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2024-09-19 09:34:06 +00:00
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commit 46b841830c
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32
CHANGELOG.md
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@@ -1,5 +1,20 @@
# biobox x.x.x
## NEW FUNCTIONALITY
* `agat`:
- `agat/agat_convert_genscan2gff`: convert a genscan file into a GFF file (PR #100).
* `bd_rhapsody/bd_rhapsody_sequence_analysis`: BD Rhapsody Sequence Analysis CWL pipeline (PR #96).
* `rsem/rsem_calculate_expression`: Calculate expression levels (PR #93).
## MINOR CHANGES
* Upgrade to Viash 0.9.0.
# biobox 0.2.0
## BREAKING CHANGES
* `star/star_align_reads`: Change all arguments from `--camelCase` to `--snake_case` (PR #62).
@@ -50,6 +65,16 @@
* `fastqc`: High throughput sequence quality control analysis tool (PR #92).
* `sortmerna`: Local sequence alignment tool for mapping, clustering, and filtering rRNA from
metatranscriptomic data (PR #146).
* `fq_subsample`: Sample a subset of records from single or paired FASTQ files (PR #147).
* `kallisto`:
- `kallisto_index`: Create a kallisto index (PR #149).
- `kallisto_quant`: Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads (PR #152).
* `trimgalore`: Quality and adapter trimming for fastq files (PR #117).
## MINOR CHANGES
@@ -139,7 +164,8 @@
- `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).
- `umi_tools/umi_tools_extract`: Flexible removal of UMI sequences from fastq reads (PR #71).
- `umi_tools/umi_tools_prepareforrsem`: Fix paired-end reads in name sorted BAM file to prepare for RSEM (PR #148).
* `falco`: A C++ drop-in replacement of FastQC to assess the quality of sequence read data (PR #43).
@@ -147,10 +173,8 @@
- `bedtools_getfasta`: extract sequences from a FASTA file for each of the
intervals defined in a BED/GFF/VCF file (PR #59).
* `sortmerna`: Local sequence alignment tool for mapping, clustering, and filtering rRNA from metatranscriptomic
data. (PR #146)
* `fq_subsample`: Sample a subset of records from single or paired FASTQ files (PR #147).
## MINOR CHANGES

2
_viash.yaml
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@@ -7,7 +7,7 @@ links:
issue_tracker: https://github.com/viash-hub/biobox/issues
repository: https://github.com/viash-hub/biobox
viash_version: 0.9.0-RC7
viash_version: 0.9.0
config_mods: |
.requirements.commands := ['ps']

95
src/agat/agat_convert_genscan2gff/config.vsh.yaml Normal file
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@@ -0,0 +1,95 @@
name: agat_convert_genscan2gff
namespace: agat
description: |
The script takes a GENSCAN file as input, and will translate it in gff
format. The GENSCAN format is described [here](http://genome.crg.es/courses/Bioinformatics2003_genefinding/results/genscan.html).
**Known problem**
You must have submited only DNA sequence, without any header!! Indeed the tool expects only DNA
sequences and does not crash/warn if an header is submited along the
sequence. e.g If you have an header ">seq" s-e-q are seen as the 3 first
nucleotides of the sequence. Then all prediction location are shifted
accordingly. (checked only on the [online version](http://argonaute.mit.edu/GENSCAN.html).
I don't know if there is the same problem elsewhere.)
keywords: [gene annotations, GFF conversion, GENSCAN]
links:
homepage: https://github.com/NBISweden/AGAT
documentation: https://agat.readthedocs.io/en/latest/tools/agat_convert_genscan2gff.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
requirements:
- commands: [agat]
authors:
- __merge__: /src/_authors/leila_paquay.yaml
roles: [ author, maintainer ]
argument_groups:
- name: Inputs
arguments:
- name: --genscan
alternatives: [-g]
description: Input genscan bed file that will be converted.
type: file
required: true
direction: input
- name: Outputs
arguments:
- name: --output
alternatives: [-o, --out, --outfile, --gff]
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: --source
description: |
The source informs about the tool used to produce the data and is stored in 2nd field of a gff file. Example: Stringtie, Maker, Augustus, etc. [default: data]
type: string
required: false
example: Stringtie
- name: --primary_tag
description: |
The primary_tag corresponds to the data type and is stored in 3rd field of a gff file. Example: gene, mRNA, CDS, etc. [default: gene]
type: string
required: false
example: gene
- name: --inflate_type
description: |
Feature type (3rd column in gff) created when inflate parameter activated [default: exon].
type: string
required: false
example: exon
- name: --verbose
description: add verbosity
type: boolean_true
- name: --config
alternatives: [-c]
description: |
AGAT config file. By default AGAT takes the original agat_config.yaml shipped with AGAT. 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

94
src/agat/agat_convert_genscan2gff/help.txt Normal file
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@@ -0,0 +1,94 @@
```sh
agat_convert_genscan2gff.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_genscan2gff.pl
Description:
The script takes a genscan file as input, and will translate it in gff
format. The genscan format is described here:
http://genome.crg.es/courses/Bioinformatics2003_genefinding/results/gens
can.html /!\ vvv Known problem vvv /!\ You must have submited only DNA
sequence, wihtout any header!! Indeed the tool expects only DNA
sequences and does not crash/warn if an header is submited along the
sequence. e.g If you have an header ">seq" s-e-q are seen as the 3 first
nucleotides of the sequence. Then all prediction location are shifted
accordingly. (checked only on the online version
http://argonaute.mit.edu/GENSCAN.html. I don't know if there is the same
pronlem elsewhere.) /!\ ^^^ Known problem ^^^^ /!\
Usage:
agat_convert_genscan2gff.pl --genscan infile.bed [ -o outfile ]
agat_convert_genscan2gff.pl -h
Options:
--genscan or -g
Input genscan bed file that will be convert.
--source
The source informs about the tool used to produce the data and
is stored in 2nd field of a gff file. Example:
Stringtie,Maker,Augustus,etc. [default: data]
--primary_tag
The primary_tag corresponf to the data type and is stored in 3rd
field of a gff file. Example: gene,mRNA,CDS,etc. [default: gene]
--inflate_off
By default we inflate the block fields (blockCount, blockSizes,
blockStarts) to create subfeatures of the main feature
(primary_tag). Type of subfeature created based on the
inflate_type parameter. If you don't want this inflating
behaviour you can deactivate it by using the option
--inflate_off.
--inflate_type
Feature type (3rd column in gff) created when inflate parameter
activated [default: exon].
--verbose
add verbosity
-o , --output , --out , --outfile or --gff
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

21
src/agat/agat_convert_genscan2gff/script.sh Normal file
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@@ -0,0 +1,21 @@
#!/bin/bash
set -eo pipefail
## VIASH START
## VIASH END
# unset flags
[[ "$par_inflate_off" == "true" ]] && unset par_inflate_off
[[ "$par_verbose" == "false" ]] && unset par_verbose
# run agat_convert_genscan2gff
agat_convert_genscan2gff.pl \
--genscan "$par_genscan" \
--output "$par_output" \
${par_source:+--source "${par_source}"} \
${par_primary_tag:+--primary_tag "${par_primary_tag}"} \
${par_inflate_off:+--inflate_off} \
${par_inflate_type:+--inflate_type "${par_inflate_type}"} \
${par_verbose:+--verbose} \
${par_config:+--config "${par_config}"}

35
src/agat/agat_convert_genscan2gff/test.sh Normal file
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@@ -0,0 +1,35 @@
#!/bin/bash
set -eo pipefail
## VIASH START
## VIASH END
test_dir="${meta_resources_dir}/test_data"
# create temporary directory and clean up on exit
TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_name-XXXXXX")
function clean_up {
[[ -d "$TMPDIR" ]] && rm -rf "$TMPDIR"
}
trap clean_up EXIT
echo "> Run $meta_name with test data"
"$meta_executable" \
--genscan "$test_dir/test.genscan" \
--output "$TMPDIR/output.gff"
echo ">> Checking output"
[ ! -f "$TMPDIR/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
echo ">> Check if output is empty"
[ ! -s "$TMPDIR/output.gff" ] && echo "Output file output.gff is empty" && exit 1
echo ">> Check if output matches expected output"
diff "$TMPDIR/output.gff" "$test_dir/agat_convert_genscan2gff_1.gff"
if [ $? -ne 0 ]; then
echo "Output file output.gff does not match expected output"
exit 1
fi
echo "> Test successful"

25
src/agat/agat_convert_genscan2gff/test_data/agat_convert_genscan2gff_1.gff Normal file
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@@ -0,0 +1,25 @@
##gff-version 3
unknown genscan gene 2223 4605 75.25 + . ID=gene_1
unknown genscan mRNA 2223 4605 75.25 + . ID=mrna_1;Parent=gene_1
unknown genscan exon 2223 3020 75.25 + . ID=exon_1;Parent=mrna_1
unknown genscan exon 4249 4605 13.03 + . ID=exon_2;Parent=mrna_1
unknown genscan CDS 2223 3020 75.25 + 0 ID=cds_1;Parent=mrna_1
unknown genscan CDS 4249 4605 13.03 + 0 ID=cds_2;Parent=mrna_1
unknown genscan gene 6829 8789 20.06 - . ID=gene_2
unknown genscan mRNA 6829 8789 20.06 - . ID=mrna_2;Parent=gene_2
unknown genscan exon 6829 7297 20.06 - . ID=exon_3;Parent=mrna_2
unknown genscan exon 7730 7888 12.78 - . ID=exon_4;Parent=mrna_2
unknown genscan exon 8029 8185 7.45 - . ID=exon_5;Parent=mrna_2
unknown genscan exon 8278 8546 17.45 - . ID=exon_6;Parent=mrna_2
unknown genscan exon 8647 8789 18.65 - . ID=exon_7;Parent=mrna_2
unknown genscan CDS 6829 7297 20.06 - 1 ID=cds_3;Parent=mrna_2
unknown genscan CDS 7730 7888 12.78 - 1 ID=cds_4;Parent=mrna_2
unknown genscan CDS 8029 8185 7.45 - 2 ID=cds_5;Parent=mrna_2
unknown genscan CDS 8278 8546 17.45 - 1 ID=cds_6;Parent=mrna_2
unknown genscan CDS 8647 8789 18.65 - 0 ID=cds_7;Parent=mrna_2
unknown genscan gene 10209 11924 16.18 + . ID=gene_3
unknown genscan mRNA 10209 11924 16.18 + . ID=mrna_3;Parent=gene_3
unknown genscan exon 10209 11313 16.18 + . ID=exon_8;Parent=mrna_3
unknown genscan exon 11850 11924 3.27 + . ID=exon_9;Parent=mrna_3
unknown genscan CDS 10209 11313 16.18 + 0 ID=cds_8;Parent=mrna_3
unknown genscan CDS 11850 11924 3.27 + 2 ID=cds_9;Parent=mrna_3

11
src/agat/agat_convert_genscan2gff/test_data/script.sh Executable file
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@@ -0,0 +1,11 @@
#!/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/in/test.genscan src/agat/agat_convert_genscan2gff/test_data/test.genscan
cp -r /tmp/agat_source/t/scripts_output/out/agat_convert_genscan2gff_1.gff src/agat/agat_convert_genscan2gff/test_data/agat_convert_genscan2gff_1.gff

127
src/agat/agat_convert_genscan2gff/test_data/test.genscan Normal file
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@@ -0,0 +1,127 @@
GENSCAN 1.0 Date run: 7-Mar-120 Time: 14:46:49
Sequence /tmp/03_07_20-14:46:49.fasta : 12217 bp : 42.83% C+G : Isochore 1 ( 0 - 43 C+G%)
Parameter matrix: HumanIso.smat
Predicted genes/exons:
Gn.Ex Type S .Begin ...End .Len Fr Ph I/Ac Do/T CodRg P.... Tscr..
----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------
1.01 Init + 2223 3020 798 2 0 55 2 924 0.940 75.25
1.02 Term + 4249 4605 357 0 0 26 38 307 0.976 13.03
1.03 PlyA + 4711 4716 6 -0.45
2.06 PlyA - 4852 4847 6 -0.45
2.05 Term - 7297 6829 469 0 1 13 42 387 0.281 20.06
2.04 Intr - 7888 7730 159 0 0 85 93 144 0.998 12.78
2.03 Intr - 8185 8029 157 2 1 65 60 144 0.787 7.45
2.02 Intr - 8546 8278 269 1 2 36 65 287 0.946 17.45
2.01 Init - 8789 8647 143 2 2 94 96 176 0.550 18.65
2.00 Prom - 9720 9681 40 -6.55
3.00 Prom + 10160 10199 40 -11.84
3.01 Init + 10209 11313 1105 2 1 66 57 269 0.512 16.18
3.02 Intr + 11850 11924 75 1 0 80 86 57 0.507 3.27
Suboptimal exons with probability > 1.000
Exnum Type S .Begin ...End .Len Fr Ph B/Ac Do/T CodRg P.... Tscr..
----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------
NO EXONS FOUND AT GIVEN PROBABILITY CUTOFF
Predicted peptide sequence(s):
>/tmp/03_03_20-07:33:11.fasta|GENSCAN_predicted_peptide_1|384_aa
MSSKNKVSKQDIDSIVESLMKKQKSYFEPRLAQIQQVGMENVQKLSAIHAELALLTASIS
TVKSDVDKLKCKVENNFSAIDGHDQAFGELELKMADMEDRSRRCNIRVIGLKERLEGFNA
IQYLTHSLPKWFPALADVPVEVMSAHRIYSDAKRGDNRTLIFNVLRYTTRQAILRAAKKD
PLSVDDRKVRFSPDYSNFTVKRCQAFHQAKDAARNKCLDFFLLYPATLKIKEGAQYRSFT
SPKEAEDYVNSAASNHAATPASPRQHGTILTIYRRIHSLYDGERARKIQLLEQAASVALT
GDNWTSVRNDNYLGVTAHFIDNVWKLRCFALEVKKKKKHSRHTAEDCAEEFIDVSNRWEI
NGKLTTLGTDSALIMLAAARLLPF
>/tmp/03_03_20-07:33:11.fasta|GENSCAN_predicted_peptide_2|398_aa
MASTMPSSSSTEDEENTPECLNKDHYHFHHYTMEYIQDKPTNVARVGGFTDKKSIAKVER
CLARERQEATEDHEAIPSTSGATSLTKKLRSRSGLPIAGSGLVLPALCIICQKKEKFINR
AGKRQRDPLSKAETLTVGQLQKAAELKDDQSILLHIKDKDCVALEVQYHKGCYNQYTRFM
TRPEKPEKEQNEPTFDVGYKILCERIIRQRLLVNQEVLRMGQLRMAFIELVKANEGLDAS
NYSIKNLERSRRADAGSQRIQIFDPDQRTPTQWKKFLSEGTKKEALAEFLYVAWKNADLT
IVGKNLCLYIAHTNQCHCVTVKEGVQSVRVVEDLLLFLHAQHAAREHKAVIIKSSDTDVA
VIAVSVQTDLPCSLYVFTGTGNRTRIIDITKVSSANKI
>/tmp/03_03_20-07:33:11.fasta|GENSCAN_predicted_peptide_3|394_aa
MQRGRAAGINGIPPEFYVAFWEQLSPFFLHMINFSIEKGGFLRDVNTALISLLMKKDKNP
TDCSSYRPLSLLNSDVKIFAKLLPLRLEPHMPELVSSDQTGFIKSRTAADNIRRLLHIIA
AAPGCETPMSVLSLDAMKAFDRLEWSFLWSVLEAMGFISTFIGMVKVLYSNPSARVLTGQ
TFSSLFPVSRSSRQGCPLSPALFVLSLEPLAQAVRLSNLVLPICICDTQHKLSLFADDVI
VFLEHPTQSLPHFLSICEEFRKLSGFKMNWSKSALMHLNDNARKSVTPVNIPLVGQLKYL
GIEVFPSLNQIVKHNYSLAFTNVLKDMDRWISLPMSIQARISIIKMNGLPRIHFVSSMVP
LPPPSDYWIKISAQGVRCPLAKPFTHSPYSKTKX

14
src/bd_rhapsody/bd_rhapsody_make_reference/config.vsh.yaml
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@@ -116,12 +116,11 @@ argument_groups:
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
- path: ../test_data
requirements:
commands: [ "cwl-runner" ]
@@ -131,12 +130,19 @@ engines:
image: bdgenomics/rhapsody:2.2.1
setup:
- type: apt
packages: [procps]
packages: [procps, git]
- type: python
packages: [cwlref-runner, cwl-runner]
- type: docker
run: |
echo "bdgenomics/rhapsody: 2.2.1" > /var/software_versions.txt
mkdir /var/bd_rhapsody_cwl && \
cd /var/bd_rhapsody_cwl && \
git clone https://bitbucket.org/CRSwDev/cwl.git . && \
git checkout 8feeace1141b24749ea6003f8e6ad6d3ad5232de
- type: docker
run:
- VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1)
- 'echo "bdgenomics/rhapsody: \"$VERSION\"" > /var/software_versions.txt'
runners:
- type: executable

115
src/bd_rhapsody/bd_rhapsody_make_reference/make_rhap_reference_2.2.1_nodocker.cwl
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@@ -1,115 +0,0 @@
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'

12
src/bd_rhapsody/bd_rhapsody_make_reference/script.py
View File

@@ -83,21 +83,21 @@ def generate_config(par: dict[str, Any], meta, config) -> str:
for config_key, arg_type, par_value in config_key_value_pairs:
if arg_type == "file":
str = strip_margin(f"""\
content = strip_margin(f"""\
|{config_key}:
|""")
if isinstance(par_value, list):
for file in par_value:
str += strip_margin(f"""\
content += strip_margin(f"""\
| - class: File
| location: "{file}"
|""")
else:
str += strip_margin(f"""\
content += strip_margin(f"""\
| class: File
| location: "{par_value}"
|""")
content_list.append(str)
content_list.append(content)
else:
content_list.append(strip_margin(f"""\
|{config_key}: {par_value}
@@ -108,9 +108,9 @@ def generate_config(par: dict[str, Any], meta, config) -> str:
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")
cwl_file="/var/bd_rhapsody_cwl/v2.2.1/Extra_Utilities/make_rhap_reference_2.2.1.cwl"
return cwl_file
return os.path.abspath(cwl_file)
def main(par: dict[str, Any], meta: dict[str, Any]):
config = read_config(meta["config"])

47
src/bd_rhapsody/bd_rhapsody_make_reference/test_data/script.sh
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@@ -1,47 +0,0 @@
#!/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

116
src/bd_rhapsody/bd_rhapsody_sequence_analysis/_process_cwl.R Normal file
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# Extract arguments from CWL file and write them to arguments.yaml
#
# This script:
# - reads the CWL file
# - extracts the main workflow arguments
# - compares cwl arguments to viash config arguments
# - writes the arguments to arguments.yaml
#
# It can be used to update the arguments in the viash config after an
# update to the CWL file has been made.
#
# Dependencies: tidyverse, jsonlite, yaml, dynutils
#
# Install dependencies:
# ```R
# install.packages(c("tidyverse", "jsonlite", "yaml", "dynutils"))
# ```
#
# Usage:
# ```bash
# Rscript src/bd_rhapsody/bd_rhapsody_sequence_analysis/_process_cwl.R
# ```
library(tidyverse)
# fetch and read cwl file
lines <- read_lines("https://bitbucket.org/CRSwDev/cwl/raw/8feeace1141b24749ea6003f8e6ad6d3ad5232de/v2.2.1/rhapsody_pipeline_2.2.1.cwl")
cwl_header <- lines[[1]]
cwl_obj <- jsonlite::fromJSON(lines[-1], simplifyVector = FALSE)
# detect main workflow arguments
gr <- dynutils::list_as_tibble(cwl_obj$`$graph`)
gr %>% print(n = 100)
main <- gr %>% filter(gr$id == "#main")
main_inputs <- main$inputs[[1]]
input_ids <- main_inputs %>% map_chr("id") %>% gsub("^#main/", "", .)
# check whether in config
config <- yaml::read_yaml("src/bd_rhapsody/bd_rhapsody_sequence_analysis/config.vsh.yaml")
config$all_arguments <- config$argument_groups %>% map("arguments") %>% list_flatten()
arg_names <- config$all_arguments %>% map_chr("name") %>% gsub("^--", "", .)
# arguments in cwl but not in config
setdiff(tolower(input_ids), arg_names)
# arguments in config but not in cwl
setdiff(arg_names, tolower(input_ids))
# create arguments from main_inputs
arguments <- map(main_inputs, function(main_input) {
input_id <- main_input$id %>% gsub("^#main/", "", .)
input_type <- main_input$type[[2]]
if (is.list(input_type) && input_type$type == "array") {
multiple <- TRUE
input_type <- input_type$items
} else {
multiple <- FALSE
}
if (is.list(input_type) && input_type$type == "enum") {
choices <- input_type$symbols %>%
gsub(paste0(input_type$name, "/"), "", .)
input_type <- "enum"
} else {
choices <- NULL
}
description <-
if (is.null(main_input$label)) {
main_input$doc
} else if (is.null(main_input$doc)) {
main_input$label
} else {
paste0(main_input$label, ". ", main_input$doc)
}
type_map <- c(
"float" = "double",
"int" = "integer",
"string" = "string",
"boolean" = "boolean",
"File" = "file",
"enum" = "string"
)
out <- list(
name = paste0("--", tolower(input_id)),
type = type_map[input_type],
# TODO: use summary when viash 0.9 is released
# summary = main_input$doc,
# description = main_input$doc,
description = description,
multiple = multiple,
choices = choices,
info = list(
config_key = input_id
)
)
out[!sapply(out, is.null)]
})
yaml::write_yaml(
arguments,
"src/bd_rhapsody/bd_rhapsody_sequence_analysis/arguments.yaml",
handlers = list(
logical = yaml::verbatim_logical
)
)

661
src/bd_rhapsody/bd_rhapsody_sequence_analysis/config.vsh.yaml Normal file
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name: bd_rhapsody_sequence_analysis
namespace: bd_rhapsody
description: |
BD Rhapsody Sequence Analysis CWL pipeline v2.2.
This pipeline performs analysis of single-cell multiomic sequence read (FASTQ) data. The supported
sequencing libraries are those generated by the BD Rhapsody™ assay kits, including: Whole Transcriptome
mRNA (WTA), Targeted mRNA, AbSeq Antibody-Oligonucleotides (ABC), Single-Cell Multiplexing (SMK),
TCR/BCR (VDJ), and ATAC-Seq.
keywords: [rna-seq, single-cell, multiomic, atac-seq, targeted, abseq, tcr, bcr]
links:
repository: https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1
documentation: https://bd-rhapsody-bioinfo-docs.genomics.bd.com
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:
- name: "--reads"
type: file
description: |
Reads (optional) - Path to your FASTQ.GZ formatted read files from libraries that may include:
- WTA mRNA
- Targeted mRNA
- AbSeq
- Sample Multiplexing
- VDJ
You may specify as many R1/R2 read pairs as you want.
required: false
multiple: true
example:
- WTALibrary_S1_L001_R1_001.fastq.gz
- WTALibrary_S1_L001_R2_001.fastq.gz
info:
config_key: Reads
- name: "--reads_atac"
type: file
description: |
Path to your FASTQ.GZ formatted read files from ATAC-Seq libraries.
You may specify as many R1/R2/I2 files as you want.
required: false
multiple: true
example:
- ATACLibrary_S2_L001_R1_001.fastq.gz
- ATACLibrary_S2_L001_R2_001.fastq.gz
- ATACLibrary_S2_L001_I2_001.fastq.gz
info:
config_key: Reads_ATAC
- name: References
description: |
Assay type will be inferred from the provided reference(s).
Do not provide both reference_archive and targeted_reference at the same time.
Valid reference input combinations:
- reference_archive: WTA only
- reference_archive & abseq_reference: WTA + AbSeq
- reference_archive & supplemental_reference: WTA + extra transgenes
- reference_archive & abseq_reference & supplemental_reference: WTA + AbSeq + extra transgenes
- reference_archive: WTA + ATAC or ATAC only
- reference_archive & supplemental_reference: WTA + ATAC + extra transgenes
- targeted_reference: Targeted only
- targeted_reference & abseq_reference: Targeted + AbSeq
- abseq_reference: AbSeq only
The reference_archive can be generated with the bd_rhapsody_make_reference component.
Alternatively, BD also provides standard references which can be downloaded from these locations:
- Human: https://bd-rhapsody-public.s3.amazonaws.com/Rhapsody-WTA/Pipeline-version2.x_WTA_references/RhapRef_Human_WTA_2023-02.tar.gz
- Mouse: https://bd-rhapsody-public.s3.amazonaws.com/Rhapsody-WTA/Pipeline-version2.x_WTA_references/RhapRef_Mouse_WTA_2023-02.tar.gz
arguments:
- name: "--reference_archive"
type: file
description: |
Path to Rhapsody WTA Reference in the tar.gz format.
Structure of the reference archive:
- `BD_Rhapsody_Reference_Files/`: top level folder
- `star_index/`: sub-folder containing STAR index, that is files created with `STAR --runMode genomeGenerate`
- GTF for gene-transcript-annotation e.g. "gencode.v43.primary_assembly.annotation.gtf"
example: "RhapRef_Human_WTA_2023-02.tar.gz"
required: false
info:
config_key: Reference_Archive
- name: "--targeted_reference"
type: file
description: |
Path to the targeted reference file in FASTA format.
example: "BD_Rhapsody_Immune_Response_Panel_Hs.fasta"
multiple: true
info:
config_key: Targeted_Reference
- name: "--abseq_reference"
type: file
description: Path to the AbSeq reference file in FASTA format. Only needed if BD AbSeq Ab-Oligos are used.
example: "AbSeq_reference.fasta"
multiple: true
info:
config_key: AbSeq_Reference
- name: "--supplemental_reference"
type: file
alternatives: [-s]
description: Path to the supplemental reference file in FASTA format. Only needed if there are additional transgene sequences to be aligned against in a WTA assay experiment.
example: "supplemental_reference.fasta"
multiple: true
info:
config_key: Supplemental_Reference
- name: Outputs
description: Outputs for all pipeline runs
# based on https://bd-rhapsody-bioinfo-docs.genomics.bd.com/outputs/top_outputs.html
arguments:
- name: "--output_dir"
type: file
direction: output
alternatives: [-o]
description: "The unprocessed output directory containing all the outputs from the pipeline."
required: true
example: output_dir/
- name: "--output_seurat"
type: file
direction: output
description: "Single-cell analysis tool inputs. Seurat (.rds) input file containing RSEC molecules data table and all cell annotation metadata."
example: output_seurat.rds
required: false
info:
template: "[sample_name]_Seurat.rds"
- name: "--output_mudata"
type: file
direction: output
description: "Single-cell analysis tool inputs. Scanpy / Muon input file containing RSEC molecules data table and all cell annotation metadata."
example: output_mudata.h5mu
required: false
info:
template: "[sample_name].h5mu"
- name: "--metrics_summary"
type: file
direction: output
description: "Metrics Summary. Report containing sequencing, molecules, and cell metrics."
example: metrics_summary.csv
required: false
info:
template: "[sample_name]_Metrics_Summary.csv"
- name: "--pipeline_report"
type: file
direction: output
description: "Pipeline Report. Summary report containing the results from the sequencing analysis pipeline run."
example: pipeline_report.html
required: false
info:
template: "[sample_name]_Pipeline_Report.html"
- name: "--rsec_mols_per_cell"
type: file
direction: output
description: "Molecules per bioproduct per cell bassed on RSEC"
example: RSEC_MolsPerCell_MEX.zip
required: false
info:
template: "[sample_name]_RSEC_MolsPerCell_MEX.zip"
- name: "--dbec_mols_per_cell"
type: file
direction: output
description: "Molecules per bioproduct per cell bassed on DBEC. DBEC data table is only output if the experiment includes targeted mRNA or AbSeq bioproducts."
example: DBEC_MolsPerCell_MEX.zip
required: false
info:
template: "[sample_name]_DBEC_MolsPerCell_MEX.zip"
- name: "--rsec_mols_per_cell_unfiltered"
type: file
direction: output
description: "Unfiltered tables containing all cell labels with ≥10 reads."
example: RSEC_MolsPerCell_Unfiltered_MEX.zip
required: false
info:
template: "[sample_name]_RSEC_MolsPerCell_Unfiltered_MEX.zip"
- name: "--bam"
type: file
direction: output
description: "Alignment file of R2 with associated R1 annotations for Bioproduct."
example: BioProduct.bam
required: false
info:
template: "[sample_name]_Bioproduct.bam"
- name: "--bam_index"
type: file
direction: output
description: "Index file for the alignment file."
example: BioProduct.bam.bai
required: false
info:
template: "[sample_name]_Bioproduct.bam.bai"
- name: "--bioproduct_stats"
type: file
direction: output
description: "Bioproduct Stats. Metrics from RSEC and DBEC Unique Molecular Identifier adjustment algorithms on a per-bioproduct basis."
example: Bioproduct_Stats.csv
required: false
info:
template: "[sample_name]_Bioproduct_Stats.csv"
- name: "--dimred_tsne"
type: file
direction: output
description: "t-SNE dimensionality reduction coordinates per cell index"
example: tSNE_coordinates.csv
required: false
info:
template: "[sample_name]_(assay)_tSNE_coordinates.csv"
- name: "--dimred_umap"
type: file
direction: output
description: "UMAP dimensionality reduction coordinates per cell index"
example: UMAP_coordinates.csv
required: false
info:
template: "[sample_name]_(assay)_UMAP_coordinates.csv"
- name: "--immune_cell_classification"
type: file
direction: output
description: "Immune Cell Classification. Cell type classification based on the expression of immune cell markers."
example: Immune_Cell_Classification.csv
required: false
info:
template: "[sample_name]_(assay)_cell_type_experimental.csv"
- name: Multiplex outputs
description: Outputs when multiplex option is selected
arguments:
- name: "--sample_tag_metrics"
type: file
direction: output
description: "Sample Tag Metrics. Metrics from the sample determination algorithm."
example: Sample_Tag_Metrics.csv
required: false
info:
template: "[sample_name]_Sample_Tag_Metrics.csv"
- name: "--sample_tag_calls"
type: file
direction: output
description: "Sample Tag Calls. Assigned Sample Tag for each putative cell"
example: Sample_Tag_Calls.csv
required: false
info:
template: "[sample_name]_Sample_Tag_Calls.csv"
- name: "--sample_tag_counts"
type: file
direction: output
description: "Sample Tag Counts. Separate data tables and metric summary for cells assigned to each sample tag. Note: For putative cells that could not be assigned a specific Sample Tag, a Multiplet_and_Undetermined.zip file is also output."
example: Sample_Tag1.zip
required: false
multiple: true
info:
template: "[sample_name]_Sample_Tag[number].zip"
- name: "--sample_tag_counts_unassigned"
type: file
direction: output
description: "Sample Tag Counts Unassigned. Data table and metric summary for cells that could not be assigned a specific Sample Tag."
example: Multiplet_and_Undetermined.zip
required: false
info:
template: "[sample_name]_Multiplet_and_Undetermined.zip"
- name: VDJ Outputs
description: Outputs when VDJ option selected
arguments:
- name: "--vdj_metrics"
type: file
direction: output
description: "VDJ Metrics. Overall metrics from the VDJ analysis."
example: VDJ_Metrics.csv
required: false
info:
template: "[sample_name]_VDJ_Metrics.csv"
- name: "--vdj_per_cell"
type: file
direction: output
description: "VDJ Per Cell. Cell specific read and molecule counts, VDJ gene segments, CDR3 sequences, paired chains, and cell type."
example: VDJ_perCell.csv
required: false
info:
template: "[sample_name]_VDJ_perCell.csv"
- name: "--vdj_per_cell_uncorrected"
type: file
direction: output
description: "VDJ Per Cell Uncorrected. Cell specific read and molecule counts, VDJ gene segments, CDR3 sequences, paired chains, and cell type."
example: VDJ_perCell_uncorrected.csv
required: false
info:
template: "[sample_name]_VDJ_perCell_uncorrected.csv"
- name: "--vdj_dominant_contigs"
type: file
direction: output
description: "VDJ Dominant Contigs. Dominant contig for each cell label chain type combination (putative cells only)."
example: VDJ_Dominant_Contigs_AIRR.csv
required: false
info:
template: "[sample_name]_VDJ_Dominant_Contigs_AIRR.csv"
- name: "--vdj_unfiltered_contigs"
type: file
direction: output
description: "VDJ Unfiltered Contigs. All contigs that were assembled and annotated successfully (all cells)."
example: VDJ_Unfiltered_Contigs_AIRR.csv
required: false
info:
template: "[sample_name]_VDJ_Unfiltered_Contigs_AIRR.csv"
- name: "ATAC-Seq outputs"
description: Outputs when ATAC-Seq option selected
arguments:
- name: "--atac_metrics"
type: file
direction: output
description: "ATAC Metrics. Overall metrics from the ATAC-Seq analysis."
example: ATAC_Metrics.csv
required: false
info:
template: "[sample_name]_ATAC_Metrics.csv"
- name: "--atac_metrics_json"
type: file
direction: output
description: "ATAC Metrics JSON. Overall metrics from the ATAC-Seq analysis in JSON format."
example: ATAC_Metrics.json
required: false
info:
template: "[sample_name]_ATAC_Metrics.json"
- name: "--atac_fragments"
type: file
direction: output
description: "ATAC Fragments. Chromosomal location, cell index, and read support for each fragment detected"
example: ATAC_Fragments.bed.gz
required: false
info:
template: "[sample_name]_ATAC_Fragments.bed.gz"
- name: "--atac_fragments_index"
type: file
direction: output
description: "Index of ATAC Fragments."
example: ATAC_Fragments.bed.gz.tbi
required: false
info:
template: "[sample_name]_ATAC_Fragments.bed.gz.tbi"
- name: "--atac_transposase_sites"
type: file
direction: output
description: "ATAC Transposase Sites. Chromosomal location, cell index, and read support for each transposase site detected"
example: ATAC_Transposase_Sites.bed.gz
required: false
info:
template: "[sample_name]_ATAC_Transposase_Sites.bed.gz"
- name: "--atac_transposase_sites_index"
type: file
direction: output
description: "Index of ATAC Transposase Sites."
example: ATAC_Transposase_Sites.bed.gz.tbi
required: false
info:
template: "[sample_name]_ATAC_Transposase_Sites.bed.gz.tbi"
- name: "--atac_peaks"
type: file
direction: output
description: "ATAC Peaks. Peak regions of transposase activity"
example: ATAC_Peaks.bed.gz
required: false
info:
template: "[sample_name]_ATAC_Peaks.bed.gz"
- name: "--atac_peaks_index"
type: file
direction: output
description: "Index of ATAC Peaks."
example: ATAC_Peaks.bed.gz.tbi
required: false
info:
template: "[sample_name]_ATAC_Peaks.bed.gz.tbi"
- name: "--atac_peak_annotation"
type: file
direction: output
description: "ATAC Peak Annotation. Estimated annotation of peak-to-gene connections"
example: peak_annotation.tsv.gz
required: false
info:
template: "[sample_name]_peak_annotation.tsv.gz"
- name: "--atac_cell_by_peak"
type: file
direction: output
description: "ATAC Cell by Peak. Peak regions of transposase activity per cell"
example: ATAC_Cell_by_Peak_MEX.zip
required: false
info:
template: "[sample_name]_ATAC_Cell_by_Peak_MEX.zip"
- name: "--atac_cell_by_peak_unfiltered"
type: file
direction: output
description: "ATAC Cell by Peak Unfiltered. Unfiltered file containing all cell labels with >=1 transposase sites in peaks."
example: ATAC_Cell_by_Peak_Unfiltered_MEX.zip
required: false
info:
template: "[sample_name]_ATAC_Cell_by_Peak_Unfiltered_MEX.zip"
- name: "--atac_bam"
type: file
direction: output
description: "ATAC BAM. Alignment file for R1 and R2 with associated I2 annotations for ATAC-Seq. Only output if the BAM generation flag is set to true."
example: ATAC.bam
required: false
info:
template: "[sample_name]_ATAC.bam"
- name: "--atac_bam_index"
type: file
direction: output
description: "Index of ATAC BAM."
example: ATAC.bam.bai
required: false
info:
template: "[sample_name]_ATAC.bam.bai"
- name: AbSeq Cell Calling outputs
description: Outputs when Cell Calling Abseq is selected
arguments:
- name: "--protein_aggregates_experimental"
type: file
direction: output
description: "Protein Aggregates Experimental"
example: Protein_Aggregates_Experimental.csv
required: false
info:
template: "[sample_name]_Protein_Aggregates_Experimental.csv"
- name: Putative Cell Calling Settings
arguments:
- name: "--cell_calling_data"
type: string
description: |
Specify the dataset to be used for putative cell calling: mRNA, AbSeq, ATAC, mRNA_and_ATAC
For putative cell calling using an AbSeq dataset, please provide an AbSeq_Reference fasta file above.
For putative cell calling using an ATAC dataset, please provide a WTA+ATAC-Seq Reference_Archive file above.
The default data for putative cell calling, will be determined the following way:
- If mRNA Reads and ATAC Reads exist: mRNA_and_ATAC
- If only ATAC Reads exist: ATAC
- Otherwise: mRNA
choices: [mRNA, AbSeq, ATAC, mRNA_and_ATAC]
example: mRNA
info:
config_key: Cell_Calling_Data
- name: "--cell_calling_bioproduct_algorithm"
type: string
description: |
Specify the bioproduct algorithm to be used for putative cell calling: Basic or Refined
By default, the Basic algorithm will be used for putative cell calling.
choices: [Basic, Refined]
example: Basic
info:
config_key: Cell_Calling_Bioproduct_Algorithm
- name: "--cell_calling_atac_algorithm"
type: string
description: |
Specify the ATAC-seq algorithm to be used for putative cell calling: Basic or Refined
By default, the Basic algorithm will be used for putative cell calling.
choices: [Basic, Refined]
example: Basic
info:
config_key: Cell_Calling_ATAC_Algorithm
- name: "--exact_cell_count"
type: integer
description: |
Set a specific number (>=1) of cells as putative, based on those with the highest error-corrected read count
example: 10000
min: 1
info:
config_key: Exact_Cell_Count
- name: "--expected_cell_count"
type: integer
description: |
Guide the basic putative cell calling algorithm by providing an estimate of the number of cells expected. Usually this can be the number of cells loaded into the Rhapsody cartridge. If there are multiple inflection points on the second derivative cumulative curve, this will ensure the one selected is near the expected.
example: 20000
min: 1
info:
config_key: Expected_Cell_Count
- name: Intronic Reads Settings
arguments:
- name: --exclude_intronic_reads
type: boolean
description: |
By default, the flag is false, and reads aligned to exons and introns are considered and represented in molecule counts. When the flag is set to true, intronic reads will be excluded.
The value can be true or false.
example: false
info:
config_key: Exclude_Intronic_Reads
- name: Multiplex Settings
arguments:
- name: "--sample_tags_version"
type: string
description: |
Specify the version of the Sample Tags used in the run:
* If Sample Tag Multiplexing was done, specify the appropriate version: human, mouse, flex, nuclei_includes_mrna, nuclei_atac_only
* If this is an SMK + Nuclei mRNA run or an SMK + Multiomic ATAC-Seq (WTA+ATAC-Seq) run (and not an SMK + ATAC-Seq only run), choose the "nuclei_includes_mrna" option.
* If this is an SMK + ATAC-Seq only run (and not SMK + Multiomic ATAC-Seq (WTA+ATAC-Seq)), choose the "nuclei_atac_only" option.
choices: [human, mouse, flex, nuclei_includes_mrna, nuclei_atac_only]
example: human
info:
config_key: Sample_Tags_Version
- name: "--tag_names"
type: string
description: |
Specify the tag number followed by '-' and the desired sample name to appear in Sample_Tag_Metrics.csv
Do not use the special characters: &, (), [], {}, <>, ?, |
multiple: true
example: [4-mySample, 9-myOtherSample, 6-alsoThisSample]
info:
config_key: Tag_Names
- name: VDJ arguments
arguments:
- name: "--vdj_version"
type: string
description: |
If VDJ was done, specify the appropriate option: human, mouse, humanBCR, humanTCR, mouseBCR, mouseTCR
choices: [human, mouse, humanBCR, humanTCR, mouseBCR, mouseTCR]
example: human
info:
config_key: VDJ_Version
- name: ATAC options
arguments:
- name: "--predefined_atac_peaks"
type: file
description: An optional BED file containing pre-established chromatin accessibility peak regions for generating the ATAC cell-by-peak matrix.
example: predefined_peaks.bed
info:
config_key: Predefined_ATAC_Peaks
- name: Additional options
arguments:
- name: "--run_name"
type: string
description: |
Specify a run name to use as the output file base name. Use only letters, numbers, or hyphens. Do not use special characters or spaces.
default: sample
info:
config_key: Run_Name
- name: "--generate_bam"
type: boolean
description: |
Specify whether to create the BAM file output
default: false
info:
config_key: Generate_Bam
- name: "--long_reads"
type: boolean
description: |
Use STARlong (default: undefined - i.e. autodetects based on read lengths) - Specify if the STARlong aligner should be used instead of STAR. Set to true if the reads are longer than 650bp.
info:
config_key: Long_Reads
- name: Advanced options
description: |
NOTE: Only change these if you are really sure about what you are doing
arguments:
- name: "--custom_star_params"
type: string
description: |
Modify STAR alignment parameters - Set this parameter to fully override default STAR mapping parameters used in the pipeline.
For reference this is the default that is used:
Short Reads: `--outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMultimapScoreRange 0 --clip3pAdapterSeq AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA --seedSearchStartLmax 50 --outFilterMatchNmin 25 --limitOutSJcollapsed 2000000`
Long Reads: Same as Short Reads + `--seedPerReadNmax 10000`
This applies to fastqs provided in the Reads user input
Do NOT set any non-mapping related params like `--genomeDir`, `--outSAMtype`, `--outSAMunmapped`, `--readFilesIn`, `--runThreadN`, etc.
We use STAR version 2.7.10b
example: "--alignIntronMax 6000 --outFilterScoreMinOverLread 0.1 --limitOutSJcollapsed 2000000"
info:
config_key: Custom_STAR_Params
- name: "--custom_bwa_mem2_params"
type: string
description: |
Modify bwa-mem2 alignment parameters - Set this parameter to fully override bwa-mem2 mapping parameters used in the pipeline
The pipeline does not specify any custom mapping params to bwa-mem2 so program default values are used
This applies to fastqs provided in the Reads_ATAC user input
Do NOT set any non-mapping related params like `-C`, `-t`, etc.
We use bwa-mem2 version 2.2.1
example: "-k 16 -w 200 -r"
info:
config_key: Custom_bwa_mem2_Params
- name: CWL-runner arguments
arguments:
- name: "--parallel"
type: boolean
description: "Run jobs in parallel."
default: true
- name: "--timestamps"
type: boolean_true
description: "Add timestamps to the errors, warnings, and notifications."
- name: Undocumented arguments
arguments:
- name: --abseq_umi
type: integer
multiple: false
info:
config_key: AbSeq_UMI
- name: --target_analysis
type: boolean
multiple: false
info:
config_key: Target_analysis
- name: --vdj_jgene_evalue
type: double
description: |
e-value threshold for J gene. The e-value threshold for J gene call by IgBlast/PyIR, default is set as 0.001
multiple: false
info:
config_key: VDJ_JGene_Evalue
- name: --vdj_vgene_evalue
type: double
description: |
e-value threshold for V gene. The e-value threshold for V gene call by IgBlast/PyIR, default is set as 0.001
multiple: false
info:
config_key: VDJ_VGene_Evalue
- name: --write_filtered_reads
type: boolean
multiple: false
info:
config_key: Write_Filtered_Reads
resources:
- type: python_script
path: script.py
test_resources:
- type: python_script
path: test.py
- path: ../test_data
- path: ../helpers
requirements:
commands: [ "cwl-runner" ]
engines:
- type: docker
image: bdgenomics/rhapsody:2.2.1
setup:
- type: apt
packages: [procps, git]
- type: python
packages: [cwlref-runner, cwl-runner]
- type: docker
run: |
mkdir /var/bd_rhapsody_cwl && \
cd /var/bd_rhapsody_cwl && \
git clone https://bitbucket.org/CRSwDev/cwl.git . && \
git checkout 8feeace1141b24749ea6003f8e6ad6d3ad5232de
- type: docker
run:
- VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1)
- 'echo "bdgenomics/rhapsody: \"$VERSION\"" > /var/software_versions.txt'
test_setup:
- type: python
packages: [biopython, gffutils]
runners:
- type: executable
- type: nextflow

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```bash
cwl-runner src/bd_rhapsody/bd_rhapsody_sequence_analysis/rhapsody_pipeline_2.2.1_nodocker.cwl --help
```
usage: src/bd_rhapsody/bd_rhapsody_sequence_analysis/rhapsody_pipeline_2.2.1_nodocker.cwl
[-h] [--AbSeq_Reference ABSEQ_REFERENCE] [--AbSeq_UMI ABSEQ_UMI]
[--Cell_Calling_ATAC_Algorithm CELL_CALLING_ATAC_ALGORITHM]
[--Cell_Calling_Bioproduct_Algorithm CELL_CALLING_BIOPRODUCT_ALGORITHM]
[--Cell_Calling_Data CELL_CALLING_DATA]
[--Custom_STAR_Params CUSTOM_STAR_PARAMS]
[--Custom_bwa_mem2_Params CUSTOM_BWA_MEM2_PARAMS]
[--Exact_Cell_Count EXACT_CELL_COUNT] [--Exclude_Intronic_Reads]
[--Expected_Cell_Count EXPECTED_CELL_COUNT] [--Generate_Bam]
[--Long_Reads] [--Maximum_Threads MAXIMUM_THREADS]
[--Predefined_ATAC_Peaks PREDEFINED_ATAC_PEAKS] [--Reads READS]
[--Reads_ATAC READS_ATAC] [--Reference_Archive REFERENCE_ARCHIVE]
[--Run_Name RUN_NAME] [--Sample_Tags_Version SAMPLE_TAGS_VERSION]
[--Supplemental_Reference SUPPLEMENTAL_REFERENCE]
[--Tag_Names TAG_NAMES] [--Target_analysis]
[--Targeted_Reference TARGETED_REFERENCE]
[--VDJ_JGene_Evalue VDJ_JGENE_EVALUE]
[--VDJ_VGene_Evalue VDJ_VGENE_EVALUE] [--VDJ_Version VDJ_VERSION]
[--Write_Filtered_Reads]
[job_order]
The BD Rhapsody™ assays are used to create sequencing libraries from single
cell transcriptomes. After sequencing, the analysis pipeline takes the FASTQ
files and a reference file for gene alignment. The pipeline generates
molecular counts per cell, read counts per cell, metrics, and an alignment
file.
positional arguments:
job_order Job input json file
options:
-h, --help show this help message and exit
--AbSeq_Reference ABSEQ_REFERENCE
AbSeq Reference
--AbSeq_UMI ABSEQ_UMI
--Cell_Calling_ATAC_Algorithm CELL_CALLING_ATAC_ALGORITHM
Specify the ATAC algorithm to be used for ATAC
putative cell calling. The Basic algorithm is the
default.
--Cell_Calling_Bioproduct_Algorithm CELL_CALLING_BIOPRODUCT_ALGORITHM
Specify the bioproduct algorithm to be used for
mRNA/AbSeq putative cell calling. The Basic algorithm
is the default.
--Cell_Calling_Data CELL_CALLING_DATA
Specify the data to be used for putative cell calling.
The default data for putative cell calling will be
determined the following way: - If mRNA and ATAC Reads
exist, mRNA_and_ATAC is the default. - If only ATAC
Reads exist, ATAC is the default. - Otherwise, mRNA is
the default.
--Custom_STAR_Params CUSTOM_STAR_PARAMS
Allows you to specify custom STAR aligner mapping
parameters. Only the mapping parameters you provide
here will be used with STAR, meaning that you must
provide the complete list of parameters that you want
to take effect. For reference, the parameters used by
default in the pipeline are: 1. Short Reads:
--outFilterScoreMinOverLread 0
--outFilterMatchNminOverLread 0
--outFilterMultimapScoreRange 0 --clip3pAdapterSeq
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
--seedSearchStartLmax 50 --outFilterMatchNmin 25
--limitOutSJcollapsed 2000000 2. Long Reads: Same
options as short reads + --seedPerReadNmax 10000
Example input: --alignIntronMax 500000
--outFilterScoreMinOverLread 0 --limitOutSJcollapsed
2000000 Important: 1. This applies to fastqs provided
in the Reads user input 2. Please do not specify any
non-mapping related params like: --runThreadN,
--genomeDir --outSAMtype, etc. 3. Please only use
params supported by STAR version 2.7.10b
--Custom_bwa_mem2_Params CUSTOM_BWA_MEM2_PARAMS
Allows you to specify custom bwa-mem2 mapping
parameters. Only the mapping parameters you provide
here will be used with bwa-mem2, meaning that you must
provide the complete list of parameters that you want
to take effect. The pipeline uses program default
mapping parameters. Example input: -k 15 -w 200 -r 2
Important: 1. This applies to fastqs provided in the
Reads_ATAC user input 2. Please do not specify any
non-mapping related params like: -C, -t, etc. 3.
Please only use params supported by bwa-mem2 version
2.2.1
--Exact_Cell_Count EXACT_CELL_COUNT
Set a specific number (>=1) of cells as putative,
based on those with the highest error-corrected read
count
--Exclude_Intronic_Reads
By default, reads aligned to exons and introns are
considered and represented in molecule counts.
Including intronic reads may increase sensitivity,
resulting in an increase in molecule counts and the
number of genes per cell for both cellular and nuclei
samples. Intronic reads may indicate unspliced mRNAs
and are also useful, for example, in the study of
nuclei and RNA velocity. When set to true, intronic
reads will be excluded.
--Expected_Cell_Count EXPECTED_CELL_COUNT
Optional. Guide the basic putative cell calling
algorithm by providing an estimate of the number of
cells expected. Usually this can be the number of
cells loaded into the Rhapsody cartridge. If there are
multiple inflection points on the second derivative
cumulative curve, this will ensure the one selected is
near the expected.
--Generate_Bam Default: false. A Bam read alignment file contains
reads from all the input libraries, but creating it
can consume a lot of compute and disk resources. By
setting this field to true, the Bam file will be
created. This option is shared for both Bioproduct and
ATAC libraries.
--Long_Reads By default, we detect if there are any reads longer
than 650bp and then flag QualCLAlign to use STARlong
instead of STAR. This flag can be explicitly set if it
is known in advance that there are reads longer than
650bp.
--Maximum_Threads MAXIMUM_THREADS
The maximum number of threads to use in the pipeline.
By default, all available cores are used.
--Predefined_ATAC_Peaks PREDEFINED_ATAC_PEAKS
An optional BED file containing pre-established
chromatin accessibility peak regions for generating
the ATAC cell-by-peak matrix. Only applies to ATAC
assays.
--Reads READS FASTQ files from libraries that may include WTA mRNA,
Targeted mRNA, AbSeq, Sample Multiplexing, and related
technologies
--Reads_ATAC READS_ATAC
FASTQ files from libraries generated using the ATAC
assay protocol. Each lane of a library is expected to
have 3 FASTQs - R1, R2 and I1/I2, where the index read
contains the Cell Barcode and UMI sequence. Only
applies to ATAC assays.
--Reference_Archive REFERENCE_ARCHIVE
Reference Files Archive
--Run_Name RUN_NAME This is a name for output files, for example
Experiment1_Metrics_Summary.csv. Default if left empty
is to name run based on a library. Any non-alpha
numeric characters will be changed to a hyphen.
--Sample_Tags_Version SAMPLE_TAGS_VERSION
The sample multiplexing kit version. This option
should only be set for a multiplexed experiment.
--Supplemental_Reference SUPPLEMENTAL_REFERENCE
Supplemental Reference
--Tag_Names TAG_NAMES
Specify the Sample Tag number followed by - (hyphen)
and a sample name to appear in the output files. For
example: 4-Ramos. Should be alpha numeric, with + -
and _ allowed. Any special characters: &, (), [], {},
<>, ?, | will be corrected to underscores.
--Target_analysis
--Targeted_Reference TARGETED_REFERENCE
Targeted Reference
--VDJ_JGene_Evalue VDJ_JGENE_EVALUE
The e-value threshold for J gene call by IgBlast/PyIR,
default is set as 0.001
--VDJ_VGene_Evalue VDJ_VGENE_EVALUE
The e-value threshold for V gene call by IgBlast/PyIR,
default is set as 0.001
--VDJ_Version VDJ_VERSION
The VDJ species and chain types. This option should
only be set for VDJ experiment.
--Write_Filtered_Reads

