Mauricio Carneiro ee9a56ad27 Fix subtle bug in the ReduceReads stash reported by Adam ... * The tailSet generated every time we flush the reads stash is still being affected by subsequent clears because it is just a pointer to the parent element in the original TreeSet. This is dangerous, and there is a weird condition where the clear will affects it. * Fix by creating a new set, given the tailSet instead of trying to do magic with just the pointer.		2012-02-23 18:35:25 -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	Fix subtle bug in the ReduceReads stash reported by Adam	2012-02-23 18:35:25 -05:00
test	Added support for breakpoint alleles	2012-02-23 12:14:48 -05:00