Package org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs

package org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs

Related Packages

Package	Description
org.broadinstitute.hellbender.tools.walkers.haplotypecaller
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading

Class	Description
AdaptiveChainPruner<V extends BaseVertex,E extends BaseEdge>
BaseEdge	Simple edge class for connecting nodes in the graph.
BaseGraph<V extends BaseVertex,E extends BaseEdge>	Common code for graphs used for local assembly.
BaseVertex	A graph vertex that holds some sequence information
ChainPruner<V extends BaseVertex,E extends BaseEdge>
CommonSuffixSplitter	Split a collection of middle nodes in a graph into their shared prefix and suffix values This code performs the following transformation.
GraphBasedKBestHaplotypeFinder<V extends BaseVertex,E extends BaseEdge>	Efficient algorithm to obtain the list of best haplotypes given the instance.
GraphUtils	Utility functions used in the graphs package
InverseAllele	Utility class for defining a "not" allele concept that is used to score haplotypes that are not supporting the allele.
JTBestHaplotype<V extends BaseVertex,E extends BaseEdge>	A best haplotype object for being used with junction trees.
JunctionTreeKBestHaplotypeFinder<V extends BaseVertex,E extends BaseEdge>
KBestHaplotype<V extends BaseVertex,E extends BaseEdge>	Represents a result from a K-best haplotype search.
KBestHaplotypeFinder<V extends BaseVertex,E extends BaseEdge>	A common interface for the different KBestHaplotypeFinder implementations to conform to
KmerSearchableGraph<V extends BaseVertex,E extends BaseEdge>	Common interface for those graphs that implement vertex by kmer look-up.
LowWeightChainPruner<V extends BaseVertex,E extends BaseEdge>	Prune all chains from this graph where all edges in the path have multiplicity < pruneFactor For A -[1]> B -[1]> C -[1]> D would be removed with pruneFactor 2 but A -[1]> B -[2]> C -[1]> D would not be because the linear chain includes an edge with weight >= 2
MultiSampleEdge	Edge class for connecting nodes in the graph that tracks some per-sample information.
Path<V extends BaseVertex,E extends BaseEdge>	A path thought a BaseGraph class to keep track of paths
SeqGraph	A graph that contains base sequence at each node
SeqVertex	A graph vertex containing a sequence of bases and a unique ID that allows multiple distinct nodes in the graph to have the same sequence.
SharedSequenceMerger	Merges the incoming vertices of a vertex V of a graph Looks at the vertices that are incoming to V (i.e., have an outgoing edge connecting to V).
SharedVertexSequenceSplitter	Split a collection of middle nodes in a graph into their shared prefix and suffix values This code performs the following transformation.