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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R	Improve queue script jobreport visualization script	2013-05-07 12:11:46 -04:00
c	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
java	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
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	ValidatingPileup was renamed to CheckPileup	2013-02-15 11:56:19 -05:00
perl	Split out contig names from Reference .fai file on white space (to support the GATK resource bundle's file human_g1k_v37.fasta.fai.gz, which does not use tab delimiters)	2012-06-07 16:56:32 -04:00
scala	Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements	2013-05-10 19:00:33 -04:00
testdata	Revert changes to exampleFASTA.fasta.fai for now to get tests passing again	2013-05-02 12:59:20 -04:00