203
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#!/usr/bin/env cwl-runner
cwl:tool: rhapsody
# This is a template YML file used to specify the inputs for a BD Rhapsody Sequence Analysis pipeline run.
# See the BD Rhapsody Sequence Analysis Pipeline User Guide for more details. Enter the following information:
## Reads (optional) - Path to your FASTQ.GZ formatted read files from libraries that may include:
# - WTA mRNA
# - Targeted mRNA
# - AbSeq
# - Sample Multiplexing
# - VDJ
# You may specify as many R1/R2 read pairs as you want.
Reads:
- class: File
location: "test/WTALibrary_S1_L001_R1_001.fastq.gz"
- class: File
location: "test/WTALibrary_S1_L001_R2_001.fastq.gz"
## Reads_ATAC (optional) - Path to your FASTQ.GZ formatted read files from ATAC-Seq libraries.
## You may specify as many R1/R2/I2 files as you want.
Reads_ATAC:
- class: File
location: "test/ATACLibrary_S2_L001_R1_001.fastq.gz"
- class: File
location: "test/ATACLibrary_S2_L001_R2_001.fastq.gz"
- class: File
location: "test/ATACLibrary_S2_L001_I2_001.fastq.gz"
## Assay type will be inferred from the provided reference(s)
## Do not provide both Reference_Archive and Targeted_Reference at the same time
##
## Valid reference input combinations:
## WTA Reference_Archive (WTA only)
## WTA Reference_Archive + AbSeq_Reference (WTA + AbSeq)
## WTA Reference_Archive + Supplemental_Reference (WTA + extra transgenes)
## WTA Reference_Archive + AbSeq_Reference + Supplemental_Reference (WTA + AbSeq + extra transgenes)
## WTA+ATAC-Seq Reference_Archive (WTA + ATAC, ATAC only)
## WTA+ATAC-Seq Reference_Archive + Supplemental_Reference (WTA + ATAC + extra transgenes)
## Targeted_Reference (Targeted only)
## Targeted_Reference + AbSeq_Reference (Targeted + AbSeq)
## AbSeq_Reference (AbSeq only)
## See the BD Rhapsody Sequence Analysis Pipeline User Guide for instructions on how to:
## - Obtain a pre-built Rhapsody Reference file
## - Create a custom Rhapsody Reference file
## WTA Reference_Archive (required for WTA mRNA assay) - Path to Rhapsody WTA Reference in the tar.gz format.
##
## --Structure of reference archive--
## BD_Rhapsody_Reference_Files/ # top level folder
## star_index/ # sub-folder containing STAR index
## [files created with STAR --runMode genomeGenerate]
## [GTF for gene-transcript-annotation e.g. "gencode.v43.primary_assembly.annotation.gtf"]
##
## WTA+ATAC-Seq Reference_Archive (required for ATAC-Seq or Multiomic ATAC-Seq (WTA+ATAC-Seq) assays) - Path to Rhapsody WTA+ATAC-Seq Reference in the tar.gz format.
##
## --Structure of reference archive--
## BD_Rhapsody_Reference_Files/ # top level folder
## star_index/ # sub-folder containing STAR index
## [files created with STAR --runMode genomeGenerate]
## [GTF for gene-transcript-annotation e.g. "gencode.v43.primary_assembly.annotation.gtf"]
##
## mitochondrial_contigs.txt # mitochondrial contigs in the reference genome - one contig name per line. e.g. chrMT or chrM, etc.
##
## bwa-mem2_index/ # sub-folder containing bwa-mem2 index
## [files created with bwa-mem2 index]
##
Reference_Archive:
class: File
location: "test/RhapRef_Human_WTA_2023-02.tar.gz"
# location: "test/RhapRef_Human_WTA-ATAC_2023-08.tar.gz"
## Targeted_Reference (required for Targeted mRNA assay) - Path to the targeted reference file in FASTA format.
#Targeted_Reference:
# - class: File
# location: "test/BD_Rhapsody_Immune_Response_Panel_Hs.fasta"
## AbSeq_Reference (optional) - Path to the AbSeq reference file in FASTA format. Only needed if BD AbSeq Ab-Oligos are used.
## For putative cell calling using an AbSeq dataset, please provide an AbSeq reference fasta file as the AbSeq_Reference.
#AbSeq_Reference:
# - class: File
# location: "test/AbSeq_reference.fasta"
## Supplemental_Reference (optional) - Path to the supplemental reference file in FASTA format. Only needed if there are additional transgene sequences to be aligned against in a WTA assay experiment
#Supplemental_Reference:
# - class: File
# location: "test/supplemental_reference.fasta"
####################################
## Putative Cell Calling Settings ##
####################################
## Putative cell calling dataset (optional) - Specify the dataset to be used for putative cell calling: mRNA, AbSeq, ATAC, mRNA_and_ATAC
## For putative cell calling using an AbSeq dataset, please provide an AbSeq_Reference fasta file above.
## For putative cell calling using an ATAC dataset, please provide a WTA+ATAC-Seq Reference_Archive file above.
## The default data for putative cell calling, will be determined the following way:
## If mRNA Reads and ATAC Reads exist:
## Cell_Calling_Data: mRNA_and_ATAC
## If only ATAC Reads exist:
## Cell_Calling_Data: ATAC
## Otherwise:
## Cell_Calling_Data: mRNA
#Cell_Calling_Data: mRNA
## Putative cell calling bioproduct algorithm (optional) - Specify the bioproduct algorithm to be used for putative cell calling: Basic or Refined
## By default, the Basic algorithm will be used for putative cell calling.
#Cell_Calling_Bioproduct_Algorithm: Basic
## Putative cell calling ATAC algorithm (optional) - Specify the ATAC-seq algorithm to be used for putative cell calling: Basic or Refined
## By default, the Basic algorithm will be used for putative cell calling.
#Cell_Calling_ATAC_Algorithm: Basic
## Exact cell count (optional) - Set a specific number (>=1) of cells as putative, based on those with the highest error-corrected read count
#Exact_Cell_Count: 10000
## Expected Cell Count (optional) - Guide the basic putative cell calling algorithm by providing an estimate of the number of cells expected. Usually this can be the number of cells loaded into the Rhapsody cartridge. If there are multiple inflection points on the second derivative cumulative curve, this will ensure the one selected is near the expected.
#Expected_Cell_Count: 20000
####################################
## Intronic Reads Settings ##
####################################
## Exclude_Intronic_Reads (optional)
## By default, the flag is false, and reads aligned to exons and introns are considered and represented in molecule counts. When the flag is set to true, intronic reads will be excluded.
## The value can be true or false.
#Exclude_Intronic_Reads: true
#######################
## Multiplex options ##
#######################
## Sample Tags Version (optional) - If Sample Tag Multiplexing was done, specify the appropriate version: human, mouse, flex, nuclei_includes_mrna, nuclei_atac_only
## If this is an SMK + Nuclei mRNA run or an SMK + Multiomic ATAC-Seq (WTA+ATAC-Seq) run (and not an SMK + ATAC-Seq only run), choose the "nuclei_includes_mrna" option.
## If this is an SMK + ATAC-Seq only run (and not SMK + Multiomic ATAC-Seq (WTA+ATAC-Seq)), choose the "nuclei_atac_only" option.
#Sample_Tags_Version: human
## Tag_Names (optional) - Specify the tag number followed by '-' and the desired sample name to appear in Sample_Tag_Metrics.csv
# Do not use the special characters: &, (), [], {}, <>, ?, |
#Tag_Names: [4-mySample, 9-myOtherSample, 6-alsoThisSample]
################
## VDJ option ##
################
## VDJ Version (optional) - If VDJ was done, specify the appropriate option: human, mouse, humanBCR, humanTCR, mouseBCR, mouseTCR
#VDJ_Version: human
##################
## ATAC options ##
##################
## Predefined ATAC Peaks - An optional BED file containing pre-established chromatin accessibility peak regions for generating the ATAC cell-by-peak matrix.
#Predefined_ATAC_Peaks:
# class: File
# location: "path/predefined_peaks.bed"
########################
## Additional Options ##
########################
## Run Name (optional)- Specify a run name to use as the output file base name. Use only letters, numbers, or hyphens. Do not use special characters or spaces.
#Run_Name: my-experiment
## Generate Bam (optional, default: false) - Specify whether to create the BAM file output
#Generate_Bam: true
## Maximum_Threads (integer, optional, default: [use all cores of CPU]) - Set the maximum number of threads to use in the read processing steps of the pipeline: QualCLAlign, AlignmentAnalysis, VDJ assembly
#Maximum_Threads: 16
## Use STARlong (optional, default: "auto" - i.e. autodetects based on read lengths) - Specify if the STARlong aligner should be used instead of STAR. Set to true if the reads are longer than 650bp.
## The value can be true or false.
#Long_Reads: true
########################
## Advanced Options ##
########################
## NOTE: Only change these if you are really sure about what you are doing
## Modify STAR alignment parameters - Set this parameter to fully override default STAR mapping parameters used in the pipeline.
## For reference this is the default that is used:
## Short Reads: --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMultimapScoreRange 0 --clip3pAdapterSeq AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA --seedSearchStartLmax 50 --outFilterMatchNmin 25 --limitOutSJcollapsed 2000000
## Long Reads: Same as Short Reads + --seedPerReadNmax 10000
## This applies to fastqs provided in the Reads user input
## Do NOT set any non-mapping related params like --genomeDir, --outSAMtype, --outSAMunmapped, --readFilesIn, --runThreadN, etc.
## We use STAR version 2.7.10b
#Custom_STAR_Params: --alignIntronMax 6000 --outFilterScoreMinOverLread 0.1 --limitOutSJcollapsed 2000000
## Modify bwa-mem2 alignment parameters - Set this parameter to fully override bwa-mem2 mapping parameters used in the pipeline
## The pipeline does not specify any custom mapping params to bwa-mem2 so program default values are used
## This applies to fastqs provided in the Reads_ATAC user input
## Do NOT set any non-mapping related params like -C, -t, etc.
## We use bwa-mem2 version 2.2.1
#Custom_bwa_mem2_Params: -k 16 -w 200 -r

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import os
import re
import subprocess
import tempfile
from typing import Any
import yaml
import shutil
import glob
## VIASH START
par = {
'reads': [
'resources_test/bdrhap_5kjrt/raw/12ABC_S1_L432_R1_001_subset.fastq.gz',
'resources_test/bdrhap_5kjrt/raw/12ABC_S1_L432_R2_001_subset.fastq.gz'
],
'reads_atac': None,
'reference_archive': "resources_test/reference_gencodev41_chr1/reference_bd_rhapsody.tar.gz",
'targeted_reference': [],
'abseq_reference': [],
'supplemental_reference': [],
'output': 'output_dir',
'cell_calling_data': None,
'cell_calling_bioproduct_algorithm': None,
'cell_calling_atac_algorithm': None,
'exact_cell_count': None,
'expected_cell_count': None,
'exclude_intronic_reads': None,
'sample_tags_version': None,
'tag_names': [],
'vdj_version': None,
'predefined_atac_peaks': None,
'run_name': "sample",
'generate_bam': None,
'alignment_star_params': None,
'alignment_bwa_mem2_params': None,
'parallel': True,
'timestamps': False,
'dryrun': False
}
meta = {
'config': "target/nextflow/bd_rhaspody/bd_rhaspody_sequence_analysis/.config.vsh.yaml",
'resources_dir': os.path.abspath('src/bd_rhaspody/bd_rhaspody_sequence_analysis'),
'temp_dir': os.getenv("VIASH_TEMP"),
'memory_mb': None,
'cpus': None
}
## VIASH END
def clean_arg(argument):
argument["clean_name"] = argument["name"].lstrip("-")
return argument
def read_config(path: str) -> dict[str, Any]:
with open(path, 'r') as f:
config = yaml.safe_load(f)
config["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, temp_dir: str) -> str:
# check input parameters
assert par["reads"] or par["reads_atac"], "Pass at least one set of inputs to --reads or --reads_atac."
# output to temp dir if output_dir was not passed
if not par["output_dir"]:
par["output_dir"] = os.path.join(temp_dir, "output")
# checking sample prefix
if par["run_name"] and re.match("[^A-Za-z0-9]", par["run_name"]):
print("--run_name should only consist of letters, numbers or hyphens. Replacing all '[^A-Za-z0-9]' with '-'.", flush=True)
par["run_name"] = re.sub("[^A-Za-z0-9\\-]", "-", par["run_name"])
# make paths absolute
for argument in config["arguments"]:
arg_clean_name = argument["clean_name"]
if not par[arg_clean_name] or not argument["type"] == "file":
continue
par_value = par[arg_clean_name]
if isinstance(par_value, list):
par_value_absolute = list(map(os.path.abspath, par_value))
else:
par_value_absolute = os.path.abspath(par_value)
par[arg_clean_name] = par_value_absolute
return par
def generate_config(par: dict[str, Any], config) -> str:
content_list = [strip_margin(f"""\
|#!/usr/bin/env cwl-runner
|
|cwl:tool: rhapsody
|""")]
for argument in config["arguments"]:
arg_clean_name = argument["clean_name"]
arg_par_value = par[arg_clean_name]
arg_info = argument.get("info") or {} # Note: .info might be None
config_key = arg_info.get("config_key")
if arg_par_value and config_key:
if argument["type"] == "file":
content = strip_margin(f"""\
|{config_key}:
|""")
if isinstance(arg_par_value, list):
for file in arg_par_value:
content += strip_margin(f"""\
| - class: File
| location: "{file}"
|""")
else:
content += strip_margin(f"""\
| class: File
| location: "{arg_par_value}"
|""")
content_list.append(content)
else:
content_list.append(strip_margin(f"""\
|{config_key}: {arg_par_value}
|"""))
## Write config to file
return ''.join(content_list)
def generate_config_file(par: dict[str, Any], config: dict[str, Any], temp_dir: str) -> str:
config_file = os.path.join(temp_dir, "config.yml")
config_content = generate_config(par, config)
with open(config_file, "w") as f:
f.write(config_content)
return config_file
def generate_cwl_file(meta: dict[str, Any], dir: str) -> str:
# create cwl file (if need be)
# orig_cwl_file=os.path.join(meta["resources_dir"], "rhapsody_pipeline_2.2.1_nodocker.cwl")
orig_cwl_file="/var/bd_rhapsody_cwl/v2.2.1/rhapsody_pipeline_2.2.1.cwl"
if not meta["memory_mb"] and not meta["cpus"]:
return os.path.abspath(orig_cwl_file)
# Inject computational requirements into pipeline
cwl_file = os.path.join(dir, "pipeline.cwl")
# Read in the file
with open(orig_cwl_file, 'r') as file :
cwl_data = file.read()
# Inject computational requirements into pipeline
if meta["memory_mb"]:
memory = int(meta["memory_mb"]) - 2000 # keep 2gb for OS
cwl_data = re.sub('"ramMin": [^\n]*[^,](,?)\n', f'"ramMin": {memory}\\1\n', cwl_data)
if meta["cpus"]:
cwl_data = re.sub('"coresMin": [^\n]*[^,](,?)\n', f'"coresMin": {meta["cpus"]}\\1\n', cwl_data)
# Write the file out again
with open(cwl_file, 'w') as file:
file.write(cwl_data)
return os.path.abspath(cwl_file)
def copy_outputs(par: dict[str, Any], config: dict[str, Any]):
for arg in config["arguments"]:
par_value = par[arg["clean_name"]]
if par_value and arg["type"] == "file" and arg["direction"] == "output":
# example template: '[sample_name]_(assay)_cell_type_experimental.csv'
template = (arg.get("info") or {}).get("template") # Note: .info might be None
if template:
template_glob = template\
.replace("[sample_name]", par["run_name"])\
.replace("(assay)", "*")\
.replace("[number]", "*")
files = glob.glob(os.path.join(par["output_dir"], template_glob))
if not files and arg["required"]:
raise ValueError(f"Expected output file '{template_glob}' not found.")
elif len(files) > 1 and not arg["multiple"]:
raise ValueError(f"Expected single output file '{template_glob}', but found multiple.")
if not arg["multiple"]:
shutil.copy(files[0], par_value)
else:
# replace '*' in par_value with index
for i, file in enumerate(files):
shutil.copy(file, par_value.replace("*", str(i)))
def main(par: dict[str, Any], meta: dict[str, Any], temp_dir: str):
config = read_config(meta["config"])
# Preprocess params
par = process_params(par, config, temp_dir)
## Process parameters
cmd = [
"cwl-runner",
"--no-container",
"--preserve-entire-environment",
"--outdir", par["output_dir"],
]
if par["parallel"]:
cmd.append("--parallel")
if par["timestamps"]:
cmd.append("--timestamps")
# Create cwl file (if need be)
cwl_file = generate_cwl_file(meta, temp_dir)
cmd.append(cwl_file)
# Create params file
config_file = generate_config_file(par, config, temp_dir)
cmd.append(config_file)
# keep environment variables but set TMPDIR to temp_dir
env = dict(os.environ)
env["TMPDIR"] = temp_dir
# Create output dir if not exists
if not os.path.exists(par["output_dir"]):
os.makedirs(par["output_dir"])
# Run command
print("> " + ' '.join(cmd), flush=True)
_ = subprocess.run(
cmd,
cwd=os.path.dirname(config_file),
env=env,
check=True
)
# Copy outputs
copy_outputs(par, config)
if __name__ == "__main__":
with tempfile.TemporaryDirectory(prefix="cwl-bd_rhapsody-", dir=meta["temp_dir"]) as temp_dir:
main(par, meta, temp_dir)

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import subprocess
import gzip
from pathlib import Path
from typing import Tuple
import numpy as np
import random
import mudata as md
## VIASH START
meta = {
"name": "bd_rhapsody_sequence_analysis",
"executable": "target/docker/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis",
"resources_dir": "src/bd_rhapsody",
"cpus": 8,
"memory_mb": 4096,
}
## VIASH END
import sys
sys.path.append(meta["resources_dir"])
from helpers.rhapsody_cell_label import index_to_sequence
meta["executable"] = Path(meta["executable"])
meta["resources_dir"] = Path(meta["resources_dir"])
#########################################################################################
# Generate index
print("> Generate index", flush=True)
# cwl_file = meta["resources_dir"] / "bd_rhapsody_make_reference.cwl"
cwl_file = "/var/bd_rhapsody_cwl/v2.2.1/Extra_Utilities/make_rhap_reference_2.2.1.cwl"
reference_small_gtf = meta["resources_dir"] / "test_data" / "reference_small.gtf"
reference_small_fa = meta["resources_dir"] / "test_data" / "reference_small.fa"
bdabseq_panel_fa = meta["resources_dir"] / "test_data" / "BDAbSeq_ImmuneDiscoveryPanel.fasta"
sampletagsequences_fa = meta["resources_dir"] / "test_data" / "SampleTagSequences_HomoSapiens_ver1.fasta"
config_file = Path("reference_config.yml")
reference_file = Path("Rhap_reference.tar.gz")
subprocess.run([
"cwl-runner",
"--no-container",
"--preserve-entire-environment",
"--outdir",
".",
str(cwl_file),
"--Genome_fasta",
str(reference_small_fa),
"--Gtf",
str(reference_small_gtf),
"--Extra_STAR_params",
"--genomeSAindexNbases 4"
])
#########################################################################################
# Load reference in memory
from Bio import SeqIO
import gffutils
# Load FASTA sequence
with open(str(reference_small_fa), "r") as handle:
reference_fasta_dict = SeqIO.to_dict(SeqIO.parse(handle, "fasta"))
with open(str(bdabseq_panel_fa), "r") as handle:
bdabseq_panel_fasta_dict = SeqIO.to_dict(SeqIO.parse(handle, "fasta"))
with open(str(sampletagsequences_fa), "r") as handle:
sampletagsequences_fasta_dict = SeqIO.to_dict(SeqIO.parse(handle, "fasta"))
# create in memory db
reference_gtf_db = gffutils.create_db(
str(reference_small_gtf),
dbfn=":memory:",
force=True,
keep_order=True,
merge_strategy="merge",
sort_attribute_values=True,
disable_infer_transcripts=True,
disable_infer_genes=True
)
#############################################
# TODO: move helper functions to separate helper file
def generate_bd_read_metadata(
instrument_id: str = "A00226",
run_id: str = "970",
flowcell_id: str = "H5FGVMXY",
lane: int = 1,
tile: int = 1101,
x: int = 1000,
y: int = 1000,
illumina_flag: str = "1:N:0",
sample_id: str = "CAGAGAGG",
) -> str:
"""
Generate a FASTQ metadata line for a BD Rhapsody FASTQ file.
Args:
instrument_id: The instrument ID.
run_id: The run ID.
flowcell_id: The flowcell ID.
lane: The lane number.
tile: The tile number. Between 1101 and 1112 in the used example data.
x: The x-coordinate. Between 1000 and 32967 in the used example data.
y: The y-coordinate. Between 1000 and 37059 in the used example data.
illumina_flag: The Illumina flag. Either 1:N:0 or 2:N:0 in the used example data.
sample_id: The sample ID.
"""
# format: @A00226:970:H5FGVDMXY:1:1101:2645:1000 2:N:0:CAGAGAGG
return f"@{instrument_id}:{run_id}:{flowcell_id}:{lane}:{tile}:{x}:{y} {illumina_flag}:{sample_id}"
def generate_bd_wta_transcript(
transcript_length: int = 42,
) -> str:
"""
Generate a WTA transcript from a given GTF and FASTA file.
"""
# Randomly select a gene
gene = random.choice(list(reference_gtf_db.features_of_type("gene")))
# Find all exons within the gene
exons = list(reference_gtf_db.children(gene, featuretype="exon", order_by="start"))
# Calculate total exon length
total_exon_length = sum(exon.end - exon.start + 1 for exon in exons)
# If total exon length is less than desired transcript length, use it as is
max_transcript_length = min(total_exon_length, transcript_length)
# Build the WTA transcript sequence
sequence = ""
for exon in exons:
exon_seq = str(reference_fasta_dict[exon.seqid].seq[exon.start - 1 : exon.end])
sequence += exon_seq
# Break if desired length is reached
if len(sequence) >= max_transcript_length:
sequence = sequence[:max_transcript_length]
break
# add padding if need be
if len(sequence) < max_transcript_length:
sequence += "N" * (max_transcript_length - len(sequence))
return sequence
def generate_bd_wta_read(
cell_index: int = 0,
bead_version: str = "EnhV2",
umi_length: int = 14,
transcript_length: int = 42,
) -> Tuple[str, str]:
"""
Generate a BD Rhapsody WTA read pair for a given cell index.
Args:
cell_index: The cell index to generate reads for.
bead_version: The bead version to use for generating the cell label.
umi_length: The length of the UMI to generate.
transcript_length: The length of the transcript to generate
Returns:
A tuple of two strings, the first string being the R1 read and the second string being the R2 read.
More info:
See structure of reads:
- https://bd-rhapsody-bioinfo-docs.genomics.bd.com/steps/top_steps.html
- https://bd-rhapsody-bioinfo-docs.genomics.bd.com/steps/steps_cell_label.html
- https://scomix.bd.com/hc/en-us/articles/360057714812-All-FAQ
R1 is Cell Label + UMI + PolyT -> 60 bp
actually, CLS1 + "GTGA" + CLS2 + "GACA" + CLS3 + UMI
R2 is the actual read -> 42 bp
Example R1
CLS1 Link CLS2 Link CLS3 UMI
AAAATCCTGT GTGA AACCAAAGT GACA GATAGAGGAG CGCATGTTTATAAC
"""
# generate metadata
per_row = np.floor((32967 - 1000) / 9)
per_col = np.floor((37059 - 1000) / 9)
assert cell_index >= 0 and cell_index < per_row * per_col, f"cell_index must be between 0 and {per_row} * {per_col}"
x = 1000 + (cell_index % per_row) * 9
y = 1000 + (cell_index // per_row) * 9
instrument_id = "A00226"
run_id = "970"
flowcell_id = "H5FGVMXY"
meta_r1 = generate_bd_read_metadata(instrument_id=instrument_id, run_id=run_id, flowcell_id=flowcell_id, x=x, y=y, illumina_flag="1:N:0")
meta_r2 = generate_bd_read_metadata(instrument_id=instrument_id, run_id=run_id, flowcell_id=flowcell_id, x=x, y=y, illumina_flag="2:N:0")
# generate r1 (cls1 + link + cls2 + link + cls3 + umi)
assert cell_index >= 0 and cell_index < 384 * 384 * 384
cell_label = index_to_sequence(cell_index + 1, bead_version=bead_version)
# sample random umi
umi = "".join(random.choices("ACGT", k=umi_length))
quality_r1 = "I" * (len(cell_label) + len(umi))
r1 = f"{meta_r1}\n{cell_label}{umi}\n+\n{quality_r1}\n"
# generate r2 by extracting sequence from fasta and gtf
wta_transcript = generate_bd_wta_transcript(transcript_length=transcript_length)
quality_r2 = "I" * transcript_length
r2 = f"{meta_r2}\n{wta_transcript}\n+\n{quality_r2}\n"
return r1, r2
def generate_bd_wta_fastq_files(
num_cells: int = 100,
num_reads_per_cell: int = 1000,
) -> Tuple[str, str]:
"""
Generate BD Rhapsody WTA FASTQ files for a given number of cells and transcripts per cell.
Args:
num_cells: The number of cells to generate
num_reads_per_cell: The number of reads to generate per cell
Returns:
A tuple of two strings, the first string being the R1 reads and the second string being the R2 reads.
"""
r1_reads = ""
r2_reads = ""
for cell_index in range(num_cells):
for _ in range(num_reads_per_cell):
r1, r2 = generate_bd_wta_read(cell_index)
r1_reads += r1
r2_reads += r2
return r1_reads, r2_reads
def generate_bd_abc_read(
cell_index: int = 0,
bead_version: str = "EnhV2",
umi_length: int = 14,
transcript_length: int = 72,
) -> Tuple[str, str]:
"""
Generate a BD Rhapsody ABC read pair for a given cell index.
Args:
cell_index: The cell index to generate reads for.
bead_version: The bead version to use for generating the cell label.
umi_length: The length of the UMI to generate.
transcript_length: The length of the transcript to generate
Returns:
A tuple of two strings, the first string being the R1 read and the second string being the R2 read.
"""
# generate metadata
per_row = np.floor((32967 - 1000) / 9)
per_col = np.floor((37059 - 1000) / 9)
assert cell_index >= 0 and cell_index < per_row * per_col, f"cell_index must be between 0 and {per_row} * {per_col}"
x = 1000 + (cell_index % per_row) * 9
y = 1000 + (cell_index // per_row) * 9
instrument_id = "A01604"
run_id = "19"
flowcell_id = "HMKLYDRXY"
meta_r1 = generate_bd_read_metadata(instrument_id=instrument_id, run_id=run_id, flowcell_id=flowcell_id, x=x, y=y, illumina_flag="1:N:0")
meta_r2 = generate_bd_read_metadata(instrument_id=instrument_id, run_id=run_id, flowcell_id=flowcell_id, x=x, y=y, illumina_flag="2:N:0")
# generate r1 (cls1 + link + cls2 + link + cls3 + umi)
assert cell_index >= 0 and cell_index < 384 * 384 * 384
cell_label = index_to_sequence(cell_index + 1, bead_version=bead_version)
# sample random umi
umi = "".join(random.choices("ACGT", k=umi_length))
quality_r1 = "I" * (len(cell_label) + len(umi))
r1 = f"{meta_r1}\n{cell_label}{umi}\n+\n{quality_r1}\n"
# generate r2 by sampling sequence from bdabseq_panel_fa
abseq_seq = str(random.choice(list(bdabseq_panel_fasta_dict.values())).seq)
abc_suffix = "AAAAAAAAAAAAAAAAAAAAAAA"
abc_data = abseq_seq[:transcript_length - len(abc_suffix) - 1]
abc_prefix = "N" + "".join(random.choices("ACGT", k=transcript_length - len(abc_data) - len(abc_suffix) - 1))
abc_transcript = f"{abc_prefix}{abc_data}{abc_suffix}"
quality_r2 = "#" + "I" * (len(abc_transcript) - 1)
r2 = f"{meta_r2}\n{abc_transcript}\n+\n{quality_r2}\n"
return r1, r2
def generate_bd_abc_fastq_files(
num_cells: int = 100,
num_reads_per_cell: int = 1000,
) -> Tuple[str, str]:
"""
Generate BD Rhapsody ABC FASTQ files for a given number of cells and transcripts per cell.
Args:
num_cells: The number of cells to generate
num_reads_per_cell: The number of reads to generate per cell
Returns:
A tuple of two strings, the first string being the R1 reads and the second string being the R2 reads.
"""
r1_reads = ""
r2_reads = ""
for cell_index in range(num_cells):
for _ in range(num_reads_per_cell):
r1, r2 = generate_bd_abc_read(cell_index)
r1_reads += r1
r2_reads += r2
return r1_reads, r2_reads
def generate_bd_smk_read(
cell_index: int = 0,
bead_version: str = "EnhV2",
umi_length: int = 14,
transcript_length: int = 72,
num_sample_tags: int = 3,
):
"""
Generate a BD Rhapsody SMK read pair for a given cell index.
Args:
cell_index: The cell index to generate reads for.
bead_version: The bead version to use for generating the cell label.
umi_length: The length of the UMI to generate.
transcript_length: The length of the transcript to generate
num_sample_tags: The number of sample tags to use
Returns:
A tuple of two strings, the first string being the R1 read and the second string being the R2 read.
"""
# generate metadata
per_row = np.floor((32967 - 1000) / 9)
per_col = np.floor((37059 - 1000) / 9)
assert cell_index >= 0 and cell_index < per_row * per_col, f"cell_index must be between 0 and {per_row} * {per_col}"
x = 1000 + (cell_index % per_row) * 9
y = 1000 + (cell_index // per_row) * 9
instrument_id = "A00226"
run_id = "970"
flowcell_id = "H5FGVDMXY"
meta_r1 = generate_bd_read_metadata(instrument_id=instrument_id, run_id=run_id, flowcell_id=flowcell_id, x=x, y=y, illumina_flag="1:N:0")
meta_r2 = generate_bd_read_metadata(instrument_id=instrument_id, run_id=run_id, flowcell_id=flowcell_id, x=x, y=y, illumina_flag="2:N:0")
# generate r1 (cls1 + link + cls2 + link + cls3 + umi)
assert cell_index >= 0 and cell_index < 384 * 384 * 384
cell_label = index_to_sequence(cell_index + 1, bead_version=bead_version)
# sample random umi
umi = "".join(random.choices("ACGT", k=umi_length))
quality_r1 = "I" * (len(cell_label) + len(umi))
r1 = f"{meta_r1}\n{cell_label}{umi}\n+\n{quality_r1}\n"
# generate r2 by selecting the cell_index %% num_sample_tags sample tags
sampletag_index = cell_index % num_sample_tags
sampletag_seq = str(list(sampletagsequences_fasta_dict.values())[sampletag_index].seq)
smk_data = sampletag_seq[:transcript_length]
smk_suffix = "A" * (transcript_length - len(smk_data))
quality_r2 = "I" * len(smk_data) + "#" * len(smk_suffix)
r2 = f"{meta_r2}\n{smk_data}{smk_suffix}\n+\n{quality_r2}\n"
return r1, r2
def generate_bd_smk_fastq_files(
num_cells: int = 100,
num_reads_per_cell: int = 1000,
num_sample_tags: int = 3,
) -> Tuple[str, str]:
"""
Generate BD Rhapsody SMK FASTQ files for a given number of cells and transcripts per cell.
Args:
num_cells: The number of cells to generate
num_reads_per_cell: The number of reads to generate per cell
num_sample_tags: The number of sample tags to use
Returns:
A tuple of two strings, the first string being the R1 reads and the second string being the R2 reads.
"""
r1_reads = ""
r2_reads = ""
for cell_index in range(num_cells):
for _ in range(num_reads_per_cell):
r1, r2 = generate_bd_smk_read(cell_index, num_sample_tags=num_sample_tags)
r1_reads += r1
r2_reads += r2
return r1_reads, r2_reads
#########################################################################################
# Prepare WTA, ABC, and SMK test data
print("> Prepare WTA test data", flush=True)
wta_reads_r1_str, wta_reads_r2_str = generate_bd_wta_fastq_files(num_cells=100, num_reads_per_cell=1000)
with gzip.open("WTAreads_R1.fq.gz", "wt") as f:
f.write(wta_reads_r1_str)
with gzip.open("WTAreads_R2.fq.gz", "wt") as f:
f.write(wta_reads_r2_str)
print("> Prepare ABC test data", flush=True)
abc_reads_r1_str, abc_reads_r2_str = generate_bd_abc_fastq_files(num_cells=100, num_reads_per_cell=1000)
with gzip.open("ABCreads_R1.fq.gz", "wt") as f:
f.write(abc_reads_r1_str)
with gzip.open("ABCreads_R2.fq.gz", "wt") as f:
f.write(abc_reads_r2_str)
print("> Prepare SMK test data", flush=True)
smk_reads_r1_str, smk_reads_r2_str = generate_bd_smk_fastq_files(num_cells=100, num_reads_per_cell=1000, num_sample_tags=3)
with gzip.open("SMKreads_R1.fq.gz", "wt") as f:
f.write(smk_reads_r1_str)
with gzip.open("SMKreads_R2.fq.gz", "wt") as f:
f.write(smk_reads_r2_str)
#########################################################################################
# Run executable
print(f">> Run {meta['name']}", flush=True)
output_dir = Path("output")
subprocess.run([
meta['executable'],
"--reads=WTAreads_R1.fq.gz;WTAreads_R2.fq.gz",
f"--reference_archive={reference_file}",
"--reads=ABCreads_R1.fq.gz;ABCreads_R2.fq.gz",
f"--abseq_reference={bdabseq_panel_fa}",
"--reads=SMKreads_R1.fq.gz;SMKreads_R2.fq.gz",
"--tag_names=1-Sample1;2-Sample2;3-Sample3",
"--sample_tags_version=human",
"--output_dir=output",
"--exact_cell_count=100",
f"---cpus={meta['cpus'] or 1}",
f"---memory={meta['memory_mb'] or 2048}mb",
# "--output_seurat=seurat.rds",
"--output_mudata=mudata.h5mu",
"--metrics_summary=metrics_summary.csv",
"--pipeline_report=pipeline_report.html",
])
# Check if output exists
print(">> Check if output exists", flush=True)
assert (output_dir / "sample_Bioproduct_Stats.csv").exists()
assert (output_dir / "sample_Metrics_Summary.csv").exists()
assert (output_dir / "sample_Pipeline_Report.html").exists()
assert (output_dir / "sample_RSEC_MolsPerCell_MEX.zip").exists()
assert (output_dir / "sample_RSEC_MolsPerCell_Unfiltered_MEX.zip").exists()
# seurat object is not generated when abc data is added
# assert (output_dir / "sample_Seurat.rds").exists()
assert (output_dir / "sample.h5mu").exists()
# check individual outputs
# assert Path("seurat.rds").exists()
assert Path("mudata.h5mu").exists()
assert Path("metrics_summary.csv").exists()
assert Path("pipeline_report.html").exists()
print(">> Check contents of output", flush=True)
data = md.read_h5mu("mudata.h5mu")
assert data.n_obs == 100, "Number of cells is incorrect"
assert "rna" in data.mod, "RNA data is missing"
assert "prot" in data.mod, "Protein data is missing"
# check rna data
data_rna = data.mod["rna"]
assert data_rna.n_vars == 1, "Number of genes is incorrect"
assert data_rna.X.sum(axis=1).min() > 950, "Number of reads per cell is incorrect"
# assert data_rna.var.Raw_Reads.sum() == 100000, "Number of reads is incorrect"
assert data_rna.var.Raw_Reads.sum() >= 99990 and data_rna.var.Raw_Reads.sum() <= 100010, \
f"Expected 100000 RNA reads, got {data_rna.var.Raw_Reads.sum()}"
# check prot data
data_prot = data.mod["prot"]
assert data_prot.n_vars == len(bdabseq_panel_fasta_dict), "Number of proteins is incorrect"
assert data_prot.X.sum(axis=1).min() > 950, "Number of reads per cell is incorrect"
assert data_prot.var.Raw_Reads.sum() >= 99990 and data_prot.var.Raw_Reads.sum() <= 100010, \
f"Expected 100000 Prot reads, got {data_prot.var.Raw_Reads.sum()}"
# check smk data
expected_sample_tags = (["SampleTag01_hs", "SampleTag02_hs", "SampleTag03_hs"] * 34)[:100]
expected_sample_names = (["Sample1", "Sample2", "Sample3"] * 34)[:100]
sample_tags = data_rna.obs["Sample_Tag"]
assert sample_tags.nunique() == 3, "Number of sample tags is incorrect"
assert sample_tags.tolist() == expected_sample_tags, "Sample tags are incorrect"
sample_names = data_rna.obs["Sample_Name"]
assert sample_names.nunique() == 3, "Number of sample names is incorrect"
assert sample_names.tolist() == expected_sample_names, "Sample names are incorrect"
# TODO: add VDJ, ATAC, and targeted RNA to test
#########################################################################################
print("> Test successful", flush=True)

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#!/usr/bin/env python
# copied from https://bd-rhapsody-public.s3.amazonaws.com/CellLabel/rhapsody_cell_label.py.txt
# documented at https://bd-rhapsody-bioinfo-docs.genomics.bd.com/steps/steps_cell_label.html
"""
Rhapsody cell label structure
Information on the cell label is captured by the combination of bases in three cell label sections (CLS1, CLS2, CLS3).
Two common linker sequences (L1, L2) separate the three CLS.
--CLS1---|-L1-|--CLS2---|-L2-|--CL3---|--UMI---|-CaptureSequence-
Each cell label section has a whitelist of 96 or 384 possible 9 base sequences.
All the capture oligos from a single bead will have the same cell label.
----------------
V1 beads:
[A96_cell_key1] + [v1_linker1] + [A96_cell_key2] + [v1_linker2] + [A96_cell_key3] + [8 random base UMI] + [18 base polyT capture]
----------------
Enhanced beads:
Enhanced beads contain two different capture oligo types, polyT and 5prime. On any one bead, the two different capture oligo types have the same cell label sequences.
Compared to the V1 bead, enhanced beads have shorter linker sequences, longer polyT, and 0-3 diversity insert bases at the beginning of the sequence.
The cell label sections use the same 3 sequence whitelists as V1 beads.
polyT capture oligo:
[Enh_insert 0-3 bases] + [A96_cell_key1] + [Enh_linker1] + [A96_cell_key2] + [Enh_linker2] + [A96_cell_key3] + [8 random base UMI] + [25 base polyT capture]
5prime capture oligo:
[Enh_5p_primer] + [A96_cell_key1] + [Enh_5p_linker1] + [A96_cell_key2] + [Enh_5p_linker2] + [A96_cell_key3] + [8 random base UMI] + [Tso_capture_seq]
----------------
Enhanced V2/V3 beads:
Enhanced V2/V3 beads have the same structure as Enhanced beads, but the cell label sections have been updated with increased diversity
polyT capture oligo:
[Enh_insert 0-3 bases] + [B384_cell_key1] + [Enh_linker1] + [B384_cell_key2] + [Enh_linker2] + [B384_cell_key3] + [8 random base UMI] + [25 base polyT capture]
5prime capture oligo:
[Enh_5p_primer] + [B384_cell_key1] + [Enh_5p_linker1] + [B384_cell_key2] + [Enh_5p_linker2] + [B384_cell_key3] + [8 random base UMI] + [Tso_capture_seq]
The only difference between Enh V2 and Enh V3 beads is a different Tso_capture_seq.
----------------
The Rhapsody Sequence Analysis Pipeline will convert each cell label into a single integer representing a unique cell label sequence - which is used in the output files as the 'Cell_index'.
This cell index integer is deterministic and derived from the 3 part cell label as follows:
- Get the 1-based index for each cell label section from the python sets of sequences below
- Apply this equation:
(CLS1index - 1) * 384 * 384 + (CLS2index - 1) * 384 + CLS3index
(See label_sections_to_index() function below)
Example: Enhanced bead sequence:
ACACATTGCAGTGAAGATAGTTCGACACTCAAGACA
Each part identified:
A CACATTGCA GTGA AGATAGTTC GACA CTCAAGACA
DiversityInsert A96_cell_key1-33 Linker1 A96_cell_key2-78 Linker2 A96_cell_key3-21
33-78-21
(33 - 1) * 384 * 384 + (78 - 1) * 384 + 21
=4748181
The original sequences of cell label can be determined from the cell index integer by reversing this conversion.
See index_to_label_sections() and index_to_sequence() functions below.
"""
v1_linker1 = 'ACTGGCCTGCGA'
v1_linker2 = 'GGTAGCGGTGACA'
Enh_linker1 = 'GTGA'
Enh_linker2 = 'GACA'
Enh_5p_primer = "ACAGGAAACTCATGGTGCGT"
Enh_5p_linker1 = "AATG"
Enh_5p_linker2 = "CCAC"
Enh_inserts = ["", "A", "GT", "TCA"]
Tso_capture_seq_Enh_EnhV2 = "TATGCGTAGTAGGTATG"
Tso_capture_seq_EnhV3 = "GTGGAGTCGTGATTATA"
A96_cell_key1 = ("GTCGCTATA","CTTGTACTA","CTTCACATA","ACACGCCGG","CGGTCCAGG","AATCGAATG","CCTAGTATA","ATTGGCTAA","AAGACATGC","AAGGCGATC",
"GTGTCCTTA","GGATTAGGA","ATGGATCCA","ACATAAGCG","AACTGTATT","ACCTTGCGG","CAGGTGTAG","AGGAGATTA","GCGATTACA","ACCGGATAG",
"CCACTTGGA","AGAGAAGTT","TAAGTTCGA","ACGGATATT","TGGCTCAGA","GAATCTGTA","ACCAAGGAC","AGTATCTGT","CACACACTA","ATTAAGTGC",
"AAGTAACCC","AAATCCTGT","CACATTGCA","GCACTGTCA","ATACTTAGG","GCAATCCGA","ACGCAATCA","GAGTATTAG","GACGGATTA","CAGCTGACA",
"CAACATATT","AACTTCTCC","CTATGAAAT","ATTATTACC","TACCGAGCA","TCTCTTCAA","TAAGCGTTA","GCCTTACAA","AGCACACAG","ACAGTTCCG",
"AGTAAAGCC","CAGTTTCAC","CGTTACTAA","TTGTTCCAA","AGAAGCACT","CAGCAAGAT","CAAACCGCC","CTAACTCGC","AATATTGGG","AGAACTTCC",
"CAAAGGCAC","AAGCTCAAC","TCCAGTCGA","AGCCATCAC","AACGAGAAG","CTACAGAAC","AGAGCTATG","GAGGATGGA","TGTACCTTA","ACACACAAA",
"TCAGGAGGA","GAGGTGCTA","ACCCTGACC","ACAAGGATC","ATCCCGGAG","TATGTGGCA","GCTGCCAAT","ATCAGAGCT","TCGAAGTGA","ATAGACGAG",
"AGCCCAATC","CAGAATCGT","ATCTCCACA","ACGAAAGGT","TAGCTTGTA","ACACGAGAT","AACCGCCTC","ATTTAGATG","CAAGCAAGC","CAAAGTGTG",
"GGCAAGCAA","GAGCCAATA","ATGTAATGG","CCTGAGCAA","GAGTACATT","TGCGATCTA"
)
A96_cell_key2 = ("TACAGGATA","CACCAGGTA","TGTGAAGAA","GATTCATCA","CACCCAAAG","CACAAAGGC","GTGTGTCGA","CTAGGTCCT","ACAGTGGTA","TCGTTAGCA",
"AGCGACACC","AAGCTACTT","TGTTCTCCA","ACGCGAAGC","CAGAAATCG","ACCAAAATG","AGTGTTGTC","TAGGGATAC","AGGGCTGGT","TCATCCTAA",
"AATCCTGAA","ATCCTAGGA","ACGACCACC","TTCCATTGA","TAGTCTTGA","ACTGTTAGA","ATTCATCGT","ACTTCGAGC","TTGCGTACA","CAGTGCCCG",
"GACACTTAA","AGGAGGCGC","GCCTGTTCA","GTACATCTA","AATCAGTTT","ACGATGAAT","TGACAGACA","ATTAGGCAT","GGAGTCTAA","TAGAACACA",
"AAATAAATA","CCGACAAGA","CACCTACCC","AAGAGTAGA","TCATTGAGA","GACCTTAGA","CAAGACCTA","GGAATGATA","AAACGTACC","ACTATCCTC",
"CCGTATCTA","ACACATGTC","TTGGTATGA","GTGCAGTAA","AGGATTCAA","AGAATGGAG","CTCTCTCAA","GCTAACTCA","ATCAACCGA","ATGAGTTAC",
"ACTTGATGA","ACTTTAACT","TTGGAGGTA","GCCAATGTA","ATCCAACCG","GATGAACTG","CCATGCACA","TAGTGACTA","AAACTGCGC","ATTACCAAG",
"CACTCGAGA","AACTCATTG","CTTGCTTCA","ACCTGAGTC","AGGTTCGCT","AAGGACTAT","CGTTCGGTA","AGATAGTTC","CAATTGATC","GCATGGCTA",
"ACCAGGTGT","AGCTGCCGT","TATAGCCCT","AGAGGACCA","ACAATATGG","CAGCACTTC","CACTTATGT","AGTGAAAGG","AACCCTCGG","AGGCAGCTA",
"AACCAAAGT","GAGTGCGAA","CGCTAAGCA","AATTATAAC","TACTAGTCA","CAACAACGG"
)
A96_cell_key3 = ("AAGCCTTCT","ATCATTCTG","CACAAGTAT","ACACCTTAG","GAACGACAA","AGTCTGTAC","AAATTACAG","GGCTACAGA","AATGTATCG","CAAGTAGAA",
"GATCTCTTA","AACAACGCG","GGTGAGTTA","CAGGGAGGG","TCCGTCTTA","TGCATAGTA","ACTTACGAT","TGTATGCGA","GCTCCTTGA","GGCACAACA",
"CTCAAGACA","ACGCTGTTG","ATATTGTAA","AAGTTTACG","CAGCCTGGC","CTATTAGCC","CAAACGTGG","AAAGTCATT","GTCTTGGCA","GATCAGCGA",
"ACATTCGGC","AGTAATTAG","TGAAGCCAA","TCTACGACA","CATAACGTT","ATGGGACTC","GATAGAGGA","CTACATGCG","CAACGATCT","GTTAGCCTA",
"AGTTGCATC","AAGGGAACT","ACTACATAT","CTAAGCTTC","ACGAACCAG","TACTTCGGA","AACATCCAT","AGCCTGGTT","CAAGTTTCC","CAGGCATTT",
"ACGTGGGAG","TCTCACGGA","GCAACATTA","ATGGTCCGT","CTATCATGA","CAATACAAG","AAAGAGGCC","GTAGAAGCA","GCTATGGAA","ACTCCAGGG",
"ACAAGTGCA","GATGGTCCA","TCCTCAATA","AATAAACAA","CTGTACGGA","CTAGATAGA","AGCTATGTG","AAATGGAGG","AGCCGCAAG","ACAGTAAAC",
"AACGTGTGA","ACTGAATTC","AAGGGTCAG","TGTCTATCA","TCAGATTCA","CACGATCCG","AACAGAAAC","CATGAATGA","CGTACTACG","TTCAGCTCA",
"AAGGCCGCA","GGTTGGACA","CGTCTAGGT","AATTCGGCG","CAACCTCCA","CAATAGGGT","ACAGGCTCC","ACAACTAGT","AGTTGTTCT","AATTACCGG",
"ACAAACTTT","TCTCGGTTA","ACTAGACCG","ACTCATACG","ATCGAGTCT","CATAGGTCA"
)
B384_cell_key1 = ("TGTGTTCGC","TGTGGCGCC","TGTCTAGCG","TGGTTGTCC","TGGTTCCTC","TGGTGTGCT","TGGCGACCG","TGCTGTGGC","TGCTGGCAC","TGCTCTTCC",
"TGCCTCACC","TGCCATTAT","TGATGTCTC","TGATGGCCT","TGATGCTTG","TGAAGGACC","TCTGTCTCC","TCTGATTAT","TCTGAGGTT","TCTCGTTCT",
"TCTCATCCG","TCCTGGATT","TCAGCATTC","TCACGCCTT","TATGTGCAC","TATGCGGCC","TATGACGAG","TATCTCGTG","TATATGACC","TAGGCTGTG",
"TACTGCGTT","TACGTGTCC","TAATCACAT","GTTGTGTTG","GTTGTGGCT","GTTGTCTGT","GTTGTCGAG","GTTGTCCTC","GTTGTATCC","GTTGGTTCT",
"GTTGGCGTT","GTTGGAGCG","GTTGCTGCC","GTTGCGCAT","GTTGCAGGT","GTTGCACTG","GTTGATGAT","GTTGATACG","GTTGAAGTC","GTTCTGTGC",
"GTTCTCTCG","GTTCTATAT","GTTCGTATG","GTTCGGCCT","GTTCGCGGC","GTTCGATTC","GTTCCGGTT","GTTCCGACG","GTTCACGCT","GTTATCACC",
"GTTAGTCCG","GTTAGGTGT","GTTAGAGAC","GTTAGACTT","GTTACCTCT","GTTAATTCC","GTTAAGCGC","GTGTTGCTT","GTGTTCGGT","GTGTTCCAG",
"GTGTTCATC","GTGTCACAC","GTGTCAAGT","GTGTACTGC","GTGGTTAGT","GTGGTACCG","GTGGCGATC","GTGCTTCTG","GTGCGTTCC","GTGCGGTAT",
"GTGCGCCTT","GTGCGAACT","GTGCAGCCG","GTGCAATTG","GTGCAAGGC","GTCTTGCGC","GTCTGGCCG","GTCTGAGGC","GTCTCAGAT","GTCTCAACC",
"GTCTATCGT","GTCGGTGTG","GTCGGAATC","GTCGCTCCG","GTCCTCGCC","GTCCTACCT","GTCCGCTTG","GTCCATTCT","GTCCAATAC","GTCATGTAT",
"GTCAGTGGT","GTCAGATAG","GTATTAACT","GTATCAGTC","GTATAGCCT","GTATACTTG","GTATAAGGT","GTAGCATCG","GTACCGTCC","GTACACCTC",
"GTAAGTGCC","GTAACAGAG","GGTTGTGTC","GGTTGGCTG","GGTTGACGC","GGTTCGTCG","GGTTCAGTT","GGTTATATT","GGTTAATAC","GGTGTACGT",
"GGTGCCGCT","GGTGCATGC","GGTCGTTGC","GGTCGAGGT","GGTAGGCAC","GGTAGCTTG","GGTACATAG","GGTAATCTG","GGCTTGGCC","GGCTTCACG",
"GGCTTATGT","GGCTTACTC","GGCTGTCTT","GGCTCTGTG","GGCTCCGGT","GGCTCACCT","GGCGTTGAG","GGCGTGTAC","GGCGTGCTG","GGCGTATCG",
"GGCGCTCGT","GGCGCTACC","GGCGAGCCT","GGCGAGATC","GGCGACTTG","GGCCTCTTC","GGCCTACAG","GGCCAGCGC","GGCCAACTT","GGCATTCCT",
"GGCATCCGC","GGCATAACC","GGCAACGAT","GGATGTCCG","GGATGAGAG","GGATCTGGC","GGATCCATG","GGATAGGTT","GGAGTCGTG","GGAGAAGGC",
"GGACTCCTT","GGACTAGTC","GGACCGTTG","GGAATTAGT","GGAATCTCT","GGAATCGAC","GGAAGCCTC","GCTTGTAGC","GCTTGACCG","GCTTCGGAC",
"GCTTCACAT","GCTTAGTCT","GCTGGATAT","GCTGGAACC","GCTGCGATG","GCTGATCAG","GCTGAGCGT","GCTCTTGTC","GCTCTCCTG","GCTCGGTCC",
"GCTCCAATT","GCTATTCGC","GCTATGAGT","GCTAGTGTT","GCTAGGATC","GCTAGCACT","GCTACGTAT","GCTAACCTT","GCGTTCCGC","GCGTGTGCC",
"GCGTGCATT","GCGTCGGTT","GCGTATGTG","GCGTATACT","GCGGTTCAC","GCGGTCTTG","GCGGCGTCG","GCGGCACCT","GCGCTGGAC","GCGCTCTCC",
"GCGCGGCAG","GCGCGATAC","GCGCCGACC","GCGAGCGAG","GCGAGAGGT","GCGAATTAC","GCCTTGCAT","GCCTGCGCT","GCCTAACTG","GCCGTCCGT",
"GCCGCTGTC","GCCATGCCG","GCCAGCTAT","GCCAACCAG","GCATGGTTG","GCATCGACG","GCAGGCTAG","GCAGGACGC","GCAGCCATC","GCAGATACC",
"GCAGACGTT","GCACTATGT","GCACACGAG","GATTGTCAT","GATTGGTAG","GATTGCACC","GATTCTACT","GATTCGCTT","GATTAGGCC","GATTACGGT",
"GATGTTGGC","GATGTTATG","GATGGCCAG","GATCGTTCG","GATCGGAGC","GATCGCCTC","GATCCTCTG","GATCCAGCG","GATACACGC","GAGTTACCT",
"GAGTCGTAT","GAGTCGCCG","GAGGTGTAG","GAGGCATTG","GAGCGGACG","GAGCCTGAG","GAGATCTGT","GAGATAATT","GAGACGGCT","GACTTCGTG",
"GACTGTTCT","GACTCTTAG","GACCGCATT","GAATTGAGC","GAATATTGC","GAAGGCTCT","GAAGAGACT","GAACTGCCG","GAACGCGTG","CTTGTGTAT",
"CTTGTGCGC","CTTGTCATG","CTTGGTCTT","CTTGGTACC","CTTGGATGT","CTTGCTCAC","CTTGCAATC","CTTGAGGCC","CTTGACGGT","CTTCTGATC",
"CTTCTCGTT","CTTCTAGGC","CTTCGTTAG","CTTATGTCC","CTTATGCTT","CTTATATAG","CTTAGGTTG","CTTAGGAGC","CTTACTTAT","CTGTTCTCG",
"CTGTGCCTC","CTGTCGCAT","CTGTCGAGC","CTGTAGCTG","CTGTACGTT","CTGCTTGCC","CTGCGTAGT","CTGCACACC","CTGATGGAT","CTGAGTCAT",
"CTGACGCCG","CTGAACGAG","CTCTTGTAG","CTCTTAGTT","CTCTTACCG","CTCTGCACC","CTCTCGTCC","CTCGTATTG","CTCGACTAT","CTCCTGACG",
"CTCACTAGC","CTATACGGC","CGTTCGCTC","CGTTCACCG","CGTATAGTT","CGGTGTTCC","CGGTGTCAG","CGGTCCTGC","CGGCGACTC","CGGCACGGT",
"CGGATAGCC","CGGAGAGAT","CGCTAATAG","CGCGTTGGC","CGCGCAGAG","CGCACTGCC","CCTTGTCTC","CCTTGGCGT","CCTTCTGAG","CCTTCTCCT",
"CCTTCGACC","CCTTACTTG","CCTGTTCGT","CCTGTATGC","CCTCGGCCG","CCGTTAATT","CCATGTGCG","CCAGTGGTT","CCAGGCATT","CCAGGATCC",
"CCAGCGTTG","CATTCCGAT","CATTATACC","CATGTTGAG","ATTGCGTGT","ATTGCGGAC","ATTGCGCCG","ATTGACTTG","ATTCGGCTG","ATTCGCGAG",
"ATTCCAAGT","ATTATCTTC","ATTACTGTT","ATTACACTC","ATGTTCTAT","ATGTTACGC","ATGTGTATC","ATGTGGCAG","ATGTCTGTG","ATGGTGCAT",
"ATGCTTACT","ATGCTGTCC","ATGCTCGGC","ATGAGGTTC","ATGAGAGTG","ATCTTGGCT","ATCTGTGCG","ATCGGTTCC","ATCATGCTC","ATCATCACT",
"ATATCTTAT","ATAGGCGCC","AGTTGGTAT","AGTTGAGCC","AGTGCGACC","AGGTGCTAC","AGGCTTGCG","AGGCCTTCC","AGGCACCTT","AGGAATATG",
"AGCGGCCAG","AGCCTGGTC","AGCCTGACT","AGCAATCCG","AGAGATGTT","AGAGAATTC","ACTCGCTTG","ACTCGACCT","ACGTACACC","ACGGATGGT",
"ACCAGTCTG","ACATTCGGC","ACATGAGGT","ACACTAATT"
)
B384_cell_key2 = ("TTGTGTTGT","TTGTGGTAG","TTGTGCGGA","TTGTCTGTT","TTGTCTAAG","TTGTCATAT","TTGTCACGA","TTGTATGAA","TTGTACAGT","TTGGTTAAT",
"TTGGTGCAA","TTGGTCGAG","TTGGTATTA","TTGGCACAG","TTGGATACA","TTGGAAGTG","TTGCGGTTA","TTGCCATTG","TTGCACGCG","TTGCAAGGT",
"TTGATGTAT","TTGATAATT","TTGAGACGT","TTGACTACT","TTGACCGAA","TTCTGGTCT","TTCTGCACA","TTCTCCTTA","TTCTCCGCT","TTCTAGGTA",
"TTCTAATCG","TTCGTCGTA","TTCGTAGAT","TTCGGCTTG","TTCGGAATA","TTCGCCAGA","TTCGATTGT","TTCGATCAG","TTCCTCGGT","TTCCGGCAG",
"TTCCGCATT","TTCCAATTA","TTCATTGAA","TTCATGCTG","TTCAGGAGT","TTCACTATA","TTCAACTCT","TTCAACGTG","TTATGCGTT","TTATGATTG",
"TTATCCTGT","TTATCCGAG","TTATATTAT","TTAGGCGCG","TTACTGGAA","TTACTAGTT","TTACGTGGT","TTACGATAT","TTACCTAGA","TTACATGAG",
"TTACAGCGT","TTACACGGA","TTACACACT","TTAATCAGT","TTAATAGGA","TTAAGTGTG","TTAACCTTG","TTAACACAA","TGTTCACTT","TGTTCAAGA",
"TGTTAAGTG","TGTGTTATG","TGTGTCCAA","TGTGGAGCG","TGTCAGTTA","TGTCAGAAG","TGGTTAGTT","TGGTTACAA","TGGCGTTAT","TGGCGCCAA",
"TGGAGTCTT","TGCGTATTG","TGATAGAGA","TGAGGTATT","TGAGAATCT","TCTTGGTAA","TCTTCATAG","TCTGTCCTT","TCTGGAATT","TCTACCGCG",
"TCGTTCGAA","TCGTCAGTG","TCGACGAGA","TCATGGCTT","TCACACTTA","TATTCCGAA","TATTATGGT","TATGCTATT","TATCAAGGA","TAGTTCAAT",
"TAGCTGCTT","TAGAGGAAG","TACCTGTTA","TACACCTGT","GTTGTGCGT","GTTGGCTAT","GTTGCCAAG","GTTGACCTT","GTTCTGCTA","GTTCTGAAT",
"GTTCTATCA","GTTCGCGTG","GTTCCTTAT","GTTAGCAGT","GTTACTGTG","GTTACTCAA","GTTAAGAGA","GTTAACTTA","GTGTCGGCA","GTGTCCATT",
"GTGCTTGAG","GTGCTCGTT","GTGCTCACA","GTGCCTGGA","GTCTTGTCG","GTCTTGATT","GTCTTCCGT","GTCTTAAGA","GTCTCATCT","GTCTACGAG",
"GTCGTTGCT","GTCGTGTTA","GTCGGTAAT","GTCGGATGT","GTCGAGCTG","GTCCGGACT","GTCCAACAT","GTCAGACGA","GTCAGAATT","GTCACTCTT",
"GTCAAGGAA","GTATGTCTT","GTATGTACA","GTATCGGTT","GTATATGTA","GTATACAAT","GTAGTTAAG","GTAGTCGAT","GTAGCCTTA","GTAGATACT",
"GTACGATTA","GTACAGTCT","GTAATTCGT","GCTTGGCAG","GCTTGCTTG","GCTTGAGGA","GCTTCATTA","GCTTATGCG","GCTGTGTAG","GCTGTCATG",
"GCTGGTTGT","GCTGGACTG","GCTGCCTAA","GCTGATATT","GCTCTTAGT","GCTCTATTG","GCTCGCCGT","GCTCCGCTG","GCTATTCTG","GCTATACGA",
"GCTACTAAG","GCTACATGT","GCTAACTCT","GCGTTGTAA","GCGTTCTCT","GCGTGCGTA","GCGTCTTGA","GCGTCCGAT","GCGTAAGAG","GCGCTTACG",
"GCGCGGATT","GCGCCATAT","GCGCATGAA","GCGATCAAT","GCGAGCCTT","GCGAGATTG","GCGAGAACA","GCCTTGGTA","GCCTTCTAG","GCCTTCACA",
"GCCTGAGTG","GCCTCACGT","GCCGGCGAA","GCCGCACAA","GCCATGCTT","GCCATATAT","GCCAATTCG","GCATTCGTT","GCATGATGT","GCAGTTGGA",
"GCAGTGTCT","GCACTTGTG","GCAATCTGT","GCAACACTT","GATTGTATT","GATTGCGAG","GATTCCAGT","GATTCATAT","GATTATCAG","GATTAGGTT",
"GATGTTGCG","GATGGATCT","GATGCTGAT","GATGCCTTG","GATCTCCTT","GATCGCTTA","GATATTGAA","GATATTACT","GAGTGTTAT","GAGCTCAGT",
"GAGCGTGCT","GAGCGTCGA","GAGCGGTTG","GAGCGACTT","GAGCCGAAT","GAGATAGAT","GAGACCTAT","GACGGTCGT","GACGCAGGT","GACGATATG",
"GACCTATCT","GAATTAGGA","GAATCAGCT","GAAGTTCAT","GAAGTGGTT","GAAGTATTG","GAAGGCATT","GAACGCTGT","CTTGTCCAG","CTTGGATTG",
"CTTGCTGAA","CTTGCCGTG","CTTGATTCT","CTTCTGTCG","CTTCGGCGT","CTTATGAGT","CTTACCGAT","CTGTTAGGT","CTGTCGTCT","CTGTATAAT",
"CTGGCTCAT","CTGGATGCG","CTGCGTGTG","CTGCGCGGT","CTGCCGATT","CTGCATTGT","CTGATTAAG","CTGAGATAT","CTGACCTGT","CTCGTATCT",
"CTCGGCAAG","CTCGCAATT","CTCCTGCTT","CTCCTAAGT","CTCCGGATG","CTCCGAGCG","CTCACAGGT","CTATTCTAT","CTATTAGTG","CTATGAATT",
"CTACATATT","CGTGGCATT","CGTCTTAAT","CGTCTGGTT","CGTCACTGT","CGTAGGTCT","CGGTTCGAG","CGGTTCATT","CGGTGCTCT","CGGTAATTG",
"CGGCCTGAT","CGGATATAG","CGGAATATT","CGCTCCAAT","CGCGTTCGT","CGCAGGTTG","CGAGGATGT","CGAGCTGTT","CGACGGCTT","CCTTGTGTG",
"CCTGTCTCA","CCTGACTAT","CCTACCTTG","CCGTAGATT","CCGGCTGGT","CATCGGACG","CATCGATAA","CATCCTTCT","CAGTTCTGT","CAGTGCCAG",
"CAGGCACTG","CAGCCTCTT","CACTTATAT","CACTGGTCG","CACTGCATG","CACGCGTTG","CACGATGTT","CACCATCTG","CACAGGCGT","ATTGTACAA",
"ATTGGTATG","ATTGCTAAT","ATTGCATAG","ATTGCAGTT","ATTCTGCAG","ATTCTACGT","ATTCGGATT","ATTCCGTTG","ATTCATCAA","ATTCAAGAG",
"ATTAGCCTT","ATTAATATT","ATGTTAGAG","ATGTTAACT","ATGTAGTCG","ATGGTGTAG","ATGGATTAT","ATCTTGAAG","ATCTGATAT","ATCTCAGAA",
"ATCGCTCAA","ATCGCGTCG","ATCCATGGT","ATCATGAGA","ATCATAGTT","ATCAGCGAG","ATCACCATT","ATAGTAATT","ATAGCTGTG","ATACTCTCG",
"ATACCTCAT","AGTTGCGCG","AGTTGAATT","AGTTATGAT","AGTGTCCGT","AGTGGCTTG","AGTGCTTCT","AGTATCATT","AGTACACAA","AGGTATGCG",
"AGGTATAGT","AGGCTACTT","AGGCCAGGT","AGGAGCGAT","AGCTTATAG","AGCTCTAGA","AGCGTGTAT","AGCGTCACA","AGCCTTCAT","AGCCTGTCG",
"AGCCTCGAG","AGCACTGAA","AGATGTACG","AGAGTTAAT","AGACCTCTG","ACTTCTATA","ACTGTCGAG","ACTGTATGT","ACTCTGTAA","ACTCGCGAA",
"ACTAGATCT","ACTAACGTT","ACGTTACTG","ACGTGGAAT","ACGGACTCT","ACGCCTAAT","ACGCCGTTA","ACGACGTGT","ACCTCGCAT","ACCATCATA",
"ACATATATT","ACAGGCACA","ACACCTGAG","ACACATTCT"
)
B384_cell_key3 = ("TTGTGGCTG","TTGTGGAGT","TTGTGCGAC","TTGTCTTCA","TTGTAAGAT","TTGGTTCTG","TTGGTGCGT","TTGGTCTAC","TTGGTAACT","TTGGCGTGC",
"TTGGATTAG","TTGGAGACG","TTGGAATCA","TTGCGGCGA","TTGCGCTCG","TTGCCTTAC","TTGCCGGAT","TTGCATGCT","TTGCACGTC","TTGCACCAT",
"TTGAACCTG","TTCTCGCGT","TTCTCAACT","TTCTACTCA","TTCGTCCAT","TTCGGATAC","TTCGGACGT","TTCGCAATC","TTCCGGTGC","TTCCGACTG",
"TTCATTATG","TTCATGGAT","TTCAGCGCA","TTCACCTCG","TTCAAGCAG","TTCAACTAC","TTATGCCAG","TTATGCATC","TTATCGTAC","TTATACCTA",
"TTATAATAG","TTATAAGTC","TTAGTTAGC","TTAGCTCAT","TTAGCACTA","TTAGATATG","TTACTACGA","TTACCGTCA","TTACAGAGC","TTAATTGCA",
"TTAACAGAT","TGTTGGCTA","TGTTGATGA","TGTTAAGCT","TGTGGCCGA","TGTGCTAGC","TGTGCGTCA","TGTCGCAGT","TGTCGAGCA","TGTACAACG",
"TGGTTCCGA","TGGTTCACT","TGGTCAAGT","TGGCTTGTA","TGGCTGTCG","TGGCGTATG","TGGCGCGCT","TGGATGTAC","TGGACTTGC","TGGAATACT",
"TGCTAGCGA","TGCGTTGCT","TGCGGTCTG","TGCGCTTAG","TGCGCGACG","TGCCTGCAT","TGCCTAGAC","TGCACGAGT","TGAGTGTGC","TGAGGCTCG",
"TCTTCCGTC","TCTTATAGT","TCTTACCAT","TCTGTTGTC","TCTGTTACT","TCTGGCTAG","TCTCAGATC","TCTAGTTGA","TCTAGTACG","TCGTACTAC",
"TCGGTGTAG","TCGGCTGCT","TCGCTACTG","TCGATCACG","TCGAGGCAT","TCCGGCGTC","TCCGGAGCT","TCCGCTCGT","TCCGAGTAC","TCCATTCAT",
"TCCATGGTC","TCCAAGTCG","TCATTACGT","TCATGCACT","TCAGGTTGC","TCAGACCGT","TCACTCAGT","TCAAGCTCA","TATTGCGCA","TATTCGGCT",
"TATTCCAGC","TATTCATCA","TATGTTCAG","TATGGTATG","TATGCAAGT","TATCTGGTC","TATCTGACT","TATCCAGAT","TATCAGTCG","TATCACGCT",
"TAGGCGCGA","TAGGCACAT","TAGGATCGT","TAGCATTGC","TAGAGTTAC","TAGACTGAT","TACTTGTCG","TACGTCCGA","TACCGTACT","TACCGCGAT",
"TACCAGGAC","TACAGAAGT","TAAGTGCAT","TAAGCTACT","GTTGACCGA","GTTCTCGAC","GTTCCTGCT","GTTATGATG","GTGCTTGCA","GTGCCGCGT",
"GTATTGCTG","GTATTCCGA","GTATTAAGC","GTATGACGT","GTAGTTGTC","GTAGTACAT","GTAGCTCGA","GGTTGCTCA","GGTTGAGTA","GGTTAACGT",
"GGTGTGGCA","GGTCTTCAG","GGTCGTCTA","GGTCGGCGT","GGTCCGACT","GGTCATGTC","GGTCACATG","GGTAGTGCT","GGTAGCGTC","GGTACCAGT",
"GGTAAGGAT","GGCTTGTGC","GGCTTGACT","GGCTTACGA","GGCTGTAGT","GGCTGGCAG","GGCTCCATC","GGCGTGGAT","GGCGTAATC","GGCGCAAGT",
"GGCGAGTAG","GGCGACCGT","GGCCTGTCA","GGCCATTGC","GGCACTCTG","GGATGTCAT","GGAGTAACT","GGAGAACGA","GGACTGGCT","GGACGTTCA",
"GGAACGTGC","GCTGTCCAT","GCTGGTTCA","GCTGCAACT","GCTCGTTAC","GCTATAGAT","GCTAGTCGT","GCTACCATG","GCGTTCTGA","GCGTGTTAG",
"GCGGTATCG","GCGGAGCAT","GCGCGGTGC","GCGCCTAGT","GCGCCGGCT","GCCTTCATG","GCCATACTG","GCATGTTGA","GCATGCTAC","GCAGTATAC",
"GCAGGTACT","GCAGCGCGT","GCACCTCAT","GCAATTCGA","GATTGCCGT","GATGAACAT","GATCTTCGA","GATCTGCAT","GAGTGGCAT","GAGTCGGAC",
"GAGTATGAT","GAGGCGAGT","GAGGCAACG","GAGCGCACT","GAATAGGCT","ATTGTCACT","ATTGTATCA","ATTGGTCAG","ATTGGCGAT","ATTGATCGT",
"ATTCGTAGT","ATTCATACG","ATTCAGGAC","ATTACTTCA","ATTAATTAG","ATTAAGCAT","ATGTCTCTA","ATGTAGCGT","ATGGCATAC","ATGGAGATC",
"ATGGACTCG","ATGGAACGA","ATGCTTCAT","ATGCTCGCT","ATGCGACGT","ATGCCGTAG","ATGAGTTCG","ATGACTATC","ATGACCGAC","ATCTTATGC",
"ATCTTACTA","ATCTATCAG","ATCGTGTAC","ATCGTCTGA","ATCGGCATG","ATCGCGAGC","ATCGCAACG","ATCGATGCT","ATCGAATAG","ATCCTTCTG",
"ATCCTGCGT","ATCCGCACT","ATCCATTAC","ATCCAAGCA","ATCAGATCA","ATCACACAT","ATCAACGTC","ATCAACCGA","ATATTGAGT","ATATTCGTC",
"ATATTACAG","ATATCTTGA","ATATCGCAT","ATATCAATC","ATAGTCCTG","ATAGGTCTA","ATAGCTGAC","ATAGCGGTA","AGTTCGCTG","AGTTACAGC",
"AGTTAACTA","AGTGCAATC","AGTCTGGTA","AGTCTGAGC","AGTCTACAT","AGTCGAACT","AGTCCATCG","AGTCATTCA","AGTATCCAG","AGTAGACTG",
"AGTAATCGA","AGTAAGTGC","AGGTTGGCT","AGGTTCTAG","AGGTGTTCA","AGGTGCCAT","AGGTCTGAT","AGGTCGTAC","AGGTCAGCA","AGGCTTATC",
"AGGCTATGA","AGGCCGACG","AGGCCAAGC","AGGCAGGTC","AGGCAAGAT","AGGAGCAGT","AGGACCGCT","AGGAATTAC","AGCTTGGAC","AGCTTAAGT",
"AGCTACACG","AGCGTTACG","AGCGGTGCA","AGCGGAGTC","AGCGGACGA","AGCGCGCTA","AGCGATAGC","AGCGACTCA","AGCCTCTAC","AGCCGTCGT",
"AGCATGATC","AGCACTTCG","AGCACGGCA","AGATTCTGA","AGATTAGAT","AGATGATAG","AGATATGTA","AGATACCGT","AGAGTGCGT","AGAGCCGAT",
"AGACTCACT","ACTTGCCTA","ACTTGAGCA","ACTTCTAGC","ACTTCGACT","ACTTAGTAC","ACTGTTGAT","ACTGTAACG","ACTGGTATC","ACTGACGTC",
"ACTGAAGCT","ACTCTGATG","ACTCCTGAC","ACTCCGCTA","ACTCAACTG","ACTATTGCA","ACTAGGCAG","ACTACGCGT","ACTAATACT","ACGTTCGTA",
"ACGTGTGCT","ACGTGTATG","ACGTGGAGC","ACGTCTTCG","ACGTCAGTC","ACGGTCTCA","ACGGTCCGT","ACGGTACAG","ACGGCGCTG","ACGCTGCGA",
"ACGCGTGTA","ACGCGCCAG","ACGATGTCG","ACGATGGAT","ACGATCTAC","ACGAGCTGA","ACGAGCATC","ACGAATCGT","ACGAACGCA","ACCTTGTAG",
"ACCTGTTGC","ACCTGTCAT","ACCTCGATC","ACCTAGGTA","ACCTACTGA","ACCTAATCG","ACCGTAGCA","ACCGGTAGT","ACCGGCTAC","ACCGCTTCA",
"ACATTGTGC","ACATTCTCG","ACATGGCTG","ACATGACGA","ACATATGAT","ACATATACG","ACAGCGTAC","ACACTTGCT","ACACTATCA","ACACGCATG",
"ACACCAGTA","ACACCAACT","ACACATAGT","ACACACCTA"
)
def label_sections_to_index(label):
"""
Return the cell_index integer based on input 3 part cell label string
"""
cl1, cl2, cl3 = [int(n) for n in label.split('-')]
return (cl1 - 1) * 384 * 384 + (cl2 - 1) * 384 + (cl3 - 1) + 1
# print(label_sections_to_index('1-1-1'))
# print(label_sections_to_index('33-78-21'))
# print(label_sections_to_index('43-12-77'))
# print(label_sections_to_index('96-96-96'))
# print(label_sections_to_index('135-43-344'))
# print(label_sections_to_index('384-384-384'))
# print('-')
#----------------------------------
def index_to_label_sections(index):
zerobased = int(index) - 1
cl1 = (int((zerobased) / 384 / 384) % 384) + 1
cl2 = (int((zerobased) / 384) % 384) + 1
cl3 = (zerobased % 384) + 1
return f'{cl1}-{cl2}-{cl3}'
# print(index_to_label_sections(1))
# print(index_to_label_sections(4748181))
# print(index_to_label_sections(6197453))
# print(index_to_label_sections(14044896))
# print(index_to_label_sections(19775576))
# print(index_to_label_sections(56623104))
# print('-')
#----------------------------------
def index_to_sequence(index, bead_version):
zerobased = int(index) - 1
cl1 = (int((zerobased) / 384 / 384) % 384) + 1
cl2 = (int((zerobased) / 384) % 384) + 1
cl3 = (zerobased % 384) + 1
if bead_version == 'v1':
cls1_sequence = A96_cell_key1[cl1-1]
cls2_sequence = A96_cell_key2[cl2-1]
cls3_sequence = A96_cell_key3[cl3-1]
return f'{cls1_sequence}{v1_linker1}{cls2_sequence}{v1_linker2}{cls3_sequence}'
elif bead_version == 'Enh':
diversityInsert = ''
if 1 <= cl1 <= 24:
diversityInsert = ''
elif 25 <= cl1 <= 48:
diversityInsert = 'A'
elif 49 <= cl1 <= 72:
diversityInsert = 'GT'
else: # 73 <= cl1 <= 96:
diversityInsert = 'TCA'
cls1_sequence = A96_cell_key1[cl1-1]
cls2_sequence = A96_cell_key2[cl2-1]
cls3_sequence = A96_cell_key3[cl3-1]
return f'{diversityInsert}{cls1_sequence}{Enh_linker1}{cls2_sequence}{Enh_linker2}{cls3_sequence}'
elif bead_version == 'EnhV2':
diversityInsert = ''
subIndex = ((cl1-1) % 96) + 1
if 1 <= subIndex <= 24:
diversityInsert = ''
elif 25 <= subIndex <= 48:
diversityInsert = 'A'
elif 49 <= subIndex <= 72:
diversityInsert = 'GT'
else: # 73 <= subIndex <= 96:
diversityInsert = 'TCA'
cls1_sequence = B384_cell_key1[cl1-1]
cls2_sequence = B384_cell_key2[cl2-1]
cls3_sequence = B384_cell_key3[cl3-1]
return f'{diversityInsert}{cls1_sequence}{Enh_linker1}{cls2_sequence}{Enh_linker2}{cls3_sequence}'
# print(index_to_sequence(4748181, 'Enh'))
# print(index_to_sequence(52923177, 'EnhV2'))
#----------------------------------
def create_cell_index_fasta_V1():
with open('Rhapsody_cellBarcodeV1_IndexToSequence.fasta', 'w') as f:
for cl1 in range(1, 96+1):
for cl2 in range(1, 96+1):
for cl3 in range(1, 96+1):
index = label_sections_to_index(f'{cl1}-{cl2}-{cl3}')
sequence = index_to_sequence(index, 'v1')
f.write(f'>{index}\n')
f.write(f'{sequence}\n')
#create_cell_index_fasta_V1()
def create_cell_index_fasta_Enh():
with open('Rhapsody_cellBarcodeEnh_IndexToSequence.fasta', 'w') as f:
for cl1 in range(1, 96+1):
for cl2 in range(1, 96+1):
for cl3 in range(1, 96+1):
index = label_sections_to_index(f'{cl1}-{cl2}-{cl3}')
sequence = index_to_sequence(index, 'Enh')
f.write(f'>{index}\n')
f.write(f'{sequence}\n')
#create_cell_index_fasta_Enh()
def create_cell_index_fasta_EnhV2():
with open('Rhapsody_cellBarcodeEnhV2_IndexToSequence.fasta', 'w') as f:
for cl1 in range(1, 384+1):
for cl2 in range(1, 384+1):
for cl3 in range(1, 384+1):
index = label_sections_to_index(f'{cl1}-{cl2}-{cl3}')
sequence = index_to_sequence(index, 'EnhV2')
f.write(f'>{index}\n')
f.write(f'{sequence}\n')
#create_cell_index_fasta_EnhV2()

