bamgroupreads.py - Group BAM file by read IDs without sorting

        This manpage was written by Andreas Tille for the Debian distribution and
        can be used for any other usage of the program.

bamgroupreads.py 0.0.1+git20170413.ccd079d          June 2020                                BAMGROUPREADS.PY(1)

       Group BAM file by read IDs without sorting

       bamgroupreads.py - Group BAM file by read IDs without sorting

optionalarguments:-h, --help
              show this help message and exit

       -i BAM, --input BAM
              Input BAM file

       -r STR, --readgroup STR
              Read group(s) to extract (comma separated)

       -d, --reset_dups
              Reset duplicate flags

       -f, --fix_flags
              Fix mate flags for secondary reads

       -S     Input is SAM format

       -b     Output BAM format

       -u     Output uncompressed BAM format (implies -b)

       -M     split  reads  are  flagged  as secondary, not supplementary. For compatibility with legacy BWA-MEM
              "-M" flag

bamgroupreads.py [-h] [-i BAM] [-r STR] [-d] [-f] [-S] [-b] [-u] [-M]