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BamConstants.h
Go to the documentation of this file.
// ***************************************************************************
// BamConstants.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 16 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides basic constants for handling BAM files.
// ***************************************************************************
#ifndef BAM_CONSTANTS_H
#define BAM_CONSTANTS_H
#include <cassert>
#include <string>
#include "api/api_global.h"
namespace BamTools {
namespace Constants {
const uint8_t BAM_SIZEOF_INT = 4;
// header magic number
const char* const BAM_HEADER_MAGIC = "BAM\1";
const uint8_t BAM_HEADER_MAGIC_LENGTH = 4;
// BAM alignment core size
const uint8_t BAM_CORE_SIZE = 32;
const uint8_t BAM_CORE_BUFFER_SIZE = 8;
// BAM alignment flags
const int BAM_ALIGNMENT_PAIRED = 0x0001;
const int BAM_ALIGNMENT_PROPER_PAIR = 0x0002;
const int BAM_ALIGNMENT_UNMAPPED = 0x0004;
const int BAM_ALIGNMENT_MATE_UNMAPPED = 0x0008;
const int BAM_ALIGNMENT_REVERSE_STRAND = 0x0010;
const int BAM_ALIGNMENT_MATE_REVERSE_STRAND = 0x0020;
const int BAM_ALIGNMENT_READ_1 = 0x0040;
const int BAM_ALIGNMENT_READ_2 = 0x0080;
const int BAM_ALIGNMENT_SECONDARY = 0x0100;
const int BAM_ALIGNMENT_QC_FAILED = 0x0200;
const int BAM_ALIGNMENT_DUPLICATE = 0x0400;
const int BAM_ALIGNMENT_SUPPLEMENTARY = 0x0800;
// CIGAR constants
const char* const BAM_CIGAR_LOOKUP = "MIDNSHP=X";
const uint8_t BAM_CIGAR_MATCH = 0;
const uint8_t BAM_CIGAR_INS = 1;
const uint8_t BAM_CIGAR_DEL = 2;
const uint8_t BAM_CIGAR_REFSKIP = 3;
const uint8_t BAM_CIGAR_SOFTCLIP = 4;
const uint8_t BAM_CIGAR_HARDCLIP = 5;
const uint8_t BAM_CIGAR_PAD = 6;
const uint8_t BAM_CIGAR_SEQMATCH = 7;
const uint8_t BAM_CIGAR_MISMATCH = 8;
const char BAM_CIGAR_MATCH_CHAR = 'M';
const char BAM_CIGAR_INS_CHAR = 'I';
const char BAM_CIGAR_DEL_CHAR = 'D';
const char BAM_CIGAR_REFSKIP_CHAR = 'N';
const char BAM_CIGAR_SOFTCLIP_CHAR = 'S';
const char BAM_CIGAR_HARDCLIP_CHAR = 'H';
const char BAM_CIGAR_PAD_CHAR = 'P';
const char BAM_CIGAR_SEQMATCH_CHAR = '=';
const char BAM_CIGAR_MISMATCH_CHAR = 'X';
const int BAM_CIGAR_SHIFT = 4;
const int BAM_CIGAR_MASK = ((1 << BAM_CIGAR_SHIFT) - 1);
// BAM tag types & sizes
const char BAM_TAG_TYPE_ASCII = 'A';
const char BAM_TAG_TYPE_INT8 = 'c';
const char BAM_TAG_TYPE_UINT8 = 'C';
const char BAM_TAG_TYPE_INT16 = 's';
const char BAM_TAG_TYPE_UINT16 = 'S';
const char BAM_TAG_TYPE_INT32 = 'i';
const char BAM_TAG_TYPE_UINT32 = 'I';
const char BAM_TAG_TYPE_FLOAT = 'f';
const char BAM_TAG_TYPE_STRING = 'Z';
const char BAM_TAG_TYPE_HEX = 'H';
const char BAM_TAG_TYPE_ARRAY = 'B';
const uint8_t BAM_TAG_TAGSIZE = 2;
const uint8_t BAM_TAG_TYPESIZE = 1;
const uint8_t BAM_TAG_ARRAYBASE_SIZE = 8;
// DNA bases