60
src/bd_rhapsody/test_data/BDAbSeq_ImmuneDiscoveryPanel.fasta Normal file
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@@ -0,0 +1,60 @@
>CD11c:B-LY6|ITGAX|AHS0056|pAbO Catalog_940024
ATGCGTTGCGAGAGATATGCGTAGGTTGCTGATTGG
>CD14:MPHIP9|CD14|AHS0037|pAbO Catalog_940005
TGGCCCGTGGTAGCGCAATGTGAGATCGTAATAAGT
>CXCR5|CXCR5|AHS0039|pAbO Catalog_940042
AGGAAGGTCGATTGTATAACGCGGCATTGTAACGGC
>CD19:SJ25C1|CD19|AHS0030|pAbO Catalog_940004
TAGTAATGTGTTCGTAGCCGGTAATAATCTTCGTGG
>CD25:2A3|IL2RA|AHS0026|pAbO Catalog_940009
AGTTGTATGGGTTAGCCGAGAGTAGTGCGTATGATT
>CD27:M-T271|CD27|AHS0025|pAbO Catalog_940018
TGTCCGGTTTAGCGAATTGGGTTGAGTCACGTAGGT
>CD278|ICOS|AHS0012|pAbO Catalog_940043
ATAGTCCGCCGTAATCGTTGTGTCGCTGAAAGGGTT
>CD279:EH12-1|PDCD1|AHS0014|pAbO Catalog_940015
ATGGTAGTATCACGACGTAGTAGGGTAATTGGCAGT
>CD3:UCHT1|CD3E|AHS0231|pAbO Catalog_940307
AGCTAGGTGTTATCGGCAAGTTGTACGGTGAAGTCG
>GITR|TNFRSF18|AHS0104|pAbO Catalog_940096
TCTGTGTGTCGGGTTGAATCGTAGTGAGTTAGCGTG
>Tim3|HAVCR2|AHS0016|pAbO Catalog_940066
TAGGTAGTAGTCCCGTATATCCGATCCGTGTTGTTT
>CD4:SK3|CD4|AHS0032|pAbO Catalog_940001
TCGGTGTTATGAGTAGGTCGTCGTGCGGTTTGATGT
>CD45RA:HI100|PTPRC|AHS0009|pAbO Catalog_940011
AAGCGATTGCGAAGGGTTAGTCAGTACGTTATGTTG
>CD56:NCAM16.2|NCAM1|AHS0019|pAbO Catalog_940007
AGAGGTTGAGTCGTAATAATAATCGGAAGGCGTTGG
>CD62L:DREG-56|SELL|AHS0049|pAbO Catalog_940041
ATGGTAAATATGGGCGAATGCGGGTTGTGCTAAAGT
>CCR7|CCR7|AHS0273|pAbO Catalog_940394
AATGTGTGATCGGCAAAGGGTTCTCGGGTTAATATG
>CXCR6|CXCR6|AHS0148|pAbO Catalog_940234
GTGGTTGGTTATTCGGACGGTTCTATTGTGAGCGCT
>CD127|IL7R|AHS0028|pAbO Catalog_940012
AGTTATTAGGCTCGTAGGTATGTTTAGGTTATCGCG
>CD134:ACT35|TNFRSF4|AHS0013|pAbO Catalog_940060
GGTGTTGGTAAGACGGACGGAGTAGATATTCGAGGT
>CD28:L293|CD28|AHS0138|pAbO Catalog_940226
TTGTTGAGGATACGATGAAGCGGTTTAAGGGTGTGG
>CD272|BTLA|AHS0052|pAbO Catalog_940105
GTAGGTTGATAGTCGGCGATAGTGCGGTTGAAAGCT
>CD8:SK1|CD8A|AHS0228|pAbO Catalog_940305
AGGACATAGAGTAGGACGAGGTAGGCTTAAATTGCT
>HLA-DR|CD74|AHS0035|pAbO Catalog_940010
TGTTGGTTATTCGTTAGTGCATCCGTTTGGGCGTGG
>CD16:3G8|FCGR3A|AHS0053|pAbO Catalog_940006
TAAATCTAATCGCGGTAACATAACGGTGGGTAAGGT
>CD183|CXCR3|AHS0031|pAbO Catalog_940030
AAAGTGTTGGCGTTATGTGTTCGTTAGCGGTGTGGG
>CD196|CCR6|AHS0034|pAbO Catalog_940033
ACGTGTTATGGTGTTGTTCGAATTGTGGTAGTCAGT
>CD137|TNFRSF9|AHS0003|pAbO Catalog_940055
TGACAAGCAACGAGCGATACGAAAGGCGAAATTAGT
>CD161:HP-3G10|KLRB1|AHS0205|pAbO Catalog_940283
TTTAGGACGATTAGTTGTGCGGCATAGGAGGTGTTC
>IgM|IGHM|AHS0198|pAbO Catalog_940276
TTTGGAGGGTAGCTAGTTGCAGTTCGTGGTCGTTTC
>IgD|IGHD|AHS0058|pAbO Catalog_940026
TGAGGGATGTATAGCGAGAATTGCGACCGTAGACTT

24
src/bd_rhapsody/test_data/SampleTagSequences_HomoSapiens_ver1.fasta Normal file
View File

@@ -0,0 +1,24 @@
>SampleTag01_hs|stAbO
GTTGTCAAGATGCTACCGTTCAGAGATTCAAGGGCAGCCGCGTCACGATTGGATACGACTGTTGGACCGG
>SampleTag02_hs|stAbO
GTTGTCAAGATGCTACCGTTCAGAGTGGATGGGATAAGTGCGTGATGGACCGAAGGGACCTCGTGGCCGG
>SampleTag03_hs|stAbO
GTTGTCAAGATGCTACCGTTCAGAGCGGCTCGTGCTGCGTCGTCTCAAGTCCAGAAACTCCGTGTATCCT
>SampleTag04_hs|stAbO
GTTGTCAAGATGCTACCGTTCAGAGATTGGGAGGCTTTCGTACCGCTGCCGCCACCAGGTGATACCCGCT
>SampleTag05_hs|stAbO
GTTGTCAAGATGCTACCGTTCAGAGCTCCCTGGTGTTCAATACCCGATGTGGTGGGCAGAATGTGGCTGG
>SampleTag06_hs|stAbO
GTTGTCAAGATGCTACCGTTCAGAGTTACCCGCAGGAAGACGTATACCCCTCGTGCCAGGCGACCAATGC
>SampleTag07_hs|stAbO
GTTGTCAAGATGCTACCGTTCAGAGTGTCTACGTCGGACCGCAAGAAGTGAGTCAGAGGCTGCACGCTGT
>SampleTag08_hs|stAbO
GTTGTCAAGATGCTACCGTTCAGAGCCCCACCAGGTTGCTTTGTCGGACGAGCCCGCACAGCGCTAGGAT
>SampleTag09_hs|stAbO
GTTGTCAAGATGCTACCGTTCAGAGGTGATCCGCGCAGGCACACATACCGACTCAGATGGGTTGTCCAGG
>SampleTag10_hs|stAbO
GTTGTCAAGATGCTACCGTTCAGAGGCAGCCGGCGTCGTACGAGGCACAGCGGAGACTAGATGAGGCCCC
>SampleTag11_hs|stAbO
GTTGTCAAGATGCTACCGTTCAGAGCGCGTCCAATTTCCGAAGCCCCGCCCTAGGAGTTCCCCTGCGTGC
>SampleTag12_hs|stAbO
GTTGTCAAGATGCTACCGTTCAGAGGCCCATTCATTGCACCCGCCAGTGATCGACCCTAGTGGAGCTAAG

0
src/bd_rhapsody/bd_rhapsody_make_reference/test_data/reference_small.fa → src/bd_rhapsody/test_data/reference_small.fa
View File

0
src/bd_rhapsody/bd_rhapsody_make_reference/test_data/reference_small.gtf → src/bd_rhapsody/test_data/reference_small.gtf
View File

141
src/bd_rhapsody/test_data/script.sh Normal file
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@@ -0,0 +1,141 @@
#!/bin/bash
TMP_DIR=/tmp/bd_rhapsody_make_reference
OUT_DIR=src/bd_rhapsody/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
# download bdabseq immunediscoverypanel fasta
# note: was contained in http://bd-rhapsody-public.s3.amazonaws.com/Rhapsody-Demo-Data-Inputs/12WTA-ABC-SMK-EB-5kJRT.tar
cat > $OUT_DIR/BDAbSeq_ImmuneDiscoveryPanel.fasta <<EOF
>CD11c:B-LY6|ITGAX|AHS0056|pAbO Catalog_940024
ATGCGTTGCGAGAGATATGCGTAGGTTGCTGATTGG
>CD14:MPHIP9|CD14|AHS0037|pAbO Catalog_940005
TGGCCCGTGGTAGCGCAATGTGAGATCGTAATAAGT
>CXCR5|CXCR5|AHS0039|pAbO Catalog_940042
AGGAAGGTCGATTGTATAACGCGGCATTGTAACGGC
>CD19:SJ25C1|CD19|AHS0030|pAbO Catalog_940004
TAGTAATGTGTTCGTAGCCGGTAATAATCTTCGTGG
>CD25:2A3|IL2RA|AHS0026|pAbO Catalog_940009
AGTTGTATGGGTTAGCCGAGAGTAGTGCGTATGATT
>CD27:M-T271|CD27|AHS0025|pAbO Catalog_940018
TGTCCGGTTTAGCGAATTGGGTTGAGTCACGTAGGT
>CD278|ICOS|AHS0012|pAbO Catalog_940043
ATAGTCCGCCGTAATCGTTGTGTCGCTGAAAGGGTT
>CD279:EH12-1|PDCD1|AHS0014|pAbO Catalog_940015
ATGGTAGTATCACGACGTAGTAGGGTAATTGGCAGT
>CD3:UCHT1|CD3E|AHS0231|pAbO Catalog_940307
AGCTAGGTGTTATCGGCAAGTTGTACGGTGAAGTCG
>GITR|TNFRSF18|AHS0104|pAbO Catalog_940096
TCTGTGTGTCGGGTTGAATCGTAGTGAGTTAGCGTG
>Tim3|HAVCR2|AHS0016|pAbO Catalog_940066
TAGGTAGTAGTCCCGTATATCCGATCCGTGTTGTTT
>CD4:SK3|CD4|AHS0032|pAbO Catalog_940001
TCGGTGTTATGAGTAGGTCGTCGTGCGGTTTGATGT
>CD45RA:HI100|PTPRC|AHS0009|pAbO Catalog_940011
AAGCGATTGCGAAGGGTTAGTCAGTACGTTATGTTG
>CD56:NCAM16.2|NCAM1|AHS0019|pAbO Catalog_940007
AGAGGTTGAGTCGTAATAATAATCGGAAGGCGTTGG
>CD62L:DREG-56|SELL|AHS0049|pAbO Catalog_940041
ATGGTAAATATGGGCGAATGCGGGTTGTGCTAAAGT
>CCR7|CCR7|AHS0273|pAbO Catalog_940394
AATGTGTGATCGGCAAAGGGTTCTCGGGTTAATATG
>CXCR6|CXCR6|AHS0148|pAbO Catalog_940234
GTGGTTGGTTATTCGGACGGTTCTATTGTGAGCGCT
>CD127|IL7R|AHS0028|pAbO Catalog_940012
AGTTATTAGGCTCGTAGGTATGTTTAGGTTATCGCG
>CD134:ACT35|TNFRSF4|AHS0013|pAbO Catalog_940060
GGTGTTGGTAAGACGGACGGAGTAGATATTCGAGGT
>CD28:L293|CD28|AHS0138|pAbO Catalog_940226
TTGTTGAGGATACGATGAAGCGGTTTAAGGGTGTGG
>CD272|BTLA|AHS0052|pAbO Catalog_940105
GTAGGTTGATAGTCGGCGATAGTGCGGTTGAAAGCT
>CD8:SK1|CD8A|AHS0228|pAbO Catalog_940305
AGGACATAGAGTAGGACGAGGTAGGCTTAAATTGCT
>HLA-DR|CD74|AHS0035|pAbO Catalog_940010
TGTTGGTTATTCGTTAGTGCATCCGTTTGGGCGTGG
>CD16:3G8|FCGR3A|AHS0053|pAbO Catalog_940006
TAAATCTAATCGCGGTAACATAACGGTGGGTAAGGT
>CD183|CXCR3|AHS0031|pAbO Catalog_940030
AAAGTGTTGGCGTTATGTGTTCGTTAGCGGTGTGGG
>CD196|CCR6|AHS0034|pAbO Catalog_940033
ACGTGTTATGGTGTTGTTCGAATTGTGGTAGTCAGT
>CD137|TNFRSF9|AHS0003|pAbO Catalog_940055
TGACAAGCAACGAGCGATACGAAAGGCGAAATTAGT
>CD161:HP-3G10|KLRB1|AHS0205|pAbO Catalog_940283
TTTAGGACGATTAGTTGTGCGGCATAGGAGGTGTTC
>IgM|IGHM|AHS0198|pAbO Catalog_940276
TTTGGAGGGTAGCTAGTTGCAGTTCGTGGTCGTTTC
>IgD|IGHD|AHS0058|pAbO Catalog_940026
TGAGGGATGTATAGCGAGAATTGCGACCGTAGACTT
EOF
# this was obtained by running the command:
# docker run bdgenomics/rhapsody:2.2.1 cat /rhapsody/control_files/SampleTagSequences_HomoSapiens_ver1.fasta
cat > $OUT_DIR/SampleTagSequences_HomoSapiens_ver1.fasta <<EOF
>SampleTag01_hs|stAbO
GTTGTCAAGATGCTACCGTTCAGAGATTCAAGGGCAGCCGCGTCACGATTGGATACGACTGTTGGACCGG
>SampleTag02_hs|stAbO
GTTGTCAAGATGCTACCGTTCAGAGTGGATGGGATAAGTGCGTGATGGACCGAAGGGACCTCGTGGCCGG
>SampleTag03_hs|stAbO
GTTGTCAAGATGCTACCGTTCAGAGCGGCTCGTGCTGCGTCGTCTCAAGTCCAGAAACTCCGTGTATCCT
>SampleTag04_hs|stAbO
GTTGTCAAGATGCTACCGTTCAGAGATTGGGAGGCTTTCGTACCGCTGCCGCCACCAGGTGATACCCGCT
>SampleTag05_hs|stAbO
GTTGTCAAGATGCTACCGTTCAGAGCTCCCTGGTGTTCAATACCCGATGTGGTGGGCAGAATGTGGCTGG
>SampleTag06_hs|stAbO
GTTGTCAAGATGCTACCGTTCAGAGTTACCCGCAGGAAGACGTATACCCCTCGTGCCAGGCGACCAATGC
>SampleTag07_hs|stAbO
GTTGTCAAGATGCTACCGTTCAGAGTGTCTACGTCGGACCGCAAGAAGTGAGTCAGAGGCTGCACGCTGT
>SampleTag08_hs|stAbO
GTTGTCAAGATGCTACCGTTCAGAGCCCCACCAGGTTGCTTTGTCGGACGAGCCCGCACAGCGCTAGGAT
>SampleTag09_hs|stAbO
GTTGTCAAGATGCTACCGTTCAGAGGTGATCCGCGCAGGCACACATACCGACTCAGATGGGTTGTCCAGG
>SampleTag10_hs|stAbO
GTTGTCAAGATGCTACCGTTCAGAGGCAGCCGGCGTCGTACGAGGCACAGCGGAGACTAGATGAGGCCCC
>SampleTag11_hs|stAbO
GTTGTCAAGATGCTACCGTTCAGAGCGCGTCCAATTTCCGAAGCCCCGCCCTAGGAGTTCCCCTGCGTGC
>SampleTag12_hs|stAbO
GTTGTCAAGATGCTACCGTTCAGAGGCCCATTCATTGCACCCGCCAGTGATCGACCCTAGTGGAGCTAAG
EOF

BIN
src/kallisto/kallisto_index/Kallisto Normal file
View File

Binary file not shown.

94
src/kallisto/kallisto_index/config.vsh.yaml Normal file
View File

@@ -0,0 +1,94 @@
name: kallisto_index
namespace: kallisto
description: |
Build a Kallisto index for the transcriptome to use Kallisto in the mapping-based mode.
keywords: [kallisto, index]
links:
homepage: https://pachterlab.github.io/kallisto/about
documentation: https://pachterlab.github.io/kallisto/manual
repository: https://github.com/pachterlab/kallisto
issue_tracker: https://github.com/pachterlab/kallisto/issues
references:
doi: https://doi.org/10.1038/nbt.3519
license: BSD 2-Clause License
argument_groups:
- name: "Input"
arguments:
- name: "--input"
type: file
description: |
Path to a FASTA-file containing the transcriptome sequences, either in plain text or
compressed (.gz) format.
required: true
- name: "--d_list"
type: file
description: |
Path to a FASTA-file containing sequences to mask from quantification.
- name: "Output"
arguments:
- name: "--index"
type: file
direction: output
example: Kallisto_index
- name: "Options"
arguments:
- name: "--kmer_size"
type: integer
description: |
Kmer length passed to indexing step of pseudoaligners (default: '31').
example: 31
- name: "--make_unique"
type: boolean_true
description: |
Replace repeated target names with unique names.
- name: "--aa"
type: boolean_true
description: |
Generate index from a FASTA-file containing amino acid sequences.
- name: "--distiguish"
type: boolean_true
description: |
Generate index where sequences are distinguished by the sequence names.
- name: "--min_size"
alternatives: ["-m"]
type: integer
description: |
Length of minimizers (default: automatically chosen).
- name: "--ec_max_size"
alternatives: ["-e"]
type: integer
description: |
Maximum number of targets in an equivalence class (default: no maximum).
- name: "--tmp"
alternatives: ["-T"]
type: string
description: |
Path to a directory for temporary files.
example: "tmp"
resources:
- type: bash_script
path: script.sh
test_resources:
- type: bash_script
path: test.sh
- path: test_data
engines:
- type: docker
image: ubuntu:22.04
setup:
- type: docker
run: |
apt-get update && \
apt-get install -y --no-install-recommends wget && \
wget --no-check-certificate https://github.com/pachterlab/kallisto/releases/download/v0.50.1/kallisto_linux-v0.50.1.tar.gz && \
tar -xzf kallisto_linux-v0.50.1.tar.gz && \
mv kallisto/kallisto /usr/local/bin/
runners:
- type: executable
- type: nextflow

21
src/kallisto/kallisto_index/help.txt Normal file
View File

@@ -0,0 +1,21 @@
```
kallisto index
```
kallisto 0.50.1
Builds a kallisto index
Usage: kallisto index [arguments] FASTA-files
Required argument:
-i, --index=STRING Filename for the kallisto index to be constructed
Optional argument:
-k, --kmer-size=INT k-mer (odd) length (default: 31, max value: 31)
-t, --threads=INT Number of threads to use (default: 1)
-d, --d-list=STRING Path to a FASTA-file containing sequences to mask from quantification
--make-unique Replace repeated target names with unique names
--aa Generate index from a FASTA-file containing amino acid sequences
--distinguish Generate index where sequences are distinguished by the sequence name
-T, --tmp=STRING Temporary directory (default: tmp)
-m, --min-size=INT Length of minimizers (default: automatically chosen)
-e, --ec-max-size=INT Maximum number of targets in an equivalence class (default: no maximum)

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#!/bin/bash
## VIASH START
## VIASH END
set -eo pipefail
unset_if_false=( par_make_unique par_aa par_distinguish )
for var in "${unset_if_false[@]}"; do
temp_var="${!var}"
[[ "$temp_var" == "false" ]] && unset $var
done
if [ -n "$par_kmer_size" ]; then
if [[ "$par_kmer_size" -lt 1 || "$par_kmer_size" -gt 31 || $(( par_kmer_size % 2 )) -eq 0 ]]; then
echo "Error: Kmer size must be an odd number between 1 and 31."
exit 1
fi
fi
kallisto index \
-i "${par_index}" \
${par_kmer_size:+--kmer-size "${par_kmer_size}"} \
${par_make_unique:+--make-unique} \
${par_aa:+--aa} \
${par_distinguish:+--distinguish} \
${par_min_size:+--min-size "${par_min_size}"} \
${par_ec_max_size:+--ec-max-size "${par_ec_max_size}"} \
${par_d_list:+--d-list "${par_d_list}"} \
${meta_cpus:+--cpu "${meta_cpus}"} \
${par_tmp:+--tmp "${par_tmp}"} \
"${par_input}"

35
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#!/bin/bash
echo ">>>Test 1: Testing $meta_functionality_name with non-default k-mer size"
"$meta_executable" \
--input "$meta_resources_dir/test_data/transcriptome.fasta" \
--index Kallisto \
--kmer_size 21
echo ">>> Checking whether output exists and is correct"
[ ! -f "Kallisto" ] && echo "Kallisto index does not exist!" && exit 1
[ ! -s "Kallisto" ] && echo "Kallisto index is empty!" && exit 1
kallisto inspect Kallisto 2> test.txt
grep "number of k-mers: 989" test.txt || { echo "The content of the index seems to be incorrect." && exit 1; }
################################################################################
echo ">>>Test 2: Testing $meta_functionality_name with d_list argument"
"$meta_executable" \
--input "$meta_resources_dir/test_data/transcriptome.fasta" \
--index Kallisto \
--d_list "$meta_resources_dir/test_data/d_list.fasta"
echo ">>> Checking whether output exists and is correct"
[ ! -f "Kallisto" ] && echo "Kallisto index does not exist!" && exit 1
[ ! -s "Kallisto" ] && echo "Kallisto index is empty!" && exit 1
kallisto inspect Kallisto 2> test.txt
grep "number of k-mers: 959" test.txt || { echo "The content of the index seems to be incorrect." && exit 1; }
echo "All tests succeeded!"
exit 0

5
src/kallisto/kallisto_index/test_data/d_list.fasta Normal file
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@@ -0,0 +1,5 @@
>YAL067W-A CDS=1-228
ATGCCAATTATAGGGGTGCCGAGGTGCCTTATAAAACCCTTTTCTGTGCCTGTGACATTTCCTTTTTCGG
TCAAAAAGAATATCCGAATTTTAGATTTGGACCCTCGTACAGAAGCTTATTGTCTAAGCCTGAATTCAGT
CTGCTTTAAACGGCTTCCGCGGAGGAAATATTTCCATCTCTTGAATTCGTACAACATTAAACGTGTGTTG
GGAGTCGTATACTGTTAG

23
src/kallisto/kallisto_index/test_data/transcriptome.fasta Normal file
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@@ -0,0 +1,23 @@
>YAL069W CDS=1-315
ATGATCGTAAATAACACACACGTGCTTACCCTACCACTTTATACCACCACCACATGCCATACTCACCCTC
ACTTGTATACTGATTTTACGTACGCACACGGATGCTACAGTATATACCATCTCAAACTTACCCTACTCTC
AGATTCCACTTCACTCCATGGCCCATCTCTCACTGAATCAGTACCAAATGCACTCACATCATTATGCACG
GCACTTGCCTCAGCGGTCTATACCCTGTGCCATTTACCCATAACGCCCATCATTATCCACATTTTGATAT
CTATATCTCATTCGGCGGTCCCAAATATTGTATAA
>YAL068W-A CDS=1-255
ATGCACGGCACTTGCCTCAGCGGTCTATACCCTGTGCCATTTACCCATAACGCCCATCATTATCCACATT
TTGATATCTATATCTCATTCGGCGGTCCCAAATATTGTATAACTGCCCTTAATACATACGTTATACCACT
TTTGCACCATATACTTACCACTCCATTTATATACACTTATGTCAATATTACAGAAAAATCCCCACAAAAA
TCACCTAAACATAAAAATATTCTACTTTTCAACAATAATACATAA
>YAL068C CDS=1-363
ATGGTCAAATTAACTTCAATCGCCGCTGGTGTCGCTGCCATCGCTGCTACTGCTTCTGCAACCACCACTC
TAGCTCAATCTGACGAAAGAGTCAACTTGGTGGAATTGGGTGTCTACGTCTCTGATATCAGAGCTCACTT
AGCCCAATACTACATGTTCCAAGCCGCCCACCCAACTGAAACCTACCCAGTCGAAGTTGCTGAAGCCGTT
TTCAACTACGGTGACTTCACCACCATGTTGACCGGTATTGCTCCAGACCAAGTGACCAGAATGATCACCG
GTGTTCCATGGTACTCCAGCAGATTAAAGCCAGCCATCTCCAGTGCTCTATCCAAGGACGGTATCTACAC
TATCGCAAACTAG
>YAL067W-A CDS=1-228
ATGCCAATTATAGGGGTGCCGAGGTGCCTTATAAAACCCTTTTCTGTGCCTGTGACATTTCCTTTTTCGG
TCAAAAAGAATATCCGAATTTTAGATTTGGACCCTCGTACAGAAGCTTATTGTCTAAGCCTGAATTCAGT
CTGCTTTAAACGGCTTCCGCGGAGGAAATATTTCCATCTCTTGAATTCGTACAACATTAAACGTGTGTTG
GGAGTCGTATACTGTTAG

105
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name: kallisto_quant
namespace: kallisto
description: |
Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
keywords: [kallisto, quant, pseudoalignment]
links:
homepage: https://pachterlab.github.io/kallisto/about
documentation: https://pachterlab.github.io/kallisto/manual
repository: https://github.com/pachterlab/kallisto
issue_tracker: https://github.com/pachterlab/kallisto/issues
references:
doi: 10.1038/nbt.3519
license: BSD 2-Clause License
argument_groups:
- name: "Input"
arguments:
- name: "--input"
type: file
description: List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
direction: "input"
multiple: true
required: true
- name: "--index"
alternatives: ["-i"]
type: file
description: Kallisto genome index.
must_exist: true
required: true
- name: "Output"
arguments:
- name: "--output_dir"
alternatives: ["-o"]
type: string
description: Directory to write output to.
required: true
- name: "Options"
arguments:
- name: "--single"
type: boolean_true
description: Single end mode.
- name: "--single_overhang"
type: boolean_true
description: Include reads where unobserved rest of fragment is predicted to lie outside a transcript.
- name: "--fr_stranded"
type: boolean_true
description: Strand specific reads, first read forward.
- name: "--rf_stranded"
type: boolean_true
description: Strand specific reads, first read reverse.
- name: "--fragment_length"
alternatives: ["-l"]
type: double
description: The estimated average fragment length.
- name: "--sd"
alternatives: ["-s"]
type: double
description: |
The estimated standard deviation of the fragment length (default: -l, -s values are estimated
from paired end data, but are required when using --single).
- name: "--plaintext"
type: boolean_true
description: Output plaintext instead of HDF5.
- name: "--bootstrap_samples"
alternatives: ["-b"]
type: integer
description: |
Number of bootstrap samples to draw. Default: '0'
example: 0
- name: "--seed"
type: integer
description: |
Random seed for bootstrap. Default: '42'
example: 42
resources:
- type: bash_script
path: script.sh
test_resources:
- type: bash_script
path: test.sh
- type: file
path: test_data
engines:
- type: docker
image: ubuntu:22.04
setup:
- type: docker
run: |
apt-get update && \
apt-get install -y --no-install-recommends wget && \
wget --no-check-certificate https://github.com/pachterlab/kallisto/releases/download/v0.50.1/kallisto_linux-v0.50.1.tar.gz && \
tar -xzf kallisto_linux-v0.50.1.tar.gz && \
mv kallisto/kallisto /usr/local/bin/
- type: docker
run: |
echo "kallisto: $(kallisto version | sed 's/kallisto, version //')" > /var/software_versions.txt
runners:
- type: executable
- type: nextflow

