[Debian-med-packaging] Bug#936989: [Help] Pysam issue in mapdamage ported to Python3 (Was: Bug#936989: mapdamage: Python2 removal in sid/bullseye)

[Andreas Tille]

Control: tags -1 help

Hi,

I've ported mapdamage to Python3 in git[1] using 2to3.  Unfortunately
there is an issue with pysam when I try to run the test suite,
particularly this command:


$ python3 rescale_test.py
EE
======================================================================
ERROR: test_longalignshortread (__main__.testCases)
Check if fails on an aligment longer than the read
----------------------------------------------------------------------
Traceback (most recent call last):
  File "rescale_test.py", line 56, in test_longalignshortread
    rescale.rescale_qual(ref,options,debug=True)
  File "/usr/lib/python3/dist-packages/mapdamage/rescale.py", line 311, in rescale_qual
    rescale_length_5p=options.rescale_length_5p,
AttributeError: 'Values' object has no attribute 'rescale_length_5p'

======================================================================
ERROR: test_paired_end_file (__main__.testPairedFile)
Test, paired end SAM file
----------------------------------------------------------------------
Traceback (most recent call last):
  File "rescale_test.py", line 46, in test_paired_end_file
    rescale.rescale_qual(ref,options,debug=True)
  File "/usr/lib/python3/dist-packages/mapdamage/rescale.py", line 311, in rescale_qual
    rescale_length_5p=options.rescale_length_5p,
AttributeError: 'Values' object has no attribute 'rescale_length_5p'

----------------------------------------------------------------------
Ran 2 tests in 0.034s

FAILED (errors=2)


Any help to finalise the Python3 port is welcome.

Kind regards

       Andreas.


[1] https://salsa.debian.org/med-team/mapdamage

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