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
  --lengths filepath  Path to genome lengths.tsv; tab-delimited
                      cols=[contig,length]
  --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 `--coverage`