Updating to use python3 and updated pysam

[DavidStreid]

Updating bamkit to use python3 and updated pysam syntax

Changes

python3

• print(), exceptions, etc.

pysam

• Samfile -> AlignmentFile; AlignedRead -> AlignedSegment [pysam-0.8.1]
• AlignedSegment:
  • opt() -> get_tag() [pysam-0.8.2]
  • is_duplicate
  • is_supplementary instead of flagcheck.flag & 2048 == 2048
  • cigar -> cigartuples
  • qname -> queryname

Testing

vyx-L-HGL63D9FVK:bamkit dstreid$ python3 
Python 3.11.6 (main, Nov  2 2023, 04:39:43) [Clang 14.0.3 (clang-1403.0.22.14.1)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import bamcleanheader
>>> import bamfilterrg
>>> import bamfixflags
>>> import bamgroupreads
>>> import bamheadrg
>>> import bamlibs
>>> import bamtofastq
>>> exit()