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gap opening realigner for BAM data streams
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ekg/ogap
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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
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