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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