SAMRecordIterator
, CloseableIterator<SAMRecord>
, Closeable
, AutoCloseable
, Iterator<SAMRecord>
public class CRAMIterator extends Object implements SAMRecordIterator
Constructor | Description |
---|---|
CRAMIterator(SeekableStream seekableStream,
CRAMReferenceSource referenceSource,
long[] coordinates) |
Deprecated.
|
CRAMIterator(SeekableStream seekableStream,
CRAMReferenceSource referenceSource,
long[] coordinates,
ValidationStringency validationStringency) |
|
CRAMIterator(InputStream inputStream,
CRAMReferenceSource referenceSource,
ValidationStringency validationStringency) |
Modifier and Type | Method | Description |
---|---|---|
boolean |
advanceToAlignmentInContainer(int refIndex,
int pos) |
Skip cached records until given alignment start position.
|
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.
|
CramHeader |
getCramHeader() |
|
SamReader |
getFileSource() |
|
SAMFileHeader |
getSAMFileHeader() |
|
ValidationStringency |
getValidationStringency() |
|
boolean |
hasNext() |
|
SAMRecord |
next() |
|
void |
remove() |
|
void |
setFileSource(SamReader mReader) |
|
void |
setValidationStringency(ValidationStringency validationStringency) |
stream, toList
forEachRemaining
public Container container
public CRAMIterator(InputStream inputStream, CRAMReferenceSource referenceSource, ValidationStringency validationStringency) throws IOException
IOException
public CRAMIterator(SeekableStream seekableStream, CRAMReferenceSource referenceSource, long[] coordinates, ValidationStringency validationStringency) throws IOException
IOException
@Deprecated public CRAMIterator(SeekableStream seekableStream, CRAMReferenceSource referenceSource, long[] coordinates) throws IOException
IOException
public ValidationStringency getValidationStringency()
public void setValidationStringency(ValidationStringency validationStringency)
public CramHeader getCramHeader()
public boolean advanceToAlignmentInContainer(int refIndex, int pos)
refIndex
- reference sequence indexpos
- alignment start to skip topublic 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 SamReader getFileSource()
public void setFileSource(SamReader mReader)
public SAMFileHeader getSAMFileHeader()