Constructor Detail

• ConvertReadsToPathUsingHMM

  ConvertReadsToPathUsingHMM()

Method Detail

• filterHaplotypeGraph

   ConvertReadsToPathUsingHMM filterHaplotypeGraph(HaplotypeGraph graph)

  This method filters a HaplotypeGraph and sets the myGraph field of the class to the result. The resulting filtered HaplotypeGraph will be used for any subsequent method calls.

  Parameters:

  graph - the HaplotypeGraph to be filtered

• filterHaplotypeGraph

   ConvertReadsToPathUsingHMM filterHaplotypeGraph(HaplotypeGraph graph, List<Integer> rangesToKeep)

  This method filters a HaplotypeGraph and sets the myGraph field of the class to the result. The resulting filtered HaplotypeGraph will be used for any subsequent method calls.

  Parameters:

  graph - the HaplotypeGraph to be filtered

• filterOnTaxa

   HaplotypeGraph filterOnTaxa(HaplotypeGraph graph)

• listTaxa

   void listTaxa()

  Writes the names of the taxa in the HaplotypeGraph, myGraph, to System.out

• haplotypeCountsToPath

   List<HaplotypeNode> haplotypeCountsToPath()

• haplotypeCountsToPathProbability

   List<Array<double>> haplotypeCountsToPathProbability()

• nodeListFromProbabilities

   List<HaplotypeNode> nodeListFromProbabilities(double minP, String infoFilename)

• nodeListFromProbabilities

   List<HaplotypeNode> nodeListFromProbabilities(double minP)

• startProbabilities

   Array<double> startProbabilities(int numberOfNodes)

• probabilityOfBeingCorrect

   Array<double> probabilityOfBeingCorrect(HaplotypeGraph hapGraph, Multiset<Integer> hapidCounts)

  Parameters:

  hapGraph - a HaplotypeGraph

  hapidCounts - a Multiset of hapids used to retrieve hapid counts

• probabilityOfBeingCorrect

   Array<double> probabilityOfBeingCorrect(Multiset<Integer> hapidCounts, TreeMap<ReferenceRange, List<HaplotypeNode>> rangeToNodesMap)

  Parameters:

  hapidCounts - a Multiset of hapids used to retrieve hapid counts

  rangeToNodesMap - a map with ReferenceRange as key and the List of nodes at that range as the associated value

• probabilityOfBeingCorrect

   Array<double> probabilityOfBeingCorrect(Map<Integer, Integer> hapidCountMap, TreeMap<ReferenceRange, List<HaplotypeNode>> rangeToNodesMap)

  Parameters:

  hapidCountMap - a Multiset of hapids used to retrieve hapid counts

  rangeToNodesMap - a map with ReferenceRange as key and the List of nodes at that range as the associated value

• filteredGraph

   HaplotypeGraph filteredGraph()

• hapidCountMap

   ConvertReadsToPathUsingHMM hapidCountMap(Map<Integer, Integer> countmap)

• minReadsPerRange

   ConvertReadsToPathUsingHMM minReadsPerRange(int minReads)

• maxReadsPerRangeKB

   ConvertReadsToPathUsingHMM maxReadsPerRangeKB(int maxReads)

• taxaFilterList

   ConvertReadsToPathUsingHMM taxaFilterList(String taxaNames)

• taxaFilterList

   ConvertReadsToPathUsingHMM taxaFilterList(TaxaList listOfTaxa)

• probabilityReadMappingCorrect

   ConvertReadsToPathUsingHMM probabilityReadMappingCorrect(double probCorrect)

• minTransitionProbability

   ConvertReadsToPathUsingHMM minTransitionProbability(double minprob)

• transitionProbabilitySameTaxon

   ConvertReadsToPathUsingHMM transitionProbabilitySameTaxon(double p)

• targetTaxon

   ConvertReadsToPathUsingHMM targetTaxon(String taxonName)

• readMap

   ConvertReadsToPathUsingHMM readMap(Multimap<ReferenceRange, HapIdSetCount> readMap)

• removeRangesWithEqualCounts

   ConvertReadsToPathUsingHMM removeRangesWithEqualCounts(boolean remove)