BamConstants.h File Reference

#include "api/api_global.h"
#include <cassert>
#include <string>

Go to the source code of this file.

Namespaces
namespace	BamTools::Constants
	Provides basic constants for handling BAM files.
namespace	BamTools
	Contains all BamTools classes & methods.
Variables
const uint8_t	BamTools::Constants::BAM_SIZEOF_INT = 4
const char *const	BamTools::Constants::BAM_HEADER_MAGIC = "BAM\1"
const uint8_t	BamTools::Constants::BAM_HEADER_MAGIC_LENGTH = 4
const uint8_t	BamTools::Constants::BAM_CORE_SIZE = 32
const uint8_t	BamTools::Constants::BAM_CORE_BUFFER_SIZE = 8
const int	BamTools::Constants::BAM_ALIGNMENT_PAIRED = 0x0001
const int	BamTools::Constants::BAM_ALIGNMENT_PROPER_PAIR = 0x0002
const int	BamTools::Constants::BAM_ALIGNMENT_UNMAPPED = 0x0004
const int	BamTools::Constants::BAM_ALIGNMENT_MATE_UNMAPPED = 0x0008
const int	BamTools::Constants::BAM_ALIGNMENT_REVERSE_STRAND = 0x0010
const int	BamTools::Constants::BAM_ALIGNMENT_MATE_REVERSE_STRAND = 0x0020
const int	BamTools::Constants::BAM_ALIGNMENT_READ_1 = 0x0040
const int	BamTools::Constants::BAM_ALIGNMENT_READ_2 = 0x0080
const int	BamTools::Constants::BAM_ALIGNMENT_SECONDARY = 0x0100
const int	BamTools::Constants::BAM_ALIGNMENT_QC_FAILED = 0x0200
const int	BamTools::Constants::BAM_ALIGNMENT_DUPLICATE = 0x0400
const char *const	BamTools::Constants::BAM_CIGAR_LOOKUP = "MIDNSHP=X"
const uint8_t	BamTools::Constants::BAM_CIGAR_MATCH = 0
const uint8_t	BamTools::Constants::BAM_CIGAR_INS = 1
const uint8_t	BamTools::Constants::BAM_CIGAR_DEL = 2
const uint8_t	BamTools::Constants::BAM_CIGAR_REFSKIP = 3
const uint8_t	BamTools::Constants::BAM_CIGAR_SOFTCLIP = 4
const uint8_t	BamTools::Constants::BAM_CIGAR_HARDCLIP = 5
const uint8_t	BamTools::Constants::BAM_CIGAR_PAD = 6
const uint8_t	BamTools::Constants::BAM_CIGAR_SEQMATCH = 7
const uint8_t	BamTools::Constants::BAM_CIGAR_MISMATCH = 8
const char	BamTools::Constants::BAM_CIGAR_MATCH_CHAR = 'M'
const char	BamTools::Constants::BAM_CIGAR_INS_CHAR = 'I'
const char	BamTools::Constants::BAM_CIGAR_DEL_CHAR = 'D'
const char	BamTools::Constants::BAM_CIGAR_REFSKIP_CHAR = 'N'
const char	BamTools::Constants::BAM_CIGAR_SOFTCLIP_CHAR = 'S'
const char	BamTools::Constants::BAM_CIGAR_HARDCLIP_CHAR = 'H'
const char	BamTools::Constants::BAM_CIGAR_PAD_CHAR = 'P'
const char	BamTools::Constants::BAM_CIGAR_SEQMATCH_CHAR = '='
const char	BamTools::Constants::BAM_CIGAR_MISMATCH_CHAR = 'X'
const int	BamTools::Constants::BAM_CIGAR_SHIFT = 4
const int	BamTools::Constants::BAM_CIGAR_MASK = ((1 << BAM_CIGAR_SHIFT) - 1)
const char	BamTools::Constants::BAM_TAG_TYPE_ASCII = 'A'
const char	BamTools::Constants::BAM_TAG_TYPE_INT8 = 'c'
const char	BamTools::Constants::BAM_TAG_TYPE_UINT8 = 'C'
const char	BamTools::Constants::BAM_TAG_TYPE_INT16 = 's'
const char	BamTools::Constants::BAM_TAG_TYPE_UINT16 = 'S'
