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gatk-3.8/protected/java/test/org/broadinstitute/sting/gatk/walkers
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Mauricio Carneiro 367f0c0ac1 Split class names into stratification and metrics 
Calling everything statistics was very confusing. Diagnose Targets stratifies the data three ways: Interval, Sample and Locus. Each stratification then has it's own set of metrics (plugin system) to calculate -- LocusMetric, SampleMetric, IntervalMetric.

 Metrics are generalized by the Metric interface. (for generic access)
 Stratifications are generalized by the AbstractStratification abstract class. (to aggressively limit code duplication)
 		2013-04-24 14:15:49 -04:00
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annotator Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
beagle Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
bqsr Trivial BQSR bug fixes and improvement 2013-04-11 17:08:35 -04:00
compression/reducereads Refactored binomial probability code in MathUtils. 2013-04-16 18:19:07 -04:00
diagnostics Split class names into stratification and metrics 2013-04-24 14:15:49 -04:00
diffengine Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs) 2013-03-12 10:57:14 -04:00
fasta Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
filters Don't allow users to specify keys and IDs that contain angle brackets or equals signs (not allowed in VCF spec). 2013-04-05 00:52:32 -04:00
genotyper UnifiedGenotyper bugfix: don't create haplotypes with 0 bases 2013-04-13 14:57:55 -04:00
haplotypecaller Bugfix for CommonSuffixSplitter 2013-04-21 19:37:01 -04:00
indels Fixed IndelRealigner reference length bug (GSA-774) 2013-02-19 16:00:36 -05:00
phasing Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
validation MathUtils.randomSubset() now uses Collections.shuffle() (indirectly, through the other methods 2013-03-29 14:52:10 -04:00
varianteval Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
variantrecalibration Update MD5s for VQSR header change 2013-04-16 11:45:45 -04:00
variantutils Using --keepOriginalAC in SelectVariants was causing it to emit bad VCFs 2013-04-05 00:53:28 -04:00