htsjdk.samtools.cram.structure

Class ContainerHeaderIO

java.lang.Object

htsjdk.samtools.cram.structure.ContainerHeaderIO

public class ContainerHeaderIO
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
ContainerHeaderIO()

Method Summary

Modifier and Type	Method and Description
static Container	readContainerHeader(int major, CountingInputStream countingStream) Reads container header only from a CountingInputStream.
static Container	readContainerHeader(int major, java.io.InputStream inputStream, long containerByteOffset) Reads container header only from an InputStream.
static Container	readContainerHeader(int major, SeekableStream seekableStream) Reads container header only from a SeekableStream.
static int	writeContainerHeader(int major, Container container, java.io.OutputStream outputStream) Write CRAM Container out into the given OutputStream.

Methods inherited from class java.lang.Object

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

Constructor Detail

ContainerHeaderIO

public ContainerHeaderIO()

Method Detail

readContainerHeader

public static Container readContainerHeader(int major,
                                            java.io.InputStream inputStream,
                                            long containerByteOffset)

Reads container header only from an InputStream.

Parameters:

major - the CRAM version to assume

inputStream - the input stream to read from

containerByteOffset - the byte offset from the start of the stream

Returns:

a new Container object with container header values filled out but empty body (no slices and blocks).

readContainerHeader

public static Container readContainerHeader(int major,
                                            SeekableStream seekableStream)

Reads container header only from a SeekableStream.

Parameters:

major - the CRAM version to assume

seekableStream - the seekable input stream to read from

Returns:

a new Container object with container header values filled out but empty body (no slices and blocks).

readContainerHeader

public static Container readContainerHeader(int major,
                                            CountingInputStream countingStream)

Reads container header only from a CountingInputStream.

Parameters:

major - the CRAM version to assume

countingStream - the counting input stream to read from

Returns:

a new Container object with container header values filled out but empty body (no slices and blocks).

writeContainerHeader

public static int writeContainerHeader(int major,
                                       Container container,
                                       java.io.OutputStream outputStream)

Write CRAM Container out into the given OutputStream.

Parameters:

major - CRAM major version

container - container to be written

outputStream - the output stream to write the container to

Returns:

number of bytes written out to the output stream