Mark DePristo 6d7d21ca47 Bugfix for incorrect branch diamond merging algorithm ... -- Previous version was just incorrectly accumulating information about nodes that were completely eliminated by the common suffix, so we were dropping some reference connections between vertices. Fixed. In the process simplified the entire algorithm and codebase -- Resolves https://jira.broadinstitute.org/browse/GSA-884		2013-03-20 22:54:37 -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	Clear ReduceReads name cache after each set of reads produced by ReduceReadsStash.	2013-03-19 14:12:33 -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	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
genotyper	Fix to issue encountered when running HaplotypeCaller in GGA mode with data from other 1000G callers.	2013-03-20 14:30:37 -04:00
haplotypecaller	Bugfix for incorrect branch diamond merging algorithm	2013-03-20 22:54:37 -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	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
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	Added new walker to split MNPs into their allelic primitives (SNPs).	2013-03-05 23:16:42 -05:00