```
inner_distance.py --help
```

Usage: inner_distance.py [options]

Calculate the inner distance (insert size)  of RNA-seq fragments. 

               RNA fragment
 _________________||_________________
|                                    |
|                                    |
||||||||||------------------||||||||||
  read_1      insert_size     read_2

fragment size = read_1 + insert_size + read_2



Options:
  --version             show program's version number and exit
  -h, --help            show this help message and exit
  -i INPUT_FILE, --input-file=INPUT_FILE
                        Alignment file in BAM or SAM format.
  -o OUTPUT_PREFIX, --out-prefix=OUTPUT_PREFIX
                        Prefix of output files(s)
  -r REF_GENE, --refgene=REF_GENE
                        Reference gene model in BED format.
  -k SAMPLESIZE, --sample-size=SAMPLESIZE
                        Number of read-pairs used to estimate inner distance.
                        default=1000000
  -l LOWER_BOUND_SIZE, --lower-bound=LOWER_BOUND_SIZE
                        Lower bound of inner distance (bp). This option is
                        used for ploting histograme. default=-250
  -u UPPER_BOUND_SIZE, --upper-bound=UPPER_BOUND_SIZE
                        Upper bound of inner distance (bp). This option is
                        used for plotting histogram. default=250
  -s STEP_SIZE, --step=STEP_SIZE
                        Step size (bp) of histograme. This option is used for
                        plotting histogram. default=5
  -q MAP_QUAL, --mapq=MAP_QUAL
                        Minimum mapping quality (phred scaled) for an
                        alignment to be called "uniquely mapped". default=30