htsjdk.samtools

Class DownsamplingIterator

java.lang.Object

htsjdk.samtools.DownsamplingIterator

All Implemented Interfaces:

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

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

An iterator of SAMRecords that can downsample on the fly. Allows for inclusion of secondary and/or supplemental records (off by default), though this will cause memory use to increase as the decisions for each read name must be cached permanently.

Constructor Summary

Constructors

Constructor and Description
DownsamplingIterator(java.util.Iterator<SAMRecord> iterator, java.util.Random random, double probabilityOfKeeping) Constructs a downsampling iterator upon the supplied iterator, using the Random as the source of randomness.

Method Summary

Methods

Modifier and Type	Method and Description
void	close()
long	getKeptReads() Returns the number of reads/records kept post-downsampling up to the point when the method is called.
long	getTotalReads() Returns the total number of reads/records considered up to the point when the method is called.
boolean	hasNext() Returns true if there is another record available post-downsampling, false otherwise.
java.util.Iterator<SAMRecord>	iterator() Simple implementation of iterable that returns this iterator.
SAMRecord	next() Returns the next record from the iterator, or throws an exception if there is no next record.
void	remove() Unsupported operation.
DownsamplingIterator	setAllowSecondaryAlignments(boolean allowSecondaryAlignments) Sets whether or not secondary alignments are allowed (true) or all discarded (false).
DownsamplingIterator	setAllowSupplementalAlignments(boolean allowSupplementalAlignments) Sets whether or not supplemental alignments are allowed (true) or all discarded (false).
DownsamplingIterator	setIncludeNoRefReads(boolean includeNoRefReads) Sets whether the iterator will stop when no-ref reads are encountered, or keep downsampling through them.

Methods inherited from class java.lang.Object

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

Constructor Detail

DownsamplingIterator

public DownsamplingIterator(java.util.Iterator<SAMRecord> iterator,
                    java.util.Random random,
                    double probabilityOfKeeping)

Constructs a downsampling iterator upon the supplied iterator, using the Random as the source of randomness.

Method Detail

setAllowSecondaryAlignments

public DownsamplingIterator setAllowSecondaryAlignments(boolean allowSecondaryAlignments)

Sets whether or not secondary alignments are allowed (true) or all discarded (false).

setAllowSupplementalAlignments

public DownsamplingIterator setAllowSupplementalAlignments(boolean allowSupplementalAlignments)

Sets whether or not supplemental alignments are allowed (true) or all discarded (false).

setIncludeNoRefReads

public DownsamplingIterator setIncludeNoRefReads(boolean includeNoRefReads)

Sets whether the iterator will stop when no-ref reads are encountered, or keep downsampling through them.

getTotalReads

public long getTotalReads()

Returns the total number of reads/records considered up to the point when the method is called.

getKeptReads

public long getKeptReads()

Returns the number of reads/records kept post-downsampling up to the point when the method is called.

iterator

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

Simple implementation of iterable that returns this iterator.

Specified by:

iterator in interface java.lang.Iterable<SAMRecord>

hasNext

public boolean hasNext()

Returns true if there is another record available post-downsampling, false otherwise.

Specified by:

hasNext in interface java.util.Iterator<SAMRecord>

next

public SAMRecord next()

Returns the next record from the iterator, or throws an exception if there is no next record.

Specified by:

next in interface java.util.Iterator<SAMRecord>

remove

public void remove()

Unsupported operation.

Specified by:

remove in interface java.util.Iterator<SAMRecord>

close

public void close()

Specified by:

close in interface CloseableIterator<SAMRecord>

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable