N/A	transcript:Os01t0104100-02	Os01t0104100-02	N/A	N/A
+1	irgsp	CDS	213490	213639	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104100-02	N/A	N/A	transcript:Os01t0104100-02	Os01t0104100-02	N/A	N/A
+1	irgsp	CDS	213741	213788	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104100-02	N/A	N/A	transcript:Os01t0104100-02	Os01t0104100-02	N/A	N/A
+1	irgsp	five_prime_UTR	209794	209794	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-52	N/A	N/A	transcript:Os01t0104100-02	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	213789	214147	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-50	N/A	N/A	transcript:Os01t0104100-02	N/A	N/A	N/A
+1	irgsp	gene	216212	217345	.	1	.	N/A	protein_coding	N/A	No apical meristem (NAM) protein domain containing protein. (Os01t0104200-00)	N/A	N/A	N/A	Os01g0104200	gene:Os01g0104200	irgspv1.0-20170804-genes	NAC DOMAIN-CONTAINING PROTEIN 16	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	216212	217345	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0104200-00	N/A	N/A	gene:Os01g0104200	N/A	N/A	Os01t0104200-00
+1	irgsp	exon	216212	216769	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0104200-00.exon1	N/A	Os01t0104200-00.exon1	N/A	Os01t0104200-00.exon1	transcript:Os01t0104200-00	N/A	1	N/A
+1	irgsp	exon	216884	217345	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0104200-00.exon2	N/A	Os01t0104200-00.exon2	N/A	Os01t0104200-00.exon2	transcript:Os01t0104200-00	N/A	2	N/A
+1	irgsp	CDS	216212	216769	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104200-00	N/A	N/A	transcript:Os01t0104200-00	Os01t0104200-00	N/A	N/A
+1	irgsp	CDS	216884	217345	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104200-00	N/A	N/A	transcript:Os01t0104200-00	Os01t0104200-00	N/A	N/A
+1	irgsp	gene	226897	229301	.	1	.	N/A	protein_coding	N/A	Ricin B-related lectin domain containing protein. (Os01t0104400-01);Ricin B-related lectin domain containing protein. (Os01t0104400-02);Ricin B-related lectin domain containing protein. (Os01t0104400-03)	N/A	N/A	N/A	Os01g0104400	gene:Os01g0104400	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	226897	229229	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0104400-01	N/A	N/A	gene:Os01g0104400	N/A	N/A	Os01t0104400-01
+1	irgsp	exon	226897	227634	.	1	.	N/A	N/A	0	N/A	0	-1	Os01t0104400-01.exon1	N/A	Os01t0104400-01.exon1	N/A	Os01t0104400-01.exon1	transcript:Os01t0104400-01	N/A	1	N/A
+1	irgsp	exon	227742	227864	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0104400-03.exon2	N/A	Os01t0104400-03.exon2	N/A	Os01t0104400-03.exon2	transcript:Os01t0104400-01	N/A	2	N/A
+1	irgsp	exon	228557	228785	.	1	.	N/A	N/A	1	N/A	1	0	Os01t0104400-03.exon3	N/A	Os01t0104400-03.exon3	N/A	Os01t0104400-03.exon3	transcript:Os01t0104400-01	N/A	3	N/A
+1	irgsp	exon	228930	229229	.	1	.	N/A	N/A	0	N/A	-1	1	Os01t0104400-01.exon4	N/A	Os01t0104400-01.exon4	N/A	Os01t0104400-01.exon4	transcript:Os01t0104400-01	N/A	4	N/A
+1	irgsp	CDS	227182	227634	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104400-01	N/A	N/A	transcript:Os01t0104400-01	Os01t0104400-01	N/A	N/A
+1	irgsp	CDS	227742	227864	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104400-01	N/A	N/A	transcript:Os01t0104400-01	Os01t0104400-01	N/A	N/A
+1	irgsp	CDS	228557	228785	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104400-01	N/A	N/A	transcript:Os01t0104400-01	Os01t0104400-01	N/A	N/A
+1	irgsp	CDS	228930	228931	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104400-01	N/A	N/A	transcript:Os01t0104400-01	Os01t0104400-01	N/A	N/A
+1	irgsp	five_prime_UTR	226897	227181	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-53	N/A	N/A	transcript:Os01t0104400-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	228932	229229	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-51	N/A	N/A	transcript:Os01t0104400-01	N/A	N/A	N/A
+1	irgsp	mRNA	227139	229301	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0104400-02	N/A	N/A	gene:Os01g0104400	N/A	N/A	Os01t0104400-02
+1	irgsp	exon	227139	227634	.	1	.	N/A	N/A	0	N/A	0	-1	Os01t0104400-02.exon1	N/A	Os01t0104400-02.exon1	N/A	Os01t0104400-02.exon1	transcript:Os01t0104400-02	N/A	1	N/A
+1	irgsp	exon	227742	227864	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0104400-03.exon2	N/A	agat-exon-13	N/A	Os01t0104400-03.exon2	transcript:Os01t0104400-02	N/A	2	N/A
+1	irgsp	exon	228557	228785	.	1	.	N/A	N/A	1	N/A	1	0	Os01t0104400-03.exon3	N/A	agat-exon-14	N/A	Os01t0104400-03.exon3	transcript:Os01t0104400-02	N/A	3	N/A
+1	irgsp	exon	228930	229301	.	1	.	N/A	N/A	0	N/A	-1	1	Os01t0104400-02.exon4	N/A	Os01t0104400-02.exon4	N/A	Os01t0104400-02.exon4	transcript:Os01t0104400-02	N/A	4	N/A
+1	irgsp	CDS	227182	227634	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104400-02	N/A	N/A	transcript:Os01t0104400-02	Os01t0104400-02	N/A	N/A
+1	irgsp	CDS	227742	227864	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104400-02	N/A	N/A	transcript:Os01t0104400-02	Os01t0104400-02	N/A	N/A
+1	irgsp	CDS	228557	228785	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104400-02	N/A	N/A	transcript:Os01t0104400-02	Os01t0104400-02	N/A	N/A
+1	irgsp	CDS	228930	228931	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104400-02	N/A	N/A	transcript:Os01t0104400-02	Os01t0104400-02	N/A	N/A
+1	irgsp	five_prime_UTR	227139	227181	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-54	N/A	N/A	transcript:Os01t0104400-02	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	228932	229301	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-52	N/A	N/A	transcript:Os01t0104400-02	N/A	N/A	N/A
+1	irgsp	mRNA	227179	229214	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0104400-03	N/A	N/A	gene:Os01g0104400	N/A	N/A	Os01t0104400-03
+1	irgsp	exon	227179	227634	.	1	.	N/A	N/A	0	N/A	0	-1	Os01t0104400-03.exon1	N/A	Os01t0104400-03.exon1	N/A	Os01t0104400-03.exon1	transcript:Os01t0104400-03	N/A	1	N/A
+1	irgsp	exon	227742	227864	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0104400-03.exon2	N/A	agat-exon-15	N/A	Os01t0104400-03.exon2	transcript:Os01t0104400-03	N/A	2	N/A
+1	irgsp	exon	228557	228785	.	1	.	N/A	N/A	1	N/A	1	0	Os01t0104400-03.exon3	N/A	agat-exon-16	N/A	Os01t0104400-03.exon3	transcript:Os01t0104400-03	N/A	3	N/A
+1	irgsp	exon	228930	229214	.	1	.	N/A	N/A	0	N/A	-1	1	Os01t0104400-03.exon4	N/A	Os01t0104400-03.exon4	N/A	Os01t0104400-03.exon4	transcript:Os01t0104400-03	N/A	4	N/A
+1	irgsp	CDS	227182	227634	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104400-03	N/A	N/A	transcript:Os01t0104400-03	Os01t0104400-03	N/A	N/A
+1	irgsp	CDS	227742	227864	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104400-03	N/A	N/A	transcript:Os01t0104400-03	Os01t0104400-03	N/A	N/A
+1	irgsp	CDS	228557	228785	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104400-03	N/A	N/A	transcript:Os01t0104400-03	Os01t0104400-03	N/A	N/A
+1	irgsp	CDS	228930	228931	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104400-03	N/A	N/A	transcript:Os01t0104400-03	Os01t0104400-03	N/A	N/A
+1	irgsp	five_prime_UTR	227179	227181	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-55	N/A	N/A	transcript:Os01t0104400-03	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	228932	229214	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-53	N/A	N/A	transcript:Os01t0104400-03	N/A	N/A	N/A
+1	irgsp	gene	241680	243440	.	1	.	N/A	protein_coding	N/A	No apical meristem (NAM) protein domain containing protein. (Os01t0104500-01)	N/A	N/A	N/A	Os01g0104500	gene:Os01g0104500	irgspv1.0-20170804-genes	NAC DOMAIN-CONTAINING PROTEIN 20	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	241680	243440	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0104500-01	N/A	N/A	gene:Os01g0104500	N/A	N/A	Os01t0104500-01
+1	irgsp	exon	241680	241702	.	1	.	N/A	N/A	1	N/A	-1	-1	Os01t0104500-01.exon1	N/A	Os01t0104500-01.exon1	N/A	Os01t0104500-01.exon1	transcript:Os01t0104500-01	N/A	1	N/A
+1	irgsp	exon	241866	242091	.	1	.	N/A	N/A	1	N/A	1	-1	Os01t0104500-01.exon2	N/A	Os01t0104500-01.exon2	N/A	Os01t0104500-01.exon2	transcript:Os01t0104500-01	N/A	2	N/A
+1	irgsp	exon	242199	243440	.	1	.	N/A	N/A	1	N/A	-1	1	Os01t0104500-01.exon3	N/A	Os01t0104500-01.exon3	N/A	Os01t0104500-01.exon3	transcript:Os01t0104500-01	N/A	3	N/A
+1	irgsp	CDS	241908	242091	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104500-01	N/A	N/A	transcript:Os01t0104500-01	Os01t0104500-01	N/A	N/A
+1	irgsp	CDS	242199	242977	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104500-01	N/A	N/A	transcript:Os01t0104500-01	Os01t0104500-01	N/A	N/A
+1	irgsp	five_prime_UTR	241680	241702	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-56	N/A	N/A	transcript:Os01t0104500-01	N/A	N/A	N/A
+1	irgsp	five_prime_UTR	241866	241907	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-57	N/A	N/A	transcript:Os01t0104500-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	242978	243440	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-54	N/A	N/A	transcript:Os01t0104500-01	N/A	N/A	N/A
+1	irgsp	gene	248828	256872	.	-1	.	N/A	protein_coding	N/A	Homolog of Arabidopsis DE-ETIOLATED1 (DET1), Modulation of the ABA signaling pathway and ABA biosynthesis, Regulation of chlorophyll content (Os01t0104600-01);Similar to Light-mediated development protein DET1 (Deetiolated1 homolog) (tDET1) (High pigmentation protein 2) (Protein dark green). (Os01t0104600-02)	N/A	N/A	N/A	Os01g0104600	gene:Os01g0104600	irgspv1.0-20170804-genes	DE-ETIOLATED1	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	248828	256571	.	-1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0104600-02	N/A	N/A	gene:Os01g0104600	N/A	N/A	Os01t0104600-02
+1	irgsp	exon	248828	249107	.	-1	.	N/A	N/A	1	N/A	-1	1	Os01t0104600-01.exon11	N/A	Os01t0104600-01.exon11	N/A	Os01t0104600-01.exon11	transcript:Os01t0104600-02	N/A	11	N/A
+1	irgsp	exon	249369	249468	.	-1	.	N/A	N/A	1	N/A	1	0	Os01t0104600-01.exon10	N/A	Os01t0104600-01.exon10	N/A	Os01t0104600-01.exon10	transcript:Os01t0104600-02	N/A	10	N/A
+1	irgsp	exon	249861	249956	.	-1	.	N/A	N/A	1	N/A	0	0	Os01t0104600-01.exon9	N/A	Os01t0104600-01.exon9	N/A	Os01t0104600-01.exon9	transcript:Os01t0104600-02	N/A	9	N/A
+1	irgsp	exon	250617	250781	.	-1	.	N/A	N/A	1	N/A	0	0	Os01t0104600-01.exon8	N/A	Os01t0104600-01.exon8	N/A	Os01t0104600-01.exon8	transcript:Os01t0104600-02	N/A	8	N/A
+1	irgsp	exon	250860	250940	.	-1	.	N/A	N/A	1	N/A	0	0	Os01t0104600-01.exon7	N/A	Os01t0104600-01.exon7	N/A	Os01t0104600-01.exon7	transcript:Os01t0104600-02	N/A	7	N/A
+1	irgsp	exon	251026	251082	.	-1	.	N/A	N/A	1	N/A	0	0	Os01t0104600-01.exon6	N/A	Os01t0104600-01.exon6	N/A	Os01t0104600-01.exon6	transcript:Os01t0104600-02	N/A	6	N/A
+1	irgsp	exon	251316	251384	.	-1	.	N/A	N/A	1	N/A	0	0	Os01t0104600-01.exon5	N/A	Os01t0104600-01.exon5	N/A	Os01t0104600-01.exon5	transcript:Os01t0104600-02	N/A	5	N/A
+1	irgsp	exon	251695	251790	.	-1	.	N/A	N/A	1	N/A	0	0	Os01t0104600-01.exon4	N/A	Os01t0104600-01.exon4	N/A	Os01t0104600-01.exon4	transcript:Os01t0104600-02	N/A	4	N/A
+1	irgsp	exon	255325	255553	.	-1	.	N/A	N/A	1	N/A	0	2	Os01t0104600-01.exon3	N/A	Os01t0104600-01.exon3	N/A	Os01t0104600-01.exon3	transcript:Os01t0104600-02	N/A	3	N/A
+1	irgsp	exon	255674	256098	.	-1	.	N/A	N/A	1	N/A	2	0	Os01t0104600-01.exon2	N/A	Os01t0104600-01.exon2	N/A	Os01t0104600-01.exon2	transcript:Os01t0104600-02	N/A	2	N/A
+1	irgsp	exon	256361	256571	.	-1	.	N/A	N/A	0	N/A	0	-1	Os01t0104600-02.exon1	N/A	Os01t0104600-02.exon1	N/A	Os01t0104600-02.exon1	transcript:Os01t0104600-02	N/A	1	N/A
+1	irgsp	CDS	248971	249107	.	-1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104600-02	N/A	N/A	transcript:Os01t0104600-02	Os01t0104600-02	N/A	N/A
+1	irgsp	CDS	249369	249468	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104600-02	N/A	N/A	transcript:Os01t0104600-02	Os01t0104600-02	N/A	N/A
+1	irgsp	CDS	249861	249956	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104600-02	N/A	N/A	transcript:Os01t0104600-02	Os01t0104600-02	N/A	N/A
+1	irgsp	CDS	250617	250781	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104600-02	N/A	N/A	transcript:Os01t0104600-02	Os01t0104600-02	N/A	N/A
+1	irgsp	CDS	250860	250940	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104600-02	N/A	N/A	transcript:Os01t0104600-02	Os01t0104600-02	N/A	N/A
+1	irgsp	CDS	251026	251082	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104600-02	N/A	N/A	transcript:Os01t0104600-02	Os01t0104600-02	N/A	N/A
+1	irgsp	CDS	251316	251384	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104600-02	N/A	N/A	transcript:Os01t0104600-02	Os01t0104600-02	N/A	N/A
+1	irgsp	CDS	251695	251790	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104600-02	N/A	N/A	transcript:Os01t0104600-02	Os01t0104600-02	N/A	N/A
+1	irgsp	CDS	255325	255553	.	-1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104600-02	N/A	N/A	transcript:Os01t0104600-02	Os01t0104600-02	N/A	N/A
+1	irgsp	CDS	255674	256098	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104600-02	N/A	N/A	transcript:Os01t0104600-02	Os01t0104600-02	N/A	N/A
+1	irgsp	CDS	256361	256441	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104600-02	N/A	N/A	transcript:Os01t0104600-02	Os01t0104600-02	N/A	N/A
+1	irgsp	five_prime_UTR	256442	256571	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-58	N/A	N/A	transcript:Os01t0104600-02	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	248828	248970	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-55	N/A	N/A	transcript:Os01t0104600-02	N/A	N/A	N/A
+1	irgsp	mRNA	248828	256872	.	-1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0104600-01	N/A	N/A	gene:Os01g0104600	N/A	N/A	Os01t0104600-01
+1	irgsp	exon	248828	249107	.	-1	.	N/A	N/A	1	N/A	-1	1	Os01t0104600-01.exon11	N/A	agat-exon-17	N/A	Os01t0104600-01.exon11	transcript:Os01t0104600-01	N/A	11	N/A
+1	irgsp	exon	249369	249468	.	-1	.	N/A	N/A	1	N/A	1	0	Os01t0104600-01.exon10	N/A	agat-exon-18	N/A	Os01t0104600-01.exon10	transcript:Os01t0104600-01	N/A	10	N/A
+1	irgsp	exon	249861	249956	.	-1	.	N/A	N/A	1	N/A	0	0	Os01t0104600-01.exon9	N/A	agat-exon-19	N/A	Os01t0104600-01.exon9	transcript:Os01t0104600-01	N/A	9	N/A
+1	irgsp	exon	250617	250781	.	-1	.	N/A	N/A	1	N/A	0	0	Os01t0104600-01.exon8	N/A	agat-exon-20	N/A	Os01t0104600-01.exon8	transcript:Os01t0104600-01	N/A	8	N/A
+1	irgsp	exon	250860	250940	.	-1	.	N/A	N/A	1	N/A	0	0	Os01t0104600-01.exon7	N/A	agat-exon-21	N/A	Os01t0104600-01.exon7	transcript:Os01t0104600-01	N/A	7	N/A
+1	irgsp	exon	251026	251082	.	-1	.	N/A	N/A	1	N/A	0	0	Os01t0104600-01.exon6	N/A	agat-exon-22	N/A	Os01t0104600-01.exon6	transcript:Os01t0104600-01	N/A	6	N/A
+1	irgsp	exon	251316	251384	.	-1	.	N/A	N/A	1	N/A	0	0	Os01t0104600-01.exon5	N/A	agat-exon-23	N/A	Os01t0104600-01.exon5	transcript:Os01t0104600-01	N/A	5	N/A
+1	irgsp	exon	251695	251790	.	-1	.	N/A	N/A	1	N/A	0	0	Os01t0104600-01.exon4	N/A	agat-exon-24	N/A	Os01t0104600-01.exon4	transcript:Os01t0104600-01	N/A	4	N/A
+1	irgsp	exon	255325	255553	.	-1	.	N/A	N/A	1	N/A	0	2	Os01t0104600-01.exon3	N/A	agat-exon-25	N/A	Os01t0104600-01.exon3	transcript:Os01t0104600-01	N/A	3	N/A
+1	irgsp	exon	255674	256098	.	-1	.	N/A	N/A	1	N/A	2	0	Os01t0104600-01.exon2	N/A	agat-exon-26	N/A	Os01t0104600-01.exon2	transcript:Os01t0104600-01	N/A	2	N/A
+1	irgsp	exon	256361	256872	.	-1	.	N/A	N/A	0	N/A	0	-1	Os01t0104600-01.exon1	N/A	Os01t0104600-01.exon1	N/A	Os01t0104600-01.exon1	transcript:Os01t0104600-01	N/A	1	N/A
+1	irgsp	CDS	248971	249107	.	-1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104600-01	N/A	N/A	transcript:Os01t0104600-01	Os01t0104600-01	N/A	N/A
+1	irgsp	CDS	249369	249468	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104600-01	N/A	N/A	transcript:Os01t0104600-01	Os01t0104600-01	N/A	N/A
+1	irgsp	CDS	249861	249956	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104600-01	N/A	N/A	transcript:Os01t0104600-01	Os01t0104600-01	N/A	N/A
+1	irgsp	CDS	250617	250781	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104600-01	N/A	N/A	transcript:Os01t0104600-01	Os01t0104600-01	N/A	N/A
+1	irgsp	CDS	250860	250940	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104600-01	N/A	N/A	transcript:Os01t0104600-01	Os01t0104600-01	N/A	N/A
+1	irgsp	CDS	251026	251082	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104600-01	N/A	N/A	transcript:Os01t0104600-01	Os01t0104600-01	N/A	N/A
+1	irgsp	CDS	251316	251384	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104600-01	N/A	N/A	transcript:Os01t0104600-01	Os01t0104600-01	N/A	N/A
+1	irgsp	CDS	251695	251790	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104600-01	N/A	N/A	transcript:Os01t0104600-01	Os01t0104600-01	N/A	N/A
+1	irgsp	CDS	255325	255553	.	-1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104600-01	N/A	N/A	transcript:Os01t0104600-01	Os01t0104600-01	N/A	N/A
+1	irgsp	CDS	255674	256098	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104600-01	N/A	N/A	transcript:Os01t0104600-01	Os01t0104600-01	N/A	N/A
+1	irgsp	CDS	256361	256441	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104600-01	N/A	N/A	transcript:Os01t0104600-01	Os01t0104600-01	N/A	N/A
+1	irgsp	five_prime_UTR	256442	256872	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-59	N/A	N/A	transcript:Os01t0104600-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	248828	248970	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-56	N/A	N/A	transcript:Os01t0104600-01	N/A	N/A	N/A
+1	irgsp	gene	261530	268145	.	1	.	N/A	protein_coding	N/A	Sas10/Utp3 family protein. (Os01t0104800-01);Hypothetical conserved gene. (Os01t0104800-02)	N/A	N/A	N/A	Os01g0104800	gene:Os01g0104800	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	261530	268145	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0104800-01	N/A	N/A	gene:Os01g0104800	N/A	N/A	Os01t0104800-01
+1	irgsp	exon	261530	261661	.	1	.	N/A	N/A	0	N/A	1	-1	Os01t0104800-01.exon1	N/A	Os01t0104800-01.exon1	N/A	Os01t0104800-01.exon1	transcript:Os01t0104800-01	N/A	1	N/A
+1	irgsp	exon	261767	261805	.	1	.	N/A	N/A	0	N/A	1	1	Os01t0104800-01.exon2	N/A	Os01t0104800-01.exon2	N/A	Os01t0104800-01.exon2	transcript:Os01t0104800-01	N/A	2	N/A
+1	irgsp	exon	261895	261941	.	1	.	N/A	N/A	0	N/A	0	1	Os01t0104800-01.exon3	N/A	Os01t0104800-01.exon3	N/A	Os01t0104800-01.exon3	transcript:Os01t0104800-01	N/A	3	N/A
+1	irgsp	exon	262582	262681	.	1	.	N/A	N/A	0	N/A	1	0	Os01t0104800-01.exon4	N/A	Os01t0104800-01.exon4	N/A	Os01t0104800-01.exon4	transcript:Os01t0104800-01	N/A	4	N/A
+1	irgsp	exon	262925	263181	.	1	.	N/A	N/A	0	N/A	0	1	Os01t0104800-01.exon5	N/A	Os01t0104800-01.exon5	N/A	Os01t0104800-01.exon5	transcript:Os01t0104800-01	N/A	5	N/A
+1	irgsp	exon	263525	263640	.	1	.	N/A	N/A	0	N/A	2	0	Os01t0104800-01.exon6	N/A	Os01t0104800-01.exon6	N/A	Os01t0104800-01.exon6	transcript:Os01t0104800-01	N/A	6	N/A
+1	irgsp	exon	264014	264098	.	1	.	N/A	N/A	1	N/A	0	2	Os01t0104800-01.exon7	N/A	Os01t0104800-01.exon7	N/A	Os01t0104800-01.exon7	transcript:Os01t0104800-01	N/A	7	N/A
+1	irgsp	exon	265236	265415	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0104800-01.exon8	N/A	Os01t0104800-01.exon8	N/A	Os01t0104800-01.exon8	transcript:Os01t0104800-01	N/A	8	N/A
+1	irgsp	exon	265506	265649	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0104800-01.exon9	N/A	Os01t0104800-01.exon9	N/A	Os01t0104800-01.exon9	transcript:Os01t0104800-01	N/A	9	N/A
+1	irgsp	exon	265740	265817	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0104800-01.exon10	N/A	Os01t0104800-01.exon10	N/A	Os01t0104800-01.exon10	transcript:Os01t0104800-01	N/A	10	N/A
+1	irgsp	exon	265909	266045	.	1	.	N/A	N/A	1	N/A	2	0	Os01t0104800-01.exon11	N/A	Os01t0104800-01.exon11	N/A	Os01t0104800-01.exon11	transcript:Os01t0104800-01	N/A	11	N/A
+1	irgsp	exon	266138	266246	.	1	.	N/A	N/A	1	N/A	0	2	Os01t0104800-01.exon12	N/A	Os01t0104800-01.exon12	N/A	Os01t0104800-01.exon12	transcript:Os01t0104800-01	N/A	12	N/A
+1	irgsp	exon	267237	267514	.	1	.	N/A	N/A	1	N/A	2	0	Os01t0104800-01.exon13	N/A	Os01t0104800-01.exon13	N/A	Os01t0104800-01.exon13	transcript:Os01t0104800-01	N/A	13	N/A
+1	irgsp	exon	267591	267657	.	1	.	N/A	N/A	1	N/A	0	2	Os01t0104800-01.exon14	N/A	Os01t0104800-01.exon14	N/A	Os01t0104800-01.exon14	transcript:Os01t0104800-01	N/A	14	N/A
+1	irgsp	exon	267734	267802	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0104800-01.exon15	N/A	Os01t0104800-01.exon15	N/A	Os01t0104800-01.exon15	transcript:Os01t0104800-01	N/A	15	N/A
+1	irgsp	exon	267880	268145	.	1	.	N/A	N/A	0	N/A	-1	0	Os01t0104800-01.exon16	N/A	Os01t0104800-01.exon16	N/A	Os01t0104800-01.exon16	transcript:Os01t0104800-01	N/A	16	N/A
+1	irgsp	CDS	261562	261661	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104800-01	N/A	N/A	transcript:Os01t0104800-01	Os01t0104800-01	N/A	N/A
+1	irgsp	CDS	261767	261805	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104800-01	N/A	N/A	transcript:Os01t0104800-01	Os01t0104800-01	N/A	N/A
+1	irgsp	CDS	261895	261941	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104800-01	N/A	N/A	transcript:Os01t0104800-01	Os01t0104800-01	N/A	N/A
+1	irgsp	CDS	262582	262681	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104800-01	N/A	N/A	transcript:Os01t0104800-01	Os01t0104800-01	N/A	N/A
+1	irgsp	CDS	262925	263181	.	1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104800-01	N/A	N/A	transcript:Os01t0104800-01	Os01t0104800-01	N/A	N/A
+1	irgsp	CDS	263525	263640	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104800-01	N/A	N/A	transcript:Os01t0104800-01	Os01t0104800-01	N/A	N/A
+1	irgsp	CDS	264014	264098	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104800-01	N/A	N/A	transcript:Os01t0104800-01	Os01t0104800-01	N/A	N/A
+1	irgsp	CDS	265236	265415	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104800-01	N/A	N/A	transcript:Os01t0104800-01	Os01t0104800-01	N/A	N/A
+1	irgsp	CDS	265506	265649	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104800-01	N/A	N/A	transcript:Os01t0104800-01	Os01t0104800-01	N/A	N/A
+1	irgsp	CDS	265740	265817	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104800-01	N/A	N/A	transcript:Os01t0104800-01	Os01t0104800-01	N/A	N/A
+1	irgsp	CDS	265909	266045	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104800-01	N/A	N/A	transcript:Os01t0104800-01	Os01t0104800-01	N/A	N/A
+1	irgsp	CDS	266138	266246	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104800-01	N/A	N/A	transcript:Os01t0104800-01	Os01t0104800-01	N/A	N/A
+1	irgsp	CDS	267237	267514	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104800-01	N/A	N/A	transcript:Os01t0104800-01	Os01t0104800-01	N/A	N/A
+1	irgsp	CDS	267591	267657	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104800-01	N/A	N/A	transcript:Os01t0104800-01	Os01t0104800-01	N/A	N/A
+1	irgsp	CDS	267734	267802	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104800-01	N/A	N/A	transcript:Os01t0104800-01	Os01t0104800-01	N/A	N/A
+1	irgsp	CDS	267880	268011	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104800-01	N/A	N/A	transcript:Os01t0104800-01	Os01t0104800-01	N/A	N/A
+1	irgsp	five_prime_UTR	261530	261561	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-60	N/A	N/A	transcript:Os01t0104800-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	268012	268145	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-57	N/A	N/A	transcript:Os01t0104800-01	N/A	N/A	N/A
+1	irgsp	mRNA	263523	268120	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0104800-02	N/A	N/A	gene:Os01g0104800	N/A	N/A	Os01t0104800-02
+1	irgsp	exon	263523	263640	.	1	.	N/A	N/A	0	N/A	2	-1	Os01t0104800-02.exon1	N/A	Os01t0104800-02.exon1	N/A	Os01t0104800-02.exon1	transcript:Os01t0104800-02	N/A	1	N/A
+1	irgsp	exon	264014	264098	.	1	.	N/A	N/A	1	N/A	0	2	Os01t0104800-01.exon7	N/A	agat-exon-27	N/A	Os01t0104800-01.exon7	transcript:Os01t0104800-02	N/A	2	N/A
+1	irgsp	exon	265236	265415	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0104800-01.exon8	N/A	agat-exon-28	N/A	Os01t0104800-01.exon8	transcript:Os01t0104800-02	N/A	3	N/A
+1	irgsp	exon	265506	265649	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0104800-01.exon9	N/A	agat-exon-29	N/A	Os01t0104800-01.exon9	transcript:Os01t0104800-02	N/A	4	N/A
+1	irgsp	exon	265740	265817	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0104800-01.exon10	N/A	agat-exon-30	N/A	Os01t0104800-01.exon10	transcript:Os01t0104800-02	N/A	5	N/A
+1	irgsp	exon	265909	266045	.	1	.	N/A	N/A	1	N/A	2	0	Os01t0104800-01.exon11	N/A	agat-exon-31	N/A	Os01t0104800-01.exon11	transcript:Os01t0104800-02	N/A	6	N/A
+1	irgsp	exon	266138	266246	.	1	.	N/A	N/A	1	N/A	0	2	Os01t0104800-01.exon12	N/A	agat-exon-32	N/A	Os01t0104800-01.exon12	transcript:Os01t0104800-02	N/A	7	N/A
+1	irgsp	exon	267237	267514	.	1	.	N/A	N/A	1	N/A	2	0	Os01t0104800-01.exon13	N/A	agat-exon-33	N/A	Os01t0104800-01.exon13	transcript:Os01t0104800-02	N/A	8	N/A
+1	irgsp	exon	267591	267657	.	1	.	N/A	N/A	1	N/A	0	2	Os01t0104800-01.exon14	N/A	agat-exon-34	N/A	Os01t0104800-01.exon14	transcript:Os01t0104800-02	N/A	9	N/A
+1	irgsp	exon	267734	267802	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0104800-01.exon15	N/A	agat-exon-35	N/A	Os01t0104800-01.exon15	transcript:Os01t0104800-02	N/A	10	N/A
+1	irgsp	exon	267880	268120	.	1	.	N/A	N/A	0	N/A	-1	0	Os01t0104800-02.exon11	N/A	Os01t0104800-02.exon11	N/A	Os01t0104800-02.exon11	transcript:Os01t0104800-02	N/A	11	N/A
+1	irgsp	CDS	263525	263640	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104800-02	N/A	N/A	transcript:Os01t0104800-02	Os01t0104800-02	N/A	N/A
+1	irgsp	CDS	264014	264098	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104800-02	N/A	N/A	transcript:Os01t0104800-02	Os01t0104800-02	N/A	N/A
+1	irgsp	CDS	265236	265415	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104800-02	N/A	N/A	transcript:Os01t0104800-02	Os01t0104800-02	N/A	N/A
+1	irgsp	CDS	265506	265649	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104800-02	N/A	N/A	transcript:Os01t0104800-02	Os01t0104800-02	N/A	N/A
+1	irgsp	CDS	265740	265817	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104800-02	N/A	N/A	transcript:Os01t0104800-02	Os01t0104800-02	N/A	N/A
+1	irgsp	CDS	265909	266045	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104800-02	N/A	N/A	transcript:Os01t0104800-02	Os01t0104800-02	N/A	N/A
+1	irgsp	CDS	266138	266246	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104800-02	N/A	N/A	transcript:Os01t0104800-02	Os01t0104800-02	N/A	N/A
+1	irgsp	CDS	267237	267514	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104800-02	N/A	N/A	transcript:Os01t0104800-02	Os01t0104800-02	N/A	N/A
+1	irgsp	CDS	267591	267657	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104800-02	N/A	N/A	transcript:Os01t0104800-02	Os01t0104800-02	N/A	N/A
+1	irgsp	CDS	267734	267802	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104800-02	N/A	N/A	transcript:Os01t0104800-02	Os01t0104800-02	N/A	N/A
+1	irgsp	CDS	267880	268011	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104800-02	N/A	N/A	transcript:Os01t0104800-02	Os01t0104800-02	N/A	N/A
+1	irgsp	five_prime_UTR	263523	263524	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-61	N/A	N/A	transcript:Os01t0104800-02	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	268012	268120	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-58	N/A	N/A	transcript:Os01t0104800-02	N/A	N/A	N/A
+1	irgsp	gene	270179	275084	.	-1	.	N/A	protein_coding	N/A	Transferase family protein. (Os01t0104900-01);Hypothetical conserved gene. (Os01t0104900-02)	N/A	N/A	N/A	Os01g0104900	gene:Os01g0104900	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	270179	275084	.	-1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0104900-01	N/A	N/A	gene:Os01g0104900	N/A	N/A	Os01t0104900-01
+1	irgsp	exon	270179	271333	.	-1	.	N/A	N/A	0	N/A	-1	0	Os01t0104900-01.exon2	N/A	Os01t0104900-01.exon2	N/A	Os01t0104900-01.exon2	transcript:Os01t0104900-01	N/A	2	N/A
+1	irgsp	exon	274529	275084	.	-1	.	N/A	N/A	0	N/A	0	-1	Os01t0104900-01.exon1	N/A	Os01t0104900-01.exon1	N/A	Os01t0104900-01.exon1	transcript:Os01t0104900-01	N/A	1	N/A
+1	irgsp	CDS	270356	271333	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104900-01	N/A	N/A	transcript:Os01t0104900-01	Os01t0104900-01	N/A	N/A
+1	irgsp	CDS	274529	274957	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104900-01	N/A	N/A	transcript:Os01t0104900-01	Os01t0104900-01	N/A	N/A
+1	irgsp	five_prime_UTR	274958	275084	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-62	N/A	N/A	transcript:Os01t0104900-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	270179	270355	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-59	N/A	N/A	transcript:Os01t0104900-01	N/A	N/A	N/A
+1	irgsp	mRNA	270250	271518	.	-1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0104900-02	N/A	N/A	gene:Os01g0104900	N/A	N/A	Os01t0104900-02
+1	irgsp	exon	270250	271333	.	-1	.	N/A	N/A	0	N/A	-1	-1	Os01t0104900-02.exon2	N/A	Os01t0104900-02.exon2	N/A	Os01t0104900-02.exon2	transcript:Os01t0104900-02	N/A	2	N/A
+1	irgsp	exon	271457	271518	.	-1	.	N/A	N/A	0	N/A	-1	-1	Os01t0104900-02.exon1	N/A	Os01t0104900-02.exon1	N/A	Os01t0104900-02.exon1	transcript:Os01t0104900-02	N/A	1	N/A
+1	irgsp	CDS	270356	271309	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0104900-02	N/A	N/A	transcript:Os01t0104900-02	Os01t0104900-02	N/A	N/A
+1	irgsp	five_prime_UTR	271310	271333	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-63	N/A	N/A	transcript:Os01t0104900-02	N/A	N/A	N/A
+1	irgsp	five_prime_UTR	271457	271518	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-64	N/A	N/A	transcript:Os01t0104900-02	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	270250	270355	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-60	N/A	N/A	transcript:Os01t0104900-02	N/A	N/A	N/A
+1	irgsp	gene	284762	291892	.	-1	.	N/A	protein_coding	N/A	Similar to HAT family dimerisation domain containing protein, expressed. (Os01t0105300-01)	N/A	N/A	N/A	Os01g0105300	gene:Os01g0105300	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	284762	291892	.	-1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0105300-01	N/A	N/A	gene:Os01g0105300	N/A	N/A	Os01t0105300-01
+1	irgsp	exon	284762	287047	.	-1	.	N/A	N/A	1	N/A	-1	-1	Os01t0105300-01.exon5	N/A	Os01t0105300-01.exon5	N/A	Os01t0105300-01.exon5	transcript:Os01t0105300-01	N/A	5	N/A
+1	irgsp	exon	291398	291436	.	-1	.	N/A	N/A	1	N/A	-1	-1	Os01t0105300-01.exon4	N/A	Os01t0105300-01.exon4	N/A	Os01t0105300-01.exon4	transcript:Os01t0105300-01	N/A	4	N/A
+1	irgsp	exon	291520	291534	.	-1	.	N/A	N/A	1	N/A	-1	-1	Os01t0105300-01.exon3	N/A	Os01t0105300-01.exon3	N/A	Os01t0105300-01.exon3	transcript:Os01t0105300-01	N/A	3	N/A
+1	irgsp	exon	291678	291738	.	-1	.	N/A	N/A	1	N/A	-1	-1	Os01t0105300-01.exon2	N/A	Os01t0105300-01.exon2	N/A	Os01t0105300-01.exon2	transcript:Os01t0105300-01	N/A	2	N/A
+1	irgsp	exon	291838	291892	.	-1	.	N/A	N/A	1	N/A	-1	-1	Os01t0105300-01.exon1	N/A	Os01t0105300-01.exon1	N/A	Os01t0105300-01.exon1	transcript:Os01t0105300-01	N/A	1	N/A
+1	irgsp	CDS	284931	285020	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0105300-01	N/A	N/A	transcript:Os01t0105300-01	Os01t0105300-01	N/A	N/A
+1	irgsp	five_prime_UTR	285021	287047	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-65	N/A	N/A	transcript:Os01t0105300-01	N/A	N/A	N/A
+1	irgsp	five_prime_UTR	291398	291436	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-66	N/A	N/A	transcript:Os01t0105300-01	N/A	N/A	N/A
+1	irgsp	five_prime_UTR	291520	291534	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-67	N/A	N/A	transcript:Os01t0105300-01	N/A	N/A	N/A
+1	irgsp	five_prime_UTR	291678	291738	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-68	N/A	N/A	transcript:Os01t0105300-01	N/A	N/A	N/A
+1	irgsp	five_prime_UTR	291838	291892	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-69	N/A	N/A	transcript:Os01t0105300-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	284762	284930	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-61	N/A	N/A	transcript:Os01t0105300-01	N/A	N/A	N/A
+1	irgsp	gene	288372	292296	.	1	.	N/A	protein_coding	N/A	Similar to Kinesin heavy chain. (Os01t0105400-01)	N/A	N/A	N/A	Os01g0105400	gene:Os01g0105400	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	288372	292296	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0105400-01	N/A	N/A	gene:Os01g0105400	N/A	N/A	Os01t0105400-01
+1	irgsp	exon	288372	288846	.	1	.	N/A	N/A	1	N/A	-1	-1	Os01t0105400-01.exon1	N/A	Os01t0105400-01.exon1	N/A	Os01t0105400-01.exon1	transcript:Os01t0105400-01	N/A	1	N/A
+1	irgsp	exon	288950	289116	.	1	.	N/A	N/A	1	N/A	-1	-1	Os01t0105400-01.exon2	N/A	Os01t0105400-01.exon2	N/A	Os01t0105400-01.exon2	transcript:Os01t0105400-01	N/A	2	N/A
+1	irgsp	exon	289202	289572	.	1	.	N/A	N/A	1	N/A	-1	-1	Os01t0105400-01.exon3	N/A	Os01t0105400-01.exon3	N/A	Os01t0105400-01.exon3	transcript:Os01t0105400-01	N/A	3	N/A
+1	irgsp	exon	289661	289830	.	1	.	N/A	N/A	1	N/A	-1	-1	Os01t0105400-01.exon4	N/A	Os01t0105400-01.exon4	N/A	Os01t0105400-01.exon4	transcript:Os01t0105400-01	N/A	4	N/A
+1	irgsp	exon	290395	290512	.	1	.	N/A	N/A	1	N/A	2	-1	Os01t0105400-01.exon5	N/A	Os01t0105400-01.exon5	N/A	Os01t0105400-01.exon5	transcript:Os01t0105400-01	N/A	5	N/A
+1	irgsp	exon	291372	291574	.	1	.	N/A	N/A	1	N/A	-1	2	Os01t0105400-01.exon6	N/A	Os01t0105400-01.exon6	N/A	Os01t0105400-01.exon6	transcript:Os01t0105400-01	N/A	6	N/A
+1	irgsp	exon	291648	291779	.	1	.	N/A	N/A	1	N/A	-1	-1	Os01t0105400-01.exon7	N/A	Os01t0105400-01.exon7	N/A	Os01t0105400-01.exon7	transcript:Os01t0105400-01	N/A	7	N/A
+1	irgsp	exon	291859	291948	.	1	.	N/A	N/A	1	N/A	-1	-1	Os01t0105400-01.exon8	N/A	Os01t0105400-01.exon8	N/A	Os01t0105400-01.exon8	transcript:Os01t0105400-01	N/A	8	N/A
+1	irgsp	exon	292073	292296	.	1	.	N/A	N/A	1	N/A	-1	-1	Os01t0105400-01.exon9	N/A	Os01t0105400-01.exon9	N/A	Os01t0105400-01.exon9	transcript:Os01t0105400-01	N/A	9	N/A
+1	irgsp	CDS	290433	290512	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0105400-01	N/A	N/A	transcript:Os01t0105400-01	Os01t0105400-01	N/A	N/A
+1	irgsp	CDS	291372	291558	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0105400-01	N/A	N/A	transcript:Os01t0105400-01	Os01t0105400-01	N/A	N/A
+1	irgsp	five_prime_UTR	288372	288846	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-70	N/A	N/A	transcript:Os01t0105400-01	N/A	N/A	N/A
+1	irgsp	five_prime_UTR	288950	289116	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-71	N/A	N/A	transcript:Os01t0105400-01	N/A	N/A	N/A
+1	irgsp	five_prime_UTR	289202	289572	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-72	N/A	N/A	transcript:Os01t0105400-01	N/A	N/A	N/A
+1	irgsp	five_prime_UTR	289661	289830	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-73	N/A	N/A	transcript:Os01t0105400-01	N/A	N/A	N/A
+1	irgsp	five_prime_UTR	290395	290432	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-74	N/A	N/A	transcript:Os01t0105400-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	291559	291574	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-62	N/A	N/A	transcript:Os01t0105400-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	291648	291779	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-63	N/A	N/A	transcript:Os01t0105400-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	291859	291948	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-64	N/A	N/A	transcript:Os01t0105400-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	292073	292296	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-65	N/A	N/A	transcript:Os01t0105400-01	N/A	N/A	N/A
+1	irgsp	gene	303233	306736	.	1	.	N/A	protein_coding	N/A	Basic helix-loop-helix dimerisation region bHLH domain containing protein. (Os01t0105700-01)	N/A	N/A	N/A	Os01g0105700	gene:Os01g0105700	irgspv1.0-20170804-genes	basic helix-loop-helix protein 071	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	303233	306736	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0105700-01	N/A	N/A	gene:Os01g0105700	N/A	N/A	Os01t0105700-01
+1	irgsp	exon	303233	303471	.	1	.	N/A	N/A	1	N/A	2	-1	Os01t0105700-01.exon1	N/A	Os01t0105700-01.exon1	N/A	Os01t0105700-01.exon1	transcript:Os01t0105700-01	N/A	1	N/A
+1	irgsp	exon	303981	304509	.	1	.	N/A	N/A	1	N/A	0	2	Os01t0105700-01.exon2	N/A	Os01t0105700-01.exon2	N/A	Os01t0105700-01.exon2	transcript:Os01t0105700-01	N/A	2	N/A
+1	irgsp	exon	305572	305718	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0105700-01.exon3	N/A	Os01t0105700-01.exon3	N/A	Os01t0105700-01.exon3	transcript:Os01t0105700-01	N/A	3	N/A
+1	irgsp	exon	305834	305899	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0105700-01.exon4	N/A	Os01t0105700-01.exon4	N/A	Os01t0105700-01.exon4	transcript:Os01t0105700-01	N/A	4	N/A
+1	irgsp	exon	305993	306058	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0105700-01.exon5	N/A	Os01t0105700-01.exon5	N/A	Os01t0105700-01.exon5	transcript:Os01t0105700-01	N/A	5	N/A
+1	irgsp	exon	306171	306245	.	1	.	N/A	N/A	1	N/A	0	0	Os01t0105700-01.exon6	N/A	Os01t0105700-01.exon6	N/A	Os01t0105700-01.exon6	transcript:Os01t0105700-01	N/A	6	N/A
+1	irgsp	exon	306353	306736	.	1	.	N/A	N/A	1	N/A	-1	0	Os01t0105700-01.exon7	N/A	Os01t0105700-01.exon7	N/A	Os01t0105700-01.exon7	transcript:Os01t0105700-01	N/A	7	N/A
+1	irgsp	CDS	303329	303471	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0105700-01	N/A	N/A	transcript:Os01t0105700-01	Os01t0105700-01	N/A	N/A
+1	irgsp	CDS	303981	304509	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0105700-01	N/A	N/A	transcript:Os01t0105700-01	Os01t0105700-01	N/A	N/A
+1	irgsp	CDS	305572	305718	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0105700-01	N/A	N/A	transcript:Os01t0105700-01	Os01t0105700-01	N/A	N/A
+1	irgsp	CDS	305834	305899	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0105700-01	N/A	N/A	transcript:Os01t0105700-01	Os01t0105700-01	N/A	N/A
+1	irgsp	CDS	305993	306058	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0105700-01	N/A	N/A	transcript:Os01t0105700-01	Os01t0105700-01	N/A	N/A
+1	irgsp	CDS	306171	306245	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0105700-01	N/A	N/A	transcript:Os01t0105700-01	Os01t0105700-01	N/A	N/A
+1	irgsp	CDS	306353	306493	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0105700-01	N/A	N/A	transcript:Os01t0105700-01	Os01t0105700-01	N/A	N/A
+1	irgsp	five_prime_UTR	303233	303328	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-75	N/A	N/A	transcript:Os01t0105700-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	306494	306736	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-66	N/A	N/A	transcript:Os01t0105700-01	N/A	N/A	N/A
+1	irgsp	gene	306871	308842	.	-1	.	N/A	protein_coding	N/A	Similar to Iron sulfur assembly protein 1. (Os01t0105800-01)	N/A	N/A	N/A	Os01g0105800	gene:Os01g0105800	irgspv1.0-20170804-genes	IRON-SULFUR CLUSTER PROTEIN 9	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	306871	308842	.	-1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0105800-01	N/A	N/A	gene:Os01g0105800	N/A	N/A	Os01t0105800-01
+1	irgsp	exon	306871	307217	.	-1	.	N/A	N/A	1	N/A	-1	2	Os01t0105800-01.exon4	N/A	Os01t0105800-01.exon4	N/A	Os01t0105800-01.exon4	transcript:Os01t0105800-01	N/A	4	N/A
+1	irgsp	exon	307296	307413	.	-1	.	N/A	N/A	1	N/A	2	1	Os01t0105800-01.exon3	N/A	Os01t0105800-01.exon3	N/A	Os01t0105800-01.exon3	transcript:Os01t0105800-01	N/A	3	N/A
+1	irgsp	exon	308397	308626	.	-1	.	N/A	N/A	1	N/A	1	-1	Os01t0105800-01.exon2	N/A	Os01t0105800-01.exon2	N/A	Os01t0105800-01.exon2	transcript:Os01t0105800-01	N/A	2	N/A
+1	irgsp	exon	308703	308842	.	-1	.	N/A	N/A	1	N/A	-1	-1	Os01t0105800-01.exon1	N/A	Os01t0105800-01.exon1	N/A	Os01t0105800-01.exon1	transcript:Os01t0105800-01	N/A	1	N/A
+1	irgsp	CDS	307124	307217	.	-1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0105800-01	N/A	N/A	transcript:Os01t0105800-01	Os01t0105800-01	N/A	N/A
+1	irgsp	CDS	307296	307413	.	-1	2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0105800-01	N/A	N/A	transcript:Os01t0105800-01	Os01t0105800-01	N/A	N/A
+1	irgsp	CDS	308397	308601	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0105800-01	N/A	N/A	transcript:Os01t0105800-01	Os01t0105800-01	N/A	N/A
+1	irgsp	five_prime_UTR	308602	308626	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-76	N/A	N/A	transcript:Os01t0105800-01	N/A	N/A	N/A
+1	irgsp	five_prime_UTR	308703	308842	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-77	N/A	N/A	transcript:Os01t0105800-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	306871	307123	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-67	N/A	N/A	transcript:Os01t0105800-01	N/A	N/A	N/A
+1	irgsp	gene	309520	313170	.	-1	.	N/A	protein_coding	N/A	Carbohydrate/purine kinase domain containing protein. (Os01t0105900-01)	N/A	N/A	N/A	Os01g0105900	gene:Os01g0105900	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	309520	313170	.	-1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0105900-01	N/A	N/A	gene:Os01g0105900	N/A	N/A	Os01t0105900-01
+1	irgsp	exon	309520	310070	.	-1	.	N/A	N/A	1	N/A	-1	0	Os01t0105900-01.exon8	N/A	Os01t0105900-01.exon8	N/A	Os01t0105900-01.exon8	transcript:Os01t0105900-01	N/A	8	N/A
+1	irgsp	exon	310256	310367	.	-1	.	N/A	N/A	1	N/A	0	2	Os01t0105900-01.exon7	N/A	Os01t0105900-01.exon7	N/A	Os01t0105900-01.exon7	transcript:Os01t0105900-01	N/A	7	N/A
+1	irgsp	exon	310455	310552	.	-1	.	N/A	N/A	1	N/A	2	0	Os01t0105900-01.exon6	N/A	Os01t0105900-01.exon6	N/A	Os01t0105900-01.exon6	transcript:Os01t0105900-01	N/A	6	N/A
+1	irgsp	exon	310632	310739	.	-1	.	N/A	N/A	1	N/A	0	0	Os01t0105900-01.exon5	N/A	Os01t0105900-01.exon5	N/A	Os01t0105900-01.exon5	transcript:Os01t0105900-01	N/A	5	N/A
+1	irgsp	exon	310880	310918	.	-1	.	N/A	N/A	1	N/A	0	0	Os01t0105900-01.exon4	N/A	Os01t0105900-01.exon4	N/A	Os01t0105900-01.exon4	transcript:Os01t0105900-01	N/A	4	N/A
+1	irgsp	exon	311002	311073	.	-1	.	N/A	N/A	1	N/A	0	0	Os01t0105900-01.exon3	N/A	Os01t0105900-01.exon3	N/A	Os01t0105900-01.exon3	transcript:Os01t0105900-01	N/A	3	N/A
+1	irgsp	exon	311163	311426	.	-1	.	N/A	N/A	1	N/A	0	0	Os01t0105900-01.exon2	N/A	Os01t0105900-01.exon2	N/A	Os01t0105900-01.exon2	transcript:Os01t0105900-01	N/A	2	N/A
+1	irgsp	exon	312867	313170	.	-1	.	N/A	N/A	1	N/A	0	-1	Os01t0105900-01.exon1	N/A	Os01t0105900-01.exon1	N/A	Os01t0105900-01.exon1	transcript:Os01t0105900-01	N/A	1	N/A
+1	irgsp	CDS	309822	310070	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0105900-01	N/A	N/A	transcript:Os01t0105900-01	Os01t0105900-01	N/A	N/A
+1	irgsp	CDS	310256	310367	.	-1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0105900-01	N/A	N/A	transcript:Os01t0105900-01	Os01t0105900-01	N/A	N/A
+1	irgsp	CDS	310455	310552	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0105900-01	N/A	N/A	transcript:Os01t0105900-01	Os01t0105900-01	N/A	N/A
+1	irgsp	CDS	310632	310739	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0105900-01	N/A	N/A	transcript:Os01t0105900-01	Os01t0105900-01	N/A	N/A
+1	irgsp	CDS	310880	310918	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0105900-01	N/A	N/A	transcript:Os01t0105900-01	Os01t0105900-01	N/A	N/A
+1	irgsp	CDS	311002	311073	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0105900-01	N/A	N/A	transcript:Os01t0105900-01	Os01t0105900-01	N/A	N/A
+1	irgsp	CDS	311163	311426	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0105900-01	N/A	N/A	transcript:Os01t0105900-01	Os01t0105900-01	N/A	N/A
+1	irgsp	CDS	312867	313064	.	-1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0105900-01	N/A	N/A	transcript:Os01t0105900-01	Os01t0105900-01	N/A	N/A
+1	irgsp	five_prime_UTR	313065	313170	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-78	N/A	N/A	transcript:Os01t0105900-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	309520	309821	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-68	N/A	N/A	transcript:Os01t0105900-01	N/A	N/A	N/A
+1	irgsp	gene	319754	322205	.	1	.	N/A	protein_coding	N/A	Similar to RER1A protein (AtRER1A). (Os01t0106200-01)	N/A	N/A	N/A	Os01g0106200	gene:Os01g0106200	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	319754	322205	.	1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0106200-01	N/A	N/A	gene:Os01g0106200	N/A	N/A	Os01t0106200-01
+1	irgsp	exon	319754	320236	.	1	.	N/A	N/A	1	N/A	2	-1	Os01t0106200-01.exon1	N/A	Os01t0106200-01.exon1	N/A	Os01t0106200-01.exon1	transcript:Os01t0106200-01	N/A	1	N/A
+1	irgsp	exon	321468	321648	.	1	.	N/A	N/A	1	N/A	0	2	Os01t0106200-01.exon2	N/A	Os01t0106200-01.exon2	N/A	Os01t0106200-01.exon2	transcript:Os01t0106200-01	N/A	2	N/A
+1	irgsp	exon	321928	322205	.	1	.	N/A	N/A	1	N/A	-1	0	Os01t0106200-01.exon3	N/A	Os01t0106200-01.exon3	N/A	Os01t0106200-01.exon3	transcript:Os01t0106200-01	N/A	3	N/A
+1	irgsp	CDS	319875	320236	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0106200-01	N/A	N/A	transcript:Os01t0106200-01	Os01t0106200-01	N/A	N/A
+1	irgsp	CDS	321468	321648	.	1	1	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0106200-01	N/A	N/A	transcript:Os01t0106200-01	Os01t0106200-01	N/A	N/A
+1	irgsp	CDS	321928	321975	.	1	0	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	CDS:Os01t0106200-01	N/A	N/A	transcript:Os01t0106200-01	Os01t0106200-01	N/A	N/A
+1	irgsp	five_prime_UTR	319754	319874	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-five_prime_utr-79	N/A	N/A	transcript:Os01t0106200-01	N/A	N/A	N/A
+1	irgsp	three_prime_UTR	321976	322205	.	1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-69	N/A	N/A	transcript:Os01t0106200-01	N/A	N/A	N/A
+1	irgsp	gene	322591	323923	.	-1	.	N/A	protein_coding	N/A	Similar to Isoflavone reductase homolog IRL (EC 1.3.1.-). (Os01t0106300-01)	N/A	N/A	N/A	Os01g0106300	gene:Os01g0106300	irgspv1.0-20170804-genes	N/A	N/A	N/A	N/A	N/A
+1	irgsp	mRNA	322591	323923	.	-1	.	N/A	protein_coding	N/A	N/A	N/A	N/A	N/A	N/A	transcript:Os01t0106300-01	N/A	N/A	gene:Os01g0106300	N/A	N/A	Os01t0106300-01
+1	irgsp	exon	322591	323923	.	-1	.	N/A	N/A	1	N/A	-1	1	Os01t0106300-01.exon2	N/A	Os01t0106300-01.exon2	N/A	Os01t0106300-01.exon2	transcript:Os01t0106300-01	N/A	2	N/A
+1	irgsp	three_prime_UTR	322591	322809	.	-1	.	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	agat-three_prime_utr-70	N/A	N/A	transcript:Os01t0106300-01	N/A	N/A	N/A
--- a/src/agat/agat_convert_sp_gff2tsv/test_data/script.sh
+++ b/src/agat/agat_convert_sp_gff2tsv/test_data/script.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+
+# clone repo
+if [ ! -d /tmp/agat_source ]; then
+  git clone --depth 1 --single-branch --branch master https://github.com/NBISweden/AGAT /tmp/agat_source
+fi
+
+# copy test data
+cp -r /tmp/agat_source/t/scripts_output/out/agat_convert_sp_gff2tsv_1.tsv src/agat/agat_convert_sp_gff2tsv/test_data
+cp -r /tmp/agat_source/t/scripts_output/in/1.gff src/agat/agat_convert_sp_gff2tsv/test_data
--- a/src/arriba/config.vsh.yaml
+++ b/src/arriba/config.vsh.yaml
@@ -0,0 +1,388 @@
+name: arriba
+description: Detect gene fusions from RNA-Seq data
+keywords: [Gene fusion, RNA-Seq]
+links:
+  homepage: https://arriba.readthedocs.io/en/latest/
+  documentation: https://arriba.readthedocs.io/en/latest/
+  repository: https://github.com/suhrig/arriba
+references:
+  doi: 10.1101/gr.257246.119
+license: MIT
+requirements:
+  cpus: 1
+  commands: [ arriba ]
+authors:
+  - __merge__: /src/_authors/robrecht_cannoodt.yaml
+    roles: [ author, maintainer ]
+argument_groups:
+  - name: Inputs
+    arguments:
+    - name: --bam
+      alternatives: -x
+      type: file
+      description: |
+        File in SAM/BAM/CRAM format with main alignments as generated by STAR
+        (Aligned.out.sam). Arriba extracts candidate reads from this file.
