net.maizegenetics.pangenome.hapCalling

Class DiploidCountsToPath

net.maizegenetics.pangenome.hapCalling.DiploidCountsToPath

public class DiploidCountsToPath

Used to find the most likely pair of paths through a graph given a set of read mappings. The two paths represent the phased haplotypes imputed from the reads.

Constructor Detail

DiploidCountsToPath

public DiploidCountsToPath(@NotNull
                           HaplotypeGraph myGraph,
                           @NotNull
                           com.google.common.collect.Multimap<net.maizegenetics.pangenome.api.ReferenceRange,net.maizegenetics.pangenome.hapCalling.HapIdSetCount> readHapids,
                           double probabilityCorrect,
                           double minTransitionProbability,
                           int maxNodesPerRange,
                           int minReadsPerRange,
                           boolean removeRangesWithEqualCounts,
                           int maxReadsPerKB,
                           boolean splitNodes,
                           double splitTransitionProb)

Used to find the most likely pair of paths through a graph given a set of read mappings. The two paths represent the phased haplotypes imputed from the reads.

Parameters:

myGraph - the HaplotypeGraph to be used for path finding

readHapids - a Multimap of class ReferenceRange -> class HapIdSetCount retrieved from a PHG DB

probabilityCorrect - the probability that a read has aligned correctly

minTransitionProbability - the minimum transition probability

maxNodesPerRange - ranges with more nodes will not be used

minReadsPerRange - ranges with fewer reads will not be used

removeRangesWithEqualCounts - ranges for which all hapid sets have the same count will not be used

maxReadsPerKB - ranges with more reads per kb will not be used

splitNodes - should nodes with more than one taxon be split into nodes of one taxon each

splitTransitionProb - the probability of a node given that the previous node was the same taxon or 1 - probability of a recombination

Method Detail

getMyLogger

@NotNull
public NonExistentClass getMyLogger()

getDiploidPath

@NotNull
public java.util.List<java.util.List> getDiploidPath()

Finds the most likely diploid path through myGraph given readHapids. Before the path is imputed, the graph is filtered based on maxNodesPerRange, minReadsPerRange, removeRangesWithEqualCounts, and maxReadsPerKB then missing sequence nodes are added and, finally, the nodes are split into individual taxa if splitNodes is true.

filteredGraph

@NotNull
public HaplotypeGraph filteredGraph()

Filters myGraph using readHapids based on maxNodesPerRange, minReadsPerRange, removeRangesWithEqualCounts, and maxReadsPerKB

getMyGraph

@NotNull
public HaplotypeGraph getMyGraph()

the HaplotypeGraph to be used for path finding

getReadHapids

@NotNull
public com.google.common.collect.Multimap<net.maizegenetics.pangenome.api.ReferenceRange,net.maizegenetics.pangenome.hapCalling.HapIdSetCount> getReadHapids()

a Multimap of

class ReferenceRange -> class HapIdSetCount retrieved from a PHG DB

See Also:

class ReferenceRange, class HapIdSetCount

getProbabilityCorrect

public double getProbabilityCorrect()

the probability that a read has aligned correctly

getMinTransitionProbability

public double getMinTransitionProbability()

the minimum transition probability

getMaxNodesPerRange

public int getMaxNodesPerRange()

ranges with more nodes will not be used

getMinReadsPerRange

public int getMinReadsPerRange()

ranges with fewer reads will not be used

getRemoveRangesWithEqualCounts

public boolean getRemoveRangesWithEqualCounts()

ranges for which all hapid sets have the same count will not be used

getMaxReadsPerKB

public int getMaxReadsPerKB()

ranges with more reads per kb will not be used

getSplitNodes

public boolean getSplitNodes()

should nodes with more than one taxon be split into nodes of one taxon each

getSplitTransitionProb

public double getSplitTransitionProb()

the probability of a node given that the previous node was the same taxon or 1

- probability of a recombination