Eric Banks ba2c3b57ed Extended the allele-biased down-sampling functionality to handle reduced reads. ... Note that this works only in the case of pileups (i.e. coming from UG); allele-biased down-sampling for RR just cannot work for haplotypes. Added lots of unit tests for new functionality.		2013-04-26 11:23:17 -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	Trivial BQSR bug fixes and improvement	2013-04-11 17:08:35 -04:00
compression/reducereads	Various bug fixes for recent Reduce Reads additions plus solution implemented for low MQ reads.	2013-04-24 18:18:50 -04:00
diagnostics	Split class names into stratification and metrics	2013-04-24 14:15:49 -04:00
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	Extended the allele-biased down-sampling functionality to handle reduced reads.	2013-04-26 11:23:17 -04:00
haplotypecaller	Bugfix for FragmentUtils.mergeOverlappingPairedFragments	2013-04-25 11:11:15 -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	Update MD5s for VQSR header change	2013-04-16 11:45:45 -04:00
variantutils	Using --keepOriginalAC in SelectVariants was causing it to emit bad VCFs	2013-04-05 00:53:28 -04:00