Source: mosdepth
Section: science
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller@debian.org>, Nilesh Patra <npatra974@gmail.com>
Build-Depends: debhelper-compat (= 13),
               nim,
               nim-docopt-dev,
               nim-regex-dev,
               nim-hts-dev,
               help2man,
               samtools,
               libhts-dev
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/mosdepth
Vcs-Git: https://salsa.debian.org/med-team/mosdepth.git
Homepage: https://github.com/brentp/mosdepth
Rules-Requires-Root: no

Package: mosdepth
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
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
     threshold 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.

Package: mosdepth-examples
Architecture: all
Depends: ${misc:Depends}
Description: Test data for mosdepth
 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
     threshold 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.
 .
 This package contains a test data set as well as sample scripts
 running some test suite provided by Debian also as autopkgtest.