gatk-3.8/protected/java/test/org/broadinstitute/sting/gatk/walkers
Mark DePristo aa7f172b18 Cap the computational cost of the kmer based error correction in the DeBruijnGraph
-- Simply don't do more than MAX_CORRECTION_OPS_TO_ALLOW = 5000 * 1000 operations to correct a graph.  If the number of ops would exceed this threshold, the original graph is used.
-- Overall the algorithm is just extremely computational expensive, and actually doesn't implement the correct correction.  So we live with this limitations while we continue to explore better algorithms
-- Updating MD5s to reflect changes in assembly algorithms
2013-03-21 09:21:35 -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 Cap the computational cost of the kmer based error correction in the DeBruijnGraph 2013-03-21 09:21:35 -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