+      required: true
+      example: Aligned.out.bam
+    - name: --genome
+      alternatives: -a
+      type: file
+      description: |
+        FastA file with genome sequence (assembly). The file may be gzip-compressed. An 
+        index with the file extension .fai must exist only if CRAM files are processed.
+      required: true
+      example: assembly.fa
+    - name: --gene_annotation
+      alternatives: -g
+      type: file
+      description: |
+        GTF file with gene annotation. The file may be gzip-compressed.
+      required: true
+      example: annotation.gtf
+    - name: --known_fusions
+      alternatives: -k
+      type: file
+      description: |
+        File containing known/recurrent fusions. Some cancer entities are often 
+        characterized by fusions between the same pair of genes. In order to boost 
+        sensitivity, a list of known fusions can be supplied using this parameter. The list 
+        must contain two columns with the names of the fused genes, separated by tabs.
+      required: false
+      example: known_fusions.tsv
+    - name: --blacklist
+      alternatives: -b
+      type: file
+      description: |
+        File containing blacklisted events (recurrent artifacts and transcripts 
+        observed in healthy tissue).
+      required: false
+      example: blacklist.tsv
+    - name: --structural_variants
+      alternatives: -d
+      type: file
+      description: |
+        Tab-separated file with coordinates of structural variants found using 
+        whole-genome sequencing data. These coordinates serve to increase sensitivity 
+        towards weakly expressed fusions and to eliminate fusions with low evidence. 
+      required: false
+      example: structural_variants_from_WGS.tsv
+    - name: --tags
+      alternatives: -t
+      type: file
+      description: |
+        Tab-separated file containing fusions to annotate with tags in the 'tags' column. 
+        The first two columns specify the genes; the third column specifies the tag. The 
+        file may be gzip-compressed. 
+      required: false
+      example: tags.tsv
+    - name: --protein_domains
+      alternatives: -p
+      type: file
+      description: |
+        File in GFF3 format containing coordinates of the protein domains of genes. The
+        protein domains retained in a fusion are listed in the column
+        'retained_protein_domains'. The file may be gzip-compressed.
+      required: false
+      example: protein_domains.gff3
+  - name: Outputs
+    arguments:
+      - name: --fusions
+        alternatives: -o
+        type: file
+        direction: output
+        description: |
+          Output file with fusions that have passed all filters.
+        required: true
+        example: fusions.tsv
+      - name: --fusions_discarded
+        alternatives: -O
+        type: file
+        direction: output
+        description: |
+          Output file with fusions that were discarded due to filtering. 
+        required: false
+        example: fusions.discarded.tsv
+  - name: Arguments
+    arguments:
+      - name: --max_genomic_breakpoint_distance
+        alternatives: -D
+        type: long
+        description: |
+          When a file with genomic breakpoints obtained via 
+          whole-genome sequencing is supplied via the --structural_variants
+          parameter, this parameter determines how far a 
+          genomic breakpoint may be away from a 
+          transcriptomic breakpoint to consider it as a 
+          related event. For events inside genes, the 
+          distance is added to the end of the gene; for 
+          intergenic events, the distance threshold is 
+          applied as is. Default: 100000.
+        required: false
+      - name: --strandedness
+        alternatives: -s
+        type: string
+        description: |
+          Whether a strand-specific protocol was used for library preparation, 
+          and if so, the type of strandedness (auto/yes/no/reverse). When 
+          unstranded data is processed, the strand can sometimes be inferred from 
+          splice-patterns. But in unclear situations, stranded data helps 
+          resolve ambiguities. Default: auto
+        choices: ["auto", "yes", "no", "reverse"]
+        required: false
+      - name: --interesting_contigs
+        alternatives: -i
+        type: string
+        description: |
+          List of interesting contigs. Fusions between genes 
+          on other contigs are ignored. Contigs can be specified with or without the 
+          prefix "chr". Asterisks (*) are treated as wild-cards. 
+          Default: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_*
+        required: false
+        multiple: true
+        example: ["1", "2", "AC_*", "NC_*"]
+      - name: --viral_contigs
+        alternatives: -v
+        type: string
+        description: |
+          List of viral contigs. Asterisks (*) are treated as 
+          wild-cards.
+          Default: AC_* NC_*
+        required: false
+        multiple: true
+        example: ["AC_*", "NC_*"]
+      - name: --disable_filters
+        alternatives: -f
+        type: string
+        description: |
+          List of filters to disable. By default all filters are 
+          enabled. 
+        choices: [ homologs, low_entropy, isoforms, 
+          top_expressed_viral_contigs, viral_contigs, uninteresting_contigs, 
+          non_coding_neighbors, mismatches, duplicates, no_genomic_support, 
+          genomic_support, intronic, end_to_end, relative_support, 
+          low_coverage_viral_contigs, merge_adjacent, mismappers, multimappers, 
+          same_gene, long_gap, internal_tandem_duplication, small_insert_size, 
+          read_through, inconsistently_clipped, intragenic_exonic, 
+          marginal_read_through, spliced, hairpin, blacklist, min_support, 
+          select_best, in_vitro, short_anchor, known_fusions, no_coverage, 
+          homopolymer, many_spliced ]
+        required: false
+        multiple: true
+      - name: --max_e_value
+        alternatives: -E
+        type: double
+        description: |
+          Arriba estimates the number of fusions with a given number of supporting 
+          reads which one would expect to see by random chance. If the expected number 
+          of fusions (e-value) is higher than this threshold, the fusion is 
+          discarded by the 'relative_support' filter. Note: Increasing this 
+          threshold can dramatically increase the number of false positives and may 
+          increase the runtime of resource-intensive steps. Fractional values are 
+          possible. Default: 0.300000 
+        required: false
+      - name: --min_supporting_reads
+        alternatives: -S
+        type: integer
+        description: |
+          The 'min_support' filter discards all fusions with fewer than 
+          this many supporting reads (split reads and discordant mates 
+          combined). Default: 2 
+        required: false
+        example: 2
+      - name: --max_mismappers
+        alternatives: -m
+        type: double
+        description: |
+          When more than this fraction of supporting reads turns out to be 
+          mismappers, the 'mismappers' filter discards the fusion. Default: 
+          0.800000
+        required: false
+        example: 0.8
+      - name: --max_homolog_identity
+        alternatives: -L
+        type: double
+        description: |
+          Genes with more than the given fraction of sequence identity are 
+          considered homologs and removed by the 'homologs' filter. 
+          Default: 0.300000 
+        required: false
+        example: 0.3
+      - name: --homopolymer_length
+        alternatives: -H
+        type: integer
+        description: |
+          The 'homopolymer' filter removes breakpoints adjacent to 
+          homopolymers of the given length or more. Default: 6
+        required: false
+        example: 6
+      - name: --read_through_distance
+        alternatives: -R
+        type: integer
+        description: |
+          The 'read_through' filter removes read-through fusions 
+          where the breakpoints are less than the given distance away 
+          from each other. Default: 10000 
+        required: false
+        example: 10000
+      - name : --min_anchor_length
+        alternatives: -A
+        type: integer
+        description: |
+          Alignment artifacts are often characterized by split reads coming 
+          from only one gene and no discordant mates. Moreover, the split 
+          reads only align to a short stretch in one of the genes. The 
+          'short_anchor' filter removes these fusions. This parameter sets 
+          the threshold in bp for what the filter considers short. Default: 23 
+        required: false
+        example: 23
+      - name: --many_spliced_events
+        alternatives: -M
+        type: integer
+        description: |
+          The 'many_spliced' filter recovers fusions between genes that 
+          have at least this many spliced breakpoints. Default: 4
+        required: false
+        example: 4
+      - name: --max_kmer_content
+        alternatives: -K
+        type: double
+        description: |
+          The 'low_entropy' filter removes reads with repetitive 3-mers. If 
+          the 3-mers make up more than the given fraction of the sequence, then 
+          the read is discarded. Default: 0.600000 
+        required: false
+        example: 0.6
+      - name: --max_mismatch_pvalue
+        alternatives: -V
+        type: double
+        description: |
+          The 'mismatches' filter uses a binomial model to calculate a 
+          p-value for observing a given number of mismatches in a read. If 
+          the number of mismatches is too high, the read is discarded. 
+          Default: 0.010000 
+        required: false
+        example: 0.05
+      - name: --fragment_length
+        alternatives: -F
+        type: integer
+        description: |
+          When paired-end data is given, the fragment length is estimated 
+          automatically and this parameter has no effect. But when single-end 
+          data is given, the mean fragment length should be specified to 
+          effectively filter fusions that arise from hairpin structures. 
+          Default: 200 
+        required: false
+        example: 200
+      - name: --max_reads
+        alternatives: -U
+        type: integer
+        description: |
+          Subsample fusions with more than the given number of supporting reads. This 
+          improves performance without compromising sensitivity, as long as the 
+          threshold is high. Counting of supporting reads beyond the threshold is 
+          inaccurate, obviously. Default: 300 
+        required: false
+        example: 300
+      - name: --quantile
+        alternatives: -Q
+        type: double
+        description: |
+          Highly expressed genes are prone to produce artifacts during library 
+          preparation. Genes with an expression above the given quantile are eligible 
+          for filtering by the 'in_vitro' filter. Default: 0.998000
+        required: false
+        example: 0.998
+      - name: --exonic_fraction
+        alternatives: -e
+        type: double
+        description: |
+          The breakpoints of false-positive predictions of intragenic events 
+          are often both in exons. True predictions are more likely to have at 
+          least one breakpoint in an intron, because introns are larger. If the 
+          fraction of exonic sequence between two breakpoints is smaller than 
+          the given fraction, the 'intragenic_exonic' filter discards the 
+          event. Default: 0.330000 
+        required: false
+        example: 0.33
+      - name: --top_n
+        alternatives: -T
+        type: integer
+        description: |
+          Only report viral integration sites of the top N most highly expressed viral 
+          contigs. Default: 5
+        required: false
+        example: 5
+      - name: --covered_fraction
+        alternatives: -C
+        type: double
+        description: |
+          Ignore virally associated events if the virus is not fully 
+          expressed, i.e., less than the given fraction of the viral contig is 
+          transcribed. Default: 0.050000 
+        required: false
+        example: 0.05
+      - name: --max_itd_length
+        alternatives: -l
+        type: integer
+        description: |
+          Maximum length of internal tandem duplications. Note: Increasing 
+          this value beyond the default can impair performance and lead to many 
+          false positives. Default: 100 
+        required: false
+        example: 100
+      - name: --min_itd_allele_fraction
+        alternatives: -z
+        type: double
+        description: |
+          Required fraction of supporting reads to report an internal 
+          tandem duplication. Default: 0.070000 
+        required: false
+        example: 0.07
+      - name: --min_itd_supporting_reads
+        alternatives: -Z
+        type: integer
+        description: |
+          Required absolute number of supporting reads to report an 
+          internal tandem duplication. Default: 10 
+        required: false
+        example: 10
+      - name: --skip_duplicate_marking
+        alternatives: -u
+        type: boolean_true
+        description: |
+          Instead of performing duplicate marking itself, Arriba relies on duplicate marking by a 
+          preceding program using the BAM_FDUP flag. This makes sense when unique molecular 
+          identifiers (UMI) are used.
+      - name: --extra_information
+        alternatives: -X
+        type: boolean_true
+        description: |
+          To reduce the runtime and file size, by default, the columns 'fusion_transcript', 
+          'peptide_sequence', and 'read_identifiers' are left empty in the file containing 
+          discarded fusion candidates (see parameter -O). When this flag is set, this extra 
+          information is reported in the discarded fusions file.
+      - name: --fill_gaps
+        alternatives: -I
+        type: boolean_true
+        description: |
+          If assembly of the fusion transcript sequence from the supporting reads is incomplete 
+          (denoted as '...'), fill the gaps using the assembly sequence wherever possible. 
+resources:
+  - type: bash_script
+    path: script.sh
+test_resources:
+  - type: bash_script
+    path: test.sh
+  - type: file
+    path: test_data
+engines:
+  - type: docker
+    image: quay.io/biocontainers/arriba:2.4.0--h0033a41_2
+    setup:
+      - type: docker
+        run: |
+          arriba -h | grep 'Version:' 2>&1 |  sed 's/Version:\s\(.*\)/arriba: "\1"/' > /var/software_versions.txt
+runners:
+  - type: executable
+  - type: nextflow
--- a/src/arriba/help.txt
+++ b/src/arriba/help.txt
@@ -0,0 +1,198 @@
+```bash
+arriba -h
+```
+
+Arriba gene fusion detector
+---------------------------
+Version: 2.4.0
+
+Arriba is a fast tool to search for aberrant transcripts such as gene fusions. 
+It is based on chimeric alignments found by the STAR RNA-Seq aligner.
+
+Usage: arriba [-c Chimeric.out.sam] -x Aligned.out.bam \
+              -g annotation.gtf -a assembly.fa [-b blacklists.tsv] [-k known_fusions.tsv] \
+              [-t tags.tsv] [-p protein_domains.gff3] [-d structural_variants_from_WGS.tsv] \
+              -o fusions.tsv [-O fusions.discarded.tsv] \
+              [OPTIONS]
+
+ -c FILE  File in SAM/BAM/CRAM format with chimeric alignments as generated by STAR 
+          (Chimeric.out.sam). This parameter is only required, if STAR was run with the 
+          parameter '--chimOutType SeparateSAMold'. When STAR was run with the parameter 
+          '--chimOutType WithinBAM', it suffices to pass the parameter -x to Arriba and -c 
+          can be omitted. 
+
+ -x FILE  File in SAM/BAM/CRAM format with main alignments as generated by STAR 
+          (Aligned.out.sam). Arriba extracts candidate reads from this file. 
+
+ -g FILE  GTF file with gene annotation. The file may be gzip-compressed. 
+
+ -G GTF_FEATURES  Comma-/space-separated list of names of GTF features. 
+                  Default: gene_name=gene_name|gene_id gene_id=gene_id 
+                  transcript_id=transcript_id feature_exon=exon feature_CDS=CDS 
+
+ -a FILE  FastA file with genome sequence (assembly). The file may be gzip-compressed. An 
+          index with the file extension .fai must exist only if CRAM files are processed. 
+
+ -b FILE  File containing blacklisted events (recurrent artifacts and transcripts 
+          observed in healthy tissue). 
+
+ -k FILE  File containing known/recurrent fusions. Some cancer entities are often 
+          characterized by fusions between the same pair of genes. In order to boost 
+          sensitivity, a list of known fusions can be supplied using this parameter. The list 
+          must contain two columns with the names of the fused genes, separated by tabs. 
+
+ -o FILE  Output file with fusions that have passed all filters. 
+
+ -O FILE  Output file with fusions that were discarded due to filtering. 
+
+ -t FILE  Tab-separated file containing fusions to annotate with tags in the 'tags' column. 
+          The first two columns specify the genes; the third column specifies the tag. The 
+          file may be gzip-compressed. 
+
+ -p FILE  File in GFF3 format containing coordinates of the protein domains of genes. The 
+          protein domains retained in a fusion are listed in the column 
+          'retained_protein_domains'. The file may be gzip-compressed. 
+
+ -d FILE  Tab-separated file with coordinates of structural variants found using 
+          whole-genome sequencing data. These coordinates serve to increase sensitivity 
+          towards weakly expressed fusions and to eliminate fusions with low evidence. 
+
+ -D MAX_GENOMIC_BREAKPOINT_DISTANCE  When a file with genomic breakpoints obtained via 
+                                     whole-genome sequencing is supplied via the -d 
+                                     parameter, this parameter determines how far a 
+                                     genomic breakpoint may be away from a 
+                                     transcriptomic breakpoint to consider it as a 
+                                     related event. For events inside genes, the 
+                                     distance is added to the end of the gene; for 
+                                     intergenic events, the distance threshold is 
+                                     applied as is. Default: 100000 
+
+ -s STRANDEDNESS  Whether a strand-specific protocol was used for library preparation, 
+                  and if so, the type of strandedness (auto/yes/no/reverse). When 
+                  unstranded data is processed, the strand can sometimes be inferred from 
+                  splice-patterns. But in unclear situations, stranded data helps 
+                  resolve ambiguities. Default: auto 
+
+ -i CONTIGS  Comma-/space-separated list of interesting contigs. Fusions between genes 
+             on other contigs are ignored. Cfontigs can be specified with or without the 
+             prefix "chr". Asterisks (*) are treated as wild-cards. 
+             Default: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_* 
+
+ -v CONTIGS  Comma-/space-separated list of viral contigs. Asterisks (*) are treated as 
+             wild-cards. 
+             Default: AC_* NC_* 
+
+ -f FILTERS  Comma-/space-separated list of filters to disable. By default all filters are 
+             enabled. Valid values: homologs, low_entropy, isoforms, 
+             top_expressed_viral_contigs, viral_contigs, uninteresting_contigs, 
+             non_coding_neighbors, mismatches, duplicates, no_genomic_support, 
+             genomic_support, intronic, end_to_end, relative_support, 
+             low_coverage_viral_contigs, merge_adjacent, mismappers, multimappers, 
+             same_gene, long_gap, internal_tandem_duplication, small_insert_size, 
+             read_through, inconsistently_clipped, intragenic_exonic, 
+             marginal_read_through, spliced, hairpin, blacklist, min_support, 
+             select_best, in_vitro, short_anchor, known_fusions, no_coverage, 
+             homopolymer, many_spliced 
+
+ -E MAX_E-VALUE  Arriba estimates the number of fusions with a given number of supporting 
+                 reads which one would expect to see by random chance. If the expected number 
+                 of fusions (e-value) is higher than this threshold, the fusion is 
+                 discarded by the 'relative_support' filter. Note: Increasing this 
+                 threshold can dramatically increase the number of false positives and may 
+                 increase the runtime of resource-intensive steps. Fractional values are 
+                 possible. Default: 0.300000 
+
+ -S MIN_SUPPORTING_READS  The 'min_support' filter discards all fusions with fewer than 
+                          this many supporting reads (split reads and discordant mates 
+                          combined). Default: 2 
+
+ -m MAX_MISMAPPERS  When more than this fraction of supporting reads turns out to be 
+                    mismappers, the 'mismappers' filter discards the fusion. Default: 
+                    0.800000 
+
+ -L MAX_HOMOLOG_IDENTITY  Genes with more than the given fraction of sequence identity are 
+                          considered homologs and removed by the 'homologs' filter. 
+                          Default: 0.300000 
+
+ -H HOMOPOLYMER_LENGTH  The 'homopolymer' filter removes breakpoints adjacent to 
+                        homopolymers of the given length or more. Default: 6 
+
+ -R READ_THROUGH_DISTANCE  The 'read_through' filter removes read-through fusions 
+                           where the breakpoints are less than the given distance away 
+                           from each other. Default: 10000 
+
+ -A MIN_ANCHOR_LENGTH  Alignment artifacts are often characterized by split reads coming 
+                       from only one gene and no discordant mates. Moreover, the split 
+                       reads only align to a short stretch in one of the genes. The 
+                       'short_anchor' filter removes these fusions. This parameter sets 
+                       the threshold in bp for what the filter considers short. Default: 23 
+
+ -M MANY_SPLICED_EVENTS  The 'many_spliced' filter recovers fusions between genes that 
+                         have at least this many spliced breakpoints. Default: 4 
+
+ -K MAX_KMER_CONTENT  The 'low_entropy' filter removes reads with repetitive 3-mers. If 
+                      the 3-mers make up more than the given fraction of the sequence, then 
+                      the read is discarded. Default: 0.600000 
+
+ -V MAX_MISMATCH_PVALUE  The 'mismatches' filter uses a binomial model to calculate a 
+                         p-value for observing a given number of mismatches in a read. If 
+                         the number of mismatches is too high, the read is discarded. 
+                         Default: 0.010000 
+
+ -F FRAGMENT_LENGTH  When paired-end data is given, the fragment length is estimated 
+                     automatically and this parameter has no effect. But when single-end 
+                     data is given, the mean fragment length should be specified to 
+                     effectively filter fusions that arise from hairpin structures. 
+                     Default: 200 
+
+ -U MAX_READS  Subsample fusions with more than the given number of supporting reads. This 
+               improves performance without compromising sensitivity, as long as the 
+               threshold is high. Counting of supporting reads beyond the threshold is 
+               inaccurate, obviously. Default: 300 
+
+ -Q QUANTILE  Highly expressed genes are prone to produce artifacts during library 
+              preparation. Genes with an expression above the given quantile are eligible 
+              for filtering by the 'in_vitro' filter. Default: 0.998000 
+
+ -e EXONIC_FRACTION  The breakpoints of false-positive predictions of intragenic events 
+                     are often both in exons. True predictions are more likely to have at 
+                     least one breakpoint in an intron, because introns are larger. If the 
+                     fraction of exonic sequence between two breakpoints is smaller than 
+                     the given fraction, the 'intragenic_exonic' filter discards the 
+                     event. Default: 0.330000 
+
+ -T TOP_N  Only report viral integration sites of the top N most highly expressed viral 
+           contigs. Default: 5 
+
+ -C COVERED_FRACTION  Ignore virally associated events if the virus is not fully 
+                      expressed, i.e., less than the given fraction of the viral contig is 
+                      transcribed. Default: 0.050000 
+
+ -l MAX_ITD_LENGTH  Maximum length of internal tandem duplications. Note: Increasing 
+                    this value beyond the default can impair performance and lead to many 
+                    false positives. Default: 100 
+
+ -z MIN_ITD_ALLELE_FRACTION  Required fraction of supporting reads to report an internal 
+                             tandem duplication. Default: 0.070000 
+
+ -Z MIN_ITD_SUPPORTING_READS  Required absolute number of supporting reads to report an 
+                              internal tandem duplication. Default: 10 
+
+ -u  Instead of performing duplicate marking itself, Arriba relies on duplicate marking by a 
+     preceding program using the BAM_FDUP flag. This makes sense when unique molecular 
+     identifiers (UMI) are used. 
+
+ -X  To reduce the runtime and file size, by default, the columns 'fusion_transcript', 
+     'peptide_sequence', and 'read_identifiers' are left empty in the file containing 
+     discarded fusion candidates (see parameter -O). When this flag is set, this extra 
+     information is reported in the discarded fusions file. 
+
+ -I  If assembly of the fusion transcript sequence from the supporting reads is incomplete 
+     (denoted as '...'), fill the gaps using the assembly sequence wherever possible. 
+
+ -h  Print help and exit. 
+
+         Code repository: https://github.com/suhrig/arriba
+    Get help/report bugs: https://github.com/suhrig/arriba/issues
+             User manual: https://arriba.readthedocs.io/
+             Please cite: https://doi.org/10.1101/gr.257246.119
--- a/src/arriba/script.sh
+++ b/src/arriba/script.sh
@@ -0,0 +1,54 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+# unset flags
+[[ "$par_skip_duplicate_marking" == "false" ]] && unset par_skip_duplicate_marking
+[[ "$par_extra_information" == "false" ]] && unset par_extra_information
+[[ "$par_fill_gaps" == "false" ]] && unset par_fill_gaps
+
+# replace ';' with ','
+par_interesting_contigs=$(echo $par_interesting_contigs | tr ';' ',')
+par_viral_contigs=$(echo $par_viral_contigs | tr ';' ',')
+par_disable_filters=$(echo $par_disable_filters | tr ';' ',')
+
+# run arriba
+arriba \
+  -x "$par_bam" \
+  -a "$par_genome" \
+  -g "$par_gene_annotation" \
+  -o "$par_fusions" \
+  ${par_known_fusions:+-k "${par_known_fusions}"} \
+  ${par_blacklist:+-b "${par_blacklist}"} \
+  ${par_structural_variants:+-d "${par_structural_variants}"} \
+  ${par_tags:+-t "${par_tags}"} \
+  ${par_protein_domains:+-p "${par_protein_domains}"} \
+  ${par_fusions_discarded:+-O "${par_fusions_discarded}"} \
+  ${par_max_genomic_breakpoint_distance:+-D "${par_max_genomic_breakpoint_distance}"} \
+  ${par_strandedness:+-s "${par_strandedness}"} \
+  ${par_interesting_contigs:+-i "${par_interesting_contigs}"} \
+  ${par_viral_contigs:+-v "${par_viral_contigs}"} \
+  ${par_disable_filters:+-f "${par_disable_filters}"} \
+  ${par_max_e_value:+-E "${par_max_e_value}"} \
+  ${par_min_supporting_reads:+-S "${par_min_supporting_reads}"} \
+  ${par_max_mismappers:+-m "${par_max_mismappers}"} \
+  ${par_max_homolog_identity:+-L "${par_max_homolog_identity}"} \
+  ${par_homopolymer_length:+-H "${par_homopolymer_length}"} \
+  ${par_read_through_distance:+-R "${par_read_through_distance}"} \
+  ${par_min_anchor_length:+-A "${par_min_anchor_length}"} \
+  ${par_many_spliced_events:+-M "${par_many_spliced_events}"} \
+  ${par_max_kmer_content:+-K "${par_max_kmer_content}"} \
+  ${par_max_mismatch_pvalue:+-V "${par_max_mismatch_pvalue}"} \
+  ${par_fragment_length:+-F "${par_fragment_length}"} \
+  ${par_max_reads:+-U "${par_max_reads}"} \
+  ${par_quantile:+-Q "${par_quantile}"} \
+  ${par_exonic_fraction:+-e "${par_exonic_fraction}"} \
+  ${par_top_n:+-T "${par_top_n}"} \
+  ${par_covered_fraction:+-C "${par_covered_fraction}"} \
+  ${par_max_itd_length:+-l "${par_max_itd_length}"} \
+  ${par_min_itd_allele_fraction:+-z "${par_min_itd_allele_fraction}"} \
+  ${par_min_itd_supporting_reads:+-Z "${par_min_itd_supporting_reads}"} \
+  ${par_skip_duplicate_marking:+-u} \
+  ${par_extra_information:+-X} \
+  ${par_fill_gaps:+-I}
--- a/src/arriba/test.sh
+++ b/src/arriba/test.sh
@@ -0,0 +1,45 @@
+#!/bin/bash
+
+set -e
+
+dir_in="$meta_resources_dir/test_data"
+
+echo "> Run arriba with blacklist"
+"$meta_executable" \
+  --bam "$dir_in/A.bam" \
+  --genome "$dir_in/genome.fasta" \
+  --gene_annotation "$dir_in/annotation.gtf" \
+  --blacklist "$dir_in/blacklist.tsv" \
+  --fusions "fusions.tsv" \
+  --fusions_discarded "fusions_discarded.tsv" \
+  --interesting_contigs "1,2"
+
+echo ">> Checking output"
+[ ! -f "fusions.tsv" ] && echo "Output file fusions.tsv does not exist" && exit 1
+[ ! -f "fusions_discarded.tsv" ] && echo "Output file fusions_discarded.tsv does not exist" && exit 1
+
+echo ">> Check if output is empty"
+[ ! -s "fusions.tsv" ] && echo "Output file fusions.tsv is empty" && exit 1
+[ ! -s "fusions_discarded.tsv" ] && echo "Output file fusions_discarded.tsv is empty" && exit 1
+
+rm fusions.tsv fusions_discarded.tsv
+
+echo "> Run arriba without blacklist"
+"$meta_executable" \
+  --bam "$dir_in/A.bam" \
+  --genome "$dir_in/genome.fasta" \
+  --gene_annotation "$dir_in/annotation.gtf" \
+  --fusions "fusions.tsv" \
+  --fusions_discarded "fusions_discarded.tsv" \
+  --interesting_contigs "1,2" \
+  --disable_filters blacklist
+
+echo ">> Checking output"
+[ ! -f "fusions.tsv" ] && echo "Output file fusions.tsv does not exist" && exit 1
+[ ! -f "fusions_discarded.tsv" ] && echo "Output file fusions_discarded.tsv does not exist" && exit 1
+
+echo ">> Check if output is empty"
+[ ! -s "fusions.tsv" ] && echo "Output file fusions.tsv is empty" && exit 1
+[ ! -s "fusions_discarded.tsv" ] && echo "Output file fusions_discarded.tsv is empty" && exit 1
+
+echo "> Test successful"
--- a/src/arriba/test_data/A.bam
+++ b/src/arriba/test_data/A.bam
--- a/src/arriba/test_data/annotation.gtf
+++ b/src/arriba/test_data/annotation.gtf
@@ -0,0 +1,6 @@
+1	havana	gene	1	80	.	+	.	gene_id "ENSG00000000000"; gene_version "5"; gene_name "A"; gene_source "havana"; gene_biotype "gene";
+1	havana	transcript	1	80	.	+	.	gene_id "ENSG00000000000"; gene_version "5"; transcript_id "ENST00000000000"; transcript_version "2"; gene_name "A"; gene_source "havana"; gene_biotype "gene"; transcript_name "A-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; tag "basic"; transcript_support_level "1";
+1	havana	exon	1	80	.	+	.	gene_id "ENSG00000000000"; gene_version "5"; transcript_id "ENST00000000000"; transcript_version "2"; exon_number "1"; gene_name "A"; gene_source "havana"; gene_biotype "gene"; transcript_name "A-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00000000000"; exon_version "1"; tag "basic"; transcript_support_level "1";
+2	havana	gene	1	80	.	+	.	gene_id "ENSG00000000001"; gene_version "5"; gene_name "B"; gene_source "havana"; gene_biotype "gene";
+2	havana	transcript	1	80	.	+	.	gene_id "ENSG00000000001"; gene_version "5"; transcript_id "ENST00000000001"; transcript_version "2"; gene_name "B"; gene_source "havana"; gene_biotype "gene"; transcript_name "B-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; tag "basic"; transcript_support_level "1";
+2	havana	exon	1	80	.	+	.	gene_id "ENSG00000000001"; gene_version "5"; transcript_id "ENST00000000001"; transcript_version "2"; exon_number "1"; gene_name "B"; gene_source "havana"; gene_biotype "gene"; transcript_name "B-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00000000001"; exon_version "1"; tag "basic"; transcript_support_level "1";
--- a/src/arriba/test_data/blacklist.tsv
+++ b/src/arriba/test_data/blacklist.tsv
--- a/src/arriba/test_data/genome.fasta
+++ b/src/arriba/test_data/genome.fasta
@@ -0,0 +1,4 @@
+>1
+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
+>2
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
--- a/src/arriba/test_data/script.sh
+++ b/src/arriba/test_data/script.sh
@@ -0,0 +1,10 @@
+# arriba test data
+
+# Test data was obtained from https://github.com/snakemake/snakemake-wrappers/tree/master/bio/arriba/test
+
+if [ ! -d /tmp/snakemake-wrappers ]; then
+  git clone --depth 1 --single-branch --branch master https://github.com/snakemake/snakemake-wrappers /tmp/snakemake-wrappers
+fi
+
+cp -r /tmp/snakemake-wrappers/bio/arriba/test/* src/arriba/test_data
+
--- a/src/bcl_convert/config.vsh.yaml
+++ b/src/bcl_convert/config.vsh.yaml
@@ -0,0 +1,170 @@
+name: bcl_convert
+description: |
+  Convert bcl files to fastq files using bcl-convert.
+  Information about upgrading from bcl2fastq via
+  [Upgrading from bcl2fastq to BCL Convert](https://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html)
+  and [BCL Convert Compatible Products](https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html)
+keywords: [demultiplex, fastq, bcl, illumina]
+links:
+  homepage: https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html
+  documentation: https://support.illumina.com/downloads/bcl-convert-user-guide.html
+license: Proprietary
+authors:
+  - __merge__: /src/_authors/toni_verbeiren.yaml
+    roles: [ author, maintainer ]
+  - __merge__: /src/_authors/dorien_roosen.yaml
+    roles: [ author ]
+
+argument_groups:
+  - name: Input arguments
+    arguments:
+      - name: "--bcl_input_directory"
+        alternatives: ["-i"]
+        type: file
+        required: true
+        description: Input run directory
+        example: bcl_dir
+      - name: "--sample_sheet"
+        alternatives: ["-s"]
+        type: file
+        description: Path to SampleSheet.csv file (default searched for in --bcl_input_directory)
+        example: bcl_dir/sample_sheet.csv
+      - name: --run_info
+        type: file
+        description: Path to RunInfo.xml file (default root of BCL input directory)
+        example: bcl_dir/RunInfo.xml
+
+  - name: Lane and tile settings
+    arguments:
+      - name: "--bcl_only_lane"
+        type: integer
+        description: Convert only specified lane number (default all lanes)
+        example: 1
+      - name: --first_tile_only
+        type: boolean
+        description: Only convert first tile of input (for testing & debugging)
+        example: true
+      - name: --tiles
+        type: string
+        description: Process only a subset of tiles by a regular expression
+        example: "s_[0-9]+_1"
+      - name: --exclude_tiles
+        type: string
+        description: Exclude set of tiles by a regular expression
+        example: "s_[0-9]+_1"
+
+  - name: Resource arguments
+    arguments:
+      - name: --shared_thread_odirect_output
+        type: boolean
+        description: Use linux native asynchronous io (io_submit) for file output (Default=false)
+        example: true
+      - name: --bcl_num_parallel_tiles
+        type: integer
+        description: "\\# of tiles to process in parallel (default 1)"
+        example: 1
+      - name: --bcl_num_conversion_threads
+        type: integer
+        description: "\\# of threads for conversion (per tile, default # cpu threads)"
+        example: 1
+      - name: --bcl_num_compression_threads
+        type: integer
+        description: "\\# of threads for fastq.gz output compression (per tile, default # cpu threads, or HW+12)"
+        example: 1
+      - name: --bcl_num_decompression_threads
+        type: integer
+        description:
+          "\\# of threads for bcl/cbcl input decompression (per tile, default half # cpu threads, or HW+8).
+          Only applies when preloading files"
+        example: 1
+
+  - name: Run arguments
+    arguments:
+      - name: --bcl_only_matched_reads
+        type: boolean
+        description: For pure BCL conversion, do not output files for 'Undetermined' [unmatched] reads (output by default)
+        example: true
+      - name: --no_lane_splitting
+        type: boolean
+        description: Do not split FASTQ file by lane (false by default)
+        example: true
+      - name: --num_unknown_barcodes_reported
+        type: integer
+        description: "\\# of Top Unknown Barcodes to output (1000 by default)"
+        example: 1000
+      - name: --bcl_validate_sample_sheet_only
+        type: boolean
+        description: Only validate RunInfo.xml & SampleSheet files (produce no FASTQ files)
+        example: true
+      - name: --strict_mode
+        type: boolean
+        description: Abort if any files are missing (false by default)
+        example: true
+      - name: --sample_name_column_enabled
+        type: boolean
+        description: Use sample sheet 'Sample_Name' column when naming fastq files & subdirectories
+        example: true
+
+  - name: Output arguments
+    arguments:
+      - name: "--output_directory"
+        alternatives: ["-o"]
+        type: file
+        direction: output
+        required: true
+        description: Output directory containig fastq files
+        example: fastq_dir
+      - name: --bcl_sampleproject_subdirectories
+        type: boolean
+        description: Output to subdirectories based upon sample sheet 'Sample_Project' column
+        example: true
+      - name: --fastq_gzip_compression_level
+        type: integer
+        description: Set fastq output compression level 0-9 (default 1)
+        example: 1
+      - name: "--reports"
+        type: file
+        direction: output
+        required: false
+        description: Reports directory
+        example: reports_dir
+      - name: "--logs"
+        type: file
+        direction: output
+        required: false
+        description: Reports directory
+        example: logs_dir
+
+# bcl-convert arguments not taken into account
+#   --force
+#   --output-legacy-stats arg              Also output stats in legacy (bcl2fastq2) format (false by default)
+#   --no-sample-sheet arg                  Enable legacy no-sample-sheet operation (No demux or trimming. No settings
+
+resources:
+  - type: bash_script
+    path: script.sh
+
+test_resources:
+  - type: bash_script
+    path: test.sh
+
+engines:
+  - type: docker
+    image: debian:trixie-slim
+    # https://support.illumina.com/sequencing/sequencing_software/bcl-convert/downloads.html
+    setup:
+      - type: apt
+        packages: [wget, gdb, which, hostname, alien, procps]
+      - type: docker
+        run: |
+          wget https://s3.amazonaws.com/webdata.illumina.com/downloads/software/bcl-convert/bcl-convert-4.2.7-2.el8.x86_64.rpm -O /tmp/bcl-convert.rpm && \
+          alien -i /tmp/bcl-convert.rpm && \
+          rm -rf /var/lib/apt/lists/* && \
+          rm /tmp/bcl-convert.rpm
+      - type: docker
+        run: |
+          echo "bcl-convert: \"$(bcl-convert -V 2>&1 >/dev/null | sed -n '/Version/ s/^bcl-convert\ Version //p')\"" > /var/software_versions.txt
+
+runners:
+  - type: executable
+  - type: nextflow
--- a/src/bcl_convert/help.txt
+++ b/src/bcl_convert/help.txt
@@ -0,0 +1,38 @@
+bcl-convert Version 00.000.000.4.2.7
+Copyright (c) 2014-2022 Illumina, Inc.
