htsjdk.samtools

Class SRAIterator

java.lang.Object

htsjdk.samtools.SRAIterator

All Implemented Interfaces:

SAMRecordIterator, CloseableIterator<SAMRecord>, java.io.Closeable, java.lang.AutoCloseable, java.util.Iterator<SAMRecord>

public class SRAIterator
extends java.lang.Object
implements SAMRecordIterator

SRA iterator which returns SAMRecords for requested list of chunks

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SRAIterator.RecordRangeInfo Describes record ranges info needed for emulating BAM index

Constructor Summary

Constructors

Constructor and Description
SRAIterator(SRAAccession accession, ngs.ReadCollection run, SAMFileHeader header, ReferenceCache cachedReferences, SRAIterator.RecordRangeInfo recordRangeInfo, java.util.List<Chunk> chunks)

Method Summary

Modifier and Type	Method and Description
SAMRecordIterator	assertSorted(SAMFileHeader.SortOrder sortOrder) Establishes that records returned by this iterator are expected to be in the specified sort order.
void	close() Should be implemented to close/release any underlying resources.
static SRAIterator.RecordRangeInfo	getRecordsRangeInfo(ngs.ReadCollection run) Loads record ranges needed for emulating BAM index
boolean	hasNext() NGS iterators implement a single method "nextObject" which return true if the operation was successful or false if there are no more objects available.
SAMRecord	next() Call hasNext to make sure that one of inner iterators points to the next record, the retrieve the record from one of them.
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 Detail

SRAIterator

public SRAIterator(SRAAccession accession,
                   ngs.ReadCollection run,
                   SAMFileHeader header,
                   ReferenceCache cachedReferences,
                   SRAIterator.RecordRangeInfo recordRangeInfo,
                   java.util.List<Chunk> chunks)

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

chunks - used to determine which records the iterator should return

Method Detail

getRecordsRangeInfo

public static SRAIterator.RecordRangeInfo getRecordsRangeInfo(ngs.ReadCollection run)

Loads record ranges needed for emulating BAM index

Parameters:

run - read collection

Returns:

record ranges

hasNext

public boolean hasNext()

NGS iterators implement a single method "nextObject" which return true if the operation was successful or false if there are no more objects available. That means that there is no way to check "hasNext" without actually moving the iterator forward. Because of that all the logic of moving iterator forward is actually happens in "hasNext". Here is explanation of how it works: Iterator holds a list of chunks of requested records. Here we have chunksIterator that walks though that list. We walk though that list using chunksIterator. If current chunk can represent aligned fragments then we create SRAAlignmentIterator iterator, pass the chunk into it and ask if it can find any record. If record was found, we say that we have next; otherwise we check if the chunk can represent unaligned fragments and then create SRAUnalignmentIterator if so and do the same steps as with alignemnt iterator. If record was not found in both SRAAlignmentIterator and SRAUnalignmentIterator (it is possible that reference range has no alignments or that reads range has all aligned fragment), we try the next chunk. When there are no more chunks and both iterators have no more records we return false.

Specified by:

hasNext in interface java.util.Iterator<SAMRecord>

Returns:

true if there are more records available

next

public SAMRecord next()

Call hasNext to make sure that one of inner iterators points to the next record, the retrieve the record from one of them.

Specified by:

next in interface java.util.Iterator<SAMRecord>

Returns:

lazy SRA record

remove

public void remove()

Specified by:

remove in interface java.util.Iterator<SAMRecord>

close

public void close()

Description copied from interface: CloseableIterator

Should be implemented to close/release any underlying resources.

Specified by:

close in interface CloseableIterator<SAMRecord>

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

assertSorted

public SAMRecordIterator assertSorted(SAMFileHeader.SortOrder sortOrder)

Description copied from interface: SAMRecordIterator

Establishes that records returned by this iterator are expected to be in the specified sort order. If this method has been called, then implementers must throw an IllegalStateException from next() when a record is read that violates the sort order. This method may be called multiple times over the course of an iteration, changing the expected sort, if desired -- from the time it is called, it validates whatever sort is set, or stops validating if it is set to null or SAMFileHeader.SortOrder.unsorted. If this method is not called, then no validation of the iterated records is done.

Specified by:

assertSorted in interface SAMRecordIterator

Parameters:

sortOrder - The order in which records are expected to be returned

Returns:

This SAMRecordIterator

setValidationStringency

public void setValidationStringency(ValidationStringency validationStringency)