gatk-3.8/protected/java/test/org/broadinstitute/sting/gatk/walkers
Mark DePristo 5226b24a11 HaplotypeCaller instructure cleanup and unit testing
-- UnitTest for isRootOfDiamond along with key bugfix detected while testing
-- Fix up the equals methods in BaseEdge.  Now called hasSameSourceAndTarget and seqEquals.  A much more meaningful naming
-- Generalize graphEquals to use seqEquals, so it works equally well with Debruijn and SeqGraphs
-- Add BaseVertex method called seqEquals that returns true if two BaseVertex objects have the same sequence
-- Reorganize SeqGraph mergeNodes into a single master function that does zipping, branch merging, and zipping again, rather than having this done in the DeBruijnAssembler itself
-- Massive expansion of the SeqGraph unit tests.  We now really test out the zipping and branch merging code.
-- Near final cleanup of the current codebase
-- DeBruijnVertex cleanup and optimizations.  Since kmer graphs don't allow sequences longer than the kmer size, the suffix is always a byte, not a byte[].  Optimize the code to make use of this constraint
2013-03-20 22:54:37 -04:00
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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 Replace uses of NestedHashMap with NestedIntegerArray. 2013-02-27 14:03:39 -05:00
compression/reducereads Clear ReduceReads name cache after each set of reads produced by ReduceReadsStash. 2013-03-19 14:12:33 -04:00
diagnostics walker to calculate per base coverage distribution 2013-02-07 16:33:05 -05:00
diffengine Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs) 2013-03-12 10:57:14 -04:00
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 Fix to issue encountered when running HaplotypeCaller in GGA mode with data from other 1000G callers. 2013-03-20 14:30:37 -04:00
haplotypecaller HaplotypeCaller instructure cleanup and unit testing 2013-03-20 22:54:37 -04:00
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