[Debian-med-packaging] Bug#797793: samtools update seems to breaks even more tests

[Afif Elghraoui]

Hi, Andreas,

على السبت  5 كانون الأول 2015 ‫23:53، كتب Andreas Tille:
> Hi,
> 
> other uploaders of pysam in CC: When building htseq with current pysam
> in unstable I get:
> 

[...]

>       File "/build/htseq-0.6.1p1/build/lib.linux-x86_64-2.7/HTSeq/__init__.py", line 976, in __getitem__
>         if not self.sf._hasIndex():
>     AttributeError: 'pysam.csamfile.Samfile' object has no attribute '_hasIndex'
> **********************************************************************
[...]
>       File "<doctest tss.rst[29]>", line 1, in <module>
>         almnt.iv.length = fragmentsize
>     AttributeError: 'NoneType' object has no attribute 'length'
> **********************************************************************
> File "../doc/tss.rst", line 221, in tss.rst
> Failed example:
>     almnt
> Expected:
>     <SAM_Alignment object: Read 'SRR001432.205754 USI-EAS21_0008_3445:8:5:217:355 length=25' aligned to 1:[145440800,145441000)/->
> Got:
>     <SAM_Alignment object: Read 'SRR001432.299973 USI-EAS21_0008_3445:8:7:811:450 length=25', not aligned>
> 
> ...
> 
>     NameError: name 'start_in_window' is not defined

[...]
> 
> Any idea how to fix this.  Htslib upstream is unresponsive even to less
> hard issues.
> 

The recent pysam release dropped support for some deprecated interfaces
and this package appears to have been affected. I can prepare a patch
for those pysam issues as I did for pbcore [1]

By the way, I had checked rdepends of pysam to look out for packages
that may have problems later on due to the change, but the only way I
know how to do that is using apt-cache rdepends. This has limitations
because I use Stable and can't get an up-to-date report without changing
my sources.list

regards
Afif

1.
http://anonscm.debian.org/cgit/debian-med/python-pbcore.git/tree/debian/patches/fix-pysam-compatibility.patch
which fixed http://bugs.debian.org/805687

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