SRAAlignmentIterator (htsjdk 2.14.3 API)

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

All Implemented Interfaces:

CloseableIterator<SAMRecord>, Closeable, AutoCloseable, Iterator<SAMRecord>
```
public class SRAAlignmentIterator
extends Object
implements CloseableIterator<SAMRecord>
```
Iterator for aligned reads. Is used from SRAIterator. Created by andrii.nikitiuk on 9/3/15.

Constructor Summary

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

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()`
`SAMRecord`	`next()`
`void`	`remove()`
`void`	`setValidationStringency(ValidationStringency validationStringency)`

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
  - SRAAlignmentIterator
```
public SRAAlignmentIterator(SRAAccession accession,
                            ngs.ReadCollection run,
                            SAMFileHeader header,
                            ReferenceCache cachedReferences,
                            SRAIterator.RecordRangeInfo recordRangeInfo,
                            Chunk chunk)
```
    Parameters:
    
    run - opened read collection
    
    header - sam header
    
    cachedReferences - list of cached references shared among all iterators from a single SRAFileReader
    
    recordRangeInfo - info about record ranges withing SRA archive
    
    chunk - used to determine which alignments 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)
```
  - 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 SRAAlignmentIterator

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

SRAAlignmentIterator

Method Detail

hasNext

next

remove

setValidationStringency

close