Scott Thibault 82dcdc01c0 Merge branch 'master' into st_fpga_hmm ... Conflicts: protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java		2013-06-28 10:13:05 -05:00
..
alignment	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
commandline	Optimization to method for getting values in ArgumentMatch	2013-04-04 23:30:47 -04:00
gatk	Move DownsampleReadsQC walker to private	2013-06-25 15:48:44 -04:00
jna	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
queue	change the default VCFs gatherer of the GATK (not just the UG)	2013-01-18 15:03:12 -05:00
tools	CatVariants accepts reference files ending in any standard extension	2013-06-19 11:10:36 -04:00
utils	Merge branch 'master' into st_fpga_hmm	2013-06-28 10:13:05 -05:00