depristo b316c9a590 Renamed StratifyAlignmentContext to AlignmentContextUtils, and StatiefyContextType to ReadOrientation. Also, went through the system and deleted all references to second bases. That ship passed long ago. This was the actual commit, the last was an intellij error ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5564 348d0f76-0448-11de-a6fe-93d51630548a		2011-04-03 15:36:17 +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	Renamed StratifyAlignmentContext to AlignmentContextUtils, and StatiefyContextType to ReadOrientation. Also, went through the system and deleted all references to second bases. That ship passed long ago. This was the actual commit, the last was an intellij error	2011-04-03 15:36:17 +00:00
test	Fix for bug GSA-441: BAM file list with blank lines gives a confusing error	2011-04-01 15:04:35 +00:00