net.maizegenetics.pangenome.hapCalling

Class ConvertGBSToSNPs

java.lang.Object

net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs

public class ConvertGBSToSNPs
extends Object

Constructor Summary

Constructors

Constructor and Description
ConvertGBSToSNPs()

Method Summary

Modifier and Type	Method and Description
ConvertGBSToSNPs	countHaplotypeNodesFromFastQ()
ConvertGBSToSNPs	emissionProbabilityMethod(ReferenceRangeEmissionProbability.METHOD method)
HaplotypeGraph	filteredGraph()
ConvertGBSToSNPs	filterHaplotypeGraph(HaplotypeGraph hapGraph) This method filters a HaplotypeGraph and sets the myGraph field of the class to the result.
ConvertGBSToSNPs	filterHaplotypeGraph(HaplotypeGraph hapGraph, List<Integer> rangesToKeep) This method filters a HaplotypeGraph and sets the myGraph field of the class to the result.
Map<Integer,Integer>	hapidCountMap()
ConvertGBSToSNPs	hapidCountMap(Map<Integer,Integer> countmap)
ConvertGBSToSNPs	hapidCounts(com.google.common.collect.Multiset<Integer> hapidCounts)
ConvertGBSToSNPs	hapidExclusionCountMap(Map<Integer,Integer> countmap)
List<HaplotypeNode>	haplotypeCountsToPath()
List<double[]>	haplotypeCountsToPathProbability()
void	listTaxa() Writes the names of the taxa in the HaplotypeGraph, myGraph, to System.out
ConvertGBSToSNPs	maxNodesPerRange(int maxNodes)
ConvertGBSToSNPs	maxReadsPerRangeKB(int maxReads)
ConvertGBSToSNPs	minReadsPerRange(int minReads)
ConvertGBSToSNPs	minTaxaPerRange(int minTaxa)
ConvertGBSToSNPs	minTransitionProbability(double minprob)
List<HaplotypeNode>	nodeListFromProbabilities(double minP)
List<HaplotypeNode>	nodeListFromProbabilities(double minP, String infoFilename)
List<HaplotypeNode>	nodesOnPath()
double[]	probabilityOfBeingCorrect(HaplotypeGraph hapGraph, com.google.common.collect.Multiset<Integer> hapidCounts)
double[]	probabilityOfBeingCorrect(Map<Integer,Integer> hapidCountMap, TreeMap<ReferenceRange,List<HaplotypeNode>> rangeToNodesMap)
double[]	probabilityOfBeingCorrect(com.google.common.collect.Multiset<Integer> hapidCounts, TreeMap<ReferenceRange,List<HaplotypeNode>> rangeToNodesMap)
ConvertGBSToSNPs	probabilityReadMappingCorrect(double probCorrect)
void	showNodeCounts() Diagnostic method that writes the HaplotypeNode counts of the first 20 ranges to System.out
ConvertGBSToSNPs	splitTaxa(boolean split)
double[]	startProbabilities(List<HaplotypeNode> nodeList)
ConvertGBSToSNPs	targetTaxon(String taxonName)
ConvertGBSToSNPs	taxaFilterList(String taxaNames)
ConvertGBSToSNPs	taxaFilterList(net.maizegenetics.taxa.TaxaList listOfTaxa)
void	testHapidCounts(HaplotypeGraph graph, String taxonName)
ConvertGBSToSNPs	transitionProbabilitySameTaxon(double p)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ConvertGBSToSNPs

public ConvertGBSToSNPs()

Method Detail

countHaplotypeNodesFromFastQ

public ConvertGBSToSNPs countHaplotypeNodesFromFastQ()

testHapidCounts

public void testHapidCounts(HaplotypeGraph graph,
                            String taxonName)

filterHaplotypeGraph

public ConvertGBSToSNPs filterHaplotypeGraph(HaplotypeGraph hapGraph)

