Package htsjdk.samtools.sra

Class SRAUnalignmentIterator

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

Method Summary

Modifier and Type	Method	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 Details

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 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)