Package org.broadinstitute.hellbender.tools

Class DownsampleableSparkReadShard

java.lang.Object

org.broadinstitute.hellbender.tools.DownsampleableSparkReadShard

All Implemented Interfaces:

htsjdk.samtools.util.Locatable, Serializable, Iterable<GATKRead>, Shard<GATKRead>

public final class DownsampleableSparkReadShard
extends Object
implements Shard<GATKRead>, Serializable

A simple shard implementation intended to be used for splitting reads by partition in Spark tools

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
DownsampleableSparkReadShard(ShardBoundary boundaries, Iterable<GATKRead> reads, ReadsDownsampler downsampler)

Method Summary

Modifier and Type	Method	Description
SimpleInterval	getInterval()
SimpleInterval	getPaddedInterval()
Iterator<GATKRead>	iterator()

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Methods inherited from interface htsjdk.samtools.util.Locatable

contains, contigsMatch, getLengthOnReference, overlaps, withinDistanceOf

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

getContig, getEnd, getStart

Constructor Details

DownsampleableSparkReadShard

public DownsampleableSparkReadShard(ShardBoundary boundaries,
 Iterable<GATKRead> reads,
 ReadsDownsampler downsampler)

Parameters:

boundaries - the boundary defining the shard

reads - the records overlapping the shard

downsampler - the downsampler to use (may be null, which signifies that no downsampling is to be performed)

Method Details

getInterval

public SimpleInterval getInterval()

Specified by:

getInterval in interface Shard<GATKRead>

Returns:

the interval this shard spans

getPaddedInterval

public SimpleInterval getPaddedInterval()

Specified by:

getPaddedInterval in interface Shard<GATKRead>

Returns:

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

iterator

public Iterator<GATKRead> iterator()

Specified by:

iterator in interface Iterable<GATKRead>