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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk/walkers
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David Roazen 24b72334b3 UnifiedGenotyper now correctly initializes the VariantAnnotator engine. 
This allows the annotation classes to perform any necessary initialization/validation.
For example, it allows the SnpEff annotator to (among other things) validate its rod binding.
This will prevent a NullPointerException when SnpEff annotation is requested but no rod binding
is present.

Added an integration test to cover this case so that it doesn't break again.
 		2011-10-11 12:02:05 -04:00
..
CNV Updating md5 for fixed file 2011-09-22 13:15:41 -04:00
annotator SnpEff annotator now assigns a functional class to each effect and distinguishes between actual effects and mere modifiers. 2011-09-23 16:06:52 -04:00
beagle 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
coverage Moving more tools over to the new rod system 2011-08-10 13:42:35 -04:00
diffengine Spelling fix requires md5 updates 2011-08-26 07:40:44 -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 UnifiedGenotyper now correctly initializes the VariantAnnotator engine. 2011-10-11 12:02:05 -04:00
indels Moving more tools over to the new rod system 2011-08-10 13:42:35 -04:00
phasing Update to new RodBinding system 2011-08-11 17:54:16 -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 Fixing syntax of BQSR and UG performance tests. 2011-08-11 17:04:09 -04:00
validation Continuing progress towards RodBinding 1.0 2011-08-03 17:19:28 -04:00
varianteval SnpEff annotator now assigns a functional class to each effect and distinguishes between actual effects and mere modifiers. 2011-09-23 16:06:52 -04:00
variantrecalibration Changing the VQSR command line syntax back to the parsed tags approach. This cleans up the code and makes sure we won't be parsing the same rod file multiple times. I've tried to update the appropriate qscripts. 2011-09-12 12:17:43 -04:00
variantutils Updating MD5s for CombineVariants 2011-09-22 10:30:25 -04:00
BAQIntegrationTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
ClipReadsWalkersIntegrationTest.java Swapped argument order but not MD5 order 2011-08-19 16:55:56 -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