delangel 0aef5c0074 Totaly experimental, possibly useless annotation that logs # of MQ0 reads / total depth, TBD if VQSR can use it. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5905 348d0f76-0448-11de-a6fe-93d51630548a		2011-05-30 14:05:39 +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	Totaly experimental, possibly useless annotation that logs # of MQ0 reads / total depth, TBD if VQSR can use it.	2011-05-30 14:05:39 +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