public class CRAMIterator extends java.lang.Object implements SAMRecordIterator
| Constructor and Description |
|---|
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, waitstream, toListpublic Container container
public CRAMIterator(java.io.InputStream inputStream,
CRAMReferenceSource referenceSource,
ValidationStringency validationStringency)
throws java.io.IOException
java.io.IOExceptionpublic 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.IOExceptionpublic 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()
CloseableIteratorclose in interface CloseableIterator<SAMRecord>close in interface java.io.Closeableclose in interface java.lang.AutoCloseablepublic SAMRecordIterator assertSorted(SAMFileHeader.SortOrder sortOrder)
SAMRecordIteratorassertSorted in interface SAMRecordIteratorsortOrder - The order in which records are expected to be returnedpublic SamReader getFileSource()
public void setFileSource(SamReader mReader)
public SAMFileHeader getSAMFileHeader()