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gatk-3.8/protected/java/test/org/broadinstitute/sting/gatk/walkers
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Mark DePristo 73a363b166 Update MD5s due to new QualityUtils calculations 
-- Increase the allowed runtime of one UG integration test
-- The GGA indels mode runs two UG commands, and was barely under the 10 minute limit before.  Some updates can push this right over the edge.  Increased limit
-- CalibrateGenotypeLikelihoods runs on a small data set now, so it's faster
-- Updating MD5s due to more correct quality utils.  DuplicatesWalkers quality estimates have changed.  One UG test has different FS and rank sum tests because the conversion to phred scores are slightly (second decimal place) different
 		2013-02-16 07:31:38 -08:00
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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 PrintReads writes a header when used with -BQSR 2013-02-14 22:19:14 -05:00
compression/reducereads Fixing the failing RR integration tests. 2013-02-06 12:40:56 -05:00
diagnostics walker to calculate per base coverage distribution 2013-02-07 16:33:05 -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 Update MD5s due to new QualityUtils calculations 2013-02-16 07:31:38 -08:00
haplotypecaller Fixed non-determinism in HaplotypeCaller and some UG calls - 2013-02-12 15:43:29 -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 Replace org.broadinstitute.variant with jar built from the Picard repo 2013-02-05 17:24:25 -05:00