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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk/walkers
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Mark DePristo 4107636144 VariantEval updates 
-- Performance optimizations
-- Tables now are cleanly formatted (floats are %.2f printed)
-- VariantSummary is a standard report now
-- Removed CompEvalGenotypes (it didn't do anything)
-- Deleted unused classes in GenotypeConcordance
-- Updates integration tests as appropriate
 		2011-11-23 13:02:07 -05:00
..
CNV Updating md5 because the file changed 2011-09-23 07:33:20 -04:00
annotator GenotypesContext no longer have immutability in constructor 2011-11-21 14:34:31 -05:00
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 Removing the legacy -L "interval1;interval2" syntax 2011-11-21 13:18:53 -05:00
diffengine DiffObjects no longer prints out the file name in the status so MD5 are stable 2011-10-10 15:10:57 -04:00
fasta Removing the legacy -L "interval1;interval2" syntax 2011-11-21 13:18:53 -05:00
filters Again, fixing the add call when we really mean replace 2011-11-21 19:15:56 -05:00
genotyper UG now encoding NO_CALLs as ./. not ./.:.:4:0,0,0 2011-11-22 08:22:32 -05:00
indels Removing all instances of -BTI (in tests and in GATKdocs) and replacing them with the appropriate alternative. 2011-10-27 23:55:11 -04:00
phasing Merge with master 2011-11-19 09:56:06 -05:00
qc First version of VariantContextBuilder 2011-11-18 11:06:15 -05:00
recalibration Update MD5s for SOLiD recalibration 2011-10-13 18:01:51 -04:00
validation Removing all instances of -BTI (in tests and in GATKdocs) and replacing them with the appropriate alternative. 2011-10-27 23:55:11 -04:00
varianteval VariantEval updates 2011-11-23 13:02:07 -05:00
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 Bug fix in SelectVariants when using a discordance track but no sample specifications. Added integration test to test this. 2011-11-07 15:25:16 -05:00
BAQIntegrationTest.java merge master 2011-10-25 16:08:39 -04:00
ClipReadsWalkersIntegrationTest.java Updating MD5s for updated BAM with read groups 2011-10-06 12:15:48 -07:00
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 GATKSAMRecord refactor 2011-11-03 15:43:26 -04:00