htsjdk.samtools.cram.structure.block

Class Block

java.lang.Object

htsjdk.samtools.cram.structure.block.Block

public class Block
extends java.lang.Object

Class representing CRAM block concept and some methods to operate with block content. CRAM block is used to hold some (usually homogeneous) binary data. An external compression can be applied to the content of a block. The class provides some instantiation static methods, for example to read a block from an input stream. Blocks can be written out to an output stream, this may be considered as a way to serialize/deserialize blocks.

Field Summary

Fields

Modifier and Type	Field and Description
static int	NO_CONTENT_ID Only external blocks have meaningful Content IDs Other blocks are required to have a Content ID of 0

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	Block(BlockCompressionMethod compressionMethod, BlockContentType contentType, int contentId, byte[] compressedContent, int uncompressedLength) Protected constructor of a generic Block, to be called by static factory methods and subclasses.

Method Summary

Modifier and Type	Method and Description
static Block	createExternalBlock(BlockCompressionMethod compressionMethod, int contentId, byte[] compressedContent, int uncompressedLength) Create a new external data block with the given compression method, uncompressed content, and content ID.
static Block	createRawCompressionHeaderBlock(byte[] rawContent) Create a new compression header block with the given uncompressed content.
static Block	createRawCoreDataBlock(byte[] rawContent) Create a new core data block with the given uncompressed content.
static Block	createRawFileHeaderBlock(byte[] rawContent) Create a new file header block with the given uncompressed content.
static Block	createRawSliceHeaderBlock(byte[] rawContent) Create a new slice header block with the given uncompressed content.
byte[]	getCompressedContent()
int	getCompressedContentSize()
BlockCompressionMethod	getCompressionMethod()
int	getContentId() Return the External Content ID for this block.
BlockContentType	getContentType() Identifies whether this is a header or data block, and which kind
byte[]	getUncompressedContent() Uncompress the stored block content (if not RAW) and return the uncompressed content.
int	getUncompressedContentSize()
static Block	read(int major, java.io.InputStream inputStream) Deserialize the Block from the InputStream.
java.lang.String	toString()
void	write(int major, java.io.OutputStream outputStream) Write the block out to the the specified OutputStream.

Methods inherited from class java.lang.Object

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

Field Detail

NO_CONTENT_ID

public static final int NO_CONTENT_ID

Only external blocks have meaningful Content IDs Other blocks are required to have a Content ID of 0

See Also:

Constant Field Values

Constructor Detail

Block

protected Block(BlockCompressionMethod compressionMethod,
                BlockContentType contentType,
                int contentId,
                byte[] compressedContent,
                int uncompressedLength)

Protected constructor of a generic Block, to be called by static factory methods and subclasses.

Parameters:

compressionMethod - the block compression method. Can be RAW, if uncompressed

contentType - whether this is a header or data block, and which kind

contentId - the External Block Content ID, or NO_CONTENT_ID for non-External block

compressedContent - the compressed form of the data to be stored in this block

uncompressedLength - the length of the content stored in this block when uncompressed

Method Detail

createRawFileHeaderBlock

public static Block createRawFileHeaderBlock(byte[] rawContent)

Create a new file header block with the given uncompressed content. The block will have RAW (no) compression and FILE_HEADER content type.

Parameters:

rawContent - the uncompressed content of the block

Returns:

a new Block object

createRawCompressionHeaderBlock

public static Block createRawCompressionHeaderBlock(byte[] rawContent)

Create a new compression header block with the given uncompressed content. The block will have RAW (no) compression and COMPRESSION_HEADER content type.

Parameters:

rawContent - the uncompressed content of the block

Returns:

a new Block object

createRawSliceHeaderBlock

public static Block createRawSliceHeaderBlock(byte[] rawContent)

Create a new slice header block with the given uncompressed content. The block will have RAW (no) compression and MAPPED_SLICE content type.

Parameters:

rawContent - the uncompressed content of the block

Returns:

a new Block object

createRawCoreDataBlock

public static Block createRawCoreDataBlock(byte[] rawContent)

Create a new core data block with the given uncompressed content. The block will have RAW (no) compression and CORE content type.

Parameters:

rawContent - the uncompressed content of the block

Returns:

a new Block object

createExternalBlock

public static Block createExternalBlock(BlockCompressionMethod compressionMethod,
                                        int contentId,
                                        byte[] compressedContent,
                                        int uncompressedLength)

Create a new external data block with the given compression method, uncompressed content, and content ID. The block will have EXTERNAL content type.

Parameters:

compressionMethod - the compression method used in this block

contentId - the external identifier for the block

compressedContent - the content of this block, in compressed mode

uncompressedLength - the length of the content stored in this block when uncompressed

getCompressionMethod

public final BlockCompressionMethod getCompressionMethod()

getContentType

public final BlockContentType getContentType()

Identifies whether this is a header or data block, and which kind

Returns:

the CRAM content type of the block

getContentId

public int getContentId()

Return the External Content ID for this block. Only ExternalBlocks have a meaningful Content ID.

Returns:

the External Content ID, or NO_CONTENT_ID

getUncompressedContent

public final byte[] getUncompressedContent()

Uncompress the stored block content (if not RAW) and return the uncompressed content.

Returns:

The uncompressed block content.

Throws:

CRAMException - The uncompressed length did not match what was expected.

getUncompressedContentSize

public int getUncompressedContentSize()

Returns:

The size of the uncompressed content in bytes.

getCompressedContent

public final byte[] getCompressedContent()

Returns:

The compressed block content.

getCompressedContentSize

public final int getCompressedContentSize()

Returns:

The size of the compressed content in bytes.

read

public static Block read(int major,
                         java.io.InputStream inputStream)

Deserialize the Block from the InputStream. The reading is parameterized by the major CRAM version number.

Parameters:

major - CRAM version major number

inputStream - input stream to read the block from

Returns:

a subtype of Block object with fields and content from the input stream

write

public final void write(int major,
                        java.io.OutputStream outputStream)

Write the block out to the the specified OutputStream. The method is parameterized with the CRAM major version number.

Parameters:

major - CRAM version major number

outputStream - output stream to write to

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object