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```
kallisto quant
```
kallisto 0.50.1
Computes equivalence classes for reads and quantifies abundances
Usage: kallisto quant [arguments] FASTQ-files
Required arguments:
-i, --index=STRING Filename for the kallisto index to be used for
quantification
-o, --output-dir=STRING Directory to write output to
Optional arguments:
-b, --bootstrap-samples=INT Number of bootstrap samples (default: 0)
--seed=INT Seed for the bootstrap sampling (default: 42)
--plaintext Output plaintext instead of HDF5
--single Quantify single-end reads
--single-overhang Include reads where unobserved rest of fragment is
predicted to lie outside a transcript
--fr-stranded Strand specific reads, first read forward
--rf-stranded Strand specific reads, first read reverse
-l, --fragment-length=DOUBLE Estimated average fragment length
-s, --sd=DOUBLE Estimated standard deviation of fragment length
(default: -l, -s values are estimated from paired
end data, but are required when using --single)
-p, --priors Priors for the EM algorithm, either as raw counts or as
probabilities. Pseudocounts are added to raw reads to
prevent zero valued priors. Supplied in the same order
as the transcripts in the transcriptome
-t, --threads=INT Number of threads to use (default: 1)
--verbose Print out progress information every 1M proccessed reads

46
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#!/bin/bash
## VIASH START
## VIASH END
set -eo pipefail
unset_if_false=( par_single par_single_overhang par_rf_stranded par_fr_stranded par_plaintext )
for var in "${unset_if_false[@]}"; do
temp_var="${!var}"
[[ "$temp_var" == "false" ]] && unset $var
done
IFS=";" read -ra input <<< $par_input
# Check if par_single is not set and ensure even number of input files
if [ -z "$par_single" ]; then
if [ $((${#input[@]} % 2)) -ne 0 ]; then
echo "Error: When running in paired-end mode, the number of input files must be even."
echo "Number of input files provided: ${#input[@]}"
exit 1
fi
fi
mkdir -p $par_output_dir
kallisto quant \
${meta_cpus:+--threads $meta_cpus} \
-i $par_index \
${par_gtf:+--gtf "${par_gtf}"} \
${par_single:+--single} \
${par_single_overhang:+--single-overhang} \
${par_fr_stranded:+--fr-stranded} \
${par_rf_stranded:+--rf-stranded} \
${par_plaintext:+--plaintext} \
${par_bootstrap_samples:+--bootstrap-samples "${par_bootstrap_samples}"} \
${par_fragment_length:+--fragment-length "${par_fragment_length}"} \
${par_sd:+--sd "${par_sd}"} \
${par_seed:+--seed "${par_seed}"} \
-o $par_output_dir \
${input[*]}

53
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#!/bin/bash
echo ">>> Testing $meta_functionality_name"
echo ">>> Test 1: Testing for paired-end reads"
"$meta_executable" \
--index "$meta_resources_dir/test_data/index/transcriptome.idx" \
--rf_stranded \
--output_dir . \
--input "$meta_resources_dir/test_data/reads/A_R1.fastq;$meta_resources_dir/test_data/reads/A_R2.fastq"
echo ">>> Checking whether output exists"
[ ! -f "run_info.json" ] && echo "run_info.json does not exist!" && exit 1
[ ! -s "run_info.json" ] && echo "run_info.json is empty!" && exit 1
[ ! -f "abundance.tsv" ] && echo "abundance.tsv does not exist!" && exit 1
[ ! -s "abundance.tsv" ] && echo "abundance.tsv is empty!" && exit 1
[ ! -f "abundance.h5" ] && echo "abundance.h5 does not exist!" && exit 1
[ ! -s "abundance.h5" ] && echo "abundance.h5 is empty!" && exit 1
echo ">>> Checking if output is correct"
diff "abundance.tsv" "$meta_resources_dir/test_data/abundance_1.tsv" || { echo "abundance.tsv is not correct"; exit 1; }
rm -rf abundance.tsv abundance.h5 run_info.json
################################################################################
echo ">>> Test 2: Testing for single-end reads"
"$meta_executable" \
--index "$meta_resources_dir/test_data/index/transcriptome.idx" \
--rf_stranded \
--output_dir . \
--single \
--input "$meta_resources_dir/test_data/reads/A_R1.fastq" \
--fragment_length 101 \
--sd 50
echo ">>> Checking whether output exists"
[ ! -f "run_info.json" ] && echo "run_info.json does not exist!" && exit 1
[ ! -s "run_info.json" ] && echo "run_info.json is empty!" && exit 1
[ ! -f "abundance.tsv" ] && echo "abundance.tsv does not exist!" && exit 1
[ ! -s "abundance.tsv" ] && echo "abundance.tsv is empty!" && exit 1
[ ! -f "abundance.h5" ] && echo "abundance.h5 does not exist!" && exit 1
[ ! -s "abundance.h5" ] && echo "abundance.h5 is empty!" && exit 1
echo ">>> Checking if output is correct"
diff "abundance.tsv" "$meta_resources_dir/test_data/abundance_2.tsv" || { echo "abundance.tsv is not correct"; exit 1; }
rm -rf abundance.tsv abundance.h5 run_info.json
################################################################################
echo "All tests succeeded!"
exit 0

2
src/kallisto/kallisto_quant/test_data/abundance_1.tsv Normal file
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@@ -0,0 +1,2 @@
target_id length eff_length est_counts tpm
Sheila 35 36 0 -nan
1 target_id length eff_length est_counts tpm
2 Sheila 35 36 0 -nan

2
src/kallisto/kallisto_quant/test_data/abundance_2.tsv Normal file
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@@ -0,0 +1,2 @@
target_id length eff_length est_counts tpm
Sheila 35 15.0373 0 -nan
1 target_id length eff_length est_counts tpm
2 Sheila 35 15.0373 0 -nan

BIN
src/kallisto/kallisto_quant/test_data/index/transcriptome.idx Normal file
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Binary file not shown.

4
src/kallisto/kallisto_quant/test_data/reads/A_R1.fastq Normal file
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@@ -0,0 +1,4 @@
@1
GCTAGCTCAGAAAAAAAAAATCGTCGCGTGCGCGT
+
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

4
src/kallisto/kallisto_quant/test_data/reads/A_R2.fastq Normal file
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@@ -0,0 +1,4 @@
@1
GCTAGCTCAGAAAAAAAAAATCGTCGCGTGCGCGT
+
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

11
src/kallisto/kallisto_quant/test_data/script.sh Executable file
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@@ -0,0 +1,11 @@
#!/bin/bash
# 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/kallisto/quant/test/* src/kallisto/kallisto_quant/test_data
rm src/kallisto/kallisto_quant/test_data/Snakefile

479
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name: "rsem_calculate_expression"
namespace: "rsem"
description: |
Calculate expression with RSEM.
keywords: [Transcriptome, Index, Alignment, RSEM]
links:
homepage: https://deweylab.github.io/RSEM/
documentation: https://deweylab.github.io/RSEM/rsem-calculate-expression.html
repository: https://github.com/deweylab/RSEM
references:
doi: https://doi.org/10.1186/1471-2105-12-323
license: GPL-3.0
argument_groups:
- name: "Input"
arguments:
- name: "--id"
type: string
description: Sample ID.
- name: "--strandedness"
type: string
description: Sample strand-specificity. Must be one of unstranded, forward, reverse
choices: [forward, reverse, unstranded]
- name: "--paired"
type: boolean_true
description: Paired-end reads or not?
- name: "--input"
type: file
description: Input reads for quantification.
multiple: true
- name: "--index"
type: file
must_exist: false
description: RSEM index.
- name: "--extra_args"
type: string
description: Extra rsem-calculate-expression arguments in addition to the examples.
- name: "Output"
arguments:
- name: "--counts_gene"
type: file
description: Expression counts on gene level
example: $id.genes.results
direction: output
- name: "--counts_transcripts"
type: file
description: Expression counts on transcript level
example: $id.isoforms.results
direction: output
- name: "--stat"
type: file
description: RSEM statistics
example: $id.stat
direction: output
- name: "--logs"
type: file
description: RSEM logs
example: $id.log
direction: output
- name: "--bam_star"
type: file
description: BAM file generated by STAR (optional)
example: $id.STAR.genome.bam
direction: output
- name: "--bam_genome"
type: file
description: Genome BAM file (optional)
example: $id.genome.bam
direction: output
- name: "--bam_transcript"
type: file
description: Transcript BAM file (optional)
example: $id.transcript.bam
direction: output
- name: "--sort_bam_by_read_name"
type: boolean_true
description: |
Sort BAM file aligned under transcript coordidate by read name. Setting this option on will produce
deterministic maximum likelihood estimations from independent runs. Note that sorting will take long
time and lots of memory.
- name: "--no_bam_output"
type: boolean_true
description: Do not output any BAM file.
- name: "--sampling_for_bam"
type: boolean_true
description: |
When RSEM generates a BAM file, instead of outputting all alignments a read has with their posterior
probabilities, one alignment is sampled according to the posterior probabilities. The sampling procedure
includes the alignment to the "noise" transcript, which does not appear in the BAM file. Only the
sampled alignment has a weight of 1. All other alignments have weight 0. If the "noise" transcript is
sampled, all alignments appeared in the BAM file should have weight 0.
- name: "--output_genome_bam"
type: boolean_true
description: |
Generate a BAM file, 'sample_name.genome.bam', with alignments mapped to genomic coordinates and
annotated with their posterior probabilities. In addition, RSEM will call samtools (included in RSEM
package) to sort and index the bam file. 'sample_name.genome.sorted.bam' and 'sample_name.genome.sorted.bam.bai'
will be generated.
- name: "--sort_bam_by_coordinate"
type: boolean_true
description: |
Sort RSEM generated transcript and genome BAM files by coordinates and build associated indices.
- name: "Basic Options"
arguments:
- name: "--no_qualities"
type: boolean_true
description: Input reads do not contain quality scores.
- name: "--alignments"
type: boolean_true
description: |
Input file contains alignments in SAM/BAM/CRAM format. The exact file format will be determined
automatically.
- name: "--fai"
type: file
description: |
If the header section of input alignment file does not contain reference sequence information,
this option should be turned on. <file> is a FAI format file containing each reference sequence's
name and length. Please refer to the SAM official website for the details of FAI format.
- name: "--bowtie2"
type: boolean_true
description: |
Use Bowtie 2 instead of Bowtie to align reads. Since currently RSEM does not handle indel, local
and discordant alignments, the Bowtie2 parameters are set in a way to avoid those alignments. In
particular, we use options '--sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score_min L,0,-0.1'
by default. The last parameter of '--score_min', '-0.1', is the negative of maximum mismatch rate.
This rate can be set by option '--bowtie2_mismatch_rate'. If reads are paired-end, we additionally
use options '--no_mixed' and '--no_discordant'.
- name: "--star"
type: boolean_true
description: |
Use STAR to align reads. Alignment parameters are from ENCODE3's STAR-RSEM pipeline. To save
computational time and memory resources, STAR's Output BAM file is unsorted. It is stored in RSEM's
temporary directory with name as 'sample_name.bam'. Each STAR job will have its own private copy of
the genome in memory.
- name: "--hisat2_hca"
type: boolean_true
description: |
Use HISAT2 to align reads to the transcriptome according to Human Cell Atlast.
- name: "--append_names"
type: boolean_true
description: |
If gene_name/transcript_name is available, append it to the end of gene_id/transcript_id (separated
by '_') in files 'sample_name.isoforms.results' and 'sample_name.genes.results'.
- name: "--seed"
type: integer
description: |
Set the seed for the random number generators used in calculating posterior mean estimates and
credibility intervals. The seed must be a non-negative 32 bit integer.
- name: "--single_cell_prior"
type: boolean_true
description: |
By default, RSEM uses Dirichlet(1) as the prior to calculate posterior mean estimates and credibility
intervals. However, much less genes are expressed in single cell RNA-Seq data. Thus, if you want to
compute posterior mean estimates and/or credibility intervals and you have single-cell RNA-Seq data,
you are recommended to turn on this option. Then RSEM will use Dirichlet(0.1) as the prior which
encourage the sparsity of the expression levels.
- name: "--calc_pme"
type: boolean_true
description: Run RSEM's collapsed Gibbs sampler to calculate posterior mean estimates.
- name: "--calc_ci"
type: boolean_true
description: |
Calculate 95% credibility intervals and posterior mean estimates. The credibility level can be
changed by setting '--ci_credibility_level'.
- name: "--quiet"
alternatives: "-q"
type: boolean_true
description: Suppress the output of logging information.
- name: "Aligner Options"
arguments:
- name: "--seed_length"
type: integer
description: |
Seed length used by the read aligner. Providing the correct value is important for RSEM. If RSEM
runs Bowtie, it uses this value for Bowtie's seed length parameter. Any read with its or at least
one of its mates' (for paired-end reads) length less than this value will be ignored. If the
references are not added poly(A) tails, the minimum allowed value is 5, otherwise, the minimum
allowed value is 25. Note that this script will only check if the value >= 5 and give a warning
message if the value < 25 but >= 5. (Default: 25)
example: 25
- name: "--phred64_quals"
type: boolean_true
description: |
Input quality scores are encoded as Phred+64 (default for GA Pipeline ver. >= 1.3). This option is
used by Bowtie, Bowtie 2 and HISAT2. Otherwise, quality score will be encoded as Phred+33. (Default: false)
- name: "--solexa_quals"
type: boolean_true
description: |
Input quality scores are solexa encoded (from GA Pipeline ver. < 1.3). This option is used by
Bowtie, Bowtie 2 and HISAT2. Otherwise, quality score will be encoded as Phred+33. (Default: false)
- name: "--bowtie_n"
type: integer
description: |
(Bowtie parameter) max # of mismatches in the seed. (Range: 0-3, Default: 2)
choices: [0, 1, 2, 3]
example: 2
- name: "--bowtie_e"
type: integer
description: |
(Bowtie parameter) max sum of mismatch quality scores across the alignment. (Default: 99999999)
example: 99999999
- name: "--bowtie_m"
type: integer
description: |
(Bowtie parameter) suppress all alignments for a read if > <int> valid alignments exist. (Default: 200)
example: 200
- name: "--bowtie_chunkmbs"
type: integer
description: |
(Bowtie parameter) memory allocated for best first alignment calculation (Default: 0 - use Bowtie's default)
example: 0
- name: "--bowtie2_mismatch_rate"
type: double
description: |
(Bowtie 2 parameter) The maximum mismatch rate allowed. (Default: 0.1)
example: 0.1
- name: "--bowtie2_k"
type: integer
description: |
(Bowtie 2 parameter) Find up to <int> alignments per read. (Default: 200)
example: 200
- name: "--bowtie2_sensitivity_level"
type: string
description: |
(Bowtie 2 parameter) Set Bowtie 2's preset options in --end-to-end mode. This option controls how
hard Bowtie 2 tries to find alignments. <string> must be one of "very_fast", "fast", "sensitive"
and "very_sensitive". The four candidates correspond to Bowtie 2's "--very-fast", "--fast",
"--sensitive" and "--very-sensitive" options. (Default: "sensitive" - use Bowtie 2's default)
choices: ["very_fast", "fast", "sensitive", "very_sensitive"]
example: sensitive
- name: "--star_gzipped_read_file"
type: boolean_true
description: |
Input read file(s) is compressed by gzip. (Default: false)
- name: "--star_bzipped_read_file"
type: boolean_true
description: |
Input read file(s) is compressed by bzip2. (Default: false)
- name: "--star_output_genome_bam"
type: boolean_true
description: |
Save the BAM file from STAR alignment under genomic coordinate to 'sample_name.STAR.genome.bam'.
This file is NOT sorted by genomic coordinate. In this file, according to STAR's manual, 'paired
ends of an alignment are always adjacent, and multiple alignments of a read are adjacent as well'.
(Default: false)
- name: "Advanced Options"
arguments:
- name: "--tag"
type: string
description: |
The name of the optional field used in the SAM input for identifying a read with too many valid
alignments. The field should have the format <tagName>:i:<value>, where a <value> bigger than 0
indicates a read with too many alignments. (Default: "")
example: ""
- name: "--fragment_length_min"
type: integer
description: |
Minimum read/insert length allowed. This is also the value for the Bowtie/Bowtie2 -I option.
(Default: 1)
example: 1
- name: "--fragment_length_max"
type: integer
description: |
Maximum read/insert length allowed. This is also the value for the Bowtie/Bowtie 2 -X option.
(Default: 1000)
example: 1000
- name: "--fragment_length_mean"
type: integer
description: |
(single-end data only) The mean of the fragment length distribution, which is assumed to be a
Gaussian. (Default: -1, which disables use of the fragment length distribution)
example: -1
- name: "--gragment_length_sd"
type: double
description: |
(single-end data only) The standard deviation of the fragment length distribution, which is
assumed to be a Gaussian. (Default: 0, which assumes that all fragments are of the same length,
given by the rounded value of --fragment_length_mean).
example: 0
- name: "--estimate_rspd"
type: boolean_true
description: |
Set this option if you want to estimate the read start position distribution (RSPD) from data.
Otherwise, RSEM will use a uniform RSPD.
- name: "--num_rspd_bins"
type: integer
description: |
Number of bins in the RSPD. Only relevant when '--estimate_rspd' is specified. Use of the default
setting is recommended. (Default: 20)
example: 20
- name: "--gibbs_burnin"
type: integer
description: |
The number of burn-in rounds for RSEM's Gibbs sampler. Each round passes over the entire data set
once. If RSEM can use multiple threads, multiple Gibbs samplers will start at the same time and all
samplers share the same burn-in number. (Default: 200)
example: 200
- name: "--gibbs_number_of_samples"
type: integer
description: |
The total number of count vectors RSEM will collect from its Gibbs samplers. (Default: 1000)
example: 1000
- name: "--gibbs_sampling_gap"
type: integer
description: |
The number of rounds between two succinct count vectors RSEM collects. If the count vector after
round N is collected, the count vector after round N + <int> will also be collected. (Default: 1)
example: 1
- name: "--ci_credibility_level"
type: double
description: |
The credibility level for credibility intervals. (Default: 0.95)
example: 0.95
- name: "--ci_number_of_samples_per_count_vector"
type: integer
description: |
The number of read generating probability vectors sampled per sampled count vector. The crebility
intervals are calculated by first sampling P(C | D) and then sampling P(Theta | C) for each sampled
count vector. This option controls how many Theta vectors are sampled per sampled count vector.
(Default: 50)
example: 50
- name: "--keep_intermediate_files"
type: boolean_true
description: |
Keep temporary files generated by RSEM. RSEM creates a temporary directory, 'sample_name.temp',
into which it puts all intermediate output files. If this directory already exists, RSEM overwrites
all files generated by previous RSEM runs inside of it. By default, after RSEM finishes, the
temporary directory is deleted. Set this option to prevent the deletion of this directory and the
intermediate files inside of it.
- name: "--temporary_folder"
type: string
description: |
Set where to put the temporary files generated by RSEM. If the folder specified does not exist,
RSEM will try to create it. (Default: sample_name.temp)
example: sample_name.temp
- name: "--time"
type: boolean_true
description: |
Output time consumed by each step of RSEM to 'sample_name.time'.
- name: "Prior-Enhanced RSEM Options"
arguments:
- name: "--run_pRSEM"
type: boolean_true
description: |
Running prior-enhanced RSEM (pRSEM). Prior parameters, i.e. isoform's initial pseudo-count for
RSEM's Gibbs sampling, will be learned from input RNA-seq data and an external data set. When pRSEM
needs and only needs ChIP-seq peak information to partition isoforms (e.g. in pRSEM's default
partition model), either ChIP-seq peak file (with the '--chipseq_peak_file' option) or ChIP-seq
FASTQ files for target and input and the path for Bowtie executables are required (with the
'--chipseq_target_read_files <string>', '--chipseq_control_read_files <string>', and '--bowtie_path
<path> options), otherwise, ChIP-seq FASTQ files for target and control and the path to Bowtie
executables are required.
- name: "--chipseq_peak_file"
type: file
must_exist: true
description: |
Full path to a ChIP-seq peak file in ENCODE's narrowPeak, i.e. BED6+4, format. This file is used
when running prior-enhanced RSEM in the default two-partition model. It partitions isoforms by
whether they have ChIP-seq overlapping with their transcription start site region or not. Each
partition will have its own prior parameter learned from a training set. This file can be either
gzipped or ungzipped.
- name: "--chipseq_target_read_files"
type: file
must_exist: true
description: |
Comma-separated full path of FASTQ read file(s) for ChIP-seq target. This option is used when running
prior-enhanced RSEM. It provides information to calculate ChIP-seq peaks and signals. The file(s)
can be either ungzipped or gzipped with a suffix '.gz' or '.gzip'. The options '--bowtie_path <path>'
and '--chipseq_control_read_files <string>' must be defined when this option is specified.
- name: "--chipseq_control_read_files"
type: file
must_exist: true
description: |
Comma-separated full path of FASTQ read file(s) for ChIP-seq conrol. This option is used when running
prior-enhanced RSEM. It provides information to call ChIP-seq peaks. The file(s) can be either
ungzipped or gzipped with a suffix '.gz' or '.gzip'. The options '--bowtie_path <path>' and
'--chipseq_target_read_files <string>' must be defined when this option is specified.
- name: "--chipseq_read_files_multi_targets"
type: file
must_exist: true
description: |
Comma-separated full path of FASTQ read files for multiple ChIP-seq targets. This option is used when
running prior-enhanced RSEM, where prior is learned from multiple complementary data sets. It provides
information to calculate ChIP-seq signals. All files can be either ungzipped or gzipped with a suffix
'.gz' or '.gzip'. When this option is specified, the option '--bowtie_path <path>' must be defined and
the option '--partition_model <string>' will be set to 'cmb_lgt' automatically.
- name: "--chipseq_bed_files_multi_targets"
type: file
must_exist: true
description: |
Comma-separated full path of BED files for multiple ChIP-seq targets. This option is used when running
prior-enhanced RSEM, where prior is learned from multiple complementary data sets. It provides information
of ChIP-seq signals and must have at least the first six BED columns. All files can be either ungzipped
or gzipped with a suffix '.gz' or '.gzip'. When this option is specified, the option '--partition_model
<string>' will be set to 'cmb_lgt' automatically.
- name: "--cap_stacked_chipseq_reads"
type: boolean_true
description: |
Keep a maximum number of ChIP-seq reads that aligned to the same genomic interval. This option is used
when running prior-enhanced RSEM, where prior is learned from multiple complementary data sets. This
option is only in use when either '--chipseq_read_files_multi_targets <string>' or
'--chipseq_bed_files_multi_targets <string>' is specified.
- name: "--n_max_stacked_chipseq_reads"
type: integer
description: |
The maximum number of stacked ChIP-seq reads to keep. This option is used when running prior-enhanced
RSEM, where prior is learned from multiple complementary data sets. This option is only in use when the
option '--cap_stacked_chipseq_reads' is set.
- name: "--partition_model"
type: string
description: |
A keyword to specify the partition model used by prior-enhanced RSEM. It must be one of the following
keywords:
* pk
* pk_lgtnopk
* lm3, lm4, lm5, or lm6
* nopk_lm2pk, nopk_lm3pk, nopk_lm4pk, or nopk_lm5pk
* pk_lm2nopk, pk_lm3nopk, pk_lm4nopk, or pk_lm5nopk
* cmb_lgt
Parameters for all the above models are learned from a training set. For detailed explanations, please
see prior-enhanced RSEM's paper. (Default: 'pk')
example: "pk"
resources:
- type: bash_script
path: script.sh
test_resources:
- type: bash_script
path: test.sh
engines:
- type: docker
image: ubuntu:22.04
setup:
- type: apt
packages:
- build-essential
- gcc
- g++
- make
- wget
- zlib1g-dev
- unzip
- type: docker
env:
- STAR_VERSION=2.7.11b
- RSEM_VERSION=1.3.3
run: |
apt-get update && \
apt-get clean && \
wget --no-check-certificate https://github.com/alexdobin/STAR/archive/refs/tags/2.7.11a.zip && \
unzip 2.7.11a.zip && \
cp STAR-2.7.11a/bin/Linux_x86_64_static/STAR /usr/local/bin && \
cd && \
wget --no-check-certificate https://github.com/deweylab/RSEM/archive/refs/tags/v1.3.3.zip && \
unzip v1.3.3.zip && \
cd RSEM-1.3.3 && \
make && \
make install
- type: docker
run: |
echo "RSEM: `rsem-calculate-expression --version | sed -e 's/Current version: RSEM v//g'`" > /var/software_versions.txt && \
echo "STAR: `STAR --version`" >> /var/software_versions.txt && \
echo "bowtie2: `bowtie2 --version | grep -oP '\d+\.\d+\.\d+'`" >> /var/software_versions.txt && \
echo "bowtie: `bowtie --version | grep -oP 'bowtie-align-s version \K\d+\.\d+\.\d+'`" >> /var/software_versions.txt && \
echo "HISAT2: `hisat2 --version | grep -oP 'hisat2-align-s version \K\d+\.\d+\.\d+'`" >> /var/software_versions.txt
runners:
- type: executable
- type: nextflow

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103
src/rsem/rsem_calculate_expression/script.sh Normal file
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@@ -0,0 +1,103 @@
#!/bin/bash
## VIASH START
## VIASH END
set -eo pipefail
function clean_up {
rm -rf "$tmpdir"
}
trap clean_up EXIT
tmpdir=$(mktemp -d "$meta_temp_dir/$meta_functionality_name-XXXXXXXX")
if [ "$par_strandedness" == 'forward' ]; then
strandedness='--strandedness forward'
elif [ "$par_strandedness" == 'reverse' ]; then
strandedness="--strandedness reverse"
else
strandedness=''
fi
IFS=";" read -ra input <<< $par_input
INDEX=$(find -L $meta_resources_dir/$par_index -name "*.grp" | sed 's/\.grp$//')
unset_if_false=( par_paired par_quiet par_no_bam_output par_sampling_for_bam par_no_qualities
par_alignments par_bowtie2 par_star par_hisat2_hca par_append_names
par_single_cell_prior par_calc_pme par_calc_ci par_phred64_quals
par_solexa_quals par_star_gzipped_read_file par_star_bzipped_read_file
par_star_output_genome_bam par_estimate_rspd par_keep_intermediate_files
par_time par_run_pRSEM par_cap_stacked_chipseq_reads par_sort_bam_by_read_name )
for par in ${unset_if_false[@]}; do
test_val="${!par}"
[[ "$test_val" == "false" ]] && unset $par
done
rsem-calculate-expression \
${par_quiet:+-q} \
${par_no_bam_output:+--no-bam-output} \
${par_sampling_for_bam:+--sampling-for-bam} \
${par_no_qualities:+--no-qualities} \
${par_alignments:+--alignments} \
${par_bowtie2:+--bowtie2} \
${par_star:+--star} \
${par_hisat2_hca:+--hisat2-hca} \
${par_append_names:+--append-names} \
${par_single_cell_prior:+--single-cell-prior} \
${par_calc_pme:+--calc-pme} \
${par_calc_ci:+--calc-ci} \
${par_phred64_quals:+--phred64-quals} \
${par_solexa_quals:+--solexa-quals} \
${par_star_gzipped_read_file:+--star-gzipped-read-file} \
${par_star_bzipped_read_file:+--star-bzipped-read-file} \
${par_star_output_genome_bam:+--star-output-genome-bam} \
${par_estimate_rspd:+--estimate-rspd} \
${par_keep_intermediate_files:+--keep-intermediate-files} \
${par_time:+--time} \
${par_run_pRSEM:+--run-pRSEM} \
${par_cap_stacked_chipseq_reads:+--cap-stacked-chipseq-reads} \
${par_sort_bam_by_read_name:+--sort-bam-by-read-name} \
${par_counts_gene:+--counts-gene "$par_counts_gene"} \
${par_counts_transcripts:+--counts-transcripts "$par_counts_transcripts"} \
${par_stat:+--stat "$par_stat"} \
${par_bam_star:+--bam-star "$par_bam_star"} \
${par_bam_genome:+--bam-genome "$par_bam_genome"} \
${par_bam_transcript:+--bam-transcript "$par_bam_transcript"} \
${par_fai:+--fai "$par_fai"} \
${par_seed:+--seed "$par_seed"} \
${par_seed_length:+--seed-length "$par_seed_length"} \
${par_bowtie_n:+--bowtie-n "$par_bowtie_n"} \
${par_bowtie_e:+--bowtie-e "$par_bowtie_e"} \
${par_bowtie_m:+--bowtie-m "$par_bowtie_m"} \
${par_bowtie_chunkmbs:+--bowtie-chunkmbs "$par_bowtie_chunkmbs"} \
${par_bowtie2_mismatch_rate:+--bowtie2-mismatch-rate "$par_bowtie2_mismatch_rate"} \
${par_bowtie2_k:+--bowtie2-k "$par_bowtie2_k"} \
${par_bowtie2_sensitivity_level:+--bowtie2-sensitivity-level "$par_bowtie2_sensitivity_level"} \
${par_tag:+--tag "$par_tag"} \
${par_fragment_length_min:+--fragment-length-min "$par_fragment_length_min"} \
${par_fragment_length_max:+--fragment-length-max "$par_fragment_length_max"} \
${par_fragment_length_mean:+--fragment-length-mean "$par_fragment_length_mean"} \
${par_fragment_length_sd:+--fragment-length-sd "$par_fragment_length_sd"} \
${par_num_rspd_bins:+--num-rspd-bins "$par_num_rspd_bins"} \
${par_gibbs_burnin:+--gibbs-burnin "$par_gibbs_burnin"} \
${par_gibbs_number_of_samples:+--gibbs-number-of-samples "$par_gibbs_number_of_samples"} \
${par_gibbs_sampling_gap:+--gibbs-sampling-gap "$par_gibbs_sampling_gap"} \
${par_ci_credibility_level:+--ci-credibility-level "$par_ci_credibility_level"} \
${par_ci_number_of_samples_per_count_vector:+--ci-number-of-samples-per-count-vector "$par_ci_number_of_samples_per_count_vector"} \
${par_temporary_folder:+--temporary-folder "$par_temporary_folder"} \
${par_chipseq_peak_file:+--chipseq-peak-file "$par_chipseq_peak_file"} \
${par_chipseq_target_read_files:+--chipseq-target-read-files "$par_chipseq_target_read_files"} \
${par_chipseq_control_read_files:+--chipseq-control-read-files "$par_chipseq_control_read_files"} \
${par_chipseq_read_files_multi_targets:+--chipseq-read-files-multi-targets "$par_chipseq_read_files_multi_targets"} \
${par_chipseq_bed_files_multi_targets:+--chipseq-bed-files-multi-targets "$par_chipseq_bed_files_multi_targets"} \
${par_n_max_stacked_chipseq_reads:+--n-max-stacked-chipseq-reads "$par_n_max_stacked_chipseq_reads"} \
${par_partition_model:+--partition-model "$par_partition_model"} \
$strandedness \
${par_paired:+--paired-end} \
${input[*]} \
$INDEX \
$par_id

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#!/bin/bash
echo ">>> Testing $meta_executable"
test_dir="${meta_resources_dir}/test_data"
# wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/rsem.tar.gz
# gunzip -k rsem.tar.gz
# tar -xf rsem.tar
# mv $test_dir/rsem $meta_resources_dir
echo "> Prepare test data"
cat > reads_R1.fastq <<'EOF'
@SEQ_ID1
ACGCTGCCTCATAAGCCTCACACAT
+
IIIIIIIIIIIIIIIIIIIIIIIII
@SEQ_ID2
ACCCGCAAGATTAGGCTCCGTACAC
+
!!!!!!!!!!!!!!!!!!!!!!!!!
EOF
cat > reads_R2.fastq <<'EOF'
@SEQ_ID1
ATGTGTGAGGCTTATGAGGCAGCGT
+
IIIIIIIIIIIIIIIIIIIIIIIII
@SEQ_ID2
GTGTACGGAGCCTAATCTTGCAGGG
+
!!!!!!!!!!!!!!!!!!!!!!!!!
EOF
cat > genome.fasta <<'EOF'
>chr1
TGGCATGAGCCAACGAACGCTGCCTCATAAGCCTCACACATCCGCGCCTATGTTGTGACTCTCTGTGAGCGTTCGTGGG
GCTCGTCACCACTATGGTTGGCCGGTTAGTAGTGTGACTCCTGGTTTTCTGGAGCTTCTTTAAACCGTAGTCCAGTCAA
TGCGAATGGCACTTCACGACGGACTGTCCTTAGGTGTGAGGCTTATGAGGCACTCAGGGGA
EOF
cat > genes.gtf <<'EOF'
chr1 example_source gene 0 50 . + . gene_id "gene1"; transcript_id "transcript1";
chr1 example_source exon 20 40 . + . gene_id "gene1"; transcript_id "transcript1";
chr1 example_source gene 100 219 . + . gene_id "gene2"; transcript_id "transcript2";
chr1 example_source exon 191 210 . + . gene_id "gene2"; transcript_id "transcript2";
EOF
cat > ref.cnt <<'EOF'
1 0 0 1
0 0 0
0 3
0 1
Inf 0
EOF
cat > ref.genes.results <<'EOF'
gene_id transcript_id(s) length effective_length expected_count TPM FPKM
gene1 transcript1 21.00 21.00 0.00 0.00 0.00
gene2 transcript2 20.00 20.00 0.00 0.00 0.00
EOF
cat > ref.isoforms.results <<'EOF'
transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct
transcript1 gene1 21 21.00 0.00 0.00 0.00 0.00
transcript2 gene2 20 20.00 0.00 0.00 0.00 0.00
EOF
echo "> Generate index"
rsem-prepare-reference \
--gtf "genes.gtf" \
"genome.fasta" \
"index"
mkdir index
mv index.* index/
STAR \
${meta_cpus:+--runThreadN $meta_cpus} \
--runMode genomeGenerate \
--genomeDir "index/" \
--genomeFastaFiles "genome.fasta" \
--sjdbGTFfile "genes.gtf" \
--genomeSAindexNbases 2
#########################################################################################
echo ">>> Test 1: Paired-end reads using STAR to align reads"
"$meta_executable" \
--star \
--paired \
--input "reads_R1.fastq;reads_R2.fastq" \
--index index \
--id test \
--seed 1 \
--quiet
echo ">>> Checking whether output exists"
[ ! -f "test.genes.results" ] && echo "Gene level expression counts file does not exist!" && exit 1
[ ! -s "test.genes.results" ] && echo "Gene level expression counts file is empty!" && exit 1
[ ! -f "test.isoforms.results" ] && echo "Transcript level expression counts file does not exist!" && exit 1
[ ! -s "test.isoforms.results" ] && echo "Transcript level expression counts file is empty!" && exit 1
[ ! -d "test.stat" ] && echo "Stats file does not exist!" && exit 1
echo ">>> Check wheter output is correct"
diff ref.genes.results test.genes.results || { echo "Gene level expression counts file is incorrect!"; exit 1; }
diff ref.isoforms.results test.isoforms.results || { echo "Transcript level expression counts file is incorrect!"; exit 1; }
diff ref.cnt test.stat/test.cnt || { echo "Stats file is incorrect!"; exit 1; }
#####################################################################################################
echo "All tests succeeded!"
exit 0

6
src/salmon/salmon_quant/config.vsh.yaml
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@@ -24,7 +24,7 @@ argument_groups:
description: |
Format string describing the library.
The library type string consists of three parts:
1. Relative orientation of the reads: This part is only provided if the library is paired-end, THe possible options are
1. Relative orientation of the reads: This part is only provided if the library is paired-end, The possible options are
I = inward
O = outward
M = matching
@@ -118,7 +118,7 @@ argument_groups:
direction: output
description: |
Salmon quantification file.
required: true
required: false
example: quant.sf
- name: Basic options
@@ -327,7 +327,7 @@ argument_groups:
If this option is provided, then the selective-alignment results will be written out in SAM-compatible format. By default, output will be directed to stdout, but an alternative file name can be provided instead.
- name: --mapping_sam
type: file
description: Path to file that should output the selective-alignment results in SAM-compatible format. THis option must be provided while using --write_mappings
description: Path to file that should output the selective-alignment results in SAM-compatible format. This option must be provided while using --write_mappings
required: false
direction: output
example: mappings.sam

107
src/umi_tools/umi_tools_prepareforrsem/config.vsh.yaml Normal file
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name: "umi_tools_prepareforrsem"
namespace: "umi_tools"
description: Make the output from umi-tools dedup or group compatible with RSEM
keywords: [umi_tools, rsem, bam, sam]
links:
homepage: https://umi-tools.readthedocs.io/en/latest/
documentation: https://umi-tools.readthedocs.io/en/latest/reference/extract.html
repository: https://github.com/CGATOxford/UMI-tools
references:
doi: 10.1101/gr.209601.116
license: MIT
argument_groups:
- name: "Input"
arguments:
- name: "--input"
alternatives: ["-I", "--stdin"]
type: file
required: true
example: $id.transcriptome.bam
- name: "Output"
arguments:
- name: "--output"
alternatives: ["-S", "--stdout"]
type: file
direction: output
example: $id.transcriptome_sorted.bam
- name: "--log"
alternatives: ["-L"]
type: file
direction: output
description: File with logging information [default = stdout].
- name: "--error"
alternatives: ["-E"]
type: file
direction: output
description: File with error information [default = stderr].
- name: "--log2stderr"
type: boolean_true
description: Send logging information to stderr [default = False].
- name: "--temp_dir"
type: string
description: |
Directory for temporary files. If not set, the bash environmental variable
TMPDIR is used.
- name: "--compresslevel"
type: integer
description: |
Level of Gzip compression to use. Default (6) matchesGNU gzip rather than python
gzip default (which is 9).
- name: "Options"
arguments:
- name: "--tags"
type: string
description: |
Comma-seperated list of tags to transfer from read1 to read2 (Default: 'UG,BX')
example: "UG,BX"
- name: "--sam"
type: boolean_true
description: Input and output SAM rather than BAM.
- name: "--timeit"
type: string
description: |
Store timeing information in file [none].
- name: "--timeit_name"
type: string
description: |
Name in timing file for this class of jobs [all].
- name: "--timeit_header"
type: boolean_true
description: Add header for timing information [none].
- name: "--verbose"
alternatives: ["-v"]
type: integer
description: |
Loglevel [1]. The higher, the more output.
- name: "--random_seed"
type: integer
description: |
Random seed to initialize number generator with [none].
resources:
- type: bash_script
path: script.sh
# copied from https://github.com/nf-core/rnaseq/blob/3.12.0/bin/prepare-for-rsem.py
- path: prepare-for-rsem.py
test_resources:
- type: bash_script
path: test.sh
- type: file
path: test_data
engines:
- type: docker
image: quay.io/biocontainers/umi_tools:1.1.5--py38h0020b31_3
setup:
- type: docker
run: |
umi_tools -v | sed 's/ version//g' > /var/software_versions.txt
runners:
- type: executable
- type: nextflow

54
src/umi_tools/umi_tools_prepareforrsem/help.txt Normal file
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@@ -0,0 +1,54 @@
```
umi_tools prepare-for-rsem --help
```
prepare_for_rsem - make output from dedup or group compatible with RSEM
Usage: umi_tools prepare_for_rsem [OPTIONS] [--stdin=IN_BAM] [--stdout=OUT_BAM]
note: If --stdout is ommited, standard out is output. To
generate a valid BAM file on standard out, please
redirect log with --log=LOGFILE or --log2stderr
For full UMI-tools documentation, see https://umi-tools.readthedocs.io/en/latest/
Options:
--version show program's version number and exit
RSEM preparation specific options:
--tags=TAGS Comma-seperated list of tags to transfer from read1 to
read2
--sam input and output SAM rather than BAM
input/output options:
-I FILE, --stdin=FILE
file to read stdin from [default = stdin].
-L FILE, --log=FILE
file with logging information [default = stdout].
-E FILE, --error=FILE
file with error information [default = stderr].
-S FILE, --stdout=FILE
file where output is to go [default = stdout].
--temp-dir=FILE Directory for temporary files. If not set, the bash
environmental variable TMPDIR is used[default = None].
--log2stderr send logging information to stderr [default = False].
--compresslevel=COMPRESSLEVEL
Level of Gzip compression to use. Default (6)
matchesGNU gzip rather than python gzip default (which
is 9)
profiling options:
--timeit=TIMEIT_FILE
store timeing information in file [none].
--timeit-name=TIMEIT_NAME
name in timing file for this class of jobs [all].
--timeit-header add header for timing information [none].
common options:
-v LOGLEVEL, --verbose=LOGLEVEL
loglevel [1]. The higher, the more output.
-h, --help output short help (command line options only).
--help-extended Output full documentation
--random-seed=RANDOM_SEED
random seed to initialize number generator with
[none].

271
src/umi_tools/umi_tools_prepareforrsem/prepare-for-rsem.py Normal file
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#!/usr/bin/env python3
"""
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Credits
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This script is a clone of the "prepare-for-rsem.py" script written by
Ian Sudbury, Tom Smith and other contributors to the UMI-tools package:
https://github.com/CGATOxford/UMI-tools
It has been included here to address problems encountered with
Salmon quant and RSEM as discussed in the issue below:
https://github.com/CGATOxford/UMI-tools/issues/465
When the "umi_tools prepare-for-rsem" command becomes available in an official
UMI-tools release this script will be replaced and deprecated.
Commit:
https://github.com/CGATOxford/UMI-tools/blob/bf8608d6a172c5ca0dcf33c126b4e23429177a72/umi_tools/prepare-for-rsem.py
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
prepare_for_rsem - make the output from dedup or group compatible with RSEM
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The SAM format specification states that the mnext and mpos fields should point
to the primary alignment of a read's mate. However, not all aligners adhere to
this standard. In addition, the RSEM software requires that the mate of a read1
appears directly after it in its input BAM. This requires that there is exactly
one read1 alignment for every read2 and vice versa.
In general (except in a few edge cases) UMI tools outputs only the read2 to that
corresponds to the read specified in the mnext and mpos positions of a selected
read1, and only outputs this read once, even if multiple read1s point to it.
This makes UMI-tools outputs incompatible with RSEM. This script takes the output
from dedup or groups and ensures that each read1 has exactly one read2 (and vice
versa), that read2 always appears directly after read1,and that pairs point to
each other (note this is technically not valid SAM format). Copy any specified
tags from read1 to read2 if they are present (by default, UG and BX, the unique
group and correct UMI tags added by _group_)
Input must to name sorted.
https://raw.githubusercontent.com/CGATOxford/UMI-tools/master/LICENSE
"""
from umi_tools import Utilities as U
from collections import defaultdict, Counter
import pysam
import sys
usage = """
prepare_for_rsem - make output from dedup or group compatible with RSEM
Usage: umi_tools prepare_for_rsem [OPTIONS] [--stdin=IN_BAM] [--stdout=OUT_BAM]
note: If --stdout is omited, standard out is output. To
generate a valid BAM file on standard out, please
redirect log with --log=LOGFILE or --log2stderr """
def chunk_bam(bamfile):
"""Take in a iterator of pysam.AlignmentSegment entries and yield
lists of reads that all share the same name"""
last_query_name = None
output_buffer = list()
for read in bamfile:
if last_query_name is not None and last_query_name != read.query_name:
yield (output_buffer)
output_buffer = list()
last_query_name = read.query_name
output_buffer.append(read)
yield (output_buffer)
def copy_tags(tags, read1, read2):
"""Given a list of tags, copies the values of these tags from read1
to read2, if the tag is set"""
for tag in tags:
try:
read1_tag = read1.get_tag(tag, with_value_type=True)
read2.set_tag(tag, value=read1_tag[0], value_type=read1_tag[1])
except KeyError:
pass
return read2
def pick_mate(read, template_dict, mate_key):
"""Find the mate of read in the template dict using key. It will retrieve
all reads at that key, and then scan to pick the one that refers to _read_
as it's mate. If there is no such read, it picks a first one it comes to"""
mate = None
# get a list of secondary reads at the correct alignment position
potential_mates = template_dict[not read.is_read1][mate_key]
# search through one at a time to find a read that points to the current read
# as its mate.
for candidate_mate in potential_mates:
if (
candidate_mate.next_reference_name == read.reference_name
and candidate_mate.next_reference_start == read.pos
):
mate = candidate_mate
# if no such read is found, then pick any old secondary alignment at that position
# note: this happens when UMI-tools outputs the wrong read as something's pair.
if mate is None and len(potential_mates) > 0:
mate = potential_mates[0]
return mate
def main(argv=None):
if argv is None:
argv = sys.argv
# setup command line parser
parser = U.OptionParser(version="%prog version: $Id$", usage=usage, description=globals()["__doc__"])
group = U.OptionGroup(parser, "RSEM preparation specific options")
group.add_option(
"--tags",
dest="tags",
type="string",
default="UG,BX",
help="Comma-separated list of tags to transfer from read1 to read2",
)
group.add_option(
"--sam", dest="sam", action="store_true", default=False, help="input and output SAM rather than BAM"
)
parser.add_option_group(group)
# add common options (-h/--help, ...) and parse command line
(options, args) = U.Start(
parser, argv=argv, add_group_dedup_options=False, add_umi_grouping_options=False, add_sam_options=False
)
skipped_stats = Counter()
if options.stdin != sys.stdin:
in_name = options.stdin.name
options.stdin.close()
else:
in_name = "-"
if options.sam:
mode = ""
else:
mode = "b"
inbam = pysam.AlignmentFile(in_name, "r" + mode)
if options.stdout != sys.stdout:
out_name = options.stdout.name
options.stdout.close()
else:
out_name = "-"
outbam = pysam.AlignmentFile(out_name, "w" + mode, template=inbam)
options.tags = options.tags.split(",")
for template in chunk_bam(inbam):
assert len(set(r.query_name for r in template)) == 1
current_template = {True: defaultdict(list), False: defaultdict(list)}
for read in template:
key = (read.reference_name, read.pos, not read.is_secondary)
current_template[read.is_read1][key].append(read)
output = set()
for read in template:
mate = None
# if this read is a non_primary alignment, we first want to check if it has a mate
# with the non-primary alignment flag set.
mate_key_primary = True
mate_key_secondary = (read.next_reference_name, read.next_reference_start, False)
# First look for a read that has the same primary/secondary status
# as read (i.e. secondary mate for secondary read, and primary mate
# for primary read)
mate_key = (read.next_reference_name, read.next_reference_start, read.is_secondary)
mate = pick_mate(read, current_template, mate_key)
# If none was found then look for the opposite (primary mate of secondary
# read or seconadary mate of primary read)
if mate is None:
mate_key = (read.next_reference_name, read.next_reference_start, not read.is_secondary)
mate = pick_mate(read, current_template, mate_key)
# If we still don't have a mate, then their can't be one?
if mate is None:
skipped_stats["no_mate"] += 1
U.warn(
"Alignment {} has no mate -- skipped".format(
"\t".join(map(str, [read.query_name, read.flag, read.reference_name, int(read.pos)]))
)
)
continue
# because we might want to make changes to the read, but not have those changes reflected
# if we need the read again,we copy the read. This is only way I can find to do this.
read = pysam.AlignedSegment().from_dict(read.to_dict(), read.header)
mate = pysam.AlignedSegment().from_dict(mate.to_dict(), read.header)
# Make it so that if our read is secondary, the mate is also secondary. We don't make the
# mate primary if the read is primary because we would otherwise end up with mulitple
# primary alignments.
if read.is_secondary:
mate.is_secondary = True
# In a situation where there is already one mate for each read, then we will come across
# each pair twice - once when we scan read1 and once when we scan read2. Thus we need
# to make sure we don't output something already output.
if read.is_read1:
mate = copy_tags(options.tags, read, mate)
output_key = str(read) + str(mate)
if output_key not in output:
output.add(output_key)
outbam.write(read)
outbam.write(mate)
skipped_stats["pairs_output"] += 1
elif read.is_read2:
read = copy_tags(options.tags, mate, read)
output_key = str(mate) + str(read)
if output_key not in output:
output.add(output_key)
outbam.write(mate)
outbam.write(read)
skipped_stats["pairs_output"] += 1
else:
skipped_stats["skipped_not_read_12"] += 1
U.warn(
"Alignment {} is neither read1 nor read2 -- skipped".format(
"\t".join(map(str, [read.query_name, read.flag, read.reference_name, int(read.pos)]))
)
)
continue
if not out_name == "-":
outbam.close()
U.info(
"Total pairs output: {}, Pairs skipped - no mates: {},"
" Pairs skipped - not read1 or 2: {}".format(
skipped_stats["pairs_output"], skipped_stats["no_mate"], skipped_stats["skipped_not_read12"]
)
)
U.Stop()
if __name__ == "__main__":
sys.exit(main(sys.argv))

32
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#!/bin/bash
set -eo pipefail
unset_if_false=(
par_sam
par_error
par_log2stderr
par_timeit_header )
for var in "${unset_if_false[@]}"; do
test_val="${!var}"
[[ "$test_val" == "false" ]] && unset $var
done
umi_tools prepare-for-rsem \
${par_log:+--log "${par_log}"} \
${par_tags:+--tags "${par_tags}"} \
${par_sam:+--sam} \
--stdin="${par_input}" \
${par_output:+--stdout "${par_output}"} \
${par_error:+--error "${par_error}"} \
${par_temp_dir:+--temp-dir "${par_temp_dir}"} \
${par_log2stderr:+--log2stderr} \
${par_verbose:+--verbose "${par_verbose}"} \
${par_random_seed:+--random-seed "${par_random_seed}"} \
${par_compresslevel:+--compresslevel "${par_compresslevel}"}
${par_timeit:+--timeit "${par_timeit}"} \
${par_timeit_name:+--timeit-name "${par_timeit_name}"} \
${par_timeit_header:+--timeit-header}

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src/umi_tools/umi_tools_prepareforrsem/test.sh Normal file
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#!/bin/bash
test_dir="$meta_resources_dir/test_data"
apt-get -q update && apt-get -q install -y samtools
################################################################################
echo ">>> Test 1: with --sam:"
"${meta_executable}" \
--input "$test_dir/test_dedup.sam" \
--output "$test_dir/test_output.sam" \
--sam
echo ">>> Check if output is present"
[[ ! -f "$test_dir/test_output.sam" ]] && echo "Output file not found" && exit 1
[[ ! -s "$test_dir/test_output.sam" ]] && echo "Output file is empty" && exit 1
echo ">>> Check if output is correct"
# use diff but ignoring the header lines (which start with @) as they may differ slightly
diff <(grep -v "^@" "$test_dir/test_output.sam") <(grep -v "^@" "$test_dir/test.sam") && echo "Output is correct" || (echo "Output is incorrect" && exit 1)
################################################################################
echo ">>> Test 2: without --sam:"
"${meta_executable}" \
--input "$test_dir/test_dedup.bam" \
--output "$test_dir/test_output.bam"
echo ">>> Check if output is present"
[[ ! -f "$test_dir/test_output.bam" ]] && echo "Output file not found" && exit 1
[[ ! -s "$test_dir/test_output.bam" ]] && echo "Output file is empty" && exit 1
echo ">>> Check if output is correct"
diff <(samtools view "$test_dir/test_output.bam") <(samtools view "$test_dir/test.bam") || (echo "Output is incorrect" && exit 1)
################################################################################
echo ">>> Test 3: with --log:"
"${meta_executable}" \
--log "$test_dir/test_log.log" \
--input "$test_dir/test_dedup.sam" \
--output "$test_dir/test_output.sam" \
--sam
echo ">>> Check if output is present"
[[ ! -f "$test_dir/test_output.sam" ]] && echo "Output file not found" && exit 1
[[ ! -s "$test_dir/test_output.sam" ]] && echo "Output file is empty" && exit 1
[[ ! -f "$test_dir/test_log.log" ]] && echo "Log file not found" && exit 1
[[ ! -s "$test_dir/test_log.log" ]] && echo "Log file is empty" && exit 1
echo ">>> Check if log file is correct"
diff <(grep -v '^#' "$test_dir/test_log.log" | sed 's/^[0-9-]* [0-9:]*,[0-9]\{3\} //') <(grep -v '^#' "$test_dir/log.log" | sed 's/^[0-9-]* [0-9:]*,[0-9]\{3\} //') || (echo "Log file is incorrect" && exit 1)
echo ">>> All test succeeded"
exit 0

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src/umi_tools/umi_tools_prepareforrsem/test_data/log.log Normal file
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# UMI-tools version: 1.1.5
# output generated by prepare-for-rsem.py --log test_data/log.log --sam --stdin test_data/test_dedup.sam --stdout jnfgioeurg.sam
# job started at Tue Sep 10 06:43:30 2024 on 4855b4607095 -- 07ae7548-56e8-4772-9b48-7406710fd838
# pid: 28, system: Linux 6.10.0-linuxkit #1 SMP PREEMPT_DYNAMIC Wed Jul 17 10:54:05 UTC 2024 x86_64
# compresslevel : 6
# log2stderr : False
# loglevel : 1
# random_seed : None
# sam : True
# short_help : None
# stderr : <_io.TextIOWrapper name='<stderr>' mode='w' encoding='utf-8'>
# stdin : <_io.TextIOWrapper name='test_data/test_dedup.sam' mode='r' encoding='UTF-8'>
# stdlog : <_io.TextIOWrapper name='test_data/log.log' mode='a' encoding='UTF-8'>
# stdout : <_io.TextIOWrapper name='jnfgioeurg.sam' mode='w' encoding='UTF-8'>
# tags : UG,BX
# timeit_file : None
# timeit_header : None
# timeit_name : all
# tmpdir : None
2024-09-10 06:43:30,918 WARNING Alignment ERR5069949.114870 99 MT192765.1 642 has no mate -- skipped
2024-09-10 06:43:30,918 WARNING Alignment ERR5069949.147998 163 MT192765.1 673 has no mate -- skipped
2024-09-10 06:43:30,919 WARNING Alignment ERR5069949.114870 147 MT192765.1 747 has no mate -- skipped
2024-09-10 06:43:30,920 WARNING Alignment ERR5069949.147998 83 MT192765.1 918 has no mate -- skipped
2024-09-10 06:43:30,921 WARNING Alignment ERR5069949.184542 99 MT192765.1 1054 has no mate -- skipped
2024-09-10 06:43:30,921 WARNING Alignment ERR5069949.184542 147 MT192765.1 1254 has no mate -- skipped
2024-09-10 06:43:30,922 WARNING Alignment ERR5069949.376959 99 MT192765.1 4104 has no mate -- skipped
2024-09-10 06:43:30,924 WARNING Alignment ERR5069949.376959 147 MT192765.1 4189 has no mate -- skipped
2024-09-10 06:43:30,925 WARNING Alignment ERR5069949.532979 99 MT192765.1 5567 has no mate -- skipped
2024-09-10 06:43:30,926 WARNING Alignment ERR5069949.540529 163 MT192765.1 5569 has no mate -- skipped
2024-09-10 06:43:30,926 WARNING Alignment ERR5069949.532979 147 MT192765.1 5620 has no mate -- skipped
2024-09-10 06:43:30,927 WARNING Alignment ERR5069949.540529 83 MT192765.1 5658 has no mate -- skipped
2024-09-10 06:43:30,930 WARNING Alignment ERR5069949.856527 99 MT192765.1 10117 has no mate -- skipped
2024-09-10 06:43:30,931 WARNING Alignment ERR5069949.870926 99 MT192765.1 10117 has no mate -- skipped
2024-09-10 06:43:30,931 WARNING Alignment ERR5069949.856527 147 MT192765.1 10198 has no mate -- skipped
2024-09-10 06:43:30,931 WARNING Alignment ERR5069949.885966 99 MT192765.1 10229 has no mate -- skipped
2024-09-10 06:43:30,932 WARNING Alignment ERR5069949.870926 147 MT192765.1 10244 has no mate -- skipped
2024-09-10 06:43:30,932 WARNING Alignment ERR5069949.885966 147 MT192765.1 10276 has no mate -- skipped
2024-09-10 06:43:30,932 WARNING Alignment ERR5069949.937422 99 MT192765.1 10421 has no mate -- skipped
2024-09-10 06:43:30,933 WARNING Alignment ERR5069949.937422 147 MT192765.1 10590 has no mate -- skipped
2024-09-10 06:43:30,934 WARNING Alignment ERR5069949.1066259 99 MT192765.1 11336 has no mate -- skipped
2024-09-10 06:43:30,935 WARNING Alignment ERR5069949.1062611 163 MT192765.1 11426 has no mate -- skipped
2024-09-10 06:43:30,936 WARNING Alignment ERR5069949.1067032 163 MT192765.1 11433 has no mate -- skipped
2024-09-10 06:43:30,936 WARNING Alignment ERR5069949.1062611 83 MT192765.1 11453 has no mate -- skipped
2024-09-10 06:43:30,936 WARNING Alignment ERR5069949.1066259 147 MT192765.1 11479 has no mate -- skipped
2024-09-10 06:43:30,937 WARNING Alignment ERR5069949.1067032 83 MT192765.1 11480 has no mate -- skipped
2024-09-10 06:43:30,938 WARNING Alignment ERR5069949.1258508 163 MT192765.1 12424 has no mate -- skipped
2024-09-10 06:43:30,939 WARNING Alignment ERR5069949.1261808 99 MT192765.1 12592 has no mate -- skipped
2024-09-10 06:43:30,940 WARNING Alignment ERR5069949.1258508 83 MT192765.1 12637 has no mate -- skipped
2024-09-10 06:43:30,940 WARNING Alignment ERR5069949.1261808 147 MT192765.1 12653 has no mate -- skipped
2024-09-10 06:43:30,941 WARNING Alignment ERR5069949.1372331 163 MT192765.1 13010 has no mate -- skipped
2024-09-10 06:43:30,941 WARNING Alignment ERR5069949.1372331 83 MT192765.1 13131 has no mate -- skipped
2024-09-10 06:43:30,942 WARNING Alignment ERR5069949.1552198 99 MT192765.1 13943 has no mate -- skipped
2024-09-10 06:43:30,943 WARNING Alignment ERR5069949.1561137 163 MT192765.1 13990 has no mate -- skipped
2024-09-10 06:43:30,943 WARNING Alignment ERR5069949.1552198 147 MT192765.1 14026 has no mate -- skipped
2024-09-10 06:43:30,944 WARNING Alignment ERR5069949.1561137 83 MT192765.1 14080 has no mate -- skipped
2024-09-10 06:43:30,947 WARNING Alignment ERR5069949.2098070 99 MT192765.1 17114 has no mate -- skipped
2024-09-10 06:43:30,947 WARNING Alignment ERR5069949.2064910 99 MT192765.1 17122 has no mate -- skipped
2024-09-10 06:43:30,947 WARNING Alignment ERR5069949.2125592 99 MT192765.1 17179 has no mate -- skipped
2024-09-10 06:43:30,947 WARNING Alignment ERR5069949.2064910 147 MT192765.1 17179 has no mate -- skipped
2024-09-10 06:43:30,948 WARNING Alignment ERR5069949.2098070 147 MT192765.1 17269 has no mate -- skipped
2024-09-10 06:43:30,948 WARNING Alignment ERR5069949.2125592 147 MT192765.1 17288 has no mate -- skipped
2024-09-10 06:43:30,948 WARNING Alignment ERR5069949.2185111 163 MT192765.1 17405 has no mate -- skipped
2024-09-10 06:43:30,949 WARNING Alignment ERR5069949.2151832 163 MT192765.1 17415 has no mate -- skipped
2024-09-10 06:43:30,949 WARNING Alignment ERR5069949.2176303 99 MT192765.1 17441 has no mate -- skipped
2024-09-10 06:43:30,949 WARNING Alignment ERR5069949.2151832 83 MT192765.1 17452 has no mate -- skipped
2024-09-10 06:43:30,949 WARNING Alignment ERR5069949.2205229 99 MT192765.1 17475 has no mate -- skipped
2024-09-10 06:43:30,950 WARNING Alignment ERR5069949.2216307 163 MT192765.1 17503 has no mate -- skipped
2024-09-10 06:43:30,950 WARNING Alignment ERR5069949.2176303 147 MT192765.1 17518 has no mate -- skipped
2024-09-10 06:43:30,950 WARNING Alignment ERR5069949.2185111 83 MT192765.1 17536 has no mate -- skipped
2024-09-10 06:43:30,951 WARNING Alignment ERR5069949.2205229 147 MT192765.1 17584 has no mate -- skipped
2024-09-10 06:43:30,951 WARNING Alignment ERR5069949.2216307 83 MT192765.1 17600 has no mate -- skipped
2024-09-10 06:43:30,952 WARNING Alignment ERR5069949.2270078 163 MT192765.1 17969 has no mate -- skipped
2024-09-10 06:43:30,953 WARNING Alignment ERR5069949.2270078 83 MT192765.1 18102 has no mate -- skipped
2024-09-10 06:43:30,953 WARNING Alignment ERR5069949.2328704 163 MT192765.1 18285 has no mate -- skipped
2024-09-10 06:43:30,954 WARNING Alignment ERR5069949.2342766 99 MT192765.1 18396 has no mate -- skipped
2024-09-10 06:43:30,954 WARNING Alignment ERR5069949.2328704 83 MT192765.1 18411 has no mate -- skipped
2024-09-10 06:43:30,954 WARNING Alignment ERR5069949.2361683 99 MT192765.1 18425 has no mate -- skipped
2024-09-10 06:43:30,954 WARNING Alignment ERR5069949.2342766 147 MT192765.1 18468 has no mate -- skipped
2024-09-10 06:43:30,955 WARNING Alignment ERR5069949.2361683 147 MT192765.1 18512 has no mate -- skipped
2024-09-10 06:43:30,955 WARNING Alignment ERR5069949.2415814 99 MT192765.1 18597 has no mate -- skipped
2024-09-10 06:43:30,955 WARNING Alignment ERR5069949.2385514 99 MT192765.1 18602 has no mate -- skipped
2024-09-10 06:43:30,956 WARNING Alignment ERR5069949.2417063 99 MT192765.1 18648 has no mate -- skipped
2024-09-10 06:43:30,956 WARNING Alignment ERR5069949.2388984 99 MT192765.1 18653 has no mate -- skipped
2024-09-10 06:43:30,956 WARNING Alignment ERR5069949.2385514 147 MT192765.1 18684 has no mate -- skipped
2024-09-10 06:43:30,956 WARNING Alignment ERR5069949.2388984 147 MT192765.1 18693 has no mate -- skipped
2024-09-10 06:43:30,957 WARNING Alignment ERR5069949.2431709 99 MT192765.1 18748 has no mate -- skipped
2024-09-10 06:43:30,957 WARNING Alignment ERR5069949.2415814 147 MT192765.1 18764 has no mate -- skipped
2024-09-10 06:43:30,957 WARNING Alignment ERR5069949.2417063 147 MT192765.1 18765 has no mate -- skipped
2024-09-10 06:43:30,958 WARNING Alignment ERR5069949.2431709 147 MT192765.1 18776 has no mate -- skipped
2024-09-10 06:43:30,959 WARNING Alignment ERR5069949.2668880 99 MT192765.1 23124 has no mate -- skipped
2024-09-10 06:43:30,960 WARNING Alignment ERR5069949.2674295 163 MT192765.1 23133 has no mate -- skipped
2024-09-10 06:43:30,960 WARNING Alignment ERR5069949.2668880 147 MT192765.1 23145 has no mate -- skipped
2024-09-10 06:43:30,960 WARNING Alignment ERR5069949.2674295 83 MT192765.1 23203 has no mate -- skipped
2024-09-10 06:43:30,963 WARNING Alignment ERR5069949.2953930 99 MT192765.1 25344 has no mate -- skipped
2024-09-10 06:43:30,963 WARNING Alignment ERR5069949.2972968 163 MT192765.1 25425 has no mate -- skipped
2024-09-10 06:43:30,963 WARNING Alignment ERR5069949.2953930 147 MT192765.1 25464 has no mate -- skipped
2024-09-10 06:43:30,964 WARNING Alignment ERR5069949.2972968 83 MT192765.1 25518 has no mate -- skipped
2024-09-10 06:43:30,966 WARNING Alignment ERR5069949.3273002 163 MT192765.1 28442 has no mate -- skipped
2024-09-10 06:43:30,966 WARNING Alignment ERR5069949.3277445 99 MT192765.1 28508 has no mate -- skipped
2024-09-10 06:43:30,966 WARNING Alignment ERR5069949.3273002 83 MT192765.1 28543 has no mate -- skipped
2024-09-10 06:43:30,966 WARNING Alignment ERR5069949.3277445 147 MT192765.1 28573 has no mate -- skipped
2024-09-10 06:43:30,968 INFO Total pairs output: 56, Pairs skipped - no mates: 82, Pairs skipped - not read1 or 2: 0
# job finished in 0 seconds at Tue Sep 10 06:43:30 2024 -- 4.44 0.25 0.00 0.00 -- 07ae7548-56e8-4772-9b48-7406710fd838

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@HD VN:1.6 SO:coordinate
@SQ SN:MT192765.1 LN:29829
@RG ID:1 LB:lib1 PL:ILLUMINA SM:test PU:barcode1
@PG ID:minimap2 PN:minimap2 VN:2.17-r941 CL:minimap2 -ax sr tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna tests/data/fastq/dna/sarscov2_1.fastq.gz tests/data/fastq/dna/sarscov2_2.fastq.gz
@PG ID:samtools PN:samtools PP:minimap2 VN:1.11 CL:samtools view -Sb sarscov2_aln.sam
@PG ID:samtools.1 PN:samtools PP:samtools VN:1.11 CL:samtools sort -o sarscov2_paired_aln.sorted.bam sarscov2_paired_aln.bam
@PG ID:samtools.2 PN:samtools PP:samtools.1 VN:1.20 CL:samtools view -h test_data/test_dedup.bam
ERR5069949.29668 83 MT192765.1 267 60 89M = 121 -235 CCTTGTCCCTGGTTACAACTAGAAACCACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAG E////6/E/EE/EE/<<///6EEE/////<AAA<A<A6AE/E/AE6A/EAEEEAEEEAEEEEEA/AEAE<EEEAEEE////6EEAA/AA s1:i:173 s2:i:0 RG:Z:1 NM:i:3 AS:i:148 de:f:0.0337 rl:i:0 cm:i:6 nn:i:0 tp:A:P ms:i:148
ERR5069949.29668 163 MT192765.1 121 60 150M = 267 235 TATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCTTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTT AAA/E/EEEEEEEEEAEEEEEEEEE/</E/E/EE<E/EEAAEA/E/EE//EA/EEEEEA/AEEE/EEEEE/E/EA/EE/EEE<E/E///E<AEE<<EEE/<EEEAA///AE/6A///A/AE/EAEE</EAEAE///AA/EEAEE/AAEAA s1:i:173 s2:i:0 RG:Z:1 NM:i:1 AS:i:290 de:f:0.0067 rl:i:0 cm:i:13 nn:i:0 tp:A:P ms:i:290
ERR5069949.155944 83 MT192765.1 1023 60 150M = 978 -195 TGAAATTAAATTGGCAAAGAAATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCACTTAAATTCCATAATCAAGACTATTCAACCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCC EA<EA/<A/6A/AEA/6/66/AAAEAEEE/EEA/6AAAAAAEE</AAEEEEAAEEEAA/EEE//A/EEEEE/AE/EEE6AEEEE/A/EAEEEEE/EEAEEEAE/AEA66AEEEEEEEEE<AEEEAEEEEEEEEE6EEEEEEEAEEAAAAA s1:i:183 s2:i:0 RG:Z:1 NM:i:1 AS:i:290 de:f:0.0067 rl:i:0 cm:i:10 nn:i:0 tp:A:P ms:i:290
ERR5069949.155944 163 MT192765.1 978 60 150M = 1023 195 GTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAAATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAACCAAGGGTTGAAAA AAAA/EEEEEEAEEEEEEEEEEEE/EEEEEEEEEE/EAEEEEEEEEEEEEEEEAEEEAEE/AEEEEEEAAEEEEEEAEAEEEE/AEE/<EAE/E<EEA<<<AAEEAEEE<AA<EE/EAAEEEE<<<EEEA/AEAEE6</EEA<AEEE<<E s1:i:183 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:17 nn:i:0 tp:A:P ms:i:300
ERR5069949.169513 99 MT192765.1 1098 60 92M = 1098 92 AATCAAGACTATTCAACCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCACCAAATG AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EE6EEEE s1:i:92 s2:i:0 RG:Z:1 NM:i:0 AS:i:184 de:f:0 rl:i:0 cm:i:11 nn:i:0 tp:A:P ms:i:184
ERR5069949.169513 147 MT192765.1 1098 48 92M = 1098 -92 AATCAAGACTATTCAACCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCACCAAATG EEEEEEEEEEEEEEEEEEEEEEE/EEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:32 s2:i:92 RG:Z:1 NM:i:0 AS:i:184 de:f:0 rl:i:0 cm:i:3 nn:i:0 tp:A:P ms:i:184
ERR5069949.257821 83 MT192765.1 2834 49 139M = 2833 -140 CCTATACAGTTGAACTCGGTACAGAAGTAAATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACCACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATA A/AE<EE<EA</EAEAAA<AEEAEE/A/E<<E</E</EEEAAE/EE<E/EEEAEEEEEEE/AEEEEEEEEEEE/EEEE<EEEE/EE/EAEEE6EEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:121 s2:i:48 RG:Z:1 NM:i:0 AS:i:278 de:f:0 rl:i:0 cm:i:1 nn:i:0 tp:A:P ms:i:278
ERR5069949.257821 163 MT192765.1 2833 60 140M = 2834 140 GCCTATACAGTTGAACTCGGTACAGAAGTAAATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACCACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEEEEEEEEEAEEEEEE s1:i:121 s2:i:0 RG:Z:1 NM:i:0 AS:i:280 de:f:0 rl:i:0 cm:i:17 nn:i:0 tp:A:P ms:i:280
ERR5069949.309410 99 MT192765.1 3184 60 151M = 3348 314 GAAGAAGATTGGTTAGATGATGATAGTCAACAAACTGTTGGTCAACAAGACGGCAGTGAGGACAATCAGACAACTACTATTCAAACAATTGTTGAGGTTCAACCTCAATTAGAGATGGAACTTACACCAGTTGTTCAGACTATTGAAGTGA AAAAA//EEEEA6EEEAE</EEE/EEEEE/EE6EEEEEEEEEEEEEEEAEEAAEEEEEEEEEAEEEEEE/EEAEEEEEAEAEEE/EEAEEE<AEEEAA////EEEEEEEEA//A/EE/EAAEA/AE<EE/E//E/</AEAEAE/AEA/AEA s1:i:274 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:22 nn:i:0 tp:A:P ms:i:302
ERR5069949.309410 147 MT192765.1 3348 60 150M = 3184 -314 TTATTTAAAACTTACTGACAATGTATACATTAAAAATGCAGACATTGTGGAAGAAGCTAAAAAGGTAAAACCAACAGTGGTTGTTAATGCAGCCAATGTTTACCTTAAACATGGAGGAGGTGTTGCAGGAGCCTTAAATACGGCTACTAA E//EEAEA<<EAAE/AAAAEAAAAEA</A/<6/E/<A<//AE/EEAAE<EEEAEEEEEEAEE/EEAEEEEEE/<E/EEE6EEAE/<EE//E</</EE/EEAAEE/EAA/EEEEAEEEEE///EA/EEEEEEEE//E66EE/E/EEA/AAA s1:i:274 s2:i:0 RG:Z:1 NM:i:1 AS:i:290 de:f:0.0067 rl:i:0 cm:i:18 nn:i:0 tp:A:P ms:i:290
ERR5069949.366975 83 MT192765.1 4166 59 106M = 4166 -106 CTAAAAAGGCTGGTGGCACTACTGAAATGCTAGCGAAAGCTTTGAGAAAAGTGCCAACAGACAATTATATAACCACTTACCCGGGTCAGGGTTTAAATGGTTACAC EEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEE6EEEEEEEEEEAEEEEEEEEEE<AEAEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:96 s2:i:0 RG:Z:1 NM:i:0 AS:i:212 de:f:0 rl:i:0 cm:i:4 nn:i:0 tp:A:P ms:i:212
ERR5069949.366975 163 MT192765.1 4166 60 106M = 4166 106 CTAAAAAGGCTGGTGGCACTACTGAAATGCTAGCGAAAGCTTTGAGAAAAGTGCCAACAGACAATTATATAACCACTTACCCGGGTCAGGGTTTAAATGGTTACAC AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE s1:i:96 s2:i:0 RG:Z:1 NM:i:0 AS:i:212 de:f:0 rl:i:0 cm:i:9 nn:i:0 tp:A:P ms:i:212
ERR5069949.465452 99 MT192765.1 4695 60 151M = 4827 282 ACCTGATGCTGTTACAGCGTATAATGGTTATCTTACTTCTTCTTCTAAAACACCTGAAGAACATTTTATTGAAACCATCTCACTTGCTGGTTCTTATAAAGATTGGTCCTATTCTGGACAATCTACACAACTAGGTATAGAATTTCTTAAG AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEE/EEAEEEE/EEEEEEEEEEAEEEEEEEEEEEEEEE<EEEEAAAEAEEEEEEAA6AAEEEEEA<EEEEE</EEAEE/EE s1:i:261 s2:i:0 RG:Z:1 NM:i:1 AS:i:292 de:f:0.0066 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:292
ERR5069949.465452 147 MT192765.1 4827 60 150M = 4695 -282 AGGTATAGAATTTCTTAAGAGAGGTGATAAAAGTGTATATTACACTAGTAATCCTACCACATTCCACCTAGATGGTGAAGTTATCACCTTTGACAATCTTAAGACACTTCTTTCTTTGAGAGAAGTGAGGACTATTAAGGTGTTTACAAC AAAEEEEEEEEEEEEAA/<EA<AA/EAEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEAEEEEEEE/EEA/EEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:261 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:300
ERR5069949.479807 83 MT192765.1 5123 60 150M = 4968 -305 CTAATGATGACACTCTACGTGTTGAGGCTTTTGAGTACTACCACACAACTGATCCTAGTTTTCTGGGTAGGTACATGTCAGCATTAAATCACACTAAAAAGTGGAAATACCCACAAGTTAATGGTTTAACTTCTATTAAATGGGCAGATA AA/EEEEAAAEAEEEAAAEEA/AAEAAEE/AAAEAAAAEEEEEEEEEEEAEEEEEEEEEEEEEAEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEAEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:280 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:23 nn:i:0 tp:A:P ms:i:300
ERR5069949.479807 163 MT192765.1 4968 60 150M = 5123 305 GTTTACAACAGTAGACAACATTAACCTCCACACGCAAGTTGTGGACATGTCAATGACATATGGACAACAGTTTGGTCCAACTTATTTGGATGGAGCTGATGTTACTAAAATAAAACCTCATAATTCACATGAAGGTAAAACATTTTATGT AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<AEEEEEEEEEE<EEE<AEE/EEEEEEEEEAEEE<AA/EAA<AEEEEEEEAEEAAA s1:i:280 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:20 nn:i:0 tp:A:P ms:i:300
ERR5069949.501486 83 MT192765.1 5423 60 146M = 5355 -214 TAGGTGAGTTAGGTGATGTTAGAGAAACAATGAGTTACTTGTTTCAACATGCCAATTTAGATTCTTGCAAAAGAGTCTTGAACGTGGTGTGTAAAACTTGTGGACAACAGCAGACAACCCTTAAGGGTGTAGAAGCTGTTATGTAC EAAAAEAEEEE6E<AEEEEEEEE<EEEEEEAAEE/EEEEEE/<EEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:207 s2:i:0 RG:Z:1 NM:i:0 AS:i:292 de:f:0 rl:i:0 cm:i:11 nn:i:0 tp:A:P ms:i:292
ERR5069949.501486 163 MT192765.1 5355 60 150M = 5423 214 TTACAGAGCAAGGGCTGGTGAAGCTGCTAACTTTTGTGCACTTATCTTAGCCTACTGTAATAAGACAGTAGGTGAGTTAGGTGATGTTAGAGAAACAATGAGTTACTTGTTTCAACATGCCAATTTAGATTCTTGCAAAAGAGTCTTGAA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEAA/EEE/<AEEAAEAEA</EEEAEAAAAAEE s1:i:207 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:18 nn:i:0 tp:A:P ms:i:300
ERR5069949.573706 99 MT192765.1 5697 60 150M = 5784 236 GTACGAACTTAAGCATGGTACATTTACTTGTGCTAGTGAGTACACTGGTAATTACCAGTGTGGTCACTATAAACATATATCTTCTAAAGAAACTTTGTATTGCATAGACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTAT AAAAA6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEAAEEEAEEEEEEEEEEE s1:i:214 s2:i:0 RG:Z:1 NM:i:2 AS:i:282 de:f:0.0133 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:282
ERR5069949.573706 147 MT192765.1 5784 60 149M = 5697 -236 AGAAACTTTGTATTGCATAGACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAGTTACACAACAACCATAAAACCAGTTACTTATAAATTGGATGGTGTTGTTTGTACAGAAA AA<E<EEEEEEEEA<AEEEAEEAA<<EEE<AEEEEEEAEAAAAEAEAEEEEEEAEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:214 s2:i:0 RG:Z:1 NM:i:0 AS:i:298 de:f:0 rl:i:0 cm:i:13 nn:i:0 tp:A:P ms:i:298
ERR5069949.576388 83 MT192765.1 5798 50 77M = 5798 -77 GCATAGACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAGT EA/AEEE/<EEEEEEEEEEEAA<EEEEEEEEEEEEEEEEEEEEEAEEEEEAEEEAEE6/EEEAEEEEEEEEEA6AAA s1:i:62 s2:i:0 RG:Z:1 NM:i:0 AS:i:154 de:f:0 rl:i:0 cm:i:1 nn:i:0 tp:A:P ms:i:154
ERR5069949.576388 163 MT192765.1 5798 60 77M = 5798 77 GCATAGACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAGT AAAAA6EEAEEEEEAEEAEEAEEEEEEA6EEEEAEEAEEEEE6EEEEEEAEEEEA///A<<EEEEEEEEEAEEEEEE s1:i:62 s2:i:0 RG:Z:1 NM:i:0 AS:i:154 de:f:0 rl:i:0 cm:i:10 nn:i:0 tp:A:P ms:i:154
ERR5069949.611123 83 MT192765.1 6481 48 125M = 6481 -125 ATTATACTTAAACCAGCAAATAATAGTTTAAAAATTACAGAAGAGGTTGGCCACACAGATCTAATGGCTGCTTATGTAGACAATTCTAGTCTTACTATTAAGAAACCTAATGAATTATCTAGAGT EEEAEEEEEEEEEEEA<EEEAEEEEA/EEEEEEEEEAEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEAEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:50 s2:i:117 RG:Z:1 NM:i:0 AS:i:250 de:f:0 rl:i:0 cm:i:8 nn:i:0 tp:A:P ms:i:250
ERR5069949.611123 163 MT192765.1 6481 60 125M = 6481 125 ATTATACTTAAACCAGCAAATAATAGTTTAAAAATTACAGAAGAGGTTGGCCACACAGATCTAATGGCTGCTTATGTAGACAATTCTAGTCTTACTATTAAGAAACCTAATGAATTATCTAGAGT AAAAAEEEEEA6EEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEE<EEEEEEEAEEEEEEEEEEEEAEEEEEEEEEEE/EEEEEEEA/AAEAAEAAEAE s1:i:117 s2:i:0 RG:Z:1 NM:i:0 AS:i:250 de:f:0 rl:i:0 cm:i:14 nn:i:0 tp:A:P ms:i:250
ERR5069949.651338 83 MT192765.1 7745 60 4S138M = 7629 -254 ACTCTGAAGAATGGTTCCATCCATCTTTACTTTGTTAAAGCTGGTCAAAAGACTTATGAAAGACATTCTCTCTCTCATTTTGTTAACTTAGACAACCTGAGAGCTAATAACACTAAAGGTTCATTGCCTATTAATGTTATAG A///A/6/<EEEA//EE/EE<AEEE/<A/EAE<</A/A<EEE/E<EEEEE<</EEEA<E/EEAAEEEEAE/EEEEEEEEEEEEEE/E/A/EE//<AE/EEEAEEA</EE/AEEEE/AEEEEAEEEEEEEEEAEAEEEAAAAA s1:i:223 s2:i:0 RG:Z:1 NM:i:1 AS:i:266 de:f:0.0072 rl:i:0 cm:i:13 nn:i:0 tp:A:P ms:i:266
ERR5069949.651338 163 MT192765.1 7629 60 149M = 7745 254 ATTCTGTGCTGGTAGTACATTTATTAGTGATGAAGATGCGAGAGACTTGTCACTACAGTTTAAAAGACCAATAAATCCTACTGACCAGTCTTCTTACATCGTTGATAGTGTTACAGTGAAGAATGGTTCCATCCATCTTTACTTTGATA AAAAAE/EAEEE/AEAEEE/EEEAAEEEEAEEEEE/EEEEAEEEEEEAEE/EEEE/EEE</EE/AEAE/<E/EEAEE<EEEE//AEEEEEE<EEAEE/EEE//E/<EE<A<A/EAA<AA/AEEA//A<A/A<A<6A6/AEE/AEEA<AE s1:i:223 s2:i:0 RG:Z:1 NM:i:1 AS:i:288 de:f:0.0067 rl:i:0 cm:i:16 nn:i:0 tp:A:P ms:i:288
ERR5069949.686090 83 MT192765.1 8097 60 150M = 7975 -272 TGCAACTGCAGAAGCTGAACTTGCAAAGAATGTGTCCTTAGACAATGTCTTATCTACTTTTATTTCAGCAGCTCGGCAAGGGTTTGTTGATTCAGATGTAGAAACTAAAGATGTTGTTGAATGTCTTAAATTGTCACATAAATCTGACAT EEEAEAEEEEEEEEEEEEEAEEEEEAEEE<EAEE/EEEEEEEEAEEE6EEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEE/EEEEAEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:252 s2:i:0 RG:Z:1 NM:i:1 AS:i:290 de:f:0.0067 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:290
ERR5069949.686090 163 MT192765.1 7975 60 151M = 8097 272 GATCAGGCATTAGTGTCTGATGTTGGTGATAGTGCGGAAGTTGCAGTTAAAATGTTTGATGCTTACGTTAATACGTTTTCATCAACTTTTAACGTACCAATGGAAAAACTCAAAACACTAGTTGCAACTGCAGAAGCTGAACTTGCAAAGA AAAAAEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEAEEEEEAEEEEEEEE/EEEEEEEEEEEEEEAEEEEEAEEEE<AEE/EEEEEEEAAAAEEEEEEEEEEEAEAEEEEEAEEEEA s1:i:252 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:27 nn:i:0 tp:A:P ms:i:302
ERR5069949.786562 83 MT192765.1 9096 60 151M = 8904 -343 AAGTTTACGCCCTGACACACGTTATGTGCTCATGGATGGCTCTATTATTCAATTTCCTAACACCTACCTTGAAGGTTCTGTTAGAGTGGTAACAACTTTTGATTCTGAGTACTGTAGGCACGGCACTTGTGAAAGATCAGAAGCTGGTGTT AEAE<AE/AAAEEAAEE<EEAEEEEAEEEEAAA/AEEEAEAEAEEEEEEEEAAEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAA6A s1:i:272 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:22 nn:i:0 tp:A:P ms:i:302
ERR5069949.786562 163 MT192765.1 8904 60 150M = 9096 343 GCATTTCTTACCTAGAGTTTTTAGTGCAGTTGGTAACATCTGTTACACACCATCAAAACTTATAGAGTACACTGACTTTGCAACATCAGCTTGTGTTTTGGCTGCTGAATGTACAATTTTTAAAGATGCTTCTGGTAAGCCAGTACCATA AAAAAEEEEEEEEAEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEAEEEEEEEEEEEEEEEAEEEEEEE<EEAEEEEE<EEEEEEEEEAEEEAEEEAEEAA6A<EEEEAAEEEEAA/AEEEEEE/EEEEEEE s1:i:272 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:20 nn:i:0 tp:A:P ms:i:300
ERR5069949.919671 83 MT192765.1 10501 60 151M = 10467 -185 ATAGATTATGACTGTGTCTCTTTTTGTTACATGCACCATATGGAATTACCAACTGGAGTTCATGCTGGCACAGACTTAGAAGGTAACTTTTATGGACCTTTTGTTGACAGGCAAACAGCACAAGCAGCTGGTACGGACACAACTATTACAG EEEEEEEEAAEAAAEEAA6AEEEEEEEEAEEAAAAE/AEEEAEEEAEEEAEEEEEEEEEEEEEEEEEEEEAAEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAAAAA s1:i:184 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:9 nn:i:0 tp:A:P ms:i:302
ERR5069949.919671 163 MT192765.1 10467 60 150M = 10501 185 CCTTAATGGTTCATGTGGTAGTGTTGGTTTTAACATAGATTATGACTGTGTCTCTTTTTGTTACATGCACCATATGGAATTACCAACTGGAGTTCATGCTGGCACAGACTTAGAAGGTAACTTTTATGGACCTTTTGTTGACAGGCAAAC AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAE/EEEEEEAEEEEEEEEAEEEEEEEEEEEAEEEEEEEAEEEEAEEEEAEEEEE6EEEEEEEAAEAEEEEEEE<EEEEEEE6AAEEAEEEAA6AEEAAAAAEEAAEEEAEAEEE s1:i:184 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:24 nn:i:0 tp:A:P ms:i:300
ERR5069949.973930 83 MT192765.1 10957 50 79M = 10924 -112 ACTTTCCAAAGTGCAGTCAAAAGAACAATCACGGGTACACACCACTGGTTGTTACTCACAATTTTGACTTCACTTTTAG <////E/EE/E//E/<//E/E//A/6EA/EE/EE///E/EAEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:101 s2:i:0 RG:Z:1 NM:i:2 AS:i:138 de:f:0.0253 rl:i:0 cm:i:1 nn:i:0 tp:A:P ms:i:138
ERR5069949.973930 163 MT192765.1 10924 60 112M = 10957 112 CCTTTTGATGTTGTTAGACAATGCTCAGGTGTTACTTTCCAAAGTGCAGTGAAAAGAACAATCAAGGGTACACACCACTGGTTGTTACTCACAATTTTGACTTCACTTTTAG AAAAAEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEAE<EAEEEEEEAEEAEE s1:i:101 s2:i:0 RG:Z:1 NM:i:0 AS:i:224 de:f:0 rl:i:0 cm:i:13 nn:i:0 tp:A:P ms:i:224
ERR5069949.986441 99 MT192765.1 11007 60 119M = 11104 247 GTTACTCACAATTTTGACTTCACTTTTAGTCTTAGTCCAGAGTACTCAATGGTCTTTGTTCTTTTTTTTGTATGAAAATGCCTTTTTACCTTTTGCTATGGGTATTATTGCTATGTCTG AAAAAEAEEEEEEE/EEE/EEEEEAEEEEEEEEEEEEEEEEEEEEE</EAAEA/EEEEEEEEAEAAEEEEEEEEEEEEE/E//<EAE/6///EE//E/EEE///E<EEEEA</A<<//< s1:i:200 s2:i:0 RG:Z:1 NM:i:1 AS:i:228 de:f:0.0084 rl:i:0 cm:i:9 nn:i:0 tp:A:P ms:i:228
ERR5069949.986441 147 MT192765.1 11104 60 150M = 11007 -247 ATGGGTATTATTGCTATGTCTGCTTTTGCAATGATGTTTGTCAAACATAAGCATGCATTTCTCTGTTTGTTTTTGTTACCTTCTCTTGCCACTGTAGCTTATTTTAATATGGTCTATATGCCTGCTAGTTGGGTGATGCGTATTATGACA A6A<AEEEEE<E<EAEAAEA<AAEEAEA</EAEEA<E/E/E/EEEEAEAA/<EAAAEAEEE/EEEEEEEAEEE/EAEAE/AEAAA/EAEEEEEEAEAEEEEEEEAEAEEEEE/EAEEEEEEAEEEEEAEEEEEEEEAEEEEEEEEAAAAA s1:i:200 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:22 nn:i:0 tp:A:P ms:i:300
ERR5069949.1014693 99 MT192765.1 11215 60 150M = 11215 150 GTCTATATGCCTGCTAGTTGGGTGATGCGTATTATGACATGGTTGGATATGGTTGATACTAGTTTGTCTGGTTTTAAGCTAAAAGACTGTGTTATGTATGCATCAGCTGTAGTGTTACTAATCCTTATGACAGCAAGAACTGTGTATGAT AAAAAAEEAEEE6EAE//E/EEE6AEAA/EAEAEE6/E//EAE/EEEEAEE/EEE/EAEEEEEAE/EEEEEAEEEEEAAEEAEEE/AE/EAEAEEEEEEEEEEEEEE/AE/E/E/<<<AA<E<AEE</EEEEA6<AEEAAAA//A//EEE s1:i:136 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:18 nn:i:0 tp:A:P ms:i:300
ERR5069949.1014693 147 MT192765.1 11215 48 150M = 11215 -150 GGCTATATGCCTGCTAGTTGGGTGATGCGTATTATGACATGGTTGGATATGGTTGATACTAGTTTGTCTGGTTTTAAGCTAAAAGACTGTGTTATGTATGCATCAGCTGTAGTGTTACTAATCCTTATGACAGCAAGAACTGTGTATGAT A/<EEEAA<<AA<AEAE<6<A<AA<EA<///EAEEE<AAEAA/EA6/EEEEE/E/EE/AEAEAEEE<AEEEEEEE6<AAEEEEE<EEEAEEEEEEAAEAEAEEEAAEEEEEEEEEE/EEEEEEEEE/EEEEEEEEAEE/EAEEEEAAAAA s1:i:33 s2:i:136 RG:Z:1 NM:i:1 AS:i:296 de:f:0.0067 rl:i:0 cm:i:3 nn:i:0 tp:A:P ms:i:296
ERR5069949.1020777 83 MT192765.1 11217 50 122M = 11217 -122 CTATATGCCTGCTAGTTGGGTGATGCGTATTATGACATGGTTGGATATGGTTGATACTAGTTTGTCTGGTTTTAAGCTAAAAGACTGTGTTATGTATGCATCAGCTGTAGTGTTACTAATCC EEEEA6AAAA6E/AA6AAAE/EEA<EE<AEEEAE<EAEAEAEAE<EEEEE/AEEAAEEEEAEEEEEEEE/EEEEE/EEEEEEEEEEEEE6EEEEEE/EEEEEE<EEEAEE6E6EEEEAAAAA s1:i:110 s2:i:41 RG:Z:1 NM:i:0 AS:i:244 de:f:0 rl:i:0 cm:i:1 nn:i:0 tp:A:P ms:i:244
ERR5069949.1020777 163 MT192765.1 11217 60 122M = 11217 122 CTATATGCCTGCTAGTTGGGTGATGCGTATTATGACATGGTTGGATATGGTTGATACTAGTTTGTCTGGTTTTAAGCTAAAAGACTGTGTTATGTATGCATCAGCTGTAGTGTTACTAATCC AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEAEEEEEEAEEEAAEEEEEEEEEAEEEEA s1:i:110 s2:i:0 RG:Z:1 NM:i:0 AS:i:244 de:f:0 rl:i:0 cm:i:15 nn:i:0 tp:A:P ms:i:244
ERR5069949.1088785 99 MT192765.1 11864 60 149M = 11912 198 CAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAATCCTTTGAAAAAAAGGTTTCACTACTTTCGGTTTTG AAAAAE/EAEE<EEA///<AEEE/EE<AEEE<EA/EEEEEEE/EAAAEEEEEE<E/E6AE<<E/EEA//</E/EEE/EEE/EE/E/<<EEAAAE<EEEEEE/EAEA//<//AA/E</A<<E/EEEE/AEE<E/<EAE</A6///AEEAA s1:i:182 s2:i:0 RG:Z:1 NM:i:3 AS:i:268 de:f:0.0201 rl:i:0 cm:i:15 nn:i:0 tp:A:P ms:i:268
ERR5069949.1088785 147 MT192765.1 11912 60 150M = 11864 -198 CTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGC AEEEEE<E//E<EAEE/AAAA<AEEEAEEEEE<AEEAEEEEEEAEAE</AE/EEE/<EEEEAEEEEEEEEEAEEEEEEE/EEEEEEEEEEEEEEEEEEEEAA/EEEAEE/EEAEEEEEEEEEEEEEEEE/EEEEEEEEEEAEEEEAAAAA s1:i:182 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:14 nn:i:0 tp:A:P ms:i:300
ERR5069949.1132353 83 MT192765.1 12075 60 150M = 12066 -159 AACCTTACAAGCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATC EEAEEEEEEEEEEEEEE<A<EEEEEEEEEEEAAEE<EAEEAAEAEEEEEEEEEEEAEEEEEEEAEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEEAAAAA s1:i:148 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:5 nn:i:0 tp:A:P ms:i:300
ERR5069949.1132353 163 MT192765.1 12066 60 151M = 12075 159 CAACAGGGCAACCTTACAAGCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTG AAAAAEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEEEEEEEEEEEEE<EEEEEEEEAAEEAAEEEEEEEEEEEEEAE<AAAAAAE/AEEAEEEEEEEEEEEEEAAAEAAEEA s1:i:148 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:21 nn:i:0 tp:A:P ms:i:302
ERR5069949.1151736 83 MT192765.1 12222 60 151M = 12126 -247 ATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGA AAAAAAEA//EE/EAAAEAEEEEAAEEAA</AEEEEEEAAEAAEEEEEA<EEEEEEAEEEEEAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEE<EE/EEEEEEAEE/EEEEEEEEEE/EEEEEEEEEEEAEEEE/EEAEEEEEAEEAAAAA s1:i:226 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:17 nn:i:0 tp:A:P ms:i:302
ERR5069949.1151736 163 MT192765.1 12126 60 151M = 12222 247 TTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGAT AAAAAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEAAEEEEEEEEEEEEEEEEEEE<EEEEAEEEEEEEEEEEEEEEEAEEEEEAEEAAEEE<AEAEEE<A/AAEEEEEEEAAAAA<AAAE<EEEEAEEEAEEEEEEAEEAEA/A s1:i:226 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:23 nn:i:0 tp:A:P ms:i:302
ERR5069949.1189252 99 MT192765.1 12486 60 98M = 12486 98 CTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTG AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEAEEE s1:i:88 s2:i:0 RG:Z:1 NM:i:0 AS:i:196 de:f:0 rl:i:0 cm:i:11 nn:i:0 tp:A:P ms:i:196
ERR5069949.1189252 147 MT192765.1 12486 52 98M = 12486 -98 CTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTG EEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:88 s2:i:27 RG:Z:1 NM:i:0 AS:i:196 de:f:0 rl:i:0 cm:i:2 nn:i:0 tp:A:P ms:i:196
ERR5069949.1246538 99 MT192765.1 12601 60 148M = 12627 177 AGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAGAATAATGAGCTTAGTCCTGTTGCACTACGACAGATGTCTTGTGCTGCCGGTACTACACAAACTGCTTGCA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEEEEEEEEEEEEA/EEEEEAEEEEEE/EEEEEEEEEEEEAAAAEEAEEEEEEEEEEEEEEEEE s1:i:168 s2:i:0 RG:Z:1 NM:i:0 AS:i:296 de:f:0 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:296
ERR5069949.1246538 147 MT192765.1 12627 60 151M = 12601 -177 ATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAGAATAATGAGCTTAGTCCTGTTGCACTACGACAGATGTCTTGTGCTGCCGGTACTACACAAACTGCTTGCACTGATGACAATGCGTTAGCTTACTACAAC AAAAAAEEEAAEEEEAAEAAAEEA<AAAEEAEEEAAEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEAAAAA s1:i:168 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:6 nn:i:0 tp:A:P ms:i:302
ERR5069949.1328186 83 MT192765.1 12953 60 151M = 12866 -238 AAGGATTAAACAACCTAAATAGAGGTATGGTACTTGGTAGTTTAGCTGCCACAGTACGTCTACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGATGCTGCTAAAGCTTACAAAGA EE/<E6/E<AAE<E<EEAEE<AAEE//EEEEEA<A6</EEAEEEEE<AAAEEEEEEEEAEEEEEEAEE/EEEAEEEEEEEE/EAEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:226 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:302
ERR5069949.1328186 163 MT192765.1 12866 60 151M = 12953 238 GTACTATCTATACAGAACTGGAACCACCTTGTAGGTTTGTTACAGACACACCTAAAGGTCCTAAAGTGAAGTATTTATACTTTATTAAAGGATTAAACAACCTAAATAGAGGTATGGTACTTGGTAGTTTAGCTGCCACAGTACGTCTACA AAAAAEEEEEEE/EEAEEEEAEEEEEAEEEEEEEEAEEEEEEEEEEEEEAE/EEEEEEAEE/EEEEEEEEEEEEEEEEEAAAEA/EEEEEEEAAEEEEE/EEEEAEEEEEAAEEEE/AAAE<A<EEEE6AEEAAA<<<<AA<AE/EEAEEA s1:i:226 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:302
ERR5069949.1331889 99 MT192765.1 13010 60 132M = 13010 132 GTCTACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGATGCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTG A/AAAEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEEAEEEEEEEEEEEEEEE/EEEEE<AEAEEEEE/EAEAEEE/AEEEEEEEEEEEEEEEEEEEEAE/EEEEEEEEEEEEEEEEEEEEEEEA<EE s1:i:122 s2:i:0 RG:Z:1 NM:i:0 AS:i:264 de:f:0 rl:i:0 cm:i:20 nn:i:0 tp:A:P ms:i:264
ERR5069949.1331889 147 MT192765.1 13010 48 132M = 13010 -132 GTCTACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGATGCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTG A/EEEEEAEEEEEEEEAEEEEEEEEEA<EEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEAAEEEEEE/EEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEAEEEEEEEEAAAAA s1:i:26 s2:i:122 RG:Z:1 NM:i:0 AS:i:264 de:f:0 rl:i:0 cm:i:3 nn:i:0 tp:A:P ms:i:264
ERR5069949.1340552 83 MT192765.1 13029 60 151M = 13021 -159 AACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGATGCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTGTTAAGATGTTGTGTACACACACTGGTACTGGTCAGGCA AEAAAAEE/A<EEAAEEE/EEEEEEEEEEAAEEEEEEEEAAEEEEEEEEE<EEEAEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEAAAAA s1:i:145 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:6 nn:i:0 tp:A:P ms:i:302
ERR5069949.1340552 163 MT192765.1 13021 60 148M = 13029 159 GGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGATGCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTGTTAAGATGTTGTGTACACACACTGGTA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEAEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEEEEAEAEEEEEEEEEE<EEEEEEEEEEEEEEAAA<AEEEEEEEEEEEEEE s1:i:145 s2:i:0 RG:Z:1 NM:i:0 AS:i:296 de:f:0 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:296
ERR5069949.1412839 83 MT192765.1 13187 60 147M = 13154 -180 TTACACCGGAAGCCAATATGGATCAAGAATCCTTTGGTGGTGCATCGTGTTGTCTGTACTGCCGTTGCCACATAGATCATCCAAATCCTAAAGGATTTTGTGACTTAAAAGGTAAGTATGTACAAATACCTACAACTTGTGCTAATG EEA<AAEAAAAAAE<A<<EA<EAE</E<EEEEE/EEEEAAAEEE/EEEE/EEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEA<EEEEEEEAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEAEEAAAAA s1:i:166 s2:i:0 RG:Z:1 NM:i:0 AS:i:294 de:f:0 rl:i:0 cm:i:10 nn:i:0 tp:A:P ms:i:294
ERR5069949.1412839 163 MT192765.1 13154 60 150M = 13187 180 GTACACACACTGGTACTGGTCAGGCAATAACAGTTACACCGGAAGCCAATATGGATCAAGAATCCTTTGGTGGTGCATCGTGTTGTCTGTACTGCCGTTGCCACATAGATCATCCAAATCCTAAAGGATTTTGTGACTTAAAAGGTAAGT AAAA6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEAEEEAAAAEEEEEEEEEEAAEEAEAE<EEEAEAEEE/<AAAEAEAA/EAEEEEAEEAAE/AEA/EEEAEEAEAA s1:i:166 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:300
ERR5069949.1476386 99 MT192765.1 13329 60 151M = 13382 201 TAATGACCCTGTGGGTTTTACACTTAAAAACACAGTCTGTACCGTCTGCGGTATGTGGAAAGGTTATGGCTGTAGTTGTGATCAACTCCGCGAACCCATGCTTCAGTCAGCTGATGCACAATCGTTTTTAAACGGGTTTGCGGTGTAAGTG AAAAA/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEAEAEEEEEEEEEEEEEEEEEEEEEEAEEEEEAEEEAEEEEEEE/AEEE/EEEEEE/AEE/EEAE/EEE<EA/<EEA/EEEEE/EEEEAAEEEAAAAEEAEEE s1:i:188 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:20 nn:i:0 tp:A:P ms:i:302
ERR5069949.1476386 147 MT192765.1 13382 60 148M = 13329 -201 TGTGGAAAGGTTATGGCTGTAGTTGTGATCAACTCCGCGAACCCATGCTTCAGTCAGCTGATGCACAATCGTTTTTAAACGGGTTTGCGGTGTAAGTGCAGCCCGTCTTACACCGTGCGGCACAGGCACTAGTACTGATGTCGTATAC AAEEEA<AEA/AAAEEE/E/AEE/E6AE/EAE/EEE<EEEAEEEEEEEEAAEE<<EEEEEEEEEEEEEEEEEEEEEA/EEEEEAA//EAEEAEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE6EEAA6AA s1:i:188 s2:i:0 RG:Z:1 NM:i:0 AS:i:296 de:f:0 rl:i:0 cm:i:10 nn:i:0 tp:A:P ms:i:296
ERR5069949.1538968 83 MT192765.1 13817 48 150M = 13799 -168 CTATGCTTTAAGGCATTTTGATGAAGGTAATTGTGACACATTAAAAGAAATACTTGTCACATACAATTGTTGTGATGATGATTATTTCAATAAAAAGGACTGGTATGATTTTGTAGAAAACCCAGATATATTACGCGTATACGCCAACTT AEE6AA<E/EA/<AE<AEA<6AA6AAEEEAAA6/6</AEEEE<EEEEEEE/EEEE//EEEAEEE/EEEA/EEEAEE/EEEE/EAEEEEEE<AEEEEAEEEEAEAEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEAEEAEEEEEEEAAAAA s1:i:41 s2:i:154 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:9 nn:i:0 tp:A:P ms:i:300
ERR5069949.1538968 163 MT192765.1 13799 60 151M = 13817 168 CACGATGGCAGACCTCGTCTATGCTTTAAGGCATTTTGATGAAGGTAATTGTGACACATTAAAAGAAATACTTGTCACATACAATTGTTGTGATGATGATTATTTCAATAAAAAGGACTGGTATGATTTTGTAGAAAACCCAGATATATTA AAAAAEEEAEEAEEEAEEEAEEEAE<EEE6EAEA<EAAAEEEEEEEEEEEEEA/</EEEEEEEEEEEEEEEEEEEEEEAEEEEE/AEEEEEEEEAEEEEEEEEEEEEEEEEAEEEAA<AEAEE<AAE<A<AEEEEE/EA6AAA/EE/EEEA s1:i:154 s2:i:0 RG:Z:1 NM:i:1 AS:i:294 de:f:0.0066 rl:i:0 cm:i:18 nn:i:0 tp:A:P ms:i:294
ERR5069949.1704586 99 MT192765.1 14601 60 149M = 14761 310 GATAAACGCACTACGTGCTTTTCAGTAGCTGCACTTACTAACAATGTTGCTTTTCAAACTGTCAAACCCGGTAATTTTAACAAAGACTTCTATGACTTTGCTGTGTCTAAGGGTTTCTTTAAGGAAGGAAGTTCTGTTGAATTAAAACA AAAA6EEEE/EE6EEEEEEEEEEEEEEEEEE<EEEEEEEE6EEAEEEEEA<EEEEE66EEEEE///EEEAEEEE<EEEEEEA/EE/EEEEEEEAE<E<AA<AAAEEAE/AEE<E<AA<EAAEEAE/AEE/E/EAEAAAEE/EA/A//EE s1:i:277 s2:i:0 RG:Z:1 NM:i:0 AS:i:298 de:f:0 rl:i:0 cm:i:21 nn:i:0 tp:A:P ms:i:298
ERR5069949.1704586 147 MT192765.1 14761 60 150M = 14601 -310 CTCAGGATGGTAATGCTGCTATCAGCGATTATGACTACTATCGTTATAATCTACCAACAATGTGTGATATCAGACAACTACTATTTGTAGTTGAAGTTGTTGATAAGTACTTTGATTGTTACGATGGTGGCTGTATTAATGCTAACCAAG A//EEAE<AAA<AEAA6EEE</<AAA6EE//A<A<<AE<E//AEEEEE<EEEEAEAA<AEA<AE/EEEEAEEAEEEAEAEEAEEE/EEEEEEAE<EEEEEEEEEEEEEE/EEEEEEAEEEEEEEEEEE/EEEEEE/EEEEE<EEEA/AAA s1:i:277 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:300
ERR5069949.1709367 83 MT192765.1 14886 50 129M = 14886 -129 GGTGGCTGTATTAATGCTAACCAAGTCATCGTCAACAACCTAGACAAATCAGCTGGTTTTCCATTTAATAAATGGGGTAAGGCTAGACTTTATTATGATTCAATGAGTTATGAGGATCAAGATACACTT AA/EEAAAEEEEAEE6A/EAAEAAEAAAAAAAAEEAEEE/AEAE<AEEAEAE/EEEEEEEEA/EEAA<AEE/EEE<AEA<EAAEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEAEEEAEEEAAAAA s1:i:117 s2:i:42 RG:Z:1 NM:i:1 AS:i:248 de:f:0.0078 rl:i:0 cm:i:1 nn:i:0 tp:A:P ms:i:248
ERR5069949.1709367 163 MT192765.1 14886 60 129M = 14886 129 GGTGGCTGTATTAATGCTAACCAAGTCATCGTCAACAACCTAGACAAATCAGCTGGTTTTCCATTTAATAAATGGGGTAAGGCTAGACTTTATTATGATTCAATGAGTTATGAGGATCAAGATACACTT AAAAAEEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEAEEEEEEAEEEEEEEEEEEEEEAEEEEEEEEEEEEEEE s1:i:117 s2:i:0 RG:Z:1 NM:i:1 AS:i:248 de:f:0.0078 rl:i:0 cm:i:15 nn:i:0 tp:A:P ms:i:248
ERR5069949.1778133 83 MT192765.1 15491 48 146M1D5M = 15485 -158 AACTGCTTATGCTAATAGTGTTTTTAACATTTGTCAAGCTGTCACGGCCAATGTTAATGCACTTTTATCTACTGATGGTAACAAAATTGCCGATAAGTATGTCCGCAATTTACAACACAGACTTTATGAGTGTCTCTATAGAAATAAGATG AEEAEEEEEAAAAAA<AEEEEEEEEEEEEEEEEEEAEEEEEEEAEAEEEEEEEEEEEEEEAEEEEAEAEAEEEEEEEEEEEE<AEEEEAAAEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:55 s2:i:139 RG:Z:1 NM:i:1 AS:i:292 de:f:0.0066 rl:i:0 cm:i:10 nn:i:0 tp:A:P ms:i:292
ERR5069949.1778133 163 MT192765.1 15485 60 150M = 15491 158 TGCCACAACTGCTTATGCTAATAGTGTTTTTAACATTTGTCAAGCTGTCACGGCCAATGTTAATGCACTTTTATCTACTGATGGTAACAAAATTGCCGATAAGTATGTCCGCAATTTACAACACAGACTTTATGAGTGTCTCTATAGAAA AAAAAEEEEEEEEEEEEEEAEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEAAEEEEEE<AEEEEEEE/AAAE<AAEEAAEEEA<EAAEEEA<AAEEEEEE/EEAAAEE/EAAAAEEEEEAEAEE s1:i:139 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:300
ERR5069949.1980512 83 MT192765.1 16852 60 151M = 16801 -202 CTGTTGTTTACCGAGGTACAACAACTTACAAATTAAATGTTGGTGATTATTTTGTGCTGACATCACATACAGTAATGCCATTAAGTGCACCTACACTAGTGCCACAAGAGCACTATGTTAGAATTACTGGCTTATACCCAACACTCAATAT EEEEEEEEEEAEEEEEEAAEEEEEAAEAEAAAEAEEEAEAEEEAEEEAEEEEEAEAAEEEEAEAEEEEEEEAEEEEEEEEEEEAEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:193 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:12 nn:i:0 tp:A:P ms:i:302
