Package htsjdk.samtools.cram.build

Class CramContainerIterator

java.lang.Object

htsjdk.samtools.cram.build.CramContainerIterator

All Implemented Interfaces:

Closeable, AutoCloseable, Iterator<Container>

Direct Known Subclasses:

CramContainerHeaderIterator, CramSpanContainerIterator

public class CramContainerIterator
extends Object
implements Iterator<Container>, Closeable

An iterator of CRAM containers read from an InputStream.

Constructor Summary

Constructors

Constructor	Description
CramContainerIterator(InputStream inputStream)

Method Summary

Modifier and Type	Method	Description
void	close()
protected Container	containerFromStream(CountingInputStream countingStream)	Consume the entirety of the next container from the stream.
CramHeader	getCramHeader()
SAMFileHeader	getSamFileHeader()
boolean	hasNext()
Container	next()
void	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 Details

CramContainerIterator

public CramContainerIterator(InputStream inputStream)

Method Details

containerFromStream

protected Container containerFromStream(CountingInputStream countingStream)

Consume the entirety of the next container from the stream.

Parameters:

countingStream - the CountingInputStream to read from

Returns:

The next Container from the stream.

See Also:

• containerFromStream(CountingInputStream)

hasNext

public boolean hasNext()

Specified by:

hasNext in interface Iterator<Container>

next

public Container next()

Specified by:

next in interface Iterator<Container>

remove

public void remove()

Specified by:

remove in interface Iterator<Container>

getCramHeader

public CramHeader getCramHeader()

getSamFileHeader

public SAMFileHeader getSamFileHeader()

close

public void close()

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable