ebanks 11d950abe0 No longer allow the lod_threshold argument - use confidence instead. ... Have UG output qscores in all cases. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1968 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-03 16:18:51 +00:00
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alignment	The BWA/C bindings were triggering the local aligner to repeatedly reload the	2009-11-03 00:01:55 +00:00
gatk	No longer allow the lod_threshold argument - use confidence instead.	2009-11-03 16:18:51 +00:00
playground	improvements to VCF and variant eval support of VCF -- now listens to the filter field	2009-11-03 12:09:30 +00:00
secondarybase	Rev'ing Picard, which includes the update to get all the reads in the query region (GSA-173). With it come a bunch of fixes, including retiring the FourBaseRecaller code, and updated md5 for some walker tests.	2009-09-30 20:37:59 +00:00
utils	improvements to VCF and variant eval support of VCF -- now listens to the filter field	2009-11-03 12:09:30 +00:00