#6 `CrossMap.py bam` broken with pysam >=0.14

[Nicola Soranzo]

Fatal error: Exit code 1 ()
Insert size = 200.000000
Insert size stdev = 30.000000
Number of stdev from the mean = 3.000000
Add tags to each alignment = False
@ 2018-05-24 20:13:02: Read chain_file:  /usr/users/ga002/soranzon/software/nsoranzo_tools-iuc/tools/crossmap/test-data/cached_locally/aToB.over.chain
Traceback (most recent call last):
File "/usr/users/ga002/soranzon/miniconda3/envs/__crossmap@0.2.7/bin/CrossMap.py", line 1686, in <module>
crossmap_bam_file(mapping = mapTree, chainfile = chain_file, infile = in_file, outfile_prefix = out_file, chrom_size = targetChromSizes, IS_size=options.insert_size, IS_std=options.insert_size_stdev, fold=options.insert_size_fold,addtag=False)
File "/usr/users/ga002/soranzon/miniconda3/envs/__crossmap@0.2.7/bin/CrossMap.py", line 773, in crossmap_bam_file
(new_header, name_to_id) = sam_header.bam_header_generator(orig_header = sam_ori_header, chrom_size = chrom_size, prog_name="CrossMap",prog_ver = __version__, format_ver=1.0,sort_type = 'coordinate',co=comments)
File "/usr/users/ga002/soranzon/miniconda3/envs/__crossmap@0.2.7/lib/python2.7/site-packages/cmmodule/sam_header.py", line 27, in bam_header_generator
bamHeaderLine['HD'] = {'VN':format_ver,'SO':sort_type}
File "pysam/libcalignmentfile.pyx", line 537, in pysam.libcalignmentfile.AlignmentHeader.__setitem__
TypeError: AlignmentHeader does not support item assignment (use header.to_dict()

[Nicola Soranzo]

Works fine if I downgrade pysam to 0.13.0 (I'm using a Conda environment).

[Liguo Wang]

This issue is now fixed in CrossMap v0.3.6.