bthomas 5b34bb9ab0 Adding three minor new features: ... + -L all now walks over all intervals + if a -L argument is passed with a .list extension, and file does not exist, returns a \ File Not Found error instead of "bad interval" error. We plan to soon revisit interval \ lists and generate a concrete list of filenames, so this is likely temporary. + Error is thrown if the start position on an interval is higher number than the end position. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3021 348d0f76-0448-11de-a6fe-93d51630548a		2010-03-17 16:24:10 +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	Adding three minor new features:	2010-03-17 16:24:10 +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