Mark DePristo 1fa5050faf Cleanup, unit test, and optimize KBestPaths and Path ... -- Split Path from inner class of KBestPaths -- Use google MinMaxPriorityQueue to track best k paths, a more efficient implementation -- Path now properly typed throughout the code -- Path maintains a on-demand hashset of BaseEdges so that path.containsEdge is fast		2013-03-20 22:54:36 -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	Cleanup, unit test, and optimize KBestPaths and Path	2013-03-20 22:54:36 -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