org.broadinstitute.hellbender.engine

Class VariantShard

java.lang.Object

org.broadinstitute.hellbender.engine.VariantShard

public final class VariantShard
extends java.lang.Object

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

Field Summary

Fields

Modifier and Type	Field and Description
static int	VARIANT_SHARDSIZE

Constructor Summary

Constructors

Constructor and Description
VariantShard(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 java.util.List<VariantShard>	getVariantShardsFromInterval(htsjdk.samtools.util.Locatable location) getVariantShardsFromInterval calculates *all* shards overlapping location.
int	hashCode()
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

VARIANT_SHARDSIZE

public static final int VARIANT_SHARDSIZE

See Also:

Constant Field Values

Constructor Detail

VariantShard

public VariantShard(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()

getVariantShardsFromInterval

public static java.util.List<VariantShard> getVariantShardsFromInterval(htsjdk.samtools.util.Locatable location)

getVariantShardsFromInterval calculates *all* shards overlapping location.

Parameters:

location - the range of sites determines which shards are overlapping

Returns:

All overlapping VariantShards

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object