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64 lines
2.1 KiB
64 lines
2.1 KiB
/*
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This file is part of BioD.
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Copyright (C) 2012 Artem Tarasov <lomereiter@gmail.com>
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BioD is free software; you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation; either version 2 of the License, or
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(at your option) any later version.
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BioD is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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You should have received a copy of the GNU General Public License
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along with this program; if not, write to the Free Software
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Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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*/
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module bio.bam.constants;
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immutable BAM_MAGIC = "BAM\1";
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immutable BAI_MAGIC = "BAI\1";
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immutable ubyte BAM_SI1 = 66;
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immutable ubyte BAM_SI2 = 67;
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immutable BGZF_MAGIC = 0x04_08_8B_1F; // little endian
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immutable ubyte[16] BLOCK_HEADER_START =
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[ 31, 139, 8, 4, // BGZF magic
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0, 0, 0, 0, // GZIP modification time
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0, // GZIP extra flags
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255, // GZIP OS identifier
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6, 0, // GZIP extra length == 6 (LE)
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66, 67, // Subfield 'BC'
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2, 0]; // Subfield length (holds 1 ushort)
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// BGZF block header length in bytes.
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// Block header holds BLOCK_HEADER_START + block size (ushort)
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immutable BLOCK_HEADER_LENGTH = BLOCK_HEADER_START.length + ushort.sizeof;
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// BGZF footer holds CRC32 and size of decompressed block.
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immutable BLOCK_FOOTER_LENGTH = uint.sizeof + uint.sizeof;
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immutable BGZF_MAX_BLOCK_SIZE = 65536;
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immutable BGZF_BLOCK_SIZE = 0xFF00;
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immutable ubyte[28] BAM_EOF =
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[31, 139, 8, 4,
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0, 0, 0, 0,
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0,
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255,
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6, 0,
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66, 67,
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2, 0,
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27, 0,
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3, 0,
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0, 0, 0, 0,
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0, 0, 0, 0];
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immutable BAI_MAX_BIN_ID = 37449;
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immutable BAI_MAX_NONLEAF_BIN_ID = 4680;
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immutable BAI_LINEAR_INDEX_WINDOW_SIZE = 16384;
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