SamPairUtil.SetMateInfoIterator (htsjdk 2.14.3 API)

java.lang.Object
- htsjdk.samtools.util.PeekableIterator<SAMRecord>
- - htsjdk.samtools.SamPairUtil.SetMateInfoIterator

All Implemented Interfaces:

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

Enclosing class:

SamPairUtil
```
public static class SamPairUtil.SetMateInfoIterator
extends PeekableIterator<SAMRecord>
```
A class to iterate through SAMRecords and set mate information on the given records, and optionally set the mate cigar tag (true by default).

Constructor Summary

Constructors
Constructor	Description
`SetMateInfoIterator(Iterator<SAMRecord> iterator)`	By default, the mate cigar tag is set
`SetMateInfoIterator(Iterator<SAMRecord> iterator, boolean setMateCigar)`
`SetMateInfoIterator(Iterator<SAMRecord> iterator, boolean setMateCigar, boolean ignoreMissingMates)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`long`	`getNumMateCigarsAdded()`
`boolean`	`hasNext()`	True if there are more items, in which case both next() and peek() will return a value.
`SAMRecord`	`next()`	Returns the next object and advances the iterator.
`SAMRecord`	`peek()`	Returns the next object but does not advance the iterator.

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

Methods inherited from class htsjdk.samtools.util.PeekableIterator
close, remove

- Constructor Detail
  - SetMateInfoIterator
```
public SetMateInfoIterator(Iterator<SAMRecord> iterator)
```
    By default, the mate cigar tag is set
    
    Parameters:
    
    iterator - the iterator to wrap
  - SetMateInfoIterator
```
public SetMateInfoIterator(Iterator<SAMRecord> iterator,
                           boolean setMateCigar)
```
    Parameters:
    
    iterator - the iterator to wrap
    
    setMateCigar - true if we are to update/create the Mate CIGAR (MC) optional tag, false if we are to clear any mate cigar tag that is present.
  - SetMateInfoIterator
```
public SetMateInfoIterator(Iterator<SAMRecord> iterator,
                           boolean setMateCigar,
                           boolean ignoreMissingMates)
```
    Parameters:
    
    iterator - the iterator to wrap
    
    setMateCigar - true if we are to update/create the Mate CIGAR (MC) optional tag, false if we are to clear any mate cigar tag that is present.
    
    ignoreMissingMates - set this to true if we are to ignore missing mates, otherwise an exception will be thrown when a missing mate is encountered
- Method Detail
  - getNumMateCigarsAdded
```
public long getNumMateCigarsAdded()
```
    Returns:
    
    the current number of mate cigars added. This could be more than the number of records returned.
  - hasNext
```
public boolean hasNext()
```
    Description copied from class: PeekableIterator
    
    True if there are more items, in which case both next() and peek() will return a value.
    
    Specified by:
    
    hasNext in interface Iterator<SAMRecord>
    
    Overrides:
    
    hasNext in class PeekableIterator<SAMRecord>
  - next
```
public SAMRecord next()
```
    Description copied from class: PeekableIterator
    
    Returns the next object and advances the iterator.
    
    Specified by:
    
    next in interface Iterator<SAMRecord>
    
    Overrides:
    
    next in class PeekableIterator<SAMRecord>
  - peek
```
public SAMRecord peek()
```
    Description copied from class: PeekableIterator
    
    Returns the next object but does not advance the iterator. Subsequent calls to peek() and next() will return the same object.
    
    Overrides:
    
    peek in class PeekableIterator<SAMRecord>

Class SamPairUtil.SetMateInfoIterator

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

Methods inherited from class htsjdk.samtools.util.PeekableIterator

Constructor Detail

SetMateInfoIterator

SetMateInfoIterator

SetMateInfoIterator

Method Detail

getNumMateCigarsAdded

hasNext

next

peek