+
+Run BCL Conversion (BCL directory to *.fastq.gz)
+  bcl-convert --bcl-input-directory <BCL_ROOT_DIR> --output-directory <PATH> [options]
+
+Options:
+  -h [ --help ]                          Print this help message
+  -V [ --version ]                       Print the version and exit
+  --output-directory arg                 Output BCL directory for BCL conversion (must be specified)
+  -f [ --force ]                         Force: allow destination diretory to already exist
+  --bcl-input-directory arg              Input BCL directory for BCL conversion (must be specified)
+  --sample-sheet arg                     Path to SampleSheet.csv file (default searched for in --bcl-input-directory)
+  --bcl-only-lane arg                    Convert only specified lane number (default all lanes)
+  --strict-mode arg                      Abort if any files are missing (false by default)
+  --first-tile-only arg                  Only convert first tile of input (for testing & debugging)
+  --tiles arg                            Process only a subset of tiles by a regular expression
+  --exclude-tiles arg                    Exclude set of tiles by a regular expression
+  --bcl-sampleproject-subdirectories arg Output to subdirectories based upon sample sheet 'Sample_Project' column
+  --sample-name-column-enabled arg       Use sample sheet 'Sample_Name' column when naming fastq files & subdirectories
+  --fastq-gzip-compression-level arg     Set fastq output compression level 0-9 (default 1)
+  --shared-thread-odirect-output arg     Use linux native asynchronous io (io_submit) for file output (Default=false)
+  --bcl-num-parallel-tiles arg           # of tiles to process in parallel (default 1)
+  --bcl-num-conversion-threads arg       # of threads for conversion (per tile, default # cpu threads)
+  --bcl-num-compression-threads arg      # of threads for fastq.gz output compression (per tile, default # cpu threads,
+                                         or HW+12)
+  --bcl-num-decompression-threads arg    # of threads for bcl/cbcl input decompression (per tile, default half # cpu
+                                         threads, or HW+8. Only applies when preloading files)
+  --bcl-only-matched-reads arg           For pure BCL conversion, do not output files for 'Undetermined' [unmatched]
+                                         reads (output by default)
+  --run-info arg                         Path to RunInfo.xml file (default root of BCL input directory)
+  --no-lane-splitting arg                Do not split FASTQ file by lane (false by default)
+  --num-unknown-barcodes-reported arg    # of Top Unknown Barcodes to output (1000 by default)
+  --bcl-validate-sample-sheet-only arg   Only validate RunInfo.xml & SampleSheet files (produce no FASTQ files)
+  --output-legacy-stats arg              Also output stats in legacy (bcl2fastq2) format (false by default)
+  --no-sample-sheet arg                  Enable legacy no-sample-sheet operation (No demux or trimming. No settings
+                                         supported. False by default, not recommended
+
--- a/src/bcl_convert/script.sh
+++ b/src/bcl_convert/script.sh
@@ -0,0 +1,40 @@
+#!/bin/bash
+
+set -eo pipefail
+
+$(which bcl-convert) \
+ --bcl-input-directory "$par_bcl_input_directory" \
+ --output-directory "$par_output_directory" \
+  ${par_sample_sheet:+ --sample-sheet "$par_sample_sheet"} \
+  ${par_run_info:+ --run-info "$par_run_info"} \
+  ${par_bcl_only_lane:+ --bcl-only-lane "$par_bcl_only_lane"} \
+  ${par_first_tile_only:+ --first-tile-only "$par_first_tile_only"} \
+  ${par_tiles:+ --tiles "$par_tiles"} \
+  ${par_exclude_tiles:+ --exclude-tiles "$par_exclude_tiles"} \
+  ${par_shared_thread_odirect_output:+ --shared-thread-odirect-output "$par_shared_thread_odirect_output"} \
+  ${par_bcl_num_parallel_tiles:+ --bcl-num-parallel-tiles "$par_bcl_num_parallel_tiles"} \
+  ${par_bcl_num_conversion_threads:+ --bcl-num-conversion-threads "$par_bcl_num_conversion_threads"} \
+  ${par_bcl_num_compression_threads:+ --bcl-num-compression-threads "$par_bcl_num_compression_threads"} \
+  ${par_bcl_num_decompression_threads:+ --bcl-num-decompression-threads "$par_bcl_num_decompression_threads"} \
+  ${par_bcl_only_matched_reads:+ --bcl-only-matched-reads "$par_bcl_only_matched_reads"} \
+  ${par_no_lane_splitting:+ --no-lane-splitting "$par_no_lane_splitting"} \
+  ${par_num_unknown_barcodes_reported:+ --num-unknown-barcodes-reported "$par_num_unknown_barcodes_reported"} \
+  ${par_bcl_validate_sample_sheet_only:+ --bcl-validate-sample-sheet-only "$par_bcl_validate_sample_sheet_only"} \
+  ${par_strict_mode:+ --strict-mode "$par_strict_mode"} \
+  ${par_sample_name_column_enabled:+ --sample-name-column-enabled "$par_sample_name_column_enabled"} \
+  ${par_bcl_sampleproject_subdirectories:+ --bcl-sampleproject-subdirectories "$par_bcl_sampleproject_subdirectories"} \
+  ${par_fastq_gzip_compression_level:+ --fastq-gzip-compression-level "$par_fastq_gzip_compression_level"}
+
+if [ ! -z "$par_reports" ]; then
+  echo "Moving reports to their own location"
+  mv "${par_output_directory}/Reports" "$par_reports"
+else
+  echo "Leaving reports alone"
+fi
+
+if [ ! -z "$par_logs" ]; then
+  echo "Moving logs to their own location"
+  mv "${par_output_directory}/Logs" "$par_logs"
+else
+  echo "Leaving logs alone"
+fi
--- a/src/bcl_convert/test.sh
+++ b/src/bcl_convert/test.sh
@@ -0,0 +1,70 @@
+#!/bin/bash
+
+# Tests are sourced from:
+#   https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/inputs/cr-direct-demultiplexing-bcl-convert
+# Test input files are fetched from:
+# https://cf.10xgenomics.com/supp/spatial-exp/demultiplexing/iseq-DI.tar.gz
+# https://cf.10xgenomics.com/supp/spatial-exp/demultiplexing/bcl_convert_samplesheet.csv
+
+set -eo pipefail
+
+echo ">> Fetching and preparing test data"
+data_src="https://cf.10xgenomics.com/supp/spatial-exp/demultiplexing/iseq-DI.tar.gz"
+sample_sheet_src="https://cf.10xgenomics.com/supp/spatial-exp/demultiplexing/bcl_convert_samplesheet.csv"
+test_data_dir="test_data"
+
+mkdir $test_data_dir
+wget -q $data_src -O $test_data_dir/data.tar.gz
+wget -q $sample_sheet_src -O $test_data_dir/sample_sheet.csv
+tar xzf $test_data_dir/data.tar.gz -C $test_data_dir
+rm $test_data_dir/data.tar.gz
+
+echo ">> Execute and verify output"
+
+$meta_executable \
+  --bcl_input_directory "$test_data_dir/iseq-DI" \
+  --sample_sheet "$test_data_dir/sample_sheet.csv" \
+  --output_directory fastq \
+  --reports reports \
+  --logs logs
+
+echo ">>> Checking whether the output dir exists"
+[[ ! -d fastq ]] && echo "Output dir could not be found!" && exit 1
+
+echo ">>> Checking whether output fastq files are created"
+[[ ! -f fastq/Undetermined_S0_L001_R1_001.fastq.gz ]] && echo "Output fastq files could not be found!" && exit 1
+[[ ! -f fastq/iseq-DI_S1_L001_R1_001.fastq.gz ]] && echo "Output fastq files could not be found!" && exit 1
+
+echo ">>> Checking whether the report dir exists"
+[[ ! -d reports ]] && echo "Reports dir could not be found!" && exit 1
+
+echo ">>> Checking whether the log dir exists"
+[[ ! -d logs ]] && echo "Logs dir could not be found!" && exit 1
+
+# print final message
+echo ">>> Test finished successfully"
+
+echo ">> Execute with additional arguments and verify output"
+
+$meta_executable \
+  --bcl_input_directory "$test_data_dir/iseq-DI" \
+  --sample_sheet "$test_data_dir/sample_sheet.csv" \
+  --output_directory fastq1 \
+  --bcl_only_matched_reads true \
+  --bcl_num_compression_threads 1 \
+  --no_lane_splitting false \
+  --fastq_gzip_compression_level 9
+
+echo ">> Checking whether the output dir exists"
+[[ ! -d fastq1 ]] && echo "Output dir could not be found!" && exit 1
+
+echo ">> Checking whether output fastq files are created"
+[[ -f fastq1/Undetermined_S0_L001_R1_001.fastq.gz ]] && echo "Undetermined should not be generated!" && exit 1
+[[ ! -f fastq1/iseq-DI_S1_L001_R1_001.fastq.gz ]] && echo "Output fastq files could not be found!" && exit 1
+
+# print final message
+echo ">> Test finished successfully"
+
+# do not remove this
+# as otherwise your test might exit with a different exit code
+exit 0
--- a/src/bd_rhapsody/bd_rhapsody_make_reference/config.vsh.yaml
+++ b/src/bd_rhapsody/bd_rhapsody_make_reference/config.vsh.yaml
@@ -0,0 +1,143 @@
+name: bd_rhapsody_make_reference
+namespace: bd_rhapsody
+description: |
+  The Reference Files Generator creates an archive containing Genome Index
+  and Transcriptome annotation files needed for the BD Rhapsody Sequencing
+  Analysis Pipeline. The app takes as input one or more FASTA and GTF files
+  and produces a compressed archive in the form of a tar.gz file. The 
+  archive contains:
+  
+  - STAR index
+  - Filtered GTF file
+keywords: [genome, reference, index, align]
+links:
+  repository: https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/
+  documentation: https://bd-rhapsody-bioinfo-docs.genomics.bd.com/resources/extra_utilities.html#make-rhapsody-reference
+license: Unknown
+authors:
+  - __merge__: /src/_authors/robrecht_cannoodt.yaml
+    roles: [ author, maintainer ]
+  - __merge__: /src/_authors/weiwei_schultz.yaml
+    roles: [ contributor ]
+
+argument_groups:
+  - name: Inputs
+    arguments:
+      - type: file
+        name: --genome_fasta
+        required: true
+        description: Reference genome file in FASTA or FASTA.GZ format. The BD Rhapsody Sequencing Analysis Pipeline uses GRCh38 for Human and GRCm39 for Mouse.
+        example: genome_sequence.fa.gz
+        multiple: true
+        info:
+          config_key: Genome_fasta
+      - type: file
+        name: --gtf
+        required: true
+        description: |
+          File path to the transcript annotation files in GTF or GTF.GZ format. The Sequence Analysis Pipeline requires the 'gene_name' or 
+          'gene_id' attribute to be set on each gene and exon feature. Gene and exon feature lines must have the same attribute, and exons
+          must have a corresponding gene with the same value. For TCR/BCR assays, the TCR or BCR gene segments must have the 'gene_type' or
+          'gene_biotype' attribute set, and the value should begin with 'TR' or 'IG', respectively.
+        example: transcriptome_annotation.gtf.gz
+        multiple: true
+        info:
+          config_key: Gtf
+      - type: file
+        name: --extra_sequences
+        description: |
+          File path to additional sequences in FASTA format to use when building the STAR index. (e.g. transgenes or CRISPR guide barcodes).
+          GTF lines for these sequences will be automatically generated and combined with the main GTF.
+        required: false
+        multiple: true
+        info:
+          config_key: Extra_sequences
+  - name: Outputs
+    arguments:
+      - type: file
+        name: --reference_archive
+        direction: output
+        required: true
+        description: |
+          A Compressed archive containing the Reference Genome Index and annotation GTF files. This archive is meant to be used as an
+          input in the BD Rhapsody Sequencing Analysis Pipeline.
+        example: star_index.tar.gz
+  - name: Arguments
+    arguments:
+      - type: string
+        name: --mitochondrial_contigs
+        description: |
+          Names of the Mitochondrial contigs in the provided Reference Genome. Fragments originating from contigs other than these are
+          identified as 'nuclear fragments' in the ATACseq analysis pipeline.
+        required: false
+        multiple: true
+        default: [chrM, chrMT, M, MT]
+        info:
+          config_key: Mitochondrial_contigs
+      - type: boolean_true
+        name: --filtering_off
+        description: |
+          By default the input Transcript Annotation files are filtered based on the gene_type/gene_biotype attribute. Only features 
+          having the following attribute values are kept:
+
+            - protein_coding
+            - lncRNA (lincRNA and antisense for Gencode < v31/M22/Ensembl97)
+            - IG_LV_gene
+            - IG_V_gene
+            - IG_V_pseudogene
+            - IG_D_gene
+            - IG_J_gene
+            - IG_J_pseudogene
+            - IG_C_gene
+            - IG_C_pseudogene
+            - TR_V_gene
+            - TR_V_pseudogene
+            - TR_D_gene
+            - TR_J_gene
+            - TR_J_pseudogene
+            - TR_C_gene
+
+            If you have already pre-filtered the input Annotation files and/or wish to turn-off the filtering, please set this option to True.
+        info:
+          config_key: Filtering_off
+      - type: boolean_true
+        name: --wta_only_index
+        description: Build a WTA only index, otherwise builds a WTA + ATAC index.
+        info:
+          config_key: Wta_Only
+      - type: string
+        name: --extra_star_params
+        description: Additional parameters to pass to STAR when building the genome index. Specify exactly like how you would on the command line.
+        example: --limitGenomeGenerateRAM 48000 --genomeSAindexNbases 11
+        required: false
+        info:
+          config_key: Extra_STAR_params
+
+resources:
+  - type: python_script
+    path: script.py
+  - path: make_rhap_reference_2.2.1_nodocker.cwl
+
+test_resources:
+  - type: bash_script
+    path: test.sh
+  - path: test_data
+
+requirements:
+  commands: [ "cwl-runner" ]
+
+engines:
+  - type: docker
+    image: bdgenomics/rhapsody:2.2.1
+    setup:
+      - type: apt
+        packages: [procps]
+      - type: python
+        packages: [cwlref-runner, cwl-runner]
+      - type: docker
+        run: |
+          echo "bdgenomics/rhapsody: 2.2.1" > /var/software_versions.txt
+
+runners:
+  - type: executable
+  - type: nextflow
--- a/src/bd_rhapsody/bd_rhapsody_make_reference/help.txt
+++ b/src/bd_rhapsody/bd_rhapsody_make_reference/help.txt
@@ -0,0 +1,66 @@
+```bash
+cwl-runner src/bd_rhapsody/bd_rhapsody_make_reference/make_rhap_reference_2.2.1_nodocker.cwl --help
+```
+
+usage: src/bd_rhapsody/bd_rhapsody_make_reference/make_rhap_reference_2.2.1_nodocker.cwl
+       [-h] [--Archive_prefix ARCHIVE_PREFIX]
+       [--Extra_STAR_params EXTRA_STAR_PARAMS]
+       [--Extra_sequences EXTRA_SEQUENCES] [--Filtering_off] --Genome_fasta
+       GENOME_FASTA --Gtf GTF [--Maximum_threads MAXIMUM_THREADS]
+       [--Mitochondrial_Contigs MITOCHONDRIAL_CONTIGS] [--WTA_Only]
+       [job_order]
+
+The Reference Files Generator creates an archive containing Genome Index and
+Transcriptome annotation files needed for the BD Rhapsodyâ„¢ Sequencing
+Analysis Pipeline. The app takes as input one or more FASTA and GTF files and
+produces a compressed archive in the form of a tar.gz file. The archive
+contains:\n - STAR index\n - Filtered GTF file
+
+positional arguments:
+  job_order             Job input json file
+
+options:
+  -h, --help            show this help message and exit
+  --Archive_prefix ARCHIVE_PREFIX
+                        A prefix for naming the compressed archive file
+                        containing the Reference genome index and annotation
+                        files. The default value is constructed based on the
+                        input Reference files.
+  --Extra_STAR_params EXTRA_STAR_PARAMS
+                        Additional parameters to pass to STAR when building
+                        the genome index. Specify exactly like how you would
+                        on the command line. Example: --limitGenomeGenerateRAM
+                        48000 --genomeSAindexNbases 11
+  --Extra_sequences EXTRA_SEQUENCES
+                        Additional sequences in FASTA format to use when
+                        building the STAR index. (E.g. phiX genome)
+  --Filtering_off       By default the input Transcript Annotation files are
+                        filtered based on the gene_type/gene_biotype
+                        attribute. Only features having the following
+                        attribute values are are kept: - protein_coding -
+                        lncRNA (lincRNA and antisense for Gencode <
+                        v31/M22/Ensembl97) - IG_LV_gene - IG_V_gene -
+                        IG_V_pseudogene - IG_D_gene - IG_J_gene -
+                        IG_J_pseudogene - IG_C_gene - IG_C_pseudogene -
+                        TR_V_gene - TR_V_pseudogene - TR_D_gene - TR_J_gene -
+                        TR_J_pseudogene - TR_C_gene If you have already pre-
+                        filtered the input Annotation files and/or wish to
+                        turn-off the filtering, please set this option to
+                        True.
+  --Genome_fasta GENOME_FASTA
+                        Reference genome file in FASTA format. The BD
+                        Rhapsodyâ„¢ Sequencing Analysis Pipeline uses GRCh38
+                        for Human and GRCm39 for Mouse.
+  --Gtf GTF             Transcript annotation files in GTF format. The BD
+                        Rhapsodyâ„¢ Sequencing Analysis Pipeline uses Gencode
+                        v42 for Human and M31 for Mouse.
+  --Maximum_threads MAXIMUM_THREADS
+                        The maximum number of threads to use in the pipeline.
+                        By default, all available cores are used.
+  --Mitochondrial_Contigs MITOCHONDRIAL_CONTIGS
+                        Names of the Mitochondrial contigs in the provided
+                        Reference Genome. Fragments originating from contigs
+                        other than these are identified as 'nuclear fragments'
+                        in the ATACseq analysis pipeline.
+  --WTA_Only            Build a WTA only index, otherwise builds a WTA + ATAC
+                        index.
--- a/src/bd_rhapsody/bd_rhapsody_make_reference/make_rhap_reference_2.2.1_nodocker.cwl
+++ b/src/bd_rhapsody/bd_rhapsody_make_reference/make_rhap_reference_2.2.1_nodocker.cwl
@@ -0,0 +1,115 @@
+requirements:
+  InlineJavascriptRequirement: {}
+class: CommandLineTool
+label: Reference Files Generator for BD Rhapsodyâ„¢ Sequencing Analysis Pipeline
+cwlVersion: v1.2
+doc: >- 
+    The Reference Files Generator creates an archive containing Genome Index and Transcriptome annotation files needed for the BD Rhapsodyâ„¢ Sequencing Analysis Pipeline. The app takes as input one or more FASTA and GTF files and produces a compressed archive in the form of a tar.gz file. The archive contains:\n  - STAR index\n  - Filtered GTF file
+
+
+baseCommand: run_reference_generator.sh 
+inputs: 
+    Genome_fasta:
+        type: File[]
+        label: Reference Genome
+        doc: |-
+            Reference genome file in FASTA format. The BD Rhapsodyâ„¢ Sequencing Analysis Pipeline uses GRCh38 for Human and GRCm39 for Mouse.
+        inputBinding:
+            prefix: --reference-genome
+            shellQuote: false
+    Gtf:
+        type: File[]
+        label: Transcript Annotations
+        doc: |-
+            Transcript annotation files in GTF format. The BD Rhapsodyâ„¢ Sequencing Analysis Pipeline uses Gencode v42 for Human and M31 for Mouse.
+        inputBinding:
+            prefix: --gtf
+            shellQuote: false
+    Extra_sequences:
+        type: File[]?
+        label: Extra Sequences
+        doc: |-
+            Additional sequences in FASTA format to use when building the STAR index. (E.g. phiX genome)
+        inputBinding:
+            prefix: --extra-sequences
+            shellQuote: false
+    Mitochondrial_Contigs:
+        type: string[]?
+        default: ["chrM", "chrMT", "M", "MT"]
+        label: Mitochondrial Contig Names
+        doc: |-
+            Names of the Mitochondrial contigs in the provided Reference Genome. Fragments originating from contigs other than these are identified as 'nuclear fragments' in the ATACseq analysis pipeline.
+        inputBinding:
+            prefix: --mitochondrial-contigs
+            shellQuote: false
+    Filtering_off:
+        type: boolean?
+        label: Turn off filtering
+        doc: |-
+            By default the input Transcript Annotation files are filtered based on the gene_type/gene_biotype attribute. Only features having the following attribute values are are kept:
+            - protein_coding
+            - lncRNA (lincRNA and antisense for Gencode < v31/M22/Ensembl97)
+            - IG_LV_gene
+            - IG_V_gene
+            - IG_V_pseudogene
+            - IG_D_gene
+            - IG_J_gene
+            - IG_J_pseudogene
+            - IG_C_gene
+            - IG_C_pseudogene
+            - TR_V_gene
+            - TR_V_pseudogene
+            - TR_D_gene
+            - TR_J_gene
+            - TR_J_pseudogene
+            - TR_C_gene
+            If you have already pre-filtered the input Annotation files and/or wish to turn-off the filtering, please set this option to True.
+        inputBinding: 
+            prefix: --filtering-off
+            shellQuote: false
+    WTA_Only:
+        type: boolean?
+        label: WTA only index
+        doc: Build a WTA only index, otherwise builds a WTA + ATAC index.
+        inputBinding:
+            prefix: --wta-only-index
+            shellQuote: false
+    Archive_prefix:
+        type: string?
+        label: Archive Prefix
+        doc: |-
+            A prefix for naming the compressed archive file containing the Reference genome index and annotation files. The default value is constructed based on the input Reference files.
+        inputBinding:
+            prefix: --archive-prefix
+            shellQuote: false
+    Extra_STAR_params:
+        type: string?
+        label: Extra STAR Params
+        doc: |-
+            Additional parameters to pass to STAR when building the genome index. Specify exactly like how you would on the command line.
+            Example:
+              --limitGenomeGenerateRAM 48000 --genomeSAindexNbases 11
+        inputBinding:
+            prefix: --extra-star-params 
+            shellQuote: true
+  
+    Maximum_threads:
+        type: int?
+        label: Maximum Number of Threads
+        doc: |-
+            The maximum number of threads to use in the pipeline. By default, all available cores are used.
+        inputBinding:
+            prefix: --maximum-threads
+            shellQuote: false
+
+outputs:
+
+    Archive:
+        type: File
+        doc: |- 
+            A Compressed archive containing the Reference Genome Index and annotation GTF files. This archive is meant to be used as an input in the BD Rhapsodyâ„¢ Sequencing Analysis Pipeline.
+        id: Reference_Archive
+        label: Reference Files Archive
+        outputBinding:
+            glob: '*.tar.gz'
+
--- a/src/bd_rhapsody/bd_rhapsody_make_reference/script.py
+++ b/src/bd_rhapsody/bd_rhapsody_make_reference/script.py
@@ -0,0 +1,161 @@
+import os
+import re
+import subprocess
+import tempfile
+from typing import Any
+import yaml
+import shutil
+
+## VIASH START
+par = {
+    "genome_fasta": [],
+    "gtf": [],
+    "extra_sequences": [],
+    "mitochondrial_contigs": ["chrM", "chrMT", "M", "MT"],
+    "filtering_off": False,
+    "wta_only_index": False,
+    "extra_star_params": None,
+    "reference_archive": "output.tar.gz",
+}
+meta = {
+    "config": "target/nextflow/reference/build_bdrhap_2_reference/.config.vsh.yaml",
+    "resources_dir": os.path.abspath("src/reference/build_bdrhap_2_reference"),
+    "temp_dir": os.getenv("VIASH_TEMP"),
+    "memory_mb": None,
+    "cpus": None
+}
+## VIASH END
+
+def clean_arg(argument):
+    argument["clean_name"] = re.sub("^-*", "", argument["name"])
+    return argument
+
+def read_config(path: str) -> dict[str, Any]:
+    with open(path, "r") as f:
+        config = yaml.safe_load(f)
+    
+    config["all_arguments"] = [
+        clean_arg(arg)
+        for grp in config["argument_groups"]
+        for arg in grp["arguments"]
+    ]
+    
+    return config
+
+def strip_margin(text: str) -> str:
+    return re.sub("(\n?)[ \t]*\|", "\\1", text)
+
+def process_params(par: dict[str, Any], config) -> str:
+    # check input parameters
+    assert par["genome_fasta"], "Pass at least one set of inputs to --genome_fasta."
+    assert par["gtf"], "Pass at least one set of inputs to --gtf."
+    assert par["reference_archive"].endswith(".tar.gz"), "Output reference_archive must end with .tar.gz."
+
+    # make paths absolute
+    for argument in config["all_arguments"]:
+        if par[argument["clean_name"]] and argument["type"] == "file":
+            if isinstance(par[argument["clean_name"]], list):
+                par[argument["clean_name"]] = [ os.path.abspath(f) for f in par[argument["clean_name"]] ]
+            else:
+                par[argument["clean_name"]] = os.path.abspath(par[argument["clean_name"]])
+    
+    return par
+
+def generate_config(par: dict[str, Any], meta, config) -> str:
+    content_list = [strip_margin(f"""\
+        |#!/usr/bin/env cwl-runner
+        |
+        |""")]
+        
+    
+    config_key_value_pairs = []
+    for argument in config["all_arguments"]:
+        config_key = (argument.get("info") or {}).get("config_key")
+        arg_type = argument["type"]
+        par_value = par[argument["clean_name"]]
+        if par_value and config_key:
+            config_key_value_pairs.append((config_key, arg_type, par_value))
+
+    if meta["cpus"]:
+        config_key_value_pairs.append(("Maximum_threads", "integer", meta["cpus"]))
+
+    # print(config_key_value_pairs)
+
+    for config_key, arg_type, par_value in config_key_value_pairs:
+        if arg_type == "file":
+            str = strip_margin(f"""\
+                |{config_key}:
+                |""")
+            if isinstance(par_value, list):
+                for file in par_value:
+                    str += strip_margin(f"""\
+                        | - class: File
+                        |   location: "{file}"
+                        |""")
+            else:
+                str += strip_margin(f"""\
+                    |   class: File
+                    |   location: "{par_value}"
+                    |""")
+            content_list.append(str)
+        else:
+            content_list.append(strip_margin(f"""\
+                |{config_key}: {par_value}
+                |"""))
+            
+    ## Write config to file
+    return "".join(content_list)
+
+def get_cwl_file(meta: dict[str, Any]) -> str:
+    # create cwl file (if need be)
+    cwl_file=os.path.join(meta["resources_dir"], "make_rhap_reference_2.2.1_nodocker.cwl")
+
+    return cwl_file
+
+def main(par: dict[str, Any], meta: dict[str, Any]):
+    config = read_config(meta["config"])
+        
+    # Preprocess params
+    par = process_params(par, config)
+
+    # fetch cwl file
+    cwl_file = get_cwl_file(meta)
+
+    # Create output dir if not exists
+    outdir = os.path.dirname(par["reference_archive"])
+    if not os.path.exists(outdir):
+        os.makedirs(outdir)
+
+    ## Run pipeline
+    with tempfile.TemporaryDirectory(prefix="cwl-bd_rhapsody_wta-", dir=meta["temp_dir"]) as temp_dir:
+        # Create params file
+        config_file = os.path.join(temp_dir, "config.yml")
+        config_content = generate_config(par, meta, config)
+        with open(config_file, "w") as f:
+            f.write(config_content)
+
+
+        cmd = [
+            "cwl-runner",
+            "--no-container",
+            "--preserve-entire-environment",
+            "--outdir",
+            temp_dir,
+            cwl_file,
+            config_file
+        ]
+
+        env = dict(os.environ)
+        env["TMPDIR"] = temp_dir
+
+        print("> " + " ".join(cmd), flush=True)
+        _ = subprocess.check_call(
+            cmd,
+            cwd=os.path.dirname(config_file),
+            env=env
+        )
+
+        shutil.move(os.path.join(temp_dir, "Rhap_reference.tar.gz"), par["reference_archive"])
+
+if __name__ == "__main__":
+    main(par, meta)
--- a/src/bd_rhapsody/bd_rhapsody_make_reference/test.sh
+++ b/src/bd_rhapsody/bd_rhapsody_make_reference/test.sh
@@ -0,0 +1,65 @@
+#!/bin/bash
+
+set -e
+
+#############################################
+# helper functions
+assert_file_exists() {
+  [ -f "$1" ] || { echo "File '$1' does not exist" && exit 1; }
+}
+assert_file_doesnt_exist() {
+  [ ! -f "$1" ] || { echo "File '$1' exists but shouldn't" && exit 1; }
+}
+assert_file_empty() {
+  [ ! -s "$1" ] || { echo "File '$1' is not empty but should be" && exit 1; }
+}
+assert_file_not_empty() {
+  [ -s "$1" ] || { echo "File '$1' is empty but shouldn't be" && exit 1; }
+}
+assert_file_contains() {
+  grep -q "$2" "$1" || { echo "File '$1' does not contain '$2'" && exit 1; }
+}
+assert_file_not_contains() {
+  grep -q "$2" "$1" && { echo "File '$1' contains '$2' but shouldn't" && exit 1; }
+}
+#############################################
+
+in_fa="$meta_resources_dir/test_data/reference_small.fa"
+in_gtf="$meta_resources_dir/test_data/reference_small.gtf"
+
+echo "#############################################"
+echo "> Simple run"
+
+mkdir simple_run
+cd simple_run
+
+out_tar="myreference.tar.gz"
+
+echo "> Running $meta_name."
+$meta_executable \
+  --genome_fasta "$in_fa" \
+  --gtf "$in_gtf" \
+  --reference_archive "$out_tar" \
+  --extra_star_params "--genomeSAindexNbases 6" \
+  ---cpus 2
+
+exit_code=$?
+[[ $exit_code != 0 ]] && echo "Non zero exit code: $exit_code" && exit 1
+
+assert_file_exists "$out_tar"
+assert_file_not_empty "$out_tar"
+
+echo ">> Checking whether output contains the expected files"
+tar -xvf "$out_tar" > /dev/null
+assert_file_exists "BD_Rhapsody_Reference_Files/star_index/genomeParameters.txt"
+assert_file_exists "BD_Rhapsody_Reference_Files/bwa-mem2_index/reference_small.ann"
+assert_file_exists "BD_Rhapsody_Reference_Files/reference_small-processed.gtf"
+assert_file_exists "BD_Rhapsody_Reference_Files/mitochondrial_contigs.txt"
+assert_file_contains "BD_Rhapsody_Reference_Files/reference_small-processed.gtf" "chr1.*HAVANA.*ENSG00000243485"
+assert_file_contains "BD_Rhapsody_Reference_Files/mitochondrial_contigs.txt" 'chrMT'
+
+cd ..
+
+echo "#############################################"
+
+echo "> Tests succeeded!"
--- a/src/bd_rhapsody/bd_rhapsody_make_reference/test_data/reference_small.fa
+++ b/src/bd_rhapsody/bd_rhapsody_make_reference/test_data/reference_small.fa
@@ -0,0 +1,27 @@
+>chr1 1
+TGGGGAAGCAAGGCGGAGTTGGGCAGCTCGTGTTCAATGGGTAGAGTTTCAGGCTGGGGT
+GATGGAAGGGTGCTGGAAATGAGTGGTAGTGATGGCGGCACAACAGTGTGAATCTACTTA
+ATCCCACTGAACTGTATGCTGAAAAATGGTTTAGACGGTGAATTTTAGGTTATGTATGTT
+TTACCACAATTTTTAAAAAGCTAGTGAAAAGCTGGTAAAAAGAAAGAAAAGAGGCTTTTT
+TAAAAAGTTAAATATATAAAAAGAGCATCATCAGTCCAAAGTCCAGCAGTTGTCCCTCCT
+GGAATCCGTTGGCTTGCCTCCGGCATTTTTGGCCCTTGCCTTTTAGGGTTGCCAGATTAA
+AAGACAGGATGCCCAGCTAGTTTGAATTTTAGATAAACAACGAATAATTTCGTAGCATAA
+ATATGTCCCAAGCTTAGTTTGGGACATACTTATGCTAAAAAACATTATTGGTTGTTTATC
+TGAGATTCAGAATTAAGCATTTTATATTTTATTTGCTGCCTCTGGCCACCCTACTCTCTT
+CCTAACACTCTCTCCCTCTCCCAGTTTTGTCCGCCTTCCCTGCCTCCTCTTCTGGGGGAG
+TTAGATCGAGTTGTAACAAGAACATGCCACTGTCTCGCTGGCTGCAGCGTGTGGTCCCCT
+TACCAGAGGTAAAGAAGAGATGGATCTCCACTCATGTTGTAGACAGAATGTTTATGTCCT
+CTCCAAATGCTTATGTTGAAACCCTAACCCCTAATGTGATGGTATGTGGAGATGGGCCTT
+TGGTAGGTAATTACGGTTAGATGAGGTCATGGGGTGGGGCCCTCATTATAGATCTGGTAA
+GAAAAGAGAGCATTGTCTCTGTGTCTCCCTCTCTCTCTCTCTCTCTCTCTCTCATTTCTC
+TCTATCTCATTTCTCTCTCTCTCGCTATCTCATTTTTCTCTCTCTCTCTTTCTCTCCTCT
+GTCTTTTCCCACCAAGTGAGGATGCGAAGAGAAGGTGGCTGTCTGCAAACCAGGAAGAGA
+GCCCTCACCGGGAACCCGTCCAGCTGCCACCTTGAACTTGGACTTCCAAGCCTCCAGAAC
+TGTGAGGGATAAATGTATGATTTTAAAGTCGCCCAGTGTGTGGTATTTTGTTTTGACTAA
+TACAACCTGAAAACATTTTCCCCTCACTCCACCTGAGCAATATCTGAGTGGCTTAAGGTA
+CTCAGGACACAACAAAGGAGAAATGTCCCATGCACAAGGTGCACCCATGCCTGGGTAAAG
+CAGCCTGGCACAGAGGGAAGCACACAGGCTCAGGGATCTGCTATTCATTCTTTGTGTGAC
+CCTGGGCAAGCCATGAATGGAGCTTCAGTCACCCCATTTGTAATGGGATTTAATTGTGCT
+TGCCCTGCCTCCTTTTGAGGGCTGTAGAGAAAAGATGTCAAAGTATTTTGTAATCTGGCT
+GGGCGTGGTGGCTCATGCCTGTAATCCTAGCACTTTGGTAGGCTGACGCGAGAGGACTGC
+T
--- a/src/bd_rhapsody/bd_rhapsody_make_reference/test_data/reference_small.gtf
+++ b/src/bd_rhapsody/bd_rhapsody_make_reference/test_data/reference_small.gtf
@@ -0,0 +1,8 @@
+chr1	HAVANA	exon	565	668	.	+	.	gene_id "ENSG00000243485.5"; transcript_id "ENST00000473358.1"; gene_type "lncRNA"; gene_name "MIR1302-2HG"; transcript_type "lncRNA"; transcript_name "MIR1302-2HG-202"; exon_number 2; exon_id "ENSE00001922571.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:52482"; tag "not_best_in_genome_evidence"; tag "dotter_confirmed"; tag "basic"; tag "Ensembl_canonical"; havana_gene "OTTHUMG00000000959.2"; havana_transcript "OTTHUMT00000002840.1";
+chr1	HAVANA	exon	977	1098	.	+	.	gene_id "ENSG00000243485.5"; transcript_id "ENST00000473358.1"; gene_type "lncRNA"; gene_name "MIR1302-2HG"; transcript_type "lncRNA"; transcript_name "MIR1302-2HG-202"; exon_number 3; exon_id "ENSE00001827679.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:52482"; tag "not_best_in_genome_evidence"; tag "dotter_confirmed"; tag "basic"; tag "Ensembl_canonical"; havana_gene "OTTHUMG00000000959.2"; havana_transcript "OTTHUMT00000002840.1";
+chr1	HAVANA	transcript	268	1110	.	+	.	gene_id "ENSG00000243485.5"; transcript_id "ENST00000469289.1"; gene_type "lncRNA"; gene_name "MIR1302-2HG"; transcript_type "lncRNA"; transcript_name "MIR1302-2HG-201"; level 2; transcript_support_level "5"; hgnc_id "HGNC:52482"; tag "not_best_in_genome_evidence"; tag "basic"; havana_gene "OTTHUMG00000000959.2"; havana_transcript "OTTHUMT00000002841.2";
+chr1	HAVANA	exon	268	668	.	+	.	gene_id "ENSG00000243485.5"; transcript_id "ENST00000469289.1"; gene_type "lncRNA"; gene_name "MIR1302-2HG"; transcript_type "lncRNA"; transcript_name "MIR1302-2HG-201"; exon_number 1; exon_id "ENSE00001841699.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:52482"; tag "not_best_in_genome_evidence"; tag "basic"; havana_gene "OTTHUMG00000000959.2"; havana_transcript "OTTHUMT00000002841.2";
+chr1	HAVANA	exon	977	1110	.	+	.	gene_id "ENSG00000243485.5"; transcript_id "ENST00000469289.1"; gene_type "lncRNA"; gene_name "MIR1302-2HG"; transcript_type "lncRNA"; transcript_name "MIR1302-2HG-201"; exon_number 2; exon_id "ENSE00001890064.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:52482"; tag "not_best_in_genome_evidence"; tag "basic"; havana_gene "OTTHUMG00000000959.2"; havana_transcript "OTTHUMT00000002841.2";
+chr1	ENSEMBL	gene	367	504	.	+	.	gene_id "ENSG00000284332.1"; gene_type "miRNA"; gene_name "MIR1302-2"; level 3; hgnc_id "HGNC:35294";
+chr1	ENSEMBL	transcript	367	504	.	+	.	gene_id "ENSG00000284332.1"; transcript_id "ENST00000607096.1"; gene_type "miRNA"; gene_name "MIR1302-2"; transcript_type "miRNA"; transcript_name "MIR1302-2-201"; level 3; transcript_support_level "NA"; hgnc_id "HGNC:35294"; tag "basic"; tag "Ensembl_canonical";
+chr1	ENSEMBL	exon	367	504	.	+	.	gene_id "ENSG00000284332.1"; transcript_id "ENST00000607096.1"; gene_type "miRNA"; gene_name "MIR1302-2"; transcript_type "miRNA"; transcript_name "MIR1302-2-201"; exon_number 1; exon_id "ENSE00003695741.1"; level 3; transcript_support_level "NA"; hgnc_id "HGNC:35294"; tag "basic"; tag "Ensembl_canonical";
--- a/src/bd_rhapsody/bd_rhapsody_make_reference/test_data/script.sh
+++ b/src/bd_rhapsody/bd_rhapsody_make_reference/test_data/script.sh
@@ -0,0 +1,47 @@
+#!/bin/bash
+
+TMP_DIR=/tmp/bd_rhapsody_make_reference
+OUT_DIR=src/bd_rhapsody/bd_rhapsody_make_reference/test_data
+
+# check if seqkit is installed
+if ! command -v seqkit &> /dev/null; then
+  echo "seqkit could not be found"
+  exit 1
+fi
+
+# create temporary directory and clean up on exit
+mkdir -p $TMP_DIR
+function clean_up {
+    rm -rf "$TMP_DIR"
+}
+trap clean_up EXIT
+
+# fetch reference
+ORIG_FA=$TMP_DIR/reference.fa.gz
+if [ ! -f $ORIG_FA ]; then
+  wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_41/GRCh38.primary_assembly.genome.fa.gz \
+    -O $ORIG_FA
+fi
+
+ORIG_GTF=$TMP_DIR/reference.gtf.gz
+if [ ! -f $ORIG_GTF ]; then
+  wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_41/gencode.v41.annotation.gtf.gz \
+    -O $ORIG_GTF
+fi
+
+# create small reference
+START=30000
+END=31500
+CHR=chr1
+
+# subset to small region
+seqkit grep -r -p "^$CHR\$" "$ORIG_FA" | \
+  seqkit subseq -r "$START:$END" > $OUT_DIR/reference_small.fa
+
+zcat "$ORIG_GTF" | \
+  awk -v FS='\t' -v OFS='\t' "
+    \$1 == \"$CHR\" && \$4 >= $START && \$5 <= $END {
+      \$4 = \$4 - $START + 1;
+      \$5 = \$5 - $START + 1;
+      print;
+    }" > $OUT_DIR/reference_small.gtf
--- a/src/bedtools/bedtools_getfasta/config.vsh.yaml
+++ b/src/bedtools/bedtools_getfasta/config.vsh.yaml
@@ -0,0 +1,106 @@
+name: bedtools_getfasta
+namespace: bedtools
+description: Extract sequences from a FASTA file for each of the intervals defined in a BED/GFF/VCF file.
+keywords: [sequencing, fasta, BED, GFF, VCF]
+links:
+  documentation: https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html
+  repository: https://github.com/arq5x/bedtools2
+references:
+  doi: 10.1093/bioinformatics/btq033
+license: GPL-2.0
+requirements:
+  commands: [bedtools]
+authors:
+  - __merge__: /src/_authors/dries_schaumont.yaml
+    roles: [ author, maintainer ]
+
+argument_groups:
+  - name: Input arguments
+    arguments:
+      - name: --input_fasta
+        type: file
+        description: |
+          FASTA file containing sequences for each interval specified in the input BED file.
+          The headers in the input FASTA file must exactly match the chromosome column in the BED file.
+      - name: "--input_bed"
+        type: file
+        description: |
+          BED file containing intervals to extract from the FASTA file.
+          BED files containing a single region require a newline character
+          at the end of the line, otherwise a blank output file is produced.
+      - name: --rna
+        type: boolean_true
+        description: |
+          The FASTA is RNA not DNA. Reverse complementation handled accordingly.
+    
+  - name: Run arguments
+    arguments:
+        - name: "--strandedness"
+          type: boolean_true
+          alternatives: ["-s"]
+          description: |
+            Force strandedness. If the feature occupies the antisense strand, the output sequence will
+            be reverse complemented. By default strandedness is not taken into account.
+
+  - name: Output arguments
+    arguments:
+      - name: --output
+        alternatives: [-o]
+        required: true
+        type: file
+        direction: output
+        description: |
+          Output file where the output from the 'bedtools getfasta' commend will
+          be written to.
+      - name: --tab
+        type: boolean_true
+        description: |
+          Report extract sequences in a tab-delimited format instead of in FASTA format.
+      - name: --bed_out
+        type: boolean_true
+        description: |
+          Report extract sequences in a tab-delimited BED format instead of in FASTA format.
+      - name: "--name"
+        type: boolean_true
+        description: |
+          Set the FASTA header for each extracted sequence to be the "name" and coordinate columns from the BED feature.
+      - name: "--name_only"
+        type: boolean_true
+        description: |
+          Set the FASTA header for each extracted sequence to be the "name" columns from the BED feature.
+      - name: "--split"
+        type: boolean_true
+        description: |
+          When --input is in BED12 format, create a separate fasta entry for each block in a BED12 record,
+          blocks being described in the 11th and 12th column of the BED.
+      - name: "--full_header"
+        type: boolean_true
+        description: |
+          Use full fasta header. By default, only the word before the first space or tab is used.
+        
+# Arguments not taken into account:
+#
+#       -fo           [Specify an output file name. By default, output goes to stdout.
+#                            
+
+resources:
+  - type: bash_script
+    path: script.sh
+
+test_resources:
+  - type: bash_script
+    path: test.sh
+
+engines:
+  - type: docker
+    image: debian:stable-slim
+    setup:
+      - type: apt
+        packages: [bedtools, procps]
+      - type: docker
+        run: |
+          echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var/software_versions.txt
+
+runners:
+  - type: executable
+  - type: nextflow
--- a/src/bedtools/bedtools_getfasta/script.sh
+++ b/src/bedtools/bedtools_getfasta/script.sh
@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+set -eo pipefail
+
+unset_if_false=( par_rna par_strandedness par_tab par_bed_out par_name par_name_only par_split par_full_header )
+
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}"
+    [[ "$test_val" == "false" ]] && unset $par
+done
+
+bedtools getfasta \
+    -fi "$par_input_fasta" \
+    -bed "$par_input_bed" \
+    ${par_rna:+-rna} \
+    ${par_name:+-name} \
+    ${par_name_only:+-nameOnly} \
+    ${par_tab:+-tab} \
+    ${par_bed_out:+-bedOut} \
+    ${par_strandedness:+-s} \
+    ${par_split:+-split} \
+    ${par_full_header:+-fullHeader} > "$par_output"
+
--- a/src/bedtools/bedtools_getfasta/test.sh
+++ b/src/bedtools/bedtools_getfasta/test.sh
@@ -0,0 +1,119 @@
+#!/usr/bin/env bash
+set -eo pipefail
+
+TMPDIR=$(mktemp -d)
+function clean_up {
+  [[ -d "$TMPDIR" ]] && rm -r "$TMPDIR"
+}
+trap clean_up EXIT
+
+# Create dummy test fasta file
+cat > "$TMPDIR/test.fa" <<EOF
+>chr1
+AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
+EOF
+
+TAB="$(printf '\t')"
+
+# Create dummy bed file
+cat > "$TMPDIR/test.bed" <<EOF
+chr1${TAB}5${TAB}10${TAB}myseq
+EOF
+
+# Create expected bed file
+cat > "$TMPDIR/expected.fasta" <<EOF
+>chr1:5-10
+AAACC
+EOF
+
+"$meta_executable" \
+  --input_bed "$TMPDIR/test.bed" \
+  --input_fasta "$TMPDIR/test.fa" \
+  --output "$TMPDIR/output.fasta"
+
+cmp --silent "$TMPDIR/output.fasta" "$TMPDIR/expected.fasta" || { echo "files are different:"; exit 1; }
+
+
+# Create expected bed file for --name
+cat > "$TMPDIR/expected_with_name.fasta" <<EOF
+>myseq::chr1:5-10
+AAACC
+EOF
+
+"$meta_executable" \
+  --input_bed "$TMPDIR/test.bed" \
+  --input_fasta "$TMPDIR/test.fa" \
+  --name \
+  --output "$TMPDIR/output_with_name.fasta"
+
+
+cmp --silent "$TMPDIR/output_with_name.fasta" "$TMPDIR/expected_with_name.fasta" || { echo "Files when using --name are different."; exit 1; }
+
+# Create expected bed file for --name_only
+cat > "$TMPDIR/expected_with_name_only.fasta" <<EOF
+>myseq
+AAACC
+EOF
+
+"$meta_executable" \
+  --input_bed "$TMPDIR/test.bed" \
+  --input_fasta "$TMPDIR/test.fa" \
+  --name_only \
+  --output "$TMPDIR/output_with_name_only.fasta"
+
+cmp --silent "$TMPDIR/output_with_name_only.fasta" "$TMPDIR/expected_with_name_only.fasta" || { echo "Files when using --name_only are different."; exit 1; }
+
+
+# Create expected tab-delimited file for --tab
+cat > "$TMPDIR/expected_tab.out" <<EOF
+myseq${TAB}AAACC
+EOF
+
+"$meta_executable" \
+  --input_bed "$TMPDIR/test.bed" \
+  --input_fasta "$TMPDIR/test.fa" \
+  --name_only \
+  --tab \
+  --output "$TMPDIR/tab.out"
+
+cmp --silent "$TMPDIR/expected_tab.out" "$TMPDIR/tab.out" || { echo "Files when using --tab are different."; exit 1; }
+
+
+# Create expected tab-delimited file for --bed_out
+cat > "$TMPDIR/expected.bed" <<EOF
+chr1${TAB}5${TAB}10${TAB}myseq${TAB}AAACC
+EOF
+
+"$meta_executable" \
+  --input_bed "$TMPDIR/test.bed" \
+  --input_fasta "$TMPDIR/test.fa" \
+  --bed_out \
+  --output "$TMPDIR/output.bed"
+
+
+cmp --silent "$TMPDIR/expected.bed" "$TMPDIR/output.bed" || { echo "Files when using --bed_out are different."; exit 1; }
+
+# Create dummy bed file for strandedness
+cat > "$TMPDIR/test_strandedness.bed" <<EOF
+chr1${TAB}20${TAB}25${TAB}forward${TAB}1${TAB}+
+chr1${TAB}20${TAB}25${TAB}reverse${TAB}1${TAB}-
+EOF
+
+# Create expected tab-delimited file for --bed_out
+cat > "$TMPDIR/expected_strandedness.fasta" <<EOF
+>forward(+)
+CGCTA
+>reverse(-)
+TAGCG
+EOF
+
+"$meta_executable" \
+  --input_bed "$TMPDIR/test_strandedness.bed" \
+  --input_fasta "$TMPDIR/test.fa" \
+  -s \
+  --name_only \
+  --output "$TMPDIR/output_strandedness.fasta"
+
+
+cmp --silent "$TMPDIR/expected_strandedness.fasta" "$TMPDIR/output_strandedness.fasta" || { echo "Files when using -s are different."; exit 1; }
+
--- a/src/busco/busco_download_datasets/config.vsh.yaml
+++ b/src/busco/busco_download_datasets/config.vsh.yaml
@@ -0,0 +1,50 @@
+name: busco_download_datasets
+namespace: busco
+description: Downloads available busco datasets
+keywords: [lineage datasets]
+links:
+  homepage: https://busco.ezlab.org/
+  documentation: https://busco.ezlab.org/busco_userguide.html
+  repository: https://gitlab.com/ezlab/busco
+references:
+  doi: 10.1007/978-1-4939-9173-0_14
+license: MIT
+authors:
+  - __merge__: /src/_authors/dorien_roosen.yaml
+    roles: [ author, maintainer ]
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: --download
+        type: string
+        description: |
+          Download dataset. Possible values are a specific dataset name, "all", "prokaryota", "eukaryota", or "virus".
