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Bug#973650: ITP: hts-nim-tools -- tools biological sequences: bam-filter, count-reads, vcf-check



Package: wnpp
Severity: wishlist

Subject: ITP: hts-nim-tools -- tools biological sequences: bam-filter, count-reads, vcf-check
Package: wnpp
Owner: Steffen Moeller <moeller@debian.org>
Severity: wishlist

* Package name    : hts-nim-tools
  Version         : 0.2.0
  Upstream Author : Brent Pedersen <@brentp>
* URL             : https://github.com/brentp/hts-nim-tools
* License         : MIT
  Programming Lang: (C, C++, C#, Perl, Python, etc.)
  Description     : tools biological sequences: bam-filter, count-reads, vcf-check
 This package provides several tools that (at least at the time of their creation)
 provide functionalities beyond the routine provided by samtools and other reverse
 dependencies of the htslib.
 .
 These new tools are
  • bam-filter    : filter BAM/CRAM/SAM files with a simple expression language
  • count-reads   : count BAM/CRAM reads in regions given in a BED file
  • vcf-check     : check regions of a VCF against a background for missing chunks
 .
 and yes, as the name suggests, these tools are all implemented in nim, using the
 nim-hts (upstream: hts-nim) wrapper for the htslib.

Remark: This package is maintained by Steffen Moeller at
   https://salsa.debian.org/med-team/hts-nim-tools

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