Mark DePristo bb42c90f2b Use LinkedHashSets in incoming and outgoing vertex functions in BaseGraph ... -- Using a LinkedHashSet changed the md5 for HCTestComplexVariants.		2013-04-02 17:58:20 -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	Use LinkedHashSets in incoming and outgoing vertex functions in BaseGraph	2013-04-02 17:58:20 -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