Package htsjdk.samtools.filter

Class FilteringSamIterator

java.lang.Object

htsjdk.samtools.filter.FilteringSamIterator

All Implemented Interfaces:

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

Direct Known Subclasses:

FilteringIterator

public class FilteringSamIterator
extends Object
implements CloseableIterator<SAMRecord>

Filtering Iterator which takes a filter and an iterator and iterates through only those records which are not rejected by the filter.

$Id$

Constructor Summary

Constructors

Constructor	Description
FilteringSamIterator(Iterator<SAMRecord> iterator, SamRecordFilter filter)	Constructor
FilteringSamIterator(Iterator<SAMRecord> iterator, SamRecordFilter filter, boolean filterByPair)	Constructor

Method Summary

Modifier and Type	Method	Description
void	close()	Should be implemented to close/release any underlying resources.
boolean	hasNext()	Returns true if the iteration has more elements.
SAMRecord	next()	Returns the next element in the iteration.
void	remove()	Required method for Iterator API.

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

Constructor Details

FilteringSamIterator

public FilteringSamIterator(Iterator<SAMRecord> iterator,
 SamRecordFilter filter,
 boolean filterByPair)

Constructor

Parameters:

iterator - the backing iterator

filter - the filter (which may be a FilterAggregator)

filterByPair - if true, filter reads in pairs

FilteringSamIterator

public FilteringSamIterator(Iterator<SAMRecord> iterator,
 SamRecordFilter filter)

Constructor

Parameters:

iterator - the backing iterator

filter - the filter (which may be a FilterAggregator)

Method Details

hasNext

public boolean hasNext()

Returns true if the iteration has more elements.

Specified by:

hasNext in interface Iterator<SAMRecord>

Returns:

true if the iteration has more elements. Otherwise returns false.

next

public SAMRecord next()

Returns the next element in the iteration.

Specified by:

next in interface Iterator<SAMRecord>

Returns:

the next element in the iteration

Throws:

NoSuchElementException

remove

public void remove()

Required method for Iterator API.

Specified by:

remove in interface Iterator<SAMRecord>

Throws:

UnsupportedOperationException

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>