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gatk-3.8/protected/java/test/org/broadinstitute/sting/gatk/walkers
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Eric Banks 9826192854 Added contracts, docs, and tests for several methods in AlignmentUtils. There are over 74K tests being run now for this class! 
* AlignmentUtils.getMismatchCount()
* AlignmentUtils.calcAlignmentByteArrayOffset()
* AlignmentUtils.readToAlignmentByteArray().
* AlignmentUtils.leftAlignIndel()
 		2013-02-07 13:04:24 -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 Added check that BaseRecalibrator is not being run on a reduced bam. 2013-02-06 10:14:27 -05:00
compression/reducereads Fixing the failing RR integration tests. 2013-02-06 12:40:56 -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 Replace org.broadinstitute.variant with jar built from the Picard repo 2013-02-05 17:24:25 -05:00
haplotypecaller Added contracts, docs, and tests for several methods in AlignmentUtils. There are over 74K tests being run now for this class! 2013-02-07 13:04:24 -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