Mark DePristo 33ecec535d Turn off the LD merging code by default ... -- It's just too hard to interpret the called variation when we merge variants via LD. -- Can now be turned on with -mergeVariantsViaLD -- Update MD5s		2013-04-09 10:08:06 -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	Don't allow users to specify keys and IDs that contain angle brackets or equals signs (not allowed in VCF spec).	2013-04-05 00:52:32 -04:00
genotyper	Fix caching indices in the PairHMM	2013-04-08 11:05:12 -04:00
haplotypecaller	Turn off the LD merging code by default	2013-04-09 10:08:06 -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	Using --keepOriginalAC in SelectVariants was causing it to emit bad VCFs	2013-04-05 00:53:28 -04:00