Package htsjdk.samtools.sra

Class SRAAlignmentIterator

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>