asivache 543aefc3d7 Fixing the bug introduced with the earlier commit. When trimming locus to the current bases, we need to take into account expanded boundaries (for windowed reference traversals) ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3059 348d0f76-0448-11de-a6fe-93d51630548a		2010-03-22 19:20:34 +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	Fixing the bug introduced with the earlier commit. When trimming locus to the current bases, we need to take into account expanded boundaries (for windowed reference traversals)	2010-03-22 19:20:34 +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