Hi Perl team,
I'm freqently stumbling upon things like
W: samclip: incorrect-path-for-interpreter usr/bin/samclip (#!/usr/bin/env
perl != /usr/bin/perl)
and my usual way to deal with this was firing up sed in d/rules. However,
I can not imagine that you have a more clever way how to deal with this.
Any hint how I can do this more elegantly?
Moreover some kind review of this pure Perl package would be nice.
Kind regards
Andreas.
On Wed, May 27, 2020 at 01:43:46PM +0200, Andreas Tille wrote:
> Package: wnpp
> Severity: wishlist
>
> Subject: ITP: samclip -- filter SAM file for soft and hard clipped alignments
> Package: wnpp
> Owner: Andreas Tille <ti...@debian.org>
> Severity: wishlist
>
> * Package name : samclip
> Version : 0.4.0
> Upstream Author : Torsten Seemann
> * URL : https://github.com/tseemann/samclip
> * License : GPL-3
> Programming Lang: (C, C++, C#, Perl, Python, etc.)
> Description : filter SAM file for soft and hard clipped alignments
> Most short read aligners perform local alignment of reads to the
> reference genome. Examples includes bwa mem, minimap2, and bowtie2
> (unless in --end-to-end mode). This means the ends of the read may not
> be part of the best alignment.
> .
> This can be caused by:
> .
> * adapter sequences (aren't in the reference)
> * poor quality bases (mismatches only make the alignment score worse)
> * structural variation in your sample compared to the reference
> * reads overlapping the start and end of contigs (including
> circular genomes)
> .
> Read aligners output a SAM file. Column 6 in this format stores the
> CIGAR string. which describes which parts of the read aligned and which
> didn't. The unaligned ends of the read can be "soft" or "hard" clipped,
> denoted with S and H at each end of the CIGAR string. It is possible for
> both types to be present, but that is not common. Soft and hard don't
> mean anything biologically, they just refer to whether the full read
> sequence is in the SAM file or not.
>
> Remark: This package is maintained by Debian Med Packaging Team at
> https://salsa.debian.org/med-team/samclip
>
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