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:

hapGraph - the HaplotypeGraph to be filtered

filterHaplotypeGraph

public ConvertGBSToSNPs filterHaplotypeGraph(HaplotypeGraph hapGraph,
                                             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:

hapGraph - the HaplotypeGraph to be filtered

listTaxa

public void listTaxa()

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

showNodeCounts

public void showNodeCounts()

Diagnostic method that writes the HaplotypeNode counts of the first 20 ranges to System.out

haplotypeCountsToPath

public List<HaplotypeNode> haplotypeCountsToPath()

Returns:

The list of HaplotypeNodes on the most likely Path for a Multiset of hapids. That is, given a HaplotypeGraph and a Multiset of hapids, the nodes on the path through the graph that is most likely to have generated the multiset of hapids.

haplotypeCountsToPathProbability

public List<double[]> haplotypeCountsToPathProbability()

Returns:

a list of node probabilities for each range in the input graph.

nodeListFromProbabilities

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

nodeListFromProbabilities

public List<HaplotypeNode> nodeListFromProbabilities(double minP)

startProbabilities

public double[] startProbabilities(List<HaplotypeNode> nodeList)

Parameters:

nodeList - the list of nodes at the first range in a linked series of ranges (a chromosome)

Returns:

the start probabilities used to initialize an HMM

probabilityOfBeingCorrect

public double[] probabilityOfBeingCorrect(HaplotypeGraph hapGraph,
                                          com.google.common.collect.Multiset<Integer> hapidCounts)

Parameters:

hapGraph - a HaplotypeGraph

hapidCounts - a Multiset of hapids used to retrieve hapid counts

Returns:

for each range in the HaplotypeGraph, the probability that a read was mapped to the correct node

probabilityOfBeingCorrect

public double[] probabilityOfBeingCorrect(com.google.common.collect.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

Returns:

for each range in the HaplotypeGraph, the probability that a read was mapped to the correct node

probabilityOfBeingCorrect

public 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

Returns:

for each range in the HaplotypeGraph, the probability that a read was mapped to the correct node

nodesOnPath

public List<HaplotypeNode> nodesOnPath()

filteredGraph

public HaplotypeGraph filteredGraph()

hapidCountMap

public Map<Integer,Integer> hapidCountMap()

hapidCounts

public ConvertGBSToSNPs hapidCounts(com.google.common.collect.Multiset<Integer> hapidCounts)

hapidCountMap

public ConvertGBSToSNPs hapidCountMap(Map<Integer,Integer> countmap)

hapidExclusionCountMap

public ConvertGBSToSNPs hapidExclusionCountMap(Map<Integer,Integer> countmap)

minReadsPerRange

public ConvertGBSToSNPs minReadsPerRange(int minReads)

maxReadsPerRangeKB

public ConvertGBSToSNPs maxReadsPerRangeKB(int maxReads)

taxaFilterList

public ConvertGBSToSNPs taxaFilterList(String taxaNames)

taxaFilterList

public ConvertGBSToSNPs taxaFilterList(net.maizegenetics.taxa.TaxaList listOfTaxa)

minTaxaPerRange

public ConvertGBSToSNPs minTaxaPerRange(int minTaxa)

maxNodesPerRange

public ConvertGBSToSNPs maxNodesPerRange(int maxNodes)

probabilityReadMappingCorrect

public ConvertGBSToSNPs probabilityReadMappingCorrect(double probCorrect)

minTransitionProbability

public ConvertGBSToSNPs minTransitionProbability(double minprob)

emissionProbabilityMethod

public ConvertGBSToSNPs emissionProbabilityMethod(ReferenceRangeEmissionProbability.METHOD method)

splitTaxa

public ConvertGBSToSNPs splitTaxa(boolean split)

transitionProbabilitySameTaxon

public ConvertGBSToSNPs transitionProbabilitySameTaxon(double p)

targetTaxon

public ConvertGBSToSNPs targetTaxon(String taxonName)