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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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	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
test	Merged bug fix from Stable into Unstable	2012-01-05 21:51:48 -05:00