chartl 7fb3f2d3eb Annotator now buffers indel calls (prevents double-output from double-calls to map) ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3413 348d0f76-0448-11de-a6fe-93d51630548a		2010-05-21 16:34:34 +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	Annotator now buffers indel calls (prevents double-output from double-calls to map)	2010-05-21 16:34:34 +00:00
test/org/broadinstitute/sting	Changes to Depth of Coverage (added maximum base and mapping quality flags; with new integration tests -- because they use b36, and the other test uses hg18, it's in a different class (integration test system can't change refs on the fly). Initial change to VariantAnnotator to allow it to see extended event pilups; you currently have to throw the -dels flag; and it's specified as "very experimental". Yet,all the integration tests pass.	2010-05-21 13:02:01 +00:00