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Searched defs:maxMnpDistance (Results 1 – 8 of 8) sorted by relevance

/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/haplotype/
H A DEventMap.java38 …final byte[] ref, final Locatable refLoc, final String sourceNameToAdd, final int maxMnpDistance) { in EventMap()
68 protected void processCigarForInitialEvents(final int maxMnpDistance) { in processCigarForInitialEvents()
296 final int maxMnpDistance) { in buildEventMapsForHaplotypes()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/
H A DAssemblyResultSet.java502 public SortedSet<VariantContext> getVariationEvents(final int maxMnpDistance) { in getVariationEvents()
514 public void regenerateVariationEvents(int maxMnpDistance) { in regenerateVariationEvents()
H A DAssemblyBasedCallerArgumentCollection.java132 public int maxMnpDistance = getDefaultMaxMnpDistance(); field in AssemblyBasedCallerArgumentCollection
H A DHaplotypeCallerGenotypingEngine.java123 final int maxMnpDistance, in assignGenotypeLikelihoods()
H A DAssemblyBasedCallerUtils.java364 assemblyResultSet.regenerateVariationEvents(maxMnpDistance); in assemblyResultSet.regenerateVariationEvents() argument
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/haplotype/
H A DEventMapUnitTest.java54 …refBases, final String haplotypeBases, final String cigar, final List<Integer> maxMnpDistance, fin… in testMNPs()
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/
H A DAssemblyBasedCallerUtilsUnitTest.java1252 final int maxMnpDistance = 0; in testAddGivenAlleles() local
1328 final int maxMnpDistance = 0; in testAddMultiallelicGivenAlleles() local
1355 final int maxMnpDistance = 0; in testGivenAllelesHugeInsertion() local
H A DHaplotypeCallerIntegrationTest.java1067 private static void checkMnpOutput(int maxMnpDistance, File outputVcf) { in checkMnpOutput()