Mark DePristo c191d7de8c Critical bugfix for CommonSuffixSplitter ... -- Graphs with cycles from the bottom node to one of the middle nodes would introduce an infinite cycle in the algorithm. Created unit test that reproduced the issue, and then fixed the underlying issue.		2013-04-02 09:22:33 -04:00
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annotator	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
beagle	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
bqsr	Replace uses of NestedHashMap with NestedIntegerArray.	2013-02-27 14:03:39 -05:00
compression/reducereads	Updated AssessReducedQuals and applied it systematically to all ReduceReads integration tests.	2013-03-31 00:27:14 -04:00
diagnostics	walker to calculate per base coverage distribution	2013-02-07 16:33:05 -05:00
diffengine	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
fasta	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
filters	Added small feature to VariantFiltration to filter sites outside of a given mask:	2013-03-31 08:48:16 -04:00
genotyper	PairHMM rework	2013-03-30 10:50:06 -04:00
haplotypecaller	Critical bugfix for CommonSuffixSplitter	2013-04-02 09:22:33 -04:00
indels	Fixed IndelRealigner reference length bug (GSA-774)	2013-02-19 16:00:36 -05:00
phasing	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
validation	MathUtils.randomSubset() now uses Collections.shuffle() (indirectly, through the other methods	2013-03-29 14:52:10 -04:00
varianteval	Move some VCF/VariantContext methods back to the GATK based on feedback	2013-01-29 16:56:55 -05:00
variantrecalibration	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
variantutils	Big bad bug fix: feature added to LeftAlignAndTrimVariants to left align multiallelic records didn't work.	2013-03-30 19:31:28 -04:00