droazen a50c40ed05 Temporary commit to aid in investigation of recent intermittent ... IndelRealignerIntegrationTest failures -- yes, it's the classic printf() debugging technique. Will revert in a day or two once I get the data I need :) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5896 348d0f76-0448-11de-a6fe-93d51630548a		2011-05-27 20:01:57 +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	Temporary commit to aid in investigation of recent intermittent	2011-05-27 20:01:57 +00:00
test	We now skip over all covering RODs in the BQSR as intended instead of just those which can be converted into a VariantContext. All the integration tests change because of subtleties in how certain dbsnp rod records are being converted into VCs. Added integration test which uses a bed file as the list of known polymorphic sites.	2011-05-27 16:32:17 +00:00