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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk/walkers
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David Roazen d78e00e5b2 Renaming VariantAnnotator SnpEff keys 
This is to head off potential confusion with the output from the SnpEff tool itself,
which also uses a key named EFF.
 		2011-09-15 17:42:15 -04:00
..
CNV Fixed bug that required symbolic alleles to be padded with reference base and added integration test to test parsing and output of symbolic alleles 2011-08-12 12:23:44 -04:00
annotator Renaming VariantAnnotator SnpEff keys 2011-09-15 17:42:15 -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 Uncomment code to add deleted bases covering an indel to per-sample genotype reporting, update integration tests accordingly 2011-09-10 19:41:01 -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 Renaming VariantAnnotator SnpEff keys 2011-09-15 17:42:15 -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 Validate Variants deletion integration test 2011-09-09 13:39:08 -04:00
BAQIntegrationTest.java
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ClipReadsWalkersIntegrationTest.java Swapped argument order but not MD5 order 2011-08-19 16:55:56 -04:00
PileupWalkerIntegrationTest.java
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PrintReadsIntegrationTest.java
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PrintReadsWalkerUnitTest.java
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