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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk/walkers
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Mark DePristo fee9b367e4 VariantContext genotypes are now stored as GenotypeMap objects 
-- Enables further sophisticated optimizations, as this class can be smarter about storing the data and will directly support operations like subset to samples
-- All instances in the gatk that used Map<String, Genotype> now use GenotypeMap type.
-- Amazingly, there were many places where HashMap<String, Genotype> is used, so that the order of the genotypes is technically undefined and could be dangerous.  Now everything uses GenotypeMap with a specific ordering of samples (by name)
-- Integrationtests updated and all pass
 		2011-11-11 15:00:35 -05:00
..
CNV Updating md5 because the file changed 2011-09-23 07:33:20 -04:00
annotator VariantContext genotypes are now stored as GenotypeMap objects 2011-11-11 15:00:35 -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 Updating MD5s 2011-10-04 15:54:45 -07:00
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 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 VariantContext genotypes are now stored as GenotypeMap objects 2011-11-11 15:00:35 -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 Moving unclaimed walker with bad integration test to archive 2011-11-07 13:16:38 -05:00
qc Removing a public -> private dependency from the test suite. 2011-10-13 21:32:52 -04:00
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 VariantEvalIntegrationTest for IntervalStratification 2011-11-10 14:10:39 -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