ERR5069949.1980512 163 MT192765.1 16801 60 150M = 16852 202 GTAAAGTACAAATAGGAGAGTACACCTTTGAAAAAGGTGACTATGGTGATGCTGTTGTTTACCGAGGTACAACAACTTACAAATTAAATGTTGGTGATTATTTTGTGCTGACATCACATACAGTAATGCCATTAAGTGCACCTACACTAG AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEAEEEEEEEEEA<EEEEEEAEEEEAAAEEAAE<EEEAAAA<AA<EEEE/AE s1:i:193 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:18 nn:i:0 tp:A:P ms:i:300
ERR5069949.2033605 83 MT192765.1 17101 48 150M = 17083 -168 TTGCTATTGGCCTAGCTCTCTACTACCCTTCTGCTCGCATAGTGTATACAGCTTGCTCTCATGCCGCTGTTGATGCACTATGTGAGAAGGCATTAAAATATTTGCCTATAGATAAATGTAGTAGAATTATACCTGCACGTGCTCGTGTAG AAA<EAA<EEEAAAA/E</EA/E6EAEE/EE/AEA<AAEEAEEA/EE<EEEEEEEEEEEE<AEE/AEEE/EAAEEEAEEAEEEEE<EEE<EEEEEAAEEEEEEEEAEEEEEAEEAEEEEEEEEEAEEEEEEEEEEEEEEEEE/EEAAAAA s1:i:34 s2:i:160 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:6 nn:i:0 tp:A:P ms:i:300
ERR5069949.2033605 163 MT192765.1 17083 60 149M = 17101 168 GTACTGGTAAGAGTCATTTTGCTATTGGCCTAGCTCTCTACTACCCTTCTGCTCGCATAGTGTATACAGCTTGCTCTCATGCCGCTGTTGATGCACTATGTGAGAAGGCATTAAAATATTTGCCTATAGATAAATGTAGTAGAATTATA AAAAAEAEEEEEEEEEEEEAEEEEEEEEEEEEE<EEEEEEEEEEE<EEEEEEEEAAEAEEEEEEEEEEEE/EAAEEEA/EEEEEEAE<EEEEEEEEE<AEEEEAAAEAE<EAEEEEEE//</A/AEAAAEA/<E<AEEEAEE<EEEEEE s1:i:160 s2:i:0 RG:Z:1 NM:i:0 AS:i:298 de:f:0 rl:i:0 cm:i:24 nn:i:0 tp:A:P ms:i:298
ERR5069949.2161340 99 MT192765.1 17482 60 80M = 17482 82 AACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGT A/AA//EEAEA/E/AEEEE6EE/EEEA/6AEEEEEEEEE6EEEAEAEE//A/EEEEEE//E/E/A//E/E/<<EE</E/E s1:i:69 s2:i:0 RG:Z:1 NM:i:0 AS:i:160 de:f:0 rl:i:0 cm:i:6 nn:i:0 tp:A:P ms:i:160
ERR5069949.2161340 147 MT192765.1 17482 55 82M = 17482 -82 AACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCC A//E/<EAEA/EE/EEEA/<AE<AE/AEA/EEEAE/EEE//EEE6////EEEEAEAE///EE//</E/E</AE/6EAAA6AA s1:i:69 s2:i:0 RG:Z:1 NM:i:0 AS:i:164 de:f:0 rl:i:0 cm:i:3 nn:i:0 tp:A:P ms:i:164
ERR5069949.2243023 83 MT192765.1 17854 60 150M = 17713 -291 ACTATGTCATATTCACTCAAACCACTGAAACAGCTCACTCTTGTAATGTAAACAGATTTAATGTTGCTATTACCAGAGCAAAAGTAGGCATACTTTGCATAATGTCTGATAGAGACCTTTATGACAAGTTGCAATTTACAAGTCTTGAAA EE<EAEEAE<EA<E/EEAEAEEEE<EEEEAA<AEEEEEEEEEAAEAEEE<EEEEAEEEEEEEEEEEEEEEEEAEEEEEEAEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:273 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:20 nn:i:0 tp:A:P ms:i:300
ERR5069949.2243023 163 MT192765.1 17713 60 151M = 17854 291 TGGTAAGAGAATTCCTTACACGTAACCCTGCTTGGAGAAAAGCTGTCTTTATTTCACCTTATAATTCACAGAATGCTGTAGCCTCAAAGATTTTGGGACTACCAACTCAAACTGTTGATTCATCACAGGGCTCAGAATATGACTATGTCAT AAAAAEEEEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEAEEEEEEEEEEEEEE/EEEEAAEEAEEA<EEEEEEEEEEEEEEAEEEEE<<AA6AAEEEAEE s1:i:273 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:20 nn:i:0 tp:A:P ms:i:302
ERR5069949.2257580 99 MT192765.1 17980 60 151M = 18039 209 AGTTGCAATTTACAAGTCTTGAAATTCCACGTAGGAATGTGGCAACTTTACAAGCTGAAAATGTAACAGGACTCTTTAAAGATTGTAGTAAGGTAATCACTGGGTTACATCCTACACAGGCACCTACACACCTCAGTGTTGACACTAAATT AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEAEEEEEEEEEAEEEEEEAEEEEEEEEEEEEAEEEEEEEEEAEEEEEEAEE/EEAEA<EAEEEAEEEEEEEEE<EEAAAEAEEE<EA s1:i:196 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:18 nn:i:0 tp:A:P ms:i:302
ERR5069949.2257580 147 MT192765.1 18039 60 150M = 17980 -209 AATGTAACAGGACTCTTTAAAGATTGTAGTAAGGTAATCACTGGGTTACATCCTACACAGGCACCTACACACCTCAGTGTTGACACTAAATTCAAAACTGAAGGTTTATGTGTTGACATACCTGGCATACCTAAGGACATGACCTATAGA EEEEEEAEEAAEEEEAAAAEEEEEEAEEEEAEAEEEAEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:196 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:11 nn:i:0 tp:A:P ms:i:300
ERR5069949.2521353 99 MT192765.1 19597 60 150M = 19698 251 CTTTTACAAGACTTCAGAGTTTAGAAATTGTGGCTTATAATGTTGTAATTAAGGGACACTTTGATGGACAACAGGGTGAAGTACCAGTTTCTATCATTAATAACTCTGTTTACACAAAAGTTGATGGTGTTGATGTAGAATTGTTTGAAA AAA/AE/6E6EEEEAEE/EE/EEE/EE/EA/EAEA//EEEEE6EAEAE/EEEEEE/EAE////EEA/EEEEEEEEEEEEEE///A/EEAEEEEEEEE<AEAEEE/AE/E<E/EEEEEA/E///AE/66AEEAEEE<E//E/EA/A<6AEE s1:i:175 s2:i:0 RG:Z:1 NM:i:4 AS:i:260 de:f:0.0267 rl:i:0 cm:i:10 nn:i:0 tp:A:P ms:i:260
ERR5069949.2521353 147 MT192765.1 19698 60 150M = 19597 -251 ATCACTGTTTTCACAAAAGTTGATGGTGTTGATGTAGAATTGTTTGAAAATAAAACAACATTACCTGTTAATGTAGCTTTTGTGCTTTGGGCTAAGCGCAACATTAAACCAGTACCAGAGGTGAAAATACTCAATAATTTGGGTGTGGAC A//A</</EE/A<AEEA//E<EEE/E<A/<<A///<6EAEEEEE/AAA</A//<<EA/EEA//</AA6EEAE</EEA//AEE//</AEEAE/EEEA/A/EEEE//E/EAA/EEE/AEE<EEE<EE/EAEEEEE6EEEE/EEEEEEAAAAA s1:i:175 s2:i:0 RG:Z:1 NM:i:4 AS:i:266 de:f:0.0267 rl:i:0 cm:i:14 nn:i:0 tp:A:P ms:i:266
ERR5069949.2605155 99 MT192765.1 21717 60 146M = 21726 159 GTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAG AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEE/EEEEEEEEEEEEEE<EEAEEEAEAEAEEEEEEEEAAEEEEE<EEAEAEEEAA<E<EAAE</E/AA s1:i:148 s2:i:0 RG:Z:1 NM:i:0 AS:i:292 de:f:0 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:292
ERR5069949.2605155 147 MT192765.1 21726 60 150M = 21717 -159 TTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGG A/EEEE/EEAEAEEEEEAEEAEEEAAAEEEAEEEEEEAEE/EEEAEAEAEEEEEEAEEAEEEEEAEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:148 s2:i:30 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:6 nn:i:0 tp:A:P ms:i:300
ERR5069949.2650879 83 MT192765.1 22710 60 150M = 22659 -201 TAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGC EAEEEAEE<EEE/EEEEEEAEEEEEEEEEEEA<AAEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEAEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:192 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:13 nn:i:0 tp:A:P ms:i:300
ERR5069949.2650879 163 MT192765.1 22659 60 151M = 22710 201 ATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATT AAAAAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEAEE<EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEAEEEEEEEEEEEEAEEE<A<EEEEAAAAEEEEEEEEEEEE s1:i:192 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:16 nn:i:0 tp:A:P ms:i:302
ERR5069949.2730382 83 MT192765.1 23528 48 142M = 23528 -142 ACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGT A<AA<A<EEEAAA/A<AEAEAEA<EAA<<AEA<EEEAAAEE<EEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEE<EEEEEAEEAEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEAEEEEEEE/EAAAAA s1:i:48 s2:i:143 RG:Z:1 NM:i:0 AS:i:284 de:f:0 rl:i:0 cm:i:9 nn:i:0 tp:A:P ms:i:284
ERR5069949.2730382 163 MT192765.1 23528 60 142M = 23528 142 ACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGT AAAAAEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAE<EE/EEEEEEE/EEAEEEEEEEEEEEEEEEEEEAEEEEA<AEA<<EA<A<AEEEEEA<EAE<66A/AEEEEEEEAE<AAEA s1:i:143 s2:i:0 RG:Z:1 NM:i:0 AS:i:284 de:f:0 rl:i:0 cm:i:20 nn:i:0 tp:A:P ms:i:284
ERR5069949.2734474 81 MT192765.1 23547 1 149M = 23548 -148 ACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCA AA/EEA/EAAAA<AAEEEEAAEEEEEEE<A/EEAEE<AEEEEEEEEAEEEEAEAAEAAEE/EEAAEEE/AEA/EEE/E/EEEEEEEEE/EEEEEEEEAEE/EEEE/EEEEEAEEEEEEEEEEEEEEEEE//EEEEAEEEEEEEAAA/AA s1:i:58 s2:i:136 RG:Z:1 NM:i:0 AS:i:298 de:f:0 rl:i:0 cm:i:11 nn:i:0 tp:A:P ms:i:298
ERR5069949.2734474 161 MT192765.1 23548 60 148M = 23547 148 CCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCA AAAA/EEEEEEEEE/E/EE6EEEEAEEEEEEAEEEEE/EEEEEEEEEEEAE/EAEE/EEEEEAE/EE<EAEEEEEEA/E<EEEEAE/EA<EEEEAEE/E/EE<EEEEE</EE/E//<<<AA6A<A<A/<AE/AE/EEEA6<A6A/</A s1:i:136 s2:i:0 RG:Z:1 NM:i:0 AS:i:296 de:f:0 rl:i:0 cm:i:20 nn:i:0 tp:A:P ms:i:296
ERR5069949.2734873 83 MT192765.1 23550 48 98M = 23550 -98 CATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGT EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEE/EEEEEEEEEEEEEEEEEEEEAAAAA s1:i:25 s2:i:92 RG:Z:1 NM:i:0 AS:i:196 de:f:0 rl:i:0 cm:i:4 nn:i:0 tp:A:P ms:i:196
ERR5069949.2734873 163 MT192765.1 23550 60 98M = 23550 98 CATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGT AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE s1:i:92 s2:i:0 RG:Z:1 NM:i:0 AS:i:196 de:f:0 rl:i:0 cm:i:9 nn:i:0 tp:A:P ms:i:196
ERR5069949.2772897 83 MT192765.1 23876 60 144M1D7M = 23809 -219 AAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTCAAC AEEEEEE<AAEEAAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEAEEEEEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEEEEEAAAAA s1:i:199 s2:i:0 RG:Z:1 NM:i:1 AS:i:294 de:f:0.0066 rl:i:0 cm:i:13 nn:i:0 tp:A:P ms:i:288
ERR5069949.2772897 163 MT192765.1 23809 60 150M = 23876 219 CTTTCGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAAT AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEA<EAEEEE<EEEEAEEAAEEEEEEEEEEE s1:i:199 s2:i:0 RG:Z:1 NM:i:1 AS:i:290 de:f:0.0067 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:290
ERR5069949.2787556 99 MT192765.1 24088 60 106M = 24088 106 GCTGCTAGAGACCTCGTTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGG AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAE s1:i:78 s2:i:0 RG:Z:1 NM:i:1 AS:i:202 de:f:0.0094 rl:i:0 cm:i:10 nn:i:0 tp:A:P ms:i:202
ERR5069949.2787556 147 MT192765.1 24088 50 106M = 24088 -106 GCTGCTAGAGACCTCGTTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGG EEAAEEEEEEEEA<EEEE<AAA<EEEEEAEEEEEEAEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:78 s2:i:0 RG:Z:1 NM:i:1 AS:i:202 de:f:0.0094 rl:i:0 cm:i:1 nn:i:0 tp:A:P ms:i:202
ERR5069949.2832676 99 MT192765.1 24409 60 139M = 24409 139 GTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCA AAAA6EEEEEEEEEEEEEEEEAEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<E/EAEEAEEEAEEAEEEEEAEEEEEEEEEEEEEEAEEAEEEEEAAEEEEEEA<AEEEAAAAEEEEE<EEAAAEEAEEAAEEEEA s1:i:132 s2:i:0 RG:Z:1 NM:i:0 AS:i:278 de:f:0 rl:i:0 cm:i:18 nn:i:0 tp:A:P ms:i:278
ERR5069949.2832676 147 MT192765.1 24409 48 139M = 24409 -139 GTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCA A<EEEE</EAEA6EEA</AEEEEAEEEAAE/EEAEE<A<AAAEEEEAAEEE/EEEEEEEEAEEAEEAA<EEEEEEEA<EEEAEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEAA6AA s1:i:37 s2:i:132 RG:Z:1 NM:i:0 AS:i:278 de:f:0 rl:i:0 cm:i:5 nn:i:0 tp:A:P ms:i:278
ERR5069949.2888794 83 MT192765.1 24853 60 151M = 24758 -246 ACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGG AAEAAAEEEEEEEEEEEEEEEAAAEEEEAAEEAAAAEEEEAEEEEEEEEE/EEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:231 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:16 nn:i:0 tp:A:P ms:i:302
ERR5069949.2888794 163 MT192765.1 24758 60 150M = 24853 246 TCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAG AAAAAEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEAEE<<<6AEE</AAAEEEEEEEAA<EEAAEA s1:i:231 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:25 nn:i:0 tp:A:P ms:i:300
ERR5069949.3017828 99 MT192765.1 26176 60 107M = 26177 107 ATGATGAACCGACGACGACTACTAGCGTGCCTTTGTAAGCACAAGCTGATGAGTACGAACTTATGTACTCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAAT AAAAAE6EEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEAEEEEE s1:i:96 s2:i:0 RG:Z:1 NM:i:0 AS:i:214 de:f:0 rl:i:0 cm:i:11 nn:i:0 tp:A:P ms:i:214
ERR5069949.3017828 147 MT192765.1 26177 48 106M = 26176 -107 TGATGAACCGACGACGACTACTAGCGTGCCTTTGTAAGCACAAGCTGATGAGTACGAACTTATGTACTCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAAT A/EAAEEEAEEAE<E</EEEEEEEEEAE<EEEEEEAE<EE/E<EEEEEEEEEEEE<EEAEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEAAAAA s1:i:37 s2:i:96 RG:Z:1 NM:i:0 AS:i:212 de:f:0 rl:i:0 cm:i:3 nn:i:0 tp:A:P ms:i:212
ERR5069949.3022231 99 MT192765.1 26228 60 147M = 26228 147 GTACGAACTTATGTACTCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTATTCTTGCTAGTTACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATAT AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEEEEEEAAAAEEEEEEEEAEEE s1:i:139 s2:i:0 RG:Z:1 NM:i:0 AS:i:294 de:f:0 rl:i:0 cm:i:21 nn:i:0 tp:A:P ms:i:294
ERR5069949.3022231 147 MT192765.1 26228 48 147M = 26228 -147 GTACGAACTTATGTACTCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTATTCTTGCTAGTTACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATAT EAAAEEEEEEAEEEEE<EEEEAE<EEAAEAAEEEEEEEEEEEEEEEEAEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:34 s2:i:139 RG:Z:1 NM:i:0 AS:i:294 de:f:0 rl:i:0 cm:i:6 nn:i:0 tp:A:P ms:i:294
ERR5069949.3057020 99 MT192765.1 26621 60 86M9S = 26621 86 CAATTTGCCTATGCCAACAGGAATAGGTTTTTGTATATAATTAAGTTAATTTTCCTCTGGCTGTTATGGCCAGTAACTTTAGCTTGGTTGTACGC AAAAAEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAE s1:i:71 s2:i:0 RG:Z:1 NM:i:0 AS:i:172 de:f:0 rl:i:0 cm:i:8 nn:i:0 tp:A:P ms:i:172
ERR5069949.3057020 147 MT192765.1 26621 51 86M9S = 26621 -86 CAATTTGCCTATGCCAACAGGAATAGGTTTTTGTATATAATTAAGTTAATTTTCCTCTGGCTGTTATGGCCAGTAACTTTAGCTTGGTTGTACGC EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:71 s2:i:33 RG:Z:1 NM:i:0 AS:i:172 de:f:0 rl:i:0 cm:i:2 nn:i:0 tp:A:P ms:i:172
ERR5069949.3122970 83 MT192765.1 26996 48 127M = 26996 -127 ATCAAGGACCTGCCTAAAGAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACAAATTGGGAGCTTCGCAGCGTGTAGCAGGTGACTCAGGTTTTGCTGCATACAGTCGCTACAGGATTGGCA A//6AAAEAEEA/AAEEEEEEAAE/EEE//A<EEEEEEEEEAEEE/EEAAEEAEEEE/<EEAEEEEEAEEAEEAEEEEEEEEA<EAEEAEAEAEEA6EEEEEEEEEEEEEAEEEAEEEEEEEA/AAA s1:i:52 s2:i:119 RG:Z:1 NM:i:0 AS:i:254 de:f:0 rl:i:0 cm:i:9 nn:i:0 tp:A:P ms:i:254
ERR5069949.3122970 163 MT192765.1 26996 60 126M = 26996 127 ATCAAGGACCTGCCTAAAGAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACAAATTGGGAGCTTCGCAGCGTGTAGCAGGTGACTCAGGTTTTGCTGCATACAGTCGCTACAGGATTGGC AAAAAEE6EEEEEEEAEEEEEEEEEEEAEEEEEEEEEEEEEE/EEEEEAE<EEAEAEEEEEEEEEAAEEEEAEAEEE/AEEE<A<A/AAAAAE/E<A66AEEEEEEEEEEEAE<</6AA<A/6/EA s1:i:119 s2:i:0 RG:Z:1 NM:i:0 AS:i:252 de:f:0 rl:i:0 cm:i:17 nn:i:0 tp:A:P ms:i:252
ERR5069949.3184655 83 MT192765.1 27352 60 150M = 27311 -191 ATGAAGAGCAACCAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGAGCTTTATCACTACCAAGAGTGTGTTAGAGGTACAACAGTACTTTTAAAAGAACCTTGCTCTTCTGGAA AAAE6E</EA6<A6/A/E6A</EEE<EEA///E/A<<</AEEEE<E<EEEEEEEEEE/E<E/EE/A<AEEAEAE/EEEEEEEAEEEEEEEEEEEEE/AEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEAAAAA s1:i:185 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:8 nn:i:0 tp:A:P ms:i:300
ERR5069949.3184655 163 MT192765.1 27311 60 150M = 27352 191 TTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGAGCTTTATCACTACCAAGAGTGTGTTAG AAAAAEEEEEEEEEEEEEEEEAEEAEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEE<EEEEE/EEEEEAEAEEEEE/EEEAEEE<EEEEEE<EEAAEEAEEEEEAAAEEE/E<AAEEAAAE6A/A<<A<AAAEE/AA6AE/A s1:i:185 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:21 nn:i:0 tp:A:P ms:i:300
ERR5069949.3249622 83 MT192765.1 28372 37 77M = 28218 -231 CGATAAAAACAAGGTCGGCCCCAAGGTTTACCCATTAATACTGCGTCTTGGTTCACCGCTCTCACTCAACATGGCAA E/E///<E<<////AE/EEA/EEEEEE/EEEEE//A//E/EEEEEEEE/EEE/EE/EAEEAEEEAEE/AE/EAAAAA s1:i:97 s2:i:0 RG:Z:1 NM:i:3 AS:i:124 de:f:0.039 rl:i:0 cm:i:3 nn:i:0 tp:A:P ms:i:124
ERR5069949.3249622 163 MT192765.1 28218 38 116M = 28372 231 ATCATGACGTTCGTGTTGTTTTAGATTTCATCGAAACGAACAAACAAAAATGTCTGATAATGGACCCCAAAATCATCGAAATGCACCCCGCATTACGGTTGGTGGACCCTCCGATT AAA/AE//EEE/EE6AE/A</EE//6AE6EE//EE/AE//A/EE//EEEE<EAA/EE//<E/A/E/EE//E/A/E/E//EE/<A/A<EE/A//</EE//E/E//A/EEE///A//6 s1:i:97 s2:i:0 RG:Z:1 NM:i:5 AS:i:182 de:f:0.0431 rl:i:0 cm:i:3 nn:i:0 tp:A:P ms:i:182
ERR5069949.3338256 83 MT192765.1 29452 60 151M = 29431 -172 CCTGCTGCAGATTTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTCAACTCAGGCCTAAACTCATGCAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGCTTTTCCGTTTACGATATATAGTCTACTCT AEEEEEEEEEEEA<AEEAEEEEEEAA<EEEEEEAEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEAAE<EEEEEAEEEEEEEEEEAEEA/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:163 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:5 nn:i:0 tp:A:P ms:i:302
ERR5069949.3338256 163 MT192765.1 29431 60 150M = 29452 172 CAGCAAACTGTGACTCTTCTTCCTGCTGCAGATTTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTCAACTCAGGCCTAAACTCATGCAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGCTTTTCCG AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEAEEEEEEEEAAAAAEA<AAAEA<AA s1:i:163 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:25 nn:i:0 tp:A:P ms:i:300

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src/umi_tools/umi_tools_prepareforrsem/test_data/test_dedup.bam Normal file
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@HD VN:1.6 SO:coordinate
@SQ SN:MT192765.1 LN:29829
@RG ID:1 LB:lib1 PL:ILLUMINA SM:test PU:barcode1
@PG ID:minimap2 PN:minimap2 VN:2.17-r941 CL:minimap2 -ax sr tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna tests/data/fastq/dna/sarscov2_1.fastq.gz tests/data/fastq/dna/sarscov2_2.fastq.gz
@PG ID:samtools PN:samtools PP:minimap2 VN:1.11 CL:samtools view -Sb sarscov2_aln.sam
@PG ID:samtools.1 PN:samtools PP:samtools VN:1.11 CL:samtools sort -o sarscov2_paired_aln.sorted.bam sarscov2_paired_aln.bam
@PG ID:samtools.2 PN:samtools PP:samtools.1 VN:1.20 CL:samtools view -h test_data/test_dedup.bam
ERR5069949.29668 163 MT192765.1 121 60 150M = 267 235 TATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCTTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTT AAA/E/EEEEEEEEEAEEEEEEEEE/</E/E/EE<E/EEAAEA/E/EE//EA/EEEEEA/AEEE/EEEEE/E/EA/EE/EEE<E/E///E<AEE<<EEE/<EEEAA///AE/6A///A/AE/EAEE</EAEAE///AA/EEAEE/AAEAA s1:i:173 s2:i:0 RG:Z:1 NM:i:1 AS:i:290 de:f:0.0067 rl:i:0 cm:i:13 nn:i:0 tp:A:P ms:i:290
ERR5069949.29668 83 MT192765.1 267 60 89M = 121 -235 CCTTGTCCCTGGTTACAACTAGAAACCACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAG E////6/E/EE/EE/<<///6EEE/////<AAA<A<A6AE/E/AE6A/EAEEEAEEEAEEEEEA/AEAE<EEEAEEE////6EEAA/AA s1:i:173 s2:i:0 RG:Z:1 NM:i:3 AS:i:148 de:f:0.0337 rl:i:0 cm:i:6 nn:i:0 tp:A:P ms:i:148
ERR5069949.114870 99 MT192765.1 643 60 150M = 748 255 AAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTAGGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTGTTACCCGTGAACTCATGCGTGAGCTTAAC AAAAA/EAEEEEEEAEEEEEEEEE/EEEAEEEEEEEEEEEEEEEEAEAEAEEAEEEEEEEEEEEEEEEEAEAA<EE</AAEEEEEEEAEEEAEEEEEEEEEEEEEEEEEEEEEAEEA<AEEEEEEA<<AAE<EEEEEAE<AAEAAAEAEE s1:i:240 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:21 nn:i:0 tp:A:P ms:i:300
ERR5069949.147998 163 MT192765.1 674 60 151M = 919 339 ATCTAAAGTCATTTGACTTAGGCCACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTGTTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAA AAAAAAE6EEE/EEE/E/EEA6E/EEE/AE/E//EEEEAA/E/E/EAEEEE/EEEEEEE<EE/E/A/A</<E</<AE<///A<AA<//E/AE/E/EEE/EEEEA//E/A</<AE/////E<AAE<EE//EA/<6/A</A//<AAAA<EE/A s1:i:215 s2:i:0 RG:Z:1 NM:i:1 AS:i:292 de:f:0.0066 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:292
ERR5069949.114870 147 MT192765.1 748 60 150M = 643 -255 AAACATAGCAGTGGTGTTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGGCCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGC AEEAA<<<AAAE/E/AA<<<<<<<</AE<AE<A/E<AAEE<EEA<AEEE/E<A<EEEEA/A/EEAEEAEAEEEE/EAEEEEEEEE<EEAEEEEEEEAEAAEAAEEEEEEAAEEEAEEEEEEEEEEEEEEEE/EEAEAEEEEEEEAAAAAA s1:i:240 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:17 nn:i:0 tp:A:P ms:i:300
ERR5069949.147998 83 MT192765.1 919 60 94M = 674 -339 TTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTGCTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGC EE<EEE//A/EEE/A</E<AEAE<EEEA<6EE/EEE/A/EAEAE<//EEEE/EEE6EEE/E/EE/EEE/EEAAEEEEEEEEEEEEEEAEAAAAA s1:i:215 s2:i:0 RG:Z:1 NM:i:0 AS:i:188 de:f:0 rl:i:0 cm:i:11 nn:i:0 tp:A:P ms:i:188
ERR5069949.155944 163 MT192765.1 978 60 150M = 1023 195 GTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAAATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAACCAAGGGTTGAAAA AAAA/EEEEEEAEEEEEEEEEEEE/EEEEEEEEEE/EAEEEEEEEEEEEEEEEAEEEAEE/AEEEEEEAAEEEEEEAEAEEEE/AEE/<EAE/E<EEA<<<AAEEAEEE<AA<EE/EAAEEEE<<<EEEA/AEAEE6</EEA<AEEE<<E s1:i:183 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:17 nn:i:0 tp:A:P ms:i:300
ERR5069949.155944 83 MT192765.1 1023 60 150M = 978 -195 TGAAATTAAATTGGCAAAGAAATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCACTTAAATTCCATAATCAAGACTATTCAACCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCC EA<EA/<A/6A/AEA/6/66/AAAEAEEE/EEA/6AAAAAAEE</AAEEEEAAEEEAA/EEE//A/EEEEE/AE/EEE6AEEEE/A/EAEEEEE/EEAEEEAE/AEA66AEEEEEEEEE<AEEEAEEEEEEEEE6EEEEEEEAEEAAAAA s1:i:183 s2:i:0 RG:Z:1 NM:i:1 AS:i:290 de:f:0.0067 rl:i:0 cm:i:10 nn:i:0 tp:A:P ms:i:290
ERR5069949.184542 99 MT192765.1 1055 60 151M = 1255 266 TCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAACAAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCTCCAAATGAATGCAACCAAATGTG AAAAAEEEEE/EA/E/EEE/EEAEE/E/EE/EEEE//AEE/E/EEE//EEE/</E/EE<<//EE/EE<EEEEEAE/E/EAAEEEAEAEE<E</EEEE/E//E<<<///E<//A<AE</<AEEEAAE///EE</EE//AA///<E</A<AEA s1:i:155 s2:i:0 RG:Z:1 NM:i:2 AS:i:282 de:f:0.0132 rl:i:0 cm:i:12 nn:i:0 tp:A:P ms:i:282
ERR5069949.169513 99 MT192765.1 1098 60 92M = 1098 92 AATCAAGACTATTCAACCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCACCAAATG AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EE6EEEE s1:i:92 s2:i:0 RG:Z:1 NM:i:0 AS:i:184 de:f:0 rl:i:0 cm:i:11 nn:i:0 tp:A:P ms:i:184
ERR5069949.169513 147 MT192765.1 1098 48 92M = 1098 -92 AATCAAGACTATTCAACCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCACCAAATG EEEEEEEEEEEEEEEEEEEEEEE/EEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:32 s2:i:92 RG:Z:1 NM:i:0 AS:i:184 de:f:0 rl:i:0 cm:i:3 nn:i:0 tp:A:P ms:i:184
ERR5069949.184542 147 MT192765.1 1255 60 66M = 1055 -266 ACGTGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGAAGGTGCC E////E/A6EAEEE<AEE///A/A/6/EEE6AA//E/EEEAAAA6EE/A/6EAAA/EEAEAA/AAA s1:i:155 s2:i:0 RG:Z:1 NM:i:1 AS:i:124 de:f:0.0152 rl:i:0 cm:i:8 nn:i:0 tp:A:P ms:i:124
ERR5069949.257821 163 MT192765.1 2833 60 140M = 2834 140 GCCTATACAGTTGAACTCGGTACAGAAGTAAATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACCACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEEEEEEEEEAEEEEEE s1:i:121 s2:i:0 RG:Z:1 NM:i:0 AS:i:280 de:f:0 rl:i:0 cm:i:17 nn:i:0 tp:A:P ms:i:280
ERR5069949.257821 83 MT192765.1 2834 49 139M = 2833 -140 CCTATACAGTTGAACTCGGTACAGAAGTAAATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACCACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATA A/AE<EE<EA</EAEAAA<AEEAEE/A/E<<E</E</EEEAAE/EE<E/EEEAEEEEEEE/AEEEEEEEEEEE/EEEE<EEEE/EE/EAEEE6EEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:121 s2:i:48 RG:Z:1 NM:i:0 AS:i:278 de:f:0 rl:i:0 cm:i:1 nn:i:0 tp:A:P ms:i:278
ERR5069949.309410 99 MT192765.1 3184 60 151M = 3348 314 GAAGAAGATTGGTTAGATGATGATAGTCAACAAACTGTTGGTCAACAAGACGGCAGTGAGGACAATCAGACAACTACTATTCAAACAATTGTTGAGGTTCAACCTCAATTAGAGATGGAACTTACACCAGTTGTTCAGACTATTGAAGTGA AAAAA//EEEEA6EEEAE</EEE/EEEEE/EE6EEEEEEEEEEEEEEEAEEAAEEEEEEEEEAEEEEEE/EEAEEEEEAEAEEE/EEAEEE<AEEEAA////EEEEEEEEA//A/EE/EAAEA/AE<EE/E//E/</AEAEAE/AEA/AEA s1:i:274 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:22 nn:i:0 tp:A:P ms:i:302
ERR5069949.309410 147 MT192765.1 3348 60 150M = 3184 -314 TTATTTAAAACTTACTGACAATGTATACATTAAAAATGCAGACATTGTGGAAGAAGCTAAAAAGGTAAAACCAACAGTGGTTGTTAATGCAGCCAATGTTTACCTTAAACATGGAGGAGGTGTTGCAGGAGCCTTAAATACGGCTACTAA E//EEAEA<<EAAE/AAAAEAAAAEA</A/<6/E/<A<//AE/EEAAE<EEEAEEEEEEAEE/EEAEEEEEE/<E/EEE6EEAE/<EE//E</</EE/EEAAEE/EAA/EEEEAEEEEE///EA/EEEEEEEE//E66EE/E/EEA/AAA s1:i:274 s2:i:0 RG:Z:1 NM:i:1 AS:i:290 de:f:0.0067 rl:i:0 cm:i:18 nn:i:0 tp:A:P ms:i:290
ERR5069949.376959 99 MT192765.1 4105 60 151M = 4190 235 GCTCCATATATAGTGGGTGATGTTGTTCAAGAGGGTGTTTTAACTGCTGTGGTTATACCTACTAAAAAGGCTGGTGGCACTACTGAAATGCTAGCGAAAGCTTTGAGAAAAGTGCCAACAGACAATTATATAACCACTTACCCGGGTCAGG AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEAAAAAEEEEEEEEEAEEAEEEEEEEEEEEEAAAEEAEA s1:i:224 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:22 nn:i:0 tp:A:P ms:i:302
ERR5069949.366975 163 MT192765.1 4166 60 106M = 4166 106 CTAAAAAGGCTGGTGGCACTACTGAAATGCTAGCGAAAGCTTTGAGAAAAGTGCCAACAGACAATTATATAACCACTTACCCGGGTCAGGGTTTAAATGGTTACAC AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE s1:i:96 s2:i:0 RG:Z:1 NM:i:0 AS:i:212 de:f:0 rl:i:0 cm:i:9 nn:i:0 tp:A:P ms:i:212
ERR5069949.366975 83 MT192765.1 4166 59 106M = 4166 -106 CTAAAAAGGCTGGTGGCACTACTGAAATGCTAGCGAAAGCTTTGAGAAAAGTGCCAACAGACAATTATATAACCACTTACCCGGGTCAGGGTTTAAATGGTTACAC EEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEE6EEEEEEEEEEAEEEEEEEEEE<AEAEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:96 s2:i:0 RG:Z:1 NM:i:0 AS:i:212 de:f:0 rl:i:0 cm:i:4 nn:i:0 tp:A:P ms:i:212
ERR5069949.376959 147 MT192765.1 4190 60 150M = 4105 -235 AAATGCTAGCGAAAGCTTTGAGAAAAGTGCCAACAGACAATTATATAACCACTTACCCGGGTCAGGGTTTAAATGGTTACACTGTAGAGGAGGCAAAGACAGTGCTTAAAAAGTGTAAAAGTGCCTTTTACATTCTACCATCTATTATCT EEAAAEAAA<AAAAAEEEA<EEEEAE<<<AAAAAAA<A<AEEEEE<EEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEAAAAA s1:i:224 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:15 nn:i:0 tp:A:P ms:i:300
ERR5069949.465452 99 MT192765.1 4695 60 151M = 4827 282 ACCTGATGCTGTTACAGCGTATAATGGTTATCTTACTTCTTCTTCTAAAACACCTGAAGAACATTTTATTGAAACCATCTCACTTGCTGGTTCTTATAAAGATTGGTCCTATTCTGGACAATCTACACAACTAGGTATAGAATTTCTTAAG AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEE/EEAEEEE/EEEEEEEEEEAEEEEEEEEEEEEEEE<EEEEAAAEAEEEEEEAA6AAEEEEEA<EEEEE</EEAEE/EE s1:i:261 s2:i:0 RG:Z:1 NM:i:1 AS:i:292 de:f:0.0066 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:292
ERR5069949.465452 147 MT192765.1 4827 60 150M = 4695 -282 AGGTATAGAATTTCTTAAGAGAGGTGATAAAAGTGTATATTACACTAGTAATCCTACCACATTCCACCTAGATGGTGAAGTTATCACCTTTGACAATCTTAAGACACTTCTTTCTTTGAGAGAAGTGAGGACTATTAAGGTGTTTACAAC AAAEEEEEEEEEEEEAA/<EA<AA/EAEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEAEEEEEEE/EEA/EEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:261 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:300
ERR5069949.479807 163 MT192765.1 4968 60 150M = 5123 305 GTTTACAACAGTAGACAACATTAACCTCCACACGCAAGTTGTGGACATGTCAATGACATATGGACAACAGTTTGGTCCAACTTATTTGGATGGAGCTGATGTTACTAAAATAAAACCTCATAATTCACATGAAGGTAAAACATTTTATGT AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<AEEEEEEEEEE<EEE<AEE/EEEEEEEEEAEEE<AA/EAA<AEEEEEEEAEEAAA s1:i:280 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:20 nn:i:0 tp:A:P ms:i:300
ERR5069949.479807 83 MT192765.1 5123 60 150M = 4968 -305 CTAATGATGACACTCTACGTGTTGAGGCTTTTGAGTACTACCACACAACTGATCCTAGTTTTCTGGGTAGGTACATGTCAGCATTAAATCACACTAAAAAGTGGAAATACCCACAAGTTAATGGTTTAACTTCTATTAAATGGGCAGATA AA/EEEEAAAEAEEEAAAEEA/AAEAAEE/AAAEAAAAEEEEEEEEEEEAEEEEEEEEEEEEEAEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEAEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:280 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:23 nn:i:0 tp:A:P ms:i:300
ERR5069949.501486 163 MT192765.1 5355 60 150M = 5423 214 TTACAGAGCAAGGGCTGGTGAAGCTGCTAACTTTTGTGCACTTATCTTAGCCTACTGTAATAAGACAGTAGGTGAGTTAGGTGATGTTAGAGAAACAATGAGTTACTTGTTTCAACATGCCAATTTAGATTCTTGCAAAAGAGTCTTGAA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEAA/EEE/<AEEAAEAEA</EEEAEAAAAAEE s1:i:207 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:18 nn:i:0 tp:A:P ms:i:300
ERR5069949.501486 83 MT192765.1 5423 60 146M = 5355 -214 TAGGTGAGTTAGGTGATGTTAGAGAAACAATGAGTTACTTGTTTCAACATGCCAATTTAGATTCTTGCAAAAGAGTCTTGAACGTGGTGTGTAAAACTTGTGGACAACAGCAGACAACCCTTAAGGGTGTAGAAGCTGTTATGTAC EAAAAEAEEEE6E<AEEEEEEEE<EEEEEEAAEE/EEEEEE/<EEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:207 s2:i:0 RG:Z:1 NM:i:0 AS:i:292 de:f:0 rl:i:0 cm:i:11 nn:i:0 tp:A:P ms:i:292
ERR5069949.532979 99 MT192765.1 5568 60 149M = 5621 204 CATGGGCACACTTTCTTATGAACAATTTAAGAAAGGTGTTCAGATACCTTGTACGTGTGGTAAACAAGCTACAAAATATCTAGTACAACAGGAGTCACCTTTTGTTATGATGTCAGCACCACCTGCTCAGTATGAACTTAAGCATGGTA AAAAAEEEEEEEEEEEEEEEEEEE/EEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/A/</EEE<EEE<<AEEEEEA/AA/AE/EE/EEEEAEA</EAEEE<<AEEEEE s1:i:196 s2:i:0 RG:Z:1 NM:i:0 AS:i:298 de:f:0 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:298
ERR5069949.540529 163 MT192765.1 5570 60 150M = 5659 238 TGGGCACACTTTCTTATGAACAATTTAAGAAAGGTGTTCAGATACCTTGTACGTGTGGTAAACAAGCTACAAAATATCTAGTACAACAGGAGTCACCTTTTGTTATGATGTCAGCACCACCTGCTCAGTATGAACTTAAGCATGGTACAT AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEAEAEEEEEEEEEEAAEEEEEEEEEEAEEEEEEE<EA<AEEEAEEEAEEEEAEEAEEEAEEEEEEEAAAEEE s1:i:226 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:300
ERR5069949.532979 147 MT192765.1 5621 60 151M = 5568 -204 CGTGTGGTAAACAAGCTACAAAATATCTAGTACAACAGGAGTCACCTTTTGTTATGATGTCAGCACCACCTGCTCAGTATGAACTTAAGCATGGTACATTTACTTGTGCTAGTGAGTACACTGGTAATTACCAGTGTGGTCACTATAAACA AE/E/<E/AA/EA<EA<EEEEAEA<AEAEE/AEAAA</<EEEE<AEEAEEE/EE/AEA<AE<EEEEEEEE/EEEEEEAE/EEEEEEEEEEE/EEAEEEEEEEEEEE/EEEAE6EEE/EEEEEEEAEEEEAEEEEEEEEEEEEEEEEAAAAA s1:i:196 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:11 nn:i:0 tp:A:P ms:i:302
ERR5069949.540529 83 MT192765.1 5659 60 149M = 5570 -238 GAGTCACCTTTTGTTATGATGTCAGCACCACCTGCTCAGTATGAACTTAAGCATGGTACATTTACTTGTGCTAGTGAGTACACTGGTAATTACCAGTGTGGTCACTATAAACATATAACTTCTAAAGAAACTTTGTATTGCATAGACGG AEAEAEE<EE<AAEA<EEE/<EE6A<AEEE<EE<EEEE<EEE/E<AEEE<E/<EAEEEEEEE<EEEAEEEAEAEAAEEEEEEEEEEEEEEAEEEEEEEEEE/EA<E/EAEEEEEEAEE6EEEEEEEAEEEAEE/AAEEEE/A/EAAAAA s1:i:226 s2:i:0 RG:Z:1 NM:i:0 AS:i:298 de:f:0 rl:i:0 cm:i:16 nn:i:0 tp:A:P ms:i:298
ERR5069949.573706 99 MT192765.1 5697 60 150M = 5784 236 GTACGAACTTAAGCATGGTACATTTACTTGTGCTAGTGAGTACACTGGTAATTACCAGTGTGGTCACTATAAACATATATCTTCTAAAGAAACTTTGTATTGCATAGACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTAT AAAAA6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEAAEEEAEEEEEEEEEEE s1:i:214 s2:i:0 RG:Z:1 NM:i:2 AS:i:282 de:f:0.0133 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:282
ERR5069949.573706 147 MT192765.1 5784 60 149M = 5697 -236 AGAAACTTTGTATTGCATAGACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAGTTACACAACAACCATAAAACCAGTTACTTATAAATTGGATGGTGTTGTTTGTACAGAAA AA<E<EEEEEEEEA<AEEEAEEAA<<EEE<AEEEEEEAEAAAAEAEAEEEEEEAEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:214 s2:i:0 RG:Z:1 NM:i:0 AS:i:298 de:f:0 rl:i:0 cm:i:13 nn:i:0 tp:A:P ms:i:298
ERR5069949.576388 163 MT192765.1 5798 60 77M = 5798 77 GCATAGACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAGT AAAAA6EEAEEEEEAEEAEEAEEEEEEA6EEEEAEEAEEEEE6EEEEEEAEEEEA///A<<EEEEEEEEEAEEEEEE s1:i:62 s2:i:0 RG:Z:1 NM:i:0 AS:i:154 de:f:0 rl:i:0 cm:i:10 nn:i:0 tp:A:P ms:i:154
ERR5069949.576388 83 MT192765.1 5798 50 77M = 5798 -77 GCATAGACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAGT EA/AEEE/<EEEEEEEEEEEAA<EEEEEEEEEEEEEEEEEEEEEAEEEEEAEEEAEE6/EEEAEEEEEEEEEA6AAA s1:i:62 s2:i:0 RG:Z:1 NM:i:0 AS:i:154 de:f:0 rl:i:0 cm:i:1 nn:i:0 tp:A:P ms:i:154
ERR5069949.611123 163 MT192765.1 6481 60 125M = 6481 125 ATTATACTTAAACCAGCAAATAATAGTTTAAAAATTACAGAAGAGGTTGGCCACACAGATCTAATGGCTGCTTATGTAGACAATTCTAGTCTTACTATTAAGAAACCTAATGAATTATCTAGAGT AAAAAEEEEEA6EEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEE<EEEEEEEAEEEEEEEEEEEEAEEEEEEEEEEE/EEEEEEEA/AAEAAEAAEAE s1:i:117 s2:i:0 RG:Z:1 NM:i:0 AS:i:250 de:f:0 rl:i:0 cm:i:14 nn:i:0 tp:A:P ms:i:250
ERR5069949.611123 83 MT192765.1 6481 48 125M = 6481 -125 ATTATACTTAAACCAGCAAATAATAGTTTAAAAATTACAGAAGAGGTTGGCCACACAGATCTAATGGCTGCTTATGTAGACAATTCTAGTCTTACTATTAAGAAACCTAATGAATTATCTAGAGT EEEAEEEEEEEEEEEA<EEEAEEEEA/EEEEEEEEEAEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEAEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:50 s2:i:117 RG:Z:1 NM:i:0 AS:i:250 de:f:0 rl:i:0 cm:i:8 nn:i:0 tp:A:P ms:i:250
ERR5069949.651338 163 MT192765.1 7629 60 149M = 7745 254 ATTCTGTGCTGGTAGTACATTTATTAGTGATGAAGATGCGAGAGACTTGTCACTACAGTTTAAAAGACCAATAAATCCTACTGACCAGTCTTCTTACATCGTTGATAGTGTTACAGTGAAGAATGGTTCCATCCATCTTTACTTTGATA AAAAAE/EAEEE/AEAEEE/EEEAAEEEEAEEEEE/EEEEAEEEEEEAEE/EEEE/EEE</EE/AEAE/<E/EEAEE<EEEE//AEEEEEE<EEAEE/EEE//E/<EE<A<A/EAA<AA/AEEA//A<A/A<A<6A6/AEE/AEEA<AE s1:i:223 s2:i:0 RG:Z:1 NM:i:1 AS:i:288 de:f:0.0067 rl:i:0 cm:i:16 nn:i:0 tp:A:P ms:i:288
ERR5069949.651338 83 MT192765.1 7745 60 4S138M = 7629 -254 ACTCTGAAGAATGGTTCCATCCATCTTTACTTTGTTAAAGCTGGTCAAAAGACTTATGAAAGACATTCTCTCTCTCATTTTGTTAACTTAGACAACCTGAGAGCTAATAACACTAAAGGTTCATTGCCTATTAATGTTATAG A///A/6/<EEEA//EE/EE<AEEE/<A/EAE<</A/A<EEE/E<EEEEE<</EEEA<E/EEAAEEEEAE/EEEEEEEEEEEEEE/E/A/EE//<AE/EEEAEEA</EE/AEEEE/AEEEEAEEEEEEEEEAEAEEEAAAAA s1:i:223 s2:i:0 RG:Z:1 NM:i:1 AS:i:266 de:f:0.0072 rl:i:0 cm:i:13 nn:i:0 tp:A:P ms:i:266
ERR5069949.686090 163 MT192765.1 7975 60 151M = 8097 272 GATCAGGCATTAGTGTCTGATGTTGGTGATAGTGCGGAAGTTGCAGTTAAAATGTTTGATGCTTACGTTAATACGTTTTCATCAACTTTTAACGTACCAATGGAAAAACTCAAAACACTAGTTGCAACTGCAGAAGCTGAACTTGCAAAGA AAAAAEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEAEEEEEAEEEEEEEE/EEEEEEEEEEEEEEAEEEEEAEEEE<AEE/EEEEEEEAAAAEEEEEEEEEEEAEAEEEEEAEEEEA s1:i:252 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:27 nn:i:0 tp:A:P ms:i:302
ERR5069949.686090 83 MT192765.1 8097 60 150M = 7975 -272 TGCAACTGCAGAAGCTGAACTTGCAAAGAATGTGTCCTTAGACAATGTCTTATCTACTTTTATTTCAGCAGCTCGGCAAGGGTTTGTTGATTCAGATGTAGAAACTAAAGATGTTGTTGAATGTCTTAAATTGTCACATAAATCTGACAT EEEAEAEEEEEEEEEEEEEAEEEEEAEEE<EAEE/EEEEEEEEAEEE6EEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEE/EEEEAEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:252 s2:i:0 RG:Z:1 NM:i:1 AS:i:290 de:f:0.0067 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:290
ERR5069949.786562 163 MT192765.1 8904 60 150M = 9096 343 GCATTTCTTACCTAGAGTTTTTAGTGCAGTTGGTAACATCTGTTACACACCATCAAAACTTATAGAGTACACTGACTTTGCAACATCAGCTTGTGTTTTGGCTGCTGAATGTACAATTTTTAAAGATGCTTCTGGTAAGCCAGTACCATA AAAAAEEEEEEEEAEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEAEEEEEEEEEEEEEEEAEEEEEEE<EEAEEEEE<EEEEEEEEEAEEEAEEEAEEAA6A<EEEEAAEEEEAA/AEEEEEE/EEEEEEE s1:i:272 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:20 nn:i:0 tp:A:P ms:i:300
ERR5069949.786562 83 MT192765.1 9096 60 151M = 8904 -343 AAGTTTACGCCCTGACACACGTTATGTGCTCATGGATGGCTCTATTATTCAATTTCCTAACACCTACCTTGAAGGTTCTGTTAGAGTGGTAACAACTTTTGATTCTGAGTACTGTAGGCACGGCACTTGTGAAAGATCAGAAGCTGGTGTT AEAE<AE/AAAEEAAEE<EEAEEEEAEEEEAAA/AEEEAEAEAEEEEEEEEAAEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAA6A s1:i:272 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:22 nn:i:0 tp:A:P ms:i:302
ERR5069949.856527 99 MT192765.1 10118 60 97M1D54M = 10199 233 CAACTACACTTAACGGTCTTTGGCTTGATGACGTAGTTTACTGTCCAAGACATGTGATCTGCACCTCTGAAGACATGCTTAACCCTAATTATGAAGATTACTCATTCGTAAGTCTAATCATAATTTCTTGGTACAGGCTGGTAATGTTCAA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAAEEEEEEEAEEEE<AAAEEAEEEAEEEE/EEEEEAEEEAEAEE//<//AE//E<E//<//EA/A<EA6EE//E/AA/6A//6/AEE<EE6AE/AE s1:i:197 s2:i:0 RG:Z:1 NM:i:1 AS:i:288 de:f:0.0066 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:288
ERR5069949.870926 99 MT192765.1 10118 60 149M = 10245 278 CAACTACACTTAACGGTCTTTGGCTTGATGACGTAGTTTACTGTCCAAGACATGTGATCTGCACCTCTGAAGACATGCTTAACCCTAATTATGAAGATTTACTCATTCGTAAGTCTAATCATAATTTCTTGGTACAGGCTGGTAATGTT AAAAAEEAEEEEEEEEEAEEEEEEAEEEEEEEEE/EEEEEEEAEEEEEEEAEEA<AE/AEEEEEEEEE<EEEEEEE/AEAEEEEAAEEEEAAEEEEEAEEEEEEEEAEEAAEEEEEAEAA/EEEAAEEEAAAA/A/EA/E/AEEEE/EE s1:i:262 s2:i:0 RG:Z:1 NM:i:0 AS:i:298 de:f:0 rl:i:0 cm:i:22 nn:i:0 tp:A:P ms:i:298
ERR5069949.856527 147 MT192765.1 10199 60 16M1D135M = 10118 -233 ACCCTAATTATGAAGATTACTCATTCGTAAGTCTAATCATAATTTCTTGGTACAGGCTGGTAATGTTCAACTAAGTGTTATTGGACATTCTATGCAAAATTGTGTACTTAAGCTTAAGGTTGATACAGCCAATCCTAAGACACCTAAGTAT A///6A/A6<//EA/EEEE<E<A<A6/<<A<A/A<EE6<EEEEE<A/AEEEE/AAA<E/E<EAEEEEEEEEE/A6/EEE/EE//E6EEEAE/EE<<AE/<EAEEEAAAEEAEEEEEE<</E<EEEEEEAEEEEEEEEAEEEE/EAAAAAAA s1:i:197 s2:i:0 RG:Z:1 NM:i:3 AS:i:268 de:f:0.0197 rl:i:0 cm:i:12 nn:i:0 tp:A:P ms:i:268
ERR5069949.885966 99 MT192765.1 10230 60 79M = 10277 118 GTCTAATCATAATTTCTTGGTACAGGCTGGTATTGTTCATCTCAGGGTTATTGGACATTCTATGCAAAATTGTGTACTT AAA//E/EAA/E//E//E//E/E//AE/A/E//EAEA///AE//E///E/EEE6EEEAEEA///E/AEE/EAEE/E//E s1:i:86 s2:i:0 RG:Z:1 NM:i:2 AS:i:138 de:f:0.0253 rl:i:0 cm:i:5 nn:i:0 tp:A:P ms:i:138
ERR5069949.870926 147 MT192765.1 10245 60 151M = 10118 -278 CTTGGTACAGGCTGGTAATGTTCAACTCAGGGTTATTGGACATTCTATGCAAAATTGTGTACTTAAGCTTAAGGTTGATACAGCCAATCCTAAGACACCTAAGTATAAGTTTGTTCGCATTCAACCAGGACAGACTTTTTCAGTGTTAGCT AAAAE////<6/EA6/</EE/EEEEAAAA<AE/EAA</</</</EEE</E/EEEAEE<E<<EEEE<EEEEEEEA//EEEA</EA<EA/EAA/EEEEEEEAEEEAEEEEEEEEEE/E/A/EEEEEEEE/EEEEEEEEEEEE6EEEE/6AAAA s1:i:262 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:22 nn:i:0 tp:A:P ms:i:302
ERR5069949.885966 147 MT192765.1 10277 60 62M2D7M = 10230 -118 TTATTGGACATTCTATGCAAAATTGTGTACTTAAGCTTAAGGTTGATACAGCCAATCCTAAGACCTAAG 6/E//AE</E/E/AAE/EAAEE/E/E/EA6EAEEEAE/EAA///AE/AEE/EEE6EEEEEAEE6AA//A s1:i:86 s2:i:0 RG:Z:1 NM:i:2 AS:i:128 de:f:0.0143 rl:i:0 cm:i:8 nn:i:0 tp:A:P ms:i:124
ERR5069949.937422 99 MT192765.1 10422 60 85M32D66M = 10591 320 TTACCAATGTGCTATGAGGCCCAATTTCACTATTAAGGGTTCATTCCTTAATGGTTCATGTGGTAGTGTTGGTTTTAACATAGATTATGGAATTACCAACTGGAGTTCATGCTGGCACAGACTTAGAAGGTAACTTTTATGGACCTTTTGT AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEEEEEEEEEEA<E<EE/EAE/E//EE/EEEEEEEAEEE<E/EEE/EEA<EEE</66EE<A/AA<EEEA<EAE/A//AEEAEE///<A<EEEEEEA s1:i:261 s2:i:0 RG:Z:1 NM:i:32 AS:i:246 de:f:0.0066 rl:i:0 cm:i:23 nn:i:0 tp:A:P ms:i:226
ERR5069949.919671 163 MT192765.1 10467 60 150M = 10501 185 CCTTAATGGTTCATGTGGTAGTGTTGGTTTTAACATAGATTATGACTGTGTCTCTTTTTGTTACATGCACCATATGGAATTACCAACTGGAGTTCATGCTGGCACAGACTTAGAAGGTAACTTTTATGGACCTTTTGTTGACAGGCAAAC AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAE/EEEEEEAEEEEEEEEAEEEEEEEEEEEAEEEEEEEAEEEEAEEEEAEEEEE6EEEEEEEAAEAEEEEEEE<EEEEEEE6AAEEAEEEAA6AEEAAAAAEEAAEEEAEAEEE s1:i:184 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:24 nn:i:0 tp:A:P ms:i:300
ERR5069949.919671 83 MT192765.1 10501 60 151M = 10467 -185 ATAGATTATGACTGTGTCTCTTTTTGTTACATGCACCATATGGAATTACCAACTGGAGTTCATGCTGGCACAGACTTAGAAGGTAACTTTTATGGACCTTTTGTTGACAGGCAAACAGCACAAGCAGCTGGTACGGACACAACTATTACAG EEEEEEEEAAEAAAEEAA6AEEEEEEEEAEEAAAAE/AEEEAEEEAEEEAEEEEEEEEEEEEEEEEEEEEAAEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAAAAA s1:i:184 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:9 nn:i:0 tp:A:P ms:i:302
ERR5069949.937422 147 MT192765.1 10591 60 151M = 10422 -320 TATGGACCTTTTGTTGACAGGCAAACAGCACAAGCAGCTGGTACGGACACAACTATTACAGTTAATGTTTTAGCTTGGTTGTACGCTGCTGTTATAAATGGAGACAGGTGGTTTCTCAATCGATTTACCACAACTCTTAATGACTTTAACC AA/A<EE/EEEAAE<EAA/AE6AAAAAAAAA<AAAAEAEEE/AEEEA<AE<AEAEEAAEAEEEEEEEAEEEEEEEEEE//EEAEEE<EEEAEEEEEEAAAAAEEEEEE/EE/6EEEEEEEEEEEEEEEEEEEEEEEEAEEEEAEEEAAAAA s1:i:261 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:22 nn:i:0 tp:A:P ms:i:302
ERR5069949.973930 163 MT192765.1 10924 60 112M = 10957 112 CCTTTTGATGTTGTTAGACAATGCTCAGGTGTTACTTTCCAAAGTGCAGTGAAAAGAACAATCAAGGGTACACACCACTGGTTGTTACTCACAATTTTGACTTCACTTTTAG AAAAAEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEAE<EAEEEEEEAEEAEE s1:i:101 s2:i:0 RG:Z:1 NM:i:0 AS:i:224 de:f:0 rl:i:0 cm:i:13 nn:i:0 tp:A:P ms:i:224
ERR5069949.973930 83 MT192765.1 10957 50 79M = 10924 -112 ACTTTCCAAAGTGCAGTCAAAAGAACAATCACGGGTACACACCACTGGTTGTTACTCACAATTTTGACTTCACTTTTAG <////E/EE/E//E/<//E/E//A/6EA/EE/EE///E/EAEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:101 s2:i:0 RG:Z:1 NM:i:2 AS:i:138 de:f:0.0253 rl:i:0 cm:i:1 nn:i:0 tp:A:P ms:i:138
ERR5069949.986441 99 MT192765.1 11007 60 119M = 11104 247 GTTACTCACAATTTTGACTTCACTTTTAGTCTTAGTCCAGAGTACTCAATGGTCTTTGTTCTTTTTTTTGTATGAAAATGCCTTTTTACCTTTTGCTATGGGTATTATTGCTATGTCTG AAAAAEAEEEEEEE/EEE/EEEEEAEEEEEEEEEEEEEEEEEEEEE</EAAEA/EEEEEEEEAEAAEEEEEEEEEEEEE/E//<EAE/6///EE//E/EEE///E<EEEEA</A<<//< s1:i:200 s2:i:0 RG:Z:1 NM:i:1 AS:i:228 de:f:0.0084 rl:i:0 cm:i:9 nn:i:0 tp:A:P ms:i:228
ERR5069949.986441 147 MT192765.1 11104 60 150M = 11007 -247 ATGGGTATTATTGCTATGTCTGCTTTTGCAATGATGTTTGTCAAACATAAGCATGCATTTCTCTGTTTGTTTTTGTTACCTTCTCTTGCCACTGTAGCTTATTTTAATATGGTCTATATGCCTGCTAGTTGGGTGATGCGTATTATGACA A6A<AEEEEE<E<EAEAAEA<AAEEAEA</EAEEA<E/E/E/EEEEAEAA/<EAAAEAEEE/EEEEEEEAEEE/EAEAE/AEAAA/EAEEEEEEAEAEEEEEEEAEAEEEEE/EAEEEEEEAEEEEEAEEEEEEEEAEEEEEEEEAAAAA s1:i:200 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:22 nn:i:0 tp:A:P ms:i:300
ERR5069949.1014693 99 MT192765.1 11215 60 150M = 11215 150 GTCTATATGCCTGCTAGTTGGGTGATGCGTATTATGACATGGTTGGATATGGTTGATACTAGTTTGTCTGGTTTTAAGCTAAAAGACTGTGTTATGTATGCATCAGCTGTAGTGTTACTAATCCTTATGACAGCAAGAACTGTGTATGAT AAAAAAEEAEEE6EAE//E/EEE6AEAA/EAEAEE6/E//EAE/EEEEAEE/EEE/EAEEEEEAE/EEEEEAEEEEEAAEEAEEE/AE/EAEAEEEEEEEEEEEEEE/AE/E/E/<<<AA<E<AEE</EEEEA6<AEEAAAA//A//EEE s1:i:136 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:18 nn:i:0 tp:A:P ms:i:300
ERR5069949.1014693 147 MT192765.1 11215 48 150M = 11215 -150 GGCTATATGCCTGCTAGTTGGGTGATGCGTATTATGACATGGTTGGATATGGTTGATACTAGTTTGTCTGGTTTTAAGCTAAAAGACTGTGTTATGTATGCATCAGCTGTAGTGTTACTAATCCTTATGACAGCAAGAACTGTGTATGAT A/<EEEAA<<AA<AEAE<6<A<AA<EA<///EAEEE<AAEAA/EA6/EEEEE/E/EE/AEAEAEEE<AEEEEEEE6<AAEEEEE<EEEAEEEEEEAAEAEAEEEAAEEEEEEEEEE/EEEEEEEEE/EEEEEEEEAEE/EAEEEEAAAAA s1:i:33 s2:i:136 RG:Z:1 NM:i:1 AS:i:296 de:f:0.0067 rl:i:0 cm:i:3 nn:i:0 tp:A:P ms:i:296
ERR5069949.1020777 163 MT192765.1 11217 60 122M = 11217 122 CTATATGCCTGCTAGTTGGGTGATGCGTATTATGACATGGTTGGATATGGTTGATACTAGTTTGTCTGGTTTTAAGCTAAAAGACTGTGTTATGTATGCATCAGCTGTAGTGTTACTAATCC AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEAEEEEEEAEEEAAEEEEEEEEEAEEEEA s1:i:110 s2:i:0 RG:Z:1 NM:i:0 AS:i:244 de:f:0 rl:i:0 cm:i:15 nn:i:0 tp:A:P ms:i:244
ERR5069949.1020777 83 MT192765.1 11217 50 122M = 11217 -122 CTATATGCCTGCTAGTTGGGTGATGCGTATTATGACATGGTTGGATATGGTTGATACTAGTTTGTCTGGTTTTAAGCTAAAAGACTGTGTTATGTATGCATCAGCTGTAGTGTTACTAATCC EEEEA6AAAA6E/AA6AAAE/EEA<EE<AEEEAE<EAEAEAEAE<EEEEE/AEEAAEEEEAEEEEEEEE/EEEEE/EEEEEEEEEEEEE6EEEEEE/EEEEEE<EEEAEE6E6EEEEAAAAA s1:i:110 s2:i:41 RG:Z:1 NM:i:0 AS:i:244 de:f:0 rl:i:0 cm:i:1 nn:i:0 tp:A:P ms:i:244
ERR5069949.1066259 99 MT192765.1 11337 60 147M = 11480 294 CCTTATGACAGCAAGAACTGTGTATGATGATGGTGCTAGGAGAGTGTGGACACTTATGAATGTCTTGACACTCGTTTATAAAGTTTATTATGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCTCTGTTACTTC AAAAAEAEEAEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEAEEEEEEEEEEEEEEEEE/EAEEEEEE/6EEEEEEEEEEAEEAEEE/EE/AEEAEEEEEAEEEA/EEAAEAE<AEEAEEEAEAEEEAEAEEAE/AEEEEAEEEEAEA s1:i:272 s2:i:0 RG:Z:1 NM:i:0 AS:i:294 de:f:0 rl:i:0 cm:i:20 nn:i:0 tp:A:P ms:i:294
ERR5069949.1062611 163 MT192765.1 11427 60 151M = 11454 178 TGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCTCTGTTACTTCTAACTACTCAGGTGTAGTTACAACTGTCATGTTTTTGGCCAGAGGTATTGTTTTTATGTGTGTTGAGTATTGCCCTATTTTCTTCATAACTGGT AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAAEEE<AAEEEEEEEEAAEEAAA6AEEEEEEEEEEEEEEEEEA s1:i:167 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:18 nn:i:0 tp:A:P ms:i:302
ERR5069949.1067032 163 MT192765.1 11434 60 150M = 11481 197 GCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCTCTGTTACTTCTAACTACTCAGGTGTAGTTACAACTGTCATGTTTTTGGCCAGAGGTATTGTTTTTATGTGTGTTGAGTATTGCCCTATTTTCTTCATAACTGGTAATACA AAAAAAEEEE666<EEEE/E/EEEAEAEEEE/EEEEEEEE/AEEEAEE/<AAEE<EAEEEA/AEEE/EAEEEE<E<AEEAEEEE<<//EEE/EEE<EEE<A/A/A<EEE///A/6<A<AE<//<EEEE6</<AAAAAAE<A//<</<A/E s1:i:171 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:16 nn:i:0 tp:A:P ms:i:300
ERR5069949.1062611 83 MT192765.1 11454 60 151M = 11427 -178 CATGTGGGCTCTTATAATCTCTGTTACTTCTAACTACTCAGGTGTAGTTACAACTGTCATGTTTTTGGCCAGAGGTATTGTTTTTATGTGTGTTGAGTATTGCCCTATTTTCTTCATAACTGGTAATACACTTCAGTGTATAATGCTAGTT AEEAAEEEAAEEEEAEAEEEAEEEEEEAEEEEEEEEEEEEEA<EEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEAEEA6EEEEEEEEAEA/EEEEAEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:167 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:5 nn:i:0 tp:A:P ms:i:302
ERR5069949.1066259 147 MT192765.1 11480 60 151M = 11337 -294 CTTCTAACTACTCAGGTGTAGTTACAACTGTCATGTTTTTGGCCAGAGGTATTGTTTTTATGTGTGTTGAGTATTGCCCTATTTTCTTCATAACTGGTAATACACTTCAGTGTATAATGCTAGTTTATTGTTTCTTAGGCTATTTTTGTAC EE//AAEEEEEEEAEE<AEEA6A<AEEAEEAAAEAA/EEEA<AA<EA<E/A//EA/EEEEEEEEEE/<AAE/AEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEAEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEAAAAA s1:i:272 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:20 nn:i:0 tp:A:P ms:i:302
ERR5069949.1067032 83 MT192765.1 11481 60 150M = 11434 -197 TTCTAACTACTCAGGTGTAGTTACAACTGTCATGTTTTTGGCCAGAGGTATTGTTTTTATGTGTGTTGAGTATTGCCCTATTTTCTTCATAACTGGAAATACACTTCAGTGTATAATGCTAGTTTATTGTTTCTTAGGCTATTTTTGTAC EE<EAAE/EEAEE/<<AEEEAA<6</E/AAA/EE/EEEAAEEEEEE<A///AAEEEE/EE<EE/A6EAE//EEE6AEEEA6EEEEEEAEEEEAAAE/EEEEAE//EE<EEEE/EEEEEEEE/E/EEEEEEEEEEEEAE/EAEEE/AAAAA s1:i:171 s2:i:0 RG:Z:1 NM:i:1 AS:i:290 de:f:0.0067 rl:i:0 cm:i:6 nn:i:0 tp:A:P ms:i:290
ERR5069949.1088785 99 MT192765.1 11864 60 149M = 11912 198 CAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAATCCTTTGAAAAAAAGGTTTCACTACTTTCGGTTTTG AAAAAE/EAEE<EEA///<AEEE/EE<AEEE<EA/EEEEEEE/EAAAEEEEEE<E/E6AE<<E/EEA//</E/EEE/EEE/EE/E/<<EEAAAE<EEEEEE/EAEA//<//AA/E</A<<E/EEEE/AEE<E/<EAE</A6///AEEAA s1:i:182 s2:i:0 RG:Z:1 NM:i:3 AS:i:268 de:f:0.0201 rl:i:0 cm:i:15 nn:i:0 tp:A:P ms:i:268
ERR5069949.1088785 147 MT192765.1 11912 60 150M = 11864 -198 CTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGC AEEEEE<E//E<EAEE/AAAA<AEEEAEEEEE<AEEAEEEEEEAEAE</AE/EEE/<EEEEAEEEEEEEEEAEEEEEEE/EEEEEEEEEEEEEEEEEEEEAA/EEEAEE/EEAEEEEEEEEEEEEEEEE/EEEEEEEEEEAEEEEAAAAA s1:i:182 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:14 nn:i:0 tp:A:P ms:i:300
ERR5069949.1132353 163 MT192765.1 12066 60 151M = 12075 159 CAACAGGGCAACCTTACAAGCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTG AAAAAEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEEEEEEEEEEEEE<EEEEEEEEAAEEAAEEEEEEEEEEEEEAE<AAAAAAE/AEEAEEEEEEEEEEEEEAAAEAAEEA s1:i:148 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:21 nn:i:0 tp:A:P ms:i:302
ERR5069949.1132353 83 MT192765.1 12075 60 150M = 12066 -159 AACCTTACAAGCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATC EEAEEEEEEEEEEEEEE<A<EEEEEEEEEEEAAEE<EAEEAAEAEEEEEEEEEEEAEEEEEEEAEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEEAAAAA s1:i:148 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:5 nn:i:0 tp:A:P ms:i:300
