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

Class AggregatedSubHaplotypeFinder<F extends org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.KBestSubHaplotypeFinder>

java.lang.Object

org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.AggregatedSubHaplotypeFinder<F>

public class AggregatedSubHaplotypeFinder<F extends org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.KBestSubHaplotypeFinder>
extends java.lang.Object

K-best sub-haplotype finder that selects the best solutions out of a collection of sub-haplotype finders.

Constructor Summary

Constructors

Constructor and Description
AggregatedSubHaplotypeFinder(java.util.Collection<F> finders) Creates a new aggregated sub-haplotype finder given its sub-finders.

Method Summary

Modifier and Type	Method and Description
int	getCount() Returns the total number of possible sub-haplotypes.
KBestHaplotype	getKBest(int k) Return the k-best sub-haplotype solution.
java.lang.String	id() Return an unique id for this sub-haplotype finder to be used when outputting diagrams.
boolean	isReference() Checks whether the top vertex for this finder is a reference haplotype vertex.
java.lang.String	label() Returns a label with human readable representation of this finder.
double	score(byte[] bases, int offset, int length) Calculate the score of a sequence of bases.
java.util.Set<org.apache.commons.lang3.tuple.Pair<? extends org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.KBestSubHaplotypeFinder,java.lang.String>>	subFinderLabels() Returns the set of subfinder from this finder together with a label for the connection with the current finder.

Methods inherited from class java.lang.Object

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

Constructor Detail

AggregatedSubHaplotypeFinder

public AggregatedSubHaplotypeFinder(java.util.Collection<F> finders)

Creates a new aggregated sub-haplotype finder given its sub-finders.

Parameters:

finders - set of sub-finders.

Method Detail

id

public java.lang.String id()

Return an unique id for this sub-haplotype finder to be used when outputting diagrams.

Returns:

never null.

label

public java.lang.String label()

Returns a label with human readable representation of this finder.

This is used when generating a diagram to illustrate the search space and costs

Returns:

never null.

subFinderLabels

public java.util.Set<org.apache.commons.lang3.tuple.Pair<? extends org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.KBestSubHaplotypeFinder,java.lang.String>> subFinderLabels()

Returns the set of subfinder from this finder together with a label for the connection with the current finder.

The label is used when generating a diagram to illustrate the search space and costs

getCount

public int getCount()

Returns the total number of possible sub-haplotypes.

Returns:

0 or greater.

score

public double score(byte[] bases,
                    int offset,
                    int length)

Calculate the score of a sequence of bases.

Parameters:

bases - array containing the query base sequence.

offset - first position of the query base sequence in bases .

length - length of the query base sequence.

Returns:

Double.NaN if there is no score for this sequence, otherwise a valid score value.

getKBest

public KBestHaplotype getKBest(int k)

Return the k-best sub-haplotype solution.

Parameters:

k - the requested solution rank.

Returns:

never null.

isReference

public boolean isReference()

Checks whether the top vertex for this finder is a reference haplotype vertex.

Returns:

true iff the top vertex for this finder is a reference vertex.