Provided by: freebayes_1.0.2-1_amd64 bug

NAME

       bamleftalign - Left-aligns and merges the insertions and deletions in all alignments

SYNOPSIS

       [BAM data stream] | bamleftalign [options]

DESCRIPTION

       Left-aligns and merges the insertions and deletions in all alignments in stdin.  Iterates until each alignment is stable through a left-realignment step.

OPTIONS

       -f --fasta-reference FILE
              FASTA reference file to use for realignment (required)

       -d --debug
              Print debugging information about realignment process

       -s --suppress-output
              Don't write BAM output stream (for debugging)

       -m --max-iterations N
              Iterate the left-realignment no more than this many times

       -c --compressed
              Write compressed BAM on stdout, default is uncompressed

AUTHOR

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