const char* const BAM_DNA_LOOKUP = "=ACMGRSVTWYHKDBN";
const uint8_t BAM_BASECODE_EQUAL = 0;
const uint8_t BAM_BASECODE_A = 1;
const uint8_t BAM_BASECODE_C = 2;
const uint8_t BAM_BASECODE_M = 3;
const uint8_t BAM_BASECODE_G = 4;
const uint8_t BAM_BASECODE_R = 5;
const uint8_t BAM_BASECODE_S = 6;
const uint8_t BAM_BASECODE_V = 7;
const uint8_t BAM_BASECODE_T = 8;
const uint8_t BAM_BASECODE_W = 9;
const uint8_t BAM_BASECODE_Y = 10;
const uint8_t BAM_BASECODE_H = 11;
const uint8_t BAM_BASECODE_K = 12;
const uint8_t BAM_BASECODE_D = 13;
const uint8_t BAM_BASECODE_B = 14;
const uint8_t BAM_BASECODE_N = 15;
const char BAM_DNA_EQUAL = '=';
const char BAM_DNA_A = 'A';
const char BAM_DNA_C = 'C';
const char BAM_DNA_M = 'M';
const char BAM_DNA_G = 'G';
const char BAM_DNA_R = 'R';
const char BAM_DNA_S = 'S';
const char BAM_DNA_V = 'V';
const char BAM_DNA_T = 'T';
const char BAM_DNA_W = 'W';
const char BAM_DNA_Y = 'Y';
const char BAM_DNA_H = 'H';
const char BAM_DNA_K = 'K';
const char BAM_DNA_D = 'D';
const char BAM_DNA_B = 'B';
const char BAM_DNA_N = 'N';
const char BAM_DNA_DEL = '-';
const char BAM_DNA_PAD = '*';
// zlib & BGZF constants
const char GZIP_ID1 = 31;
const char GZIP_ID2 = static_cast<char>(139);
const char CM_DEFLATE = 8;
const char FLG_FEXTRA = 4;
const char OS_UNKNOWN = static_cast<char>(255);
const char BGZF_XLEN = 6;
const char BGZF_ID1 = 66;
const char BGZF_ID2 = 67;
const char BGZF_LEN = 2;
const int8_t GZIP_WINDOW_BITS = -15;
const int8_t Z_DEFAULT_MEM_LEVEL = 8;
const uint8_t BGZF_BLOCK_HEADER_LENGTH = 18;
const uint8_t BGZF_BLOCK_FOOTER_LENGTH = 8;
const uint32_t BGZF_MAX_BLOCK_SIZE = 65536;
const uint32_t BGZF_DEFAULT_BLOCK_SIZE = 65536;
} // namespace Constants
// -------------------------
// tag-type helper structs
// -------------------------
// fail on any types not specified below
template <typename T>
struct TagTypeHelper
{
static bool CanConvertFrom(const char)
{
assert(false);
return false;
}
static bool CanConvertTo(const char)
{
assert(false);
return false;
}
static char TypeCode()
{
assert(false);
return 0;
}
};
template <>
struct TagTypeHelper<uint8_t>
{
static bool CanConvertFrom(const char c)
{
return (c == Constants::BAM_TAG_TYPE_ASCII || c == Constants::BAM_TAG_TYPE_UINT8);
}
static bool CanConvertTo(const char c)
{
return (c == Constants::BAM_TAG_TYPE_ASCII || c == Constants::BAM_TAG_TYPE_UINT8 ||
c == Constants::BAM_TAG_TYPE_UINT16 || c == Constants::BAM_TAG_TYPE_UINT32);
}
static char TypeCode()
{
return Constants::BAM_TAG_TYPE_UINT8;
}
};
template <>
struct TagTypeHelper<int8_t>
{
static bool CanConvertFrom(const char c)
{
return (c == Constants::BAM_TAG_TYPE_ASCII || c == Constants::BAM_TAG_TYPE_INT8);
}
static bool CanConvertTo(const char c)
{
return (c == Constants::BAM_TAG_TYPE_ASCII || c == Constants::BAM_TAG_TYPE_INT8 ||