+          The full list of available datasets can be viewed [here](https://busco-data.ezlab.org/v5/data/lineages/) or by running the busco/busco_list_datasets component.
+        required: true
+        example: stramenopiles_odb10
+  - name: Outputs
+    arguments:
+      - name: --download_path
+        direction: output
+        type: file
+        description: |
+          Local filepath for storing BUSCO dataset downloads
+        required: false
+        default: busco_downloads
+        example: busco_downloads
+resources:
+  - type: bash_script
+    path: script.sh
+test_resources:
+  - type: bash_script
+    path: test.sh
+engines:
+  - type: docker
+    image: quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0
+    setup:
+      - type: docker
+        run: |
+          busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_versions.txt
+runners:
+  - type: executable
+  - type: nextflow
--- a/src/busco/busco_download_datasets/script.sh
+++ b/src/busco/busco_download_datasets/script.sh
@@ -0,0 +1,14 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+
+if [ ! -d "$par_download_path" ]; then
+    mkdir -p "$par_download_path"
+fi
+
+busco \
+    --download_path "$par_download_path" \
+    --download "$par_download"
+    
--- a/src/busco/busco_download_datasets/test.sh
+++ b/src/busco/busco_download_datasets/test.sh
@@ -0,0 +1,15 @@
+echo "> Downloading busco stramenopiles_odb10 dataset"
+
+"$meta_executable" \
+    --download stramenopiles_odb10 \
+    --download_path downloads 
+
+echo ">> Checking output"
+[ ! -f "downloads/file_versions.tsv" ] && echo "file_versions.tsv does not exist" && exit 1
+[ ! -f "downloads/lineages/stramenopiles_odb10/dataset.cfg" ] && echo "dataset.cfg does not exist" && exit 1
+
+echo ">> Checking if output is empty"
+[ ! -s "downloads/file_versions.tsv" ] && echo "file_versions.tsv is empty" && exit 1
+[ ! -s "downloads/lineages/stramenopiles_odb10/dataset.cfg" ] && echo "dataset.cfg is empty" && exit 1
+
+rm -r downloads
--- a/src/busco/busco_list_datasets/config.vsh.yaml
+++ b/src/busco/busco_list_datasets/config.vsh.yaml
@@ -0,0 +1,42 @@
+name: busco_list_datasets
+namespace: busco
+description: Lists the available busco datasets
+keywords: [lineage datasets]
+links:
+  homepage: https://busco.ezlab.org/
+  documentation: https://busco.ezlab.org/busco_userguide.html
+  repository: https://gitlab.com/ezlab/busco
+references:
+  doi: 10.1007/978-1-4939-9173-0_14
+license: MIT
+authors:
+  - __merge__: /src/_authors/dorien_roosen.yaml
+    roles: [ author, maintainer ]
+argument_groups:
+  - name: Outputs
+    arguments:
+      - name: --output
+        alternatives: ["-o"]
+        direction: output
+        type: file
+        description: |
+          Output file of the available busco datasets
+        required: false
+        default: busco_dataset_list.txt
+        example: file.txt
+resources:
+  - type: bash_script
+    path: script.sh
+test_resources:
+  - type: bash_script
+    path: test.sh
+engines:
+  - type: docker
+    image: quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0
+    setup:
+      - type: docker
+        run: |
+          busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_versions.txt
+runners:
+  - type: executable
+  - type: nextflow
--- a/src/busco/busco_list_datasets/script.sh
+++ b/src/busco/busco_list_datasets/script.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+busco --list-datasets | awk '/^#{40}/{flag=1; next} flag{print}' > $par_output
--- a/src/busco/busco_list_datasets/test.sh
+++ b/src/busco/busco_list_datasets/test.sh
@@ -0,0 +1,15 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+"$meta_executable" \
+    --output datasets.txt 
+
+echo ">> Checking output"
+[ ! -f "datasets.txt" ] && echo "datasets.txt does not exist" && exit 1
+
+echo ">> Checking if output is empty"
+[ ! -s "datasets.txt" ] && echo "datasets.txt is empty" && exit 1
+
+rm datasets.txt
--- a/src/busco/busco_run/config.vsh.yaml
+++ b/src/busco/busco_run/config.vsh.yaml
@@ -0,0 +1,221 @@
+name: busco_run
+namespace: busco
+description: Assessment of genome assembly and annotation completeness with single copy orthologs
+keywords: [Genome assembly, quality control]
+links:
+  homepage: https://busco.ezlab.org/
+  documentation: https://busco.ezlab.org/busco_userguide.html
+  repository: https://gitlab.com/ezlab/busco
+references:
+  doi: 10.1007/978-1-4939-9173-0_14
+license: MIT
+authors:
+  - __merge__: /src/_authors/dorien_roosen.yaml
+    roles: [ author, maintainer ]
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: --input
+        alternatives: ["-i"]
+        type: file
+        description: |
+          Input sequence file in FASTA format. Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set. Also possible to use a path to a directory containing multiple input files.
+        required: true
+        example: file.fasta
+      - name: --mode
+        alternatives: ["-m"]
+        type: string
+        choices: [genome, geno, transcriptome, tran, proteins, prot]
+        required: true
+        description: |
+          Specify which BUSCO analysis mode to run. There are three valid modes:
+            - geno or genome, for genome assemblies (DNA)
+            - tran or transcriptome, for transcriptome assemblies (DNA)
+            - prot or proteins, for annotated gene sets (protein)
+        example: proteins
+      - name: --lineage_dataset
+        alternatives: ["-l"]
+        type: string
+        required: false
+        description: |
+          Specify a BUSCO lineage dataset that is most closely related to the assembly or gene set being assessed. 
+          The full list of available datasets can be viewed [here](https://busco-data.ezlab.org/v5/data/lineages/) or by running the busco/busco_list_datasets component.
+          When unsure, the "--auto_lineage" flag can be set to automatically find the optimal lineage path.
+          BUSCO will automatically download the requested dataset if it is not already present in the download folder. 
+          You can optionally provide a path to a local dataset instead of a name, e.g. path/to/dataset.
+          Datasets can be downloaded using the busco/busco_download_dataset component.
+        example: stramenopiles_odb10
+
+  - name: Outputs
+    arguments:
+      - name: --short_summary_json
+        required: false
+        direction: output
+        type: file
+        example: short_summary.json
+        description: |
+          Output file for short summary in JSON format.
+      - name: --short_summary_txt
+        required: false
+        direction: output
+        type: file
+        example: short_summary.txt
+        description: |
+          Output file for short summary in TXT format.
+      - name: --full_table
+        required: false
+        direction: output
+        type: file
+        example: full_table.tsv
+        description: |
+          Full table output in TSV format.
+      - name: --missing_busco_list
+        required: false
+        direction: output
+        type: file
+        example: missing_busco_list.tsv
+        description: |
+          Missing list output in TSV format.
+      - name: --output_dir
+        required: false
+        direction: output
+        type: file
+        example: output_dir/
+        description: |
+          The full output directory, if so desired.
+
+  - name: Resource and Run Settings
+    arguments:
+      - name: --force
+        type: boolean_true
+        description: |
+          Force rewriting of existing files. Must be used when output files with the provided name already exist.
+      - name: --quiet
+        alternatives: ["-q"]
+        type: boolean_true
+        description: |
+          Disable the info logs, displays only errors.
+      - name: --restart
+        alternatives: ["-r"]
+        type: boolean_true
+        description: |
+          Continue a run that had already partially completed. Restarting skips calls to tools that have completed but performs all pre- and post-processing steps.
+      - name: --tar
+        type: boolean_true
+        description: |
+          Compress some subdirectories with many files to save space.
+
+  - name: Lineage Dataset Settings
+    arguments:
+      - name: --auto_lineage
+        type: boolean_true
+        description: |
+          Run auto-lineage pipelilne to automatically determine BUSCO lineage dataset that is most closely related to the assembly or gene set being assessed.
+      - name: --auto_lineage_euk
+        type: boolean_true
+        description: |
+          Run auto-placement just on eukaryota tree to find optimal lineage path.
+      - name: --auto_lineage_prok
+        type: boolean_true
+        description: |
+          Run auto_lineage just on prokaryota trees to find optimum lineage path.
+      - name: --datasets_version
+        type: string
+        required: false
+        description: |
+          Specify the version of BUSCO datasets
+        example: odb10
+
+  - name: Augustus Settings
+    arguments:
+      - name: --augustus
+        type: boolean_true
+        description: |
+          Use augustus gene predictor for eukaryote runs.
+      - name: --augustus_parameters
+        type: string
+        required: false
+        description: |
+          Additional parameters to be passed to Augustus (see Augustus documentation: https://github.com/Gaius-Augustus/Augustus/blob/master/docs/RUNNING-AUGUSTUS.md).
+          Parameters should be contained within a single string, without whitespace and seperated by commas.
+        example: "--PARAM1=VALUE1,--PARAM2=VALUE2"
+      - name: --augustus_species
+        type: string
+        required: false
+        description: |
+          Specify the augustus species
+      - name: --long
+        type: boolean_true
+        description: |
+          Optimize Augustus self-training mode. This adds considerably to the run time, but can improve results for some non-model organisms.
+
+  - name: BBTools Settings
+    arguments:
+      - name: --contig_break
+        type: integer
+        required: false
+        description: |
+          Number of contiguous Ns to signify a break between contigs in BBTools analysis.
+      - name: --limit
+        type: integer
+        required: false
+        description: |
+          Number of candidate regions (contig or transcript) from the BLAST output to consider per BUSCO.
+          This option is only effective in pipelines using BLAST, i.e. the genome pipeline (see --augustus) or the prokaryota transcriptome pipeline.
+      - name: --scaffold_composition
+        type: boolean_true
+        description: |
+          Writes ACGTN content per scaffold to a file scaffold_composition.txt.
+
+  - name: BLAST Settings
+    arguments:
+      - name: --e_value
+        type: double
+        required: false
+        description: |
+          E-value cutoff for BLAST searches.
+
+  - name: Protein Gene Prediction settings
+    arguments:
+      - name: --miniprot
+        type: boolean_true
+        description: |
+          Use Miniprot gene predictor.
+
+  - name: MetaEuk Settings
+    arguments:
+      - name: --metaeuk
+        type: boolean_true
+        description: |
+          Use Metaeuk gene predictor.
+      - name: --metaeuk_parameters
+        type: string
+        description: |
+          Pass additional arguments to Metaeuk for the first run (see Metaeuk documentation https://github.com/soedinglab/metaeuk).
+          All parameters should be contained within a single string with no white space, with each parameter separated by a comma.
+        example: "--max-overlap=15,--min-exon-aa=15"
+      - name: --metaeuk_rerun_parameters
+        type: string
+        description: |
+          Pass additional arguments to Metaeuk for the second run (see Metaeuk documentation https://github.com/soedinglab/metaeuk).
+          All parameters should be contained within a single string with no white space, with each parameter separated by a comma.
+        example: "--max-overlap=15,--min-exon-aa=15"
+
+resources:
+  - type: bash_script
+    path: script.sh
+test_resources:
+  - type: bash_script
+    path: test.sh
+  - type: file
+    path: test_data
+engines:
+  - type: docker
+    image: quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0
+    setup:
+      - type: docker
+        run: |
+          busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_versions.txt
+runners:
+  - type: executable
+  - type: nextflow
--- a/src/busco/busco_run/help.txt
+++ b/src/busco/busco_run/help.txt
@@ -0,0 +1,63 @@
+```bash
+busco -h
+```
+
+usage: busco -i [SEQUENCE_FILE] -l [LINEAGE] -o [OUTPUT_NAME] -m [MODE] [OTHER OPTIONS]
+
+Welcome to BUSCO 5.7.1: the Benchmarking Universal Single-Copy Ortholog assessment tool.
+For more detailed usage information, please review the README file provided with this distribution and the BUSCO user guide. Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
+
+optional arguments:
+  -i SEQUENCE_FILE, --in SEQUENCE_FILE
+                        Input sequence file in FASTA format. Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set. Also possible to use a path to a directory containing multiple input files.
+  -o OUTPUT, --out OUTPUT
+                        Give your analysis run a recognisable short name. Output folders and files will be labelled with this name. The path to the output folder is set with --out_path.
+  -m MODE, --mode MODE  Specify which BUSCO analysis mode to run.
+                        There are three valid modes:
+                        - geno or genome, for genome assemblies (DNA)
+                        - tran or transcriptome, for transcriptome assemblies (DNA)
+                        - prot or proteins, for annotated gene sets (protein)
+  -l LINEAGE, --lineage_dataset LINEAGE
+                        Specify the name of the BUSCO lineage to be used.
+  --augustus            Use augustus gene predictor for eukaryote runs
+  --augustus_parameters "--PARAM1=VALUE1,--PARAM2=VALUE2"
+                        Pass additional arguments to Augustus. All arguments should be contained within a single string with no white space, with each argument separated by a comma.
+  --augustus_species AUGUSTUS_SPECIES
+                        Specify a species for Augustus training.
+  --auto-lineage        Run auto-lineage to find optimum lineage path
+  --auto-lineage-euk    Run auto-placement just on eukaryote tree to find optimum lineage path
+  --auto-lineage-prok   Run auto-lineage just on non-eukaryote trees to find optimum lineage path
+  -c N, --cpu N         Specify the number (N=integer) of threads/cores to use.
+  --config CONFIG_FILE  Provide a config file
+  --contig_break n      Number of contiguous Ns to signify a break between contigs. Default is n=10.
+  --datasets_version DATASETS_VERSION
+                        Specify the version of BUSCO datasets, e.g. odb10
+  --download [dataset [dataset ...]]
+                        Download dataset. Possible values are a specific dataset name, "all", "prokaryota", "eukaryota", or "virus". If used together with other command line arguments, make sure to place this last.
+  --download_base_url DOWNLOAD_BASE_URL
+                        Set the url to the remote BUSCO dataset location
+  --download_path DOWNLOAD_PATH
+                        Specify local filepath for storing BUSCO dataset downloads
+  -e N, --evalue N      E-value cutoff for BLAST searches. Allowed formats, 0.001 or 1e-03 (Default: 1e-03)
+  -f, --force           Force rewriting of existing files. Must be used when output files with the provided name already exist.
+  -h, --help            Show this help message and exit
+  --limit N             How many candidate regions (contig or transcript) to consider per BUSCO (default: 3)
+  --list-datasets       Print the list of available BUSCO datasets
+  --long                Optimization Augustus self-training mode (Default: Off); adds considerably to the run time, but can improve results for some non-model organisms
+  --metaeuk             Use Metaeuk gene predictor
+  --metaeuk_parameters "--PARAM1=VALUE1,--PARAM2=VALUE2"
+                        Pass additional arguments to Metaeuk for the first run. All arguments should be contained within a single string with no white space, with each argument separated by a comma.
+  --metaeuk_rerun_parameters "--PARAM1=VALUE1,--PARAM2=VALUE2"
+                        Pass additional arguments to Metaeuk for the second run. All arguments should be contained within a single string with no white space, with each argument separated by a comma.
+  --miniprot            Use Miniprot gene predictor
+  --skip_bbtools        Skip BBTools for assembly statistics
+  --offline             To indicate that BUSCO cannot attempt to download files
+  --opt-out-run-stats   Opt out of data collection. Information on the data collected is available in the user guide.
+  --out_path OUTPUT_PATH
+                        Optional location for results folder, excluding results folder name. Default is current working directory.
+  -q, --quiet           Disable the info logs, displays only errors
+  -r, --restart         Continue a run that had already partially completed.
+  --scaffold_composition
+                        Writes ACGTN content per scaffold to a file scaffold_composition.txt
+  --tar                 Compress some subdirectories with many files to save space
+  -v, --version         Show this version and exit
--- a/src/busco/busco_run/script.sh
+++ b/src/busco/busco_run/script.sh
@@ -0,0 +1,72 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+
+[[ "$par_tar" == "false" ]] && unset par_tar
+[[ "$par_force" == "false" ]] && unset par_force
+[[ "$par_quiet" == "false" ]] && unset par_quiet
+[[ "$par_restart" == "false" ]] && unset par_restart
+[[ "$par_auto_lineage" == "false" ]] && unset par_auto_lineage
+[[ "$par_auto_lineage_euk" == "false" ]] && unset par_auto_lineage_euk
+[[ "$par_auto_lineage_prok" == "false" ]] && unset par_auto_lineage_prok
+[[ "$par_augustus" == "false" ]] && unset par_augustus
+[[ "$par_long" == "false" ]] && unset par_long
+[[ "$par_scaffold_composition" == "false" ]] && unset par_scaffold_composition
+[[ "$par_miniprot" == "false" ]] && unset par_miniprot
+
+tmp_dir=$(mktemp -d -p "$meta_temp_dir" busco_XXXXXXXXX)
+prefix=$(openssl rand -hex 8)
+
+busco \
+    --in "$par_input" \
+    --mode "$par_mode" \
+    --out "$prefix" \
+    --out_path "$tmp_dir" \
+    --opt-out-run-stats \
+    ${meta_cpus:+--cpu "${meta_cpus}"} \
+    ${par_lineage_dataset:+--lineage_dataset "$par_lineage_dataset"} \
+    ${par_augustus:+--augustus} \
+    ${par_augustus_parameters:+--augustus_parameters "$par_augustus_parameters"} \
+    ${par_augustus_species:+--augustus_species "$par_augustus_species"} \
+    ${par_auto_lineage:+--auto-lineage} \
+    ${par_auto_lineage_euk:+--auto-lineage-euk} \
+    ${par_auto_lineage_prok:+--auto-lineage-prok} \
+    ${par_contig_break:+--contig_break $par_contig_break} \
+    ${par_datasets_version:+--datasets_version "$par_datasets_version"} \
+    ${par_e_value:+--evalue "$par_e_value"} \
+    ${par_force:+--force} \
+    ${par_limit:+--limit "$par_limit"} \
+    ${par_long:+--long} \
+    ${par_metaeuk:+--metaeuk} \
+    ${par_metaeuk_parameters:+--metaeuk_parameters "$par_metaeuk_parameters"} \
+    ${par_metaeuk_rerun_parameters:+--metaeuk_rerun_parameters "$par_metaeuk_rerun_parameters"} \
+    ${par_miniprot:+--miniprot} \
+    ${par_quiet:+--quiet} \
+    ${par_restart:+--restart} \
+    ${par_scaffold_composition:+--scaffold_composition} \
+    ${par_tar:+--tar} \
+
+
+out_dir=$(find "$tmp_dir/$prefix" -maxdepth 1 -name 'run_*')
+
+if [[ -n "$par_short_summary_json" ]]; then
+    cp "$out_dir/short_summary.json" "$par_short_summary_json"
+fi
+if [[ -n "$par_short_summary_txt" ]]; then
+    cp "$out_dir/short_summary.txt" "$par_short_summary_txt"
+fi
+if [[ -n "$par_full_table" ]]; then
+    cp "$out_dir/full_table.tsv" "$par_full_table"
+fi
+if [[ -n "$par_missing_busco_list" ]]; then
+    cp "$out_dir/missing_busco_list.tsv" "$par_missing_busco_list"
+fi
+if [[ -n "$par_output_dir" ]]; then
+    if [[ -d "$par_output_dir" ]]; then
+        rm -r "$par_output_dir"
+    fi
+    cp -r -L "$out_dir" "$par_output_dir"
+fi
+
--- a/src/busco/busco_run/test.sh
+++ b/src/busco/busco_run/test.sh
@@ -0,0 +1,88 @@
+test_dir="$meta_resources_dir/test_data"
+
+mkdir "run_prot_stramenopiles"
+cd "run_prot_stramenopiles"
+
+echo "> Running busco with lineage dataset"
+
+"$meta_executable" \
+    --input $test_dir/protein.fasta \
+    --mode proteins \
+    --lineage_dataset stramenopiles_odb10 \
+    --output_dir output \
+    --short_summary_json short_summary.json \
+    --short_summary_txt short_summary.txt \
+    --full_table full_table.tsv \
+    --missing_busco_list missing_busco_list.tsv
+
+echo ">> Checking output"
+[ ! -f "output/full_table.tsv" ] && echo "full_table.tsv does not exist" && exit 1
+[ ! -f "output/missing_busco_list.tsv" ] && echo "missing_busco_list.tsv does not exist" && exit 1
+[ ! -f "output/short_summary.json" ] && echo "short_summary.json does not exist" && exit 1
+[ ! -f "output/short_summary.txt" ] && echo "short_summary.txt does not exist" && exit 1
+[ ! -f "full_table.tsv" ] && echo "full_table.tsv does not exist" && exit 1
+[ ! -f "missing_busco_list.tsv" ] && echo "missing_busco_list.tsv does not exist" && exit 1
+[ ! -f "short_summary.json" ] && echo "short_summary.json does not exist" && exit 1
+[ ! -f "short_summary.txt" ] && echo "short_summary.txt does not exist" && exit 1
+
+echo ">> Checking if output is empty"
+[ ! -s "output/full_table.tsv" ] && echo "full_table.tsv is empty" && exit 1
+[ ! -s "output/missing_busco_list.tsv" ] && echo "missing_busco_list.tsv is empty" && exit 1
+[ ! -s "output/short_summary.json" ] && echo "short_summary.json is empty" && exit 1
+[ ! -s "output/short_summary.txt" ] && echo "short_summary.txt is empty" && exit 1
+[ ! -s "full_table.tsv" ] && echo "full_table.tsv is empty" && exit 1
+[ ! -s "missing_busco_list.tsv" ] && echo "missing_busco_list.tsv is empty" && exit 1
+[ ! -s "short_summary.json" ] && echo "short_summary.json is empty" && exit 1
+[ ! -s "short_summary.txt" ] && echo "short_summary.txt is empty" && exit 1
+
+cd ..
+mkdir "run_prot_autolineage"
+cd "run_prot_autolineage"
+
+echo "> Running busco with auto lineage"
+
+"$meta_executable" \
+    --input $test_dir/protein.fasta \
+    --mode proteins \
+    --auto_lineage \
+    --output_dir output 
+
+echo ">> Checking output"
+[ ! -f "output/full_table.tsv" ] && echo "full_table.tsv does not exist in output folder" && exit 1
+[ ! -f "output/missing_busco_list.tsv" ] && echo "missing_busco_list.tsv does not exist in output folder" && exit 1
+[ ! -f "output/short_summary.json" ] && echo "short_summary.json does not exist in output folder" && exit 1
+[ ! -f "output/short_summary.txt" ] && echo "short_summary.txt does not exist in output folder" && exit 1
+
+echo ">> Checking if output is empty"
+[ ! -s "output/full_table.tsv" ] && echo "full_table.tsv in output folder is empty" && exit 1
+[ ! -s "output/missing_busco_list.tsv" ] && echo "missing_busco_list.tsv in output folder is empty" && exit 1
+[ ! -s "output/short_summary.json" ] && echo "short_summary.json in output folder is empty" && exit 1
+[ ! -s "output/short_summary.txt" ] && echo "short_summary.txt in output folder is empty" && exit 1
+
+rm -r output/ 
+
+cd ..
+mkdir "run_genome"
+cd "run_genome"
+
+echo "> Running busco with genome data"
+
+"$meta_executable" \
+    --input $test_dir/genome.fna \
+    --mode genome \
+    --lineage_dataset saccharomycetes_odb10 \
+    --output_dir output 
+
+echo ">> Checking output"
+[ ! -f "output/full_table.tsv" ] && echo "full_table.tsv does not exist in output folder" && exit 1
+[ ! -f "output/missing_busco_list.tsv" ] && echo "missing_busco_list.tsv does not exist in output folder" && exit 1
+[ ! -f "output/short_summary.json" ] && echo "short_summary.json does not exist in output folder" && exit 1
+[ ! -f "output/short_summary.txt" ] && echo "short_summary.txt does not exist in output folder" && exit 1
+
+echo ">> Checking if output is empty"
+[ ! -s "output/full_table.tsv" ] && echo "full_table.tsv in output folder is empty" && exit 1
+[ ! -s "output/missing_busco_list.tsv" ] && echo "missing_busco_list.tsv in output folder is empty" && exit 1
+[ ! -s "output/short_summary.json" ] && echo "short_summary.json in output folder is empty" && exit 1
+[ ! -s "output/short_summary.txt" ] && echo "short_summary.txt in output folder is empty" && exit 1
+
+rm -r output/ 
--- a/src/busco/busco_run/test_data/genome.fna
+++ b/src/busco/busco_run/test_data/genome.fna
--- a/src/busco/busco_run/test_data/protein.fasta
+++ b/src/busco/busco_run/test_data/protein.fasta
@@ -0,0 +1,64 @@
+>341721at2759_1001832_1:000010
+MASRPVKKRKLTPPGDDEASSRKSGGKIQKAFLKNAANWDLEQDYETRARKGKKKEKESTRLPLKLPGGRVQHVSAPDNDFQAIESDEDWLDGAEDVSEDEESKDKKAPEEPEKPEHEQILEAKEELAKIALMLNESPDENTGAFKALAKIGQSRIITIKKLALATQLTVYKDVIPGYRIRPVAEDGPEEKLSKDVRKLRTYETCLISGYQAYVKELTKHAKTGHANGLASVAITCACNLLTAVPHFNFRSDLVKILVGKLSTRRVDDDFNKCLQALETLFEEDEEGRPSMEAVSLLSKMMKAREYQVNESVVNLFLHLRLLSDFSGKGSKDSVDRMDDGPSKKPKSKREFRTKRERKQIKEQKALQKDMAQADALVQHEERDRMEGETLKLVFGTYFRVLKMRVPHLMGAVLEGLSKYAHLINQNFFGDLLEALKDLIRHSDASEKDDAEEKEDEEADDDAPVRNPSREALLCTTTAFALLAGQDAHNARADLHLDLSFFTTHLYQSLFPLSLHPDLELGARSLHLPDPDKPSQNRKSNSSNKVNLQTTTVLLIRCLTAVLLPPWNVRSVPPVRLAAFAKQLMTAALHVPEKSAQALLALLADVAGTHGRRIAALWNTEERKGDGAFNPLAESAEASNPFAATVWEGEILRRHYCPAVRRGVGIVEKSLSLAER
+>296129at2759_1069680_1:000010
+MMKKKQIDSRIPTLIKNGVQEKKRTLFVIVGDRGRDQIVNLHWLLSQTRIASRPSVLWMYKKDLLGFTSHRKKREAKIKKEIKKGIRDPNEATTPFELFISVTNIRYTYYKESEKILGQTFGMLVLQDFEAITPNLLARTIETVEGGGIIVILFKTMENLKQLYTMTMDIHSRYRTEAHQDVVARFNGRFILSLGHCSSCLFVDDELNVLPISEAKKVKPLPKPQLEEPKKELEELKQKYEDKQLLRSLIDVAKTVDQARALITFVEAISEKTLRSTVALTAARGRGKSAALGLAISAAVAYGYSNIFITSPNPENLKTLFEFTFKGFNSLKYEEHIDYDIIQSLNPSFNKSIVRVNIFRNHRQTIQYIHPSDAYVLGQAELLVIDEAAAIPMPLVKKLLGPYLTFMASTVNGYEGTGRSLSLKLIQQLREQSRGFAHENTKSGNSEKSMINRSEKLNKESGINSIGGRKLREITLEEPIRYSYGDPVEEWLNKLLCLDINISLKQFLEQGCPHPSQCELYYVNRDTLFSYHPVSESFLQMMMSLYVASHYKNSPNDLQLMADAPAHQLFVLLPPVKEDDNKLPEPLCVIQVALEGEISRESVVNNLTRGYRTGGDLIPWVITEQFQDDKFASLSGARIVRIATNPEYIRMGYGSHALKLLENFYEGKYLNLSEETISESNENIKIINNNLESSLLTDDIKIKDLKIMPPLLLKLSEKKPGLIHYLGVSYGLTPQLYKFWKRAEFIPVYLRQTPNDLTGEHTCLMLKLLQDKSETWLNEFSNDFRKRFLSLLSFSFRSFPTILCLNIIESINNDLIQKDNVHVITKSEIDINLSPFDLKRLESYANNMLDYHTIIDMLPYIADLYFKGRFGKDLKMTGVQSAILLALGLQKRLLEDIEKELNLPSNQVLAMLVKILRKLSSFFKDIYYKAIDNTLPIERKNLKNQLQTHADENDNFRGFIPLKATLKEELDHLSSEMEDSIKEKQRELINSLDLQKYIIKGQEEDWDKAEQHIKNGIYSGKSSVVSIQSHSLKREHESLTDIPHIKKKHQKKHKRKV
+>1217666at2759_1073089_1:000010
+MPINQPSNQIKFTNVSVVRLKKGKKRFELACYKNKLLEYRSGAEKDLDNVLQVPTIFLSVSKAQTAPSAELTKAFGANIPADEIRQEILRKGEVQVGERERKEISERVEKELLDIVSGRLVDPTTKRVYTPGMISKALDQLSSASGQMQQTQGEGSGATDEKGAAQPRKPMWTGVAPNKSAKSQALDAMKALIAWQPIPVMRARMRLRVTCPVSILKHSVKAPSGGGASKEKEAPSGNSKSNKGKKGPKSRAARQQDSDAEDGKSDAEAAPKTPSNVKDKILGYIESIESQEVIGGDEWEVVGFAEPGAYKGLNEFVGNETRGRGRVEVLDMTVTHEE
+>513979at2759_1159556_1:000010
+MAVVDIQARFSPHHPLEPDLLYEIQSILRLHGLSVDDLFFKWDAYCIRMDLDAQAALSLANVRSLKQSIQDDLEKSHRSTTQVRSERKVAAAPKAVSGGDVYGMLDGLVPSTPAAGGKRSRGVAAGGGGSGLKKKMDSLKMNSSPAGMKEQLSAFNGLPATSFAERANAGDVVEILNAQLPPCEAPLAPFPEPRIKLTAASDQKKMAYKPLAVKLSEASEVLDDRIDEFAALVQDYHGLEDSAFGSAASQGTTEVVAVGRIASDAMEGKLNAAALVLETSRRTGMGLRVPLKMHKVPSWSFFPGQVVALRGTNATGGEFVVEQVLDVPLLPSAASTPSALEAHRARMSGVPPGGGAAAATTDSDAAAPAPAPAPLTILYAAGPYTADDNLDYEPLHALCSQAADALADALVLAGPFLDIDHPLVAAGDFDLPPEDEAALDPDTATMSAVFRHLVAPALNRACAANPHLTVVLVPSVRDVLARHVSWPQDAIARKELGLAKAARIVSNPMTLSMNEVVVGVSSQDVLHELRNEECSRACPPGDLMGRLCRYLVEQRHYFPLFPPTDRARLPRTGTQSGLATGAVLDPSYLRLGEMVNVRPDVMVVPSSLPPFAKASSVVESVLAINPGPLSKRKGAGTFARMTLHAPPVGGGSEMTSHRVFDRARVEIVRI
+>543764at2759_1165861_1:000010
+MALGRAARPVGWTDCCAAVEKKPNYKSGMTQPARTITAGDNLLLKLPSGQTRTIKNVTSDSSISLGKFGKFQTNELIDQPFGLTFDILEDGKLVRNEQINLALELNPMLDELNSFESIKGMANGISNVEDIEATNEMIKESDGAQKLTNVEIEELKKSGLSGREIILRQIQQHSAFELKSEFSKAKYIKRKEKKFLKMFTCIDPTIHNMSQYLFENHNFAIKGLRPDTLSQMLSLSNVRPGWKGIVVDDIGGLLVAAVLIRMGGEGTIFVLNNADSPPDLHLLELFNLPKSVLGPLKSLNWAQTEADWTTSDIEELLLLHRDPPQPLPILDSTLPDPQLKQLSQRTKKQPNNRSKSMRKFERVQELLSMRQEFLDTQFEGLLTCSEYEPESIVTKLVNKLSGSSTIVIYSCHLRPLSDLQTLLKKSSMPSTSSSSLGGSSSLVEQNELTKRMKENKTEFIQITISEPWLRAYQVLVGRTHPEMAGTHHGGFVFSAIKVFNSCS
+>1558822at2759_1266660_1:000010
+MSIAEILPLEIIDKTVGQPVLVMLTSHREFSGTLVGYDDFVNVVLEEVVEYDHDQEIKRHAGKMLLSGNNIAMLVPGGKRVQ
+>1287094at2759_1291522_0:000010
+MGNILVKKNRVTITEADRAILTLRTQRRKMEEHRRRVEALMERETTVARTLVAKQQRPAALLALKKKRLHETQLEGLDNCLLTLEETLTQVESAQRTARLMAALKQGADVLSALQRAMPLESVEQLMEQGAESREYEMRLQALLGESLGEDQSAAAERELDEMEAQLIEEDVLDLPKVPSHAVARPASARAIGQAASERQLEPEIAA
+>83779at2759_1296121_1:000010
+MCGLTLTIRPLSLSLSSPSVSDCSSSDSTEDADLALLDSFRSTNAQRGPDSQRTFKHTVTLDDDDNGVTTTTTTKSTTKSKVEICLTATVLGLRGDLTAQPLVGNRGVLGWNGQVFEGIDIGTEENDTRKIFERLEKGERVEDVLSGVEGPFAFIYLDLENDILHYQLDPLSRRSLLIHPAEVAVDSNPSVTRHFILSSSRSTLAREHGVDMRALLGGEGGTIDLRRIKVVQNQGFLTMDMSDALKHRHTLSPDQDASCSSSSGSWTKVAPINTALPPDNLPLDNPKIKEEVPKFIEQLKESVKRRVENIPNPEKGCSRVAVLFSGGIDCTFLAYLIHLCLPPEDPIDLINVAFSPAPKLSSLSSNGADKGKGKSPALPAAPTYDVPDRLSGRDALVELKQVCPDREWRFVEIDVPYDEARAHRQNVLDLMYPSSTEMDHSLALPLYFASRGYGSVRKEGSNHSEPYRVKAKVYISGLGADEQLGGYARHRHAYQREGWQGLISETQMDIARLPTRNLSRDDRMLSSHARDARYPYLSLSFISYLSSLPVHLKCDPRLGEGQGDKILLRKAVESVGLVRASGRVKRAMQFGTRSSKLGGRGSGVKGPKAGERQVE
+>1057950at2759_1314783_1:000010
+MSSRQATHADSWYVGDGRRLDSELSKNLAAVEGDANYSPPIKGCKAVIAPHAGYSYSGRAAAWAYKSIDTTGIKRIFILGPSHHVYLDGCALSKCEKYETPLGELPIDLDTVKELRATGEFQDMDIQTDEDEHSIEMHLPYVRKVFEGLDIAIVPILIGAINLNKENKFGTVLAPYLAKDDTFFVISSDFCHWGTRFQYTFYYPRPPPTSTPAIRLSKADPNPSTLATHPIHASISAIDHEAMDLMTMPPQTAQQAHIDFAEYLRTTKNTICGRHPIGVLLGALAVLQSQGRVPHLKFVRYEQSSQCQTVRDSSVSYASAYITV
+>453044at2759_1330018_1:000010
+MPAAPQDPFFKSIGSAAADTEALREQPDEQDEQETDLEPIDEDRPLQEVESLCMSCGEQGVTRMLLTSIPYFREVIVMSFRCEHCGNQNNEIQSASTIREHGAMYTVKILNQGDLNRQLVKSEAATVTIPEFELTIPPLRGQLTTVEGTLRDTIQDLAADQPLRRIQDPPTFDKIEALLAKLKEVVPDDEDEAAPTMKERHPEDPVRPFTVILDDPTGNSFIEFSGSMSDPKWSLREYARSMDQNITLGLSQPEDEEKEKVTQKGGPFTEEDEDGLPAEEVFIFPGICSSCGHPVDTRMKKVNIPYFKDIIIMSTNCSACGYRDNEVKSGGAISDKGKRITLKVEDAEDLSRDILKSETCGLEIPEIDLALHAGTLGGRFTTVEGILTQVYDELSEKVFRGDSVGSANSKDNQEFETFLGSMKEVMTAARPFTLILDDPLANSYLQNLYAPDPDPNMEIVTYDRTFDQNEDLGLNDMKVEGYEAPS
+>1323575at2759_1392248_1:000010
+MSQPQPPPLRYIRYEPSREDEYVAAMRQLISKDLSEPYSIYVYRYFLYQWGDLCFMTVDDSRPEDPIVGVVVSKLEPHRGGPMRGYIAMLAVREEYRGRGIATKLVRMAIDAMIARDADEIALETEITNTAAMKLYERLGFLRSKRLHRYYLNGNSAYRLVLYLKEGVGNMRTSFDPYAAPAEARPEMSGAAAVPAAPAPPPLLQGNGR
+>160593at2759_139723_0:000010
+MADAELAKALKDLPNRVLNVPVEERPELFQNVIAVLPNPGINATIVRGICKVIGTTLTKYKDPESQTLVKELLVAVLKQHPDLTYEHFNAVLKALLAKDLAGAPPIKAAQASALALGWANLIALHADHETAVGKKEFPKLLEVQAGLYQLSLTSGIQKISDKAYSFLRDFFASDESLAQRYFDKLLAMEPSSGVIVMLCTIVRYLHQEQGTVELLDQHKPKLLDHLVKGLITVKTKPHASDIVACSILLKAITKDELRTIIVPALQRSMLRSAEVILRAVGAIVNEIELDVSDYALDLGKPLVQNLASKEETVRQEAVESLKQVALKCGTPNAIETLLKEVFAVLNGSGGKITVAELRINLLQGAGNLSYNKIPSQKIQTILPAACDHFTKVIEAEIQEKVVCHALEMFGLWTVNHRGEIPAKIVQLFKKGLDAKAQTIRTSYLQWFLSCLHDGKLPNGIDFTTTLSKIVERAAQSPTQTPVVSEGVGAACILLLTNPSVSEKLKDFWNIVLDTNKSPFLSERFLSTTNAETRCYVMVICEQLLIKHRNELKGSSTTDPLIRAATVCVMSAQAKVRRYCLPLVTKIVNSEDGVSLAKFLLAELTRYVECTKILSEGEPAEEGIAPAQALVDAVCTVCNVEKVANPDAQSLALSALLCSHHPAAVSVRGDLWESILERYGLYGKQFIALNTAQIEEVFFNSYKATAMYENTLATLSRISPELILSVLVKNVTDQLNNSRMSNVTDEEYFTYLTPDGELYDKSVIPNTDEQVQTAHLKRENKAYSYKEQLEELQLRRELEEKRRKEGKWKPPQLTPKQKEVIDKQREKENAIKARLQALHDTITTLISQIEGAAKGTPKQLPLFFPALLPAILRVFSSPLAAPAMVKLYYRLKDICFGEERVELGRDIAIATIRLSKPHCDLEESWCTANLVELVSDILVALYDETIDMYNVHREEEASKRYLLDAPAFSYTFEFLKRALTLPEAKKDESLLINGVQIIAYHAQLKGDTVDGKDLGDVYHPLYMPRLEMIRLLLRLIQQHRGRVQTQAVAALLDVAESCSGREYTTRAEQREIEALLVALQEELDAVRDVALRALAIMIDVLPSIADDYEFGLRLTRRLWVAKHDLSADIKQLATGIWQDGAYEVPIVMADELMKDIIHPELCVQKAAAAALVSILVEDSSTIDGVVEQLLEIYREKVVMIPAKLDQFDREVEPAIDPWGPRRGVAITLGSISPFLTPELVKSVIQFMVRSGLRDRQEIVHKEMLAASLAIVEHHGKDSVTYLLPTFEYFLDKAPSKGAYDNIRQAVVILMGSLARHLDREDERIQPIIDRLLAALETPSQQVQEAVANCIPHLIPSVKDKAPEIVKKLLQQLVKSEKYGVRRGAAYGIAGVVKGLGILSLKQLDIMSKLTHYIQDKKNYKSREGALFAFEMLCSTLGRLFEPYIVHVLPHLLQCFGDSSVYVRQAADECAKTVMAKLSAHGVKLVLPSLLNALDEDSWRTKTASVELLGSMAFCAPKQLSSCLPSIVPKLMEVLGDSHIKVQEAGANALRVIGSVIKNPEIQAIVPVLLTALEDPSSKTSACLQSLLETKFVHFIDAPSLALIMPVVQRAFMDRSTETRKMAAQIIGNMYSLTDQKDLTPYLPNIIPGLKTSLLDPVPEVRGVSARALGAMVRGMGESSFEDLLPWLMQTLTSESSSVDRSGAAQGLSEVVGGLGVEKLHKLMPEIIATAERTDIAPHVKDGYIMMFIYMPSAFPNDFTPYIGQIINPILKALADENEYVRDTALKAGQRIVNLYAESAITLLLPELEKGLFDDNWRIRYSSVQLLGDLLYKISGVSGKMTTQTASEDDNFGTEQSHKAIIRSLGADRRNRVLAGLYMGRSDVSLMVRQAALHVWKVVVTNTPRTLREILPTLFSLLLGCLASTSYDKRQVAARTLGDLVRKLGERVLPEIIPILERGLSSDQADQRQGVCIGLSEIMASTSRDMVLTFVNSLVPTVRKALADPLPEVRHAAAKTFDSLHTTVGARALEDILPSMLESLADPDPDVAEWTLDGLRQVMAIKSRVVLPYLIPQLTAKPVNTKALSILASVAGEALTKYLPKILPALLAALAAAQGTPEEVQELEYCQAVILSVSDEVGIRTIMDTVMESTKSEIPETRRAAATLLCAFCTHSPGDYSQYVPQLLRGLLWLLSDGDREVLQRSWDALNAVTKTLDSAQQIAHVTDVRQAVKFASSDLPKGGELPGFCLPKGITPLLPVFREAILNGLPEEKENAAQGLGEVIKLTSPASLQPSVVHITGPLIRILGDRFNAGVKAAVLETLAILLHKVGIMLKQFLPQLQTTFLKALHDPSRTVRIKAGHALAELIVIHTRPDPLFVEMHNGIKSADDSAVRETMLQALRGIVTPAGDKMTEPLRKQIYATLAGMLAHPEDVSRAAAAGCFGALCRWLTPEQVDDALTSHMLNEDYGDDATLRHGRTAALFVALKEHPGGIVTTKYEPKICKVITGALVSDKISVAMNGVRAGGYLLQYGMTDGTAKLSTAVIGPFVKSMNHSSNEVKQLLAKTCTYLARVVPAERIAPEYLKLAIPMLVNGTKEKNGYVRSNSEIALVHVLRLRDGEEFHQRCITLLEPGARESLSEVVSKVLRKVAMQAVGKEEELDDTILT
+>1346432at2759_1447883_1:000010
+MSSMRNAVQRRVHRERAQPANREKWGILEKHKDYSLRARDYSVKKAKLQRLREKADTRNPDEFAFGMMSGKSRTQGKHGARDTESAALSLETVKLLKTQDAGYLRVVGERIRRQMMAVDEEVRVQEGISGVSANGAAAGGGGGGGRKVVFVDSVEEQRERALEDEGKSDDDEEQGDFDEVDEEEQRQQKTQPKSKKQLEAEKLAQKEMLKARKLKIKAAEARSKKLQALTDQHKNIVAAEQELDWQRGKMENSVGGVNKHGLRWKVRERKR
+>761109at2759_198730_1:000010
+MAMTFTEDSIKELRLRLEDAVVKCSERCLYQSAKWAAEMLNSLVSTDGNDTDAESPMETDLQPTVNPFSLQSDPTEATLELQEAHKYLLAKSYFDTREYDRCAAVFLPPTIPPVPLSTVSPNVKSRASLTPQKGKRKSFIRPGLKSGQALPRNPYPNLSQKSLFLALYAKYLAGEKRRDEETEMVLGPADGGMTVNRELPDLARGLEGWFEERRERGLQDQGQGWLEYLYAVILIKGKNEEEAKKWLVRSVHLFPFHWGAWQELNDLLPSVDDLKQVAETLPQNIMSFIFQVHCSQELYQATDETHQTLNGLESIFPTSAFLKTERALLYYHSRDFEDASAIFADILIDSPHRLDSLDHYSNILYVMGARPQLAFVAQLATATDKFRPETCCVVGNYYSLKSEHEKAVMYFRRALTLDRNFLSAWTLMGHEYIEMKNTHAAIESYRRAVDVNRKDYRAWYGLGQAYEVLDMCFYALYYYQRTAALKPYDPKMWQAVGTCYAKMNQIPQSIKAMKRALVAGAYYEQRADAATADHPAAGRKILDPDLLHQIALLYEKMNNEDEAAAYMELTLQQESGEIERTETDSDDDDGDDNSDDGTTQRRSRRQRRRQKSRDDDNEIEAVGGTGVTATTSKARLWLARWALKHGDLNRADQLAGELCQDGVEVEEAKALMRDVRARREGGGG
+>1617752at2759_2004952_1:000010
+MPSSFVTPGQQRYLRACMVCSIVMTYSRFRDEGCPNCDEFLHLAGSQDQIESCTSQVFEGLITLANPAKSWIAKWQRLDGYVGGVYAIKVSGQLPDEIRTTLEDEYRIQYIPRDGTQTEADA
+>1588798at2759_215358_0:000010
+MTLPPTQQEPHTPEAFSLFVSFNHREPQNDDVMADLGIKAGDKVMMVWTQPSAPEGLKQHAEELAAIVGADGKVSVENLERLLLSSHSASSFDCVLSCLLADSSPVHTSETLEELARVLKPGGKLVLDEAVTGAETSQVRTAEKLISALKLSGFMSVTEVSKAELTAEALSALRTATGYQGNTLSRVRVSASKPNFEVGSSSQIKLSFGKKTPKPAEKPALDPNTVKMWTLSANDMGDDDVDLVDSDALLDEEDLKKPDPASLKVSCRDSGKKKACKNCSCGLAEELEQESTGKQKTNLPKSACGSCYLGDAFRCASCPYAGMPAFKPGEKIVLDKKTLTDA
+>1275837at2759_28005_1:000010
+MSSRDKASPSSPKETKGEHHLNEESDNDNNERRDEQQVTASAYLPSASRVDVHPLVLLSLVDHFARMNTKVRQKKRVVGLLLGRYKTDAAGTQVLDINNSFAVPFDEDPHNSDVWFFDTNYAEEMFVMHRRVHPKTKIVGWYASGPTVQQNDMLLHLLVADRFCANPVYCVVNTDPSHKGVPVLAYTTVQGREGARSLEFRNIPTHVGAEEAEEIGVEHLLRDLTDSTVTTLSSQLEERERSLEHMARVLVQIEEYLSDVASGALPASEDVLEALQELISLQPETYLKKKSLELNRFTNDRTIATFLGSIARCIGGLHEVILNRRVLARELKEIKARRAEAEEQRMDNEKNKIAEASPERKQ
+>1264469at2759_29058_0:000010
+MRPPLAIVRTYCTTAAPKSSNFIDEMKRNFIATNTFQKTLLSCGSAAISLLNPHRGDMIACLGEVTGESAIKYMRQKMTETEEGTEILKEKPRINSGTVSFDKLSQMPDNTLGRVYADFMTENNITADSRLPVQFIEDPELAYVMQRYREVHDLVHATLFMRTSMLGEVTVKWVEGIQTRLPMCISGGIWGAARLKPKHRQMYLKYYLPWAIKTGNNAKFMQGIYFEKRWDQDIDDFHKEMNIVRLVKK
+>673132at2759_326594_0:000010
+MTLLTVFKQFKKFQDAGKSVARSLSIKDDQESKKTCLYDLHIENNGKMVNFSGWLLPIQYRDSITASHQHTRTHASLFDVGHMLQSHVSGCDSGEFLESLTTADLQNLAQGGAALTVFTNKSGGILDDLIITKDRNDRFFVVSNAGRRNEDIELMLGRQAEMKSQGKNVTIEFLDPLEQGLIALQGPSAATTLQTLVKIDLTKLKFMNSVETKINQKSVRISRCGYTGEDGFEISVNGKDARTISEMILEVPDIKLAGLGARDSLRLEAGFCLYGHDINESITPVEASLQWLIAKRRREAANFPGAEFILEQIKNGPKKKRVGLILGQGPPARENATILTSAGERVGIVTSGGPSPTLGKPIAMGYVPLEHVHTGTPVLTEIRGKTYKALITKMPFVKPHYYSDKR
+>887370at2759_331117_1:000010
+MVVRSFLPLLSLLIALATFTSAASDYHEALVLQPLPQSSLLASFNFRGNTSQEAFDQRHFRYFPRALGQILQHTHTKELHIRFTTGRWDAESWGTRPWNGTKEGNTGVELWAWIDAPDSESAFARWISLTQSLSGLFCASLNFIDSTRTTRPVVSFEPIGDHSPSSDLHLLHGTLPGEVVCTENLTPFLKLLPCKGKAGVSSLLDGHKLFDASWQSMSVDVRPVCPQGGECLMQIEQTVDIVLDIERSKRPRDNPIPRPVPNDQLNCDNSKPYHSDDTCYPLERGSGKGWSLNEIFGRTLNGVCSLDEGQRPGEEAICLRVPHEQGVYTTSGVEETKRPDGYTRCFTLQPSGTFDLVIPEQSHTSLAPRDEPVLSAERTIVGHGQERGGMRIIFDNPSDAHPVDFIYFETLPWFLRPYVHTLRATITGRDGATRSVPVSHIVKETFYRPAIDRERGTQLELALSVPAASIVTLTYDFEKAILRYTEYPPDANRGFNVAPAVIKLSSANGNTIAHDTPIYMRTTSLLLPLPTPDFSMPYNVIILTSTVIALAFGSIFNLLVRRFVAADQAAALTAQTLKGRLLGKIVALRDRISGKRSKVE
+>166920at2759_38123_0:000010
+MAFLDFVFPLSKDELLERSDSQYYVRDQVTTSELPEKLKGCFESLHDDGPLFILENFDTLYGLLAHFKSVDFNQLHKVYTKLLIKSITEFIPILENYFSKETPDDELQNKYLNVIKMTVYILTEFIISFESRLQKEYQKVVIDVRARKVKVRAAIKHKEKYNWDWDFHLSNGLNSIHQLLKAKINKLWDPPVVEEEFVNTIANCCYKIIEDPCIASVKHKELRIFIFQVIGYLIKKYNHGISCTVKIVQLLKNCDHLVSPLAQAVTMFIRNHGCKSLVREIVREISEMDDGNEAAGQGQDNSKMVAAFLNEIAAEGPEYVIPAMDELLLNLEKESYMMRNCTLTILTELLLQVYKKENLSSEAKDQRDEYLNSLMEHIYDVHTFVRTKVLQLFQKLVIEKALPLAFTLQLVDRAIGRLMDKSSNVVKYAVQLLRTMIVSNPFAAKLGVEELKKKLAEAKATLTELEKNLPETSAQLSLVDEWNNIHYPVLLKIIREILEDGMYGCFLFYFL
+>1275837at2759_402676_1:000010
+MESMNDMFKKINAREKLVGWYHTGPQLRSSDLEINNLFKKYIPNPVLVIIDVQSKAVGLPTSAYFAVDEIKDDGTKSSLTFVHLPSSIEAEEAEEIGVEHLLRDTRDITAGTLATRVTEQVQSLRALEQRLDEIAVYLRKVVDGQLPINHTILGELQGVFNLLPNIFKTSNENDPLGLENGDERSFNINSNDQLMTVYLSSIVRSVIALHDLLDSLAASKAAEQEQDKLDLKQESTDSEKRATTAAVDEDPFMPN
+>1284731at2759_42254_0:000010
+MAEAGAVAAEYPSGGRARAARTLLDQVVLPGEELLLPEQEDADGPGGAGERPLQARDPYLKWGVRRACCEIPYVPVRGDHVIGIVTAKSGDTFKVDVGGSEPASLSYLAFEGATKRNRPNVQVGDLIYGQFVVANKDMEPEMVCIDGCGRANGMGVIGQDGLLFKVTLGLIRKLLAPDCEIIQELGKLYPLEIVFGMNGRIWVKAKTIQQTLILANILEACEHMTTDQRKQIFSRLAES
+>1228942at2759_45354_1:000010
+MNHDPFQWGRPRDEIYGHYDHKIAQASTSEFPSMHTQQPIITGTSVLGLKFDTGVVIAADHMGSYGSLLRFNNLERLICVGSETIVGVSGDISDFQHIERLLHELETEEEVYDTDGGHNLRAPNIHEYLSRVLYNRRLKMDPLWNAILVAGFNDDRTPFIRYVDLLGVTYGALALATGFGAHLAIPLLRKLVPYDLDYVKVKEADAREAVVNAMRVLYYRDARASDKYTLAVLSFKDGKVDVHFDQELKVTNQSWKFAEKVIGYGSKQQ
+>759498at2759_502779_1:000010
+MDGSRGSRKRKAVTRDLGEEPGVVSGNELHLDSADGSLADHSEDLDGSSDSEIELADDLNSDDDEEEEEEEEEDEDEINSDEVPSDIEPKVVGKKSGPGGEVDIIVRGDDTASDDDDDDDDDFESDDRPNYRVVKDANGNERYVYDEINPDDNSDYSETDENANTIGNIPLSFYDQYPHIGYNINGKKIMRPAKGQALDALLDSIELPKGFTGLTDPATGKPLELTQDELELLRKVQMNEITEEGYDPYQPTIEYFTSKLEVMPLSAAPEPKRRFVPSKHEAKRVMKLVKAIREGRILPYKQPAEEDEAEEGVQTYDIWANETPRADHPMHIPAPKLPPPGYEESYHPPPEYLPDEKEKSAWLNTDPEDRETEYLPTDHDALRKVPGYESFVKEKFERCLDLYLAPRVRRSKLNIDPESLLPKLPSPEELKPFPSTCATLFRGHQGRVRTLAIDPTGVWLASGGDDGTVRVWDILTGRQFWSVALSGDDAINVVRWRPGKDAVVLAAAAGDSIFLMVPPVLDPEMEKASFEVVDAGWGYAKTSPSTFTSTDSTKTSPVQWTRPSSSLLDSGVQAVISLGYVAKSLSWHRRGDYFVTVCPGTSTPVSLAIAIHTLSKHLTQQPFRRRLKGGGPPQTAHFHPSKPILFVANQRTIRAYDLSRQTLVKILQPGARWISSFDIHPTSSSTSGGDNLIVGSYDRRLLWHDVDLSPRPYKTLRYHQKAIRAVRYHANYPLFADASDDGSLQIFHGSVTGDLLSNASIVPLKVLRGHKVTGELGVLDLDWHPKEAWCVSAGADGTCRLWM
+>375960at2759_51337_0:000010
+MFFREHIFNIIGAFDIPRFVYNSERKKFLPLLMTNHPAPNLLGTAKDKAELYRERYTLLHQRTHRHELFTPPVIGSYPNESGSKFQLKTIETLLGSTTKIGDVIVLGMITQLKEGKFFLEDPTRTVQLDLSQAQFHSGLYTEACFVLAEGKAYYGSINFFGGPSNTSVKTSTKLKQLEEENKDAMFVFVSDVWLDRAEVLEKLHIMFSGYSPAPPSCFILCGNFSSAPYGKNQIQALKDSLKTLADIICEYPNIHQSSRFVFVPGPKDPGFGSILPRPPLAESITSEFRQKIPFSVFTTNPCRIQYCTEEIIIFREDIVNKMCRNCVRFPSSNLDIPNHFVKTILSQGHLTPLPLYVCPVYWARFPSSNLDIPNHGSFPRSGFSFKVFYPSSKTVEDSKLQGF
+>919955at2759_5643_1:000010
+MAAPMAVDKAKAPKIDVDEFLTLAISETPAELHPFFESFRSLYSRKLWHQLTNKLFEFFDHPLSKPYRVDVFNKFVRDFGLRLNQLRLVEMGVKVSKEIDNPVTHLQFLTDLLERVNIEKSPEAHVLLLSSLAHAKLLYGDHEGTKNDIDAAWKVLDELSSVDPSVNAAYYGVAADYYKSKAEYAPYYKNSLLYLACIDPAKDLTAEERLLRAHDLGIAAFLGDTIYNFGELPILQENYPFLRQKICLMALIESVFKRGSYDRTMSFQTIAEETHLPLDEVEHLVMKALSLKLIKGSLDQVDQKAQITWVQPRVLSREQIGQLAQRLAAWNSKLHQVEERIAPEVLVNS
+>817008at2759_5849_1:000010
+MDKLKTIYIDSALSIIKGALCVILQIPTGRTTESIKKKQNNVGIITVKSIFKEPTISQYNDIKQLIKTKIEENCPFYNYQINRTIAEKIYGDTIYDNYGLSKEINEVNLIILEEWNINCNRNRVLKHSGLIKNIEINKFKYLNNKESLEVHFLVNPKYTFEELNTIYKNEEELNNFLLSPIIKVTNKKIYEIEDKKSEFSYLYEEDILPKNKVLPPSGIENVNYESSKVVTPWDVNIGEEGINYNKLIKEFGCSKISDEHIRKIEKLTNRKAHHFIRRGIFFSHRDLDFLLNYYEQNGYFYIYTGRGPSSLSMHLGHLIPFYFCKYLQDAFNVPLIIQLSDDEKFLFNQNYSLDDINRFTKENVKDIIAVGFNPELTFIFKNTEYANHLYPTVLAIHKKTTLNQSMNVFGFNNSDNIGKISYPSFQIAPCFSQCFPNFLKKNIPCLVPQGIDQDPYFRLSRDIAVKLALYKPVVIHSVFMPGLQGVNTKMSSTKKKDNKNMDSKQDINNSVIFLTDSPEQIKNKINKYAFSGGGATIAEHKEKGADLEKDISYQYLRYFLVDDEKLNEIGEKYKKGEMLSGEIKKILIDILTDLVQKHQEKRNSLTDEDILYFFNDNKSSLKKFKDM
+>1426075at2759_61621_0:000010
+MTASQPNPQLPQSLPALKTSGTCARLPSTGRKLHLRIARAHPRVSRELFRRSGCGCGAGLSSAETDIAFLFSASGYRSHILKTMSGSFYFVIVGHHDNPVLKWSFXPAGKAESKDDHRHLNQFIAHAALDLVDENMWLSNNMYLKTVDKFNEWFVSAFVTAGHMRFIMLHDIRQEDGIKNFFTDVYDLYIKFSMNPFYEPNSPIRSSAFDRKVQFLGKKHLLS
+>655400at2759_688394_1:000010
