Ryan Poplin 11001ab9a2 Adding option to HaplotypeCaller to genotype the events on the chosen haplotypes as independent events. The filtered reads are now kept around so they can be passed to the variant annotations. Unfortunately the filtered reads aren't assigned a likelihood yet so they are all thrown in the Allele.NO_CALL bin.		2012-04-19 11:32:10 -04:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Adding option to HaplotypeCaller to genotype the events on the chosen haplotypes as independent events. The filtered reads are now kept around so they can be passed to the variant annotations. Unfortunately the filtered reads aren't assigned a likelihood yet so they are all thrown in the Allele.NO_CALL bin.	2012-04-19 11:32:10 -04:00
test	minor misc optimizations to PairHMM	2012-04-18 15:02:26 -04:00