ebanks a048f5cdf1 -Refactored JointEstimation code so that pooled calling will work ... -Use phred-scale for fisher strand test -Use only 2N allele frequency estimation points git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2059 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-17 20:21:15 +00:00
..
alignment	Finally reinstate the iterator-style interface. Get rid of some scaffolding code.	2009-11-16 02:34:19 +00:00
gatk	-Refactored JointEstimation code so that pooled calling will work	2009-11-17 20:21:15 +00:00
playground	CountCovariates now warns the user if they didn't supply a dbSNP rod file. Thanks Kiran for the use case.	2009-11-16 18:44:54 +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	Ignoring deletions in the primary pileup by default was causing the primary pileup to become shorter than the secondary pileup when building up the secondary base pileup string. This fix makes sure to include the primary Ds within the pileup so that not only are the pileups guaranteed to be the same size, the same offsets will truly correspond with the same read.	2009-11-17 17:20:13 +00:00