org.broadinstitute.hellbender.utils.downsampling

Class ReadsDownsampler

java.lang.Object

org.broadinstitute.hellbender.utils.downsampling.Downsampler<GATKRead>

org.broadinstitute.hellbender.utils.downsampling.ReadsDownsampler

All Implemented Interfaces:

PushPullTransformer<GATKRead>

Direct Known Subclasses:

FractionalDownsampler, MutectDownsampler, PassThroughDownsampler, PositionalDownsampler, ReservoirDownsampler

public abstract class ReadsDownsampler
extends Downsampler<GATKRead>

An extension of the basic downsampler API with reads-specific operations

Constructor Summary

Constructors

Constructor and Description
ReadsDownsampler()

Method Summary

Modifier and Type	Method and Description
abstract boolean	requiresCoordinateSortOrder() Does this downsampler require that reads be fed to it in coordinate order?
abstract void	signalNoMoreReadsBefore(GATKRead read) Tell this downsampler that no more reads located before the provided read (according to the sort order of the read stream) will be fed to it.

Methods inherited from class org.broadinstitute.hellbender.utils.downsampling.Downsampler

clearItems, consumeFinalizedItems, getNumberOfDiscardedItems, hasFinalizedItems, hasPendingItems, incrementNumberOfDiscardedItems, peekFinalized, peekPending, resetStats, signalEndOfInput, size, submit, submit

Methods inherited from class java.lang.Object

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

Constructor Detail

ReadsDownsampler

public ReadsDownsampler()

Method Detail

requiresCoordinateSortOrder

public abstract boolean requiresCoordinateSortOrder()

Does this downsampler require that reads be fed to it in coordinate order?

Returns:

true if reads must be submitted to this downsampler in coordinate order, otherwise false

signalNoMoreReadsBefore

public abstract void signalNoMoreReadsBefore(GATKRead read)

Tell this downsampler that no more reads located before the provided read (according to the sort order of the read stream) will be fed to it. Allows position-aware downsamplers to finalize pending reads earlier than they would otherwise be able to, particularly when doing per-sample downsampling and reads for certain samples are sparser than average.

Parameters:

read - the downsampler will assume that no reads located before this read will ever be submitted to it in the future