ERR5069949.1151736 163 MT192765.1 12126 60 151M = 12222 247 TTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGAT AAAAAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEAAEEEEEEEEEEEEEEEEEEE<EEEEAEEEEEEEEEEEEEEEEAEEEEEAEEAAEEE<AEAEEE<A/AAEEEEEEEAAAAA<AAAE<EEEEAEEEAEEEEEEAEEAEA/A s1:i:226 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:23 nn:i:0 tp:A:P ms:i:302
ERR5069949.1151736 83 MT192765.1 12222 60 151M = 12126 -247 ATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGA AAAAAAEA//EE/EAAAEAEEEEAAEEAA</AEEEEEEAAEAAEEEEEA<EEEEEEAEEEEEAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEE<EE/EEEEEEAEE/EEEEEEEEEE/EEEEEEEEEEEAEEEE/EEAEEEEEAEEAAAAA s1:i:226 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:17 nn:i:0 tp:A:P ms:i:302
ERR5069949.1258508 163 MT192765.1 12425 60 151M = 12638 364 GTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAG AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE/EEEEEEEEEAEEEEEEEEA/AEAEAAAEAEEEEEAEEEEE<<EEEEEEE<AEAEAAA<EEE s1:i:268 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:302
ERR5069949.1189252 99 MT192765.1 12486 60 98M = 12486 98 CTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTG AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEAEEE s1:i:88 s2:i:0 RG:Z:1 NM:i:0 AS:i:196 de:f:0 rl:i:0 cm:i:11 nn:i:0 tp:A:P ms:i:196
ERR5069949.1189252 147 MT192765.1 12486 52 98M = 12486 -98 CTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTG EEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:88 s2:i:27 RG:Z:1 NM:i:0 AS:i:196 de:f:0 rl:i:0 cm:i:2 nn:i:0 tp:A:P ms:i:196
ERR5069949.1261808 99 MT192765.1 12593 60 149M = 12654 166 GTGAAATTAGTATGGACAAATCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATAACAGAATAATGAGCTTAGTCCTGTTGCACTACGACAGATGTCTTGTGCTGCCGGAACTACACAAACT AAAA/AAA/EEEE/AE<EE//EE/EEEEEA<EAEEE66//EE/E/A6EEEA/E<<E/E//A/EE/AEEE6/E6EA<EEE/E//EAAEEEA/E//EEE/EA/A/A</<<E/AA<EEE<E<EEEE<A6</<A//A/AA/<<<AA<<A<AEA s1:i:134 s2:i:47 RG:Z:1 NM:i:3 AS:i:268 de:f:0.0201 rl:i:0 cm:i:5 nn:i:0 tp:A:P ms:i:268
ERR5069949.1246538 99 MT192765.1 12601 60 148M = 12627 177 AGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAGAATAATGAGCTTAGTCCTGTTGCACTACGACAGATGTCTTGTGCTGCCGGTACTACACAAACTGCTTGCA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEEEEEEEEEEEEA/EEEEEAEEEEEE/EEEEEEEEEEEEAAAAEEAEEEEEEEEEEEEEEEEE s1:i:168 s2:i:0 RG:Z:1 NM:i:0 AS:i:296 de:f:0 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:296
ERR5069949.1246538 147 MT192765.1 12627 60 151M = 12601 -177 ATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAGAATAATGAGCTTAGTCCTGTTGCACTACGACAGATGTCTTGTGCTGCCGGTACTACACAAACTGCTTGCACTGATGACAATGCGTTAGCTTACTACAAC AAAAAAEEEAAEEEEAAEAAAEEA<AAAEEAEEEAAEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEAAAAA s1:i:168 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:6 nn:i:0 tp:A:P ms:i:302
ERR5069949.1258508 83 MT192765.1 12638 60 151M = 12425 -364 TTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAGAATAATGAGCTTAGTCCTGTTGCACTACGACAGATGTCTTGTGCTGCCGGTACTACACAAACTGCTTGCACTGATGACAATGCGTTAGCTTACTACAACACAACAAAGGG EAAEEA/EEEAAAEEEAEEEEEEAA/AAEEEE/<EA/EAAEEEAAAAAAEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEAAAAA s1:i:268 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:20 nn:i:0 tp:A:P ms:i:302
ERR5069949.1261808 147 MT192765.1 12654 60 105M = 12593 -166 GGCCAATTCTGCTGTCAAATTACAGAATAATGAGCTTAGTCCTGTTGCACTACGACAGATGTCTTGTGCTGCCGGTACTACACAAACTGCTTGCACTGATGACAA <//</EEE/<<EE<E/A<AEAE/<E6////EE/E/EAE<E/EEEE//AEAEEEEA/A/EEAE/EEEEEE/EE/E//AEEEEEEEAE/EEAE/EAE6AEEEA//AA s1:i:134 s2:i:0 RG:Z:1 NM:i:0 AS:i:210 de:f:0 rl:i:0 cm:i:16 nn:i:0 tp:A:P ms:i:210
ERR5069949.1328186 163 MT192765.1 12866 60 151M = 12953 238 GTACTATCTATACAGAACTGGAACCACCTTGTAGGTTTGTTACAGACACACCTAAAGGTCCTAAAGTGAAGTATTTATACTTTATTAAAGGATTAAACAACCTAAATAGAGGTATGGTACTTGGTAGTTTAGCTGCCACAGTACGTCTACA AAAAAEEEEEEE/EEAEEEEAEEEEEAEEEEEEEEAEEEEEEEEEEEEEAE/EEEEEEAEE/EEEEEEEEEEEEEEEEEAAAEA/EEEEEEEAAEEEEE/EEEEAEEEEEAAEEEE/AAAE<A<EEEE6AEEAAA<<<<AA<AE/EEAEEA s1:i:226 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:302
ERR5069949.1328186 83 MT192765.1 12953 60 151M = 12866 -238 AAGGATTAAACAACCTAAATAGAGGTATGGTACTTGGTAGTTTAGCTGCCACAGTACGTCTACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGATGCTGCTAAAGCTTACAAAGA EE/<E6/E<AAE<E<EEAEE<AAEE//EEEEEA<A6</EEAEEEEE<AAAEEEEEEEEAEEEEEEAEE/EEEAEEEEEEEE/EAEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:226 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:302
ERR5069949.1331889 99 MT192765.1 13010 60 132M = 13010 132 GTCTACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGATGCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTG A/AAAEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEEAEEEEEEEEEEEEEEE/EEEEE<AEAEEEEE/EAEAEEE/AEEEEEEEEEEEEEEEEEEEEAE/EEEEEEEEEEEEEEEEEEEEEEEA<EE s1:i:122 s2:i:0 RG:Z:1 NM:i:0 AS:i:264 de:f:0 rl:i:0 cm:i:20 nn:i:0 tp:A:P ms:i:264
ERR5069949.1331889 147 MT192765.1 13010 48 132M = 13010 -132 GTCTACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGATGCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTG A/EEEEEAEEEEEEEEAEEEEEEEEEA<EEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEAAEEEEEE/EEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEAEEEEEEEEAAAAA s1:i:26 s2:i:122 RG:Z:1 NM:i:0 AS:i:264 de:f:0 rl:i:0 cm:i:3 nn:i:0 tp:A:P ms:i:264
ERR5069949.1372331 163 MT192765.1 13011 60 150M = 13132 272 TCTACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGATGCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTGTTAAGATGTTGTGTACACA AAAAAEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEEEEEEE/EEEEEEE<EEAEEEEEEA/EEA<EAEEEEEEAEAAAEEAAAEEEEEAAA<AAAEEEA s1:i:257 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:25 nn:i:0 tp:A:P ms:i:300
ERR5069949.1340552 163 MT192765.1 13021 60 148M = 13029 159 GGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGATGCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTGTTAAGATGTTGTGTACACACACTGGTA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEAEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEEEEAEAEEEEEEEEEE<EEEEEEEEEEEEEEAAA<AEEEEEEEEEEEEEE s1:i:145 s2:i:0 RG:Z:1 NM:i:0 AS:i:296 de:f:0 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:296
ERR5069949.1340552 83 MT192765.1 13029 60 151M = 13021 -159 AACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGATGCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTGTTAAGATGTTGTGTACACACACTGGTACTGGTCAGGCA AEAAAAEE/A<EEAAEEE/EEEEEEEEEEAAEEEEEEEEAAEEEEEEEEE<EEEAEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEAAAAA s1:i:145 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:6 nn:i:0 tp:A:P ms:i:302
ERR5069949.1372331 83 MT192765.1 13132 60 151M = 13011 -272 ACTAATTGTGTTAAGATGTTGTGTACACACACTGGTACTGGTCAGGCAATAACAGTTACACCGGAAGCCAATATGGATCAAGAATCCTTTGGTGGTGCATCGTGTTGTCTGTACTGCCGTTGCCACATAGATCATCCAAATCCTAAAGGAT EE<<EEEEEEEAAAEEEEEAEEEEEEEEEAEEEEEEEEAEEEEAEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:257 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:21 nn:i:0 tp:A:P ms:i:302
ERR5069949.1412839 163 MT192765.1 13154 60 150M = 13187 180 GTACACACACTGGTACTGGTCAGGCAATAACAGTTACACCGGAAGCCAATATGGATCAAGAATCCTTTGGTGGTGCATCGTGTTGTCTGTACTGCCGTTGCCACATAGATCATCCAAATCCTAAAGGATTTTGTGACTTAAAAGGTAAGT AAAA6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEAEEEAAAAEEEEEEEEEEAAEEAEAE<EEEAEAEEE/<AAAEAEAA/EAEEEEAEEAAE/AEA/EEEAEEAEAA s1:i:166 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:300
ERR5069949.1412839 83 MT192765.1 13187 60 147M = 13154 -180 TTACACCGGAAGCCAATATGGATCAAGAATCCTTTGGTGGTGCATCGTGTTGTCTGTACTGCCGTTGCCACATAGATCATCCAAATCCTAAAGGATTTTGTGACTTAAAAGGTAAGTATGTACAAATACCTACAACTTGTGCTAATG EEA<AAEAAAAAAE<A<<EA<EAE</E<EEEEE/EEEEAAAEEE/EEEE/EEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEA<EEEEEEEAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEAEEAAAAA s1:i:166 s2:i:0 RG:Z:1 NM:i:0 AS:i:294 de:f:0 rl:i:0 cm:i:10 nn:i:0 tp:A:P ms:i:294
ERR5069949.1476386 99 MT192765.1 13329 60 151M = 13382 201 TAATGACCCTGTGGGTTTTACACTTAAAAACACAGTCTGTACCGTCTGCGGTATGTGGAAAGGTTATGGCTGTAGTTGTGATCAACTCCGCGAACCCATGCTTCAGTCAGCTGATGCACAATCGTTTTTAAACGGGTTTGCGGTGTAAGTG AAAAA/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEAEAEEEEEEEEEEEEEEEEEEEEEEAEEEEEAEEEAEEEEEEE/AEEE/EEEEEE/AEE/EEAE/EEE<EA/<EEA/EEEEE/EEEEAAEEEAAAAEEAEEE s1:i:188 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:20 nn:i:0 tp:A:P ms:i:302
ERR5069949.1476386 147 MT192765.1 13382 60 148M = 13329 -201 TGTGGAAAGGTTATGGCTGTAGTTGTGATCAACTCCGCGAACCCATGCTTCAGTCAGCTGATGCACAATCGTTTTTAAACGGGTTTGCGGTGTAAGTGCAGCCCGTCTTACACCGTGCGGCACAGGCACTAGTACTGATGTCGTATAC AAEEEA<AEA/AAAEEE/E/AEE/E6AE/EAE/EEE<EEEAEEEEEEEEAAEE<<EEEEEEEEEEEEEEEEEEEEEA/EEEEEAA//EAEEAEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE6EEAA6AA s1:i:188 s2:i:0 RG:Z:1 NM:i:0 AS:i:296 de:f:0 rl:i:0 cm:i:10 nn:i:0 tp:A:P ms:i:296
ERR5069949.1538968 163 MT192765.1 13799 60 151M = 13817 168 CACGATGGCAGACCTCGTCTATGCTTTAAGGCATTTTGATGAAGGTAATTGTGACACATTAAAAGAAATACTTGTCACATACAATTGTTGTGATGATGATTATTTCAATAAAAAGGACTGGTATGATTTTGTAGAAAACCCAGATATATTA AAAAAEEEAEEAEEEAEEEAEEEAE<EEE6EAEA<EAAAEEEEEEEEEEEEEA/</EEEEEEEEEEEEEEEEEEEEEEAEEEEE/AEEEEEEEEAEEEEEEEEEEEEEEEEAEEEAA<AEAEE<AAE<A<AEEEEE/EA6AAA/EE/EEEA s1:i:154 s2:i:0 RG:Z:1 NM:i:1 AS:i:294 de:f:0.0066 rl:i:0 cm:i:18 nn:i:0 tp:A:P ms:i:294
ERR5069949.1538968 83 MT192765.1 13817 48 150M = 13799 -168 CTATGCTTTAAGGCATTTTGATGAAGGTAATTGTGACACATTAAAAGAAATACTTGTCACATACAATTGTTGTGATGATGATTATTTCAATAAAAAGGACTGGTATGATTTTGTAGAAAACCCAGATATATTACGCGTATACGCCAACTT AEE6AA<E/EA/<AE<AEA<6AA6AAEEEAAA6/6</AEEEE<EEEEEEE/EEEE//EEEAEEE/EEEA/EEEAEE/EEEE/EAEEEEEE<AEEEEAEEEEAEAEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEAEEAEEEEEEEAAAAA s1:i:41 s2:i:154 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:9 nn:i:0 tp:A:P ms:i:300
ERR5069949.1552198 99 MT192765.1 13944 60 150M = 14027 234 ATATTACGCGTATACGCCAACTTAGGTGAACGTGTACGCCAAGCTTTGTTAAAAACAGTACAATTCTGTGATGCCATGCGAAATGCTGGTATTGTTGGTGTACTGACATTAGATAATCAAGATCTCAATGGTAACTGGTATGATTTCGGT AAAAAEEEEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEAEAEEEEEEEEEEEAEEEEEEEEEAEEEEEEEEEEEEEEA s1:i:229 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:20 nn:i:0 tp:A:P ms:i:300
ERR5069949.1561137 163 MT192765.1 13991 60 149M = 14081 240 GTTAAAAACAGTACAATTCTGTGATGCCATGCGAAATGCTGGTATTGTTGGTGTACTGACATTAGATAATCAAGATCTCAATGGTAACTGGTATGATTTCGGTGATTTCATACAAACCACGCCAGGTAGTGGAGTTCCTGTTGTAGATT AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEEEEEEEEEE<EAEEEAEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEE<EEEEAEEEE/EEEEAAAEEEA<AEEEAEEEEEAEAEEA/AA<A s1:i:223 s2:i:0 RG:Z:1 NM:i:0 AS:i:298 de:f:0 rl:i:0 cm:i:20 nn:i:0 tp:A:P ms:i:298
ERR5069949.1552198 147 MT192765.1 14027 60 151M = 13944 -234 TGCTGGTATTGTTGGTGTACTGACATTAGATAATCAAGATCTCAATGGTAACTGGTATGATTTCGGTGATTTCATACAAACCACGCCAGGTAGTGGAGTTCCTGTTGTAGATTCTTATTATTCATTGTTAATGCCTATATTAACCTTGACC AE/AAE<AEAAA/A<///<AA6AAAE<E/E/EA<AEE/</EEEEEAEE/EE/AEA/E/<EEE/AEA//EE</AA<AEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:229 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:15 nn:i:0 tp:A:P ms:i:302
ERR5069949.1561137 83 MT192765.1 14081 60 150M = 13991 -240 GTATGATTTCGGTGATTTCATACAAACCACGCCAGGTAGTGGAGTTCCTGTTGTAGATTCTTATTATTCATTGTTAATGCCTATATTAACCTTGACCAGGGCTTTAACTGCAGAGTCACATGTTGACACTGACTTAACAAAGCCTTACAT AE<EAAA/EEAEE<A<A/AAEE<EE/EEAAAEEEEEAEEEEEEE/EEEEEEEEEEEEEEEEAEEAEEAEEEEEEEEEEEEEEEEEE/EEEEEEEEEEAEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:223 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:13 nn:i:0 tp:A:P ms:i:300
ERR5069949.1704586 99 MT192765.1 14601 60 149M = 14761 310 GATAAACGCACTACGTGCTTTTCAGTAGCTGCACTTACTAACAATGTTGCTTTTCAAACTGTCAAACCCGGTAATTTTAACAAAGACTTCTATGACTTTGCTGTGTCTAAGGGTTTCTTTAAGGAAGGAAGTTCTGTTGAATTAAAACA AAAA6EEEE/EE6EEEEEEEEEEEEEEEEEE<EEEEEEEE6EEAEEEEEA<EEEEE66EEEEE///EEEAEEEE<EEEEEEA/EE/EEEEEEEAE<E<AA<AAAEEAE/AEE<E<AA<EAAEEAE/AEE/E/EAEAAAEE/EA/A//EE s1:i:277 s2:i:0 RG:Z:1 NM:i:0 AS:i:298 de:f:0 rl:i:0 cm:i:21 nn:i:0 tp:A:P ms:i:298
ERR5069949.1704586 147 MT192765.1 14761 60 150M = 14601 -310 CTCAGGATGGTAATGCTGCTATCAGCGATTATGACTACTATCGTTATAATCTACCAACAATGTGTGATATCAGACAACTACTATTTGTAGTTGAAGTTGTTGATAAGTACTTTGATTGTTACGATGGTGGCTGTATTAATGCTAACCAAG A//EEAE<AAA<AEAA6EEE</<AAA6EE//A<A<<AE<E//AEEEEE<EEEEAEAA<AEA<AE/EEEEAEEAEEEAEAEEAEEE/EEEEEEAE<EEEEEEEEEEEEEE/EEEEEEAEEEEEEEEEEE/EEEEEE/EEEEE<EEEA/AAA s1:i:277 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:300
ERR5069949.1709367 163 MT192765.1 14886 60 129M = 14886 129 GGTGGCTGTATTAATGCTAACCAAGTCATCGTCAACAACCTAGACAAATCAGCTGGTTTTCCATTTAATAAATGGGGTAAGGCTAGACTTTATTATGATTCAATGAGTTATGAGGATCAAGATACACTT AAAAAEEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEAEEEEEEAEEEEEEEEEEEEEEAEEEEEEEEEEEEEEE s1:i:117 s2:i:0 RG:Z:1 NM:i:1 AS:i:248 de:f:0.0078 rl:i:0 cm:i:15 nn:i:0 tp:A:P ms:i:248
ERR5069949.1709367 83 MT192765.1 14886 50 129M = 14886 -129 GGTGGCTGTATTAATGCTAACCAAGTCATCGTCAACAACCTAGACAAATCAGCTGGTTTTCCATTTAATAAATGGGGTAAGGCTAGACTTTATTATGATTCAATGAGTTATGAGGATCAAGATACACTT AA/EEAAAEEEEAEE6A/EAAEAAEAAAAAAAAEEAEEE/AEAE<AEEAEAE/EEEEEEEEA/EEAA<AEE/EEE<AEA<EAAEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEAEEEAEEEAAAAA s1:i:117 s2:i:42 RG:Z:1 NM:i:1 AS:i:248 de:f:0.0078 rl:i:0 cm:i:1 nn:i:0 tp:A:P ms:i:248
ERR5069949.1778133 163 MT192765.1 15485 60 150M = 15491 158 TGCCACAACTGCTTATGCTAATAGTGTTTTTAACATTTGTCAAGCTGTCACGGCCAATGTTAATGCACTTTTATCTACTGATGGTAACAAAATTGCCGATAAGTATGTCCGCAATTTACAACACAGACTTTATGAGTGTCTCTATAGAAA AAAAAEEEEEEEEEEEEEEAEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEAAEEEEEE<AEEEEEEE/AAAE<AAEEAAEEEA<EAAEEEA<AAEEEEEE/EEAAAEE/EAAAAEEEEEAEAEE s1:i:139 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:300
ERR5069949.1778133 83 MT192765.1 15491 48 146M1D5M = 15485 -158 AACTGCTTATGCTAATAGTGTTTTTAACATTTGTCAAGCTGTCACGGCCAATGTTAATGCACTTTTATCTACTGATGGTAACAAAATTGCCGATAAGTATGTCCGCAATTTACAACACAGACTTTATGAGTGTCTCTATAGAAATAAGATG AEEAEEEEEAAAAAA<AEEEEEEEEEEEEEEEEEEAEEEEEEEAEAEEEEEEEEEEEEEEAEEEEAEAEAEEEEEEEEEEEE<AEEEEAAAEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:55 s2:i:139 RG:Z:1 NM:i:1 AS:i:292 de:f:0.0066 rl:i:0 cm:i:10 nn:i:0 tp:A:P ms:i:292
ERR5069949.1980512 163 MT192765.1 16801 60 150M = 16852 202 GTAAAGTACAAATAGGAGAGTACACCTTTGAAAAAGGTGACTATGGTGATGCTGTTGTTTACCGAGGTACAACAACTTACAAATTAAATGTTGGTGATTATTTTGTGCTGACATCACATACAGTAATGCCATTAAGTGCACCTACACTAG AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEAEEEEEEEEEA<EEEEEEAEEEEAAAEEAAE<EEEAAAA<AA<EEEE/AE s1:i:193 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:18 nn:i:0 tp:A:P ms:i:300
ERR5069949.1980512 83 MT192765.1 16852 60 151M = 16801 -202 CTGTTGTTTACCGAGGTACAACAACTTACAAATTAAATGTTGGTGATTATTTTGTGCTGACATCACATACAGTAATGCCATTAAGTGCACCTACACTAGTGCCACAAGAGCACTATGTTAGAATTACTGGCTTATACCCAACACTCAATAT EEEEEEEEEEAEEEEEEAAEEEEEAAEAEAAAEAEEEAEAEEEAEEEAEEEEEAEAAEEEEAEAEEEEEEEAEEEEEEEEEEEAEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:193 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:12 nn:i:0 tp:A:P ms:i:302
ERR5069949.2033605 163 MT192765.1 17083 60 149M = 17101 168 GTACTGGTAAGAGTCATTTTGCTATTGGCCTAGCTCTCTACTACCCTTCTGCTCGCATAGTGTATACAGCTTGCTCTCATGCCGCTGTTGATGCACTATGTGAGAAGGCATTAAAATATTTGCCTATAGATAAATGTAGTAGAATTATA AAAAAEAEEEEEEEEEEEEAEEEEEEEEEEEEE<EEEEEEEEEEE<EEEEEEEEAAEAEEEEEEEEEEEE/EAAEEEA/EEEEEEAE<EEEEEEEEE<AEEEEAAAEAE<EAEEEEEE//</A/AEAAAEA/<E<AEEEAEE<EEEEEE s1:i:160 s2:i:0 RG:Z:1 NM:i:0 AS:i:298 de:f:0 rl:i:0 cm:i:24 nn:i:0 tp:A:P ms:i:298
ERR5069949.2033605 83 MT192765.1 17101 48 150M = 17083 -168 TTGCTATTGGCCTAGCTCTCTACTACCCTTCTGCTCGCATAGTGTATACAGCTTGCTCTCATGCCGCTGTTGATGCACTATGTGAGAAGGCATTAAAATATTTGCCTATAGATAAATGTAGTAGAATTATACCTGCACGTGCTCGTGTAG AAA<EAA<EEEAAAA/E</EA/E6EAEE/EE/AEA<AAEEAEEA/EE<EEEEEEEEEEEE<AEE/AEEE/EAAEEEAEEAEEEEE<EEE<EEEEEAAEEEEEEEEAEEEEEAEEAEEEEEEEEEAEEEEEEEEEEEEEEEEE/EEAAAAA s1:i:34 s2:i:160 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:6 nn:i:0 tp:A:P ms:i:300
ERR5069949.2098070 99 MT192765.1 17115 60 151M = 17270 304 GCTCTCTACTACCCTTCTGCTCGCATAGTGTATACAGCTTGCTCTCATGCCGCTGTTGATGCACTATGTGAGAAGGCATTAAAATATTTGCCTATAGATAAATGTAGTAGAATTATACCTGCACGTGCTCGTGTAGAGTGTTTTGATAAAT AAAAAEEEEEEE/EE/EA/EEA/EEEEA/<6EEEEEEA<AE/EAEEEE/AAA<A<E<EEA<EEA/EEAEEEEAEEAEE/EAEEEEE//6/6AEEA</EEAEEEEA<EE/AE66AEAEAAAA/<AA<<<<EAAEAEAEE/EA6EEEEEAEEE s1:i:269 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:23 nn:i:0 tp:A:P ms:i:302
ERR5069949.2064910 99 MT192765.1 17123 60 149M = 17180 174 CTACCCTTCTGCTCGCATAGTGTATACAGCTTGCTCTCATGCCGCTGTTGATGCACTATGTGAGAAGGCATTAAAATATTTGCATATAGATAAATGTAGTAGAATTATACCTGCACGTGCTCGTGTAGAGTGTTTTGATAAATTCAAAG AAAAAEA<AEEE/EE/EE/EEE/EEE//E/EA/EEEEEEEEEEE<E/A</</A/AEAEEEE/EAE/AEEE<AAE/E//EA</<//E<A/AE<EAEEE///<EA/E<AEAAAA/A/</EEEEEAE/A/<A/AA/EAE<AE/6/<<A</<A s1:i:141 s2:i:0 RG:Z:1 NM:i:1 AS:i:288 de:f:0.0067 rl:i:0 cm:i:18 nn:i:0 tp:A:P ms:i:288
ERR5069949.2125592 99 MT192765.1 17180 60 150M = 17289 245 ATGTGAGAAGGCATTAAAATATTTGCCTATAGATAAATGTAGTAGAATTATACCTGCACGTGCTCGTGTAGAGTGTTTTGATAAATTCAAAGTGAATTCAACATTAGAACAGTATGTCTTTTGTACTGTAAATGCATTGCCTGAGACGAC AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEAEEEEEEEAEEEEA<EEEEEEEAEEEEEEAEEEEEEAAEEEEEE<EE/A/EEEA s1:i:237 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:20 nn:i:0 tp:A:P ms:i:300
ERR5069949.2064910 147 MT192765.1 17180 48 117M = 17123 -174 ATGTGAGTAGGCATTAAAATATTTGCCTATAGATAAATGTAGTAGAATTATACCTGCACGTGCTCGTGTAGAGTGTTTTGATAAATTCAAAGTGACTTCAACATTAGAACAGTATGT <<////A/AAAE<EA///AA<EAAE/EEEEEEEE//E<AE/EEAEA/EAEAEEEEEAAE<AEE6/AE</<E/EEEEEE<EAE<AA6EAEEEE/EE6EEE/A/EEE/AEEE/EAA//A s1:i:38 s2:i:141 RG:Z:1 NM:i:2 AS:i:214 de:f:0.0171 rl:i:0 cm:i:8 nn:i:0 tp:A:P ms:i:214
ERR5069949.2098070 147 MT192765.1 17270 60 149M = 17115 -304 AGTGAATTCAACATTAGAACAGTATGTCTTTTGTACTGTAAATGCATTGCCTGAGACGACAGCAGATATAGTTGTCTTTGATGAAATTTCAATGGCCACAAATTATGATTTGAGTGTTGTCAATGCCAGATTACGTGCTAAGCACTATG A6A/6EEE6/</6EEAAE//<<EA/EE/EEEAAEA/A<E/A6AAA/AEEA/E</AEAEEAEA<A6EE/EEEE<AAEEEEA/EA<EEEEAEEEEEE<<E/E/AEEEEAAEEEEAAEEEEEEE/EEEEEEEEEEEEEEEEEEEEE/AAAAA s1:i:269 s2:i:0 RG:Z:1 NM:i:0 AS:i:298 de:f:0 rl:i:0 cm:i:22 nn:i:0 tp:A:P ms:i:298
ERR5069949.2125592 147 MT192765.1 17289 60 136M = 17180 -245 CAGTATGTCTTTTGTACTGTAAATGCATTGCCTGAGACGACAGCAGATATAGTTGTCTTTGATGAAATTTCAATGGCCACAAATTATGATTTGAGTGTTGTCAATGCCAGATTACGTGCTAAGCACTATGTGTACA A//<//E//EE</</</<//AA6//</A//EE<E//EEEEEEEEEEEE<EEE/EEAEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:237 s2:i:0 RG:Z:1 NM:i:0 AS:i:272 de:f:0 rl:i:0 cm:i:20 nn:i:0 tp:A:P ms:i:272
ERR5069949.2185111 163 MT192765.1 17406 60 147M = 17537 281 GCTAAGCACTATGTGTACATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACAAGAATATATCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGT AAAAA6/E//AEEAEEEEE/EEE/E/EEEE/E/E6E///E<E/<EE</A/<EEE//E6/<EEEAE<//<E/E/6EEE/EAAA<//EE//<EEE/AEEAA/A<EAE/EEA<//AEAEEE/<A/E</AA<EEA<<EAAEA<<</E/EEE s1:i:248 s2:i:0 RG:Z:1 NM:i:2 AS:i:274 de:f:0.0136 rl:i:0 cm:i:14 nn:i:0 tp:A:P ms:i:274
ERR5069949.2151832 163 MT192765.1 17416 60 150M = 17453 187 ATGTGTACATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTG AAAAAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEAEEEEEAAEEEEEEEEEAAEAAA<<EAAEEEEEEEAAA<<<AE s1:i:183 s2:i:47 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:14 nn:i:0 tp:A:P ms:i:300
ERR5069949.2176303 99 MT192765.1 17442 60 151M = 17519 227 TTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTGCTGAAATTGTTGACACTGTGAGTGCTT AAAAAEEEEEEAEEEEEEAEEEEEEEEEEEEEEAEAEEEEEAEEEEEEEEEAEEEEEEEEEEE<EEEEAEEEEEEEEEEEEEEEEEEEEEEAEEEE<A<AEEEAE/EE<EEEEAAAAAAEEAA<AAAEEEEEE<EEEEEEEEAEE<EEEEA s1:i:217 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:20 nn:i:0 tp:A:P ms:i:302
ERR5069949.2151832 83 MT192765.1 17453 60 150M = 17416 -187 ACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGA AAAA<EEEEEEAEEEAEAAAAEEEEEEEEEAAAEE<EEEEEAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAAA s1:i:183 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:13 nn:i:0 tp:A:P ms:i:300
ERR5069949.2205229 99 MT192765.1 17476 60 137M1D13M = 17585 259 CACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGATAATAAGCTTAAGCACATAAAGA AAAAAEEEEEEA/EEEEEEEAEEEEEEEEEAEAEAEEEEEEEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEEAEEEEEEAEEEEEE6EE<E<<EEEAEEEEEEEEEEEEEEEEA<AEEEEEEAAAEEEEEEEEEEEEEEEE<EAAEEEEE s1:i:252 s2:i:0 RG:Z:1 NM:i:1 AS:i:286 de:f:0.0066 rl:i:0 cm:i:18 nn:i:0 tp:A:P ms:i:286
ERR5069949.2161340 99 MT192765.1 17482 60 80M = 17482 82 AACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGT A/AA//EEAEA/E/AEEEE6EE/EEEA/6AEEEEEEEEE6EEEAEAEE//A/EEEEEE//E/E/A//E/E/<<EE</E/E s1:i:69 s2:i:0 RG:Z:1 NM:i:0 AS:i:160 de:f:0 rl:i:0 cm:i:6 nn:i:0 tp:A:P ms:i:160
ERR5069949.2161340 147 MT192765.1 17482 55 82M = 17482 -82 AACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCC A//E/<EAEA/EE/EEEA/<AE<AE/AEA/EEEAE/EEE//EEE6////EEEEAEAE///EE//</E/E</AE/6EAAA6AA s1:i:69 s2:i:0 RG:Z:1 NM:i:0 AS:i:164 de:f:0 rl:i:0 cm:i:3 nn:i:0 tp:A:P ms:i:164
ERR5069949.2216307 163 MT192765.1 17504 60 145M = 17601 244 GTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTGCTGAAATTGATGACACTGTGAGTGCTTTGGTTTATGATAATAAGCTTAAAGCACATAAAGACAAATCAGCTCAATGCTTTAAA A//AA6EEE/EEEEAEEEEE/EE/A/6E/EAE</EE/AEE/AEEAEAE/E//AA<6AA6<E/EE/EEE/AE/6/EEE<//E/E6A/<E/////EAE<E<</AAAEE//AAEE/6AAA6/AEA/AAEEAAAA////AA/6E<6AAE s1:i:218 s2:i:0 RG:Z:1 NM:i:1 AS:i:280 de:f:0.0069 rl:i:0 cm:i:14 nn:i:0 tp:A:P ms:i:280
ERR5069949.2176303 147 MT192765.1 17519 60 150M = 17442 -227 AACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGATAATAAGCTTAAAGCACATAAAGACAAATCAGCTCAATGCTTTAAAATGTTTTATAAGGGTGTTAT EAEAEEEAEAEAAAEEEEEEAAA<AAAA<A/EEAEE/A</EAAEEAAEEEEEEEAEEEEEEAEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEAEAEAEEAEAEEEEEAAEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEAAAAA s1:i:217 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:13 nn:i:0 tp:A:P ms:i:300
ERR5069949.2185111 83 MT192765.1 17537 60 150M = 17406 -281 GTTCCTCGGAACTTGTCGGCGTTGTCCTGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGATAATAAGCTTTAAGCACATAAAGACAAATCAGCTCAATGCTTTAAAATGTTTTATAAGGGTGTTATCACGCATGATGTTTCATC AEA/EE<EEA/E<A<<EA//6<6A/EEEEEEEEEAAAEE<A//A/AEEA/AEAEE/EEAEAEEEEEE//EA/AAEA/EEE</E/EAEE/<A<E/A/<AAE//AA<EEE/EEEE/<EEEA/EEE<<AEEEEEEAEEEAAAAAEAEE6AAAA s1:i:248 s2:i:0 RG:Z:1 NM:i:1 AS:i:290 de:f:0.0067 rl:i:0 cm:i:16 nn:i:0 tp:A:P ms:i:290
ERR5069949.2205229 147 MT192765.1 17585 60 28M1D121M = 17476 -259 GAGTGCTTTGGTTTATGATAATAAGCTTAAGCACATAAAGACAAATCAGCTCAATGCTTTAAAATGTTTTATAAGGGTGTTATCACGCATGATGTTTCATCTGCAATTAACAGGCCACAAATAGGCGTGGTAAGAGAATTCCTTACACG A<A<<EE/EEE/EEAEEAEA/AAAAEEEAEEA<EEEAA<//<E<<EEAEEE<E/EEE/EEEEEEEEEEEAEEEAE/E/E/EEEAEEEEEEEEAEEEAEEE/EEEEEEE/AEEEEEE<EEEEEEEEEE/AEEAEEEEEEEAEEEEAAAAA s1:i:252 s2:i:0 RG:Z:1 NM:i:1 AS:i:284 de:f:0.0067 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:284
ERR5069949.2216307 83 MT192765.1 17601 60 147M = 17504 -244 GATAATAAGCTTAAAGCACATAAAGACAAATCAGCTCAATGCTTTAAAATGTTTTATAAGGGTGTTATCACGCATGATGTTTCATCTGCAATTATCAGGCCACAAATAGGCGTGGTAAGAGAATTCCTTACACGTAACCCTGCTTGG AEA/AAAE<<A<6AEAAAA<//A6A6A/EEEAAA<A<<A/<<AA</<EEE<AEE<<EAE//AEAEEEEEEAE/AEAEEEEEE/EEAE</<<EAE/EEA/A<E6EE/E6<<EAE</EEEEEEEEEE/AEEE6EA/EEE/AAEA/EAAA s1:i:218 s2:i:0 RG:Z:1 NM:i:1 AS:i:284 de:f:0.0068 rl:i:0 cm:i:15 nn:i:0 tp:A:P ms:i:284
ERR5069949.2243023 163 MT192765.1 17713 60 151M = 17854 291 TGGTAAGAGAATTCCTTACACGTAACCCTGCTTGGAGAAAAGCTGTCTTTATTTCACCTTATAATTCACAGAATGCTGTAGCCTCAAAGATTTTGGGACTACCAACTCAAACTGTTGATTCATCACAGGGCTCAGAATATGACTATGTCAT AAAAAEEEEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEAEEEEEEEEEEEEEE/EEEEAAEEAEEA<EEEEEEEEEEEEEEAEEEEE<<AA6AAEEEAEE s1:i:273 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:20 nn:i:0 tp:A:P ms:i:302
ERR5069949.2243023 83 MT192765.1 17854 60 150M = 17713 -291 ACTATGTCATATTCACTCAAACCACTGAAACAGCTCACTCTTGTAATGTAAACAGATTTAATGTTGCTATTACCAGAGCAAAAGTAGGCATACTTTGCATAATGTCTGATAGAGACCTTTATGACAAGTTGCAATTTACAAGTCTTGAAA EE<EAEEAE<EA<E/EEAEAEEEE<EEEEAA<AEEEEEEEEEAAEAEEE<EEEEAEEEEEEEEEEEEEEEEEAEEEEEEAEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:273 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:20 nn:i:0 tp:A:P ms:i:300
ERR5069949.2270078 163 MT192765.1 17970 60 151M = 18103 284 CTTTATGACAAGTTGCAATTTACAAGTCTTGAAATTCCACGTAGGAATGTGGCAACTTTACAAGCTGAAAATGTAACAGGACTCTTTAAAGATTGTAGTAAGGTAATCACTGGGTTACATCCTACACAGGCACCTACACACCTCAGTGTTG AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEAEEEEEEEEEEEAEEAAEEEEAEEEEEAEEAEEEAAEAEEEEEAEAEEAEA<EAA s1:i:275 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:302
ERR5069949.2257580 99 MT192765.1 17980 60 151M = 18039 209 AGTTGCAATTTACAAGTCTTGAAATTCCACGTAGGAATGTGGCAACTTTACAAGCTGAAAATGTAACAGGACTCTTTAAAGATTGTAGTAAGGTAATCACTGGGTTACATCCTACACAGGCACCTACACACCTCAGTGTTGACACTAAATT AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEAEEEEEEEEEAEEEEEEAEEEEEEEEEEEEAEEEEEEEEEAEEEEEEAEE/EEAEA<EAEEEAEEEEEEEEE<EEAAAEAEEE<EA s1:i:196 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:18 nn:i:0 tp:A:P ms:i:302
ERR5069949.2257580 147 MT192765.1 18039 60 150M = 17980 -209 AATGTAACAGGACTCTTTAAAGATTGTAGTAAGGTAATCACTGGGTTACATCCTACACAGGCACCTACACACCTCAGTGTTGACACTAAATTCAAAACTGAAGGTTTATGTGTTGACATACCTGGCATACCTAAGGACATGACCTATAGA EEEEEEAEEAAEEEEAAAAEEEEEEAEEEEAEAEEEAEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:196 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:11 nn:i:0 tp:A:P ms:i:300
ERR5069949.2270078 83 MT192765.1 18103 60 151M = 17970 -284 CTACACACCTCAGTGTTGACACTAAATTCAAAACTGAAGGTTTATGTGTTGACATACCTGGCATACCTAAGGACATGACCTATAGAAGACTCATCTCTATGATGGGTTTTAAAATGAATTATCAAGTTAATGGTTACCCTAACATGTTTAT AEEEEEEAEEA//EEEEAEEEEEEEEEA<EEA6<A<A<AEEE<AEE<</EEEEEAEEEEE<EEEEEEAEEE/EEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:275 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:23 nn:i:0 tp:A:P ms:i:302
ERR5069949.2328704 163 MT192765.1 18286 60 150M = 18412 276 CATGGATTGGCTTCGATGTCGAGGGGTGTCATGCTACTAGAGAAGCTGTTGGTACCAATTTACCTTTACAGCTAGGTTTTTCTACAGGTGTTAACCTAGTTGCTGTACCTACAGGTTATGTTGATACACCTAATAATACAGATTTTTCCA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEAEEEEEEEEEEEEAEEEEEEAEEEEEEEEEEEAEEEAEAEEEA<AEEEEEEEE/EEEEEEEAEEEEEEE/EEEEAEE s1:i:264 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:18 nn:i:0 tp:A:P ms:i:300
ERR5069949.2342766 99 MT192765.1 18397 60 151M = 18469 222 CAGGTTATGTTGATACACCTAATAATACAGATTTTTCCAGAGTTAGTGCTAAACCACCGCCTGGAGATCAATTTAAACACCTCATACCACTTATGTACAAAGGACTTCCTTGGAATGTAGTGCGTATAAAGATTGTACAAATGTTAAGTGA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEAEEEEEEEAEAEAAAAEAEEEAEEAEEE/EEEE<AAEEAEA s1:i:215 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:302
ERR5069949.2328704 83 MT192765.1 18412 60 150M = 18286 -276 CACCTAATAATACAGATTTTTCCAGAGTTAGTGCTAAACCACCGCCTGGAGATCAATTTAAACACCTCATACCACTTATGTACAAAGGACTTCCTTGGAATGTAGTGCGTATAAAGATTGTACAAATGTTAAGTGACACACTTAAAAATC AEAAEAEEEEEEAAEEEEEEEAEE/EAAEE</EAAAEAEEAEAEEEEEE/AEA<EEEEEAEAAEEEEEAAEEEEEEE/E/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:264 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:20 nn:i:0 tp:A:P ms:i:300
ERR5069949.2361683 99 MT192765.1 18426 60 149M = 18513 235 GATTTTTCCAGAGTTAGTGCTAAACCACCGCCTGGAGATCAATTTAAACACCTCATACCACTTATGTACAAAGGACTTCCTTGGAATGTAGTGCGTATAAAGATTGTACAAATGTTAAGTGACACACTTAAAAATCTCTCTGACAGAGT AAAAA/AA/EAEEAAEEEEAEE/EAEAAA<EEAAEEEEEE/EEEEEEEEEAAEEE/AEEE/EEEA<EEEAEEEEE<AAA<EEEEEEEEEAAEEA<AEEEEEEEEE<EEE/<AEEEEEAEEA<//A<EEAAEE6EAEEAAAEEAA6AEEA s1:i:227 s2:i:0 RG:Z:1 NM:i:0 AS:i:298 de:f:0 rl:i:0 cm:i:21 nn:i:0 tp:A:P ms:i:298
ERR5069949.2342766 147 MT192765.1 18469 60 150M = 18397 -222 TTAAACACCTCATACCACTTATGTACAAAGGACTTCCTTGGAATGTAGTGCGTATAAAGATTGTACAAATGTTAAGTGACACACTTAAAAATCTCTCTGACAGAGTCGTATTTGTCTTATGGGCACATGGCTTTGAGTTGACATCTATGA EAEAEAEEEEA<<AAAAEEEAEEEEEAEEEEEEEEEEEAAAEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:215 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:16 nn:i:0 tp:A:P ms:i:300
ERR5069949.2361683 147 MT192765.1 18513 60 148M = 18426 -235 GTAGTGCGTATAAAGATTGTACAAATGTTAAGTGACACACTTAAAAATCTCTCTGACAGAGTCGTATTTGTCTTATGGGCACATGGCTTTGAGTTGACATCTATGAAGTATTTTGTGAAAATAGGACCTGAGCGCACCTGTTGTCTAT A<6EA</AEEAA/<AEE<EEEEAAAA//E<A/EAEE6EAA/AA/E/</EAEEEEEE/AEEEE/EAE/6EEE/EE<EA6<</E<E/AE/AAEE/EEE<EEEE</E/EEEEEEEEEEE<EAEEEEEEA/EEEEEEAEE/EEAEEAAAAAA s1:i:227 s2:i:0 RG:Z:1 NM:i:0 AS:i:296 de:f:0 rl:i:0 cm:i:17 nn:i:0 tp:A:P ms:i:296
ERR5069949.2415814 99 MT192765.1 18598 60 150M = 18765 318 GCTTTGAGTTGACATCTATGAAGTATTTTGTGAAAATAGGACCTGAGCGCACCTGTTGTCTATGTGATAGACGTGCCACATGCTTTTCCACTGCTTCAGACACTTATGCCTGTTGGCATCATTCTATTGGATTTGATTACGTCTATAATC AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEAEEEEEEAEEEEEEEAEEEAEEEEEAEEEEEAEAAAE<AEA s1:i:258 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:21 nn:i:0 tp:A:P ms:i:300
ERR5069949.2385514 99 MT192765.1 18603 60 150M = 18685 232 GAGTTGACATCTATGAAGTATTTTGTGAAAATAGGACCTGAGCGCACCTGTTGTCTATGTGATAGACGTGCCACATGCTTTTCCACTGCTTCAGACACTTATGCCTGTTGGCATCATTCTATTGGATTTGATTACGTCTATAATCCGTTT A/AAAE6EEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EE<EEEEE/A/AE6EEA/E/EEEEEA/AEEEEEEE<EEEAAEEEEEEE/EAEEEEEE/EEAAAEEE/<<AEEEEEEAEAEA<E/AAAAAAAA/<EE/EEAEEAE s1:i:199 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:22 nn:i:0 tp:A:P ms:i:300
ERR5069949.2417063 99 MT192765.1 18649 60 150M = 18766 267 CCTGTTGTCTATGTGATAGACGTGCCACATGCTTTTCCACTGCTTCAGACACTTATGCCTGTTGGCATCATTCTATTGGATTTGATTACGTCTATAATCCGTTTATGATTGATGTTCAACAATGGGGTTTTACAGGTAACCTACAAAGCA AAAAAEEEAEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEAEEEE/EEEEAEEEEE<EEEEAEE<AAEAEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEAEAEEE<AEE<EAE/EEA<EEEEAEEEAEEEEEEEA/EEEAE/AEEEA s1:i:245 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:300
ERR5069949.2388984 99 MT192765.1 18654 60 150M = 18694 189 TGTCTATGTGATAGACGTGCCACATGCTTTTCCACTGCTTCAGACACTTATGCCTGTTGGCATCATTCTATTGGATTTGATTACGTCTATAATCCGTTTATGATTGATGTTCAACAATGGGGTTTTACAGGTAACCTACAAAGCAACCAT AAAAAEEEEEEEEE/EEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEAAEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEAEEEEAE/EAEEEEEEEEEEAEEEE/EEEEEEEEAEEAEEAEEEEEAEEEEAEEEE<A/EA<E s1:i:161 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:17 nn:i:0 tp:A:P ms:i:300
ERR5069949.2385514 147 MT192765.1 18685 60 150M = 18603 -232 CCACTGCTTCAGACACTTATGCCTGTTGGCATCATTCTATTGGATTTGATTACGTCTATAATCCGTTTATGATTGATGTTCAACAATGGGGTTTTACAGGTAACCTACAAAGCAACCATGATCTGTATTGTCAAGTCCATGGTAATGCAC AA<EAAE<AA<EEAAEE/AAEEAAEE<<AAEEEAEAEAEEEAEEEEAEEEEAAEEEEE/EAEAEEEEAAEEEEEEEEEEAAEEEEAAEEEEEEEEEAEEEEEEEAEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEEEEEEEEAAA/A s1:i:199 s2:i:0 RG:Z:1 NM:i:1 AS:i:290 de:f:0.0067 rl:i:0 cm:i:9 nn:i:0 tp:A:P ms:i:290
ERR5069949.2388984 147 MT192765.1 18694 60 149M = 18654 -189 CAGACACTTATGCCTGTTGGCATCATTCTATTGGATTTGATTACGTCTATAATCCGTTTATGATTGATGTTCAACAATGGGGTTTTACAGGTAACCTACAAAGCAACCATGATCTGTATTGTCAAGTCCATGGTAATGCACATGTAGCT EAAAA6EEE<EEAEEEAAAAEE/AE<AAAAEAEEEAAEEEEEAEEEEEEEEAEAA<<EEEEEEAAAEEEEAEEEA<EE<EE</EEEEEAEEEEEEEEEEEEEEEAEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:161 s2:i:0 RG:Z:1 NM:i:1 AS:i:288 de:f:0.0067 rl:i:0 cm:i:5 nn:i:0 tp:A:P ms:i:288
ERR5069949.2431709 99 MT192765.1 18749 60 72M1D78M = 18777 180 GTTTATGATTGATGTTCAACAATGGGGTTTTACAGGTAACCTACAAAGCAACCATGATCTGTATTGTCAAGTCATGGTAATGCACATGTAGCTAGTTGTGATGCAATCATGACTAGGTGTCTAGCTGTCCACGAGTGCTTTGTTAAGCGT AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAAAEAEAEE<AEEEEAEEAA<AEA s1:i:148 s2:i:0 RG:Z:1 NM:i:2 AS:i:276 de:f:0.0132 rl:i:0 cm:i:15 nn:i:0 tp:A:P ms:i:276
ERR5069949.2415814 147 MT192765.1 18765 60 151M = 18598 -318 CAACAATGGGGTTTTACAGGTAACCTACAAAGCAACCATGATCTGTATTGTCAAGTCCATGGTAATGCACATGTAGCTAGTTGTGATGCAATCATGACTAGGTGTCTAGCTGTCCACGAGTGCTTTGTTAAGCGTGTTGACTGGACTATTG AEEEA<EEEEE/EEEEAEEEEEEEEEEEEAEAEAAEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:258 s2:i:0 RG:Z:1 NM:i:1 AS:i:292 de:f:0.0066 rl:i:0 cm:i:16 nn:i:0 tp:A:P ms:i:292
ERR5069949.2417063 147 MT192765.1 18766 60 150M = 18649 -267 AACAATGGGGTTTTACAGGTAACCTACAAAGCAACCATGATCCGTATTGTCAAGTCCATGGTAATGCACATGTAGCTAGTTGTGATGCAATCATGACTAGGTGTCTAGCTGTCCACGAGTGCTTTGTTAAGCGTGTTGACTGGACTATTG AEEA<EEEEE//<EAEAEE/EAEAE/E<A6AAAAEEE/EAEE/EEAEAAEEEEEAEEEEEAEEEEEEEAEEEEEEAEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEE6E/EEEEEEEEEAAAAA s1:i:245 s2:i:0 RG:Z:1 NM:i:2 AS:i:280 de:f:0.0133 rl:i:0 cm:i:16 nn:i:0 tp:A:P ms:i:280
ERR5069949.2431709 147 MT192765.1 18777 60 44M1D107M = 18749 -180 TTTACAGGTAACCTACAAAGCAACCATGATCTGTATTGTCAAGTCATGGTAATGCACATGTAGCTAGTTGTGATGCAATCATGACTAGGTGTCTAGCTGTCCACGAGTGCTTTGTTAAGCGTGTTGACTGGACTATTGAATATCCTATAAT AAAAAAAE<AAAAEEEEAEAAAEEAEEEEEEEEEEEEEEEEEEAEEEAEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEAEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:148 s2:i:0 RG:Z:1 NM:i:2 AS:i:278 de:f:0.0132 rl:i:0 cm:i:5 nn:i:0 tp:A:P ms:i:278
ERR5069949.2521353 99 MT192765.1 19597 60 150M = 19698 251 CTTTTACAAGACTTCAGAGTTTAGAAATTGTGGCTTATAATGTTGTAATTAAGGGACACTTTGATGGACAACAGGGTGAAGTACCAGTTTCTATCATTAATAACTCTGTTTACACAAAAGTTGATGGTGTTGATGTAGAATTGTTTGAAA AAA/AE/6E6EEEEAEE/EE/EEE/EE/EA/EAEA//EEEEE6EAEAE/EEEEEE/EAE////EEA/EEEEEEEEEEEEEE///A/EEAEEEEEEEE<AEAEEE/AE/E<E/EEEEEA/E///AE/66AEEAEEE<E//E/EA/A<6AEE s1:i:175 s2:i:0 RG:Z:1 NM:i:4 AS:i:260 de:f:0.0267 rl:i:0 cm:i:10 nn:i:0 tp:A:P ms:i:260
ERR5069949.2521353 147 MT192765.1 19698 60 150M = 19597 -251 ATCACTGTTTTCACAAAAGTTGATGGTGTTGATGTAGAATTGTTTGAAAATAAAACAACATTACCTGTTAATGTAGCTTTTGTGCTTTGGGCTAAGCGCAACATTAAACCAGTACCAGAGGTGAAAATACTCAATAATTTGGGTGTGGAC A//A</</EE/A<AEEA//E<EEE/E<A/<<A///<6EAEEEEE/AAA</A//<<EA/EEA//</AA6EEAE</EEA//AEE//</AEEAE/EEEA/A/EEEE//E/EAA/EEE/AEE<EEE<EE/EAEEEEE6EEEE/EEEEEEAAAAA s1:i:175 s2:i:0 RG:Z:1 NM:i:4 AS:i:266 de:f:0.0267 rl:i:0 cm:i:14 nn:i:0 tp:A:P ms:i:266
ERR5069949.2605155 99 MT192765.1 21717 60 146M = 21726 159 GTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAG AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEE/EEEEEEEEEEEEEE<EEAEEEAEAEAEEEEEEEEAAEEEEE<EEAEAEEEAA<E<EAAE</E/AA s1:i:148 s2:i:0 RG:Z:1 NM:i:0 AS:i:292 de:f:0 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:292
ERR5069949.2605155 147 MT192765.1 21726 60 150M = 21717 -159 TTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGG A/EEEE/EEAEAEEEEEAEEAEEEAAAEEEAEEEEEEAEE/EEEAEAEAEEEEEEAEEAEEEEEAEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:148 s2:i:30 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:6 nn:i:0 tp:A:P ms:i:300
ERR5069949.2650879 163 MT192765.1 22659 60 151M = 22710 201 ATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATT AAAAAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEAEE<EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEAEEEEEEEEEEEEAEEE<A<EEEEAAAAEEEEEEEEEEEE s1:i:192 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:16 nn:i:0 tp:A:P ms:i:302
ERR5069949.2650879 83 MT192765.1 22710 60 150M = 22659 -201 TAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGC EAEEEAEE<EEE/EEEEEEAEEEEEEEEEEEA<AAEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEAEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:192 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:13 nn:i:0 tp:A:P ms:i:300
ERR5069949.2668880 99 MT192765.1 23125 60 147M = 23146 171 GTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACT AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAE<EEAEEEEA<EAA<AAAEEEEEE<AEA<EAAEE s1:i:158 s2:i:0 RG:Z:1 NM:i:0 AS:i:294 de:f:0 rl:i:0 cm:i:20 nn:i:0 tp:A:P ms:i:294
ERR5069949.2674295 163 MT192765.1 23134 60 150M = 23204 218 CCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTC AAAAAEEEEEEEEEEAEEEEEEEEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEE<EEEEEEAEEE/EEEEEEE<EEAEEAEEEEEAEEAEE<EEAEE<E/AAAAAAE<AEAAAEEEEAEEAEAEE/EEAAAEE s1:i:209 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:20 nn:i:0 tp:A:P ms:i:300
ERR5069949.2668880 147 MT192765.1 23146 60 150M = 23125 -171 ACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAG AE/EAEAEAEEEEEEA<A6EEEEEE<EAAEEEAEEEEEEEAEEEEEAEEEEEEEEEEEEAEEAEEEEEEEEEAEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:158 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:6 nn:i:0 tp:A:P ms:i:300
ERR5069949.2674295 83 MT192765.1 23204 60 148M = 23134 -218 GTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAAC EEEAEEEEEEEEEEEE<EEEEAA<EEEAA<AAEEE/EAAE<AAAEA<EEEEEEE<EEEEEE<EEEEEEEEEEEEEEAEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:209 s2:i:0 RG:Z:1 NM:i:0 AS:i:296 de:f:0 rl:i:0 cm:i:14 nn:i:0 tp:A:P ms:i:296
ERR5069949.2730382 163 MT192765.1 23528 60 142M = 23528 142 ACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGT AAAAAEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAE<EE/EEEEEEE/EEAEEEEEEEEEEEEEEEEEEAEEEEA<AEA<<EA<A<AEEEEEA<EAE<66A/AEEEEEEEAE<AAEA s1:i:143 s2:i:0 RG:Z:1 NM:i:0 AS:i:284 de:f:0 rl:i:0 cm:i:20 nn:i:0 tp:A:P ms:i:284
ERR5069949.2730382 83 MT192765.1 23528 48 142M = 23528 -142 ACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGT A<AA<A<EEEAAA/A<AEAEAEA<EAA<<AEA<EEEAAAEE<EEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEE<EEEEEAEEAEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEAEEEEEEE/EAAAAA s1:i:48 s2:i:143 RG:Z:1 NM:i:0 AS:i:284 de:f:0 rl:i:0 cm:i:9 nn:i:0 tp:A:P ms:i:284
ERR5069949.2734474 81 MT192765.1 23547 1 149M = 23548 -148 ACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCA AA/EEA/EAAAA<AAEEEEAAEEEEEEE<A/EEAEE<AEEEEEEEEAEEEEAEAAEAAEE/EEAAEEE/AEA/EEE/E/EEEEEEEEE/EEEEEEEEAEE/EEEE/EEEEEAEEEEEEEEEEEEEEEEE//EEEEAEEEEEEEAAA/AA s1:i:58 s2:i:136 RG:Z:1 NM:i:0 AS:i:298 de:f:0 rl:i:0 cm:i:11 nn:i:0 tp:A:P ms:i:298
ERR5069949.2734474 161 MT192765.1 23548 60 148M = 23547 148 CCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCA AAAA/EEEEEEEEE/E/EE6EEEEAEEEEEEAEEEEE/EEEEEEEEEEEAE/EAEE/EEEEEAE/EE<EAEEEEEEA/E<EEEEAE/EA<EEEEAEE/E/EE<EEEEE</EE/E//<<<AA6A<A<A/<AE/AE/EEEA6<A6A/</A s1:i:136 s2:i:0 RG:Z:1 NM:i:0 AS:i:296 de:f:0 rl:i:0 cm:i:20 nn:i:0 tp:A:P ms:i:296
ERR5069949.2734873 163 MT192765.1 23550 60 98M = 23550 98 CATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGT AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE s1:i:92 s2:i:0 RG:Z:1 NM:i:0 AS:i:196 de:f:0 rl:i:0 cm:i:9 nn:i:0 tp:A:P ms:i:196
ERR5069949.2734873 83 MT192765.1 23550 48 98M = 23550 -98 CATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGT EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEE/EEEEEEEEEEEEEEEEEEEEAAAAA s1:i:25 s2:i:92 RG:Z:1 NM:i:0 AS:i:196 de:f:0 rl:i:0 cm:i:4 nn:i:0 tp:A:P ms:i:196
ERR5069949.2772897 163 MT192765.1 23809 60 150M = 23876 219 CTTTCGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAAT AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEA<EAEEEE<EEEEAEEAAEEEEEEEEEEE s1:i:199 s2:i:0 RG:Z:1 NM:i:1 AS:i:290 de:f:0.0067 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:290
ERR5069949.2772897 83 MT192765.1 23876 60 144M1D7M = 23809 -219 AAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTCAAC AEEEEEE<AAEEAAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEAEEEEEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEEEEEAAAAA s1:i:199 s2:i:0 RG:Z:1 NM:i:1 AS:i:294 de:f:0.0066 rl:i:0 cm:i:13 nn:i:0 tp:A:P ms:i:288
ERR5069949.2787556 99 MT192765.1 24088 60 106M = 24088 106 GCTGCTAGAGACCTCGTTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGG AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAE s1:i:78 s2:i:0 RG:Z:1 NM:i:1 AS:i:202 de:f:0.0094 rl:i:0 cm:i:10 nn:i:0 tp:A:P ms:i:202
ERR5069949.2787556 147 MT192765.1 24088 50 106M = 24088 -106 GCTGCTAGAGACCTCGTTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGG EEAAEEEEEEEEA<EEEE<AAA<EEEEEAEEEEEEAEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:78 s2:i:0 RG:Z:1 NM:i:1 AS:i:202 de:f:0.0094 rl:i:0 cm:i:1 nn:i:0 tp:A:P ms:i:202
ERR5069949.2832676 99 MT192765.1 24409 60 139M = 24409 139 GTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCA AAAA6EEEEEEEEEEEEEEEEAEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<E/EAEEAEEEAEEAEEEEEAEEEEEEEEEEEEEEAEEAEEEEEAAEEEEEEA<AEEEAAAAEEEEE<EEAAAEEAEEAAEEEEA s1:i:132 s2:i:0 RG:Z:1 NM:i:0 AS:i:278 de:f:0 rl:i:0 cm:i:18 nn:i:0 tp:A:P ms:i:278
ERR5069949.2832676 147 MT192765.1 24409 48 139M = 24409 -139 GTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCA A<EEEE</EAEA6EEA</AEEEEAEEEAAE/EEAEE<A<AAAEEEEAAEEE/EEEEEEEEAEEAEEAA<EEEEEEEA<EEEAEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEAA6AA s1:i:37 s2:i:132 RG:Z:1 NM:i:0 AS:i:278 de:f:0 rl:i:0 cm:i:5 nn:i:0 tp:A:P ms:i:278
ERR5069949.2888794 163 MT192765.1 24758 60 150M = 24853 246 TCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAG AAAAAEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEAEE<<<6AEE</AAAEEEEEEEAA<EEAAEA s1:i:231 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:25 nn:i:0 tp:A:P ms:i:300
ERR5069949.2888794 83 MT192765.1 24853 60 151M = 24758 -246 ACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGG AAEAAAEEEEEEEEEEEEEEEAAAEEEEAAEEAAAAEEEEAEEEEEEEEE/EEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:231 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:16 nn:i:0 tp:A:P ms:i:302
ERR5069949.2953930 99 MT192765.1 25345 60 151M = 25465 268 GTGCTCAAAGGAGTCAAATTACATTACACATAAACGAACTTATGGATTTGTTTATGAGAATCTTCACAATTGGAACTGTAACTTTGAAGCAAGGTGAAATCAAGGATGCTACTCCTTCAGATTTTGTTCGCGCTACTGCAACGATACCGAT AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEAEEAEEEEEEEEEEEEEEEEEEEEE/EEEEEE<AA/EA<A<AAAA<AAEAAEAEE/E<<E<EAAEA s1:i:256 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:22 nn:i:0 tp:A:P ms:i:302
ERR5069949.2972968 163 MT192765.1 25426 60 147M = 25519 234 CTTTGAAGCAAGGTGAAATCAAGGATGCTACTCCTTCAGATTTTCTTCGCGCTACTGCAACGATACCGATACAAGCCTCACTCCCTTACGGATGGCTTATTGTAGGCGTTGCACTTCTAGCTGTTTTTCAGAGCGCTTCCAAAAACA AAAAAEEEEEEA/E/EEEEEEE/EEEEEEEAEEEEE/EEE/E/E/<66<6/EEEE///EEE<<E/<AEAEEEE/EEEEE6A/EEA/E//AE<EEE</6E/E/E/A<AAEA/A//AE<A/E<EE//6A/A<AAA6<E<<A66</E/AA s1:i:188 s2:i:0 RG:Z:1 NM:i:5 AS:i:248 de:f:0.034 rl:i:0 cm:i:8 nn:i:0 tp:A:P ms:i:248
ERR5069949.2953930 147 MT192765.1 25465 60 148M = 25345 -268 ATTTTGTTCGCGCTACTGCAACGATACCGATACAAGCCTCACTCCCTTTCGGATGGCTTATTGTTGGCGTTGCACTTCTTGCTGTTTTTCAGAGCGCTTCCAAAATCATAACCCTCAAAAAGAGATGGCAACTAGCACTCTCCAAGGG EEEEEE/EEEEEEEEEEAAEEEEAAAAAEEEEEE/EEEEEEAAEEEEAEEEEEEEAEEEEEEEEEAEEEE/EEAEEEEEEEEEEAAEEEEEEAEEEE/EEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:256 s2:i:0 RG:Z:1 NM:i:0 AS:i:296 de:f:0 rl:i:0 cm:i:15 nn:i:0 tp:A:P ms:i:296
ERR5069949.2972968 83 MT192765.1 25519 60 141M = 25426 -234 GTCTTATTGTTGGCGTTGCACTTCTTGCTGTTTTTCAGAGCGATTCCAAAATCATAACCCTCAAAAAGAGATGGCAACTAGCACTCTCCAAGGGTGTTCACTTTGTTTGCAACTTGCTGTTGTTGTTTGTAACAGTTTACT 6//A//A/EE/EE/A//6/E/EEEEEE66AAE//EEAEE/AE//EEEE//EA/A///<E/E/E/EE<E<E/EE/<E</EEEEAEEEEEEEAE<A/AEE//EEEEE/E//EEEEEEEE6E/EA/EA6EEEE//EEEEAAAAA s1:i:188 s2:i:0 RG:Z:1 NM:i:2 AS:i:268 de:f:0.0142 rl:i:0 cm:i:14 nn:i:0 tp:A:P ms:i:268
ERR5069949.3017828 99 MT192765.1 26176 60 107M = 26177 107 ATGATGAACCGACGACGACTACTAGCGTGCCTTTGTAAGCACAAGCTGATGAGTACGAACTTATGTACTCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAAT AAAAAE6EEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEAEEEEE s1:i:96 s2:i:0 RG:Z:1 NM:i:0 AS:i:214 de:f:0 rl:i:0 cm:i:11 nn:i:0 tp:A:P ms:i:214
ERR5069949.3017828 147 MT192765.1 26177 48 106M = 26176 -107 TGATGAACCGACGACGACTACTAGCGTGCCTTTGTAAGCACAAGCTGATGAGTACGAACTTATGTACTCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAAT A/EAAEEEAEEAE<E</EEEEEEEEEAE<EEEEEEAE<EE/E<EEEEEEEEEEEE<EEAEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEAAAAA s1:i:37 s2:i:96 RG:Z:1 NM:i:0 AS:i:212 de:f:0 rl:i:0 cm:i:3 nn:i:0 tp:A:P ms:i:212
ERR5069949.3022231 99 MT192765.1 26228 60 147M = 26228 147 GTACGAACTTATGTACTCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTATTCTTGCTAGTTACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATAT AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEEEEEEAAAAEEEEEEEEAEEE s1:i:139 s2:i:0 RG:Z:1 NM:i:0 AS:i:294 de:f:0 rl:i:0 cm:i:21 nn:i:0 tp:A:P ms:i:294
ERR5069949.3022231 147 MT192765.1 26228 48 147M = 26228 -147 GTACGAACTTATGTACTCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTATTCTTGCTAGTTACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATAT EAAAEEEEEEAEEEEE<EEEEAE<EEAAEAAEEEEEEEEEEEEEEEEAEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:34 s2:i:139 RG:Z:1 NM:i:0 AS:i:294 de:f:0 rl:i:0 cm:i:6 nn:i:0 tp:A:P ms:i:294
ERR5069949.3057020 99 MT192765.1 26621 60 86M9S = 26621 86 CAATTTGCCTATGCCAACAGGAATAGGTTTTTGTATATAATTAAGTTAATTTTCCTCTGGCTGTTATGGCCAGTAACTTTAGCTTGGTTGTACGC AAAAAEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAE s1:i:71 s2:i:0 RG:Z:1 NM:i:0 AS:i:172 de:f:0 rl:i:0 cm:i:8 nn:i:0 tp:A:P ms:i:172
ERR5069949.3057020 147 MT192765.1 26621 51 86M9S = 26621 -86 CAATTTGCCTATGCCAACAGGAATAGGTTTTTGTATATAATTAAGTTAATTTTCCTCTGGCTGTTATGGCCAGTAACTTTAGCTTGGTTGTACGC EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:71 s2:i:33 RG:Z:1 NM:i:0 AS:i:172 de:f:0 rl:i:0 cm:i:2 nn:i:0 tp:A:P ms:i:172
ERR5069949.3122970 163 MT192765.1 26996 60 126M = 26996 127 ATCAAGGACCTGCCTAAAGAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACAAATTGGGAGCTTCGCAGCGTGTAGCAGGTGACTCAGGTTTTGCTGCATACAGTCGCTACAGGATTGGC AAAAAEE6EEEEEEEAEEEEEEEEEEEAEEEEEEEEEEEEEE/EEEEEAE<EEAEAEEEEEEEEEAAEEEEAEAEEE/AEEE<A<A/AAAAAE/E<A66AEEEEEEEEEEEAE<</6AA<A/6/EA s1:i:119 s2:i:0 RG:Z:1 NM:i:0 AS:i:252 de:f:0 rl:i:0 cm:i:17 nn:i:0 tp:A:P ms:i:252
