ebanks b3f561710f Optimizations: ... 1. Only do calculations in UG for alternate allele with highest sum of quality scores (note that this also constitutes a bug fix for a precision problem we were having). 2. Avoid using Strings in DiploidGenotype when we can (it was taking 1.5% of my compute according to JProfiler) UG now runs in half the time for JOINT_ESTIMATE model. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2141 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-24 16:27:39 +00:00
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org/broadinstitute/sting	Optimizations:	2009-11-24 16:27:39 +00:00