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

Class SeqVertex

java.lang.Object

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

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

public final class SeqVertex
extends BaseVertex

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. This is essential when thinking about representing the actual sequence of a haplotype in a graph. There can be many parts of the sequence that have the same sequence, but are distinct elements in the graph because they have a different position in the graph. For example: A -> C -> G -> A -> T The two As are not the same, because they occur with different connections. In a kmer graph equals() is based on the sequence itself, as each distinct kmer can only be represented once. But the transformation of the kmer graph into a graph of base sequences, without their kmer prefixes, means that nodes that where once unique including their prefix can become equal after shedding the prefix. So we need to use some mechanism -- here a unique ID per node -- to separate nodes that have the same sequence but are distinct elements of the graph.

Field Summary

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

sequence

Constructor Summary

Constructors

Constructor and Description
SeqVertex(byte[] sequence) Create a new SeqVertex with sequence and the next available id
SeqVertex(java.lang.String sequence) Create a new SeqVertex having bases of sequence.getBytes()

Method Summary

Modifier and Type	Method and Description
boolean	equals(java.lang.Object o) Two SeqVertex are equal only if their ids are equal
int	getId() Get the unique ID for this SeqVertex
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()
SeqVertex	withoutPrefixAndSuffix(byte[] prefix, byte[] suffix) Return a new SeqVertex derived from this one but not including prefix or suffix bases
SeqVertex	withoutSuffix(byte[] suffix) Return a new SeqVertex derived from this one but not including the suffix bases

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

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

Methods inherited from class java.lang.Object

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

Constructor Detail

SeqVertex

public SeqVertex(byte[] sequence)

Create a new SeqVertex with sequence and the next available id

Parameters:

sequence - our base sequence

SeqVertex

public SeqVertex(java.lang.String sequence)

Create a new SeqVertex having bases of sequence.getBytes()

Parameters:

sequence - the string representation of our bases

Method Detail

getId

public int getId()

Get the unique ID for this SeqVertex

Returns:

a positive integer >= 0

toString

public java.lang.String toString()

Overrides:

toString in class BaseVertex

equals

public boolean equals(java.lang.Object o)

Two SeqVertex are equal only if their ids are equal

Overrides:

equals in class BaseVertex

Parameters:

o -

Returns:

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

withoutSuffix

public SeqVertex withoutSuffix(byte[] suffix)

Return a new SeqVertex derived from this one but not including the suffix bases

Parameters:

suffix - the suffix bases to remove from this vertex

Returns:

a newly allocated SeqVertex with appropriate prefix, or null if suffix removes all bases from this node

withoutPrefixAndSuffix

public SeqVertex withoutPrefixAndSuffix(byte[] prefix,
                                        byte[] suffix)

Return a new SeqVertex derived from this one but not including prefix or suffix bases

Parameters:

prefix - the previx bases to remove

suffix - the suffix bases to remove from this vertex

Returns:

a newly allocated SeqVertex