depristo 349661b958 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. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5563 348d0f76-0448-11de-a6fe-93d51630548a		2011-04-03 15:35:09 +00:00
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qscript	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.	2011-04-03 15:35:09 +00:00
src/org/broadinstitute/sting	When getCanonicalHostName fails use getHostName instead of getHostAddress as it's more compatible with our mail servers.	2011-04-01 20:26:26 +00:00
test/org/broadinstitute/sting/queue	When @Gather annotation is missing (probably due to an unclean build) printing out the full field+class name for debugging purposes.	2011-03-30 21:43:37 +00:00