Mark DePristo 12475cc027 Display the active MappingQualityFilter if mmq > 0 in the HaplotypeCaller		2013-03-26 14:27:18 -04:00
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alignment	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
commandline	Fixed the logic of the @Output annotation and its interaction with 'required'.	2013-03-14 11:58:51 -04:00
gatk	Display the active MappingQualityFilter if mmq > 0 in the HaplotypeCaller	2013-03-26 14:27:18 -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	Created ListAnnotations utility (extends CommandLineProgram)	2013-03-20 06:15:27 -04:00
utils	PerReadAlleleLikelihoodMap getMostLikelyAllele returns an MostLikelyAllele objects now	2013-03-26 14:27:13 -04:00