jmaguire 4f6d26849f Behold MultiSampleCaller! ... Complete re-write of PoolCaller algorithm, now basically beta quality code. Improvements over PoolCaller include: - more correct strand test - fractional counts from genotypes (which means no individual lod threshold needed) - signifigantly cleaner code; first beta-quality code I've written since BaitDesigner so long ago. - faster, less likely to crash! git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1020 348d0f76-0448-11de-a6fe-93d51630548a		2009-06-16 20:03:24 +00:00
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gatk	Behold MultiSampleCaller!	2009-06-16 20:03:24 +00:00
indels	border case bug fixes	2009-06-09 04:33:15 +00:00
samples	Hypen-style xml output. Much sexier.	2009-05-08 01:04:40 +00:00
somaticcoverage	checked in a sample xml file used to store the defaults for the SomaticCoverage tool, and added it to the SomaticCoverage.jar in build.sml. Also added a inputStream marshalling method to the GATKArgumentCollection.	2009-06-10 20:46:16 +00:00
utils	Behold MultiSampleCaller!	2009-06-16 20:03:24 +00:00
ValidateSAM.java	Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard...	2009-05-28 20:13:01 +00:00