Re: HTSlib code copy in python-pysam.

[Andreas Tille <andreas@an3as.eu>]

Hi Charles,

On Wed, Aug 20, 2014 at 07:08:40PM +0900, Charles Plessy wrote:
> Le Wed, Aug 20, 2014 at 07:06:53PM +0900, Charles Plessy a écrit :
> > Le Wed, Aug 20, 2014 at 11:10:32AM +0200, Andreas Tille a écrit :
> > > 
> > > --- a/setup.py
> > > +++ b/setup.py
> > > @@ -32,7 +32,7 @@ IS_PYTHON3 = sys.version_info[0] >= 3
> > >  #         pysam.
> > >  # external: use shared libhts.so compiled outside of
> > >  #           pysam
> > > -HTSLIB = "separate"
> > > +HTSLIB = "external"
> > >  HTSLIB_DIR = []
> > 
> > Thanks for the hint.  For the moment it causes the build to fail
> 
> I see on the commit list that you solved the problem.  Thanks !

It seems to be a simple problem in setup.py.  However, independently
whether I activate the patch or not the tests do not work.  While I
checked that the symbol sam_itr_queryi is known via

$ strings /usr/lib/python2.7/dist-packages/pysam/csamfile.x86_64-linux-gnu.so | grep sam_itr_queryi
sam_itr_queryi

I get

$ python pysam_test.py 
Traceback (most recent call last):
  File "pysam_test.py", line 8, in <module>
    import pysam
  File "/usr/lib/python2.7/dist-packages/pysam/__init__.py", line 5, in <module>
    import pysam.csamfile as csamfile
ImportError: /usr/lib/python2.7/dist-packages/pysam/csamfile.x86_64-linux-gnu.so: undefined symbol: sam_itr_queryi

(same for tabix_test.py).  So I guess this is no issue connected to
htslib.  Any idea why the tests are failing would be helpful.

Kind regards

      Andreas.

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