CloseableIterator<SAMRecord>
, Closeable
, AutoCloseable
, Iterator<SAMRecord>
public class SRAAlignmentIterator extends Object implements CloseableIterator<SAMRecord>
Constructor | Description |
---|---|
SRAAlignmentIterator(SRAAccession accession,
ngs.ReadCollection run,
SAMFileHeader header,
ReferenceCache cachedReferences,
SRAIterator.RecordRangeInfo recordRangeInfo,
Chunk chunk) |
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) |
stream, toList
forEachRemaining
public SRAAlignmentIterator(SRAAccession accession, ngs.ReadCollection run, SAMFileHeader header, ReferenceCache cachedReferences, SRAIterator.RecordRangeInfo recordRangeInfo, Chunk chunk)
run
- opened read collectionheader
- sam headercachedReferences
- list of cached references shared among all iterators from a single SRAFileReaderrecordRangeInfo
- info about record ranges withing SRA archivechunk
- used to determine which alignments the iterator should returnpublic void setValidationStringency(ValidationStringency validationStringency)
public void close()
CloseableIterator
close
in interface AutoCloseable
close
in interface Closeable
close
in interface CloseableIterator<SAMRecord>