htsjdk.samtools.cram.build

Class CramSpanContainerIterator

java.lang.Object

htsjdk.samtools.cram.build.CramContainerIterator

htsjdk.samtools.cram.build.CramSpanContainerIterator

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, java.util.Iterator<Container>

public final class CramSpanContainerIterator
extends CramContainerIterator

An iterator of CRAM containers read from locations in a SeekableStream. The locations are specified with pairs of coordinates, and are basically file pointers as returned for example by SamReader.Indexing.getFilePointerSpanningReads()

Method Summary

Modifier and Type	Method and Description
static CramSpanContainerIterator	fromFileSpan(SeekableStream seekableStream, long[] coordinates)
boolean	hasNext()
Container	next()
void	remove()

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

close, containerFromStream, getCramHeader, getSamFileHeader

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

Method Detail

fromFileSpan

public static CramSpanContainerIterator fromFileSpan(SeekableStream seekableStream,
                                                     long[] coordinates)

hasNext

public boolean hasNext()

Specified by:

hasNext in interface java.util.Iterator<Container>

Overrides:

hasNext in class CramContainerIterator

next

public Container next()

Specified by:

next in interface java.util.Iterator<Container>

Overrides:

next in class CramContainerIterator

remove

public void remove()

Specified by:

remove in interface java.util.Iterator<Container>

Overrides:

remove in class CramContainerIterator