hanna 3767adb0bb Processing intervals as they stream in means much lower memory usage and ... quicker runtime. Making change as minimal as possible to avoid conflicts with BT's incoming patch. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3061 348d0f76-0448-11de-a6fe-93d51630548a		2010-03-22 22:04:45 +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	Processing intervals as they stream in means much lower memory usage and	2010-03-22 22:04:45 +00:00
test/org/broadinstitute/sting	Test updated. Now we do not throw an exception when locus interval is out of bounds, we just return silently a reference context trimmed to the current shard boundaries. New test checks for trimming.	2010-03-22 17:37:52 +00:00