htsjdk.samtools.cram.io

Class CramInt

java.lang.Object

htsjdk.samtools.cram.io.CramInt

public class CramInt
extends java.lang.Object

Methods to read and write CRAM int values as given in the file format specification.

Constructor Summary

Constructors

Constructor and Description
CramInt()

Method Summary

Modifier and Type	Method and Description
static int	int32(byte[] data) Read unsigned little-endian 4 byte integer from an array of bytes.
static int	int32(java.nio.ByteBuffer buffer) Read unsigned little-endian 4 byte integer from an ByteBuffer.
static int	int32(java.io.InputStream inputStream) Read unsigned little-endian 4 byte integer from an InputStream.
static byte[]	writeInt32(int value) Write int value to OutputStream encoded as CRAM int data type.
static int	writeInt32(int value, java.io.OutputStream outputStream) Write int value to OutputStream encoded as CRAM int data type.

Methods inherited from class java.lang.Object

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

Constructor Detail

CramInt

public CramInt()

Method Detail

int32

public static int int32(java.io.InputStream inputStream)
                 throws java.io.IOException

Read unsigned little-endian 4 byte integer from an InputStream.

Parameters:

inputStream - input stream to read from

Returns:

an integer value read

Throws:

java.io.IOException - as per java IO contract

int32

public static int int32(byte[] data)

Read unsigned little-endian 4 byte integer from an array of bytes.

Parameters:

data - input stream to read from

Returns:

an integer value read

int32

public static int int32(java.nio.ByteBuffer buffer)

Read unsigned little-endian 4 byte integer from an ByteBuffer.

Parameters:

buffer - ByteBuffer to read from

Returns:

an integer value read from the buffer

writeInt32

public static int writeInt32(int value,
                             java.io.OutputStream outputStream)
                      throws java.io.IOException

Write int value to OutputStream encoded as CRAM int data type.

Parameters:

value - value to be written out

outputStream - the output stream

Returns:

the number of bits written out

Throws:

java.io.IOException - as per java IO contract

writeInt32

public static byte[] writeInt32(int value)

Write int value to OutputStream encoded as CRAM int data type.

Parameters:

value - value to be written out

Returns:

the byte array holding the value encoded as CRAM int data type