public class SRAAlignmentIterator extends java.lang.Object implements CloseableIterator<SAMRecord>
| Constructor and Description |
|---|
SRAAlignmentIterator(SRAAccession accession,
ngs.ReadCollection run,
SAMFileHeader header,
ReferenceCache cachedReferences,
SRAIterator.RecordRangeInfo recordRangeInfo,
Chunk chunk) |
| Modifier and Type | Method and Description |
|---|---|
void |
close()
Should be implemented to close/release any underlying resources.
|
boolean |
hasNext() |
SAMRecord |
next() |
void |
remove() |
void |
setValidationStringency(ValidationStringency validationStringency) |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitstream, toListpublic 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 boolean hasNext()
hasNext in interface java.util.Iterator<SAMRecord>public void remove()
remove in interface java.util.Iterator<SAMRecord>public void setValidationStringency(ValidationStringency validationStringency)
public void close()
CloseableIteratorclose in interface CloseableIterator<SAMRecord>close in interface java.io.Closeableclose in interface java.lang.AutoCloseable