hanna c3b68cc58d Rethinking DownsamplingLocusIteratorByState with a flattened read structure. Samples are kept ... independent while processing, and only merged back in a priority queue if necessary in a special variant of the ReadBackedPileup. This code is not live yet except in the case of naive deduping. Downsampling by sample temporarily disabled, and the ReadBackedPileup variant is sketchy and not well integrated with StratifiedAlignmentContext or the walkers. Cleanup to follow. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3540 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-13 01:47:02 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src/org/broadinstitute/sting	Rethinking DownsamplingLocusIteratorByState with a flattened read structure. Samples are kept	2010-06-13 01:47:02 +00:00
test/org/broadinstitute/sting	Fixing a VCF bug for Sendu: we weren't emitting flags (booleans) correctly in VCF3.3 (rev'ed tribble for this).	2010-06-11 16:42:06 +00:00