SRAUnalignmentIterator (htsjdk 2.8.1 API)

java.lang.Object
- htsjdk.samtools.sra.SRAUnalignmentIterator

All Implemented Interfaces:

Iterator<SAMRecord>
```
public class SRAUnalignmentIterator
extends Object
implements Iterator<SAMRecord>
```
Iterator for unaligned reads. Is used from SRAIterator. Created by andrii.nikitiuk on 9/3/15.

Constructor Summary

Constructors
Constructor and Description
`SRAUnalignmentIterator(SRAAccession accession, ngs.ReadCollection run, SAMFileHeader header, SRAIterator.RecordRangeInfo recordRangeInfo, Chunk chunk)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`hasNext()`
`SAMRecord`	`next()`
`void`	`remove()`
`void`	`setValidationStringency(ValidationStringency validationStringency)`

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

Methods inherited from interface java.util.Iterator
forEachRemaining

Constructor Detail

SRAUnalignmentIterator

public SRAUnalignmentIterator(SRAAccession accession,
                              ngs.ReadCollection run,
                              SAMFileHeader header,
                              SRAIterator.RecordRangeInfo recordRangeInfo,
                              Chunk chunk)

Parameters:: run - opened read collection; header - sam header; recordRangeInfo - info about record ranges withing SRA archive; chunk - used to determine which unaligned reads the iterator should return

Method Detail
- hasNext
```
public boolean hasNext()
```
  Specified by:
  
  hasNext in interface Iterator<SAMRecord>
- next
```
public SAMRecord next()
```
  Specified by:
  
  next in interface Iterator<SAMRecord>
- remove
```
public void remove()
```
  Specified by:
  
  remove in interface Iterator<SAMRecord>
- setValidationStringency
```
public void setValidationStringency(ValidationStringency validationStringency)
```

Class SRAUnalignmentIterator

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface java.util.Iterator

Constructor Detail

SRAUnalignmentIterator

Method Detail

hasNext

next

remove

setValidationStringency