ebanks 0a55fa5bb1 Completely refactored the Genotype Concordance module(s). ... Now PooledConcordance and GenotypeConcordance inherit from the same super class (and can therefore share data structures and functionality). Also, they now use ConcordanceTruthTable to keep track of necessary info. GenotypeConcordance passes integration tests. PooledConcordance needs to be finished by Chris. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1979 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-06 16:27:16 +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	Completely refactored the Genotype Concordance module(s).	2009-11-06 16:27:16 +00:00
test/org/broadinstitute/sting	a fix for a bug Andrey discovered: in read-based interval traversals we're dupplicating reads in rare cases. The problem was that to accomidate a bug in SAM JDK indexing, we were forced to add one to the stop of our QueryOverlapping() calls to ensure we always got all of the overlapping reads.	2009-11-05 05:26:33 +00:00