c == Constants::BAM_TAG_TYPE_INT16 || c == Constants::BAM_TAG_TYPE_INT32);
}
static char TypeCode()
{
return Constants::BAM_TAG_TYPE_INT8;
}
};
template <>
struct TagTypeHelper<uint16_t>
{
static bool CanConvertFrom(const char c)
{
return (c == Constants::BAM_TAG_TYPE_ASCII || c == Constants::BAM_TAG_TYPE_UINT8 ||
c == Constants::BAM_TAG_TYPE_UINT16);
}
static bool CanConvertTo(const char c)
{
return (c == Constants::BAM_TAG_TYPE_UINT16 || c == Constants::BAM_TAG_TYPE_UINT32);
}
static char TypeCode()
{
return Constants::BAM_TAG_TYPE_UINT16;
}
};
template <>
struct TagTypeHelper<int16_t>
{
static bool CanConvertFrom(const char c)
{
return (c == Constants::BAM_TAG_TYPE_ASCII || c == Constants::BAM_TAG_TYPE_INT8 ||
c == Constants::BAM_TAG_TYPE_INT16);
}
static bool CanConvertTo(const char c)
{
return (c == Constants::BAM_TAG_TYPE_INT16 || c == Constants::BAM_TAG_TYPE_INT32);
}
static char TypeCode()
{
return Constants::BAM_TAG_TYPE_INT16;
}
};
template <>
struct TagTypeHelper<uint32_t>
{
static bool CanConvertFrom(const char c)
{
return (c == Constants::BAM_TAG_TYPE_ASCII || c == Constants::BAM_TAG_TYPE_UINT8 ||
c == Constants::BAM_TAG_TYPE_UINT16 || c == Constants::BAM_TAG_TYPE_UINT32);
}
static bool CanConvertTo(const char c)
{
return (c == Constants::BAM_TAG_TYPE_UINT32);
}
static char TypeCode()
{
return Constants::BAM_TAG_TYPE_UINT32;
}
};
template <>
struct TagTypeHelper<int32_t>
{
static bool CanConvertFrom(const char c)
{
return (c == Constants::BAM_TAG_TYPE_ASCII || c == Constants::BAM_TAG_TYPE_INT8 ||
c == Constants::BAM_TAG_TYPE_INT16 || c == Constants::BAM_TAG_TYPE_INT32);
}
static bool CanConvertTo(const char c)
{
return (c == Constants::BAM_TAG_TYPE_INT32);
}
static char TypeCode()
{
return Constants::BAM_TAG_TYPE_INT32;
}
};
template <>
struct TagTypeHelper<float>
{
static bool CanConvertFrom(const char c)
{
return (c == Constants::BAM_TAG_TYPE_ASCII || c == Constants::BAM_TAG_TYPE_UINT8 ||
c == Constants::BAM_TAG_TYPE_INT8 || c == Constants::BAM_TAG_TYPE_UINT16 ||
c == Constants::BAM_TAG_TYPE_INT16 || c == Constants::BAM_TAG_TYPE_UINT32 ||
c == Constants::BAM_TAG_TYPE_INT32 || c == Constants::BAM_TAG_TYPE_FLOAT);
}
static bool CanConvertTo(const char c)
{
return (c == Constants::BAM_TAG_TYPE_FLOAT);
}
static char TypeCode()
{
return Constants::BAM_TAG_TYPE_FLOAT;
}
};
template <>
struct TagTypeHelper<std::string>
{
static bool CanConvertFrom(const char c)
{
return (c == Constants::BAM_TAG_TYPE_HEX || c == Constants::BAM_TAG_TYPE_STRING);
}
static bool CanConvertTo(const char c)
{
return (c == Constants::BAM_TAG_TYPE_HEX || c == Constants::BAM_TAG_TYPE_STRING);
}
static char TypeCode()
{
return Constants::BAM_TAG_TYPE_STRING;
}
};
} // namespace BamTools
#endif // BAM_CONSTANTS_H
api_global.h
BamTools::Constants
Provides basic constants for handling BAM files.
