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gatk-3.8/protected/java/test/org/broadinstitute/sting/gatk/walkers
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Eric Banks 05e69b6294 Refactoring of SlidingWindow class in RR to reduce complexity and fix important bug. 
* Allow RR to write its BAM to stdout by setting required=true for @Output.
  * Fixed bug in sliding window where a break in coverage after a long stretch without
     a variant region was causing a doubling of all the reads before the break.
  * Refactored SlidingWindow.updateHeaderCounts() into 3 separate tested methods.
  * Refactored polyploid consensus code out of SlidingWindow.compressVariantRegion().
 		2013-03-12 09:06:55 -04:00
..
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 Replace uses of NestedHashMap with NestedIntegerArray. 2013-02-27 14:03:39 -05:00
compression/reducereads Refactoring of SlidingWindow class in RR to reduce complexity and fix important bug. 2013-03-12 09:06:55 -04:00
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 Two features useful for ancient DNA processing. 2013-03-09 18:18:13 -05:00
haplotypecaller Expanded functionality for writing BAMs from HaplotypeCaller 2013-03-03 12:07:29 -05:00
indels Fixed IndelRealigner reference length bug (GSA-774) 2013-02-19 16:00:36 -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 Added new walker to split MNPs into their allelic primitives (SNPs). 2013-03-05 23:16:42 -05:00