+MAASRSPRLSSLLLRTTPLSRPTWQRTLSTRGFATAISNKLDNVYDMVIVGGGIAGTALACSLATNPSMKDYRIALIEAMDLSNTNNWAPATGRYSNRVVSLTPASMQFFEKIGVADELYRDRIQPYNCMKVSDGVTNASIEFDTNLLSSSTNPDDLPIAYMIENVHLQHSILKTLQTSKGKGATVDILQKARVASIRMQEQDAKETKDTLDLSDWPIIEMENGQSLQARLLVGADGVNSPVRSFAKIESLGWDYNMHGVVATFKTDPSRKNDTAYQRFLPTGPIAMLPLGDGHASMVWSMPPDMAHKVKKIPAQAFCTLVNSAFRLSMEDLDYLRSKIDPTTFEPLCDFDSEYNWRQGVAKHGLGDMEMMERELAFPPIVESVDETSRASFPLRMRNSQQYFADRVVLVGDAAHTVHPLAGQGLNQGILDVACLSDILQRGASEGQDIGNLHLLREYASVRYLRNLLMISACDKLHRLYSTDFAPITWIRSLGLSSVNQLDFVKAEIMKYAMGIEQ
+>946128at2759_765440_1:000010
+MPTTVCTAKASYKKTPGQLELTETHLQWFADGKKAPSVRVLYAEAASLFCSKEGAAQIRLKLGLVGDDTGHNFTFTSPQSVAYKERETFKKELTNIISRNRSVPNVTTPRPPLNTSISSTTPAISNAPTPRSVVPPSRASTSRAPSVSSDGRTPIVPGSDPTSDFRLRKQVLVSNPELGALHRDLVMSGQITEAEFWEGREHLLLAQTATESQKRGRPGQLVDPRPETVEGGEVKIVITPQLVHDIFEEYPVVAKAYNDNVPNKLSEAEFWKRYFQSKLFNAHRASIRSSAAQHVVKDDKIFDKYLEKDDDELEPRRQRDEGINLFVNLGATREDHGETGNEQDITMQAGRQRGALPLIRKFNEHSERLLNSALGDEPTAKRRRIDAGKEDAYSQIDLDDLHDPEASAGIILEMQDRQRYFEGQMASAASAEAAAGKNLDIRAILGETKVNLHDWETNLAQLKINKKSGDAALLSMTENVSARLEIKMKKNDIPPELFSQMTTCQTAANEFLRQFWLSMYPPAADHQVLAPATPAQKAAKAAKMIGYLGKTHEKVDALIRTAQVEAVDAAKVEIVRAVCFVYIITVNFNANLQAMKPILDAVDRALAFYRSRKPPK
+>1287401at2759_870435_1:000010
+MSSSIVGSLTRGCRTPSVNINPHPFFRCRTSLYHGIGKPPSWLHSRTQLWRTIGTSSSKHTPPSSASVSARRPTAIPSYNASREQMYKTRNRNLLMYTSAVVILGVGITYAAVPLYRMFCSATGFAGTPSVVSTSSGRFDPSRLTPDTDARRIRVHFNADRAEALPWKFFPQQKYVEVLPGESSLAFYKARNESKKDIIGIATYNVTPDRVAPYFSKVECFCFEEQKLLAGEEVDMPLLFFIDKDILDDPSCRGVNDVVLSYTFFKARRNAQGHLEPDAEEDVVQRSLGFEGYEHSPRAETKKVEGSKANS
--- a/src/busco/busco_run/test_data/script.sh
+++ b/src/busco/busco_run/test_data/script.sh
@@ -0,0 +1,12 @@
+# busco test data
+
+# Test data from https://github.com/snakemake/snakemake-wrappers/tree/master/bio/busco/test
+
+if [ ! -d /tmp/snakemake-wrappers ]; then
+  git clone --depth 1 --single-branch --branch master https://github.com/snakemake/snakemake-wrappers /tmp/snakemake-wrappers
+fi
+
+cp -r /tmp/snakemake-wrappers/bio/busco/test/protein.fasta src/busco/test_data
+
+# Test data from busco test data at https://gitlab.com/ezlab/busco/-/tree/master/test_data?ref_type=heads
+wget -O src/busco/test_data/genome.fna "https://gitlab.com/ezlab/busco/-/raw/master/test_data/eukaryota/genome.fna?ref_type=heads&inline=false"
--- a/src/cutadapt/config.vsh.yaml
+++ b/src/cutadapt/config.vsh.yaml
@@ -0,0 +1,484 @@
+name: cutadapt
+description: |
+  Cutadapt removes adapter sequences from high-throughput sequencing reads.
+keywords: [RNA-seq, scRNA-seq, high-throughput]
+links:
+  homepage: https://cutadapt.readthedocs.io
+  documentation: https://cutadapt.readthedocs.io
+  repository: https://github.com/marcelm/cutadapt
+references:
+  doi: 10.14806/ej.17.1.200
+license: MIT
+authors:
+  - __merge__: /src/_authors/toni_verbeiren.yaml
+    roles: [ author, maintainer ]
+argument_groups:
+  ####################################################################
+  - name: Specify Adapters for R1
+    arguments:
+      - name: --adapter
+        alternatives: [-a]
+        type: string
+        multiple: true
+        description: |
+          Sequence of an adapter ligated to the 3' end (paired data:
+          of the first read). The adapter and subsequent bases are
+          trimmed. If a '$' character is appended ('anchoring'), the
+          adapter is only found if it is a suffix of the read.
+        required: false
+      - name: --front
+        alternatives: [-g]
+        type: string
+        multiple: true
+        description: |
+          Sequence of an adapter ligated to the 5' end (paired data:
+          of the first read). The adapter and any preceding bases
+          are trimmed. Partial matches at the 5' end are allowed. If
+          a '^' character is prepended ('anchoring'), the adapter is
+          only found if it is a prefix of the read.
+        required: false
+      - name: --anywhere
+        alternatives: [-b]
+        type: string
+        multiple: true
+        description: |
+          Sequence of an adapter that may be ligated to the 5' or 3'
+          end (paired data: of the first read). Both types of
+          matches as described under -a and -g are allowed. If the
+          first base of the read is part of the match, the behavior
+          is as with -g, otherwise as with -a. This option is mostly
+          for rescuing failed library preparations - do not use if
+          you know which end your adapter was ligated to!
+        required: false
+
+  ####################################################################
+  - name: Specify Adapters using Fasta files for R1
+    arguments:
+      - name: --adapter_fasta
+        type: file
+        multiple: true
+        description: |
+          Fasta file containing sequences of an adapter ligated to the 3' end (paired data:
+          of the first read). The adapter and subsequent bases are
+          trimmed. If a '$' character is appended ('anchoring'), the
+          adapter is only found if it is a suffix of the read.
+        required: false
+      - name: --front_fasta
+        type: file
+        description: |
+          Fasta file containing sequences of an adapter ligated to the 5' end (paired data:
+          of the first read). The adapter and any preceding bases
+          are trimmed. Partial matches at the 5' end are allowed. If
+          a '^' character is prepended ('anchoring'), the adapter is
+          only found if it is a prefix of the read.
+        required: false
+      - name: --anywhere_fasta
+        type: file
+        description: |
+          Fasta file containing sequences of an adapter that may be ligated to the 5' or 3'
+          end (paired data: of the first read). Both types of
+          matches as described under -a and -g are allowed. If the
+          first base of the read is part of the match, the behavior
+          is as with -g, otherwise as with -a. This option is mostly
+          for rescuing failed library preparations - do not use if
+          you know which end your adapter was ligated to!
+        required: false
+
+  ####################################################################
+  - name: Specify Adapters for R2
+    arguments:
+      - name: --adapter_r2
+        alternatives: [-A]
+        type: string
+        multiple: true
+        description: |
+          Sequence of an adapter ligated to the 3' end (paired data:
+          of the first read). The adapter and subsequent bases are
+          trimmed. If a '$' character is appended ('anchoring'), the
+          adapter is only found if it is a suffix of the read.
+        required: false
+      - name: --front_r2
+        alternatives: [-G]
+        type: string
+        multiple: true
+        description: |
+          Sequence of an adapter ligated to the 5' end (paired data:
+          of the first read). The adapter and any preceding bases
+          are trimmed. Partial matches at the 5' end are allowed. If
+          a '^' character is prepended ('anchoring'), the adapter is
+          only found if it is a prefix of the read.
+        required: false
+      - name: --anywhere_r2
+        alternatives: [-B]
+        type: string
+        multiple: true
+        description: |
+          Sequence of an adapter that may be ligated to the 5' or 3'
+          end (paired data: of the first read). Both types of
+          matches as described under -a and -g are allowed. If the
+          first base of the read is part of the match, the behavior
+          is as with -g, otherwise as with -a. This option is mostly
+          for rescuing failed library preparations - do not use if
+          you know which end your adapter was ligated to!
+        required: false
+
+  ####################################################################
+  - name: Specify Adapters using Fasta files for R2
+    arguments:
+      - name: --adapter_r2_fasta
+        type: file
+        description: |
+          Fasta file containing sequences of an adapter ligated to the 3' end (paired data:
+          of the first read). The adapter and subsequent bases are
+          trimmed. If a '$' character is appended ('anchoring'), the
+          adapter is only found if it is a suffix of the read.
+        required: false
+      - name: --front_r2_fasta
+        type: file
+        description: |
+          Fasta file containing sequences of an adapter ligated to the 5' end (paired data:
+          of the first read). The adapter and any preceding bases
+          are trimmed. Partial matches at the 5' end are allowed. If
+          a '^' character is prepended ('anchoring'), the adapter is
+          only found if it is a prefix of the read.
+        required: false
+      - name: --anywhere_r2_fasta
+        type: file
+        description: |
+          Fasta file containing sequences of an adapter that may be ligated to the 5' or 3'
+          end (paired data: of the first read). Both types of
+          matches as described under -a and -g are allowed. If the
+          first base of the read is part of the match, the behavior
+          is as with -g, otherwise as with -a. This option is mostly
+          for rescuing failed library preparations - do not use if
+          you know which end your adapter was ligated to!
+        required: false
+
+  ####################################################################
+  - name: Paired-end options
+    arguments:
+      - name: --pair_adapters
+        type: boolean_true
+        description: |
+          Treat adapters given with -a/-A etc. as pairs. Either both
+          or none are removed from each read pair.
+      - name: --pair_filter
+        type: string
+        choices: [any, both, first]
+        description: |
+          Which of the reads in a paired-end read have to match the
+          filtering criterion in order for the pair to be filtered.
+      - name: --interleaved
+        type: boolean_true
+        description: |
+          Read and/or write interleaved paired-end reads.
+
+  ####################################################################
+  - name: Input parameters
+    arguments:
+      - name: --input
+        type: file
+        required: true
+        description: |
+          Input fastq file for single-end reads or R1 for paired-end reads.
+      - name: --input_r2
+        type: file
+        required: false
+        description: |
+          Input fastq file for R2 in the case of paired-end reads.
+      - name: --error_rate
+        alternatives: [-E, --errors]
+        type: double
+        description: |
+          Maximum allowed error rate (if 0 <= E < 1), or absolute
+          number of errors for full-length adapter match (if E is an
+          integer >= 1). Error rate = no. of errors divided by
+          length of matching region. Default: 0.1 (10%).
+        example: 0.1
+      - name: --no_indels
+        type: boolean_false
+        description: |
+          Allow only mismatches in alignments.
+
+      - name: --times
+        type: integer
+        alternatives: [-n]
+        description: |
+          Remove up to COUNT adapters from each read. Default: 1.
+        example: 1
+      - name: --overlap
+        alternatives: [-O]
+        type: integer
+        description: |
+          Require MINLENGTH overlap between read and adapter for an
+          adapter to be found. The default is 3.
+        example: 3
+      - name: --match_read_wildcards
+        type: boolean_true
+        description: |
+          Interpret IUPAC wildcards in reads.
+      - name: --no_match_adapter_wildcards
+        type: boolean_false
+        description: |
+          Do not interpret IUPAC wildcards in adapters.
+      - name: --action
+        type: string
+        choices:
+          - trim
+          - retain
+          - mask
+          - lowercase
+          - none
+        description: |
+          What to do if a match was found. trim: trim adapter and
+          up- or downstream sequence; retain: trim, but retain
+          adapter; mask: replace with 'N' characters; lowercase:
+          convert to lowercase; none: leave unchanged.
+          The default is trim.
+        example: trim
+      - name: --revcomp
+        alternatives: [--rc]
+        type: boolean_true
+        description: |
+          Check both the read and its reverse complement for adapter
+          matches. If match is on reverse-complemented version,
+          output that one.
+  
+  ####################################################################
+  - name: "Demultiplexing options"
+    arguments:
+      - name: "--demultiplex_mode"
+        type: string
+        choices: ["single", "unique_dual", "combinatorial_dual"]
+        required: false
+        description: |
+          Enable demultiplexing and set the mode for it.
+          With mode 'unique_dual', adapters from the first and second read are used,
+          and the indexes from the reads are only used in pairs. This implies
+          --pair_adapters.
+          Enabling mode 'combinatorial_dual' allows all combinations of the sets of indexes
+          on R1 and R2. It is necessary to write each read pair to an output
+          file depending on the adapters found on both R1 and R2.
+          Mode 'single', uses indexes or barcodes located at the 5'
+          end of the R1 read (single). 
+
+  ####################################################################
+  - name: Read modifications
+    arguments:
+      - name: --cut
+        alternatives: [-u]
+        type: integer
+        multiple: true
+        description: |
+          Remove LEN bases from each read (or R1 if paired; use --cut_r2
+          option for R2). If LEN is positive, remove bases from the
+          beginning. If LEN is negative, remove bases from the end.
+          Can be used twice if LENs have different signs. Applied
+          *before* adapter trimming.
+      - name: --cut_r2
+        type: integer
+        multiple: true
+        description: |
+          Remove LEN bases from each read (for R2). If LEN is positive, remove bases from the
+          beginning. If LEN is negative, remove bases from the end.
+          Can be used twice if LENs have different signs. Applied
+          *before* adapter trimming.
+      - name: --nextseq_trim
+        type: string
+        description: |
+          NextSeq-specific quality trimming (each read). Trims also
+          dark cycles appearing as high-quality G bases.
+      - name: --quality_cutoff
+        alternatives: [-q]
+        type: string
+        description: |
+          Trim low-quality bases from 5' and/or 3' ends of each read
+          before adapter removal. Applied to both reads if data is
+          paired. If one value is given, only the 3' end is trimmed.
+          If two comma-separated cutoffs are given, the 5' end is
+          trimmed with the first cutoff, the 3' end with the second.
+      - name: --quality_cutoff_r2
+        alternatives: [-Q]
+        type: string
+        description: |
+          Quality-trimming cutoff for R2. Default: same as for R1
+      - name: --quality_base
+        type: integer
+        description: |
+          Assume that quality values in FASTQ are encoded as
+          ascii(quality + N). This needs to be set to 64 for some
+          old Illumina FASTQ files. The default is 33.
+        example: 33
+      - name: --poly_a
+        type: boolean_true
+        description: Trim poly-A tails
+      - name: --length
+        alternatives: [-l]
+        type: integer
+        description: |
+          Shorten reads to LENGTH. Positive values remove bases at
+          the end while negative ones remove bases at the beginning.
+          This and the following modifications are applied after
+          adapter trimming.
+      - name: --trim_n
+        type: boolean_true
+        description: Trim N's on ends of reads.
+      - name: --length_tag
+        type: string
+        description: |
+          Search for TAG followed by a decimal number in the
+          description field of the read. Replace the decimal number
+          with the correct length of the trimmed read. For example,
+          use --length-tag 'length=' to correct fields like
+          'length=123'.
+        example: "length="
+      - name: --strip_suffix
+        type: string
+        description: |
+          Remove this suffix from read names if present. Can be
+          given multiple times.
+      - name: --prefix
+        alternatives: [-x]
+        type: string
+        description: |
+          Add this prefix to read names. Use {name} to insert the
+          name of the matching adapter.
+      - name: --suffix
+        alternatives: [-y]
+        type: string
+        description: |
+          Add this suffix to read names; can also include {name}
+      - name: --rename
+        type: string
+        description: |
+          Rename reads using TEMPLATE containing variables such as
+          {id}, {adapter_name} etc. (see documentation)
+      - name: --zero_cap
+        alternatives: [-z]
+        type: boolean_true
+        description: Change negative quality values to zero.
+
+  ####################################################################
+  - name: Filtering of processed reads
+    description: |
+      Filters are applied after above read modifications. Paired-end reads are
+      always discarded pairwise (see also --pair_filter).
+    arguments:
+      - name: --minimum_length
+        alternatives: [-m]
+        type: string
+        description: |
+          Discard reads shorter than LEN. Default is 0.
+          When trimming paired-end reads, the minimum lengths for R1 and R2 can be specified separately by separating them with a colon (:).
+          If the colon syntax is not used, the same minimum length applies to both reads, as discussed above.
+          Also, one of the values can be omitted to impose no restrictions.
+          For example, with -m 17:, the length of R1 must be at least 17, but the length of R2 is ignored.
+        example: "0"
+      - name: --maximum_length
+        alternatives: [-M]
+        type: string
+        description: |
+          Discard reads longer than LEN. Default: no limit.
+          For paired reads, see the remark for --minimum_length
+      - name: --max_n
+        type: string
+        description: |
+          Discard reads with more than COUNT 'N' bases. If COUNT is
+          a number between 0 and 1, it is interpreted as a fraction
+          of the read length.
+      - name: --max_expected_errors
+        alternatives: [--max_ee]
+        type: long
+        description: |
+          Discard reads whose expected number of errors (computed
+          from quality values) exceeds ERRORS.
+      - name: --max_average_error_rate
+        alternatives: [--max_aer]
+        type: long
+        description: |
+          as --max_expected_errors (see above), but divided by
+          length to account for reads of varying length.
+      - name: --discard_trimmed
+        alternatives: [--discard]
+        type: boolean_true
+        description: |
+          Discard reads that contain an adapter. Use also -O to
+          avoid discarding too many randomly matching reads.
+      - name: --discard_untrimmed
+        alternatives: [--trimmed_only]
+        type: boolean_true
+        description: |
+          Discard reads that do not contain an adapter.
+      - name: --discard_casava
+        type: boolean_true
+        description: |
+          Discard reads that did not pass CASAVA filtering (header
+          has :Y:).
+
+  ####################################################################
+  - name: Output parameters
+    arguments:
+      - name: --report
+        type: string
+        choices: [full, minimal]
+        description: |
+          Which type of report to print: 'full' (default) or 'minimal'.
+        example: full
+      - name: --json
+        type: boolean_true
+        description: |
+          Write report in JSON format to this file.
+      - name: --output
+        type: file
+        description: |
+          Glob pattern for matching the expected output files.
+          Should include `$output_dir`.
+        example: "fastq/*_001.fast[a,q]"
+        direction: output
+        required: true
+        must_exist: true
+        multiple: true
+      - name: --fasta
+        type: boolean_true
+        description: |
+          Output FASTA to standard output even on FASTQ input.
+      - name: --info_file
+        type: boolean_true
+        description: |
+          Write information about each read and its adapter matches
+          into info.txt in the output directory.
+          See the documentation for the file format.
+      # - name: -Z
+      # - name: --rest_file
+      # - name: --wildcard-file
+      # - name: --too_short_output
+      # - name: --too_long_output
+      # - name: --untrimmed_output
+      # - name: --untrimmed_paired_output
+      # - name: too_short_paired_output
+      # - name: too_long_paired_output
+  - name: Debug
+    arguments:
+      - type: boolean_true
+        name: --debug
+        description: Print debug information
+resources:
+  - type: bash_script
+    path: script.sh
+test_resources:
+  - type: bash_script
+    path: test.sh
+
+engines:
+  - type: docker
+    image: python:3.12
+    setup:
+      - type: python
+        pip:
+          - cutadapt
+      - type: docker
+        run: |
+          cutadapt --version | sed 's/\(.*\)/cutadapt: "\1"/' > /var/software_versions.txt
+runners:
+  - type: executable
+  - type: nextflow
--- a/src/cutadapt/help.txt
+++ b/src/cutadapt/help.txt
@@ -0,0 +1,218 @@
+cutadapt version 4.6
+
+Copyright (C) 2010 Marcel Martin <marcel.martin@scilifelab.se> and contributors
+
+Cutadapt removes adapter sequences from high-throughput sequencing reads.
+
+Usage:
+    cutadapt -a ADAPTER [options] [-o output.fastq] input.fastq
+
+For paired-end reads:
+    cutadapt -a ADAPT1 -A ADAPT2 [options] -o out1.fastq -p out2.fastq in1.fastq in2.fastq
+
+Replace "ADAPTER" with the actual sequence of your 3' adapter. IUPAC wildcard
+characters are supported. All reads from input.fastq will be written to
+output.fastq with the adapter sequence removed. Adapter matching is
+error-tolerant. Multiple adapter sequences can be given (use further -a
+options), but only the best-matching adapter will be removed.
+
+Input may also be in FASTA format. Compressed input and output is supported and
+auto-detected from the file name (.gz, .xz, .bz2). Use the file name '-' for
+standard input/output. Without the -o option, output is sent to standard output.
+
+Citation:
+
+Marcel Martin. Cutadapt removes adapter sequences from high-throughput
+sequencing reads. EMBnet.Journal, 17(1):10-12, May 2011.
+http://dx.doi.org/10.14806/ej.17.1.200
+
+Run "cutadapt --help" to see all command-line options.
+See https://cutadapt.readthedocs.io/ for full documentation.
+
+Options:
+  -h, --help            Show this help message and exit
+  --version             Show version number and exit
+  --debug               Print debug log. Use twice to also print DP matrices
+  -j CORES, --cores CORES
+                        Number of CPU cores to use. Use 0 to auto-detect. Default:
+                        1
+
+Finding adapters:
+  Parameters -a, -g, -b specify adapters to be removed from each read (or from
+  R1 if data is paired-end. If specified multiple times, only the best matching
+  adapter is trimmed (but see the --times option). Use notation 'file:FILE' to
+  read adapter sequences from a FASTA file.
+
+  -a ADAPTER, --adapter ADAPTER
+                        Sequence of an adapter ligated to the 3' end (paired data:
+                        of the first read). The adapter and subsequent bases are
+                        trimmed. If a '$' character is appended ('anchoring'), the
+                        adapter is only found if it is a suffix of the read.
+  -g ADAPTER, --front ADAPTER
+                        Sequence of an adapter ligated to the 5' end (paired data:
+                        of the first read). The adapter and any preceding bases
+                        are trimmed. Partial matches at the 5' end are allowed. If
+                        a '^' character is prepended ('anchoring'), the adapter is
+                        only found if it is a prefix of the read.
+  -b ADAPTER, --anywhere ADAPTER
+                        Sequence of an adapter that may be ligated to the 5' or 3'
+                        end (paired data: of the first read). Both types of
+                        matches as described under -a and -g are allowed. If the
+                        first base of the read is part of the match, the behavior
+                        is as with -g, otherwise as with -a. This option is mostly
+                        for rescuing failed library preparations - do not use if
+                        you know which end your adapter was ligated to!
+  -e E, --error-rate E, --errors E
+                        Maximum allowed error rate (if 0 <= E < 1), or absolute
+                        number of errors for full-length adapter match (if E is an
+                        integer >= 1). Error rate = no. of errors divided by
+                        length of matching region. Default: 0.1 (10%)
+  --no-indels           Allow only mismatches in alignments. Default: allow both
+                        mismatches and indels
+  -n COUNT, --times COUNT
+                        Remove up to COUNT adapters from each read. Default: 1
+  -O MINLENGTH, --overlap MINLENGTH
+                        Require MINLENGTH overlap between read and adapter for an
+                        adapter to be found. Default: 3
+  --match-read-wildcards
+                        Interpret IUPAC wildcards in reads. Default: False
+  -N, --no-match-adapter-wildcards
+                        Do not interpret IUPAC wildcards in adapters.
+  --action {trim,retain,mask,lowercase,none}
+                        What to do if a match was found. trim: trim adapter and
+                        up- or downstream sequence; retain: trim, but retain
+                        adapter; mask: replace with 'N' characters; lowercase:
+                        convert to lowercase; none: leave unchanged. Default: trim
+  --rc, --revcomp       Check both the read and its reverse complement for adapter
+                        matches. If match is on reverse-complemented version,
+                        output that one. Default: check only read
+
+Additional read modifications:
+  -u LEN, --cut LEN     Remove LEN bases from each read (or R1 if paired; use -U
+                        option for R2). If LEN is positive, remove bases from the
+                        beginning. If LEN is negative, remove bases from the end.
+                        Can be used twice if LENs have different signs. Applied
+                        *before* adapter trimming.
+  --nextseq-trim 3'CUTOFF
+                        NextSeq-specific quality trimming (each read). Trims also
+                        dark cycles appearing as high-quality G bases.
+  -q [5'CUTOFF,]3'CUTOFF, --quality-cutoff [5'CUTOFF,]3'CUTOFF
+                        Trim low-quality bases from 5' and/or 3' ends of each read
+                        before adapter removal. Applied to both reads if data is
+                        paired. If one value is given, only the 3' end is trimmed.
+                        If two comma-separated cutoffs are given, the 5' end is
+                        trimmed with the first cutoff, the 3' end with the second.
+  --quality-base N      Assume that quality values in FASTQ are encoded as
+                        ascii(quality + N). This needs to be set to 64 for some
+                        old Illumina FASTQ files. Default: 33
+  --poly-a              Trim poly-A tails
+  --length LENGTH, -l LENGTH
+                        Shorten reads to LENGTH. Positive values remove bases at
+                        the end while negative ones remove bases at the beginning.
+                        This and the following modifications are applied after
+                        adapter trimming.
+  --trim-n              Trim N's on ends of reads.
+  --length-tag TAG      Search for TAG followed by a decimal number in the
+                        description field of the read. Replace the decimal number
+                        with the correct length of the trimmed read. For example,
+                        use --length-tag 'length=' to correct fields like
+                        'length=123'.
+  --strip-suffix STRIP_SUFFIX
+                        Remove this suffix from read names if present. Can be
+                        given multiple times.
+  -x PREFIX, --prefix PREFIX
+                        Add this prefix to read names. Use {name} to insert the
+                        name of the matching adapter.
+  -y SUFFIX, --suffix SUFFIX
+                        Add this suffix to read names; can also include {name}
+  --rename TEMPLATE     Rename reads using TEMPLATE containing variables such as
+                        {id}, {adapter_name} etc. (see documentation)
+  --zero-cap, -z        Change negative quality values to zero.
+
+Filtering of processed reads:
+  Filters are applied after above read modifications. Paired-end reads are
+  always discarded pairwise (see also --pair-filter).
+
+  -m LEN[:LEN2], --minimum-length LEN[:LEN2]
+                        Discard reads shorter than LEN. Default: 0
+  -M LEN[:LEN2], --maximum-length LEN[:LEN2]
+                        Discard reads longer than LEN. Default: no limit
+  --max-n COUNT         Discard reads with more than COUNT 'N' bases. If COUNT is
+                        a number between 0 and 1, it is interpreted as a fraction
+                        of the read length.
+  --max-expected-errors ERRORS, --max-ee ERRORS
+                        Discard reads whose expected number of errors (computed
+                        from quality values) exceeds ERRORS.
+  --max-average-error-rate ERROR_RATE, --max-aer ERROR_RATE
+                        as --max-expected-errors (see above), but divided by
+                        length to account for reads of varying length.
+  --discard-trimmed, --discard
+                        Discard reads that contain an adapter. Use also -O to
+                        avoid discarding too many randomly matching reads.
+  --discard-untrimmed, --trimmed-only
+                        Discard reads that do not contain an adapter.
+  --discard-casava      Discard reads that did not pass CASAVA filtering (header
+                        has :Y:).
+
+Output:
+  --quiet               Print only error messages.
+  --report {full,minimal}
+                        Which type of report to print: 'full' or 'minimal'.
+                        Default: full
+  --json FILE           Dump report in JSON format to FILE
+  -o FILE, --output FILE
+                        Write trimmed reads to FILE. FASTQ or FASTA format is
+                        chosen depending on input. Summary report is sent to
+                        standard output. Use '{name}' for demultiplexing (see
+                        docs). Default: write to standard output
+  --fasta               Output FASTA to standard output even on FASTQ input.
+  -Z                    Use compression level 1 for gzipped output files (faster,
+                        but uses more space)
+  --info-file FILE      Write information about each read and its adapter matches
+                        into FILE. See the documentation for the file format.
+  -r FILE, --rest-file FILE
+                        When the adapter matches in the middle of a read, write
+                        the rest (after the adapter) to FILE.
+  --wildcard-file FILE  When the adapter has N wildcard bases, write adapter bases
+                        matching wildcard positions to FILE. (Inaccurate with
+                        indels.)
+  --too-short-output FILE
+                        Write reads that are too short (according to length
+                        specified by -m) to FILE. Default: discard reads
+  --too-long-output FILE
+                        Write reads that are too long (according to length
+                        specified by -M) to FILE. Default: discard reads
+  --untrimmed-output FILE
+                        Write reads that do not contain any adapter to FILE.
+                        Default: output to same file as trimmed reads
+
+Paired-end options:
+  The -A/-G/-B/-U/-Q options work like their lowercase counterparts, but are
+  applied to R2 (second read in pair)
+
+  -A ADAPTER            3' adapter to be removed from R2
+  -G ADAPTER            5' adapter to be removed from R2
+  -B ADAPTER            5'/3 adapter to be removed from R2
+  -U LENGTH             Remove LENGTH bases from R2
+  -Q [5'CUTOFF,]3'CUTOFF
+                        Quality-trimming cutoff for R2. Default: same as for R1
+  -p FILE, --paired-output FILE
+                        Write R2 to FILE.
+  --pair-adapters       Treat adapters given with -a/-A etc. as pairs. Either both
+                        or none are removed from each read pair.
+  --pair-filter {any,both,first}
+                        Which of the reads in a paired-end read have to match the
+                        filtering criterion in order for the pair to be filtered.
+                        Default: any
+  --interleaved         Read and/or write interleaved paired-end reads.
+  --untrimmed-paired-output FILE
+                        Write second read in a pair to this FILE when no adapter
+                        was found. Use with --untrimmed-output. Default: output to
+                        same file as trimmed reads
+  --too-short-paired-output FILE
+                        Write second read in a pair to this file if pair is too
+                        short.
+  --too-long-paired-output FILE
+                        Write second read in a pair to this file if pair is too
+                        long.
+
--- a/src/cutadapt/script.sh
+++ b/src/cutadapt/script.sh
@@ -0,0 +1,258 @@
+#!/bin/bash
+
+## VIASH START
+par_adapter='AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC;GGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
+par_input='src/cutadapt/test_data/se/a.fastq'
+par_report='full'
+par_json='false'
+par_fasta='false'
+par_info_file='false'
+par_debug='true'
+## VIASH END
+
+function debug {
+  [[ "$par_debug" == "true" ]] && echo "DEBUG: $@"
+}
+
+output_dir=$(dirname $par_output)
+[[ ! -d $output_dir ]] && mkdir -p $output_dir
+
+# Init
+###########################################################
+
+echo ">> Paired-end data or not?"
+
+mode=""
+if [[ -z $par_input_r2 ]]; then
+  mode="se"
+  echo "  Single end"
+  input="$par_input"
+else
+  echo "  Paired end"
+  mode="pe"
+  input="$par_input $par_input_r2"
+fi
+
+# Adapter arguments
+#   - paired and single-end
+#   - string and fasta
+###########################################################
+
+function add_flags {
+  local arg=$1
+  local flag=$2
+  local prefix=$3
+  [[ -z $prefix ]] && prefix=""
+
+  # This function should not be called if the input is empty
+  # but check for it just in case
+  if [[ -z $arg ]]; then
+    return
+  fi
+
+  local output=""
+  IFS=';' read -r -a array <<< "$arg"
+  for a in "${array[@]}"; do
+    output="$output $flag $prefix$a"
+  done
+  echo $output
+}
+
+debug ">> Parsing arguments dealing with adapters"
+adapter_args=$(echo \
+  ${par_adapter:+$(add_flags "$par_adapter" "--adapter")} \
+  ${par_adapter_fasta:+$(add_flags "$par_adapter_fasta" "--adapter" "file:")} \
+  ${par_front:+$(add_flags "$par_front" "--front")} \
+  ${par_front_fasta:+$(add_flags "$par_front_fasta" "--front" "file:")} \
+  ${par_anywhere:+$(add_flags "$par_anywhere" "--anywhere")} \
+  ${par_anywhere_fasta:+$(add_flags "$par_anywhere_fasta" "--anywhere" "file:")} \
+  ${par_adapter_r2:+$(add_flags "$par_adapter_r2" "-A")} \
+  ${par_adapter_fasta_r2:+$(add_flags "$par_adapter_fasta_r2" "-A" "file:")} \
+  ${par_front_r2:+$(add_flags "$par_front_r2" "-G")} \
+  ${par_front_fasta_r2:+$(add_flags "$par_front_fasta_r2" "-G" "file:")} \
+  ${par_anywhere_r2:+$(add_flags "$par_anywhere_r2" "-B")} \
+  ${par_anywhere_fasta_r2:+$(add_flags "$par_anywhere_fasta_r2" "-B" "file:")} \
+)
+
+debug "Arguments to cutadapt:"
+debug "$adapter_args"
+debug
+
+# Paired-end options
+###########################################################
+echo ">> Parsing arguments for paired-end reads"
+[[ "$par_pair_adapters" == "false" ]] && unset par_pair_adapters
+[[ "$par_interleaved" == "false" ]] && unset par_interleaved
+
+paired_args=$(echo \
+  ${par_pair_adapters:+--pair-adapters} \
+  ${par_pair_filter:+--pair-filter "${par_pair_filter}"} \
+  ${par_interleaved:+--interleaved}
+)
+debug "Arguments to cutadapt:"
+debug $paired_args
+debug
+
+# Input arguments 
+###########################################################
+echo ">> Parsing input arguments"
+[[ "$par_no_indels" == "true" ]] && unset par_no_indels
+[[ "$par_match_read_wildcards" == "false" ]] && unset par_match_read_wildcards
+[[ "$par_no_match_adapter_wildcards" == "true" ]] && unset par_no_match_adapter_wildcards
+[[ "$par_revcomp" == "false" ]] && unset par_revcomp
+
+input_args=$(echo \
+  ${par_error_rate:+--error-rate "${par_error_rate}"} \
+  ${par_no_indels:+--no-indels} \
+  ${par_times:+--times "${par_times}"} \
+  ${par_overlap:+--overlap "${par_overlap}"} \
+  ${par_match_read_wildcards:+--match-read-wildcards} \
+  ${par_no_match_adapter_wildcards:+--no-match-adapter-wildcards} \
+  ${par_action:+--action "${par_action}"} \
+  ${par_revcomp:+--revcomp} \
+)
+debug "Arguments to cutadapt:"
+debug $input_args
+debug
+
+# Read modifications
+###########################################################
+echo ">> Parsing read modification arguments"
+[[ "$par_poly_a" == "false" ]] && unset par_poly_a
+[[ "$par_trim_n" == "false" ]] && unset par_trim_n
+[[ "$par_zero_cap" == "false" ]] && unset par_zero_cap
+
+mod_args=$(echo \
+  ${par_cut:+--cut "${par_cut}"} \
+  ${par_cut_r2:+--cut_r2 "${par_cut_r2}"} \
+  ${par_nextseq_trim:+--nextseq-trim "${par_nextseq_trim}"} \
+  ${par_quality_cutoff:+--quality-cutoff "${par_quality_cutoff}"} \
+  ${par_quality_cutoff_r2:+-Q "${par_quality_cutoff_r2}"} \
+  ${par_quality_base:+--quality-base "${par_quality_base}"} \
+  ${par_poly_a:+--poly-a} \
+  ${par_length:+--length "${par_length}"} \
+  ${par_trim_n:+--trim-n} \
+  ${par_length_tag:+--length-tag "${par_length_tag}"} \
+  ${par_strip_suffix:+--strip-suffix "${par_strip_suffix}"} \
+  ${par_prefix:+--prefix "${par_prefix}"} \
+  ${par_suffix:+--suffix "${par_suffix}"} \
+  ${par_rename:+--rename "${par_rename}"} \
+  ${par_zero_cap:+--zero-cap} \
+)
+debug "Arguments to cutadapt:"
+debug $mod_args
+debug
+
+# Filtering of processed reads arguments
+###########################################################
+echo ">> Filtering of processed reads arguments"
+[[ "$par_discard_trimmed" == "false" ]] && unset par_discard_trimmed
+[[ "$par_discard_untrimmed" == "false" ]] && unset par_discard_untrimmed
+[[ "$par_discard_casava" == "false" ]] && unset par_discard_casava
+
+# Parse and transform the minimum and maximum length arguments
+[[ -z $par_minimum_length   ]]
+
+filter_args=$(echo \
+  ${par_minimum_length:+--minimum-length "${par_minimum_length}"} \
+  ${par_maximum_length:+--maximum-length "${par_maximum_length}"} \
+  ${par_max_n:+--max-n "${par_max_n}"} \
+  ${par_max_expected_errors:+--max-expected-errors "${par_max_expected_errors}"} \
+  ${par_max_average_error_rate:+--max-average-error-rate "${par_max_average_error_rate}"} \
+  ${par_discard_trimmed:+--discard-trimmed} \
+  ${par_discard_untrimmed:+--discard-untrimmed} \
+  ${par_discard_casava:+--discard-casava} \
+)
+debug "Arguments to cutadapt:"
+debug $filter_args
+debug
+
+# Optional output arguments
+###########################################################
+echo ">> Optional arguments"
+[[ "$par_json" == "false" ]] && unset par_json
+[[ "$par_fasta" == "false" ]] && unset par_fasta
+[[ "$par_info_file" == "false" ]] && unset par_info_file
+
+optional_output_args=$(echo \
+  ${par_report:+--report "${par_report}"} \
+  ${par_json:+--json "report.json"} \
+  ${par_fasta:+--fasta} \
+  ${par_info_file:+--info-file "info.txt"} \
+)
+
+debug "Arguments to cutadapt:"
+debug $optional_output_args
+debug
+
+# Output arguments
+# We write the output to a directory rather than
+# individual files.
