[Debian-med-packaging] Bug#799698: samtools: Unknown command "faidx" on (kfreebsd-)i386

[Afif Elghraoui]

Control: severity -1 serious
Control: tags -1 + pending

>   In the later case, this bug will be fixed by just adding a
> Breaks: python-pysam (<< version-that-fixe-pysam-with-new-samtools)
> in the samtools package. But, python-pysam will then need to be
> fixed/updated in order to work with the new samtools.
> 
>> Builds of python-pysam for i386 and kfreebsd-i386 failed:
>>
>>    samtools faidx ex1.fa
>>    Unknown command "faidx".
>>
>> This error appears to indicate a deficiency in samtools; could you
>> please take a look?
> 
> deficiency or removal/change of a old tool ? I did not checked into
> samtools changelog yet.
>

Aaron is right that something is wrong. It appears to be that, in my
push towards more stringent policy compliance, I inadvertently replaced
the main samtools executable with a renamed version of samtools.pl


The fixed package is now in git and awaits upload.

Thanks and regards
Afif


-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name