Eric Banks 2f5ef6db44 New faster Smith-Waterman implementation that is edge greedy and assumes that ref and haplotype have same global start/end points. ... * This version inherits from the original SW implementation so it can use the same matrix creation method. * A bunch of refactoring was done to the original version to clean it up a bit and to have it do the right thing for indels at the edges of the alignments. * Enum added for the overhang strategy to use; added implementation for the INDEL version of this strategy. * Lots of systematic testing added for this implementation. * NOT HOOKED UP TO HAPLOTYPE CALLER YET. Committing so that people can play around with this for now.		2013-05-13 09:36:39 -04:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	New faster Smith-Waterman implementation that is edge greedy and assumes that ref and haplotype have same global start/end points.	2013-05-13 09:36:39 -04:00
test	New faster Smith-Waterman implementation that is edge greedy and assumes that ref and haplotype have same global start/end points.	2013-05-13 09:36:39 -04:00