htsjdk.samtools.cram.structure

Class Block

java.lang.Object

htsjdk.samtools.cram.structure.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.

Constructor Summary

Constructors

Constructor and Description
Block()

Method Summary

Modifier and Type	Method and Description
static Block	buildNewCore(byte[] rawContent) Create a new core block with the given uncompressed content.
static Block	buildNewFileHeaderBlock(byte[] rawContent) Create a new core block with the given uncompressed content.
static Block	buildNewSliceHeaderBlock(byte[] rawContent) Create a new slice header block with the given uncompressed content.
int	getCompressedContentSize()
int	getContentId()
BlockContentType	getContentType()
byte[]	getRawContent()
int	getRawContentSize()
static Block	readFromInputStream(int major, java.io.InputStream inputStream) Deserialize the block from the InputStream.
void	setContent(byte[] raw, byte[] compressed)
void	setContentId(int contentId)
void	setContentType(BlockContentType contentType)
void	setMethod(BlockCompressionMethod method)
void	setRawContent(byte[] raw)
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

Constructor Detail

Block

public Block()

Method Detail

readFromInputStream

public static Block readFromInputStream(int major,
                                        java.io.InputStream inputStream)
                                 throws java.io.IOException

Deserialize the block from the InputStream. The reading is parametrized by the major CRAM version number.

Parameters:

major - CRAM version major number

inputStream - input stream to read the block from

Returns:

a new Block object with fields and content from the input stream

Throws:

java.io.IOException - as per java IO contract

buildNewSliceHeaderBlock

public static Block buildNewSliceHeaderBlock(byte[] rawContent)

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

Parameters:

rawContent - the content of the block

Returns:

a new mapped slice Block object

buildNewCore

public static Block buildNewCore(byte[] rawContent)

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

Parameters:

rawContent - the content of the block

Returns:

a new core Block object

buildNewFileHeaderBlock

public static Block buildNewFileHeaderBlock(byte[] rawContent)

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

Parameters:

rawContent - the content of the block

Returns:

a new core Block object

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

setRawContent

public void setRawContent(byte[] raw)

getRawContent

public byte[] getRawContent()

getRawContentSize

public int getRawContentSize()

setContent

public void setContent(byte[] raw,
                       byte[] compressed)

write

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

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

Parameters:

major - CRAM version major number

outputStream - output stream to write to

Throws:

java.io.IOException - as per java IO contract

setMethod

public void setMethod(BlockCompressionMethod method)

getContentType

public BlockContentType getContentType()

setContentType

public void setContentType(BlockContentType contentType)

getContentId

public int getContentId()

setContentId

public void setContentId(int contentId)

getCompressedContentSize

public int getCompressedContentSize()