ebanks 5d85bd9671 By default, VF should ask for deleted bases so that they show up in coverage. ... The Strand filter then needs to ignore those bases when determining bias. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1636 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-16 16:46:09 +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	By default, VF should ask for deleted bases so that they show up in coverage.	2009-09-16 16:46:09 +00:00
test/org/broadinstitute/sting	Fix for problem where err stream remapped to output stream in certain cases, (hopefully) completing Matt's hat trick of fail. Thanks, unit tests.	2009-09-16 08:33:56 +00:00