ebanks cfb33d8e12 Filtering optimizations are now live for UGv2. Instead of re-computing filtered bases at every locus, they are computed just once per read and stored in the read itself. Eyeballing the results on the ~600 sample set from 1kg, we cut out ~40% of the runtime! QUALs are now sometimes different from UGv1 because I noticed a bug in v1 where samples with spanning deletions only were assigned ref calls instead of no-calls which ever so slightly affects the QUAL. Not a big deal though. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4494 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-14 05:04:28 +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	Filtering optimizations are now live for UGv2. Instead of re-computing filtered bases at every locus, they are computed just once per read and stored in the read itself. Eyeballing the results on the ~600 sample set from 1kg, we cut out ~40% of the runtime! QUALs are now sometimes different from UGv1 because I noticed a bug in v1 where samples with spanning deletions only were assigned ref calls instead of no-calls which ever so slightly affects the QUAL. Not a big deal though.	2010-10-14 05:04:28 +00:00
test	This is simultaneously a minor and major change to VariantEval, so take heed:	2010-10-13 22:26:15 +00:00