gatk-3.8/protected/java/test/org/broadinstitute/sting/gatk/walkers
Mark DePristo 66910b036c Added new and improved suffix and node merging algorithms
-- These new algorithms are more powerful than the restricted diamond merging algoriths, in that they can merge nodes with multiple incoming and outgoing edges.  Together the splitter + merger algorithms will correctly merge many more cases than the original headless and tailless diamond merger.
-- Refactored haplotype caller infrastructure into graphs package, code cleanup
-- Cleanup new merging / splitting algorithms, with proper docs and unit tests
-- Fix bug in zipping of linear chains.  Because the multiplicity can be 0, protect ourselves with a max function call
-- Fix BaseEdge.max unit test
-- Add docs and some more unit tests
-- Move error correct from DeBruijnGraph to DeBruijnAssembler
-- Replaced uses of System.out.println with logger.info
-- Don't make multiplicity == 0 nodes look like they should be pruned
-- Fix toString of Path
2013-03-27 15:31:18 -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 Added new and improved suffix and node merging algorithms 2013-03-27 15:31:18 -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