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gatk-3.8/protected/java/test/org/broadinstitute/sting/gatk/walkers
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David Roazen a536e1da84 Move some VCF/VariantContext methods back to the GATK based on feedback 
-Moved some of the more specialized / complex VariantContext and VCF utility
 methods back to the GATK.

-Due to this re-shuffling, was able to return things like the Pair class back
 to the GATK as well.
 		2013-01-29 16:56:55 -05:00
..
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 updating BQSR integration test values for the PR half of BQSR. 2013-01-29 09:47:57 -05:00
compression/reducereads First pass at adding unit tests for the RR framework: I have added 3 tests and all 3 uncovered RR bugs! 2013-01-29 15:51:07 -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 Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
haplotypecaller Updating HC md5s for new cutting algorithm and default band pass filter parameters 2013-01-25 11:07:29 -05:00
indels Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -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 some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00