ebanks fddca032bb Initial commit of v2.0 of the cleaner. DO NOT USE. (this means you, Chris) ... Cleaned up SW code and started moving over everything to use byte[] instead of String or char[]. Added a wrapper class for SAMFileWriter that allows for adding reads out of order. Not even close to done, but I need to commit now to sync up with Andrey. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2712 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-27 21:36:42 +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	Initial commit of v2.0 of the cleaner. DO NOT USE. (this means you, Chris)	2010-01-27 21:36:42 +00:00
test/org/broadinstitute/sting	Incremental update 2 -- refined allele and VariantContext classes; support for AttributedObject class; extensive testing for Allele class, and partial for VariantContext. Now possible to easily convert dbSNP to VariantContext.	2010-01-27 17:19:37 +00:00