org.broadinstitute.hellbender.engine

Class ShardBoundary

java.lang.Object

org.broadinstitute.hellbender.engine.ShardBoundary

All Implemented Interfaces:

htsjdk.samtools.util.Locatable, java.io.Serializable

Direct Known Subclasses:

ReadlessAssemblyRegion

public class ShardBoundary
extends java.lang.Object
implements htsjdk.samtools.util.Locatable, java.io.Serializable

Holds the bounds of a Shard, both with and without padding

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected SimpleInterval	interval
protected boolean	padded
protected SimpleInterval	paddedSpan

Constructor Summary

Constructors

Modifier	Constructor and Description
	ShardBoundary(SimpleInterval interval, SimpleInterval paddedSpan) Create a new ShardBoundary from the given intervals
protected	ShardBoundary(SimpleInterval interval, SimpleInterval paddedSpan, boolean padded)

Method Summary

Modifier and Type	Method and Description
<T> Shard<T>	createShard(java.lang.Iterable<T> locatables)
boolean	equals(java.lang.Object o)
java.lang.String	getContig()
int	getEnd()
SimpleInterval	getInterval()
SimpleInterval	getPaddedSpan()
int	getStart()
int	hashCode()
ShardBoundary	paddedShardBoundary()
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.samtools.util.Locatable

contains, contigsMatch, getLengthOnReference, overlaps, withinDistanceOf

Field Detail

interval

protected final SimpleInterval interval

paddedSpan

protected final SimpleInterval paddedSpan

padded

protected final boolean padded

Constructor Detail

ShardBoundary

public ShardBoundary(SimpleInterval interval,
                     SimpleInterval paddedSpan)

Create a new ShardBoundary from the given intervals

Parameters:

interval - the interval covered by the shard

paddedSpan - the interval covered by the shard's padding, must contain the shard interval

ShardBoundary

protected ShardBoundary(SimpleInterval interval,
                        SimpleInterval paddedSpan,
                        boolean padded)

Method Detail

getContig

public java.lang.String getContig()

Specified by:

getContig in interface htsjdk.samtools.util.Locatable

getStart

public int getStart()

Specified by:

getStart in interface htsjdk.samtools.util.Locatable

Returns:

start of the shard boundary without padding

getEnd

public int getEnd()

Specified by:

getEnd in interface htsjdk.samtools.util.Locatable

Returns:

end of the shard boundary without padding

getInterval

public SimpleInterval getInterval()

Returns:

the interval this boundary covers without padding

getPaddedSpan

public SimpleInterval getPaddedSpan()

Returns:

the interval this boundary covers including padding

paddedShardBoundary

public ShardBoundary paddedShardBoundary()

createShard

public <T> Shard<T> createShard(java.lang.Iterable<T> locatables)

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

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object