gatk-3.8/protected/java/test/org/broadinstitute/sting/gatk/walkers
Mauricio Carneiro d004bfbe6f walker to calculate per base coverage distribution
-- Base distribution optionally includes deletions
-- Implemented an optional filtered coverage distribution option
-- Integration tests added for every feature of the traversal

This walker is specially fast for the task due to the ability to calculate uncovered bases without having to visit the loci. This capability should be made generic in the future for the advantage of DiagnoseTargets and DepthOfCoverage.
GSATDG-45 #resolve
2013-02-07 16:33:05 -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 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 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 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