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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genotyper	Extended the allele-biased down-sampling functionality to handle reduced reads.	2013-04-26 11:23:17 -04:00
haplotype	LD-based merging algorithm for nearby events in the haplotypes	2013-04-08 12:47:48 -04:00
haplotypeBAMWriter	Slightly improved Smith-Waterman parameter values for HaplotypeCaller Path comparisons	2013-04-11 18:22:55 -04:00
nanoScheduler	Fix caching indices in the PairHMM	2013-04-08 11:05:12 -04:00
pairhmm	Fix caching indices in the PairHMM	2013-04-08 11:05:12 -04:00
recalibration	Added hidden mode for BQSR to force all read groups to be the same one.	2013-05-06 19:09:10 -04:00
smithwaterman	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
ContigComparatorUnitTest.java	Generalize and fixup ContigComparator	2013-02-09 09:52:13 -05:00