SRAAlignmentIterator (htsjdk 3.0.4 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

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 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
- 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 Details
- 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>