Chris Hartl 74a17359a8 MathUtils.randomSubset() now uses Collections.shuffle() (indirectly, through the other methods ... that are tested), resulting in slightly different numbers of calls to the RNG, and ultimately different sets of selected variants. This commits updates the md5 values for the validation site selector integration test to reflect these new random subsets of variants that are selected.		2013-03-29 14:52:10 -04:00
..
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	Refactored the het (polyploid) consensus creation in ReduceReads.	2013-03-25 09:34:54 -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	Refactored the het (polyploid) consensus creation in ReduceReads.	2013-03-25 09:34:54 -04:00
haplotypecaller	Updating md5s due to changes in assembly graph creation algorithms and default parameter	2013-03-27 15:31:24 -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	Upgrades and changes to LeftAlignVariants, motivated by 1000G consensus indel production:	2013-03-29 10:02:06 -04:00