Thank you John I will update to the last version of Samtools
On Wed, Dec 3, 2014 at 2:28 PM, John Marshall <j...@sanger.ac.uk> wrote:
> On 3 Dec 2014, at 18:39, Radhouane Aniba <arad...@gmail.com> wrote:
> > I noticed that samtools is not managing exit code for its programs the
> same way
>
> This is in general https://github.com/samtools/samtools/issues/51 . It
> takes somewhat disproportionate effort to fix all these as each instance
> reflects a separate piece of code, but we're gradually working through them.
>
> > where we have 'samtools sort' and 'samtools view' given files that do
> not exist, both should return an exit code of 1
> >
> > sort => exit code 0
> > view => exit code 1
> >
> > Any thoughts ?
>
>
> You are testing an old version of samtools. In the particular case of
> samtools sort's exit status, this was fixed a little over a year ago [1]:
>
> $ samtools-1.0 sort S222.bam S22.sorted; echo "exit code $?"
> [E::hts_open] fail to open file 'S222.bam'
> [bam_sort_core] fail to open file S222.bam
> exit code 1
>
> To be sure, there is room for improvement (and deduplication) in the error
> message, but the exit status indicates the failure as expected.
>
> John
>
> [1] See
> https://github.com/samtools/samtools/commit/d60c730cb9b87cb4b0d58e3dc7c184b551607bbd
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.
>
--
*Radhouane Aniba*
*Bioinformatics Scientist*
*BC Cancer Agency, Vancouver, Canada*
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