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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk
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David Roazen d9ea764611 SnpEff annotator now adds OriginalSnpEffVersion and OriginalSnpEffCmd lines to the header of the VCF output file. 
This change is urgently required for production, which is why it's going into Stable+Unstable
instead of just Unstable.

The keys for the SnpEff version and command header lines in the VCF file output by
VariantAnnotator (OriginalSnpEffVersion and OriginalSnpEffCmd) are intentionally
different from the keys for those same lines in the SnpEff output file (SnpEffVersion
and SnpEffCmd), so that output files from VariantAnnotator won't be confused
with output files from SnpEff itself.
 		2011-09-20 16:30:55 -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 SnpEff annotator now adds OriginalSnpEffVersion and OriginalSnpEffCmd lines to the header of the VCF output file. 2011-09-20 16:30:55 -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