BamTools::Constants::BAM_ALIGNMENT_UNMAPPED
const int BAM_ALIGNMENT_UNMAPPED
Definition BamConstants.h:37
BamTools::Constants::BAM_TAG_TYPE_UINT8
const char BAM_TAG_TYPE_UINT8
Definition BamConstants.h:76
BamTools::Constants::CM_DEFLATE
const char CM_DEFLATE
Definition BamConstants.h:131
BamTools::Constants::BAM_BASECODE_S
const uint8_t BAM_BASECODE_S
Definition BamConstants.h:98
BamTools::Constants::BAM_DNA_N
const char BAM_DNA_N
Definition BamConstants.h:124
BamTools::Constants::BAM_CIGAR_MISMATCH
const uint8_t BAM_CIGAR_MISMATCH
Definition BamConstants.h:58
BamTools::Constants::BAM_DNA_H
const char BAM_DNA_H
Definition BamConstants.h:120
BamTools::Constants::BAM_TAG_TYPE_HEX
const char BAM_TAG_TYPE_HEX
Definition BamConstants.h:83
BamTools::Constants::BGZF_DEFAULT_BLOCK_SIZE
const uint32_t BGZF_DEFAULT_BLOCK_SIZE
Definition BamConstants.h:144
BamTools::Constants::BAM_TAG_TYPE_INT32
const char BAM_TAG_TYPE_INT32
Definition BamConstants.h:79
BamTools::Constants::BAM_DNA_D
const char BAM_DNA_D
Definition BamConstants.h:122
BamTools::Constants::BAM_TAG_TYPE_ASCII
const char BAM_TAG_TYPE_ASCII
Definition BamConstants.h:74
BamTools::Constants::BAM_DNA_V
const char BAM_DNA_V
Definition BamConstants.h:116
BamTools::Constants::BAM_BASECODE_M
const uint8_t BAM_BASECODE_M
Definition BamConstants.h:95
BamTools::Constants::BAM_CIGAR_SHIFT
const int BAM_CIGAR_SHIFT
Definition BamConstants.h:70
BamTools::Constants::BAM_DNA_T
const char BAM_DNA_T
Definition BamConstants.h:117
BamTools::Constants::BAM_CIGAR_REFSKIP
const uint8_t BAM_CIGAR_REFSKIP
Definition BamConstants.h:53
BamTools::Constants::BAM_CIGAR_SEQMATCH
const uint8_t BAM_CIGAR_SEQMATCH
Definition BamConstants.h:57
BamTools::Constants::BAM_CIGAR_PAD
const uint8_t BAM_CIGAR_PAD
Definition BamConstants.h:56
BamTools::Constants::BGZF_BLOCK_FOOTER_LENGTH
const uint8_t BGZF_BLOCK_FOOTER_LENGTH
Definition BamConstants.h:142
BamTools::Constants::BAM_CIGAR_INS_CHAR
const char BAM_CIGAR_INS_CHAR
Definition BamConstants.h:61
BamTools::Constants::BAM_ALIGNMENT_DUPLICATE
const int BAM_ALIGNMENT_DUPLICATE
Definition BamConstants.h:45
BamTools::Constants::BAM_DNA_G
const char BAM_DNA_G
Definition BamConstants.h:113
BamTools::Constants::BAM_DNA_B
const char BAM_DNA_B
Definition BamConstants.h:123
BamTools::Constants::BAM_BASECODE_N
const uint8_t BAM_BASECODE_N
Definition BamConstants.h:107
BamTools::Constants::BGZF_XLEN
const char BGZF_XLEN
Definition BamConstants.h:134
BamTools::Constants::BAM_CIGAR_SEQMATCH_CHAR
const char BAM_CIGAR_SEQMATCH_CHAR
Definition BamConstants.h:67
BamTools::Constants::BAM_ALIGNMENT_PAIRED
const int BAM_ALIGNMENT_PAIRED
Definition BamConstants.h:35
BamTools::Constants::BAM_BASECODE_C
const uint8_t BAM_BASECODE_C
Definition BamConstants.h:94
BamTools::Constants::BGZF_LEN
const char BGZF_LEN
Definition BamConstants.h:137
BamTools::Constants::BAM_CIGAR_MATCH_CHAR
const char BAM_CIGAR_MATCH_CHAR
Definition BamConstants.h:60
BamTools::Constants::BAM_BASECODE_B
const uint8_t BAM_BASECODE_B
Definition BamConstants.h:106
BamTools::Constants::BAM_DNA_DEL
const char BAM_DNA_DEL
Definition BamConstants.h:125
BamTools::Constants::BAM_BASECODE_T
const uint8_t BAM_BASECODE_T
Definition BamConstants.h:100
BamTools::Constants::BAM_CIGAR_SOFTCLIP_CHAR
const char BAM_CIGAR_SOFTCLIP_CHAR
