Eric Banks 8b9c6aae3e Fix bug in Reduce Reads that arises in multi-sample mode. ... * bitset could legitimately be in an unfinished state but we were trying to access it without finalizing. * added --cancer_mode argument per Mark's suggestion to force the user to explicitly enable multi-sample mode. * tests were easiest to implement as integration tests (this was a really complicated case).		2013-05-08 23:23:51 -04:00
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annotator	Update expected test output for Java 7	2013-05-01 16:18:01 -04:00
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	Fix bug in Reduce Reads that arises in multi-sample mode.	2013-05-08 23:23:51 -04:00
diagnostics	e# This is a combination of 2 commits.	2013-05-03 11:19:14 -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	Re-fix md5's that changed due to conflicting pushes	2013-05-03 14:59:16 -04:00
haplotypecaller	Re-fix md5's that changed due to conflicting pushes	2013-05-03 14:59:16 -04:00
indels	Secondary alignments were not handled correctly in IndelRealigner	2013-05-06 19:09:10 -04:00
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	- Fixed a small bug in the printout of molten data in GenotypeConcordance	2013-05-02 09:16:07 -04:00