Searched defs:maxMnpDistance (Results 1 – 8 of 8) sorted by relevance
38 …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()
502 public SortedSet<VariantContext> getVariationEvents(final int maxMnpDistance) { in getVariationEvents()514 public void regenerateVariationEvents(int maxMnpDistance) { in regenerateVariationEvents()
132 public int maxMnpDistance = getDefaultMaxMnpDistance(); field in AssemblyBasedCallerArgumentCollection
123 final int maxMnpDistance, in assignGenotypeLikelihoods()
364 assemblyResultSet.regenerateVariationEvents(maxMnpDistance); in assemblyResultSet.regenerateVariationEvents() argument
54 …refBases, final String haplotypeBases, final String cigar, final List<Integer> maxMnpDistance, fin… in testMNPs()
1252 final int maxMnpDistance = 0; in testAddGivenAlleles() local1328 final int maxMnpDistance = 0; in testAddMultiallelicGivenAlleles() local1355 final int maxMnpDistance = 0; in testGivenAllelesHugeInsertion() local
1067 private static void checkMnpOutput(int maxMnpDistance, File outputVcf) { in checkMnpOutput()