Definition BamConstants.h:64
BamTools::Constants::BAM_TAG_TAGSIZE
const uint8_t BAM_TAG_TAGSIZE
Definition BamConstants.h:86
BamTools::Constants::BAM_HEADER_MAGIC
const char *const BAM_HEADER_MAGIC
Definition BamConstants.h:27
BamTools::Constants::BAM_CORE_BUFFER_SIZE
const uint8_t BAM_CORE_BUFFER_SIZE
Definition BamConstants.h:32
BamTools::Constants::BAM_BASECODE_W
const uint8_t BAM_BASECODE_W
Definition BamConstants.h:101
BamTools::Constants::BAM_TAG_TYPE_ARRAY
const char BAM_TAG_TYPE_ARRAY
Definition BamConstants.h:84
BamTools::Constants::BAM_ALIGNMENT_SECONDARY
const int BAM_ALIGNMENT_SECONDARY
Definition BamConstants.h:43
BamTools::Constants::BAM_CIGAR_INS
const uint8_t BAM_CIGAR_INS
Definition BamConstants.h:51
BamTools::Constants::BAM_DNA_R
const char BAM_DNA_R
Definition BamConstants.h:114
BamTools::Constants::BAM_DNA_K
const char BAM_DNA_K
Definition BamConstants.h:121
BamTools::Constants::BAM_CIGAR_LOOKUP
const char *const BAM_CIGAR_LOOKUP
Definition BamConstants.h:49
BamTools::Constants::BAM_TAG_TYPE_FLOAT
const char BAM_TAG_TYPE_FLOAT
Definition BamConstants.h:81
BamTools::Constants::BAM_BASECODE_V
const uint8_t BAM_BASECODE_V
Definition BamConstants.h:99
BamTools::Constants::BAM_TAG_TYPE_UINT32
const char BAM_TAG_TYPE_UINT32
Definition BamConstants.h:80
BamTools::Constants::BAM_CORE_SIZE
const uint8_t BAM_CORE_SIZE
Definition BamConstants.h:31
BamTools::Constants::BAM_BASECODE_EQUAL
const uint8_t BAM_BASECODE_EQUAL
Definition BamConstants.h:92
BamTools::Constants::BAM_DNA_A
const char BAM_DNA_A
Definition BamConstants.h:110
BamTools::Constants::BAM_ALIGNMENT_QC_FAILED
const int BAM_ALIGNMENT_QC_FAILED
Definition BamConstants.h:44
BamTools::Constants::FLG_FEXTRA
const char FLG_FEXTRA
Definition BamConstants.h:132
BamTools::Constants::BAM_CIGAR_DEL
const uint8_t BAM_CIGAR_DEL
Definition BamConstants.h:52
BamTools::Constants::Z_DEFAULT_MEM_LEVEL
const int8_t Z_DEFAULT_MEM_LEVEL
Definition BamConstants.h:140
BamTools::Constants::BAM_TAG_TYPE_STRING
const char BAM_TAG_TYPE_STRING
Definition BamConstants.h:82
BamTools::Constants::BAM_CIGAR_MISMATCH_CHAR
const char BAM_CIGAR_MISMATCH_CHAR
Definition BamConstants.h:68
BamTools::Constants::BAM_DNA_LOOKUP
const char *const BAM_DNA_LOOKUP
Definition BamConstants.h:91
BamTools::Constants::BAM_DNA_S
const char BAM_DNA_S
Definition BamConstants.h:115
BamTools::Constants::BGZF_MAX_BLOCK_SIZE
const uint32_t BGZF_MAX_BLOCK_SIZE
Definition BamConstants.h:143
BamTools::Constants::BAM_CIGAR_PAD_CHAR
const char BAM_CIGAR_PAD_CHAR
Definition BamConstants.h:66
BamTools::Constants::BGZF_BLOCK_HEADER_LENGTH
const uint8_t BGZF_BLOCK_HEADER_LENGTH
Definition BamConstants.h:141
BamTools::Constants::BAM_TAG_TYPE_INT8
const char BAM_TAG_TYPE_INT8
Definition BamConstants.h:75
BamTools::Constants::BAM_CIGAR_MASK
const int BAM_CIGAR_MASK
Definition BamConstants.h:71
BamTools::Constants::BAM_ALIGNMENT_READ_1
const int BAM_ALIGNMENT_READ_1
Definition BamConstants.h:41
BamTools::Constants::BGZF_ID1
const char BGZF_ID1
Definition BamConstants.h:135
BamTools::Constants::BAM_ALIGNMENT_REVERSE_STRAND
const int BAM_ALIGNMENT_REVERSE_STRAND
Definition BamConstants.h:39
BamTools::Constants::BAM_DNA_C
const char BAM_DNA_C
Definition BamConstants.h:111
BamTools::Constants::BAM_BASECODE_K
const uint8_t BAM_BASECODE_K
