Guillermo del Angel d4e7655d14 Added ability to call multiallelic indels, if -multiallelic is included in UG arguments. Simple idea: we genotype all alleles with count >= minIndelCnt. ... To support this, refactored code that computes consensus alleles. To ease merging of mulitple alt alleles, we create a single vc for each alt alleles and then use VariantContextUtils.simpleMerge to carry out merging, which takes care of handling all corner conditions already. In order to use this, interface to GenotypeLikelihoodsCalculationModel changed to pass in a GenomeLocParser object (why are these objects to hard to handle??). More testing is required and feature turned off my default.		2012-01-06 11:24:38 -05:00
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alignment	GATKSAMRecord refactor	2011-11-03 15:43:26 -04:00
analyzecovariates	No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path.	2011-10-27 14:17:07 -04:00
commandline	A toString() method for IntervalBindings	2011-11-23 11:56:12 -05:00
gatk	Added ability to call multiallelic indels, if -multiallelic is included in UG arguments. Simple idea: we genotype all alleles with count >= minIndelCnt.	2012-01-06 11:24:38 -05:00
jna	Updates to JobRunners from the Queue developer community and from running the WholeGenomePipeline:	2011-08-22 15:13:27 -04:00
queue	General improvements to Queue	2011-12-20 14:05:09 -05:00
utils	Initial commit of the Active Region Traversal. Not ready to be used by anyone yet.	2012-01-04 17:03:21 -05:00