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gatk-3.8/protected/java/test/org/broadinstitute/sting/gatk/walkers
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Chris Hartl 41a030f4b7 Apparently I'm a failure at rebasing...there should have been only one commit message to write. But whatever, here it is again: 
Part 1 of Variant Annotator Unit tests: PerReadAlleleLikelihoodMap

 - Added contract enforcement for public methods
 - Refactored the conversion from read -> (allele -> likelihood) to allele -> list[read] into its own method
 - added method documentation for non getters/setters
 - finals, finals everywhere
 - Add in a unit test for the PerReadAlleleLikelihoodMap. Complete coverage except for .clear() and a method that is a straight call into a separately-tested utility class.
 		2013-02-04 14:16:28 -05:00
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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 Update MD5s to reflect version number change in the BAM header 2013-02-01 13:51:31 -05:00
compression/reducereads More RR-related updates and tests. 2013-02-04 12:57:43 -05:00
diagnostics Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
diffengine Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
fasta Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
filters Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
genotyper Apparently I'm a failure at rebasing...there should have been only one commit message to write. But whatever, here it is again: 2013-02-04 14:16:28 -05:00
haplotypecaller Somehow these md5 updates got lost in my previous git rebase disaster. Sorry for the trouble. 2013-02-04 13:26:18 -05:00
indels Update MD5s to reflect version number change in the BAM header 2013-02-01 13:51:31 -05:00
phasing Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
validation Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
varianteval Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
variantrecalibration Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
variantutils Move BaseUtils back to the GATK by request, along with associated utility methods 2013-01-30 13:09:44 -05:00