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

Class MultiDeBruijnVertex

java.lang.Object

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

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

public final class MultiDeBruijnVertex
extends BaseVertex

A DeBruijnVertex that supports multiple copies of the same kmer

Field Summary

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

sequence

Constructor Summary

Constructors

Constructor and Description
MultiDeBruijnVertex(byte[] sequence) Create a new MultiDeBruijnVertex with kmer sequence
MultiDeBruijnVertex(byte[] sequence, boolean mergeIdenticalNodes) Create a new MultiDeBruijnVertex with kmer sequence

Method Summary

Modifier and Type	Method and Description
void	addRead(java.lang.String name) Add name information to this vertex for debugging This information will be captured as a list of strings, and displayed in DOT if this graph is written out to disk This functionality is only enabled when KEEP_TRACK_OF_READS is true
boolean	equals(java.lang.Object o)
java.lang.String	getAdditionalInfo()
byte[]	getAdditionalSequence(boolean source) Get the sequence unique to this vertex This function may not return the entire sequence stored in the vertex, as kmer graphs really only provide 1 base of additional sequence (the last base of the kmer).
int	getKmerSize() Get the kmer size for this DeBruijnVertex
byte	getSuffix() Get the suffix byte of this DeBruijnVertex The suffix byte is simply the last byte of the kmer sequence, so if this is holding sequence ACT getSuffix would return T
java.lang.String	getSuffixString() Get the string representation of the suffix of this DeBruijnVertex
int	hashCode() necessary to override here so that graph.containsVertex() works the same way as vertex.equals() as one might expect
java.lang.String	toString()

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

getSequence, getSequenceString, hasAmbiguousSequence, isEmpty, length, seqEquals, setAdditionalInfo

Methods inherited from class java.lang.Object

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

Constructor Detail

MultiDeBruijnVertex

public MultiDeBruijnVertex(byte[] sequence,
                           boolean mergeIdenticalNodes)

Create a new MultiDeBruijnVertex with kmer sequence

Parameters:

mergeIdenticalNodes - should nodes with the same sequence be treated as equal?

sequence - the kmer sequence

MultiDeBruijnVertex

public MultiDeBruijnVertex(byte[] sequence)

Create a new MultiDeBruijnVertex with kmer sequence

Parameters:

sequence - the kmer sequence

Method Detail

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class BaseVertex

hashCode

public int hashCode()

Description copied from class: BaseVertex

necessary to override here so that graph.containsVertex() works the same way as vertex.equals() as one might expect

Overrides:

hashCode in class BaseVertex

toString

public java.lang.String toString()

Overrides:

toString in class BaseVertex

addRead

public void addRead(java.lang.String name)

Add name information to this vertex for debugging This information will be captured as a list of strings, and displayed in DOT if this graph is written out to disk This functionality is only enabled when KEEP_TRACK_OF_READS is true

Parameters:

name - a non-null string

getAdditionalInfo

public java.lang.String getAdditionalInfo()

Overrides:

getAdditionalInfo in class BaseVertex

Returns:

the additional information for display about this vertex

getKmerSize

public int getKmerSize()

Get the kmer size for this DeBruijnVertex

Returns:

integer >= 1

getSuffixString

public java.lang.String getSuffixString()

Get the string representation of the suffix of this DeBruijnVertex

Returns:

a non-null non-empty string

getSuffix

public byte getSuffix()

Get the suffix byte of this DeBruijnVertex The suffix byte is simply the last byte of the kmer sequence, so if this is holding sequence ACT getSuffix would return T

Returns:

a byte

getAdditionalSequence

public byte[] getAdditionalSequence(boolean source)

Get the sequence unique to this vertex This function may not return the entire sequence stored in the vertex, as kmer graphs really only provide 1 base of additional sequence (the last base of the kmer). The base implementation simply returns the sequence.

Overrides:

getAdditionalSequence in class BaseVertex

Parameters:

source - is this vertex a source vertex (i.e., no in nodes) in the graph

Returns:

a byte[] of the sequence added by this vertex to the overall sequence