asivache ee1dc6092f 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. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3058 348d0f76-0448-11de-a6fe-93d51630548a		2010-03-22 17:37:52 +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	We also have to allow the window to be (partially) outside the bounds and trimming to the contig size is not enough (thanks to shards). Now we trim to the current bounds too (i.e. if the interval is not completely within current bounds, we create reference context that contains only bases from the overlap between the interval and the bounds).	2010-03-22 17:36:29 +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