bamfixflags.py - filter readgroup(s) from a BAM file

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

bamfixflags.py 0.0.1+git20170413.ccd079d            June 2020                                  BAMFIXFLAGS.PY(1)

       filter readgroup(s) from a BAM file

       bamfixflags.py - filter readgroup(s) from a BAM file

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

       -i BAM, --input BAM
              Input BAM file

       -l FILE, --lib_info FILE
              SVTyper JSON file of library information

       -n INT Output first n alignments and quit

       -S     Input is SAM format

       -b     Output BAM format

       -u     Output uncompressed BAM format (implies -b)

bamfixflags.py [-h] [-i BAM] -l FILE [-n INT] [-S] [-b] [-u]