bedtools.py

usage: bedtools.py

Compute genome coverage from sorted BAM file

optional arguments:
  -h, --help         show this help message and exit
  --ibam filepath    Path to sorted alignment.bam
  --bed filepath     Path to write alignment.bed; tab-delimited
                     cols=[contig,length]
  --output filepath  Path to output coverage.tsv
  --force-bed        force overwrite `bed`
  --force-cov        force overwrite `--output`