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gatk-3.8/protected/java/test/org/broadinstitute/sting/gatk/walkers
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Eric Banks 75ceddf9e5 Adding new unit tests for RR. These tests took a frustratingly long time to get to pass, but now we have a framework for 
testing the adding of reads into the SlidingWindow plus consensus creation.  Will flesh these out more after I take care of
some other items on my plate.
 		2013-01-31 09:46:38 -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 md5s to reflect the updates to the hierarchicalBayesianQualityEstimate function 2013-01-30 13:30:18 -05:00
compression/reducereads Adding new unit tests for RR. These tests took a frustratingly long time to get to pass, but now we have a framework for 2013-01-31 09:46:38 -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 BaseUtils back to the GATK by request, along with associated utility methods 2013-01-30 13:09:44 -05:00
haplotypecaller Breaking up my massive commits into smaller pieces that I can successfully merge and digest. This one enables downsampling in the HaplotypeCaller (by lowering the default dcov to 20) and removes my long-standing, temporary region-based downsampling. 2013-01-30 16:14:07 -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 BaseUtils back to the GATK by request, along with associated utility methods 2013-01-30 13:09:44 -05:00