hanna 7389077b3b A few misc usability fixes: ... - Clarify the message emitted when -XL is supplied so I don't spend another half day chasing a bug that doesn't exist. - Crash with a helpful message when running -nt with non-TreeReducible walkers. - Crash with a helpful message when running -nt with reduceByInterval walkers. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3405 348d0f76-0448-11de-a6fe-93d51630548a		2010-05-20 19:02:02 +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	A few misc usability fixes:	2010-05-20 19:02:02 +00:00
test/org/broadinstitute/sting	Removing unused methods in QualityUtils; ReferenceContext now converting all bases to upper case, but can be disabled with static boolean	2010-05-20 12:38:06 +00:00