htsjdk.samtools.cram.structure

Class ContainerIO

java.lang.Object

htsjdk.samtools.cram.structure.ContainerIO

public class ContainerIO
extends java.lang.Object

Methods to read and write CRAM containers.

Constructor Summary

Constructors

Constructor and Description
ContainerIO()

Method Summary

Modifier and Type	Method and Description
static Container	readContainer(Version version, CountingInputStream countingInputStream) Reads a CRAM container from a Counting input stream.
static Container	readContainer(Version version, SeekableStream seekableInputStream) Reads a CRAM container from a Seekable input stream.
static int	writeContainer(Version version, Container container, java.io.OutputStream outputStream) Writes a complete Container with it's header to a OutputStream.

Methods inherited from class java.lang.Object

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

Constructor Detail

ContainerIO

public ContainerIO()

Method Detail

readContainer

public static Container readContainer(Version version,
                                      SeekableStream seekableInputStream)

Reads a CRAM container from a Seekable input stream. Returns an EOF container when there is no more data or the EOF marker found.

Parameters:

version - CRAM version to expect

seekableInputStream - the SeekableStream stream to read from

Returns:

a new container object read from the stream

readContainer

public static Container readContainer(Version version,
                                      CountingInputStream countingInputStream)

Reads a CRAM container from a Counting input stream. Returns an EOF container when there is no more data or the EOF marker found.

Parameters:

version - CRAM version to expect

countingInputStream - the CountingInputStream stream to read from

Returns:

a new container object read from the stream

writeContainer

public static int writeContainer(Version version,
                                 Container container,
                                 java.io.OutputStream outputStream)

Writes a complete Container with it's header to a OutputStream. The method is aware of file header containers and is suitable for general purpose use: basically any container is allowed.

Parameters:

version - the CRAM version to assume

container - the container to write

outputStream - the stream to write to

Returns:

the number of bytes written out