htsjdk.samtools

Class CRAMIterator

java.lang.Object

htsjdk.samtools.CRAMIterator

All Implemented Interfaces:

SAMRecordIterator, CloseableIterator<SAMRecord>, java.io.Closeable, java.lang.AutoCloseable, java.util.Iterator<SAMRecord>

public class CRAMIterator
extends java.lang.Object
implements SAMRecordIterator

Field Summary

Fields

Modifier and Type	Field and Description
Container	container

Constructor Summary

Constructors

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)

Method Summary

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)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface htsjdk.samtools.util.CloseableIterator

stream, toList

Methods inherited from interface java.util.Iterator

forEachRemaining

Field Detail

container

public Container container

Constructor Detail

CRAMIterator

public CRAMIterator(java.io.InputStream inputStream,
                    CRAMReferenceSource referenceSource,
                    ValidationStringency validationStringency)
             throws java.io.IOException

Throws:

java.io.IOException

CRAMIterator

public CRAMIterator(SeekableStream seekableStream,
                    CRAMReferenceSource referenceSource,
                    long[] coordinates,
                    ValidationStringency validationStringency)
             throws java.io.IOException

Throws:

java.io.IOException

CRAMIterator

@Deprecated
public CRAMIterator(SeekableStream seekableStream,
                                CRAMReferenceSource referenceSource,
                                long[] coordinates)
                         throws java.io.IOException

Deprecated.

Throws:

java.io.IOException

Method Detail

getValidationStringency

public ValidationStringency getValidationStringency()

setValidationStringency

public void setValidationStringency(ValidationStringency validationStringency)

getCramHeader

public CramHeader getCramHeader()

advanceToAlignmentInContainer

public boolean advanceToAlignmentInContainer(int refIndex,
                                             int pos)

Skip cached records until given alignment start position.

Parameters:

refIndex - reference sequence index

pos - alignment start to skip to

hasNext

public boolean hasNext()

Specified by:

hasNext in interface java.util.Iterator<SAMRecord>

next

public SAMRecord next()

Specified by:

next in interface java.util.Iterator<SAMRecord>

remove

public void remove()

Specified by:

remove in interface java.util.Iterator<SAMRecord>

close

public void close()

Description copied from interface: CloseableIterator

Should be implemented to close/release any underlying resources.

Specified by:

close in interface CloseableIterator<SAMRecord>

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

assertSorted

public SAMRecordIterator assertSorted(SAMFileHeader.SortOrder sortOrder)

Description copied from interface: SAMRecordIterator

Establishes that records returned by this iterator are expected to be in the specified sort order. If this method has been called, then implementers must throw an IllegalStateException from next() when a record is read that violates the sort order. This method may be called multiple times over the course of an iteration, changing the expected sort, if desired -- from the time it is called, it validates whatever sort is set, or stops validating if it is set to null or SAMFileHeader.SortOrder.unsorted. If this method is not called, then no validation of the iterated records is done.

Specified by:

assertSorted in interface SAMRecordIterator

Parameters:

sortOrder - The order in which records are expected to be returned

Returns:

This SAMRecordIterator

getFileSource

public SamReader getFileSource()

setFileSource

public void setFileSource(SamReader mReader)

getSAMFileHeader

public SAMFileHeader getSAMFileHeader()