SAM headers can't be modified – a new incompatible version of PySAM

[karel-brinda]

[samsift] 2018-02-26 17:39:53 SAMsift is starting.
Traceback (most recent call last):
  File "/Users/karel/miniconda/lib/python3.6/site-packages/samsift/samsift.py", line 276, in run
    header['PG'].insert(0,pg)
  File "pysam/libcalignmentfile.pyx", line 539, in pysam.libcalignmentfile.AlignmentHeader.__getitem__
KeyError: 'PG'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/karel/miniconda/bin/samsift", line 6, in <module>
    sys.exit(samsift.samsift.main())
  File "/Users/karel/miniconda/lib/python3.6/site-packages/samsift/samsift.py", line 418, in main
    sam_sift.run()
  File "/Users/karel/miniconda/lib/python3.6/site-packages/samsift/samsift.py", line 278, in run
    header['PG']=[pg]
  File "pysam/libcalignmentfile.pyx", line 536, in pysam.libcalignmentfile.AlignmentHeader.__setitem__
TypeError: AlignmentHeader does not support item assignment (use header.to_dict()

Refs:

• https://github.com/pysam-developers/pysam/pull/620/files
• AlignmentFile.header attribute has changed type pysam-developers/pysam#618