[Debian-med-packaging] How to deal with lintian warning "incorrect-path-for-interpreter" properly (Was: Bug#961661: ITP: samclip -- filter SAM file for soft and hard clipped alignments)

[Andreas Tille]

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 <tille at 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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