hanna d9398dc347 Remove some of the restrictions on getStart() and getStop(); getStart() and getStop() ... now do the minimum validation rather than the more rigorous only-within-the-contig-bounds header validation. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3027 348d0f76-0448-11de-a6fe-93d51630548a		2010-03-17 19:39:30 +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	Remove some of the restrictions on getStart() and getStop(); getStart() and getStop()	2010-03-17 19:39:30 +00:00
test/org/broadinstitute/sting	-Pushed base quals back down into SAMRecord; if -OQ is used, the SAMRecord quals get updated automatically	2010-03-17 16:00:10 +00:00