FilteringSamIterator (htsjdk 2.14.3 API)

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

All Methods Instance Methods Concrete Methods
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 interface htsjdk.samtools.util.CloseableIterator
stream, toList

Methods inherited from interface java.util.Iterator
forEachRemaining

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - 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 Detail
  - 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>

Class FilteringSamIterator

Constructor Summary

Method Summary

Methods inherited from interface htsjdk.samtools.util.CloseableIterator

Methods inherited from interface java.util.Iterator

Methods inherited from class java.lang.Object

Constructor Detail

FilteringSamIterator

FilteringSamIterator

Method Detail

hasNext

next

remove

close