ERR5069949.3122970 83 MT192765.1 26996 48 127M = 26996 -127 ATCAAGGACCTGCCTAAAGAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACAAATTGGGAGCTTCGCAGCGTGTAGCAGGTGACTCAGGTTTTGCTGCATACAGTCGCTACAGGATTGGCA A//6AAAEAEEA/AAEEEEEEAAE/EEE//A<EEEEEEEEEAEEE/EEAAEEAEEEE/<EEAEEEEEAEEAEEAEEEEEEEEA<EAEEAEAEAEEA6EEEEEEEEEEEEEAEEEAEEEEEEEA/AAA s1:i:52 s2:i:119 RG:Z:1 NM:i:0 AS:i:254 de:f:0 rl:i:0 cm:i:9 nn:i:0 tp:A:P ms:i:254
ERR5069949.3184655 163 MT192765.1 27311 60 150M = 27352 191 TTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGAGCTTTATCACTACCAAGAGTGTGTTAG AAAAAEEEEEEEEEEEEEEEEAEEAEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEE<EEEEE/EEEEEAEAEEEEE/EEEAEEE<EEEEEE<EEAAEEAEEEEEAAAEEE/E<AAEEAAAE6A/A<<A<AAAEE/AA6AE/A s1:i:185 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:21 nn:i:0 tp:A:P ms:i:300
ERR5069949.3184655 83 MT192765.1 27352 60 150M = 27311 -191 ATGAAGAGCAACCAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGAGCTTTATCACTACCAAGAGTGTGTTAGAGGTACAACAGTACTTTTAAAAGAACCTTGCTCTTCTGGAA AAAE6E</EA6<A6/A/E6A</EEE<EEA///E/A<<</AEEEE<E<EEEEEEEEEE/E<E/EE/A<AEEAEAE/EEEEEEEAEEEEEEEEEEEEE/AEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEAAAAA s1:i:185 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:8 nn:i:0 tp:A:P ms:i:300
ERR5069949.3249622 163 MT192765.1 28218 38 116M = 28372 231 ATCATGACGTTCGTGTTGTTTTAGATTTCATCGAAACGAACAAACAAAAATGTCTGATAATGGACCCCAAAATCATCGAAATGCACCCCGCATTACGGTTGGTGGACCCTCCGATT AAA/AE//EEE/EE6AE/A</EE//6AE6EE//EE/AE//A/EE//EEEE<EAA/EE//<E/A/E/EE//E/A/E/E//EE/<A/A<EE/A//</EE//E/E//A/EEE///A//6 s1:i:97 s2:i:0 RG:Z:1 NM:i:5 AS:i:182 de:f:0.0431 rl:i:0 cm:i:3 nn:i:0 tp:A:P ms:i:182
ERR5069949.3249622 83 MT192765.1 28372 37 77M = 28218 -231 CGATAAAAACAAGGTCGGCCCCAAGGTTTACCCATTAATACTGCGTCTTGGTTCACCGCTCTCACTCAACATGGCAA E/E///<E<<////AE/EEA/EEEEEE/EEEEE//A//E/EEEEEEEE/EEE/EE/EAEEAEEEAEE/AE/EAAAAA s1:i:97 s2:i:0 RG:Z:1 NM:i:3 AS:i:124 de:f:0.039 rl:i:0 cm:i:3 nn:i:0 tp:A:P ms:i:124
ERR5069949.3273002 163 MT192765.1 28443 60 150M = 28544 249 TGGCAAGGAAGACCTTAAATTCCCTCGAGGACAAGGCGTTCCAATTAACACCAATAGCAGTCCAGATGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGGTGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTA AAAAAEEEEEEEEEEEEEEEEEEAEEAEEEEEEEAEEE/EEA/EEEEEE6EEEAEEEEEEEEEAEEEEAEEEEE<EEEE<EEE/EE//AE/EEAEAEAE/EAAEEA6AEEE/<E<</EEE/E</AEA//A/EA6<AAEEEA/AEE6AE/E s1:i:235 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:300
ERR5069949.3277445 99 MT192765.1 28509 60 151M = 28574 166 TGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGGTGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTATTTCTACTACCTAGGAACTGGGCCAGAAGCTGGACTTCCCTATGGTGCTAACAAAGACGGCATCATA AA/AAEEEEEEEEEEEEEEEEEEEAEEEEEEEEAEEEEAEEEEEEEEEEEAEEEEEEEEEEEEEE/AEEEAEEEAAEEAEEE<E/EEEEEEEEAEEEEA/EEEEEEEAAA//EEEEEAEA<AEEAAEAEAEAEAEEEEAEEEEEEA/EEAA s1:i:154 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:21 nn:i:0 tp:A:P ms:i:302
ERR5069949.3273002 83 MT192765.1 28544 60 148M = 28443 -249 GAATGGGTGGTGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTATTTCTACTACCTCGGAACTGGGCCAGAAGCTGGACTTCCCTATGGTGCTAACAAAGACGGCATCATATGGGTTGCAACTGAGGGAGCCTTGAATACACC AE/A//A/E</EE/AEAE<EEEA//A6E6/E/AA<EE<<<E/AEAAAEE<//EAEEE<EA</E/E/A/EEEE</EEAEA/EAEEE<EEEEEEEEEEEEAEAEEEAEEEEEEEEEAE/EEEE/EEEEEEEEEEEEEEEEEEEEAAAAAA s1:i:235 s2:i:0 RG:Z:1 NM:i:3 AS:i:274 de:f:0.0203 rl:i:0 cm:i:17 nn:i:0 tp:A:P ms:i:274
ERR5069949.3277445 147 MT192765.1 28574 57 101M = 28509 -166 ATCTCAGTCCAAGATGGTATTTCTACTACCTAGGAACGGGGCCAGAAGCGGGACTTCCCTATGGTGCTAACAAAGACGGCATCATATGGGTTGCAACTGAG </</A///EA<//</<AE/EA/AE<E//</E/A/<///EE/E///E/E//E/E/A/EAAE<EEA/A//EAEE6//EEEEEEEEEEEEEEE6EEEEEAAAAA s1:i:154 s2:i:0 RG:Z:1 NM:i:2 AS:i:182 de:f:0.0198 rl:i:0 cm:i:3 nn:i:0 tp:A:P ms:i:182
ERR5069949.3338256 163 MT192765.1 29431 60 150M = 29452 172 CAGCAAACTGTGACTCTTCTTCCTGCTGCAGATTTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTCAACTCAGGCCTAAACTCATGCAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGCTTTTCCG AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEAEEEEEEEEAAAAAEA<AAAEA<AA s1:i:163 s2:i:0 RG:Z:1 NM:i:0 AS:i:300 de:f:0 rl:i:0 cm:i:25 nn:i:0 tp:A:P ms:i:300
ERR5069949.3338256 83 MT192765.1 29452 60 151M = 29431 -172 CCTGCTGCAGATTTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTCAACTCAGGCCTAAACTCATGCAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGCTTTTCCGTTTACGATATATAGTCTACTCT AEEEEEEEEEEEA<AEEAEEEEEEAA<EEEEEEAEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEAAE<EEEEEAEEEEEEEEEEAEEA/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA s1:i:163 s2:i:0 RG:Z:1 NM:i:0 AS:i:302 de:f:0 rl:i:0 cm:i:5 nn:i:0 tp:A:P ms:i:302

9
target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml
View File

@@ -234,15 +234,16 @@ build_info:
engine: "docker|native"
output: "target/executable/agat/agat_convert_bed2gff"
executable: "target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff"
viash_version: "0.9.0-RC7"
git_commit: "90735159b7bafa4aa8643eb132534d078ea299cf"
git_remote: "https://x-access-token:ghs_f5MGzzY8TnzQWjJSiZ9z9t1HGTq1aI25g7mw@github.com/viash-hub/biobox"
viash_version: "0.9.0"
git_commit: "58fff63a79486cc6ef8154ce25968f0d33233bbd"
git_remote: "https://x-access-token:ghs_bkyUSr3AiRiiBMZsG4a0cVtxksNgov2SKmdL@github.com/viash-hub/biobox"
git_tag: "v0.2.0-17-g58fff63"
package_config:
name: "biobox"
version: "add_trimgalore"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0-RC7"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:

10
target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff
View File

@@ -2,9 +2,9 @@
# agat_convert_bed2gff add_trimgalore
#
# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
# Data Intuitive.
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
@@ -515,9 +515,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
LABEL org.opencontainers.image.authors="Leïla Paquay"
LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_bed2gff"
LABEL org.opencontainers.image.created="2024-09-19T08:36:04Z"
LABEL org.opencontainers.image.created="2024-09-19T09:11:38Z"
LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
LABEL org.opencontainers.image.revision="90735159b7bafa4aa8643eb132534d078ea299cf"
LABEL org.opencontainers.image.revision="58fff63a79486cc6ef8154ce25968f0d33233bbd"
LABEL org.opencontainers.image.version="add_trimgalore"
VIASHDOCKER

9
target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml
View File

@@ -224,15 +224,16 @@ build_info:
engine: "docker|native"
output: "target/executable/agat/agat_convert_embl2gff"
executable: "target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff"
viash_version: "0.9.0-RC7"
git_commit: "90735159b7bafa4aa8643eb132534d078ea299cf"
git_remote: "https://x-access-token:ghs_f5MGzzY8TnzQWjJSiZ9z9t1HGTq1aI25g7mw@github.com/viash-hub/biobox"
viash_version: "0.9.0"
git_commit: "58fff63a79486cc6ef8154ce25968f0d33233bbd"
git_remote: "https://x-access-token:ghs_bkyUSr3AiRiiBMZsG4a0cVtxksNgov2SKmdL@github.com/viash-hub/biobox"
git_tag: "v0.2.0-17-g58fff63"
package_config:
name: "biobox"
version: "add_trimgalore"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0-RC7"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:

10
target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff
View File

@@ -2,9 +2,9 @@
# agat_convert_embl2gff add_trimgalore
#
# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
# Data Intuitive.
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
@@ -505,9 +505,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
LABEL org.opencontainers.image.authors="Leïla Paquay"
LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_embl2gff"
LABEL org.opencontainers.image.created="2024-09-19T08:36:04Z"
LABEL org.opencontainers.image.created="2024-09-19T09:11:37Z"
LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
LABEL org.opencontainers.image.revision="90735159b7bafa4aa8643eb132534d078ea299cf"
LABEL org.opencontainers.image.revision="58fff63a79486cc6ef8154ce25968f0d33233bbd"
LABEL org.opencontainers.image.version="add_trimgalore"
VIASHDOCKER

257
target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml Normal file
View File

@@ -0,0 +1,257 @@
name: "agat_convert_genscan2gff"
namespace: "agat"
version: "add_trimgalore"
authors:
- name: "Leïla Paquay"
roles:
- "author"
- "maintainer"
info:
links:
email: "leila@data-intuitive.com"
github: "Leila011"
linkedin: "leilapaquay"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Software Developer"
argument_groups:
- name: "Inputs"
arguments:
- type: "file"
name: "--genscan"
alternatives:
- "-g"
description: "Input genscan bed file that will be converted."
info: null
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Outputs"
arguments:
- type: "file"
name: "--output"
alternatives:
- "-o"
- "--out"
- "--outfile"
- "--gff"
description: "Output GFF file. If no output file is specified, the output will\
\ be written to STDOUT."
info: null
example:
- "output.gff"
must_exist: true
create_parent: true
required: true
direction: "output"
multiple: false
multiple_sep: ";"
- name: "Arguments"
arguments:
- type: "string"
name: "--source"
description: "The source informs about the tool used to produce the data and is\
\ stored in 2nd field of a gff file. Example: Stringtie, Maker, Augustus, etc.\
\ [default: data]\n"
info: null
example:
- "Stringtie"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--primary_tag"
description: "The primary_tag corresponds to the data type and is stored in 3rd\
\ field of a gff file. Example: gene, mRNA, CDS, etc. [default: gene]\n"
info: null
example:
- "gene"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--inflate_type"
description: "Feature type (3rd column in gff) created when inflate parameter\
\ activated [default: exon].\n"
info: null
example:
- "exon"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--verbose"
description: "add verbosity"
info: null
direction: "input"
- type: "file"
name: "--config"
alternatives:
- "-c"
description: "AGAT config file. By default AGAT takes the original agat_config.yaml\
\ shipped with AGAT. The `--config` option gives you the possibility to use\
\ your own AGAT config file (located elsewhere or named differently).\n"
info: null
example:
- "custom_agat_config.yaml"
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
resources:
- type: "bash_script"
path: "script.sh"
is_executable: true
description: "The script takes a GENSCAN file as input, and will translate it in gff\n\
format. The GENSCAN format is described [here](http://genome.crg.es/courses/Bioinformatics2003_genefinding/results/genscan.html).\n\
\n**Known problem** \n\nYou must have submited only DNA sequence, without any header!!\
\ Indeed the tool expects only DNA\nsequences and does not crash/warn if an header\
\ is submited along the\nsequence. e.g If you have an header \">seq\" s-e-q are\
\ seen as the 3 first\nnucleotides of the sequence. Then all prediction location\
\ are shifted\naccordingly. (checked only on the [online version](http://argonaute.mit.edu/GENSCAN.html).\
\ \nI don't know if there is the same problem elsewhere.)\n"
test_resources:
- type: "bash_script"
path: "test.sh"
is_executable: true
- type: "file"
path: "test_data"
info: null
status: "enabled"
requirements:
commands:
- "ps"
keywords:
- "gene annotations"
- "GFF conversion"
- "GENSCAN"
license: "GPL-3.0"
references:
doi:
- "10.5281/zenodo.3552717"
links:
repository: "https://github.com/NBISweden/AGAT"
homepage: "https://github.com/NBISweden/AGAT"
documentation: "https://agat.readthedocs.io/en/latest/tools/agat_convert_genscan2gff.html"
issue_tracker: "https://github.com/NBISweden/AGAT/issues"
runners:
- type: "executable"
id: "executable"
docker_setup_strategy: "ifneedbepullelsecachedbuild"
- type: "nextflow"
id: "nextflow"
directives:
tag: "$id"
auto:
simplifyInput: true
simplifyOutput: false
transcript: false
publish: false
config:
labels:
mem1gb: "memory = 1000000000.B"
mem2gb: "memory = 2000000000.B"
mem5gb: "memory = 5000000000.B"
mem10gb: "memory = 10000000000.B"
mem20gb: "memory = 20000000000.B"
mem50gb: "memory = 50000000000.B"
mem100gb: "memory = 100000000000.B"
mem200gb: "memory = 200000000000.B"
mem500gb: "memory = 500000000000.B"
mem1tb: "memory = 1000000000000.B"
mem2tb: "memory = 2000000000000.B"
mem5tb: "memory = 5000000000000.B"
mem10tb: "memory = 10000000000000.B"
mem20tb: "memory = 20000000000000.B"
mem50tb: "memory = 50000000000000.B"
mem100tb: "memory = 100000000000000.B"
mem200tb: "memory = 200000000000000.B"
mem500tb: "memory = 500000000000000.B"
mem1gib: "memory = 1073741824.B"
mem2gib: "memory = 2147483648.B"
mem4gib: "memory = 4294967296.B"
mem8gib: "memory = 8589934592.B"
mem16gib: "memory = 17179869184.B"
mem32gib: "memory = 34359738368.B"
mem64gib: "memory = 68719476736.B"
mem128gib: "memory = 137438953472.B"
mem256gib: "memory = 274877906944.B"
mem512gib: "memory = 549755813888.B"
mem1tib: "memory = 1099511627776.B"
mem2tib: "memory = 2199023255552.B"
mem4tib: "memory = 4398046511104.B"
mem8tib: "memory = 8796093022208.B"
mem16tib: "memory = 17592186044416.B"
mem32tib: "memory = 35184372088832.B"
mem64tib: "memory = 70368744177664.B"
mem128tib: "memory = 140737488355328.B"
mem256tib: "memory = 281474976710656.B"
mem512tib: "memory = 562949953421312.B"
cpu1: "cpus = 1"
cpu2: "cpus = 2"
cpu5: "cpus = 5"
cpu10: "cpus = 10"
cpu20: "cpus = 20"
cpu50: "cpus = 50"
cpu100: "cpus = 100"
cpu200: "cpus = 200"
cpu500: "cpus = 500"
cpu1000: "cpus = 1000"
debug: false
container: "docker"
engines:
- type: "docker"
id: "docker"
image: "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0"
target_registry: "images.viash-hub.com"
target_tag: "add_trimgalore"
namespace_separator: "/"
setup:
- type: "docker"
run:
- "agat --version | sed 's/AGAT\\s\\(.*\\)/agat: \"\\1\"/' > /var/software_versions.txt\n"
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/agat/agat_convert_genscan2gff/config.vsh.yaml"
runner: "executable"
engine: "docker|native"
output: "target/executable/agat/agat_convert_genscan2gff"
executable: "target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff"
viash_version: "0.9.0"
git_commit: "58fff63a79486cc6ef8154ce25968f0d33233bbd"
git_remote: "https://x-access-token:ghs_bkyUSr3AiRiiBMZsG4a0cVtxksNgov2SKmdL@github.com/viash-hub/biobox"
git_tag: "v0.2.0-17-g58fff63"
package_config:
name: "biobox"
version: "add_trimgalore"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'add_trimgalore'"
keywords:
- "bioinformatics"
- "modules"
- "sequencing"
license: "MIT"
organization: "vsh"
links:
repository: "https://github.com/viash-hub/biobox"
issue_tracker: "https://github.com/viash-hub/biobox/issues"

1252
target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff Executable file
View File

File diff suppressed because it is too large Load Diff

9
target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
View File

@@ -227,15 +227,16 @@ build_info:
engine: "docker|native"
output: "target/executable/agat/agat_convert_sp_gff2gtf"
executable: "target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf"
viash_version: "0.9.0-RC7"
git_commit: "90735159b7bafa4aa8643eb132534d078ea299cf"
git_remote: "https://x-access-token:ghs_f5MGzzY8TnzQWjJSiZ9z9t1HGTq1aI25g7mw@github.com/viash-hub/biobox"
viash_version: "0.9.0"
git_commit: "58fff63a79486cc6ef8154ce25968f0d33233bbd"
git_remote: "https://x-access-token:ghs_bkyUSr3AiRiiBMZsG4a0cVtxksNgov2SKmdL@github.com/viash-hub/biobox"
git_tag: "v0.2.0-17-g58fff63"
package_config:
name: "biobox"
version: "add_trimgalore"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0-RC7"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:

10
target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf
View File

@@ -2,9 +2,9 @@
# agat_convert_sp_gff2gtf add_trimgalore
#
# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
# Data Intuitive.
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
@@ -519,9 +519,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
LABEL org.opencontainers.image.authors="Leïla Paquay"
LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gff2gtf"
LABEL org.opencontainers.image.created="2024-09-19T08:36:04Z"
LABEL org.opencontainers.image.created="2024-09-19T09:11:38Z"
LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
LABEL org.opencontainers.image.revision="90735159b7bafa4aa8643eb132534d078ea299cf"
LABEL org.opencontainers.image.revision="58fff63a79486cc6ef8154ce25968f0d33233bbd"
LABEL org.opencontainers.image.version="add_trimgalore"
VIASHDOCKER

9
target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
View File

@@ -187,15 +187,16 @@ build_info:
engine: "docker|native"
output: "target/executable/agat/agat_convert_sp_gff2tsv"
executable: "target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv"
viash_version: "0.9.0-RC7"
git_commit: "90735159b7bafa4aa8643eb132534d078ea299cf"
git_remote: "https://x-access-token:ghs_f5MGzzY8TnzQWjJSiZ9z9t1HGTq1aI25g7mw@github.com/viash-hub/biobox"
viash_version: "0.9.0"
git_commit: "58fff63a79486cc6ef8154ce25968f0d33233bbd"
git_remote: "https://x-access-token:ghs_bkyUSr3AiRiiBMZsG4a0cVtxksNgov2SKmdL@github.com/viash-hub/biobox"
git_tag: "v0.2.0-17-g58fff63"
package_config:
name: "biobox"
version: "add_trimgalore"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0-RC7"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:

10
target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv
View File

@@ -2,9 +2,9 @@
# agat_convert_sp_gff2tsv add_trimgalore
#
# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
# Data Intuitive.
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
@@ -484,9 +484,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
LABEL org.opencontainers.image.authors="Leïla Paquay"
LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gff2tsv"
LABEL org.opencontainers.image.created="2024-09-19T08:36:03Z"
LABEL org.opencontainers.image.created="2024-09-19T09:11:37Z"
LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
LABEL org.opencontainers.image.revision="90735159b7bafa4aa8643eb132534d078ea299cf"
LABEL org.opencontainers.image.revision="58fff63a79486cc6ef8154ce25968f0d33233bbd"
LABEL org.opencontainers.image.version="add_trimgalore"
VIASHDOCKER

9
target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
View File

@@ -194,15 +194,16 @@ build_info:
engine: "docker|native"
output: "target/executable/agat/agat_convert_sp_gxf2gxf"
executable: "target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf"
viash_version: "0.9.0-RC7"
git_commit: "90735159b7bafa4aa8643eb132534d078ea299cf"
git_remote: "https://x-access-token:ghs_f5MGzzY8TnzQWjJSiZ9z9t1HGTq1aI25g7mw@github.com/viash-hub/biobox"
viash_version: "0.9.0"
git_commit: "58fff63a79486cc6ef8154ce25968f0d33233bbd"
git_remote: "https://x-access-token:ghs_bkyUSr3AiRiiBMZsG4a0cVtxksNgov2SKmdL@github.com/viash-hub/biobox"
git_tag: "v0.2.0-17-g58fff63"
package_config:
name: "biobox"
version: "add_trimgalore"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0-RC7"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:

10
target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf
View File

@@ -2,9 +2,9 @@
# agat_convert_sp_gxf2gxf add_trimgalore
#
# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
# Data Intuitive.
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
@@ -493,9 +493,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
LABEL org.opencontainers.image.authors="Leïla Paquay"
LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gxf2gxf"
LABEL org.opencontainers.image.created="2024-09-19T08:36:03Z"
LABEL org.opencontainers.image.created="2024-09-19T09:11:37Z"
LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
LABEL org.opencontainers.image.revision="90735159b7bafa4aa8643eb132534d078ea299cf"
LABEL org.opencontainers.image.revision="58fff63a79486cc6ef8154ce25968f0d33233bbd"
LABEL org.opencontainers.image.version="add_trimgalore"
VIASHDOCKER

9
target/executable/arriba/.config.vsh.yaml
View File

@@ -705,15 +705,16 @@ build_info:
engine: "docker|native"
output: "target/executable/arriba"
executable: "target/executable/arriba/arriba"
viash_version: "0.9.0-RC7"
git_commit: "90735159b7bafa4aa8643eb132534d078ea299cf"
git_remote: "https://x-access-token:ghs_f5MGzzY8TnzQWjJSiZ9z9t1HGTq1aI25g7mw@github.com/viash-hub/biobox"
viash_version: "0.9.0"
git_commit: "58fff63a79486cc6ef8154ce25968f0d33233bbd"
git_remote: "https://x-access-token:ghs_bkyUSr3AiRiiBMZsG4a0cVtxksNgov2SKmdL@github.com/viash-hub/biobox"
git_tag: "v0.2.0-17-g58fff63"
package_config:
name: "biobox"
version: "add_trimgalore"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0-RC7"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:

10
target/executable/arriba/arriba
View File

@@ -2,9 +2,9 @@
# arriba add_trimgalore
#
# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
# Data Intuitive.
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
@@ -754,9 +754,9 @@ RUN arriba -h | grep 'Version:' 2>&1 | sed 's/Version:\s\(.*\)/arriba: "\1"/' >
LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
LABEL org.opencontainers.image.description="Companion container for running component arriba"
LABEL org.opencontainers.image.created="2024-09-19T08:36:07Z"
LABEL org.opencontainers.image.created="2024-09-19T09:11:40Z"
LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
LABEL org.opencontainers.image.revision="90735159b7bafa4aa8643eb132534d078ea299cf"
LABEL org.opencontainers.image.revision="58fff63a79486cc6ef8154ce25968f0d33233bbd"
LABEL org.opencontainers.image.version="add_trimgalore"
VIASHDOCKER

9
target/executable/bcftools/bcftools_annotate/.config.vsh.yaml
View File

@@ -468,15 +468,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bcftools/bcftools_annotate"
executable: "target/executable/bcftools/bcftools_annotate/bcftools_annotate"
viash_version: "0.9.0-RC7"
git_commit: "90735159b7bafa4aa8643eb132534d078ea299cf"
git_remote: "https://x-access-token:ghs_f5MGzzY8TnzQWjJSiZ9z9t1HGTq1aI25g7mw@github.com/viash-hub/biobox"
viash_version: "0.9.0"
git_commit: "58fff63a79486cc6ef8154ce25968f0d33233bbd"
git_remote: "https://x-access-token:ghs_bkyUSr3AiRiiBMZsG4a0cVtxksNgov2SKmdL@github.com/viash-hub/biobox"
git_tag: "v0.2.0-17-g58fff63"
package_config:
name: "biobox"
version: "add_trimgalore"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0-RC7"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:

10
target/executable/bcftools/bcftools_annotate/bcftools_annotate
View File

@@ -2,9 +2,9 @@
# bcftools_annotate add_trimgalore
#
# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
# Data Intuitive.
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
@@ -650,9 +650,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_annotate"
LABEL org.opencontainers.image.created="2024-09-19T08:35:57Z"
LABEL org.opencontainers.image.created="2024-09-19T09:11:31Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
LABEL org.opencontainers.image.revision="90735159b7bafa4aa8643eb132534d078ea299cf"
LABEL org.opencontainers.image.revision="58fff63a79486cc6ef8154ce25968f0d33233bbd"
LABEL org.opencontainers.image.version="add_trimgalore"
VIASHDOCKER

9
target/executable/bcftools/bcftools_concat/.config.vsh.yaml
View File

@@ -334,15 +334,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bcftools/bcftools_concat"
executable: "target/executable/bcftools/bcftools_concat/bcftools_concat"
viash_version: "0.9.0-RC7"
git_commit: "90735159b7bafa4aa8643eb132534d078ea299cf"
git_remote: "https://x-access-token:ghs_f5MGzzY8TnzQWjJSiZ9z9t1HGTq1aI25g7mw@github.com/viash-hub/biobox"
viash_version: "0.9.0"
git_commit: "58fff63a79486cc6ef8154ce25968f0d33233bbd"
git_remote: "https://x-access-token:ghs_bkyUSr3AiRiiBMZsG4a0cVtxksNgov2SKmdL@github.com/viash-hub/biobox"
git_tag: "v0.2.0-17-g58fff63"
package_config:
name: "biobox"
version: "add_trimgalore"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0-RC7"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:

10
target/executable/bcftools/bcftools_concat/bcftools_concat
View File

@@ -2,9 +2,9 @@
# bcftools_concat add_trimgalore
#
# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
# Data Intuitive.
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
@@ -566,9 +566,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_concat"
LABEL org.opencontainers.image.created="2024-09-19T08:35:58Z"
LABEL org.opencontainers.image.created="2024-09-19T09:11:31Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
LABEL org.opencontainers.image.revision="90735159b7bafa4aa8643eb132534d078ea299cf"
LABEL org.opencontainers.image.revision="58fff63a79486cc6ef8154ce25968f0d33233bbd"
LABEL org.opencontainers.image.version="add_trimgalore"
VIASHDOCKER

9
target/executable/bcftools/bcftools_norm/.config.vsh.yaml
View File

@@ -415,15 +415,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bcftools/bcftools_norm"
executable: "target/executable/bcftools/bcftools_norm/bcftools_norm"
viash_version: "0.9.0-RC7"
git_commit: "90735159b7bafa4aa8643eb132534d078ea299cf"
git_remote: "https://x-access-token:ghs_f5MGzzY8TnzQWjJSiZ9z9t1HGTq1aI25g7mw@github.com/viash-hub/biobox"
viash_version: "0.9.0"
git_commit: "58fff63a79486cc6ef8154ce25968f0d33233bbd"
git_remote: "https://x-access-token:ghs_bkyUSr3AiRiiBMZsG4a0cVtxksNgov2SKmdL@github.com/viash-hub/biobox"
git_tag: "v0.2.0-17-g58fff63"
package_config:
name: "biobox"
version: "add_trimgalore"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0-RC7"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:

10
target/executable/bcftools/bcftools_norm/bcftools_norm
View File

@@ -2,9 +2,9 @@
# bcftools_norm add_trimgalore
#
# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
# Data Intuitive.
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
@@ -589,9 +589,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_norm"
LABEL org.opencontainers.image.created="2024-09-19T08:35:59Z"
LABEL org.opencontainers.image.created="2024-09-19T09:11:32Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
LABEL org.opencontainers.image.revision="90735159b7bafa4aa8643eb132534d078ea299cf"
LABEL org.opencontainers.image.revision="58fff63a79486cc6ef8154ce25968f0d33233bbd"
LABEL org.opencontainers.image.version="add_trimgalore"
VIASHDOCKER

9
target/executable/bcftools/bcftools_sort/.config.vsh.yaml
View File

@@ -184,15 +184,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bcftools/bcftools_sort"
executable: "target/executable/bcftools/bcftools_sort/bcftools_sort"
viash_version: "0.9.0-RC7"
git_commit: "90735159b7bafa4aa8643eb132534d078ea299cf"
git_remote: "https://x-access-token:ghs_f5MGzzY8TnzQWjJSiZ9z9t1HGTq1aI25g7mw@github.com/viash-hub/biobox"
viash_version: "0.9.0"
git_commit: "58fff63a79486cc6ef8154ce25968f0d33233bbd"
git_remote: "https://x-access-token:ghs_bkyUSr3AiRiiBMZsG4a0cVtxksNgov2SKmdL@github.com/viash-hub/biobox"
git_tag: "v0.2.0-17-g58fff63"
package_config:
name: "biobox"
version: "add_trimgalore"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0-RC7"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:

10
target/executable/bcftools/bcftools_sort/bcftools_sort
View File

@@ -2,9 +2,9 @@
# bcftools_sort add_trimgalore
#
# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
# Data Intuitive.
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
@@ -483,9 +483,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_sort"
LABEL org.opencontainers.image.created="2024-09-19T08:35:57Z"
LABEL org.opencontainers.image.created="2024-09-19T09:11:30Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
LABEL org.opencontainers.image.revision="90735159b7bafa4aa8643eb132534d078ea299cf"
LABEL org.opencontainers.image.revision="58fff63a79486cc6ef8154ce25968f0d33233bbd"
LABEL org.opencontainers.image.version="add_trimgalore"
VIASHDOCKER

9
target/executable/bcftools/bcftools_stats/.config.vsh.yaml
View File

@@ -457,15 +457,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bcftools/bcftools_stats"
executable: "target/executable/bcftools/bcftools_stats/bcftools_stats"
viash_version: "0.9.0-RC7"
git_commit: "90735159b7bafa4aa8643eb132534d078ea299cf"
git_remote: "https://x-access-token:ghs_f5MGzzY8TnzQWjJSiZ9z9t1HGTq1aI25g7mw@github.com/viash-hub/biobox"
viash_version: "0.9.0"
git_commit: "58fff63a79486cc6ef8154ce25968f0d33233bbd"
git_remote: "https://x-access-token:ghs_bkyUSr3AiRiiBMZsG4a0cVtxksNgov2SKmdL@github.com/viash-hub/biobox"
git_tag: "v0.2.0-17-g58fff63"
package_config:
name: "biobox"
version: "add_trimgalore"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0-RC7"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:

10
target/executable/bcftools/bcftools_stats/bcftools_stats
View File

@@ -2,9 +2,9 @@
# bcftools_stats add_trimgalore
#
# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
# Data Intuitive.
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
@@ -626,9 +626,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_stats"
LABEL org.opencontainers.image.created="2024-09-19T08:35:58Z"
LABEL org.opencontainers.image.created="2024-09-19T09:11:31Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
LABEL org.opencontainers.image.revision="90735159b7bafa4aa8643eb132534d078ea299cf"
LABEL org.opencontainers.image.revision="58fff63a79486cc6ef8154ce25968f0d33233bbd"
LABEL org.opencontainers.image.version="add_trimgalore"
VIASHDOCKER

9
target/executable/bcl_convert/.config.vsh.yaml
View File

@@ -417,15 +417,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bcl_convert"
executable: "target/executable/bcl_convert/bcl_convert"
viash_version: "0.9.0-RC7"
git_commit: "90735159b7bafa4aa8643eb132534d078ea299cf"
git_remote: "https://x-access-token:ghs_f5MGzzY8TnzQWjJSiZ9z9t1HGTq1aI25g7mw@github.com/viash-hub/biobox"
viash_version: "0.9.0"
git_commit: "58fff63a79486cc6ef8154ce25968f0d33233bbd"
git_remote: "https://x-access-token:ghs_bkyUSr3AiRiiBMZsG4a0cVtxksNgov2SKmdL@github.com/viash-hub/biobox"
git_tag: "v0.2.0-17-g58fff63"
package_config:
name: "biobox"
version: "add_trimgalore"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0-RC7"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:

10
target/executable/bcl_convert/bcl_convert
View File

@@ -2,9 +2,9 @@
# bcl_convert add_trimgalore
#
# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
# Data Intuitive.
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
@@ -599,9 +599,9 @@ RUN echo "bcl-convert: \"$(bcl-convert -V 2>&1 >/dev/null | sed -n '/Version/ s/
LABEL org.opencontainers.image.authors="Toni Verbeiren, Dorien Roosen"
LABEL org.opencontainers.image.description="Companion container for running component bcl_convert"
LABEL org.opencontainers.image.created="2024-09-19T08:36:06Z"
LABEL org.opencontainers.image.created="2024-09-19T09:11:40Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
LABEL org.opencontainers.image.revision="90735159b7bafa4aa8643eb132534d078ea299cf"
LABEL org.opencontainers.image.revision="58fff63a79486cc6ef8154ce25968f0d33233bbd"
LABEL org.opencontainers.image.version="add_trimgalore"
VIASHDOCKER

19
target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
View File

@@ -146,8 +146,6 @@ resources:
- type: "python_script"
path: "script.py"
is_executable: true
- type: "file"
path: "make_rhap_reference_2.2.1_nodocker.cwl"
description: "The Reference Files Generator creates an archive containing Genome Index\n\
and Transcriptome annotation files needed for the BD Rhapsody Sequencing\nAnalysis\
\ Pipeline. The app takes as input one or more FASTA and GTF files\nand produces\
@@ -249,6 +247,7 @@ engines:
- type: "apt"
packages:
- "procps"
- "git"
interactive: false
- type: "python"
user: false
@@ -258,7 +257,12 @@ engines:
upgrade: true
- type: "docker"
run:
- "echo \"bdgenomics/rhapsody: 2.2.1\" > /var/software_versions.txt\n"
- "mkdir /var/bd_rhapsody_cwl && \\\n cd /var/bd_rhapsody_cwl && \\\n git clone\
\ https://bitbucket.org/CRSwDev/cwl.git . && \\\n git checkout 8feeace1141b24749ea6003f8e6ad6d3ad5232de\n"
- type: "docker"
run:
- "VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1)"
- "echo \"bdgenomics/rhapsody: \\\"$VERSION\\\"\" > /var/software_versions.txt"
entrypoint: []
cmd: null
- type: "native"
@@ -269,15 +273,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bd_rhapsody/bd_rhapsody_make_reference"
executable: "target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference"
viash_version: "0.9.0-RC7"
git_commit: "90735159b7bafa4aa8643eb132534d078ea299cf"
git_remote: "https://x-access-token:ghs_f5MGzzY8TnzQWjJSiZ9z9t1HGTq1aI25g7mw@github.com/viash-hub/biobox"
viash_version: "0.9.0"
git_commit: "58fff63a79486cc6ef8154ce25968f0d33233bbd"
git_remote: "https://x-access-token:ghs_bkyUSr3AiRiiBMZsG4a0cVtxksNgov2SKmdL@github.com/viash-hub/biobox"
git_tag: "v0.2.0-17-g58fff63"
package_config:
name: "biobox"
version: "add_trimgalore"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0-RC7"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:

31
target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference
View File

@@ -2,9 +2,9 @@
# bd_rhapsody_make_reference add_trimgalore
#
# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
# Data Intuitive.
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
@@ -539,19 +539,24 @@ function ViashDockerfile {
FROM bdgenomics/rhapsody:2.2.1
ENTRYPOINT []
RUN apt-get update && \
DEBIAN_FRONTEND=noninteractive apt-get install -y procps && \
DEBIAN_FRONTEND=noninteractive apt-get install -y procps git && \
rm -rf /var/lib/apt/lists/*
RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "cwlref-runner" "cwl-runner"
RUN echo "bdgenomics/rhapsody: 2.2.1" > /var/software_versions.txt
RUN mkdir /var/bd_rhapsody_cwl && \
cd /var/bd_rhapsody_cwl && \
git clone https://bitbucket.org/CRSwDev/cwl.git . && \
git checkout 8feeace1141b24749ea6003f8e6ad6d3ad5232de
RUN VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1)
RUN echo "bdgenomics/rhapsody: \"$VERSION\"" > /var/software_versions.txt
LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz"
LABEL org.opencontainers.image.description="Companion container for running component bd_rhapsody bd_rhapsody_make_reference"
LABEL org.opencontainers.image.created="2024-09-19T08:36:09Z"
LABEL org.opencontainers.image.created="2024-09-19T09:11:44Z"
LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/"
LABEL org.opencontainers.image.revision="90735159b7bafa4aa8643eb132534d078ea299cf"
LABEL org.opencontainers.image.revision="58fff63a79486cc6ef8154ce25968f0d33233bbd"
LABEL org.opencontainers.image.version="add_trimgalore"
VIASHDOCKER
@@ -1360,21 +1365,21 @@ def generate_config(par: dict[str, Any], meta, config) -> str:
for config_key, arg_type, par_value in config_key_value_pairs:
if arg_type == "file":
str = strip_margin(f"""\\
content = strip_margin(f"""\\
|{config_key}:
|""")
if isinstance(par_value, list):
for file in par_value:
str += strip_margin(f"""\\
content += strip_margin(f"""\\
| - class: File
| location: "{file}"
|""")
else:
str += strip_margin(f"""\\
content += strip_margin(f"""\\
| class: File
| location: "{par_value}"
|""")
content_list.append(str)
content_list.append(content)
else:
content_list.append(strip_margin(f"""\\
|{config_key}: {par_value}
@@ -1385,9 +1390,9 @@ def generate_config(par: dict[str, Any], meta, config) -> str:
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")
cwl_file="/var/bd_rhapsody_cwl/v2.2.1/Extra_Utilities/make_rhap_reference_2.2.1.cwl"
return cwl_file
return os.path.abspath(cwl_file)
def main(par: dict[str, Any], meta: dict[str, Any]):
config = read_config(meta["config"])

115
target/executable/bd_rhapsody/bd_rhapsody_make_reference/make_rhap_reference_2.2.1_nodocker.cwl
View File

@@ -1,115 +0,0 @@
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'

1142
target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml Normal file
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3469
target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis Executable file
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9
target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml
View File

@@ -186,15 +186,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bedtools/bedtools_bamtofastq"
executable: "target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq"
viash_version: "0.9.0-RC7"
git_commit: "90735159b7bafa4aa8643eb132534d078ea299cf"
git_remote: "https://x-access-token:ghs_f5MGzzY8TnzQWjJSiZ9z9t1HGTq1aI25g7mw@github.com/viash-hub/biobox"
viash_version: "0.9.0"
git_commit: "58fff63a79486cc6ef8154ce25968f0d33233bbd"
git_remote: "https://x-access-token:ghs_bkyUSr3AiRiiBMZsG4a0cVtxksNgov2SKmdL@github.com/viash-hub/biobox"
git_tag: "v0.2.0-17-g58fff63"
package_config:
name: "biobox"
version: "add_trimgalore"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0-RC7"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:

10
target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq
View File

@@ -2,9 +2,9 @@
# bedtools_bamtofastq add_trimgalore
#
# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
# Data Intuitive.
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
@@ -483,9 +483,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bamtofastq"
LABEL org.opencontainers.image.created="2024-09-19T08:35:50Z"
LABEL org.opencontainers.image.created="2024-09-19T09:11:23Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="90735159b7bafa4aa8643eb132534d078ea299cf"
LABEL org.opencontainers.image.revision="58fff63a79486cc6ef8154ce25968f0d33233bbd"
LABEL org.opencontainers.image.version="add_trimgalore"
VIASHDOCKER

9
target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml
View File

@@ -175,15 +175,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bedtools/bedtools_bed12tobed6"
executable: "target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6"
viash_version: "0.9.0-RC7"
git_commit: "90735159b7bafa4aa8643eb132534d078ea299cf"
git_remote: "https://x-access-token:ghs_f5MGzzY8TnzQWjJSiZ9z9t1HGTq1aI25g7mw@github.com/viash-hub/biobox"
viash_version: "0.9.0"
git_commit: "58fff63a79486cc6ef8154ce25968f0d33233bbd"
git_remote: "https://x-access-token:ghs_bkyUSr3AiRiiBMZsG4a0cVtxksNgov2SKmdL@github.com/viash-hub/biobox"
git_tag: "v0.2.0-17-g58fff63"
package_config:
name: "biobox"
version: "add_trimgalore"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0-RC7"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:

10
target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6
View File

@@ -2,9 +2,9 @@
# bedtools_bed12tobed6 add_trimgalore
#
# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
# Data Intuitive.
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
@@ -480,9 +480,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bed12tobed6"
LABEL org.opencontainers.image.created="2024-09-19T08:35:49Z"
LABEL org.opencontainers.image.created="2024-09-19T09:11:22Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="90735159b7bafa4aa8643eb132534d078ea299cf"
LABEL org.opencontainers.image.revision="58fff63a79486cc6ef8154ce25968f0d33233bbd"
LABEL org.opencontainers.image.version="add_trimgalore"
VIASHDOCKER

9
target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml
View File

@@ -213,15 +213,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bedtools/bedtools_bedtobam"
executable: "target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam"
viash_version: "0.9.0-RC7"
git_commit: "90735159b7bafa4aa8643eb132534d078ea299cf"
git_remote: "https://x-access-token:ghs_f5MGzzY8TnzQWjJSiZ9z9t1HGTq1aI25g7mw@github.com/viash-hub/biobox"
viash_version: "0.9.0"
git_commit: "58fff63a79486cc6ef8154ce25968f0d33233bbd"
git_remote: "https://x-access-token:ghs_bkyUSr3AiRiiBMZsG4a0cVtxksNgov2SKmdL@github.com/viash-hub/biobox"
git_tag: "v0.2.0-17-g58fff63"
package_config:
name: "biobox"
version: "add_trimgalore"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0-RC7"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:

10
target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam
View File

@@ -2,9 +2,9 @@
# bedtools_bedtobam add_trimgalore
#
# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
# Data Intuitive.
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
@@ -496,9 +496,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bedtobam"
LABEL org.opencontainers.image.created="2024-09-19T08:35:51Z"
LABEL org.opencontainers.image.created="2024-09-19T09:11:24Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="90735159b7bafa4aa8643eb132534d078ea299cf"
LABEL org.opencontainers.image.revision="58fff63a79486cc6ef8154ce25968f0d33233bbd"
LABEL org.opencontainers.image.version="add_trimgalore"
VIASHDOCKER

9
target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml
View File

@@ -336,15 +336,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bedtools/bedtools_genomecov"
executable: "target/executable/bedtools/bedtools_genomecov/bedtools_genomecov"
viash_version: "0.9.0-RC7"
git_commit: "90735159b7bafa4aa8643eb132534d078ea299cf"
git_remote: "https://x-access-token:ghs_f5MGzzY8TnzQWjJSiZ9z9t1HGTq1aI25g7mw@github.com/viash-hub/biobox"
viash_version: "0.9.0"
git_commit: "58fff63a79486cc6ef8154ce25968f0d33233bbd"
git_remote: "https://x-access-token:ghs_bkyUSr3AiRiiBMZsG4a0cVtxksNgov2SKmdL@github.com/viash-hub/biobox"
git_tag: "v0.2.0-17-g58fff63"
package_config:
name: "biobox"
version: "add_trimgalore"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0-RC7"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:

10
target/executable/bedtools/bedtools_genomecov/bedtools_genomecov
View File

@@ -2,9 +2,9 @@
# bedtools_genomecov add_trimgalore
#
# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
# Data Intuitive.
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
@@ -591,9 +591,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_genomecov"
LABEL org.opencontainers.image.created="2024-09-19T08:35:48Z"
LABEL org.opencontainers.image.created="2024-09-19T09:11:21Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="90735159b7bafa4aa8643eb132534d078ea299cf"
LABEL org.opencontainers.image.revision="58fff63a79486cc6ef8154ce25968f0d33233bbd"
LABEL org.opencontainers.image.version="add_trimgalore"
VIASHDOCKER

9
target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
View File

@@ -231,15 +231,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bedtools/bedtools_getfasta"
executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta"
viash_version: "0.9.0-RC7"
git_commit: "90735159b7bafa4aa8643eb132534d078ea299cf"
git_remote: "https://x-access-token:ghs_f5MGzzY8TnzQWjJSiZ9z9t1HGTq1aI25g7mw@github.com/viash-hub/biobox"
viash_version: "0.9.0"
git_commit: "58fff63a79486cc6ef8154ce25968f0d33233bbd"
git_remote: "https://x-access-token:ghs_bkyUSr3AiRiiBMZsG4a0cVtxksNgov2SKmdL@github.com/viash-hub/biobox"
git_tag: "v0.2.0-17-g58fff63"
package_config:
name: "biobox"
version: "add_trimgalore"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0-RC7"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:

10
target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
View File

@@ -2,9 +2,9 @@
# bedtools_getfasta add_trimgalore
#
# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
# Data Intuitive.
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
@@ -526,9 +526,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Dries Schaumont"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_getfasta"
LABEL org.opencontainers.image.created="2024-09-19T08:35:49Z"
LABEL org.opencontainers.image.created="2024-09-19T09:11:22Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="90735159b7bafa4aa8643eb132534d078ea299cf"
LABEL org.opencontainers.image.revision="58fff63a79486cc6ef8154ce25968f0d33233bbd"
LABEL org.opencontainers.image.version="add_trimgalore"
VIASHDOCKER

9
target/executable/bedtools/bedtools_groupby/.config.vsh.yaml
View File

@@ -272,15 +272,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bedtools/bedtools_groupby"
executable: "target/executable/bedtools/bedtools_groupby/bedtools_groupby"
viash_version: "0.9.0-RC7"
git_commit: "90735159b7bafa4aa8643eb132534d078ea299cf"
git_remote: "https://x-access-token:ghs_f5MGzzY8TnzQWjJSiZ9z9t1HGTq1aI25g7mw@github.com/viash-hub/biobox"
viash_version: "0.9.0"
git_commit: "58fff63a79486cc6ef8154ce25968f0d33233bbd"
git_remote: "https://x-access-token:ghs_bkyUSr3AiRiiBMZsG4a0cVtxksNgov2SKmdL@github.com/viash-hub/biobox"
git_tag: "v0.2.0-17-g58fff63"
package_config:
name: "biobox"
version: "add_trimgalore"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0-RC7"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:

10
target/executable/bedtools/bedtools_groupby/bedtools_groupby
View File

@@ -2,9 +2,9 @@
# bedtools_groupby add_trimgalore
#
# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
# Data Intuitive.
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
@@ -552,9 +552,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_groupby"
LABEL org.opencontainers.image.created="2024-09-19T08:35:50Z"
LABEL org.opencontainers.image.created="2024-09-19T09:11:23Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="90735159b7bafa4aa8643eb132534d078ea299cf"
LABEL org.opencontainers.image.revision="58fff63a79486cc6ef8154ce25968f0d33233bbd"
LABEL org.opencontainers.image.version="add_trimgalore"
VIASHDOCKER

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