hanna 1843684cd2 Cleanup: GATKEngine no longer needs to be lazy loaded, b/c the plugin directory no longer exists. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1287 348d0f76-0448-11de-a6fe-93d51630548a		2009-07-21 18:50:51 +00:00
..
examples	Update naming for consistency.	2009-06-30 22:03:21 +00:00
gatk	Switched to Reflections (http://code.google.com/p/reflections/) project for	2009-07-21 18:32:22 +00:00
indels	count X/N/etc. as mismatches for the NM attribute in the BAMs	2009-06-30 16:08:55 +00:00
piecemealannotator	Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.	2009-07-08 18:49:08 +00:00
somaticcoverage	Cleanup: GATKEngine no longer needs to be lazy loaded, b/c the plugin directory no longer exists.	2009-07-21 18:50:51 +00:00
utils	adding the GenotypeLikelihoodsWalker, which generates GLF genotype likelihoods that are pretty much identical to the samtools calls.	2009-07-14 16:57:18 +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