+###########################################################
+
+if [[ -z $par_fasta ]]; then
+  ext="fastq"
+else
+  ext="fasta"
+fi
+
+demultiplex_mode="$par_demultiplex_mode"
+if [[ $mode == "se" ]]; then
+  if [[ "$demultiplex_mode" == "unique_dual" ]] || [[ "$demultiplex_mode" == "combinatorial_dual" ]]; then
+    echo "Demultiplexing dual indexes is not possible with single-end data."
+    exit 1
+  fi
+  prefix="trimmed_"
+  if [[ ! -z "$demultiplex_mode" ]]; then
+    prefix="{name}_"
+  fi
+  output_args=$(echo \
+    --output "$output_dir/${prefix}001.$ext" \
+  )
+else
+  demultiplex_indicator_r1='{name}_'
+  demultiplex_indicator_r2=$demultiplex_indicator_r1
+  if [[ "$demultiplex_mode" == "combinatorial_dual" ]]; then
+    demultiplex_indicator_r1='{name1}_{name2}_'
+    demultiplex_indicator_r2='{name1}_{name2}_'
+  fi
+  prefix_r1="trimmed_"
+  prefix_r2="trimmed_"
+  if [[ ! -z "$demultiplex_mode" ]]; then
+    prefix_r1=$demultiplex_indicator_r1
+    prefix_r2=$demultiplex_indicator_r2
+  fi
+  output_args=$(echo \
+    --output "$output_dir/${prefix_r1}R1_001.$ext" \
+    --paired-output "$output_dir/${prefix_r2}R2_001.$ext" \
+  )
+fi
+
+debug "Arguments to cutadapt:"
+debug $output_args
+debug
+
+# Full CLI
+# Set the --cores argument to 0 unless meta_cpus is set
+###########################################################
+echo ">> Running cutadapt"
+par_cpus=0
+[[ ! -z $meta_cpus ]] && par_cpus=$meta_cpus
+
+cli=$(echo \
+  $input \
+  $adapter_args \
+  $paired_args \
+  $input_args \
+  $mod_args \
+  $filter_args \
+  $optional_output_args \
+  $output_args \
+  --cores $par_cpus
+)
+
+debug ">> Full CLI to be run:"
+debug cutadapt $cli | sed -e 's/--/\r\n  --/g'
+debug
+
+cutadapt $cli
--- a/src/cutadapt/test.sh
+++ b/src/cutadapt/test.sh
@@ -0,0 +1,261 @@
+#!/bin/bash
+
+set -e
+set -eo pipefail
+
+#############################################
+# helper functions
+assert_file_exists() {
+  [ -f "$1" ] || { echo "File '$1' does not exist" && exit 1; }
+}
+assert_file_doesnt_exist() {
+  [ ! -f "$1" ] || { echo "File '$1' exists but shouldn't" && exit 1; }
+}
+assert_file_empty() {
+  [ ! -s "$1" ] || { echo "File '$1' is not empty but should be" && exit 1; }
+}
+assert_file_not_empty() {
+  [ -s "$1" ] || { echo "File '$1' is empty but shouldn't be" && exit 1; }
+}
+assert_file_contains() {
+  grep -q "$2" "$1" || { echo "File '$1' does not contain '$2'" && exit 1; }
+}
+assert_file_not_contains() {
+  grep -q "$2" "$1" && { echo "File '$1' contains '$2' but shouldn't" && exit 1; }
+}
+#############################################
+
+mkdir test_multiple_output
+cd test_multiple_output
+
+echo "#############################################"
+echo "> Run cutadapt with multiple outputs"
+
+cat > example.fa <<'EOF'
+>read1
+MYSEQUENCEADAPTER
+>read2
+MYSEQUENCEADAP
+>read3
+MYSEQUENCEADAPTERSOMETHINGELSE
+>read4
+MYSEQUENCEADABTER
+>read5
+MYSEQUENCEADAPTR
+>read6
+MYSEQUENCEADAPPTER
+>read7
+ADAPTERMYSEQUENCE
+>read8
+PTERMYSEQUENCE
+>read9
+SOMETHINGADAPTERMYSEQUENCE
+EOF
+
+"$meta_executable" \
+  --report minimal \
+  --output "out_test/*.fasta" \
+  --adapter ADAPTER \
+  --input example.fa \
+  --fasta \
+  --demultiplex_mode single \
+  --no_match_adapter_wildcards \
+  --json
+
+echo ">> Checking output"
+assert_file_exists "report.json"
+assert_file_exists "out_test/1_001.fasta"
+assert_file_exists "out_test/unknown_001.fasta"
+
+cd ..
+echo
+
+#############################################
+mkdir test_simple_single_end
+cd test_simple_single_end
+
+echo "#############################################"
+echo "> Run cutadapt on single-end data"
+
+cat > example.fa <<'EOF'
+>read1
+MYSEQUENCEADAPTER
+>read2
+MYSEQUENCEADAP
+>read3
+MYSEQUENCEADAPTERSOMETHINGELSE
+>read4
+MYSEQUENCEADABTER
+>read5
+MYSEQUENCEADAPTR
+>read6
+MYSEQUENCEADAPPTER
+>read7
+ADAPTERMYSEQUENCE
+>read8
+PTERMYSEQUENCE
+>read9
+SOMETHINGADAPTERMYSEQUENCE
+EOF
+
+"$meta_executable" \
+  --report minimal \
+  --output "out_test1/*.fasta" \
+  --adapter ADAPTER \
+  --input example.fa \
+  --demultiplex_mode single \
+  --fasta \
+  --no_match_adapter_wildcards \
+  --json
+
+echo ">> Checking output"
+assert_file_exists "report.json"
+assert_file_exists "out_test1/1_001.fasta"
+assert_file_exists "out_test1/unknown_001.fasta"
+
+echo ">> Check if output is empty"
+assert_file_not_empty "report.json"
+assert_file_not_empty "out_test1/1_001.fasta"
+assert_file_not_empty "out_test1/unknown_001.fasta"
+
+echo ">> Check contents"
+for i in 1 2 3 7 9; do
+  assert_file_contains "out_test1/1_001.fasta" ">read$i"
+done
+for i in 4 5 6 8; do
+  assert_file_contains "out_test1/unknown_001.fasta" ">read$i"
+done
+
+cd ..
+echo
+
+#############################################
+mkdir test_multiple_single_end
+cd test_multiple_single_end
+
+echo "#############################################"
+echo "> Run with a combination of inputs"
+
+cat > example.fa <<'EOF'
+>read1
+ACGTACGTACGTAAAAA
+>read2
+ACGTACGTACGTCCCCC
+>read3
+ACGTACGTACGTGGGGG
+>read4
+ACGTACGTACGTTTTTT
+EOF
+
+cat > adapters1.fasta <<'EOF'
+>adapter1
+CCCCC
+EOF
+
+cat > adapters2.fasta <<'EOF'
+>adapter2
+GGGGG
+EOF
+
+"$meta_executable" \
+  --report minimal \
+  --output "out_test2/*.fasta" \
+  --adapter AAAAA \
+  --adapter_fasta adapters1.fasta \
+  --adapter_fasta adapters2.fasta \
+  --demultiplex_mode single \
+  --input example.fa \
+  --fasta \
+  --json
+
+echo ">> Checking output"
+assert_file_exists "report.json"
+assert_file_exists "out_test2/1_001.fasta"
+assert_file_exists "out_test2/adapter1_001.fasta"
+assert_file_exists "out_test2/adapter2_001.fasta"
+assert_file_exists "out_test2/unknown_001.fasta"
+
+echo ">> Check if output is empty"
+assert_file_not_empty "report.json"
+assert_file_not_empty "out_test2/1_001.fasta"
+assert_file_not_empty "out_test2/adapter1_001.fasta"
+assert_file_not_empty "out_test2/adapter2_001.fasta"
+assert_file_not_empty "out_test2/unknown_001.fasta"
+
+echo ">> Check contents"
+assert_file_contains "out_test2/1_001.fasta" ">read1"
+assert_file_contains "out_test2/adapter1_001.fasta" ">read2"
+assert_file_contains "out_test2/adapter2_001.fasta" ">read3"
+assert_file_contains "out_test2/unknown_001.fasta" ">read4"
+
+cd ..
+echo
+
+#############################################
+mkdir test_simple_paired_end
+cd test_simple_paired_end
+
+echo "#############################################"
+echo "> Run cutadapt on paired-end data"
+
+cat > example_R1.fastq <<'EOF'
+@read1
+ACGTACGTACGTAAAAA
+
+IIIIIIIIIIIIIIIII
+@read2
+ACGTACGTACGTCCCCC
+
+IIIIIIIIIIIIIIIII
+EOF
+
+cat > example_R2.fastq <<'EOF'
+@read1
+ACGTACGTACGTGGGGG
+
+IIIIIIIIIIIIIIIII
+@read2
+ACGTACGTACGTTTTTT
+
+IIIIIIIIIIIIIIIII
+EOF
+
+"$meta_executable" \
+  --report minimal \
+  --output "out_test3/*.fastq" \
+  --adapter AAAAA \
+  --adapter_r2 GGGGG \
+  --input example_R1.fastq \
+  --input_r2 example_R2.fastq \
+  --quality_cutoff 20 \
+  --demultiplex_mode unique_dual \
+  --json \
+  ---cpus 1
+
+echo ">> Checking output"
+assert_file_exists "report.json"
+assert_file_exists "out_test3/1_R1_001.fastq"
+assert_file_exists "out_test3/1_R2_001.fastq"
+assert_file_exists "out_test3/unknown_R1_001.fastq"
+assert_file_exists "out_test3/unknown_R2_001.fastq"
+
+echo ">> Check if output is empty"
+assert_file_not_empty "report.json"
+assert_file_not_empty "out_test3/1_R1_001.fastq"
+assert_file_not_empty "out_test3/1_R2_001.fastq"
+assert_file_not_empty "out_test3/unknown_R1_001.fastq"
+
+echo ">> Check contents"
+assert_file_contains "out_test3/1_R1_001.fastq" "@read1"
+assert_file_contains "out_test3/1_R2_001.fastq" "@read1"
+assert_file_contains "out_test3/unknown_R1_001.fastq" "@read2"
+assert_file_contains "out_test3/unknown_R2_001.fastq" "@read2"
+
+cd ..
+echo
+
+#############################################
+
+echo "#############################################"
+echo "> Test successful"
+
--- a/src/falco/config.vsh.yaml
+++ b/src/falco/config.vsh.yaml
@@ -0,0 +1,199 @@
+name: falco
+description: A C++ drop-in replacement of FastQC to assess the quality of sequence read data
+keywords: [qc, fastqc, sequencing]
+links:
+  documentation: https://falco.readthedocs.io/en/latest/
+  repository: https://github.com/smithlabcode/falco
+references:
+  doi: 10.12688/f1000research.21142.2
+license: GPL-3.0
+requirements:
+  commands: [falco]
+authors:
+  - __merge__: /src/_authors/toni_verbeiren.yaml
+    roles: [ author, maintainer ]
+
+# Notes:
+# - falco as arguments similar to -subsample and we update those to --subsample
+# - The outdir argument is not required
+# - The input argument in falco is positional but we changed this to --input
+argument_groups:
+  - name: Input arguments
+    arguments:
+      - name: --input
+        required: true
+        type: file
+        multiple: true
+        description: input fastq files
+        example: input1.fastq;input2.fastq
+
+  - name: Run arguments
+    arguments:
+      - name: --nogroup
+        type: boolean_true
+        description: |
+          Disable grouping of bases for reads >50bp. 
+          All reports will show data for every base in 
+          the read. WARNING: When using this option, 
+          your plots may end up a ridiculous size. You 
+          have been warned!
+      - name: --contaminents
+        type: file
+        description: |
+          Specifies a non-default file which contains 
+          the list of contaminants to screen 
+          overrepresented sequences against. The file 
+          must contain sets of named contaminants in 
+          the form name[tab]sequence. Lines prefixed 
+          with a hash will be ignored. Default: 
+          https://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/contaminant_list.txt
+      - name: --adapters
+        type: file
+        description: |
+          Specifies a non-default file which contains 
+          the list of adapter sequences which will be 
+          explicity searched against the library. The 
+          file must contain sets of named adapters in 
+          the form name[tab]sequence. Lines prefixed 
+          with a hash will be ignored. Default:
+          https://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/adapter_list.txt
+      - name: --limits
+        type: file
+        description: |
+          Specifies a non-default file which contains 
+          a set of criteria which will be used to 
+          determine the warn/error limits for the 
+          various modules. This file can also be used 
+          to selectively remove some modules from the 
+          output all together. The format needs to 
+          mirror the default limits.txt file found in 
+          the Configuration folder. Default: 
+          https://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/limits.txt
+      - name: --subsample
+        alternatives: [-s]
+        type: integer
+        example: 10
+        description: |
+          [Falco only] makes falco faster (but 
+          possibly less accurate) by only processing 
+          reads that are a multiple of this value (using 
+          0-based indexing to number reads).
+      - name: --bisulfite
+        alternatives: [-b]
+        type: boolean_true
+        description: |
+          [Falco only] reads are whole genome 
+          bisulfite sequencing, and more Ts and fewer 
+          Cs are therefore expected and will be 
+          accounted for in base content.
+      - name: --reverse_complliment
+        alternatives: [-r]
+        type: boolean_true
+        description: |
+          [Falco only] The input is a 
+          reverse-complement. All modules will be 
+          tested by swapping A/T and C/G
+
+  - name: Output arguments
+    arguments:
+      - name: --outdir
+        alternatives: [-o]
+        required: true
+        type: file
+        direction: output
+        description: |
+          Create all output files in the specified 
+          output directory. FALCO-SPECIFIC: If the 
+          directory does not exists, the program will 
+          create it.
+        example: output
+      - name: --format
+        type: string
+        choices: [bam, sam, bam_mapped, sam_mapped, fastq, fq, fastq.gz, fq.gz]
+        alternatives: ["-f"]
+        description: |
+          Bypasses the normal sequence file format 
+          detection and forces the program to use the 
+          specified format. Validformats are bam, sam, 
+          bam_mapped, sam_mapped, fastq, fq, fastq.gz 
+          or fq.gz.
+      - name: --data_filename
+        alternatives: [-D]
+        type: file
+        direction: output
+        description: |
+          [Falco only] Specify filename for FastQC 
+          data output (TXT). If not specified, it will 
+          be called fastq_data.txt in either the input 
+          file's directory or the one specified in the 
+          --output flag. Only available when running 
+          falco with a single input.
+      - name: --report_filename
+        alternatives: [-R]
+        type: file
+        direction: output
+        description: |
+          [Falco only] Specify filename for FastQC 
+          report output (HTML). If not specified, it 
+          will be called fastq_report.html in either 
+          the input file's directory or the one 
+          specified in the --output flag. Only 
+          available when running falco with a single 
+          input.
+      - name: --summary_filename
+        alternatives: [-S]
+        type: file
+        direction: output
+        description: |
+          [Falco only] Specify filename for the short 
+          summary output (TXT). If not specified, it 
+          will be called fastq_report.html in either 
+          the input file's directory or the one 
+          specified in the --output flag. Only 
+          available when running falco with a single 
+          input.
+
+# Arguments not taken into account:
+#
+#       -skip-data           [Falco only] Do not create FastQC data text
+#                            file.
+#       -skip-report         [Falco only] Do not create FastQC report
+#                            HTML file.
+#       -skip-summary        [Falco only] Do not create FastQC summary
+#                            file
+#       -K, -add-call        [Falco only] add the command call call to
+#                            FastQC data output and FastQC report HTML
+#                            (this may break the parse of fastqc_data.txt
+#                            in programs that are very strict about the
+#                            FastQC output format).
+
+resources:
+  - type: bash_script
+    path: script.sh
+
+test_resources:
+  - type: bash_script
+    path: test.sh
+
+engines:
+  - type: docker
+    image: debian:trixie-slim
+    setup:
+      - type: apt
+        packages: [wget, build-essential, g++, zlib1g-dev, procps]
+      - type: docker
+        run: |
+          wget https://github.com/smithlabcode/falco/releases/download/v1.2.2/falco-1.2.2.tar.gz -O /tmp/falco.tar.gz && \
+          cd /tmp && \
+          tar xvf falco.tar.gz && \
+          cd falco-1.2.2 && \
+          ./configure && \
+          make all && \
+          make install
+      - type: docker
+        run: |
+          echo "falco: \"$(falco -v | sed -n 's/^falco //p')\"" > /var/software_versions.txt
+
+runners:
+  - type: executable
+  - type: nextflow
--- a/src/falco/help.txt
+++ b/src/falco/help.txt
@@ -0,0 +1,156 @@
+Usage: falco [OPTIONS] <seqfile1> <seqfile2> ...
+
+Options:
+  -h, --help               Print this help file and exit  
+  -v, --version            Print the version of the program and exit  
+  -o, --outdir             Create all output files in the specified 
+                           output directory. FALCO-SPECIFIC: If the 
+                           directory does not exists, the program will 
+                           create it. If this option is not set then 
+                           the output file for each sequence file is 
+                           created in the same directory as the 
+                           sequence file which was processed.  
+      --casava             [IGNORED BY FALCO] Files come from raw 
+                           casava output. Files in the same sample 
+                           group (differing only by the group number) 
+                           will be analysed as a set rather than 
+                           individually. Sequences with the filter flag 
+                           set in the header will be excluded from the 
+                           analysis. Files must have the same names 
+                           given to them by casava (including being 
+                           gzipped and ending with .gz) otherwise they 
+                           won't be grouped together correctly.  
+      --nano               [IGNORED BY FALCO] Files come from nanopore 
+                           sequences and are in fast5 format. In this 
+                           mode you can pass in directories to process 
+                           and the program will take in all fast5 files 
+                           within those directories and produce a 
+                           single output file from the sequences found 
+                           in all files.  
+      --nofilter           [IGNORED BY FALCO] If running with --casava 
+                           then don't remove read flagged by casava as 
+                           poor quality when performing the QC 
+                           analysis.  
+      --extract            [ALWAYS ON IN FALCO] If set then the zipped 
+                           output file will be uncompressed in the same 
+                           directory after it has been created. By 
+                           default this option will be set if fastqc is 
+                           run in non-interactive mode.  
+  -j, --java               [IGNORED BY FALCO] Provides the full path to 
+                           the java binary you want to use to launch 
+                           fastqc. If not supplied then java is assumed 
+                           to be in your path.  
+      --noextract          [IGNORED BY FALCO] Do not uncompress the 
+                           output file after creating it. You should 
+                           set this option if you do not wish to 
+                           uncompress the output when running in 
+                           non-interactive mode.  
+      --nogroup            Disable grouping of bases for reads >50bp. 
+                           All reports will show data for every base in 
+                           the read. WARNING: When using this option, 
+                           your plots may end up a ridiculous size. You 
+                           have been warned!  
+      --min_length         [NOT YET IMPLEMENTED IN FALCO] Sets an 
+                           artificial lower limit on the length of the 
+                           sequence to be shown in the report. As long 
+                           as you set this to a value greater or equal 
+                           to your longest read length then this will 
+                           be the sequence length used to create your 
+                           read groups. This can be useful for making 
+                           directly comaparable statistics from 
+                           datasets with somewhat variable read 
+                           lengths.  
+  -f, --format             Bypasses the normal sequence file format 
+                           detection and forces the program to use the 
+                           specified format. Validformats are bam, sam, 
+                           bam_mapped, sam_mapped, fastq, fq, fastq.gz 
+                           or fq.gz.  
+  -t, --threads            [NOT YET IMPLEMENTED IN FALCO] Specifies the 
+                           number of files which can be processed 
+                           simultaneously. Each thread will be 
+                           allocated 250MB of memory so you shouldn't 
+                           run more threads than your available memory 
+                           will cope with, and not more than 6 threads 
+                           on a 32 bit machine [1] 
+  -c, --contaminants       Specifies a non-default file which contains 
+                           the list of contaminants to screen 
+                           overrepresented sequences against. The file 
+                           must contain sets of named contaminants in 
+                           the form name[tab]sequence. Lines prefixed 
+                           with a hash will be ignored. Default: 
+                           /tmp/falco-1.2.2/Configuration/contaminant_list.txt 
+  -a, --adapters           Specifies a non-default file which contains 
+                           the list of adapter sequences which will be 
+                           explicity searched against the library. The 
+                           file must contain sets of named adapters in 
+                           the form name[tab]sequence. Lines prefixed 
+                           with a hash will be ignored. Default: 
+                           /tmp/falco-1.2.2/Configuration/adapter_list.txt 
+  -l, --limits             Specifies a non-default file which contains 
+                           a set of criteria which will be used to 
+                           determine the warn/error limits for the 
+                           various modules. This file can also be used 
+                           to selectively remove some modules from the 
+                           output all together. The format needs to 
+                           mirror the default limits.txt file found in 
+                           the Configuration folder. Default: 
+                           /tmp/falco-1.2.2/Configuration/limits.txt 
+  -k, --kmers              [IGNORED BY FALCO AND ALWAYS SET TO 7] 
+                           Specifies the length of Kmer to look for in 
+                           the Kmer content module. Specified Kmer 
+                           length must be between 2 and 10. Default 
+                           length is 7 if not specified.  
+  -q, --quiet              Supress all progress messages on stdout and 
+                           only report errors.  
+  -d, --dir                [IGNORED: FALCO DOES NOT CREATE TMP FILES] 
+                           Selects a directory to be used for temporary 
+                           files written when generating report images. 
+                           Defaults to system temp directory if not 
+                           specified.  
+  -s, -subsample           [Falco only] makes falco faster (but 
+                           possibly less accurate) by only processing 
+                           reads that are multiple of this value (using 
+                           0-based indexing to number reads). [1] 
+  -b, -bisulfite           [Falco only] reads are whole genome 
+                           bisulfite sequencing, and more Ts and fewer 
+                           Cs are therefore expected and will be 
+                           accounted for in base content.  
+  -r, -reverse-complement  [Falco only] The input is a 
+                           reverse-complement. All modules will be 
+                           tested by swapping A/T and C/G  
+      -skip-data           [Falco only] Do not create FastQC data text 
+                           file.  
+      -skip-report         [Falco only] Do not create FastQC report 
+                           HTML file.  
+      -skip-summary        [Falco only] Do not create FastQC summary 
+                           file  
+  -D, -data-filename       [Falco only] Specify filename for FastQC 
+                           data output (TXT). If not specified, it will 
+                           be called fastq_data.txt in either the input 
+                           file's directory or the one specified in the 
+                           --output flag. Only available when running 
+                           falco with a single input.  
+  -R, -report-filename     [Falco only] Specify filename for FastQC 
+                           report output (HTML). If not specified, it 
+                           will be called fastq_report.html in either 
+                           the input file's directory or the one 
+                           specified in the --output flag. Only 
+                           available when running falco with a single 
+                           input.  
+  -S, -summary-filename    [Falco only] Specify filename for the short 
+                           summary output (TXT). If not specified, it 
+                           will be called fastq_report.html in either 
+                           the input file's directory or the one 
+                           specified in the --output flag. Only 
+                           available when running falco with a single 
+                           input.  
+  -K, -add-call            [Falco only] add the command call call to 
+                           FastQC data output and FastQC report HTML 
+                           (this may break the parse of fastqc_data.txt 
+                           in programs that are very strict about the 
+                           FastQC output format).  
+
+Help options:
+  -?, -help                print this help message  
+      -about               print about message  
+
--- a/src/falco/script.sh
+++ b/src/falco/script.sh
@@ -0,0 +1,24 @@
+#!/bin/bash
+
+set -eo pipefail
+
+[[ "$par_nogroup" == "false" ]] && unset par_nogroup
+[[ "$par_bisulfite" == "false" ]] && unset par_bisulfite
+[[ "$par_reverse_compliment" == "false" ]] && unset par_reverse_compliment
+
+IFS=";" read -ra input <<< $par_input
+
+$(which falco) \
+  ${par_nogroup:+--nogroup} \
+  ${par_contaminants:+--contaminants "$par_contaminants"} \
+  ${par_adapters:+--adapters "$par_adapters"} \
+  ${par_limits:+--limits "$par_limits"} \
+  ${par_subsample:+-subsample $par_subsample} \
+  ${par_bisulfite:+-bisulfite} \
+  ${par_reverse_compliment:+-reverse-compliment} \
+  ${par_outdir:+--outdir "$par_outdir"} \
+  ${par_format:+--format "$par_format"} \
+  ${par_data_filename:+-data-filename "$par_data_filename"} \
+  ${par_report_filename:+-report-filename "$par_report_filename"} \
+  ${par_summary_filename:+-summary-filename "$par_summary_filename"} \
+  ${input[*]}
--- a/src/falco/test.sh
+++ b/src/falco/test.sh
@@ -0,0 +1,79 @@
+#!/bin/bash
+
+set -e
+
+echo "> Prepare test data"
+
+# We use data from this repo: https://github.com/hartwigmedical/testData
+echo ">> Fetching and preparing test data"
+fastq1="https://github.com/hartwigmedical/testdata/raw/master/100k_reads_hiseq/TESTX/TESTX_H7YRLADXX_S1_L001_R1_001.fastq.gz"
+fastq2="https://github.com/hartwigmedical/testdata/raw/master/100k_reads_hiseq/TESTX/TESTX_H7YRLADXX_S1_L001_R2_001.fastq.gz"
+TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_functionality_name-XXXXXX")
+function clean_up {
+  [[ -d "$TMPDIR" ]] && rm -r "$TMPDIR"
+}
+trap clean_up EXIT
+
+test_data_dir="$TMPDIR/test_data"
+
+mkdir $test_data_dir
+wget -q $fastq1 -O $test_data_dir/R1.fastq.gz
+wget -q $fastq2 -O $test_data_dir/R2.fastq.gz
+
+echo ">> Run falco on test data, output to dir"
+echo ">>> Run falco"
+$meta_executable \
+  --input "$test_data_dir/R1.fastq.gz;$test_data_dir/R2.fastq.gz" \
+  --outdir "$TMPDIR/output1"
+
+echo ">>> Checking whether output exists"
+[ ! -d "$TMPDIR/output1" ] && echo "Output directory not created" && exit 1
+[ ! -f "$TMPDIR/output1/R1.fastq.gz_fastqc_report.html" ] && echo "Report not created" && exit 1
+[ ! -f "$TMPDIR/output1/R1.fastq.gz_summary.txt" ] && echo "Summary not created" && exit 1
+[ ! -f "$TMPDIR/output1/R1.fastq.gz_fastqc_data.txt" ] && echo "fastqc_data not created" && exit 1
+[ ! -f "$TMPDIR/output1/R2.fastq.gz_fastqc_report.html" ] && echo "Report not created" && exit 1
+[ ! -f "$TMPDIR/output1/R2.fastq.gz_summary.txt" ] && echo "Summary not created" && exit 1
+[ ! -f "$TMPDIR/output1/R2.fastq.gz_fastqc_data.txt" ] && echo "fastqc_data not created" && exit 1
+
+echo ">>> cleanup"
+rm -rf "$TMPDIR/output1"
+
+echo ">> Run falco on test data, output to individual files"
+echo ">>> Please note this is only possible for 1 input fastq file!"
+echo ">>> Run falco"
+$meta_executable \
+  --input "$test_data_dir/R1.fastq.gz" \
+  --data_filename "$TMPDIR/output2/data.txt" \
+  --report_filename "$TMPDIR/output2/report.html" \
+  --summary_filename "$TMPDIR/output2/summary.txt" \
+  --outdir "$TMPDIR/output2/"
+
+echo ">>> Checking whether output exists"
+[ ! -d "$TMPDIR/output2" ] && echo "Output directory not created" && exit 1
+[ ! -f "$TMPDIR/output2/report.html" ] && echo "Report not created" && exit 1
+[ ! -f "$TMPDIR/output2/summary.txt" ] && echo "Summary not created" && exit 1
+[ ! -f "$TMPDIR/output2/data.txt" ] && echo "fastqc_data not created" && exit 1
+
+echo ">>> cleanup"
+rm -rf $TMPDIR/output2/
+
+echo ">> Run falco on test data, subsample"
+echo ">>> Run falco"
+$meta_executable \
+  --input "$test_data_dir/R1.fastq.gz" \
+  --data_filename "$TMPDIR/output3/data.txt" \
+  --report_filename "$TMPDIR/output3/report.html" \
+  --summary_filename "$TMPDIR/output3/summary.txt" \
+  --subsample 100 \
+  --outdir "$TMPDIR/output3"
+
+echo ">>> Checking whether output exists"
+[ ! -d "$TMPDIR/output3" ] && echo "Output directory not created" && exit 1
+[ ! -f "$TMPDIR/output3/report.html" ] && echo "Report not created" && exit 1
+[ ! -f "$TMPDIR/output3/summary.txt" ] && echo "Summary not created" && exit 1
+[ ! -f "$TMPDIR/output3/data.txt" ] && echo "fastqc_data not created" && exit 1
+
+echo ">>> cleanup"
+rm -rf "$TMPDIR/output3/"
+
+echo "All tests succeeded!"
--- a/src/fastp/config.vsh.yaml
+++ b/src/fastp/config.vsh.yaml
@@ -0,0 +1,579 @@
+name: fastp
+description: |
+  An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...).
+
+  Features:
+
+    - comprehensive quality profiling for both before and after filtering data (quality curves, base contents, KMER, Q20/Q30, GC Ratio, duplication, adapter contents...)
+    - filter out bad reads (too low quality, too short, or too many N...)
+    - cut low quality bases for per read in its 5' and 3' by evaluating the mean quality from a sliding window (like Trimmomatic but faster).
+    - trim all reads in front and tail
+    - cut adapters. Adapter sequences can be automatically detected, which means you don't have to input the adapter sequences to trim them.
+    - correct mismatched base pairs in overlapped regions of paired end reads, if one base is with high quality while the other is with ultra low quality
+    - trim polyG in 3' ends, which is commonly seen in NovaSeq/NextSeq data. Trim polyX in 3' ends to remove unwanted polyX tailing (i.e. polyA tailing for mRNA-Seq data)
+    - preprocess unique molecular identifier (UMI) enabled data, shift UMI to sequence name.
+    - report JSON format result for further interpreting.
+    - visualize quality control and filtering results on a single HTML page (like FASTQC but faster and more informative).
+    - split the output to multiple files (0001.R1.gz, 0002.R1.gz...) to support parallel processing. Two modes can be used, limiting the total split file number, or limitting the lines of each split file.
+    - support long reads (data from PacBio / Nanopore devices).
+    - support reading from STDIN and writing to STDOUT
+    - support interleaved input
+    - support ultra-fast FASTQ-level deduplication
+keywords: [RNA-Seq, Trimming, Quality control]
+links:
+  repository: https://github.com/OpenGene/fastp
+  documentation: https://github.com/OpenGene/fastp/blob/master/README.md
+references:
+  doi: "10.1093/bioinformatics/bty560"
+license: MIT
+authors:
+  - __merge__: /src/_authors/robrecht_cannoodt.yaml
+    roles: [ author, maintainer ]
+argument_groups:
+  - name: Inputs
+    description: |
+      `fastp` supports both single-end (SE) and paired-end (PE) input.
+
+      - for SE data, you only have to specify read1 input by `-i` or `--in1`.
+      - for PE data, you should also specify read2 input by `-I` or `--in2`.
+    arguments:
+      - name: --in1
+        alternatives: [-i]
+        type: file
+        description: Input FastQ file. Must be single-end or paired-end R1. Can be gzipped.
+        required: true
+        example: in.R1.fq.gz
+      - name: --in2
+        alternatives: [-I]
+        type: file
+        description: Input FastQ file. Must be paired-end R2. Can be gzipped.
+        required: false
+        example: in.R2.fq.gz
+  - name: Outputs
+    description: |
+
+      - for SE data, you only have to specify read1 output by `-o` or `--out1`.
+      - for PE data, you should also specify read2 output by `-O` or `--out2`.
+      - if you don't specify the output file names, no output files will be written, but the QC will still be done for both data before and after filtering.
+      - the output will be gzip-compressed if its file name ends with `.gz`
+    arguments:
+      - name: --out1
+        alternatives: [-o]
+        type: file
+        description: The single-end or paired-end R1 reads that pass QC. Will be gzipped if its file name ends with `.gz`.
+        required: true
+        example: out.R1.fq.gz
+        direction: output
+      - name: --out2
+        alternatives: [-O]
+        type: file
+        description: The paired-end R2 reads that pass QC. Will be gzipped if its file name ends with `.gz`.
+        required: false
+        example: out.R2.fq.gz
+        direction: output
+      - name: --unpaired1
+        type: file
+        description: Store the reads that `read1` passes filters but its paired `read2` doesn't.
+        required: false
+        example: unpaired.R1.fq.gz
+        direction: output
+      - name: --unpaired2
+        type: file
+        description: Store the reads that `read2` passes filters but its paired `read1` doesn't.
+        required: false
+        example: unpaired.R2.fq.gz
+        direction: output
+      - name: --failed_out
+        type: file
+        description: |
+          Store the reads that fail filters.
+
+          If one read failed and is written to --failed_out, its failure reason will be appended to its read name. For example, failed_quality_filter, failed_too_short etc.
+          For PE data, if unpaired reads are not stored (by giving --unpaired1 or --unpaired2), the failed pair of reads will be put together. If one read passes the filters but its pair doesn't, the failure reason will be paired_read_is_failing.
+        required: false
+        example: failed.fq.gz
+        direction: output
+      - name: --overlapped_out
+        type: file
+        description: |
+          For each read pair, output the overlapped region if it has no any mismatched base.
+        direction: output
+  - name: Report output arguments
+    arguments:
+      - name: --json
+        alternatives: [-j]
+        type: file
+        description: |
+          The json format report file name
+        example: out.json
+        direction: output
+      - name: --html
+        type: file
+        description: |
+          The html format report file name
+        example: out.html
+        direction: output
+      - name: --report_title
+        type: string
+        description: |
+          The title of the html report, default is "fastp report".
+        example: fastp report
+  - name: Adapter trimming
+    description: |
+      Adapter trimming is enabled by default, but you can disable it by `-A` or `--disable_adapter_trimming`. Adapter sequences can be automatically detected for both PE/SE data.
+
+      - For SE data, the adapters are evaluated by analyzing the tails of first ~1M reads. This evaluation may be inacurrate, and you can specify the adapter sequence by `-a` or `--adapter_sequence` option. If adapter sequence is specified, the auto detection for SE data will be disabled.
+      - For PE data, the adapters can be detected by per-read overlap analysis, which seeks for the overlap of each pair of reads. This method is robust and fast, so normally you don't have to input the adapter sequence even you know it. But you can still specify the adapter sequences for read1 by `--adapter_sequence`, and for read2 by `--adapter_sequence_r2`. If `fastp` fails to find an overlap (i.e. due to low quality bases), it will use these sequences to trim adapters for read1 and read2 respectively.
+      - For PE data, the adapter sequence auto-detection is disabled by default since the adapters can be trimmed by overlap analysis. However, you can specify `--detect_adapter_for_pe` to enable it.
+      - For PE data, `fastp` will run a little slower if you specify the sequence adapters or enable adapter auto-detection, but usually result in a slightly cleaner output, since the overlap analysis may fail due to sequencing errors or adapter dimers.
+      - The most widely used adapter is the Illumina TruSeq adapters. If your data is from the TruSeq library, you can add `--adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT` to your command lines, or enable auto detection for PE data by specifing `detect_adapter_for_pe`.
+      - `fastp` contains some built-in known adapter sequences for better auto-detection. If you want to make some adapters to be a part of the built-in adapters, please file an issue.
+
+      You can also specify --adapter_fasta to give a FASTA file to tell fastp to trim multiple adapters in this FASTA file. Here is a sample of such adapter FASTA file:
+
+      ```
+      >Illumina TruSeq Adapter Read 1
+      AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
+      >Illumina TruSeq Adapter Read 2
+      AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
+      >polyA
+      AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+      ```
+
+      The adapter sequence in this file should be at least 6bp long, otherwise it will be skipped. And you can give whatever you want to trim, rather than regular sequencing adapters (i.e. polyA).
+
+      `fastp` first trims the auto-detected adapter or the adapter sequences given by `--adapter_sequence | --adapter_sequence_r2`, then trims the adapters given by `--adapter_fasta` one by one.
+
+      The sequence distribution of trimmed adapters can be found at the HTML/JSON reports.
+    arguments:
+      - name: --disable_adapter_trimming
+        alternatives: [-A]
+        type: boolean_true
+        description: |
+          Disable adapter trimming.
+      - name: --detect_adapter_for_pe
+        type: boolean_true
+        description: |
+          By default, the auto-detection for adapter is for SE data input only, turn on this option to enable it for PE data.
+      - name: --adapter_sequence
+        alternatives: [-a]
+        type: string
+        description: |
+          The adapter sequences to be trimmed. For SE data, if not specified, the adapters will be auto-detected. For PE data, this is used if R1/R2 are found not overlapped
+      - name: --adapter_sequence_r2
+        type: string
+        description: |
+          The adapter sequences to be trimmed for R2. This is used for PE data if R1/R2 are found overlapped.
+      - name: --adapter_fasta
+        type: file
+        description: |
+          A FASTA file containing all the adapter sequences to be trimmed. For SE data, if not specified, the adapters will be auto-detected. For PE data, this is used if R1/R2 are found not overlapped.
+  - name: Base trimming
+    arguments:
+      - name: --trim_front1
+        alternatives: [-f]
+        type: integer
+        description: |
+          Trimming how many bases in front for read1, default is 0.
+        example: 0
+      - name: --trim_tail1
+        alternatives: [-t]
+        type: integer
+        description: |
+          Trimming how many bases in tail for read1, default is 0.
+        example: 0
+      - name: --max_len1
+        alternatives: [-b]
+        type: integer
+        min: 0
+        description: |
+          If read1 is longer than max_len1, then trim read1 at its tail to make it as long as max_len1. Default 0 means no limitation.
+      - name: --trim_front2
+        alternatives: [-F]
+        type: integer
+        description: |
+          Trimming how many bases in front for read2, default is 0.
+        example: 0
+      - name: --trim_tail2
+        alternatives: [-T]
+        type: integer
+        description: |
+          Trimming how many bases in tail for read2, default is 0.
+        example: 0
+      - name: --max_len2
+        alternatives: [-B]
+        type: integer
+        min: 0
+        description: |
+          If read2 is longer than max_len2, then trim read2 at its tail to make it as long as max_len2. Default 0 means no limitation.
+  - name: Merging mode
+    description: Allows merging paired-end reads into a single longer read if they are overlapping.
+    arguments:
+      - name: --merge
+        alternatives: [-m]
+        type: boolean_true
+        description: |
+          For paired-end input, merge each pair of reads into a single read if they are overlapped. The merged reads will be written to the file given by --merged_out, the unmerged reads will be written to the files specified by --out1 and --out2. The merging mode is disabled by default.
+      - name: --merged_out
+        type: file
+        description: |
+          In the merging mode, specify the file name to store merged output, or specify --stdout to stream the merged output.
+        direction: output
+        example: merged.fq.gz
+      - name: --include_unmerged
+        type: boolean_true
+        description: |
+          In the merging mode, write the unmerged or unpaired reads to the file specified by --merge. Disabled by default.
+  - name: Additional input arguments
+    description: Affects how the input is read.
+    arguments:
+      - name: --interleaved_in
+        type: boolean_true
+        description: |
+          Indicate that <in1> is an interleaved FASTQ which contains both read1 and read2. Disabled by default.
+      - name: --fix_mgi_id
+        type: boolean_true
+        description: |
+          The MGI FASTQ ID format is not compatible with many BAM operation tools, enable this option to fix it.
+      - name: --phred64
+        alternatives: ["-6"]
+        type: boolean_true
+        description: |
+          Indicate the input is using phred64 scoring (it'll be converted to phred33, so the output will still be phred33)
+  - name: Additional output arguments
+    description: Affects how the output is written.
+    arguments:
+      - name: --compression
+        alternatives: ["-z"]
+        type: integer
+        description: |
+          Compression level for gzip output (1 ~ 9). 1 is fastest, 9 is smallest, default is 4.
+        example: 4
+        min: 1
+        max: 9
+      - name: --dont_overwrite
+        type: boolean_true
+        description: |
+          Don't overwrite existing files. Overwritting is allowed by default.
+  - name: Logging arguments
+    arguments:
+      - name: --verbose
+        alternatives: [-V]
+        type: boolean_true
+        description: Output verbose log information (i.e. when every 1M reads are processed).
+  - name: Processing arguments
+    arguments:
+      - name: --reads_to_process
+        type: long
+        description: |
+          Specify how many reads/pairs to be processed. Default 0 means process all reads.
+        example: 1000000
+        min: 0
+  - name: Deduplication arguments
+    arguments:
+      - name: --dedup
+        type: boolean_true
+        description: |
+          Enable deduplication to drop the duplicated reads/pairs
+      - name: --dup_calc_accuracy
+        type: integer
+        description: |
+          Accuracy level to calculate duplication (1~6). Higher level uses more memory (1G, 2G, 4G, 8G, 16G, 24G). Default 1 for no-dedup mode, and 3 for dedup mode.
+        example: 3
+        min: 1
+        max: 6
+      - name: --dont_eval_duplication
+        type: boolean_true
+        description: |
+          Don't evaluate duplication rate to save time and use less memory.
+  - name: PolyG tail trimming arguments
+    arguments:
+      - name: --trim_poly_g
+        alternatives: [-g]
+        type: boolean_true
+        description: |
+          Force polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data
+      - name: --poly_g_min_len
+        type: integer
+        description: |
+          The minimum length to detect polyG in the read tail. 10 by default.
+        example: 10
+        min: 1
+      - name: --disable_trim_poly_g
+        alternatives: [-G]
+        type: boolean_true
+        description: |
+          Disable polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data
+  - name: PolyX tail trimming arguments
+    arguments:
+      - name: --trim_poly_x
+        alternatives: [-x]
+        type: boolean_true
+        description: |
+          Enable polyX trimming in 3' ends.
+      - name: --poly_x_min_len
+        type: integer
+        description: |
+          The minimum length to detect polyX in the read tail. 10 by default.
+        example: 10
+        min: 1
+  - name: Cut arguments
+    arguments:
+      - name: --cut_front
+        alternatives: ["-5"]
+        type: integer
+        description: |
+          Move a sliding window from front (5') to tail, drop the bases in the window if its mean quality < threshold, stop otherwise.
+      - name: --cut_tail
+        alternatives: ["-3"]
+        type: integer
+        description: |
+          Move a sliding window from tail (3') to front, drop the bases in the window if its mean quality < threshold, stop otherwise.
+      - name: --cut_right
+        alternatives: ["-r"]
+        type: integer
+        description: |
+          Move a sliding window from front to tail, if meet one window with mean quality < threshold, drop the bases in the window and the right part, and then stop.
+      - name: --cut_window_size
+        alternatives: ["-W"]
+        type: integer
+        description: |
+          The window size option shared by cut_front, cut_tail or cut_sliding. Range: 1~1000, default: 4.
+        example: 4
+        min: 1
+      - name: --cut_mean_quality
+        alternatives: ["-M"]
+        type: integer
+        description: |
+          The mean quality requirement option shared by cut_front, cut_tail or cut_sliding. Range: 1~36 default: 20 (Q20)
+        example: 20
+        min: 0
+      - name: --cut_front_window_size
+        type: integer
+        description: |
+          The window size option of cut_front, default to cut_window_size if not specified.
+        example: 4
+        min: 1
+      - name: --cut_front_mean_quality
+        type: integer
+        description: |
+          The mean quality requirement option of cut_front, default to cut_mean_quality if not specified.
+        example: 20
+        min: 0
+      - name: --cut_tail_window_size
+        type: integer
+        description: |
+          The window size option of cut_tail, default to cut_window_size if not specified.
+        example: 4
+        min: 1
+      - name: --cut_tail_mean_quality
+        type: integer
+        description: |
+          The mean quality requirement option of cut_tail, default to cut_mean_quality if not specified.
+        example: 20
+        min: 0
+      - name: --cut_right_window_size
+        type: integer
+        description: |
+          The window size option of cut_right, default to cut_window_size if not specified.
+        example: 4
+        min: 1
+      - name: --cut_right_mean_quality
+        type: integer
+        description: |
+          The mean quality requirement option of cut_right, default to cut_mean_quality if not specified.
+        example: 20
+        min: 0
+  - name: Quality filtering arguments
+    arguments:
+      - name: --disable_quality_filtering
+        alternatives: [-Q]
+        type: boolean_true
+        description: |
+          Quality filtering is enabled by default. If this option is specified, quality filtering is disabled.
+      - name: --qualified_quality_phred
+        alternatives: [-q]
+        type: integer
+        description: |
+          The quality value that a base is qualified. Default 15 means phred quality >=Q15 is qualified.
+        example: 15
+        min: 0
+      - name: --unqualified_percent_limit
+        alternatives: [-u]
+        type: integer
+        description: |
+          How many percents of bases are allowed to be unqualified (0~100). Default 40 means 40%.
+        example: 40
+        min: 0
+        max: 100
+      - name: --n_base_limit
+        alternatives: [-n]
+        type: integer
+        description: |
+          If one read's number of N base is >n_base_limit, then this read/pair is discarded. Default is 5.
