ebanks 47c4a70ac1 It turns out that it is legitimately possible for there to be reads that won't overlap within a target interval for cleaning. While we don't want to attempt cleaning, we also don't want to fail. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3682 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-30 15:50:44 +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	It turns out that it is legitimately possible for there to be reads that won't overlap within a target interval for cleaning. While we don't want to attempt cleaning, we also don't want to fail.	2010-06-30 15:50:44 +00:00
test/org/broadinstitute/sting	Added ability to clean using only known indels. Added integration test for it. Fixed vcf->vc conversion for indels which was busted.	2010-06-30 01:20:56 +00:00