Bamkit

• bamcleanheader.py(1) remove illegal and malformed fields from a BAM file's header
• bamfilterrg.py(1) filter readgroup(s) from a BAM file
• bamfixflags.py(1) filter readgroup(s) from a BAM file
• bamgroupreads.py(1) Group BAM file by read IDs without sorting
• bamheadrg.py(1) Inject readgroup info
• bamlibs.py(1) output comma delimited string of read group IDs for each library
• bamtofastq.py(1) Convert a coordinate sorted BAM file to FASTQ