+        example: 5
+        min: 0
+      - name: --average_qual
+        alternatives: [-e]
+        type: integer
+        description: |
+          If one read's average quality score <avg_qual, then this read/pair is discarded. Default 0 means no requirement.
+        example: 0
+        min: 0
+  - name: Length filtering arguments
+    arguments:
+      - name: --disable_length_filtering
+        alternatives: [-L]
+        type: boolean_true
+        description: |
+          Length filtering is enabled by default. If this option is specified, length filtering is disabled.
+      - name: --length_required
+        alternatives: [-l]
+        type: integer
+        description: |
+          Reads shorter than length_required will be discarded, default is 15.
+        example: 15
+        min: 0
+      - name: --length_limit
+        type: integer
+        description: |
+          Reads longer than length_limit will be discarded, default 0 means no limitation.
+        example: 0
+        min: 0
+  - name: Low complexity filtering arguments
+    arguments:
+      - name: --low_complexity_filter
+        alternatives: [-y]
+        type: boolean_true
+        description: |
+          Enable low complexity filter. The complexity is defined as the percentage of base that is different from its next base (base[i] != base[i+1]).
+      - name: --complexity_threshold
+        alternatives: [-Y]
+        type: integer
+        description: |
+          The threshold for low complexity filter (0~100). Default is 30, which means 30% complexity is required.
+        example: 30
+        min: 0
+  - name: Index filtering arguments
+    arguments:
+      - name: --filter_by_index1
+        type: file
+        description: |
+          Specify a file contains a list of barcodes of index1 to be filtered out, one barcode per line.
+      - name: --filter_by_index2
+        type: file
+        description: |
+          Specify a file contains a list of barcodes of index2 to be filtered out, one barcode per line.
+      - name: --filter_by_index_threshold
+        type: integer
+        description: |
+          The allowed difference of index barcode for index filtering, default 0 means completely identical.
+        example: 0
+        min: 0
+  - name: Overlapped region correction
+    arguments:
+      - type: boolean_true
+        name: --correction
+        alternatives: [-c]
+        description: |
+          Enable base correction in overlapped regions (only for PE data), default is disabled.
+      - name: --overlap_len_require
+        type: integer
+        description: |
+          The minimum length to detect overlapped region of PE reads. This will affect overlap analysis based PE merge, adapter trimming and correction. 30 by default.
+        example: 30
+        min: 0
+      - name: --overlap_diff_limit
+        type: integer
+        description: |
+          The maximum number of mismatched bases to detect overlapped region of PE reads. This will affect overlap analysis based PE merge, adapter trimming and correction. 5 by default.
+        example: 5
+        min: 0
+      - name: --overlap_diff_percent_limit
+        type: integer
+        description: |
+          The maximum percentage of mismatched bases to detect overlapped region of PE reads. This will affect overlap analysis based PE merge, adapter trimming and correction. Default 20 means 20%.
+        example: 20
+        min: 0
+        max: 100
+  - name: UMI arguments
+    arguments:
+      - name: --umi
+        alternatives: [-U]
+        type: boolean_true
+        description: |
+          Enable unique molecular identifier (UMI) preprocessing.
+      - name: --umi_loc
+        type: string
+        description: |
+          Specify the location of UMI, can be (index1/index2/read1/read2/per_index/per_read, default is none.
+        choices: [index1, index2, read1, read2, per_index, per_read]
+      - name: --umi_len
+        type: integer
+        description: |
+          If the UMI is in read1/read2, its length should be provided.
+        example: 0
+        min: 0
+      - name: --umi_prefix
+        type: string
+        description: |
+          If specified, an underline will be used to connect prefix and UMI (i.e. prefix=UMI, UMI=AATTCG, final=UMI_AATTCG). No prefix by default.
+      - name: --umi_skip
+        type: integer
+        description: |
+          If the UMI is in read1/read2, fastp can skip several bases following UMI, default is 0.
+        example: 0
+        min: 0
+      - name: --umi_delim
+        type: string
+        description: |
+          If the UMI is in index1/index2, fastp can use a delimiter to separate UMI from the read sequence, default is none.
+  - name: Overrepresentation analysis arguments
+    arguments:
+      - name: --overrepresentation_analysis
+        alternatives: [-p]
+        type: boolean_true
+        description: |
+          Enable overrepresentation analysis.
+      - name: --overrepresentation_sampling
+        type: integer
+        description: |
+          One in (--overrepresentation_sampling) reads will be computed for overrepresentation analysis (1~10000), smaller is slower, default is 20.
+        example: 20
+        min: 1
+  # # would need to set all outputs to multiple: true
+  # - name: Split arguments
+  #   arguments:
+  #     - name: --split
+  #       alternatives: [-s]
+  #       type: boolean_true
+  #       description: |
+  #         Split output by limiting total split file number with this option (2~999), a sequential number prefix will be added to output name ( 0001.out.fq, 0002.out.fq...), disabled by default.
+  #     - name: --split_by_lines
+  #       alternatives: [-S]
+  #       type: long
+  #       description: |
+  #         Split output by limiting lines of each file with this option(>=1000), a sequential number prefix will be added to output name ( 0001.out.fq, 0002.out.fq...), disabled by default.
+  #     - name: --split_prefix_digits
+  #       type: integer
+  #       description: |
+  #         The digits for the sequential number padding (1~10), default is 4, so the filename will be padded as 0001.xxx, 0 to disable padding.
+  #       example: 4
+resources:
+  - type: bash_script
+    path: script.sh
+test_resources:
+  - type: bash_script
+    path: test.sh
+  - type: file
+    path: test_data
+engines:
+  - type: docker
+    image: quay.io/biocontainers/fastp:0.23.4--hadf994f_2
+    setup:
+      - type: docker
+        run: |
+          fastp --version 2>&1 | sed 's# #: "#;s#$#"#' > /var/software_versions.txt
+runners:
+  - type: executable
+  - type: nextflow
--- a/src/fastp/help.txt
+++ b/src/fastp/help.txt
@@ -0,0 +1,93 @@
+```bash
+fastp --help
+```
+
+usage: fastp [options] ... 
+options:
+  -i, --in1                            read1 input file name (string [=])
+  -o, --out1                           read1 output file name (string [=])
+  -I, --in2                            read2 input file name (string [=])
+  -O, --out2                           read2 output file name (string [=])
+      --unpaired1                      for PE input, if read1 passed QC but read2 not, it will be written to unpaired1. Default is to discard it. (string [=])
+      --unpaired2                      for PE input, if read2 passed QC but read1 not, it will be written to unpaired2. If --unpaired2 is same as --unpaired1 (default mode), both unpaired reads will be written to this same file. (string [=])
+      --overlapped_out                 for each read pair, output the overlapped region if it has no any mismatched base. (string [=])
+      --failed_out                     specify the file to store reads that cannot pass the filters. (string [=])
+  -m, --merge                          for paired-end input, merge each pair of reads into a single read if they are overlapped. The merged reads will be written to the file given by --merged_out, the unmerged reads will be written to the files specified by --out1 and --out2. The merging mode is disabled by default.
+      --merged_out                     in the merging mode, specify the file name to store merged output, or specify --stdout to stream the merged output (string [=])
+      --include_unmerged               in the merging mode, write the unmerged or unpaired reads to the file specified by --merge. Disabled by default.
+  -6, --phred64                        indicate the input is using phred64 scoring (it'll be converted to phred33, so the output will still be phred33)
+  -z, --compression                    compression level for gzip output (1 ~ 9). 1 is fastest, 9 is smallest, default is 4. (int [=4])
+      --stdin                          input from STDIN. If the STDIN is interleaved paired-end FASTQ, please also add --interleaved_in.
+      --stdout                         stream passing-filters reads to STDOUT. This option will result in interleaved FASTQ output for paired-end output. Disabled by default.
+      --interleaved_in                 indicate that <in1> is an interleaved FASTQ which contains both read1 and read2. Disabled by default.
+      --reads_to_process               specify how many reads/pairs to be processed. Default 0 means process all reads. (int [=0])
+      --dont_overwrite                 don't overwrite existing files. Overwritting is allowed by default.
+      --fix_mgi_id                     the MGI FASTQ ID format is not compatible with many BAM operation tools, enable this option to fix it.
+  -V, --verbose                        output verbose log information (i.e. when every 1M reads are processed).
+  -A, --disable_adapter_trimming       adapter trimming is enabled by default. If this option is specified, adapter trimming is disabled
+  -a, --adapter_sequence               the adapter for read1. For SE data, if not specified, the adapter will be auto-detected. For PE data, this is used if R1/R2 are found not overlapped. (string [=auto])
+      --adapter_sequence_r2            the adapter for read2 (PE data only). This is used if R1/R2 are found not overlapped. If not specified, it will be the same as <adapter_sequence> (string [=auto])
+      --adapter_fasta                  specify a FASTA file to trim both read1 and read2 (if PE) by all the sequences in this FASTA file (string [=])
+      --detect_adapter_for_pe          by default, the auto-detection for adapter is for SE data input only, turn on this option to enable it for PE data.
+  -f, --trim_front1                    trimming how many bases in front for read1, default is 0 (int [=0])
+  -t, --trim_tail1                     trimming how many bases in tail for read1, default is 0 (int [=0])
+  -b, --max_len1                       if read1 is longer than max_len1, then trim read1 at its tail to make it as long as max_len1. Default 0 means no limitation (int [=0])
+  -F, --trim_front2                    trimming how many bases in front for read2. If it's not specified, it will follow read1's settings (int [=0])
+  -T, --trim_tail2                     trimming how many bases in tail for read2. If it's not specified, it will follow read1's settings (int [=0])
+  -B, --max_len2                       if read2 is longer than max_len2, then trim read2 at its tail to make it as long as max_len2. Default 0 means no limitation. If it's not specified, it will follow read1's settings (int [=0])
+  -D, --dedup                          enable deduplication to drop the duplicated reads/pairs
+      --dup_calc_accuracy              accuracy level to calculate duplication (1~6), higher level uses more memory (1G, 2G, 4G, 8G, 16G, 24G). Default 1 for no-dedup mode, and 3 for dedup mode. (int [=0])
+      --dont_eval_duplication          don't evaluate duplication rate to save time and use less memory.
+  -g, --trim_poly_g                    force polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data
+      --poly_g_min_len                 the minimum length to detect polyG in the read tail. 10 by default. (int [=10])
+  -G, --disable_trim_poly_g            disable polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data
+  -x, --trim_poly_x                    enable polyX trimming in 3' ends.
+      --poly_x_min_len                 the minimum length to detect polyX in the read tail. 10 by default. (int [=10])
+  -5, --cut_front                      move a sliding window from front (5') to tail, drop the bases in the window if its mean quality < threshold, stop otherwise.
+  -3, --cut_tail                       move a sliding window from tail (3') to front, drop the bases in the window if its mean quality < threshold, stop otherwise.
+  -r, --cut_right                      move a sliding window from front to tail, if meet one window with mean quality < threshold, drop the bases in the window and the right part, and then stop.
+  -W, --cut_window_size                the window size option shared by cut_front, cut_tail or cut_sliding. Range: 1~1000, default: 4 (int [=4])
+  -M, --cut_mean_quality               the mean quality requirement option shared by cut_front, cut_tail or cut_sliding. Range: 1~36 default: 20 (Q20) (int [=20])
+      --cut_front_window_size          the window size option of cut_front, default to cut_window_size if not specified (int [=4])
+      --cut_front_mean_quality         the mean quality requirement option for cut_front, default to cut_mean_quality if not specified (int [=20])
+      --cut_tail_window_size           the window size option of cut_tail, default to cut_window_size if not specified (int [=4])
+      --cut_tail_mean_quality          the mean quality requirement option for cut_tail, default to cut_mean_quality if not specified (int [=20])
+      --cut_right_window_size          the window size option of cut_right, default to cut_window_size if not specified (int [=4])
+      --cut_right_mean_quality         the mean quality requirement option for cut_right, default to cut_mean_quality if not specified (int [=20])
+  -Q, --disable_quality_filtering      quality filtering is enabled by default. If this option is specified, quality filtering is disabled
+  -q, --qualified_quality_phred        the quality value that a base is qualified. Default 15 means phred quality >=Q15 is qualified. (int [=15])
+  -u, --unqualified_percent_limit      how many percents of bases are allowed to be unqualified (0~100). Default 40 means 40% (int [=40])
+  -n, --n_base_limit                   if one read's number of N base is >n_base_limit, then this read/pair is discarded. Default is 5 (int [=5])
+  -e, --average_qual                   if one read's average quality score <avg_qual, then this read/pair is discarded. Default 0 means no requirement (int [=0])
+  -L, --disable_length_filtering       length filtering is enabled by default. If this option is specified, length filtering is disabled
+  -l, --length_required                reads shorter than length_required will be discarded, default is 15. (int [=15])
+      --length_limit                   reads longer than length_limit will be discarded, default 0 means no limitation. (int [=0])
+  -y, --low_complexity_filter          enable low complexity filter. The complexity is defined as the percentage of base that is different from its next base (base[i] != base[i+1]).
+  -Y, --complexity_threshold           the threshold for low complexity filter (0~100). Default is 30, which means 30% complexity is required. (int [=30])
+      --filter_by_index1               specify a file contains a list of barcodes of index1 to be filtered out, one barcode per line (string [=])
+      --filter_by_index2               specify a file contains a list of barcodes of index2 to be filtered out, one barcode per line (string [=])
+      --filter_by_index_threshold      the allowed difference of index barcode for index filtering, default 0 means completely identical. (int [=0])
+  -c, --correction                     enable base correction in overlapped regions (only for PE data), default is disabled
+      --overlap_len_require            the minimum length to detect overlapped region of PE reads. This will affect overlap analysis based PE merge, adapter trimming and correction. 30 by default. (int [=30])
+      --overlap_diff_limit             the maximum number of mismatched bases to detect overlapped region of PE reads. This will affect overlap analysis based PE merge, adapter trimming and correction. 5 by default. (int [=5])
+      --overlap_diff_percent_limit     the maximum percentage of mismatched bases to detect overlapped region of PE reads. This will affect overlap analysis based PE merge, adapter trimming and correction. Default 20 means 20%. (int [=20])
+  -U, --umi                            enable unique molecular identifier (UMI) preprocessing
+      --umi_loc                        specify the location of UMI, can be (index1/index2/read1/read2/per_index/per_read, default is none (string [=])
+      --umi_len                        if the UMI is in read1/read2, its length should be provided (int [=0])
+      --umi_prefix                     if specified, an underline will be used to connect prefix and UMI (i.e. prefix=UMI, UMI=AATTCG, final=UMI_AATTCG). No prefix by default (string [=])
+      --umi_skip                       if the UMI is in read1/read2, fastp can skip several bases following UMI, default is 0 (int [=0])
+      --umi_delim                      delimiter to use between the read name and the UMI, default is : (string [=:])
+  -p, --overrepresentation_analysis    enable overrepresented sequence analysis.
+  -P, --overrepresentation_sampling    one in (--overrepresentation_sampling) reads will be computed for overrepresentation analysis (1~10000), smaller is slower, default is 20. (int [=20])
+  -j, --json                           the json format report file name (string [=fastp.json])
+  -h, --html                           the html format report file name (string [=fastp.html])
+  -R, --report_title                   should be quoted with ' or ", default is "fastp report" (string [=fastp report])
+  -w, --thread                         worker thread number, default is 3 (int [=3])
+  -s, --split                          split output by limiting total split file number with this option (2~999), a sequential number prefix will be added to output name ( 0001.out.fq, 0002.out.fq...), disabled by default (int [=0])
+  -S, --split_by_lines                 split output by limiting lines of each file with this option(>=1000), a sequential number prefix will be added to output name ( 0001.out.fq, 0002.out.fq...), disabled by default (long [=0])
+  -d, --split_prefix_digits            the digits for the sequential number padding (1~10), default is 4, so the filename will be padded as 0001.xxx, 0 to disable padding (int [=4])
+      --cut_by_quality5                DEPRECATED, use --cut_front instead.
+      --cut_by_quality3                DEPRECATED, use --cut_tail instead.
+      --cut_by_quality_aggressive      DEPRECATED, use --cut_right instead.
+      --discard_unmerged               DEPRECATED, no effect now, see the introduction for merging.
+  -?, --help                           print this message
--- a/src/fastp/script.sh
+++ b/src/fastp/script.sh
@@ -0,0 +1,105 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+# disable flags
+[[ "$par_disable_adapter_trimming" == "false" ]] && unset par_disable_adapter_trimming
+[[ "$par_detect_adapter_for_pe" == "false" ]] && unset par_detect_adapter_for_pe
+[[ "$par_merge" == "false" ]] && unset par_merge
+[[ "$par_include_unmerged" == "false" ]] && unset par_include_unmerged
+[[ "$par_interleaved_in" == "false" ]] && unset par_interleaved_in
+[[ "$par_fix_mgi_id" == "false" ]] && unset par_fix_mgi_id
+[[ "$par_phred64" == "false" ]] && unset par_phred64
+[[ "$par_dont_overwrite" == "false" ]] && unset par_dont_overwrite
+[[ "$par_verbose" == "false" ]] && unset par_verbose
+[[ "$par_dedup" == "false" ]] && unset par_dedup
+[[ "$par_dont_eval_duplication" == "false" ]] && unset par_dont_eval_duplication
+[[ "$par_trim_poly_g" == "false" ]] && unset par_trim_poly_g
+[[ "$par_disable_trim_poly_g" == "false" ]] && unset par_disable_trim_poly_g
+[[ "$par_trim_poly_x" == "false" ]] && unset par_trim_poly_x
+[[ "$par_disable_quality_filtering" == "false" ]] && unset par_disable_quality_filtering
+[[ "$par_disable_length_filtering" == "false" ]] && unset par_disable_length_filtering
+[[ "$par_low_complexity_filter" == "false" ]] && unset par_low_complexity_filter
+[[ "$par_umi" == "false" ]] && unset par_umi
+[[ "$par_overrepresentation_analysis" == "false" ]] && unset par_overrepresentation_analysis
+
+# run command
+fastp \
+  -i "$par_in1" \
+  -o "$par_out1" \
+  ${par_in2:+--in2 "${par_in2}"} \
+  ${par_out2:+--out2 "${par_out2}"} \
+  ${par_unpaired1:+--unpaired1 "${par_unpaired1}"} \
+  ${par_unpaired2:+--unpaired2 "${par_unpaired2}"} \
+  ${par_failed_out:+--failed_out "${par_failed_out}"} \
+  ${par_overlapped_out:+--overlapped_out "${par_overlapped_out}"} \
+  ${par_json:+--json "${par_json}"} \
+  ${par_html:+--html "${par_html}"} \
+  ${par_report_title:+--report_title "${par_report_title}"} \
+  ${par_disable_adapter_trimming:+--disable_adapter_trimming} \
+  ${par_detect_adapter_for_pe:+--detect_adapter_for_pe} \
+  ${par_adapter_sequence:+--adapter_sequence "${par_adapter_sequence}"} \
+  ${par_adapter_sequence_r2:+--adapter_sequence_r2 "${par_adapter_sequence_r2}"} \
+  ${par_adapter_fasta:+--adapter_fasta "${par_adapter_fasta}"} \
+  ${par_trim_front1:+--trim_front1 "${par_trim_front1}"} \
+  ${par_trim_tail1:+--trim_tail1 "${par_trim_tail1}"} \
+  ${par_max_len1:+--max_len1 "${par_max_len1}"} \
+  ${par_trim_front2:+--trim_front2 "${par_trim_front2}"} \
+  ${par_trim_tail2:+--trim_tail2 "${par_trim_tail2}"} \
+  ${par_max_len2:+--max_len2 "${par_max_len2}"} \
+  ${par_merge:+--merge} \
+  ${par_merged_out:+--merged_out "${par_merged_out}"} \
+  ${par_include_unmerged:+--include_unmerged} \
+  ${par_interleaved_in:+--interleaved_in} \
+  ${par_fix_mgi_id:+--fix_mgi_id} \
+  ${par_phred64:+--phred64} \
+  ${par_compression:+--compression "${par_compression}"} \
+  ${par_dont_overwrite:+--dont_overwrite} \
+  ${par_verbose:+--verbose} \
+  ${par_reads_to_process:+--reads_to_process "${par_reads_to_process}"} \
+  ${par_dedup:+--dedup} \
+  ${par_dup_calc_accuracy:+--dup_calc_accuracy "${par_dup_calc_accuracy}"} \
+  ${par_dont_eval_duplication:+--dont_eval_duplication} \
+  ${par_trim_poly_g:+--trim_poly_g} \
+  ${par_poly_g_min_len:+--poly_g_min_len "${par_poly_g_min_len}"} \
+  ${par_disable_trim_poly_g:+--disable_trim_poly_g} \
+  ${par_trim_poly_x:+--trim_poly_x} \
+  ${par_poly_x_min_len:+--poly_x_min_len "${par_poly_x_min_len}"} \
+  ${par_cut_front:+--cut_front "${par_cut_front}"} \
+  ${par_cut_tail:+--cut_tail "${par_cut_tail}"} \
+  ${par_cut_right:+--cut_right "${par_cut_right}"} \
+  ${par_cut_window_size:+--cut_window_size "${par_cut_window_size}"} \
+  ${par_cut_mean_quality:+--cut_mean_quality "${par_cut_mean_quality}"} \
+  ${par_cut_front_window_size:+--cut_front_window_size "${par_cut_front_window_size}"} \
+  ${par_cut_front_mean_quality:+--cut_front_mean_quality "${par_cut_front_mean_quality}"} \
+  ${par_cut_tail_window_size:+--cut_tail_window_size "${par_cut_tail_window_size}"} \
+  ${par_cut_tail_mean_quality:+--cut_tail_mean_quality "${par_cut_tail_mean_quality}"} \
+  ${par_cut_right_window_size:+--cut_right_window_size "${par_cut_right_window_size}"} \
+  ${par_cut_right_mean_quality:+--cut_right_mean_quality "${par_cut_right_mean_quality}"} \
+  ${par_disable_quality_filtering:+--disable_quality_filtering} \
+  ${par_qualified_quality_phred:+--qualified_quality_phred "${par_qualified_quality_phred}"} \
+  ${par_unqualified_percent_limit:+--unqualified_percent_limit "${par_unqualified_percent_limit}"} \
+  ${par_n_base_limit:+--n_base_limit "${par_n_base_limit}"} \
+  ${par_average_qual:+--average_qual "${par_average_qual}"} \
+  ${par_disable_length_filtering:+--disable_length_filtering} \
+  ${par_length_required:+--length_required "${par_length_required}"} \
+  ${par_length_limit:+--length_limit "${par_length_limit}"} \
+  ${par_low_complexity_filter:+--low_complexity_filter} \
+  ${par_complexity_threshold:+--complexity_threshold "${par_complexity_threshold}"} \
+  ${par_filter_by_index1:+--filter_by_index1 "${par_filter_by_index1}"} \
+  ${par_filter_by_index2:+--filter_by_index2 "${par_filter_by_index2}"} \
+  ${par_filter_by_index_threshold:+--filter_by_index_threshold "${par_filter_by_index_threshold}"} \
+  ${par_correction:+--correction} \
+  ${par_overlap_len_require:+--overlap_len_require "${par_overlap_len_require}"} \
+  ${par_overlap_diff_limit:+--overlap_diff_limit "${par_overlap_diff_limit}"} \
+  ${par_overlap_diff_percent_limit:+--overlap_diff_percent_limit "${par_overlap_diff_percent_limit}"} \
+  ${par_umi:+--umi} \
+  ${par_umi_loc:+--umi_loc "${par_umi_loc}"} \
+  ${par_umi_len:+--umi_len "${par_umi_len}"} \
+  ${par_umi_prefix:+--umi_prefix "${par_umi_prefix}"} \
+  ${par_umi_skip:+--umi_skip "${par_umi_skip}"} \
+  ${par_umi_delim:+--umi_delim "${par_umi_delim}"} \
+  ${par_overrepresentation_analysis:+--overrepresentation_analysis} \
+  ${par_overrepresentation_sampling:+--overrepresentation_sampling "${par_overrepresentation_sampling}"} \
+  ${meta_cpus:+--thread "${meta_cpus}"}
--- a/src/fastp/test.sh
+++ b/src/fastp/test.sh
@@ -0,0 +1,74 @@
+#!/bin/bash
+
+set -e
+
+## VIASH START
+meta_executable="target/docker/fastp/fastp"
+meta_resources_dir="src/fastp"
+## VIASH END
+
+#########################################################################################
+mkdir fastp_se
+cd fastp_se
+
+echo "> Run fastp on SE"
+"$meta_executable" \
+  --in1 "$meta_resources_dir/test_data/se/a.fastq" \
+  --out1 "trimmed.fastq" \
+  --failed_out "failed.fastq" \
+  --json "report.json" \
+  --html "report.html" \
+  --adapter_sequence ACGGCTAGCTA
+
+echo ">> Check if output exists"
+[ ! -f "trimmed.fastq" ] && echo ">> trimmed.fastq does not exist" && exit 1
+[ ! -f "failed.fastq" ] && echo ">> failed.fastq does not exist" && exit 1
+[ ! -f "report.json" ] && echo ">> report.json does not exist" && exit 1
+[ ! -f "report.html" ] && echo ">> report.html does not exist" && exit 1
+
+#########################################################################################
+cd ..
+mkdir fastp_pe_minimal
+cd fastp_pe_minimal
+
+echo ">> Run fastp on PE with minimal parameters"
+"$meta_executable" \
+  --in1 "$meta_resources_dir/test_data/pe/a.1.fastq" \
+  --in2 "$meta_resources_dir/test_data/pe/a.2.fastq" \
+  --out1 "trimmed_1.fastq" \
+  --out2 "trimmed_2.fastq"
+
+echo ">> Check if output exists"
+[ ! -f "trimmed_1.fastq" ] && echo ">> trimmed_1.fastq does not exist" && exit 1
+[ ! -f "trimmed_2.fastq" ] && echo ">> trimmed_2.fastq does not exist" && exit 1
+
+#########################################################################################
+cd ..
+mkdir fastp_pe_many
+cd fastp_pe_many
+
+echo ">> Run fastp on PE with many parameters"
+"$meta_executable" \
+  --in1 "$meta_resources_dir/test_data/pe/a.1.fastq" \
+  --in2 "$meta_resources_dir/test_data/pe/a.2.fastq" \
+  --out1 "trimmed_1.fastq" \
+  --out2 "trimmed_2.fastq" \
+  --failed_out "failed.fastq" \
+  --json "report.json" \
+  --html "report.html" \
+  --adapter_sequence ACGGCTAGCTA \
+  --adapter_sequence_r2 AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC \
+  --merge \
+  --merged_out "merged.fastq"
+
+echo ">> Check if output exists"
+[ ! -f "trimmed_1.fastq" ] && echo ">> trimmed_1.fastq does not exist" && exit 1
+[ ! -f "trimmed_2.fastq" ] && echo ">> trimmed_2.fastq does not exist" && exit 1
+[ ! -f "failed.fastq" ] && echo ">> failed.fastq does not exist" && exit 1
+[ ! -f "report.json" ] && echo ">> report.json does not exist" && exit 1
+[ ! -f "report.html" ] && echo ">> report.html does not exist" && exit 1
+[ ! -f "merged.fastq" ] && echo ">> merged.fastq does not exist" && exit 1
+
+#########################################################################################
+
+echo "> Test successful"
--- a/src/fastp/test_data/pe/a.1.fastq
+++ b/src/fastp/test_data/pe/a.1.fastq
@@ -0,0 +1,4 @@
+@1
+ACGGCAT
+
+!!!!!!!
--- a/src/fastp/test_data/pe/a.2.fastq
+++ b/src/fastp/test_data/pe/a.2.fastq
@@ -0,0 +1,4 @@
+@1
+ACGGCAT
+
+!!!!!!!
--- a/src/fastp/test_data/script.sh
+++ b/src/fastp/test_data/script.sh
@@ -0,0 +1,10 @@
+# fastp test data
+
+# Test data was obtained from https://github.com/snakemake/snakemake-wrappers/tree/master/bio/fastp/test
+
+if [ ! -d /tmp/snakemake-wrappers ]; then
+  git clone --depth 1 --single-branch --branch master https://github.com/snakemake/snakemake-wrappers /tmp/snakemake-wrappers
+fi
+
+cp -r /tmp/snakemake-wrappers/bio/fastp/test/reads/* src/fastp/test_data
+
--- a/src/fastp/test_data/se/a.fastq
+++ b/src/fastp/test_data/se/a.fastq
@@ -0,0 +1,4 @@
+@1
+ACGGCAT
+
+!!!!!!!
--- a/src/featurecounts/config.vsh.yaml
+++ b/src/featurecounts/config.vsh.yaml
@@ -0,0 +1,338 @@
+name: featurecounts
+description: |
+  featureCounts is a read summarization program for counting reads generated from either RNA or genomic DNA sequencing experiments by implementing highly efficient chromosome hashing and feature blocking techniques. It works with either single or paired-end reads and provides a wide range of options appropriate for different sequencing applications.
+keywords: ["Read counting", "Genomic features"]
+links:
+  homepage: https://subread.sourceforge.net/
+  documentation: https://subread.sourceforge.net/SubreadUsersGuide.pdf
+  repository: https://github.com/ShiLab-Bioinformatics/subread
+references:
+  doi: "10.1093/bioinformatics/btt656"
+license: GPL-3.0 
+requirements:
+  commands: [ featureCounts ]
+authors:
+  - __merge__: /src/_authors/sai_nirmayi_yasa.yaml
+    roles: [ author, maintainer ]
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: --annotation
+        alternatives: ["-a"]
+        type: file
+        description: | 
+          Name of an annotation file. GTF/GFF format by default. See '--format' option for more format information.
+        required: true
+        example: annotation.gtf
+      - name: --input
+        alternatives: ["-i"]
+        type: file
+        multiple: true
+        description: |
+          A list of SAM or BAM format files separated by semi-colon (;). They can be either name or location sorted. Location-sorted paired-end reads are automatically sorted by read names.
+        required: true
+        example: input_file1.bam
+  
+  - name: Outputs
+    arguments:
+      - name: --counts
+        alternatives: ["-o"]
+        type: file
+        direction: output
+        description: | 
+          Name of output file including read counts in tab delimited format.
+        required: true
+        example: features.tsv
+      - name: --summary
+        type: file
+        direction: output
+        description: | 
+          Summary statistics of counting results in tab delimited format.
+        required: false
+        example: summary.tsv
+      - name: --junctions
+        type: file
+        direction: output
+        description: | 
+          Count number of reads supporting each exon-exon junction. Junctions were identified from those exon-spanning reads in the input (containing 'N' in CIGAR string).
+        example: junctions.txt
+        required: false
+
+  - name: Annotation
+    arguments:
+      - name: --format
+        alternatives: ["-F"]
+        type: string
+        description: | 
+          Specify format of the provided annotation file. Acceptable formats include 'GTF' (or compatible GFF format) and 'SAF'. 'GTF' by default. 
+        choices: [GTF, GFF, SAF]
+        example: "GTF"
+        required: false
+      - name: --feature_type
+        alternatives: ["-t"]
+        type: string
+        description: | 
+          Specify feature type(s) in a GTF annotation. If multiple types are provided, they should be separated by ';' with no space in between. 'exon' by default. Rows in the annotation with a matched feature will be extracted and used for read mapping.
+        example: "exon"
+        required: false
+        multiple: true
+      - name: --attribute_type
+        alternatives: ["-g"]
+        type: string
+        description: | 
+          Specify attribute type in GTF annotation. 'gene_id' by default. Meta-features used for read counting will be extracted from annotation using the provided value.
+        example: "gene_id"
+        required: false
+      - name: --extra_attributes
+        type: string
+        description: | 
+          Extract extra attribute types from the provided GTF annotation and include them in the counting output. These attribute types will not be used to group features. If more than one attribute type is provided they should be separated by semicolon (;).
+        required: false
+        multiple: true
+      - name: --chrom_alias
+        alternatives: ["-A"]
+        type: file
+        description: | 
+          Provide a chromosome name alias file to match chr names in annotation with those in the reads. This should be a two-column comma-delimited text file. Its first column should include chr names in the annotation and its second column should include chr names in the reads. Chr names are case sensitive. No column header should be included in the file.
+        required: false
+        example: chrom_alias.csv
+  
+  - name: Level of summarization
+    arguments:
+      - name: --feature_level
+        alternatives: ["-f"]
+        type: boolean_true
+        description: | 
+          Perform read counting at feature level (eg. counting reads for exons rather than genes).
+  
+  - name: Overlap between reads and features
+    arguments:
+      - name: --overlapping
+        alternatives: ["-O"]
+        type: boolean_true
+        description: | 
+          Assign reads to all their overlapping meta-features (or features if '--feature_level' is specified).
+      - name: --min_overlap
+        type: integer
+        description: | 
+          Minimum number of overlapping bases in a read that is required for read assignment. 1 by default. Number of overlapping bases is counted from both reads if paired end. If a negative value is provided, then a gap of up to specified size will be allowed between read and the feature that the read is assigned to.
+        required: false
+        example: 1
+      - name: --frac_overlap
+        type: double
+        description: | 
+          Minimum fraction of overlapping bases in a read that is required for read assignment. Value should be within range [0,1]. 0 by default. Number of overlapping bases is counted from both reads if paired end. Both this option and '--min_overlap' option need to be satisfied for read assignment.
+        required: false
+        min: 0
+        max: 1
+        example: 0
+      - name: --frac_overlap_feature
+        type: double
+        description: | 
+          Minimum fraction of overlapping bases in a feature that is required for read assignment. Value should be within range [0,1]. 0 by default.
+        required: false
+        min: 0
+        max: 1
+        example: 0
+      - name: --largest_overlap
+        type: boolean_true
+        description: | 
+          Assign reads to a meta-feature/feature that has the largest number of overlapping bases.
+      - name: --non_overlap
+        type: integer
+        description: | 
+          Maximum number of non-overlapping bases in a read (or a read pair) that is allowed when being assigned to a feature. No limit is set by default.
+        required: false
+      - name: --non_overlap_feature
+        type: integer
+        description: | 
+          Maximum number of non-overlapping bases in a feature that is allowed in read assignment. No limit is set by default.
+        required: false
+      - name: --read_extension5
+        type: integer
+        description: | 
+          Reads are extended upstream by <int> bases from their 5' end.
+        required: false
+      - name: --read_extension3
+        type: integer
+        description: | 
+          Reads are extended upstream by <int> bases from their 3' end.
+        required: false
+      - name: --read2pos
+        type: integer
+        description: | 
+          Reduce reads to their 5' most base or 3' most base. Read counting is then performed based on the single base the read is reduced to.
+        required: false
+        choices: [3, 5]
+  
+  - name: Multi-mapping reads
+    arguments:
+      - name: --multi_mapping
+        alternatives: ["-M"]
+        type: boolean_true
+        description: | 
+          Multi-mapping reads will also be counted. For a multi-mapping read, all its reported alignments will be counted. The 'NH' tag in BAM/SAM input is used to detect multi-mapping reads.
+  
+  - name: Fractional counting
+    arguments:
+      - name: --fraction
+        type: boolean_true
+        description: | 
+          Assign fractional counts to features. This option must be used together with '--multi_mapping' or '--overlapping' or both. When '--multi_mapping' is specified, each reported alignment from a multi-mapping read (identified via 'NH' tag) will carry a fractional count of 1/x, instead of 1 (one), where x is the total number of alignments reported for the same read. When '--overlapping' is specified, each overlapping feature will receive a fractional count of 1/y, where y is the total number of features overlapping with the read. When both '--multi_mapping' and '--overlapping' are specified, each alignment will carry a fractional count of 1/(x*y).
+
+  - name: Read filtering
+    arguments:
+      - name: --min_map_quality
+        alternatives: ["-Q"]
+        type: integer
+        description: | 
+          The minimum mapping quality score a read must satisfy in order to be counted. For paired-end reads, at least one end should satisfy this criteria. 0 by default.
+        required: false
+        example: 0
+      - name: --split_only
+        type: boolean_true
+        description: | 
+          Count split alignments only (ie. alignments with CIGAR string containing 'N'). An example of split alignments is exon-spanning reads in RNA-seq data.
+      - name: --non_split_only
+        type: boolean_true
+        description: | 
+          If specified, only non-split alignments (CIGAR strings do not contain letter 'N') will be counted. All the other alignments will be ignored.
+      - name: --primary
+        type: boolean_true
+        description: | 
+          Count primary alignments only. Primary alignments are identified using bit 0x100 in SAM/BAM FLAG field.
+      - name: --ignore_dup
+        type: boolean_true
+        description: | 
+          Ignore duplicate reads in read counting. Duplicate reads are identified using bit Ox400 in BAM/SAM FLAG field. The whole read pair is ignored if one of the reads is a duplicate read for paired end data.
+  
+  - name: Strandedness
+    arguments:
+      - name: --strand
+        alternatives: ["-s"]
+        type: integer
+        description: | 
+          Perform strand-specific read counting. A single integer value (applied to all input files) should be provided. Possible values include: 0 (unstranded), 1 (stranded) and 2 (reversely stranded). Default value is 0 (ie. unstranded read counting carried out for all input files).
+        choices: [0, 1, 2] 
+        example: 0
+        required: false
+
+  - name: Exon-exon junctions
+    arguments:
+      - name: --ref_fasta
+        alternatives: ["-G"]
+        type: file
+        description: | 
+          Provide the name of a FASTA-format file that contains the reference sequences used in read mapping that produced the provided SAM/BAM files.
+        required: false
+        example: reference.fasta
+      
+  - name: Parameters specific to paired end reads
+    arguments:
+      - name: --paired
+        alternatives: ["-p"]
+        type: boolean_true
+        description: | 
+          Specify that input data contain paired-end reads. To perform fragment counting (ie. counting read pairs), the '--countReadPairs' parameter should also be specified in addition to this parameter.
+      - name: --count_read_pairs
+        type: boolean_true
+        description: | 
+          Count read pairs (fragments) instead of reads. This option is only applicable for paired-end reads.
+      - name: --both_aligned
+        alternatives: ["-B"]
+        type: boolean_true
+        description: | 
+          Count read pairs (fragments) instead of reads. This option is only applicable for paired-end reads.
+      - name: --check_pe_dist
+        alternatives: ["-P"]
+        type: boolean_true
+        description: | 
+          Check validity of paired-end distance when counting read pairs. Use '--min_length' and '--max_length' to set thresholds.
+      - name: --min_length
+        alternatives: ["-d"]
+        type: integer
+        description: | 
+          Minimum fragment/template length, 50 by default.
+        required: false
+        example: 50
+      - name: --max_length
+        alternatives: ["-D"]
+        type: integer
+        description: | 
+          Maximum fragment/template length, 600 by default.
+        required: false
+        example: 600
+      - name: --same_strand
+        alternatives: ["-C"]
+        type: boolean_true
+        description: | 
+          Do not count read pairs that have their two ends mapping to different chromosomes or mapping to same chromosome but on different strands.
+      - name: --donotsort
+        type: boolean_true
+        description: | 
+          Do not sort reads in BAM/SAM input. Note that reads from the same pair are required to be located next to each other in the input.
+  
+  - name: Read groups
+    arguments:
+      - name: --by_read_group
+        type: boolean_true
+        description: | 
+          Assign reads by read group. "RG" tag is required to be present in the input BAM/SAM files.
+  
+  - name: Long reads
+    arguments:
+      - name: --long_reads
+        type: boolean_true
+        description: | 
+          Count long reads such as Nanopore and PacBio reads. Long read counting can only run in one thread and only reads (not read-pairs) can be counted. There is no limitation on the number of 'M' operations allowed in a CIGAR string in long read counting.
+  
+  - name: Assignment results for each read
+    arguments:
+      - name: --detailed_results
+        type: file
+        direction: output
+        description: | 
+          Directory to save the detailed assignment results. Use `--detailed_results_format` to determine the format of the detailed results.
+        example: detailed_results/
+        required: false
+      - name: --detailed_results_format
+        alternatives: ["-R"]
+        type: string
+        description: | 
+          Output detailed assignment results for each read or read-pair. Results are saved to a file that is in one of the following formats: CORE, SAM and BAM. See documentaiton for more info about these formats.
+        required: false
+        choices: [CORE, SAM, BAM]
+      
+  - name: Miscellaneous
+    arguments:
+      - name: --max_M_op
+        type: integer
+        description: | 
+          Maximum number of 'M' operations allowed in a CIGAR string. 10 by default. Both 'X' and '=' are treated as 'M' and adjacent 'M' operations are merged in the CIGAR string.
+        required: false
+        example: 10
+      - name: --verbose
+        type: boolean_true
+        description: | 
+          Output verbose information for debugging, such as un-matched chromosome/contig names.
+
+resources:
+  - type: bash_script
+    path: script.sh
+
+test_resources:
+  - type: bash_script
+    path: test.sh
+  - type: file
+    path: test_data
+
+engines: 
+  - type: docker
+    image: quay.io/biocontainers/subread:2.0.6--he4a0461_0
+    setup:
+      - type: docker
+        run: |
+          featureCounts -v 2>&1 | sed 's/featureCounts v\([0-9.]*\)/featureCounts: \1/' > /var/software_versions.txt
+runners:
+  - type: executable
+  - type: nextflow
--- a/src/featurecounts/help.txt
+++ b/src/featurecounts/help.txt
@@ -0,0 +1,242 @@
+```bash
+featureCounts
+```
+
+Version 2.0.3
+
+Usage: featureCounts [options] -a <annotation_file> -o <output_file> input_file1 [input_file2] ... 
+
+## Mandatory arguments:
+
+  -a <string>         Name of an annotation file. GTF/GFF format by default. See
+                      -F option for more format information. Inbuilt annotations
+                      (SAF format) is available in 'annotation' directory of the
+                      package. Gzipped file is also accepted.
+
+  -o <string>         Name of output file including read counts. A separate file
+                      including summary statistics of counting results is also
+                      included in the output ('<string>.summary'). Both files
+                      are in tab delimited format.
+
+  input_file1 [input_file2] ...   A list of SAM or BAM format files. They can be
+                      either name or location sorted. If no files provided,
+                      <stdin> input is expected. Location-sorted paired-end reads
+                      are automatically sorted by read names.
+
+## Optional arguments:
+# Annotation
+
+  -F <string>         Specify format of the provided annotation file. Acceptable
+                      formats include 'GTF' (or compatible GFF format) and
+                      'SAF'. 'GTF' by default.  For SAF format, please refer to
+                      Users Guide.
+
+  -t <string>         Specify feature type(s) in a GTF annotation. If multiple
+                      types are provided, they should be separated by ',' with
+                      no space in between. 'exon' by default. Rows in the
+                      annotation with a matched feature will be extracted and
+                      used for read mapping. 
+
+  -g <string>         Specify attribute type in GTF annotation. 'gene_id' by 
+                      default. Meta-features used for read counting will be 
+                      extracted from annotation using the provided value.
+
+  --extraAttributes   Extract extra attribute types from the provided GTF
+                      annotation and include them in the counting output. These
+                      attribute types will not be used to group features. If
+                      more than one attribute type is provided they should be
+                      separated by comma.
+
+  -A <string>         Provide a chromosome name alias file to match chr names in
+                      annotation with those in the reads. This should be a two-
+                      column comma-delimited text file. Its first column should
+                      include chr names in the annotation and its second column
+                      should include chr names in the reads. Chr names are case
+                      sensitive. No column header should be included in the
+                      file.
+
+# Level of summarization
+
+  -f                  Perform read counting at feature level (eg. counting 
+                      reads for exons rather than genes).
+
+# Overlap between reads and features
+
+  -O                  Assign reads to all their overlapping meta-features (or 
+                      features if -f is specified).
+
+  --minOverlap <int>  Minimum number of overlapping bases in a read that is
+                      required for read assignment. 1 by default. Number of
+                      overlapping bases is counted from both reads if paired
+                      end. If a negative value is provided, then a gap of up
+                      to specified size will be allowed between read and the
+                      feature that the read is assigned to.
+
+  --fracOverlap <float> Minimum fraction of overlapping bases in a read that is
+                      required for read assignment. Value should be within range
+                      [0,1]. 0 by default. Number of overlapping bases is
+                      counted from both reads if paired end. Both this option
+                      and '--minOverlap' option need to be satisfied for read
+                      assignment.
+
+  --fracOverlapFeature <float> Minimum fraction of overlapping bases in a
+                      feature that is required for read assignment. Value
+                      should be within range [0,1]. 0 by default.
+
+  --largestOverlap    Assign reads to a meta-feature/feature that has the 
+                      largest number of overlapping bases.
+
+  --nonOverlap <int>  Maximum number of non-overlapping bases in a read (or a
+                      read pair) that is allowed when being assigned to a
+                      feature. No limit is set by default.
+
+  --nonOverlapFeature <int> Maximum number of non-overlapping bases in a feature
+                      that is allowed in read assignment. No limit is set by
+                      default.
+
+  --readExtension5 <int> Reads are extended upstream by <int> bases from their
+                      5' end.
+
+  --readExtension3 <int> Reads are extended upstream by <int> bases from their
+                      3' end.
+
+  --read2pos <5:3>    Reduce reads to their 5' most base or 3' most base. Read
+                      counting is then performed based on the single base the 
+                      read is reduced to.
+
+# Multi-mapping reads
+
+  -M                  Multi-mapping reads will also be counted. For a multi-
+                      mapping read, all its reported alignments will be 
+                      counted. The 'NH' tag in BAM/SAM input is used to detect 
+                      multi-mapping reads.
+
+# Fractional counting
+
+  --fraction          Assign fractional counts to features. This option must
+                      be used together with '-M' or '-O' or both. When '-M' is
+                      specified, each reported alignment from a multi-mapping
+                      read (identified via 'NH' tag) will carry a fractional
+                      count of 1/x, instead of 1 (one), where x is the total
+                      number of alignments reported for the same read. When '-O'
+                      is specified, each overlapping feature will receive a
+                      fractional count of 1/y, where y is the total number of
+                      features overlapping with the read. When both '-M' and
+                      '-O' are specified, each alignment will carry a fractional
+                      count of 1/(x*y).
+
+# Read filtering
+
+  -Q <int>            The minimum mapping quality score a read must satisfy in
+                      order to be counted. For paired-end reads, at least one
+                      end should satisfy this criteria. 0 by default.
+
+  --splitOnly         Count split alignments only (ie. alignments with CIGAR
+                      string containing 'N'). An example of split alignments is
+                      exon-spanning reads in RNA-seq data.
+
+  --nonSplitOnly      If specified, only non-split alignments (CIGAR strings do
+                      not contain letter 'N') will be counted. All the other
+                      alignments will be ignored.
+
+  --primary           Count primary alignments only. Primary alignments are 
+                      identified using bit 0x100 in SAM/BAM FLAG field.
+
+  --ignoreDup         Ignore duplicate reads in read counting. Duplicate reads 
+                      are identified using bit Ox400 in BAM/SAM FLAG field. The 
+                      whole read pair is ignored if one of the reads is a 
+                      duplicate read for paired end data.
+
+# Strandness
+
+  -s <int or string>  Perform strand-specific read counting. A single integer
+                      value (applied to all input files) or a string of comma-
+                      separated values (applied to each corresponding input
+                      file) should be provided. Possible values include:
+                      0 (unstranded), 1 (stranded) and 2 (reversely stranded).
+                      Default value is 0 (ie. unstranded read counting carried
+                      out for all input files).
+
+# Exon-exon junctions
+
+  -J                  Count number of reads supporting each exon-exon junction.
