htsjdk.samtools.cram.build

Class CramContainerHeaderIterator

java.lang.Object

htsjdk.samtools.cram.build.CramContainerIterator

htsjdk.samtools.cram.build.CramContainerHeaderIterator

All Implemented Interfaces:

java.util.Iterator<Container>

public class CramContainerHeaderIterator
extends CramContainerIterator

Iterate over CRAM containers from an input stream, and unlike CramContainerIterator only the header of each container is read, rather than the whole stream. As a result, the container block data is *not* populated, including the compression header block and slices. This class is useful when you are not interested in the contents of containers, for example when indexing container start positions.

Constructor Summary

Constructors

Constructor and Description
CramContainerHeaderIterator(java.io.InputStream inputStream)

Method Summary

Modifier and Type	Method and Description
protected Container	containerFromStream(CountingInputStream countingStream) Consume the entirety of the next container from the stream, but retain only the header.

Methods inherited from class htsjdk.samtools.cram.build.CramContainerIterator

close, getCramHeader, hasNext, next, remove

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Iterator

forEachRemaining

Constructor Detail

CramContainerHeaderIterator

public CramContainerHeaderIterator(java.io.InputStream inputStream)

Method Detail

containerFromStream

protected Container containerFromStream(CountingInputStream countingStream)

Consume the entirety of the next container from the stream, but retain only the header. This is intended as a performance optimization, because it does not decode block data.

Overrides:

containerFromStream in class CramContainerIterator

Parameters:

countingStream - the CountingInputStream to read from

Returns:

The next Container's header from the stream, returned as a Container.

See Also:

CramContainerIterator.containerFromStream(CountingInputStream)