Constructor Detail

Method Detail

• createGtvalueMap

   static Map<Byte, Integer> createGtvalueMap()

• getLongFromRefAltData

   static long getLongFromRefAltData(RefAltData rad)

  RefAltData comes from processing the Longs stored for each haplotype. It is used for consensus processing. Different data is available than is with the VariantMappingData used for processing single haplotypes.

• findTaxonRefCoverage

   static RefAltData findTaxonRefCoverage(Position startPos, int maxRefLen, TaxaList tList, Map<Taxon, RangeMap<Position, RefAltData>> taxonToPosDataMap, double maxError, double minTaxaCoverage)

• splitConsensusTaxa

   static TaxaList splitConsensusTaxa(TaxaList tList)

• chooseVarIdForSNPPositionFromGenotypeTable

   static Map<Position, Integer> chooseVarIdForSNPPositionFromGenotypeTable(GenotypeTable genotypeTable, Map<Integer, BiMap<Integer, Integer>> posCallVarIdMap)

• createVarIDtoRefAltData

   static Map<Integer, RefAltData> createVarIDtoRefAltData(Map<Taxon, RangeMap<Position, RefAltData>> taxonToPosDataMap)

  Returns a map of variantID to RefAltData for each variantId/data lookup. variantID of -1 (ref) is handled in calling method.

• convertVariantsToSequence

   static String convertVariantsToSequence(List<HaplotypeNode.VariantInfo> variants, ReferenceRange refRange, GenomeSequence refSequence)

• variantsInOrder

   static boolean variantsInOrder(List<HaplotypeNode.VariantInfo> variants)

• encodeRefBlockToLong

   static Long encodeRefBlockToLong(int refLength, int refDepth, int pos)

  Encode a reference block to a Long

  Parameters:

  refLength - length of the reference block

  refDepth - readDepth in the reference block.

  pos - the start position of the block on a chromosome

• encodeVariantToLong

   static Long encodeVariantToLong(int variantId, int refDepth, int altDepth, boolean isIndel)

  Encode variant information as a Long

  Parameters:

  refDepth - read depth of the reference allele.

  altDepth - read depth of the alt allele.

  isIndel - true if the variant is an indel, false otherwise.

• areGraphTaxaInRankingMap

   static boolean areGraphTaxaInRankingMap(HaplotypeGraph graph, Map<String, Double> rankingMap)

  Method to verify that the taxa in the graph are in the ranking file. We can have more taxon in the ranking file than in the graph, but not the other way around.

• areRankingsUnique

   static boolean areRankingsUnique(Map<String, Double> rankingMap)

  Method to verify that rankings are unique. This is used to throw a Warning message in the Assembly consensus.

• createDistanceMatrix

   static DistanceMatrix createDistanceMatrix(int ntaxa, Chromosome chr, ReferenceRange currentRefRange, TaxaList taxaWithInfo, Map<Taxon, RangeMap<Integer, HaplotypeNode.VariantInfo>> taxonToVariantInfoMap)

  Function to create a disntance matrix given a set of variants for a single reference range. This will ignore Ns and indels Distance is #SNPs/(#SNPs + #RefPos)

• setNsToMax

   static DistanceMatrix setNsToMax(DistanceMatrix originalDM)

  Function to create a new DistanceMatrix setting NaNs to the maximum value in both its row and column.

• maxDistance

   static float maxDistance(DistanceMatrix matrix, int row, int col)

  Function to figure out what the maximum row and col distance are for a given position in the oringinal distance Matrix.