David Roazen 1213b2f8c6 SnpEff 2.0.2 support ... -Rewrote SnpEff support in VariantAnnotator to support the latest SnpEff release (version 2.0.2) -Removed support for SnpEff 1.9.6 (and associated tribble codec) -Will refuse to parse SnpEff output files produced by unsupported versions (or without a version tag) -Correctly matches ref/alt alleles before annotating a record, unlike the previous version -Correctly handles indels (again, unlike the previous version		2011-09-14 07:09:47 -04:00
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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 2.0.2 support	2011-09-14 07:09:47 -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