Eric Banks 07ad8c78a9 More tools moved over. Fixed the VariantContextIntegrationTest which was not useful because the md5s were all removed. In the future, instead of removing md5s (putting it in 'parameterization' mode), you should instead use @Test{enabled=false} since it's easier to track.		2011-08-10 14:24:40 -04:00
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annotator	SnpEffCodec now implements SelfScopingFeatureCodec so that we no longer have to specify the codec name on the command line for SnpEff files.	2011-08-10 13:12:09 -04:00
beagle	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
coverage	Moving more tools over to the new rod system	2011-08-10 13:42:35 -04:00
diffengine	GATKReport v0.2:	2011-08-03 00:24:47 -04:00
fasta	More updates to be consistent with the new rod syntax.	2011-08-09 10:11:37 -04:00
filters	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
genotyper	Moving more tools over to the new rod system	2011-08-10 13:42:35 -04:00
indels	Moving more tools over to the new rod system	2011-08-10 13:42:35 -04:00
phasing	Moving more tools over to the new rod system	2011-08-10 13:42:35 -04:00
qc	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
recalibration	Reverting a bunch of bad -B type drops	2011-08-08 16:57:38 -04:00
validation	Continuing progress towards RodBinding 1.0	2011-08-03 17:19:28 -04:00
varianteval	Reverting a bunch of bad -B type drops	2011-08-08 16:57:38 -04:00
variantrecalibration	Updating VQSR for new RodBinding syntax. Cleaning up indel specific parts of VQSR.	2011-08-10 10:20:37 -04:00
variantutils	More tools moved over. Fixed the VariantContextIntegrationTest which was not useful because the md5s were all removed. In the future, instead of removing md5s (putting it in 'parameterization' mode), you should instead use @Test{enabled=false} since it's easier to track.	2011-08-10 14:24:40 -04:00
BAQIntegrationTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
ClipReadsWalkersIntegrationTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
PileupWalkerIntegrationTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
PrintReadsIntegrationTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
PrintReadsWalkerUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00