hanna 23e9e29964 Changed reads traversals from providing a LocusContext from which the reference sequence ... could be extracted to a char[] containing the reference bases. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@657 348d0f76-0448-11de-a6fe-93d51630548a		2009-05-11 22:45:11 +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	Changed reads traversals from providing a LocusContext from which the reference sequence	2009-05-11 22:45:11 +00:00
test/org/broadinstitute/sting	Switch over to the GenomeAnalysisEngine/CommandLineGATK system from the GenomeAnalysisTK code.	2009-05-11 22:05:58 +00:00