org.broadinstitute.hellbender.engine

Class ShardToMultiIntervalShardAdapter<T>

java.lang.Object

org.broadinstitute.hellbender.engine.ShardToMultiIntervalShardAdapter<T>

All Implemented Interfaces:

htsjdk.samtools.util.Locatable, java.io.Serializable, java.lang.Iterable<T>, MultiIntervalShard<T>, Shard<T>

public class ShardToMultiIntervalShardAdapter<T>
extends java.lang.Object
implements MultiIntervalShard<T>, Shard<T>, java.io.Serializable

adapts a normal Shard into a MultiIntervalShard that contains only the single wrapped shard this is a temporary shim until we can fully adopt MultiIntervalShard in HaplotypeCallerSpark

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
ShardToMultiIntervalShardAdapter(Shard<T> shard)

Method Summary

Modifier and Type	Method and Description
SimpleInterval	getInterval()
java.util.List<SimpleInterval>	getIntervals()
SimpleInterval	getPaddedInterval()
java.util.List<SimpleInterval>	getPaddedIntervals()
java.util.Iterator<T>	iterator()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.broadinstitute.hellbender.engine.Shard

divideIntervalIntoShards, divideIntervalIntoShards, getContig, getEnd, getStart

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Methods inherited from interface htsjdk.samtools.util.Locatable

contains, contigsMatch, getLengthOnReference, overlaps, withinDistanceOf

Constructor Detail

ShardToMultiIntervalShardAdapter

public ShardToMultiIntervalShardAdapter(Shard<T> shard)

Method Detail

getIntervals

public java.util.List<SimpleInterval> getIntervals()

Specified by:

getIntervals in interface MultiIntervalShard<T>

Returns:

A List of this shard's intervals

getPaddedIntervals

public java.util.List<SimpleInterval> getPaddedIntervals()

Specified by:

getPaddedIntervals in interface MultiIntervalShard<T>

Returns:

A List of this shard's intervals, with padding added to each interval on both sides

iterator

public java.util.Iterator<T> iterator()

Specified by:

iterator in interface java.lang.Iterable<T>

getInterval

public SimpleInterval getInterval()

Specified by:

getInterval in interface Shard<T>

Returns:

the interval this shard spans

getPaddedInterval

public SimpleInterval getPaddedInterval()

Specified by:

getPaddedInterval in interface Shard<T>

Returns:

the interval this shard spans, potentially with additional padding on each side it must be the case that for a given Shard getPaddedInterval().contains(getInterval())