rpoplin f0a234ab29 TableRecalibration is now much smarter about hashing calculations, taking advantage of the sequential recalibration formulation. Instead of hashing RecalDatums it hashes the empirical quality score itself. This cuts the runtime by 20 percent. TableRecalibration also now skips over reads with zero mapping quality (outputs them to the new bam but doesn't touch their base quality scores). ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2069 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-18 16:47:44 +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	TableRecalibration is now much smarter about hashing calculations, taking advantage of the sequential recalibration formulation. Instead of hashing RecalDatums it hashes the empirical quality score itself. This cuts the runtime by 20 percent. TableRecalibration also now skips over reads with zero mapping quality (outputs them to the new bam but doesn't touch their base quality scores).	2009-11-18 16:47:44 +00:00
test/org/broadinstitute/sting	Added - a walker that outputs relevant information about false negatives given a bunch of hapmap individuals and corresponding integration tests for it.	2009-11-18 15:47:52 +00:00