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. -- http://fam-tille.de