public class CRAMIterator extends java.lang.Object implements SAMRecordIterator
Constructor and Description |
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CRAMIterator(java.io.InputStream inputStream,
CRAMReferenceSource referenceSource,
ValidationStringency validationStringency) |
CRAMIterator(SeekableStream seekableStream,
CRAMReferenceSource referenceSource,
long[] coordinates)
Deprecated.
|
CRAMIterator(SeekableStream seekableStream,
CRAMReferenceSource referenceSource,
long[] coordinates,
ValidationStringency validationStringency) |
Modifier and Type | Method and 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) |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
stream, toList
public Container container
public CRAMIterator(java.io.InputStream inputStream, CRAMReferenceSource referenceSource, ValidationStringency validationStringency) throws java.io.IOException
java.io.IOException
public CRAMIterator(SeekableStream seekableStream, CRAMReferenceSource referenceSource, long[] coordinates, ValidationStringency validationStringency) throws java.io.IOException
java.io.IOException
@Deprecated public CRAMIterator(SeekableStream seekableStream, CRAMReferenceSource referenceSource, long[] coordinates) throws java.io.IOException
java.io.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 boolean hasNext()
hasNext
in interface java.util.Iterator<SAMRecord>
public void remove()
remove
in interface java.util.Iterator<SAMRecord>
public void close()
CloseableIterator
close
in interface CloseableIterator<SAMRecord>
close
in interface java.io.Closeable
close
in interface java.lang.AutoCloseable
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()