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- All Implemented Interfaces:
public class ConvertReadsToPathUsingHMM
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Constructor Summary
Constructors Constructor Description ConvertReadsToPathUsingHMM()
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Method Summary
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Method Detail
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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
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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
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filterOnTaxa
HaplotypeGraph filterOnTaxa(HaplotypeGraph graph)
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listTaxa
void listTaxa()
Writes the names of the taxa in the HaplotypeGraph, myGraph, to System.out
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haplotypeCountsToPath
List<HaplotypeNode> haplotypeCountsToPath()
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haplotypeCountsToPathProbability
List<Array<double>> haplotypeCountsToPathProbability()
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nodeListFromProbabilities
List<HaplotypeNode> nodeListFromProbabilities(double minP, String infoFilename)
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nodeListFromProbabilities
List<HaplotypeNode> nodeListFromProbabilities(double minP)
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startProbabilities
Array<double> startProbabilities(int numberOfNodes)
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probabilityOfBeingCorrect
Array<double> probabilityOfBeingCorrect(HaplotypeGraph hapGraph, Multiset<Integer> hapidCounts)
- Parameters:
hapGraph
- a HaplotypeGraphhapidCounts
- a Multiset of hapids used to retrieve hapid counts
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probabilityOfBeingCorrect
Array<double> probabilityOfBeingCorrect(Multiset<Integer> hapidCounts, TreeMap<ReferenceRange, List<HaplotypeNode>> rangeToNodesMap)
- Parameters:
hapidCounts
- a Multiset of hapids used to retrieve hapid countsrangeToNodesMap
- a map with ReferenceRange as key and the List of nodes at that range as the associated value
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probabilityOfBeingCorrect
Array<double> probabilityOfBeingCorrect(Map<Integer, Integer> hapidCountMap, TreeMap<ReferenceRange, List<HaplotypeNode>> rangeToNodesMap)
- Parameters:
hapidCountMap
- a Multiset of hapids used to retrieve hapid countsrangeToNodesMap
- a map with ReferenceRange as key and the List of nodes at that range as the associated value
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filteredGraph
HaplotypeGraph filteredGraph()
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hapidCountMap
ConvertReadsToPathUsingHMM hapidCountMap(Map<Integer, Integer> countmap)
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minReadsPerRange
ConvertReadsToPathUsingHMM minReadsPerRange(int minReads)
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maxReadsPerRangeKB
ConvertReadsToPathUsingHMM maxReadsPerRangeKB(int maxReads)
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taxaFilterList
ConvertReadsToPathUsingHMM taxaFilterList(String taxaNames)
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taxaFilterList
ConvertReadsToPathUsingHMM taxaFilterList(TaxaList listOfTaxa)
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probabilityReadMappingCorrect
ConvertReadsToPathUsingHMM probabilityReadMappingCorrect(double probCorrect)
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minTransitionProbability
ConvertReadsToPathUsingHMM minTransitionProbability(double minprob)
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transitionProbabilitySameTaxon
ConvertReadsToPathUsingHMM transitionProbabilitySameTaxon(double p)
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targetTaxon
ConvertReadsToPathUsingHMM targetTaxon(String taxonName)
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readMap
ConvertReadsToPathUsingHMM readMap(Multimap<ReferenceRange, HapIdSetCount> readMap)
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removeRangesWithEqualCounts
ConvertReadsToPathUsingHMM removeRangesWithEqualCounts(boolean remove)
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