README

usage: [BAM data stream] | ./ogap [options]

Realigns alignments meeting specified criteria (number of gaps, mismatches) using
Smith-Waterman parameters optimized to open gaps and eliminate mismatches and
writes the stream of alignments as BAM on stdout.

arguments:
    -f --fasta-reference FILE  FASTA reference file to use for realignment (required)
    -d --debug                 Print debugging information about realignment process
    -w --flanking-window BP    The number of bases on the left and right to attempt to
                               align to (default 300bp).
    -c --max-position-delta    Maximum number of bases the start or end of the alignment
                               may change when realigning (default 200bp)
    -m --match-score           The match score (default 10.0)
    -n --mismatch-score        The mismatch score (default -20.0)
    -g --gap-open-penalty      The gap open penalty (default 15.0)
    -e --gap-extend-penalty    The gap extend penalty (default 0.0)
    -s --suppress-output       Don't output BAM on stdout