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

[Andreas Tille]

Hi,

other uploaders of pysam in CC: When building htseq with current pysam
in unstable I get:

...
All 26 tests passed.

Doctest of tss.rst:
**********************************************************************
File "../doc/tss.rst", line 211, in tss.rst
Failed example:
    for almnt in sortedbamfile[ window ]:
        print almnt   #doctest:+ELLIPSIS +NORMALIZE_WHITESPACE
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest tss.rst[27]>", line 1, in <module>
        for almnt in sortedbamfile[ window ]:
      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 "../doc/tss.rst", line 220, in tss.rst
Failed example:
    almnt.iv.length = fragmentsize
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      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
**********************************************************************
1 items had failures:
   6 of  37 in tss.rst
***Test Failed*** 6 failures.
6 of 37 tests failed.


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

Kind regards

    Andreas.

-- 
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