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brittneybrinsfield / pysam

Automatically exported from code.google.com/p/pysam
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pysam.SamtoolsError #90

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?

>>> import pysam
>>> pysam.merge('o.bam 1.bam 2.bam')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/srv/raijen/lib/python2.7/site-packages/pysam-0.6-py2.7-linux-x86_64.egg/pysam/__init__.py", line 51, in __call__
    if retval: raise SamtoolsError( "\n".join( stderr ) )
pysam.SamtoolsError: ''

>>> pysam.view('aln.sorted.bam chr2:20,100,000-20,200,000')
open: No such file or directory
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/srv/raijen/lib/python2.7/site-packages/pysam-0.6-py2.7-linux-x86_64.egg/pysam/__init__.py", line 51, in __call__
    if retval: raise SamtoolsError( "\n".join( stderr ) )
pysam.SamtoolsError: ''

>>> pysam.idxstats('a.bam')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/srv/raijen/lib/python2.7/site-packages/pysam-0.6-py2.7-linux-x86_64.egg/pysam/__init__.py", line 51, in __call__
    if retval: raise SamtoolsError( "\n".join( stderr ) )
pysam.SamtoolsError: ''

What version of the product are you using? On what operating system?
pysam 0.6 with 64 bit ubuntu

Original issue reported on code.google.com by mictadlo on 29 Feb 2012 at 10:38

GoogleCodeExporter commented 9 years ago 
Hi,

thanks, I have changed the way error messages are caught from c-samtools.

Best wishes,
Andreas

Original comment by andreas....@gmail.com on 20 Nov 2012 at 9:00