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, wait
stream, toList
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 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()
CloseableIterator
close
in interface CloseableIterator<SAMRecord>
close
in interface java.io.Closeable
close
in interface java.lang.AutoCloseable