[Debian-med-packaging] Bug#671524: Dropping coverage patch in Samtools ?

[Dominique Belhachemi]

On Wed, Nov 26, 2014 at 3:49 AM, Charles Plessy <plessy at debian.org> wrote:

>
> in recent versions of samtools, the mpileup command has a new option
> to specify the coverage at run time.
>
> Would it be fine to drop our patch that was raising the default coverage
> cap
> from 8,000 to 1,000,000 ?  If yes, do you think we need to mention it as a
> NEWS
> entry ?
>
>
Hi Charles,

I think we still need the patch. samtools depth doesn't support the -d flag.

$ samtools --version
samtools 1.1
Using htslib 1.1
Copyright (C) 2014 Genome Research Ltd.

$ samtools depth

Usage: samtools depth [options] in1.bam [in2.bam [...]]
Options:
   -b <bed>            list of positions or regions
   -f <list>           list of input BAM filenames, one per line [null]
   -l <int>            minQLen
   -q <int>            base quality threshold
   -Q <int>            mapping quality threshold
   -r <chr:from-to>    region

$ ./samtools mpileup

Usage: samtools mpileup [options] in1.bam [in2.bam [...]]

Input options:
...
  -d, --max-depth INT     max per-BAM depth; avoids excessive memory usage
[250]
...

Best
-Dominique
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