hanna 05deb8796b Simplify handling of reference sequence for unmapped reads. Improvement made based on a suggestion from Alec. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2475 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-29 21:06:20 +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	Simplify handling of reference sequence for unmapped reads. Improvement made based on a suggestion from Alec.	2009-12-29 21:06:20 +00:00
test/org/broadinstitute/sting	Recalibrator now uses NestedHashMap instead of NHashMap. The keys are now nested hash maps instead of Lists of Comparables. These results in a big speed up (thanks Tim!). There is still a little bit of clean up to do, but everything works now.	2009-12-29 21:01:32 +00:00