htsjdk.samtools

Class DownsamplingIterator

java.lang.Object

htsjdk.samtools.DownsamplingIterator

All Implemented Interfaces:

CloseableIterator<SAMRecord>, java.io.Closeable, java.lang.AutoCloseable, java.util.Iterator<SAMRecord>

public abstract class DownsamplingIterator
extends java.lang.Object
implements CloseableIterator<SAMRecord>

Abstract base class for all DownsamplingIterators that provides a uniform interface for recording and reporting statistics bout how many records have been kept and discarded. A DownsamplingIterator is an iterator that takes another iterator of SAMRecords and filters out a subset of those records in a random way, while ensuring that all records for a template (i.e. record name) are either retained or discarded. Strictly speaking the proportion parameter applies to templates, though in most instances it is safe to think about it being applied to records.

Constructor Summary

Constructors

Constructor and Description
DownsamplingIterator(double targetProportion) Constructs a downsampling iterator that aims to retain the targetProportion of reads.

Method Summary

Modifier and Type	Method and Description
void	close() Does nothing.
long	getAcceptedCount() Returns the number of records returned since creation of the last call to resetStatistics.
double	getAcceptedFraction() Gets the fraction of records accepted since creation or the last call to resetStatistics().
long	getDiscardedCount() Returns the number of records discarded since creation of the last call to resetStatistics.
double	getDiscardedFraction() Gets the fraction of records discarded since creation or the last call to resetStatistics().
long	getSeenCount() Returns the number of records seen, including accepted and discarded, since creation of the last call to resetStatistics.
double	getTargetProportion() Gets the target proportion of records that should be retained during downsampling.
boolean	isHigherAccuracy() Indicates whether or not the strategy implemented by this DownsamplingIterator makes any effort to increase accuracy beyond random sampling (i.e.
protected void	recordAcceptedRecord() Method for subclasses to record a specific record as being accepted.
protected void	recordAcceptedRecords(long n) Record one or more records as having been discarded.
protected void	recordDiscardedRecord() Method for subclasses to record a record as being discarded.
protected void	recordDiscardRecords(long n) Record one or more records as having been discarded.
void	remove() Not supported.
void	resetStatistics() Resets the statistics for records seen/accepted/discarded.

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.samtools.util.CloseableIterator

stream, toList

Methods inherited from interface java.util.Iterator

forEachRemaining, hasNext, next

Constructor Detail

DownsamplingIterator

public DownsamplingIterator(double targetProportion)

Constructs a downsampling iterator that aims to retain the targetProportion of reads.

Method Detail

close

public void close()

Does nothing.

Specified by:

close in interface CloseableIterator<SAMRecord>

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

getSeenCount

public long getSeenCount()

Returns the number of records seen, including accepted and discarded, since creation of the last call to resetStatistics.

getAcceptedCount

public long getAcceptedCount()

Returns the number of records returned since creation of the last call to resetStatistics.

getDiscardedCount

public long getDiscardedCount()

Returns the number of records discarded since creation of the last call to resetStatistics.

getDiscardedFraction

public double getDiscardedFraction()

Gets the fraction of records discarded since creation or the last call to resetStatistics().

getAcceptedFraction

public double getAcceptedFraction()

Gets the fraction of records accepted since creation or the last call to resetStatistics().

resetStatistics

public void resetStatistics()

Resets the statistics for records seen/accepted/discarded.

getTargetProportion

public double getTargetProportion()

Gets the target proportion of records that should be retained during downsampling.

recordDiscardedRecord

protected final void recordDiscardedRecord()

Method for subclasses to record a record as being discarded.

recordAcceptedRecord

protected final void recordAcceptedRecord()

Method for subclasses to record a specific record as being accepted. Null may be passed if a record was discarded but access to the object is no longer available.

recordDiscardRecords

protected final void recordDiscardRecords(long n)

Record one or more records as having been discarded.

recordAcceptedRecords

protected final void recordAcceptedRecords(long n)

Record one or more records as having been discarded.

isHigherAccuracy

public boolean isHigherAccuracy()

Indicates whether or not the strategy implemented by this DownsamplingIterator makes any effort to increase accuracy beyond random sampling (i.e. to reduce the delta between the requested proportion of reads and the actually emitted proportion of reads).

remove

public void remove()

Not supported.

Specified by:

remove in interface java.util.Iterator<SAMRecord>