Trying to upgrade python-pysam for Debian

[Andreas Tille <andreas@an3as.eu>]

Hi,

I tried to upgrade the Debian package of python-pysam to the latest upstream version
but realised two major problems:

   1. We would like to link against the Debian packaged copy of htslib but it
      seems the code copy inside python-pysam relies on symbols only available
      in version 0.0.1 while Debian currently has 0.2.0.  This is discussed on
      our mailing list here[1].

   2. Even if I try to ignore the Debian packaged version and use the internal
      code copy the test suite fails as well since the file TestUtils-py seems
      to be missing:

PYTHONPATH=/tmp/buildd/python-pysam-0.8.0/.pybuild/pythonX.Y_2.7/build python2.7 ./tabix_test.py 
Traceback (most recent call last):
  File "./pysam_test.py", line 15, in <module>
    from TestUtils import checkBinaryEqual
ImportError: No module named TestUtils

Any help to solve this issues would be appreciated.

Kind regards and thanks for providing pysam as free software

      Andreas.


[1] https://lists.debian.org/debian-med/2014/08/msg00091.html

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