htsjdk.samtools.util

Class SAMRecordPrefetchingIterator

java.lang.Object

htsjdk.samtools.util.SAMRecordPrefetchingIterator

All Implemented Interfaces:

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

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

Iterator that uses a dedicated background thread to prefetch SAMRecords, reading ahead by a set number of bases to improve throughput.

Note that this implementation is not synchronized. If multiple threads access an instance concurrently, it must be synchronized externally.

Constructor Summary

Constructors

Constructor and Description
SAMRecordPrefetchingIterator(CloseableIterator<SAMRecord> iterator, int basePrefetchLimit) Creates a new iterator that traverses the given iterator on a background thread

Method Summary

Modifier and Type	Method and Description
void	close() Should be implemented to close/release any underlying resources.
boolean	hasNext()
SAMRecord	next()
protected int	readsInQueue()

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, remove

Constructor Detail

SAMRecordPrefetchingIterator

public SAMRecordPrefetchingIterator(CloseableIterator<SAMRecord> iterator,
                                    int basePrefetchLimit)

Creates a new iterator that traverses the given iterator on a background thread

Parameters:

iterator - the iterator to traverse

basePrefetchLimit - the number of bases to prefetch

Method Detail

close

public void close()

Description copied from interface: CloseableIterator

Should be implemented to close/release any underlying resources.

Specified by:

close in interface CloseableIterator<SAMRecord>

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

hasNext

public boolean hasNext()

Specified by:

hasNext in interface java.util.Iterator<SAMRecord>

next

public SAMRecord next()

Specified by:

next in interface java.util.Iterator<SAMRecord>

readsInQueue

protected int readsInQueue()