Many resources are needed to download a project. Please understand that we have to compensate our server costs. Thank you in advance. Project price only 1 $
You can buy this project and download/modify it how often you want.
/*
* The MIT License
*
* Copyright (c) 2009 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package htsjdk.samtools.util;
import htsjdk.samtools.Defaults;
/**
* Constants shared by BlockCompressed{Input,Output}Stream classes
*/
public class BlockCompressedStreamConstants {
// Number of bytes in the gzip block before the deflated data.
// This is not the standard header size, because we include one optional subfield,
// but it is the standard for us.
public static final int BLOCK_HEADER_LENGTH = 18;
// Location in the gzip block of the total block size (actually total block size - 1)
public static final int BLOCK_LENGTH_OFFSET = 16;
// Number of bytes that follow the deflated data
public static final int BLOCK_FOOTER_LENGTH = 8;
// We require that a compressed block (including header and footer, be <= this)
public static final int MAX_COMPRESSED_BLOCK_SIZE = 64 * 1024;
// Gzip overhead is the header, the footer, and the block size (encoded as a short).
public static final int GZIP_OVERHEAD = BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH + 2;
// If Deflater has compression level == NO_COMPRESSION, 10 bytes of overhead (determined experimentally).
public static final int NO_COMPRESSION_OVERHEAD = 10;
// Push out a gzip block when this many uncompressed bytes have been accumulated.
// This size is selected so that if data is not compressible, if Deflater is given
// compression level == NO_COMPRESSION, compressed size is guaranteed to be <= MAX_COMPRESSED_BLOCK_SIZE.
public static final int DEFAULT_UNCOMPRESSED_BLOCK_SIZE = 64 * 1024 - (GZIP_OVERHEAD + NO_COMPRESSION_OVERHEAD);
// Magic numbers
public static final byte GZIP_ID1 = 31;
public static final int GZIP_ID2 = 139;
// FEXTRA flag means there are optional fields
public static final int GZIP_FLG = 4;
// extra flags
public static final int GZIP_XFL = 0;
// length of extra subfield
public static final short GZIP_XLEN = 6;
// The deflate compression, which is customarily used by gzip
public static final byte GZIP_CM_DEFLATE = 8;
public static final int DEFAULT_COMPRESSION_LEVEL = Defaults.COMPRESSION_LEVEL;
// We don't care about OS because we're not doing line terminator translation
public static final int GZIP_OS_UNKNOWN = 255;
// The subfield ID
public static final byte BGZF_ID1 = 66;
public static final byte BGZF_ID2 = 67;
// subfield length in bytes
public static final byte BGZF_LEN = 2;
public static final byte[] EMPTY_GZIP_BLOCK = {
BlockCompressedStreamConstants.GZIP_ID1,
(byte)BlockCompressedStreamConstants.GZIP_ID2,
BlockCompressedStreamConstants.GZIP_CM_DEFLATE,
BlockCompressedStreamConstants.GZIP_FLG,
0, 0, 0, 0, // Modification time
BlockCompressedStreamConstants.GZIP_XFL,
(byte)BlockCompressedStreamConstants.GZIP_OS_UNKNOWN,
BlockCompressedStreamConstants.GZIP_XLEN, 0, // Little-endian short
BlockCompressedStreamConstants.BGZF_ID1,
BlockCompressedStreamConstants.BGZF_ID2,
BlockCompressedStreamConstants.BGZF_LEN, 0, // Little-endian short
// Total block size - 1
BlockCompressedStreamConstants.BLOCK_HEADER_LENGTH +
BlockCompressedStreamConstants.BLOCK_FOOTER_LENGTH - 1 + 2, 0, // Little-endian short
// Dummy payload?
3, 0,
0, 0, 0, 0, // crc
0, 0, 0, 0, // uncompressedSize
};
public static final byte[] GZIP_BLOCK_PREAMBLE = {
BlockCompressedStreamConstants.GZIP_ID1,
(byte)BlockCompressedStreamConstants.GZIP_ID2,
BlockCompressedStreamConstants.GZIP_CM_DEFLATE,
BlockCompressedStreamConstants.GZIP_FLG,
0, 0, 0, 0, // Modification time
BlockCompressedStreamConstants.GZIP_XFL,
(byte)BlockCompressedStreamConstants.GZIP_OS_UNKNOWN,
BlockCompressedStreamConstants.GZIP_XLEN, 0, // Little-endian short
BlockCompressedStreamConstants.BGZF_ID1,
BlockCompressedStreamConstants.BGZF_ID2,
BlockCompressedStreamConstants.BGZF_LEN, 0, // Little-endian short
};
}
