[Debian-med-packaging] Bug#973658: ITP: mosdepth -- BAM/CRAM depth calculation biological sequencing

[Steffen Moeller]

Package: wnpp
Severity: wishlist

Subject: ITP: mosdepth -- BAM/CRAM depth calculation biological sequencing
Package: wnpp
Owner: Steffen Moeller <moeller at debian.org>
Severity: wishlist

* Package name    : mosdepth
  Version         : 0.3.1
  Upstream Author : Brent Pedersen
* URL             : https://github.com/brentp/mosdepth
* License         : Expat
  Programming Lang: Python
  Description     : BAM/CRAM depth calculation biological sequencing
 Many small reads are produced by high-throughput "next generation"
 sequencing technologies. The final sequence is derived from how
 these reads are overlapping towards a consensus.
 The more reads are covering/confirming parts of a nucleotide seq,
 the higher the confidence is. Too many reads would be indicative
 of e.g. repeats in the genome.
 .
 mosdepth can output:
  *  per-base depth about 2x as fast samtools depth--about 25 minutes
     of CPU time for a 30X genome.
  *  mean per-window depth given a window size--as would be used for
     CNV calling.
  *  the mean per-region given a BED file of regions.
  *  a distribution of proportion of bases covered at or above a given
     threshhold for each chromosome and genome-wide.
  *  quantized output that merges adjacent bases as long as they fall
     in the same coverage bins e.g. (10-20)
  *  threshold output to indicate how many bases in each region are
     covered at the given thresholds.
 when appropriate, the output files are bgzipped and indexed for ease
 of use.

Remark: This package is maintained by Debian Med Packaging Team at
   https://salsa.debian.org/med-team/mosdepth