SAMRecordIterator
, CloseableIterator<SAMRecord>
, Closeable
, AutoCloseable
, Iterator<SAMRecord>
public class SRAIterator extends Object implements SAMRecordIterator
Modifier and Type | Class | Description |
---|---|---|
static class |
SRAIterator.RecordRangeInfo |
Describes record ranges info needed for emulating BAM index
|
Constructor | Description |
---|---|
SRAIterator(SRAAccession accession,
ngs.ReadCollection run,
SAMFileHeader header,
ReferenceCache cachedReferences,
SRAIterator.RecordRangeInfo recordRangeInfo,
List<Chunk> chunks) |
Modifier and Type | Method | 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) |
stream, toList
forEachRemaining
public SRAIterator(SRAAccession accession, ngs.ReadCollection run, SAMFileHeader header, ReferenceCache cachedReferences, SRAIterator.RecordRangeInfo recordRangeInfo, List<Chunk> chunks)
run
- opened read collectionheader
- sam headercachedReferences
- list of cached references shared among all iterators from a single SRAFileReaderrecordRangeInfo
- info about record ranges withing SRA archivechunks
- used to determine which records the iterator should returnpublic static SRAIterator.RecordRangeInfo getRecordsRangeInfo(ngs.ReadCollection run)
run
- read collectionpublic boolean hasNext()
public SAMRecord next()
public void close()
CloseableIterator
close
in interface AutoCloseable
close
in interface Closeable
close
in interface CloseableIterator<SAMRecord>
public SAMRecordIterator assertSorted(SAMFileHeader.SortOrder sortOrder)
SAMRecordIterator
assertSorted
in interface SAMRecordIterator
sortOrder
- The order in which records are expected to be returnedpublic void setValidationStringency(ValidationStringency validationStringency)