Guillermo del Angel c6672f2397 Intermediate (but necessary) fix for Beagle walkers: if a marker is absent in the Beagle output files, but present in the input vcf, there's no reason why it should be omitted in the output vcf. Rather, the vc is written as is from the input vcf		2011-09-13 16:57:37 -04:00
..
arguments	Removed -B support. Now explodes with error if -B provided.	2011-08-16 16:13:47 -04:00
datasources	Cleanup of codec locations. No more dbSNPHelper	2011-08-18 10:02:46 -04:00
executive	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
filters	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
iterators	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
refdata	Dynamic typing of vcf.gz files	2011-08-19 09:05:11 -04:00
report	GATKReport v0.2:	2011-08-03 00:24:47 -04:00
traversals	BugFix for unit test	2011-09-07 14:54:10 -04:00
walkers	Intermediate (but necessary) fix for Beagle walkers: if a marker is absent in the Beagle output files, but present in the input vcf, there's no reason why it should be omitted in the output vcf. Rather, the vc is written as is from the input vcf	2011-09-13 16:57:37 -04:00
EngineFeaturesIntegrationTest.java	Thanks to Mark for agreeing to transition from 'variants' back to 'variant'. I think I got them all but I've been jumping all around the code, so there might be a straggler or two.	2011-08-09 12:04:55 -04:00
GenomeAnalysisEngineUnitTest.java	Fixing broken paths to the testdata directory throughout the codebase.	2011-06-29 17:36:47 -04:00
WalkerManagerUnitTest.java	Moving more tools over to use the standard VC arg collection. Also, while I'm in there, I removed all of the empty references to @Requires given that it's no longer relevant.	2011-08-10 12:20:18 -04:00