aaron 4d75b26b7a Removing the code that made the ROD system case insensitive. Anyone using specific ROD names in their classes should take care in naming required tracks; All lowercase is the best practice. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3184 348d0f76-0448-11de-a6fe-93d51630548a		2010-04-16 06:17:31 +00:00
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alignment	adding the initial ROD for Reads support; more convenience methods in ReadMetaDataTracker to come.	2010-03-03 15:56:44 +00:00
analyzecovariates	Removed the StingException when mkdir fails for Sendu in AnalyzeCovariates. Incremental updates to VariantOptimizer.	2010-03-16 19:45:02 +00:00
gatk	Removing the code that made the ROD system case insensitive. Anyone using specific ROD names in their classes should take care in naming required tracks; All lowercase is the best practice.	2010-04-16 06:17:31 +00:00
oneoffprojects	Moving VE2 to core; calling it "VariantEval" (one more checkin coming)	2010-04-15 20:25:47 +00:00
playground	Moving to archive as it's no longer supported	2010-04-15 22:10:42 +00:00
utils	Utility method added: getQualsInCycleOrder(read) - examines the read and returns its quals in the order the machine read them (i.e. always from cycle 1 to cycle N). Simply inverts quals if the read happens to be rc-aligned :)	2010-04-16 00:15:57 +00:00