org.broadinstitute.hellbender.testutils

Class TestingReadThreadingGraph

java.lang.Object

org.jgrapht.graph.AbstractGraph<V,E>

org.jgrapht.graph.AbstractBaseGraph<V,E>

org.jgrapht.graph.DefaultDirectedGraph<V,E>

org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph<MultiDeBruijnVertex,MultiSampleEdge>

org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph

org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph

org.broadinstitute.hellbender.testutils.TestingReadThreadingGraph

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, KmerSearchableGraph<MultiDeBruijnVertex,MultiSampleEdge>, org.jgrapht.DirectedGraph<MultiDeBruijnVertex,MultiSampleEdge>, org.jgrapht.Graph<MultiDeBruijnVertex,MultiSampleEdge>

public final class TestingReadThreadingGraph
extends ReadThreadingGraph

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph

AbstractReadThreadingGraph.MyEdgeFactory, AbstractReadThreadingGraph.TraversalDirection

Nested classes/interfaces inherited from class org.jgrapht.graph.AbstractBaseGraph

org.jgrapht.graph.AbstractBaseGraph.DirectedEdgeContainer<VV,EE>, org.jgrapht.graph.AbstractBaseGraph.DirectedSpecifics, org.jgrapht.graph.AbstractBaseGraph.UndirectedSpecifics

Field Summary

Fields inherited from class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph

logger, nonUniqueKmers

Fields inherited from class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph

alreadyBuilt, debugGraphTransformations, kmerToVertexMap, minBaseQualityToUseInAssembly, pending, referencePath

Fields inherited from class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph

kmerSize

Constructor Summary

Constructors

Constructor and Description
TestingReadThreadingGraph(java.lang.String s) Constructs a read-threading-graph for a string representation.

Method Summary

Modifier and Type	Method and Description
TestingReadThreadingGraph	clone()

Methods inherited from class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph

getNextKmerVertexForChainExtension, isLowQualityGraph, isThreadingStart, postProcessForHaplotypeFinding, preprocessReads, shouldRemoveReadsAfterGraphConstruction, toSequenceGraph, toString, trackKmer

Methods inherited from class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph

addSequence, addSequence, addSequence, addSequence, baseIsUsableForAssembly, buildGraphIfNecessary, extendChainByOne, findKmer, findStart, getKmerVertex, getReferencePath, recoverDanglingHeads, recoverDanglingTails, removeSingletonOrphanVertices, removeVertex, setAlreadyBuilt, setThreadingStartOnlyAtExistingVertex

Methods inherited from class org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph

addEdges, addEdges, addOrUpdateEdge, addVertices, addVertices, cleanNonRefPaths, containsAllVertices, getAdditionalSequence, getAdditionalSequence, getExtraGraphFileLines, getKmerSize, getNextReferenceVertex, getNextReferenceVertex, getPrevReferenceVertex, getReferenceBytes, getReferenceSinkVertex, getReferenceSourceVertex, getSinks, getSources, graphEquals, hasCycles, incomingEdgeOf, incomingVerticesOf, isReferenceNode, isRefSink, isRefSource, isSink, isSource, neighboringVerticesOf, outgoingEdgeOf, outgoingVerticesOf, printGraph, printGraph, removePathsNotConnectedToRef, removeVerticesNotConnectedToRefRegardlessOfEdgeDirection, subsetToNeighbors, subsetToRefSource

Methods inherited from class org.jgrapht.graph.DefaultDirectedGraph

builder, builder

Methods inherited from class org.jgrapht.graph.AbstractBaseGraph

addEdge, addEdge, addVertex, containsEdge, containsVertex, createDirectedSpecifics, createUndirectedSpecifics, degreeOf, edgeSet, edgesOf, getAllEdges, getEdge, getEdgeFactory, getEdgeSource, getEdgeTarget, getEdgeWeight, incomingEdgesOf, inDegreeOf, isAllowingLoops, isAllowingMultipleEdges, outDegreeOf, outgoingEdgesOf, removeEdge, removeEdge, setEdgeSetFactory, setEdgeWeight, vertexSet

Methods inherited from class org.jgrapht.graph.AbstractGraph

assertVertexExist, containsEdge, equals, hashCode, removeAllEdges, removeAllEdges, removeAllEdges, removeAllVertices, toStringFromSets

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.KmerSearchableGraph

getKmerSize

Methods inherited from interface org.jgrapht.DirectedGraph

incomingEdgesOf, inDegreeOf, outDegreeOf, outgoingEdgesOf

Methods inherited from interface org.jgrapht.Graph

addEdge, addEdge, addVertex, containsEdge, containsEdge, containsVertex, edgeSet, edgesOf, getAllEdges, getEdge, getEdgeFactory, getEdgeSource, getEdgeTarget, getEdgeWeight, removeAllEdges, removeAllEdges, removeAllVertices, removeEdge, removeEdge, vertexSet

Constructor Detail

TestingReadThreadingGraph

public TestingReadThreadingGraph(java.lang.String s)

Constructs a read-threading-graph for a string representation.

Note: only used for testing. Checkout HaplotypeGraphUnitTest for examples.

Parameters:

s - the string representation of the graph null.

Method Detail

clone

public TestingReadThreadingGraph clone()

Overrides:

clone in class ReadThreadingGraph