Package htsjdk.samtools

Class BAMFileReader.BAMQueryFilteringIterator

java.lang.Object

htsjdk.samtools.BAMFileReader.BAMQueryFilteringIterator

All Implemented Interfaces:

CloseableIterator<SAMRecord>, Closeable, AutoCloseable, Iterator<SAMRecord>

Enclosing class:

BAMFileReader

public class BAMFileReader.BAMQueryFilteringIterator
extends Object

Pull SAMRecords from a coordinate-sorted iterator, and filter out any that do not match the filter.

Field Summary

Fields

Modifier and Type	Field	Description
protected SAMRecord	mNextRecord	The next record to be returned.
protected final CloseableIterator<SAMRecord>	wrappedIterator	The wrapped iterator.

Constructor Summary

Constructors

Constructor	Description
BAMQueryFilteringIterator(CloseableIterator<SAMRecord> iterator, htsjdk.samtools.BAMIteratorFilter iteratorFilter)

Method Summary

Modifier and Type	Method	Description
protected void	assertOpen()
void	close()	Should be implemented to close/release any underlying resources.
boolean	hasNext()	Returns true if a next element exists; false otherwise.
SAMRecord	next()	Gets the next record from the given iterator.
void	remove()

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

Field Details

wrappedIterator

protected final CloseableIterator<SAMRecord> wrappedIterator

The wrapped iterator.

mNextRecord

protected SAMRecord mNextRecord

The next record to be returned. Will be null if no such record exists.

Constructor Details

BAMQueryFilteringIterator

public BAMQueryFilteringIterator(CloseableIterator<SAMRecord> iterator,
 htsjdk.samtools.BAMIteratorFilter iteratorFilter)

Method Details

hasNext

public boolean hasNext()

Returns true if a next element exists; false otherwise.

next

public SAMRecord next()

Gets the next record from the given iterator.

Returns:

The next SAM record in the iterator.

close

public void close()

Description copied from interface: CloseableIterator

Should be implemented to close/release any underlying resources.

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable

Specified by:

close in interface CloseableIterator<SAMRecord>

assertOpen

protected void assertOpen()

remove

public void remove()

Specified by:

remove in interface Iterator<SAMRecord>