org.broadinstitute.hellbender.engine

Class ReferenceShard

java.lang.Object

org.broadinstitute.hellbender.engine.ReferenceShard

All Implemented Interfaces:

java.io.Serializable

public final class ReferenceShard
extends java.lang.Object
implements java.io.Serializable

ReferenceShard is section of the reference genome that's used for sharding work for pairing things with the reference. The primary use case is pairing reads with the reference. This class is designed to be a simple data-storage class with related static utilities.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static int	REFERENCE_SHARD_SIZE

Constructor Summary

Constructors

Constructor and Description
ReferenceShard(int shardNumber, java.lang.String contig)

Method Summary

Modifier and Type	Method and Description
boolean	equals(java.lang.Object o)
java.lang.String	getContig()
int	getShardNumber()
static ReferenceShard	getShardNumberFromInterval(htsjdk.samtools.util.Locatable location) getShardNumberFromInterval returns the ReferenceShard that overlap the read's start position.
int	hashCode()
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

REFERENCE_SHARD_SIZE

public static final int REFERENCE_SHARD_SIZE

See Also:

Constant Field Values

Constructor Detail

ReferenceShard

public ReferenceShard(int shardNumber,
                      java.lang.String contig)

Method Detail

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

getContig

public java.lang.String getContig()

getShardNumber

public int getShardNumber()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getShardNumberFromInterval

public static ReferenceShard getShardNumberFromInterval(htsjdk.samtools.util.Locatable location)

getShardNumberFromInterval returns the ReferenceShard that overlap the read's start position.

Parameters:

location, - the start of which is used to determine the shard

Returns:

the shard (contig + id)