htsjdk.samtools.sra

Class SRAAlignmentIterator

java.lang.Object

htsjdk.samtools.sra.SRAAlignmentIterator

All Implemented Interfaces:

java.util.Iterator<SAMRecord>

public class SRAAlignmentIterator
extends java.lang.Object
implements java.util.Iterator<SAMRecord>

Iterator for aligned reads. Is used from SRAIterator. Created by andrii.nikitiuk on 9/3/15.

Constructor Summary

Constructors

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

Method Summary

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

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 java.util.Iterator<SAMRecord>

next

public SAMRecord next()

Specified by:

next in interface java.util.Iterator<SAMRecord>

remove

public void remove()

Specified by:

remove in interface java.util.Iterator<SAMRecord>

setValidationStringency

public void setValidationStringency(ValidationStringency validationStringency)