Definition BamConstants.h:104
BamTools::Constants::BAM_TAG_TYPE_UINT16
const char BAM_TAG_TYPE_UINT16
Definition BamConstants.h:78
BamTools::Constants::BAM_HEADER_MAGIC_LENGTH
const uint8_t BAM_HEADER_MAGIC_LENGTH
Definition BamConstants.h:28
BamTools::Constants::BAM_ALIGNMENT_READ_2
const int BAM_ALIGNMENT_READ_2
Definition BamConstants.h:42
BamTools::Constants::BAM_TAG_TYPE_INT16
const char BAM_TAG_TYPE_INT16
Definition BamConstants.h:77
BamTools::Constants::BAM_BASECODE_Y
const uint8_t BAM_BASECODE_Y
Definition BamConstants.h:102
BamTools::Constants::BAM_CIGAR_MATCH
const uint8_t BAM_CIGAR_MATCH
Definition BamConstants.h:50
BamTools::Constants::BAM_SIZEOF_INT
const uint8_t BAM_SIZEOF_INT
Definition BamConstants.h:24
BamTools::Constants::BAM_BASECODE_D
const uint8_t BAM_BASECODE_D
Definition BamConstants.h:105
BamTools::Constants::BGZF_ID2
const char BGZF_ID2
Definition BamConstants.h:136
BamTools::Constants::BAM_CIGAR_DEL_CHAR
const char BAM_CIGAR_DEL_CHAR
Definition BamConstants.h:62
BamTools::Constants::BAM_ALIGNMENT_MATE_REVERSE_STRAND
const int BAM_ALIGNMENT_MATE_REVERSE_STRAND
Definition BamConstants.h:40
BamTools::Constants::BAM_ALIGNMENT_SUPPLEMENTARY
const int BAM_ALIGNMENT_SUPPLEMENTARY
Definition BamConstants.h:46
BamTools::Constants::BAM_DNA_M
const char BAM_DNA_M
Definition BamConstants.h:112
BamTools::Constants::GZIP_WINDOW_BITS
const int8_t GZIP_WINDOW_BITS
Definition BamConstants.h:139
BamTools::Constants::BAM_DNA_PAD
const char BAM_DNA_PAD
Definition BamConstants.h:126
BamTools::Constants::BAM_BASECODE_A
const uint8_t BAM_BASECODE_A
Definition BamConstants.h:93
BamTools::Constants::BAM_ALIGNMENT_PROPER_PAIR
const int BAM_ALIGNMENT_PROPER_PAIR
Definition BamConstants.h:36
BamTools::Constants::BAM_TAG_TYPESIZE
const uint8_t BAM_TAG_TYPESIZE
Definition BamConstants.h:87
BamTools::Constants::BAM_DNA_W
const char BAM_DNA_W
Definition BamConstants.h:118
BamTools::Constants::BAM_CIGAR_SOFTCLIP
const uint8_t BAM_CIGAR_SOFTCLIP
Definition BamConstants.h:54
BamTools::Constants::OS_UNKNOWN
const char OS_UNKNOWN
Definition BamConstants.h:133
BamTools::Constants::BAM_CIGAR_REFSKIP_CHAR
const char BAM_CIGAR_REFSKIP_CHAR
Definition BamConstants.h:63
BamTools::Constants::BAM_BASECODE_G
const uint8_t BAM_BASECODE_G
Definition BamConstants.h:96
BamTools::Constants::BAM_DNA_EQUAL
const char BAM_DNA_EQUAL
Definition BamConstants.h:109
BamTools::Constants::BAM_ALIGNMENT_MATE_UNMAPPED
const int BAM_ALIGNMENT_MATE_UNMAPPED
Definition BamConstants.h:38
BamTools::Constants::BAM_CIGAR_HARDCLIP_CHAR
const char BAM_CIGAR_HARDCLIP_CHAR
Definition BamConstants.h:65
BamTools::Constants::GZIP_ID1
const char GZIP_ID1
Definition BamConstants.h:129
BamTools::Constants::BAM_BASECODE_H
const uint8_t BAM_BASECODE_H
Definition BamConstants.h:103
BamTools::Constants::GZIP_ID2
const char GZIP_ID2
Definition BamConstants.h:130
BamTools::Constants::BAM_BASECODE_R
const uint8_t BAM_BASECODE_R
Definition BamConstants.h:97
BamTools::Constants::BAM_DNA_Y
const char BAM_DNA_Y
Definition BamConstants.h:119
BamTools::Constants::BAM_CIGAR_HARDCLIP
const uint8_t BAM_CIGAR_HARDCLIP
Definition BamConstants.h:55
BamTools::Constants::BAM_TAG_ARRAYBASE_SIZE
const uint8_t BAM_TAG_ARRAYBASE_SIZE
Definition BamConstants.h:88
BamTools
Contains all BamTools classes & methods.
Definition Sort.h:24