asivache 94d74d4f78 Multiple instances of the same consensus were all living happily together in the set of alt consensuses. As the result, we have been taking considerable performance hit from trying to align all reads to those instances over and over again. Fixed. Only one copy of any given alt consensus is now stored. ... in class Consensus: 1) use Arrays.equals() to compare java arrays!! 2) if object overrides equals() it also MUST provide appropriate hashCode() (thanks, Matt) As a side effect, a number of commented out debug prints are committed, still need them... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2879 348d0f76-0448-11de-a6fe-93d51630548a		2010-02-24 02:09:50 +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	Multiple instances of the same consensus were all living happily together in the set of alt consensuses. As the result, we have been taking considerable performance hit from trying to align all reads to those instances over and over again. Fixed. Only one copy of any given alt consensus is now stored.	2010-02-24 02:09:50 +00:00
test/org/broadinstitute/sting	adding code to deal with the off-spec situation where our minimum likelihood is above the GLF max of 255.	2010-02-22 22:27:39 +00:00