Eric Banks 0055a6f1cd Merge pull request #45 from broadinstitute/mc_fix_indelrealigner_GSA-774 ... Fix to the Indel Realigner bug described in GSA-774		2013-02-19 16:16:48 -08:00
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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	PrintReads writes a header when used with -BQSR	2013-02-14 22:19:14 -05:00
compression/reducereads	Fixing the failing RR integration tests.	2013-02-06 12:40:56 -05:00
diagnostics	walker to calculate per base coverage distribution	2013-02-07 16:33:05 -05:00
diffengine	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
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 for calculating read pos rank sum test with reads that are informative but don't actually overlap the variant due to some hard clipping.	2013-02-19 14:09:24 -05:00
haplotypecaller	Fix for calculating read pos rank sum test with reads that are informative but don't actually overlap the variant due to some hard clipping.	2013-02-19 14:09:24 -05:00
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	Replace org.broadinstitute.variant with jar built from the Picard repo	2013-02-05 17:24:25 -05:00