+                      Junctions were identified from those exon-spanning reads
+                      in the input (containing 'N' in CIGAR string). Counting
+                      results are saved to a file named '<output_file>.jcounts'
+
+  -G <string>         Provide the name of a FASTA-format file that contains the
+                      reference sequences used in read mapping that produced the
+                      provided SAM/BAM files. This optional argument can be used
+                      with '-J' option to improve read counting for junctions.
+
+# Parameters specific to paired end reads
+
+  -p                  Specify that input data contain paired-end reads. To
+                      perform fragment counting (ie. counting read pairs), the
+                      '--countReadPairs' parameter should also be specified in
+                      addition to this parameter.
+
+  --countReadPairs    Count read pairs (fragments) instead of reads. This option
+                      is only applicable for paired-end reads.
+
+  -B                  Only count read pairs that have both ends aligned.
+
+  -P                  Check validity of paired-end distance when counting read 
+                      pairs. Use -d and -D to set thresholds.
+
+  -d <int>            Minimum fragment/template length, 50 by default.
+
+  -D <int>            Maximum fragment/template length, 600 by default.
+
+  -C                  Do not count read pairs that have their two ends mapping 
+                      to different chromosomes or mapping to same chromosome 
+                      but on different strands.
+
+  --donotsort         Do not sort reads in BAM/SAM input. Note that reads from 
+                      the same pair are required to be located next to each 
+                      other in the input.
+
+# Number of CPU threads
+
+  -T <int>            Number of the threads. 1 by default.
+
+# Read groups
+
+  --byReadGroup       Assign reads by read group. "RG" tag is required to be
+                      present in the input BAM/SAM files.
+                      
+
+# Long reads
+
+  -L                  Count long reads such as Nanopore and PacBio reads. Long
+                      read counting can only run in one thread and only reads
+                      (not read-pairs) can be counted. There is no limitation on
+                      the number of 'M' operations allowed in a CIGAR string in
+                      long read counting.
+
+# Assignment results for each read
+
+  -R <format>         Output detailed assignment results for each read or read-
+                      pair. Results are saved to a file that is in one of the
+                      following formats: CORE, SAM and BAM. See Users Guide for
+                      more info about these formats.
+
+  --Rpath <string>    Specify a directory to save the detailed assignment
+                      results. If unspecified, the directory where counting
+                      results are saved is used.
+
+# Miscellaneous
+
+  --tmpDir <string>   Directory under which intermediate files are saved (later
+                      removed). By default, intermediate files will be saved to
+                      the directory specified in '-o' argument.
+
+  --maxMOp <int>      Maximum number of 'M' operations allowed in a CIGAR
+                      string. 10 by default. Both 'X' and '=' are treated as 'M'
+                      and adjacent 'M' operations are merged in the CIGAR
+                      string.
+
+  --verbose           Output verbose information for debugging, such as un-
+                      matched chromosome/contig names.
+
+  -v                  Output version of the program.
--- a/src/featurecounts/script.sh
+++ b/src/featurecounts/script.sh
@@ -0,0 +1,94 @@
+#!/bin/bash
+
+set -e
+
+## VIASH START
+## VIASH END
+
+# create temporary directory
+tmp_dir=$(mktemp -d -p "$meta_temp_dir" "${meta_functionality_name}_XXXXXX")
+mkdir -p "$tmp_dir/temp"
+
+# create detailed_results directory if variable is set and directory does not exist
+if [[ ! -z "$par_detailed_results" ]] && [[ ! -d "$par_detailed_results" ]]; then
+  mkdir -p "$par_detailed_results"
+fi
+
+# replace comma with semicolon
+par_feature_type=$(echo $par_feature_type | tr ',' ';')
+par_extra_attributes=$(echo $par_extra_attributes | tr ',' ';')
+
+# unset flag variables
+[[ "$par_feature_level" == "false" ]] && unset par_feature_level
+[[ "$par_overlapping" == "false" ]] && unset par_overlapping
+[[ "$par_largest_overlap" == "false" ]] && unset par_largest_overlap
+[[ "$par_multi_mapping" == "false" ]] && unset par_multi_mapping
+[[ "$par_fraction" == "false" ]] && unset par_fraction
+[[ "$par_split_only" == "false" ]] && unset par_split_only
+[[ "$par_non_split_only" == "false" ]] && unset par_non_split_only
+[[ "$par_primary" == "false" ]] && unset par_primary
+[[ "$par_ignore_dup" == "false" ]] && unset par_ignore_dup
+[[ "$par_paired" == "false" ]] && unset par_paired
+[[ "$par_count_read_pairs" == "false" ]] && unset par_count_read_pairs
+[[ "$par_both_aligned" == "false" ]] && unset par_both_aligned
+[[ "$par_check_pe_dist" == "false" ]] && unset par_check_pe_dist
+[[ "$par_same_strand" == "false" ]] && unset par_same_strand
+[[ "$par_donotsort" == "false" ]] && unset par_donotsort
+[[ "$par_by_read_group" == "false" ]] && unset par_by_read_group
+[[ "$par_long_reads" == "false" ]] && unset par_long_reads
+[[ "$par_verbose" == "false" ]] && unset par_verbose
+
+IFS=";" read -ra input <<< $par_input
+
+featureCounts \
+  ${par_format:+-F "${par_format}"} \
+  ${par_feature_type:+-t "${par_feature_type}"} \
+  ${par_attribute_type:+-g "${par_attribute_type}"} \
+  ${par_extra_attributes:+--extraAttributes "${extra_attributes}"} \
+  ${par_chrom_alias:+-A "${par_chrom_alias}"} \
+  ${par_feature_level:+-f} \
+  ${par_overlapping:+-O} \
+  ${par_min_overlap:+--minOverlap "${par_min_overlap}"} \
+  ${par_frac_overlap:+--fracOverlap "${par_frac_overlap}"} \
+  ${par_frac_overlap_feature:+--fracOverlapFeature "${par_frac_overlap_feature}"} \
+  ${par_largest_overlap:+--largestOverlap} \
+  ${par_non_overlap:+--nonOverlap "${par_non_overlap}"} \
+  ${par_non_overlap_feature:+--nonOverlapFeature "${par_non_overlap_feature}"} \
+  ${par_read_extension5:+--readExtension5 "${par_read_extension5}"} \
+  ${par_read_extension3:+--readExtension3 "${par_read_extension3}"} \
+  ${par_read2pos:+--read2pos "${par_read2pos}"} \
+  ${par_multi_mapping:+-M} \
+  ${par_fraction:+--fraction} \
+  ${par_min_map_quality:+-Q "${par_min_map_quality}"} \
+  ${par_split_only:+--splitOnly} \
+  ${par_non_split_only:+--nonSplitOnly} \
+  ${par_primary:+--primary} \
+  ${par_ignore_dup:+--ignoreDup} \
+  ${par_strand:+-s "${par_strand}"} \
+  ${par_junctions:+-J} \
+  ${par_ref_fasta:+-G "${par_ref_fasta}"} \
+  ${par_paired:+-p} \
+  ${par_count_read_pairs:+--countReadPairs} \
+  ${par_both_aligned:+-B} \
+  ${par_check_pe_dist:+-P} \
+  ${par_min_length:+-d "${par_min_length}"} \
+  ${par_max_length:+-D "${par_max_length}"} \
+  ${par_same_strand:+-C} \
+  ${par_donotsort:+--donotsort} \
+  ${par_by_read_group:+--byReadGroup} \
+  ${par_long_reads:+-L} \
+  ${par_detailed_results:+--Rpath "${par_detailed_results}"} \
+  ${par_detailed_results_format:+-R "${par_detailed_results_format}"} \
+  ${par_max_M_op:+--maxMOp "${par_max_M_op}"} \
+  ${par_verbose:+--verbose} \
+  ${meta_cpus:+-T "${meta_cpus}"} \
+  --tmpDir "$tmp_dir/temp" \
+  -a "$par_annotation" \
+  -o "$tmp_dir/output.txt" \
+  "${input[*]}"
+
+[[ ! -z "$par_counts" ]] && mv "$tmp_dir/output.txt" "$par_counts"
+[[ ! -z "$par_summary" ]] && mv "$tmp_dir/output.txt.summary" "$par_summary"
+if [[ ! -z "$par_junctions" ]] && [[ -e "$tmp_dir/output.txt.jcounts" ]]; then 
+  mv "$tmp_dir/output.txt.jcounts" "$par_junctions"
+fi
--- a/src/featurecounts/test.sh
+++ b/src/featurecounts/test.sh
@@ -0,0 +1,59 @@
+#!/bin/bash
+
+set -e
+
+dir_in="$meta_resources_dir/test_data"
+
+echo "> Run featureCounts (with junctions)"
+"$meta_executable" \
+  --input "$dir_in/a.bam" \
+  --annotation "$dir_in/annotation.gtf" \
+  --counts "features.tsv" \
+  --summary "summary.tsv" \
+  --junctions "junction_counts.txt" \
+  --ref_fasta "$dir_in/genome.fasta" \
+  --overlapping \
+  --frac_overlap 0.2 \
+  --paired \
+  --strand 0 \
+  --detailed_results detailed_results \
+  --detailed_results_format SAM
+
+echo ">> Checking output"
+[ ! -f "features.tsv" ] && echo "Output file features.tsv does not exist" && exit 1
+[ ! -f "summary.tsv" ] && echo "Output file summary.tsv does not exist" && exit 1
+[ ! -f "junction_counts.txt" ] && echo "Output file junction_counts.txt does not exist" && exit 1
+[ ! -d "detailed_results" ] && echo "Output directory detailed_results does not exist" && exit 1
+[ ! -f "detailed_results/a.bam.featureCounts.sam" ] && echo "Output file detailed_results/a.bam.featureCounts.sam does not exist" && exit 1
+
+echo ">> Check if output is empty"
+[ ! -s "features.tsv" ] && echo "Output file features.tsv is empty" && exit 1
+[ ! -s "summary.tsv" ] && echo "Output file summary.tsv is empty" && exit 1
+[ ! -s "junction_counts.txt" ] && echo "Output file junction_counts.txt is empty" && exit 1
+[ ! -s "detailed_results/a.bam.featureCounts.sam" ] && echo "Output file detailed_results/a.bam.featureCounts.sam is empty" && exit 1
+
+echo "> Run featureCounts (without junctions)"
+"$meta_executable" \
+  --input "$dir_in/a.bam" \
+  --annotation "$dir_in/annotation.gtf" \
+  --counts "features.tsv" \
+  --summary "summary.tsv" \
+  --overlapping \
+  --frac_overlap 0.2 \
+  --paired \
+  --strand 0 \
+  --detailed_results detailed_results \
+  --detailed_results_format SAM
+
+echo ">> Checking output"
+[ ! -f "features.tsv" ] && echo "Output file features.tsv does not exist" && exit 1
+[ ! -f "summary.tsv" ] && echo "Output file summary.tsv does not exist" && exit 1
+[ ! -d "detailed_results" ] && echo "Output directory detailed_results does not exist" && exit 1
+[ ! -f "detailed_results/a.bam.featureCounts.sam" ] && echo "Output file detailed_results/a.bam.featureCounts.sam does not exist" && exit 1
+
+echo ">> Check if output is empty"
+[ ! -s "features.tsv" ] && echo "Output file features.tsv is empty" && exit 1
+[ ! -s "summary.tsv" ] && echo "Output file summary.tsv is empty" && exit 1
+[ ! -s "detailed_results/a.bam.featureCounts.sam" ] && echo "Output file detailed_results/a.bam.featureCounts.sam is empty" && exit 1
+
+echo "> Test successful"
--- a/src/featurecounts/test_data/a.bam
+++ b/src/featurecounts/test_data/a.bam
--- a/src/featurecounts/test_data/annotation.gtf
+++ b/src/featurecounts/test_data/annotation.gtf
@@ -0,0 +1,6 @@
+1	havana	gene	1	80	.	+	.	gene_id "ENSG00000000000"; gene_version "5"; gene_name "A"; gene_source "havana"; gene_biotype "gene";
+1	havana	transcript	1	80	.	+	.	gene_id "ENSG00000000000"; gene_version "5"; transcript_id "ENST00000000000"; transcript_version "2"; gene_name "A"; gene_source "havana"; gene_biotype "gene"; transcript_name "A-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; tag "basic"; transcript_support_level "1";
+1	havana	exon	1	80	.	+	.	gene_id "ENSG00000000000"; gene_version "5"; transcript_id "ENST00000000000"; transcript_version "2"; exon_number "1"; gene_name "A"; gene_source "havana"; gene_biotype "gene"; transcript_name "A-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00000000000"; exon_version "1"; tag "basic"; transcript_support_level "1";
+2	havana	gene	1	80	.	+	.	gene_id "ENSG00000000001"; gene_version "5"; gene_name "B"; gene_source "havana"; gene_biotype "gene";
+2	havana	transcript	1	80	.	+	.	gene_id "ENSG00000000001"; gene_version "5"; transcript_id "ENST00000000001"; transcript_version "2"; gene_name "B"; gene_source "havana"; gene_biotype "gene"; transcript_name "B-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; tag "basic"; transcript_support_level "1";
+2	havana	exon	1	80	.	+	.	gene_id "ENSG00000000001"; gene_version "5"; transcript_id "ENST00000000001"; transcript_version "2"; exon_number "1"; gene_name "B"; gene_source "havana"; gene_biotype "gene"; transcript_name "B-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00000000001"; exon_version "1"; tag "basic"; transcript_support_level "1";
--- a/src/featurecounts/test_data/genome.fasta
+++ b/src/featurecounts/test_data/genome.fasta
@@ -0,0 +1,4 @@
+>1
+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
+>2
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
--- a/src/featurecounts/test_data/script.sh
+++ b/src/featurecounts/test_data/script.sh
@@ -0,0 +1,9 @@
+# featureCounts test data
+
+# Test data was obtained from https://github.com/snakemake/snakemake-wrappers/tree/master/bio/subread/featurecounts/test
+
+if [ ! -d /tmp/snakemake-wrappers ]; then
+  git clone --depth 1 --single-branch --branch master https://github.com/snakemake/snakemake-wrappers /tmp/snakemake-wrappers
+fi
+
+cp -r /tmp/snakemake-wrappers/bio/subread/featurecounts/test/* src/subread/featurecounts/test_data
--- a/src/gffread/config.vsh.yaml
+++ b/src/gffread/config.vsh.yaml
@@ -0,0 +1,397 @@
+name: gffread
+description: Validate, filter, convert and perform various other operations on GFF files.
+keywords: [gff, conversion, validation, filtering]
+links:
+  homepage: https://ccb.jhu.edu/software/stringtie/gff.shtml#gffread
+  documentation: https://ccb.jhu.edu/software/stringtie/gff.shtml#gffread
+  repository: https://github.com/gpertea/gffread
+references: 
+  doi: 10.12688/f1000research.23297.2
+license: MIT
+authors:
+  - __merge__: /src/_authors/emma_rousseau.yaml
+    roles: [ author, maintainer ]
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: --input
+        type: file 
+        direction: input
+        description: |
+          A reference file in either the GFF3, GFF2 or GTF format.
+        required: true
+        example: annotation.gff
+      - name: --chr_mapping
+        alternatives: -m
+        type: file
+        direction: input
+        description: |
+          <chr_replace> is a name mapping table for converting reference sequence names, 
+          having this 2-column format: <original_ref_ID> <new_ref_ID>.
+      - name: --seq_info
+        alternatives: -s
+        type: file
+        direction: input
+        description: |
+          <seq_info.fsize> is a tab-delimited file providing this info for each of the mapped 
+          sequences: <seq-name> <seq-length> <seq-description> (useful for --description option with 
+          mRNA/EST/protein mappings).
+      - name: --genome
+        alternatives: -g
+        type: file
+        description: |
+          Full path to a multi-fasta file with the genomic sequences for all input mappings, 
+          OR a directory with single-fasta files (one per genomic sequence, with file names 
+          matching sequence names).
+        example: genome.fa
+  - name: Outputs
+    arguments:
+      - name: --outfile
+        alternatives: -o
+        type: file
+        direction: output
+        required: true
+        description: |
+          Write the output records into <outfile>.
+        example: output.gff
+      - name: --force_exons
+        type: boolean_true
+        description: |
+          Make sure that the lowest level GFF features are considered "exon" features.
+      - name: --gene2exon
+        type: boolean_true
+        description: |
+          For single-line genes not parenting any transcripts, add an exon feature spanning 
+          the entire gene (treat it as a transcript).
+      - name: --t_adopt
+        type: boolean_true
+        description: |
+          Try to find a parent gene overlapping/containing a transcript that does not have 
+          any explicit gene Parent.
+      - name: --decode
+        alternatives: -D
+        type: boolean_true
+        description: |
+          Decode url encoded characters within attributes.
+      - name: --merge_exons
+        alternatives: -Z
+        type: boolean_true
+        description: |
+          Merge very close exons into a single exon (when intron size<4).
+      - name: --junctions
+        alternatives: -j
+        type: boolean_true
+        description: |
+          Output the junctions and the corresponding transcripts.
+      - name: --spliced_exons
+        alternatives: -w
+        type: file
+        direction: output
+        must_exist: false
+        description: |
+          Write a fasta file with spliced exons for each transcript.
+        example: exons.fa
+      - name: --w_add
+        type: integer
+        description: |
+          For the --spliced_exons option, extract additional <N> bases both upstream and 
+          downstream of the transcript boundaries.
+      - name: --w_nocds
+        type: boolean_true
+        description: |
+          For --spliced_exons, disable the output of CDS info in the FASTA file.
+      - name: --spliced_cds
+        alternatives: -x
+        type: file
+        must_exist: false
+        example: cds.fa
+        description: |
+          Write a fasta file with spliced CDS for each GFF transcript.
+      - name: --tr_cds
+        alternatives: -y
+        type: file
+        must_exist: false
+        example: tr_cds.fa
+        description: |
+          Write a protein fasta file with the translation of CDS for each record.
+      - name: --w_coords
+        alternatives: -W
+        type: boolean_true
+        description: |
+          For --spliced_exons, --spliced_cds and -tr_cds options, write in the FASTA defline 
+          all the exon coordinates projected onto the spliced sequence.
+      - name: --stop_dot
+        alternatives: -S
+        type: boolean_true
+        description: |
+          For --tr_cds option, use '*' instead of '.' as stop codon translation.
+      - name: --id_version
+        alternatives: -L
+        type: boolean_true
+        description: |
+          Ensembl GTF to GFF3 conversion, adds version to IDs.
+      - name: --trackname
+        alternatives: -t
+        type: string
+        description: |
+          Use <trackname> in the 2nd column of each GFF/GTF output line.
+      - name: --gtf_output
+        alternatives: -T
+        type: boolean_true
+        description: |
+          Main output will be GTF instead of GFF3.
+      - name: --bed
+        type: boolean_true
+        description: |
+          Output records in BED format instead of default GFF3.
+      - name: --tlf
+        type: boolean_true
+        description: |
+          Output "transcript line format" which is like GFF but with exons and CDS related 
+          features stored as GFF attributes in the transcript feature line, like this:
+            exoncount=N;exons=<exons>;CDSphase=<N>;CDS=<CDScoords>
+          <exons> is a comma-delimited list of exon_start-exon_end coordinates;
+          <CDScoords> is CDS_start:CDS_end coordinates or a list like <exons>.
+      - name: --table
+        type: string
+        multiple: true
+        description: |
+          Output a simple tab delimited format instead of GFF, with columns having the values 
+          of GFF attributes given in <attrlist>; special pseudo-attributes (prefixed by @) are 
+          recognized:
+            @id, @geneid, @chr, @start, @end, @strand, @numexons, @exons, @cds, @covlen, @cdslen
+          If any of --spliced_exons/--tr_cds/--spliced_cds FASTA output files are enabled, the 
+          same fields (excluding @id) are appended to the definition line of corresponding FASTA
+          records.
+      - name: --expose_dups
+        type: boolean_true
+        alternatives: [-E, -v]
+        description: |
+          Expose (warn about) duplicate transcript IDs and other potential problems with the 
+          given GFF/GTF records.
+  - name: Options
+    arguments:
+      - name: --ids
+        type: file
+        description: |
+          Discard records/transcripts if their IDs are not listed in <IDs.lst>.
+      - name: --nids
+        type: file
+        description: |
+          Discard records/transcripts if their IDs are listed in <IDs.lst>.
+      - name: --maxintron
+        alternatives: -i
+        type: integer
+        description: |
+          Discard transcripts having an intron larger than <maxintron>.
+      - name: --minlen
+        alternatives: -l
+        type: integer
+        description: |
+          Discard transcripts shorter than <minlen> bases.
+      - name: --range
+        alternatives: -r
+        type: string
+        description: |
+          Only show transcripts overlapping coordinate range <start>..<end> (on chromosome/contig 
+          <chr>, strand <strand> if provided).
+      - name: --strict_range
+        alternatives: -R
+        type: boolean_true
+        description: |
+          For --range option, discard all transcripts that are not fully contained within the given 
+          range.
+      - name: --jmatch
+        type: string
+        description: |
+          Only output transcripts matching the given junction.
+      - name: --no_single_exon
+        alternatives: -U
+        type: boolean_true
+        description: |
+          Discard single-exon transcripts.
+      - name: --coding
+        alternatives: -C
+        type: boolean_true
+        description: |
+          Coding only: discard mRNAs that have no CDS features.
+      - name: --nc
+        type: boolean_true
+        description: |
+          Non-coding only: discard mRNAs that have CDS features.
+      - name: --ignore_locus
+        type: boolean_true
+        description: |
+          Discard locus features and attributes found in the input.
+      - name: --description
+        alternatives: -A
+        type: boolean_true
+        description: |
+          Use the description field from <seq_info.fsize> and add it as the value for a 'descr' 
+          attribute to the GFF record.
+
+  - name: Sorting
+    arguments:
+      - name: --sort_alpha
+        type: boolean_true
+        description: |
+          Chromosomes (reference sequences) are sorted alphabetically.
+      - name: --sort_by
+        type: file
+        must_exist: true
+        description: |
+          Sort the reference sequences by the order in which their names are given in the 
+          <refseq.lst> file.
+  - name: Misc options
+    arguments:
+      - name: --keep_attrs
+        alternatives: -F
+        type: boolean_true
+        description: |
+          Keep all GFF attributes (for non-exon features).
+      - name: --keep_exon_attrs
+        type: boolean_true
+        description: |
+          For -F option, do not attempt to reduce redundant exon/CDS attributes.
+      - name: --no_exon_attrs
+        alternatives: -G
+        type: boolean_true
+        description: |
+          Do not keep exon attributes, move them to the transcript feature (for GFF3 output).
+      - name: --attrs
+        type: string
+        description: |
+          Only output the GTF/GFF attributes listed in <attr-list> which is a comma delimited 
+          list of attribute names to.
+      - name: --keep_genes
+        type: boolean_true
+        description: |
+          In transcript-only mode (default), also preserve gene records.
+      - name: --keep_comments
+        type: boolean_true
+        description: |
+          For GFF3 input/output, try to preserve comments.
+      - name: --process_other
+        alternatives: -O
+        type: boolean_true
+        description: |
+          process other non-transcript GFF records (by default non-transcript records are ignored).
+      - name: --rm_stop_codons
+        alternatives: -V
+        type: boolean_true
+        description: |
+          Discard any mRNAs with CDS having in-frame stop codons (requires --genome).
+      - name: --adj_cds_start
+        alternatives: -H
+        type: boolean_true
+        description: |
+          For --rm_stop_codons option, check and adjust the starting CDS phase if the original phase
+          leads to a translation with an in-frame stop codon.
+      - name: --opposite_strand
+        alternatives: -B
+        type: boolean_true
+        description: |
+          For -V option, single-exon transcripts are also checked on the opposite strand (requires 
+          --genome).  
+      - name: --coding_status
+        alternatives: -P
+        type: boolean_true
+        description: |
+          Add transcript level GFF attributes about the coding status of each transcript, including 
+          partialness or in-frame stop codons (requires --genome).
+      - name: --add_hasCDS
+        type: boolean_true
+        description: |
+          Add a "hasCDS" attribute with value "true" for transcripts that have CDS features. 
+      - name: --adj_stop
+        type: boolean_true
+        description: |
+          Stop codon adjustment: enables --coding_status and performs automatic adjustment of the CDS stop 
+          coordinate if premature or downstream.
+      - name: --rm_noncanon
+        alternatives: -N
+        type: boolean_true
+        description: |
+          Discard multi-exon mRNAs that have any intron with a non-canonical splice site consensus 
+          (i.e. not GT-AG, GC-AG or AT-AC).
+      - name: --complete_cds
+        alternatives: -J
+        type: boolean_true
+        description: |
+          Discard any mRNAs that either lack initial START codon or the terminal STOP codon, or 
+          have an in-frame stop codon (i.e. only print mRNAs with a complete CDS).
+      - name: --no_pseudo
+        type: boolean_true
+        description: |
+          Filter out records matching the 'pseudo' keyword.
+      - name: --in_bed
+        type: boolean_true
+        description: |
+          Input should be parsed as BED format (automatic if the input filename ends with .bed*).
+      - name: --in_tlf
+        type: boolean_true
+        description: |
+          Input GFF-like one-line-per-transcript format without exon/CDS features (see --tlf option 
+          below); automatic if the input filename ends with .tlf).
+      - name: --stream
+        type: boolean_true
+        description: |
+          Fast processing of input GFF/BED transcripts as they are received (no sorting, exons must 
+          be grouped by transcript in the input data).
+
+  - name: Clustering
+    arguments:
+      - name: --merge
+        alternatives: -M
+        type: boolean_true
+        description: |
+          Cluster the input transcripts into loci, discarding "redundant" transcripts (those with 
+          the same exact introns and fully contained or equal boundaries).
+      - name: --dupinfo
+        alternatives: -d
+        type: file
+        description: |
+          For --merge option, write duplication info to file <dupinfo>.
+      - name: --cluster_only
+        type: boolean_true
+        description: |
+          Same as --merge but without discarding any of the "duplicate" transcripts, only create 
+          "locus" features.
+      - name: --rm_redundant
+        alternatives: -K
+        type: boolean_true
+        description: |
+          For --merge option: also discard as redundant the shorter, fully contained transcripts (intron 
+          chains matching a part of the container).
+      - name: --no_boundary
+        alternatives: -Q
+        type: boolean_true
+        description: |
+          For --merge option, no longer require boundary containment when assessing redundancy (can be 
+          combined with --rm_redundant); only introns have to match for multi-exon transcripts, and >=80%
+          overlap for single-exon transcripts.
+      - name: --no_overlap
+        alternatives: -Y
+        type: boolean_true
+        description: |
+          For --merge option, enforce --no_boundary but also discard overlapping single-exon transcripts,
+          even on the opposite strand (can be combined with --rm_redudant).
+
+resources:
+  - type: bash_script
+    path: script.sh
+test_resources:
+  - type: bash_script
+    path: test.sh
+  - type: file
+    path: test_data
+engines:
+- type: docker
+  image: quay.io/biocontainers/gffread:0.12.7--hdcf5f25_3
+  setup:
+    - type: docker
+      run: |
+        echo "gffread: \"$(gffread --version 2>&1)\"" > /var/software_versions.txt
+runners:
+- type: executable
+- type: nextflow
--- a/src/gffread/help.txt
+++ b/src/gffread/help.txt
@@ -0,0 +1,140 @@
+```sh
+gffread --help
+```
+
+gffread v0.12.7. Usage:
+gffread [-g <genomic_seqs_fasta> | <dir>] [-s <seq_info.fsize>] 
+ [-o <outfile>] [-t <trackname>] [-r [<strand>]<chr>:<start>-<end> [-R]]
+ [--jmatch <chr>:<start>-<end>] [--no-pseudo] 
+ [-CTVNJMKQAFPGUBHZWTOLE] [-w <exons.fa>] [-x <cds.fa>] [-y <tr_cds.fa>]
+ [-j ][--ids <IDs.lst> | --nids <IDs.lst>] [--attrs <attr-list>] [-i <maxintron>]
+ [--stream] [--bed | --gtf | --tlf] [--table <attrlist>] [--sort-by <ref.lst>]
+ [<input_gff>] 
+
+ Filter, convert or cluster GFF/GTF/BED records, extract the sequence of
+ transcripts (exon or CDS) and more.
+ By default (i.e. without -O) only transcripts are processed, discarding any
+ other non-transcript features. Default output is a simplified GFF3 with only
+ the basic attributes.
+ 
+Options:
+ --ids discard records/transcripts if their IDs are not listed in <IDs.lst>
+ --nids discard records/transcripts if their IDs are listed in <IDs.lst>
+ -i   discard transcripts having an intron larger than <maxintron>
+ -l   discard transcripts shorter than <minlen> bases
+ -r   only show transcripts overlapping coordinate range <start>..<end>
+      (on chromosome/contig <chr>, strand <strand> if provided)
+ -R   for -r option, discard all transcripts that are not fully 
+      contained within the given range
+ --jmatch only output transcripts matching the given junction
+ -U   discard single-exon transcripts
+ -C   coding only: discard mRNAs that have no CDS features
+ --nc non-coding only: discard mRNAs that have CDS features
+ --ignore-locus : discard locus features and attributes found in the input
+ -A   use the description field from <seq_info.fsize> and add it
+      as the value for a 'descr' attribute to the GFF record
+ -s   <seq_info.fsize> is a tab-delimited file providing this info
+      for each of the mapped sequences:
+      <seq-name> <seq-length> <seq-description>
+      (useful for -A option with mRNA/EST/protein mappings)
+Sorting: (by default, chromosomes are kept in the order they were found)
+ --sort-alpha : chromosomes (reference sequences) are sorted alphabetically
+ --sort-by : sort the reference sequences by the order in which their
+      names are given in the <refseq.lst> file
+Misc options: 
+ -F   keep all GFF attributes (for non-exon features)
+ --keep-exon-attrs : for -F option, do not attempt to reduce redundant
+      exon/CDS attributes
+ -G   do not keep exon attributes, move them to the transcript feature
+      (for GFF3 output)
+ --attrs <attr-list> only output the GTF/GFF attributes listed in <attr-list>
+    which is a comma delimited list of attribute names to
+ --keep-genes : in transcript-only mode (default), also preserve gene records
+ --keep-comments: for GFF3 input/output, try to preserve comments
+ -O   process other non-transcript GFF records (by default non-transcript
+      records are ignored)
+ -V   discard any mRNAs with CDS having in-frame stop codons (requires -g)
+ -H   for -V option, check and adjust the starting CDS phase
+      if the original phase leads to a translation with an 
+      in-frame stop codon
+ -B   for -V option, single-exon transcripts are also checked on the
+      opposite strand (requires -g)
+ -P   add transcript level GFF attributes about the coding status of each
+      transcript, including partialness or in-frame stop codons (requires -g)
+ --add-hasCDS : add a "hasCDS" attribute with value "true" for transcripts
+      that have CDS features
+ --adj-stop stop codon adjustment: enables -P and performs automatic
+      adjustment of the CDS stop coordinate if premature or downstream
+ -N   discard multi-exon mRNAs that have any intron with a non-canonical
+      splice site consensus (i.e. not GT-AG, GC-AG or AT-AC)
+ -J   discard any mRNAs that either lack initial START codon
+      or the terminal STOP codon, or have an in-frame stop codon
+      (i.e. only print mRNAs with a complete CDS)
+ --no-pseudo: filter out records matching the 'pseudo' keyword
+ --in-bed: input should be parsed as BED format (automatic if the input
+           filename ends with .bed*)
+ --in-tlf: input GFF-like one-line-per-transcript format without exon/CDS
+           features (see --tlf option below); automatic if the input
+           filename ends with .tlf)
+ --stream: fast processing of input GFF/BED transcripts as they are received
+           ((no sorting, exons must be grouped by transcript in the input data)
+Clustering:
+ -M/--merge : cluster the input transcripts into loci, discarding
+      "redundant" transcripts (those with the same exact introns
+      and fully contained or equal boundaries)
+ -d <dupinfo> : for -M option, write duplication info to file <dupinfo>
+ --cluster-only: same as -M/--merge but without discarding any of the
+      "duplicate" transcripts, only create "locus" features
+ -K   for -M option: also discard as redundant the shorter, fully contained
+       transcripts (intron chains matching a part of the container)
+ -Q   for -M option, no longer require boundary containment when assessing
+      redundancy (can be combined with -K); only introns have to match for
+      multi-exon transcripts, and >=80% overlap for single-exon transcripts
+ -Y   for -M option, enforce -Q but also discard overlapping single-exon 
+      transcripts, even on the opposite strand (can be combined with -K)
+Output options:
+ --force-exons: make sure that the lowest level GFF features are considered
+       "exon" features
+ --gene2exon: for single-line genes not parenting any transcripts, add an
+       exon feature spanning the entire gene (treat it as a transcript)
+ --t-adopt:  try to find a parent gene overlapping/containing a transcript
+       that does not have any explicit gene Parent
+ -D    decode url encoded characters within attributes
+ -Z    merge very close exons into a single exon (when intron size<4)
+ -g   full path to a multi-fasta file with the genomic sequences
+      for all input mappings, OR a directory with single-fasta files
+      (one per genomic sequence, with file names matching sequence names)
+ -j    output the junctions and the corresponding transcripts
+ -w    write a fasta file with spliced exons for each transcript
+ --w-add <N> for the -w option, extract additional <N> bases
+       both upstream and downstream of the transcript boundaries
+ --w-nocds for -w, disable the output of CDS info in the FASTA file
+ -x    write a fasta file with spliced CDS for each GFF transcript
+ -y    write a protein fasta file with the translation of CDS for each record
+ -W    for -w, -x and -y options, write in the FASTA defline all the exon
+       coordinates projected onto the spliced sequence;
+ -S    for -y option, use '*' instead of '.' as stop codon translation
+ -L    Ensembl GTF to GFF3 conversion, adds version to IDs
+ -m    <chr_replace> is a name mapping table for converting reference 
+       sequence names, having this 2-column format:
+       <original_ref_ID> <new_ref_ID>
+ -t    use <trackname> in the 2nd column of each GFF/GTF output line
+ -o    write the output records into <outfile> instead of stdout
+ -T    main output will be GTF instead of GFF3
+ --bed output records in BED format instead of default GFF3
+ --tlf output "transcript line format" which is like GFF
+       but with exons and CDS related features stored as GFF 
+       attributes in the transcript feature line, like this:
+         exoncount=N;exons=<exons>;CDSphase=<N>;CDS=<CDScoords> 
+       <exons> is a comma-delimited list of exon_start-exon_end coordinates;
+       <CDScoords> is CDS_start:CDS_end coordinates or a list like <exons>
+ --table output a simple tab delimited format instead of GFF, with columns
+       having the values of GFF attributes given in <attrlist>; special
+       pseudo-attributes (prefixed by @) are recognized:
+       @id, @geneid, @chr, @start, @end, @strand, @numexons, @exons, 
+       @cds, @covlen, @cdslen
+       If any of -w/-y/-x FASTA output files are enabled, the same fields
+       (excluding @id) are appended to the definition line of corresponding
+       FASTA records
+ -v,-E expose (warn about) duplicate transcript IDs and other potential
+       problems with the given GFF/GTF records
--- a/src/gffread/script.sh
+++ b/src/gffread/script.sh
@@ -0,0 +1,121 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+# unset flags
+[[ "$par_coding" == "false" ]] && unset par_coding
+[[ "$par_strict_range" == "false" ]] && unset par_strict_range
+[[ "$par_no_single_exon" == "false" ]] && unset par_no_single_exon
+[[ "$par_no_exon_attrs" == "false" ]] && unset par_no_exon_attrs
+[[ "$par_nc" == "false" ]] && unset par_nc
+[[ "$par_ignore_locus" == "false" ]] && unset par_ignore_locus
+[[ "$par_description" == "false" ]] && unset par_description
+[[ "$par_sort_alpha" == "false" ]] && unset par_sort_alpha
+[[ "$par_keep_genes" == "false" ]] && unset par_keep_genes
+[[ "$par_keep_attrs" == "false" ]] && unset par_keep_attrs
+[[ "$par_keep_exon_attrs" == "false" ]] && unset par_keep_exon_attrs
+[[ "$par_keep_comments" == "false" ]] && unset par_keep_comments
+[[ "$par_process_other" == "false" ]] && unset par_process_other
+[[ "$par_rm_stop_codons" == "false" ]] && unset par_rm_stop_codons
+[[ "$par_adj_cds_start" == "false" ]] && unset par_adj_cds_start
+[[ "$par_opposite_strand" == "false" ]] && unset par_opposite_strand
+[[ "$par_coding_status" == "false" ]] && unset par_coding_status
+[[ "$par_add_hasCDS" == "false" ]] && unset par_add_hasCDS
+[[ "$par_adj_stop" == "false" ]] && unset par_adj_stop
+[[ "$par_rm_noncanon" == "false" ]] && unset par_rm_noncanon
+[[ "$par_complete_cds" == "false" ]] && unset par_complete_cds
+[[ "$par_no_pseudo" == "false" ]] && unset par_no_pseudo
+[[ "$par_in_bed" == "false" ]] && unset par_in_bed
+[[ "$par_in_tlf" == "false" ]] && unset par_in_tlf
+[[ "$par_stream" == "false" ]] && unset par_stream
+[[ "$par_merge" == "false" ]] && unset par_merge
+[[ "$par_rm_redundant" == "false" ]] && unset par_rm_redundant
+[[ "$par_no_boundary" == "false" ]] && unset par_no_boundary
+[[ "$par_no_overlap" == "false" ]] && unset par_no_overlap
+[[ "$par_force_exons" == "false" ]] && unset par_force_exons
+[[ "$par_gene2exon" == "false" ]] && unset par_gene2exon
+[[ "$par_t_adopt" == "false" ]] && unset par_t_adopt
+[[ "$par_decode" == "false" ]] && unset par_decode
+[[ "$par_merge_exons" == "false" ]] && unset par_merge_exons
+[[ "$par_junctions" == "false" ]] && unset par_junctions
+[[ "$par_w_nocds" == "false" ]] && unset par_w_nocds
+[[ "$par_tr_cds" == "false" ]] && unset par_tr_cds
+[[ "$par_w_coords" == "false" ]] && unset par_w_coords
+[[ "$par_stop_dot" == "false" ]] && unset par_stop_dot
+[[ "$par_id_version" == "false" ]] && unset par_id_version
+[[ "$par_gtf_output" == "false" ]] && unset par_gtf_output
+[[ "$par_bed" == "false" ]] && unset par_bed
+[[ "$par_tlf" == "false" ]] && unset par_tlf
+[[ "$par_expose_dups" == "false" ]] && unset par_expose_dups
+[[ "$par_cluster_only" == "false" ]] && unset par_cluster_only
+
+# if par_table is not empty, replace ";" with ","
+par_table=$(echo "$par_table" | tr ';' ',')
+
+$(which gffread) \
+    "$par_input" \
+    ${par_chr_mapping:+-m "$par_chr_mapping"} \
+    ${par_seq_info:+-s "$par_seq_info"} \
+    -o "$par_outfile" \
+    ${par_force_exons:+--force-exons} \
+    ${par_gene2exon:+--gene2exon} \
+    ${par_t_adopt:+--t-adopt} \
+    ${par_decode:+-D} \
+    ${par_merge_exons:+-Z} \
+    ${par_genome:+-g "$par_genome"} \
+    ${par_junctions:+-j} \
+    ${par_spliced_exons:+-w "$par_spliced_exons"} \
+    ${par_w_add:+--w-add "$par_w_add"} \
+    ${par_w_nocds:+--w-nocds} \
+    ${par_spliced_cds:+-x "$par_spliced_cds"} \
+    ${par_tr_cds:+-y "$par_tr_cds"} \
+    ${par_w_coords:+-W} \
+    ${par_stop_dot:+-S} \
+    ${par_id_version:+-L} \
+    ${par_trackname:+-t "$par_trackname"} \
+    ${par_gtf_output:+-T} \
+    ${par_bed:+--bed} \
+    ${par_tlf:+--tlf} \
+    ${par_table:+--table "$par_table"} \
+    ${par_expose_dups:+-E} \
+    ${par_ids:+--ids "$par_ids"} \
+    ${par_nids:+--nids "$par_nids"} \
+    ${par_maxintron:+-i "$par_maxintron"} \
+    ${par_minlen:+-l "$par_minlen"} \
+    ${par_range:+-r "$par_range"} \
+    ${par_strict_range:+-R} \
+    ${par_jmatch:+--jmatch "$par_jmatch"} \
+    ${par_no_single_exon:+-U} \
+    ${par_coding:+-C} \
+    ${par_nc:+--nc} \
+    ${par_ignore_locus:+--ignore-locus} \
+    ${par_description:+-A} \
+    ${par_sort_alpha:+--sort-alpha} \
+    ${par_sort_by:+--sort-by "$par_sort_by"} \
+    ${par_keep_attrs:+-F} \
+    ${par_keep_exon_attrs:+--keep-exon-attrs} \
+    ${par_no_exon_attrs:+-G} \
+    ${par_attrs:+--attrs "$par_attrs"} \
+    ${par_keep_genes:+--keep-genes} \
+    ${par_keep_comments:+--keep-comments} \
+    ${par_process_other:+-O} \
+    ${par_rm_stop_codons:+-V} \
+    ${par_adj_cds_start:+-H} \
+    ${par_opposite_strand:+-B} \
+    ${par_coding_status:+-P} \
+    ${par_add_hasCDS:+--add-hasCDS} \
+    ${par_adj_stop:+--adj-stop} \
+    ${par_rm_noncanon:+-N} \
+    ${par_complete_cds:+-J} \
+    ${par_no_pseudo:+--no-pseudo} \
+    ${par_in_bed:+--in-bed} \
+    ${par_in_tlf:+--in-tlf} \
+    ${par_stream:+--stream} \
+    ${par_merge:+-M} \
+    ${par_dupinfo:+-d "$par_dupinfo"} \
+    ${par_cluster_only:+--cluster-only} \
+    ${par_rm_redundant:+-K} \
+    ${par_no_boundary:+-Q} \
+    ${par_no_overlap:+-Y} 
+
--- a/src/gffread/test.sh
+++ b/src/gffread/test.sh
@@ -0,0 +1,111 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+set -e
+
+test_output_dir="${meta_resources_dir}/test_data/test_output"
+test_dir="${meta_resources_dir}/test_data"
+expected_output_dir="${meta_resources_dir}/test_data/output"
+
+mkdir -p "$test_output_dir"
+
+
+################################################################################
+
+echo "> Test 1 - Read annotation file, output GFF" 
+
+"$meta_executable" \
+  --expose_dups \
+  --outfile "$test_output_dir/ann_simple.gff" \
+  --input "$test_dir/sequence.gff3" 
+ 
+
+echo ">> Check if output exists"
+[ ! -f "$test_output_dir/ann_simple.gff" ] \
+    && echo "Output file test_output/ann_simple.gff does not exist" && exit 1
+
+echo ">> Check if output is empty"
+[ ! -s "$test_output_dir/ann_simple.gff" ] \
+    && echo "Output file test_output/ann_simple.gff is empty" && exit 1
+
+echo ">> Compare output to expected output"
+
+# compare file expect lines starting with "#"
+diff <(grep -v "^#" "$expected_output_dir/ann_simple.gff") \
+    <(grep -v "^#" "$test_output_dir/ann_simple.gff") || \
+    (echo "Output file ann_simple.gff does not match expected output" && exit 1)
+
+################################################################################
+
+echo "> Test 2 - Read annotation file, output GTF"
+
+"$meta_executable" \
+  --gtf_output \
+  --outfile "$test_output_dir/annotation.gtf" \
+  --input "$test_dir/sequence.gff3"
+
+echo ">> Check if output exists"
+[ ! -f "$test_output_dir/annotation.gtf" ] \
+    && echo "Output file test_output/annotation.gtf does not exist" && exit 1
+
+echo ">> Check if output is empty"
+[ ! -s "$test_output_dir/annotation.gtf" ] \
+    && echo "Output file test_output/annotation.gtf is empty" && exit 1
+
+echo ">> Compare output to expected output"
+diff "$expected_output_dir/annotation.gtf" "$test_output_dir/annotation.gtf" || \
+    (echo "Output file annotation.gtf does not match expected output" && exit 1)
+
+################################################################################
+
+echo "> Test 3 - Generate fasta file from annotation file"
+
+
+"$meta_executable" \
+  --genome "$test_dir/sequence.fasta" \
+  --spliced_exons "$test_output_dir/transcripts.fa" \
+  --outfile "$test_output_dir/output.gff" \
+  --input "$test_dir/sequence.gff3"
+
+echo ">> Check if output exists"
+[ ! -f "$test_output_dir/transcripts.fa" ] \
+    && echo "Output file transcripts.fa does not exist" && exit 1
+
+echo ">> Check if output is empty"
+[ ! -s "$test_output_dir/transcripts.fa" ] \
+    && echo "Output file transcripts.fa is empty" && exit 1
+
+echo ">> Compare output to expected output"
+diff "$expected_output_dir/transcripts.fa" "$test_output_dir/transcripts.fa" || \
+    (echo "Output file transcripts.fa does not match expected output" && exit 1)
+
+################################################################################
+
+echo "> Test 4 - Generate table from GFF annotation file"
+
+"$meta_executable" \
+  --table "@id;@chr;@start;@end;@strand;@exons;Name;gene;product" \
+  --outfile "$test_output_dir/annotation.tbl" \
+  --input "$test_dir/sequence.gff3"
+
+echo ">> Check if output exists"
+[ ! -f "$test_output_dir/annotation.tbl" ] \
+    && echo "Output file test_output/annotation.tbl does not exist" && exit 1
+
+echo ">> Check if output is empty"
+[ ! -s "$test_output_dir/annotation.tbl" ] \
+    && echo "Output file test_output/annotation.tbl is empty" && exit 1
+
+echo ">> Compare output to expected output"
+diff "$expected_output_dir/annotation.tbl" "$test_output_dir/annotation.tbl" || \
+    (echo "Output file annotation.tbl does not match expected output" && exit 1)
+
+################################################################################
+
+rm -r "$test_output_dir"
+
+echo "> All tests successful"
+
+exit 0
--- a/src/gffread/test_data/README.md
+++ b/src/gffread/test_data/README.md
@@ -0,0 +1,38 @@
+## GffRead usage examples
+
+GffRead can be used to simply read an annotation file in a GFF format, and print it in either GFF3 (default) or 
+GTF2 format (with the -T option), while discarding any non-trasncript features and optional attributes. 
+It can also report some potential issues found in the input GFF records. The command line for such a quick GFF/GTF 
+file cleanup would be:
+```
+gffread -E annotation.gff -o ann_simple.gff
+```
+
+This will create a minimalist GFF3 re-formatting of the transcript records found in the input file (`annotation.gff` in this example). 
+The -E option directs GffRead to "expose" (display warnings about) any potential formatting issues 
+encountered while parsing the input file.
+
+In order to obtain the GTF2 version of the same transcript records, the `-T` option should be added:
+```
+gffread annotation.gff -T -o annotation.gtf
+```
+
+GffRead can be used to generate a FASTA file with the DNA sequences for all transcripts in a GFF file. For this operation 
+a fasta file with the genomic sequences has to be provided as well. This can be accomplished with a command line like this:
+```
+gffread -w transcripts.fa -g genome.fa annotation.gff
+```
+The file `genome.fa` in this example would be a multi-fasta file with the chromosome/contig sequences of the target genome. 
+This also requires that every contig or chromosome name found in the 1st column of the input GFF file 
+(`annotation.gff` in this example) must have a corresponding sequence entry in the `genome.fa` file.
+
+
+```
+gffread --table @id,@chr,@start,@end,@strand,@exons,Name,gene,product \
+  -o annotation.tbl annotation.gff
+```
+This shows how the `--table` option can make a tab delimited table out of a GFF3 input.
+
+The `output` directory contains all the output files that should be generated by the above examples.
+
+
--- a/Show More
+++ b/Show More