const char	BamTools::Constants::BAM_TAG_TYPE_INT32 = 'i'
const char	BamTools::Constants::BAM_TAG_TYPE_UINT32 = 'I'
const char	BamTools::Constants::BAM_TAG_TYPE_FLOAT = 'f'
const char	BamTools::Constants::BAM_TAG_TYPE_STRING = 'Z'
const char	BamTools::Constants::BAM_TAG_TYPE_HEX = 'H'
const char	BamTools::Constants::BAM_TAG_TYPE_ARRAY = 'B'
const uint8_t	BamTools::Constants::BAM_TAG_TAGSIZE = 2
const uint8_t	BamTools::Constants::BAM_TAG_TYPESIZE = 1
const uint8_t	BamTools::Constants::BAM_TAG_ARRAYBASE_SIZE = 8
const char *const	BamTools::Constants::BAM_DNA_LOOKUP = "=ACMGRSVTWYHKDBN"
const uint8_t	BamTools::Constants::BAM_BASECODE_EQUAL = 0
const uint8_t	BamTools::Constants::BAM_BASECODE_A = 1
const uint8_t	BamTools::Constants::BAM_BASECODE_C = 2
const uint8_t	BamTools::Constants::BAM_BASECODE_M = 3
const uint8_t	BamTools::Constants::BAM_BASECODE_G = 4
const uint8_t	BamTools::Constants::BAM_BASECODE_R = 5
const uint8_t	BamTools::Constants::BAM_BASECODE_S = 6
const uint8_t	BamTools::Constants::BAM_BASECODE_V = 7
const uint8_t	BamTools::Constants::BAM_BASECODE_T = 8
const uint8_t	BamTools::Constants::BAM_BASECODE_W = 9
const uint8_t	BamTools::Constants::BAM_BASECODE_Y = 10
const uint8_t	BamTools::Constants::BAM_BASECODE_H = 11
const uint8_t	BamTools::Constants::BAM_BASECODE_K = 12
const uint8_t	BamTools::Constants::BAM_BASECODE_D = 13
const uint8_t	BamTools::Constants::BAM_BASECODE_B = 14
const uint8_t	BamTools::Constants::BAM_BASECODE_N = 15
const char	BamTools::Constants::BAM_DNA_EQUAL = '='
const char	BamTools::Constants::BAM_DNA_A = 'A'
const char	BamTools::Constants::BAM_DNA_C = 'C'
const char	BamTools::Constants::BAM_DNA_M = 'M'
const char	BamTools::Constants::BAM_DNA_G = 'G'
const char	BamTools::Constants::BAM_DNA_R = 'R'
const char	BamTools::Constants::BAM_DNA_S = 'S'
const char	BamTools::Constants::BAM_DNA_V = 'V'
const char	BamTools::Constants::BAM_DNA_T = 'T'
const char	BamTools::Constants::BAM_DNA_W = 'W'
const char	BamTools::Constants::BAM_DNA_Y = 'Y'
const char	BamTools::Constants::BAM_DNA_H = 'H'
const char	BamTools::Constants::BAM_DNA_K = 'K'
const char	BamTools::Constants::BAM_DNA_D = 'D'
const char	BamTools::Constants::BAM_DNA_B = 'B'
const char	BamTools::Constants::BAM_DNA_N = 'N'
const char	BamTools::Constants::BAM_DNA_DEL = '-'
const char	BamTools::Constants::BAM_DNA_PAD = '*'
const char	BamTools::Constants::GZIP_ID1 = 31
const char	BamTools::Constants::GZIP_ID2 = 139
const char	BamTools::Constants::CM_DEFLATE = 8
const char	BamTools::Constants::FLG_FEXTRA = 4
const char	BamTools::Constants::OS_UNKNOWN = 255
const char	BamTools::Constants::BGZF_XLEN = 6
const char	BamTools::Constants::BGZF_ID1 = 66
const char	BamTools::Constants::BGZF_ID2 = 67
const char	BamTools::Constants::BGZF_LEN = 2
const int8_t	BamTools::Constants::GZIP_WINDOW_BITS = -15
const int8_t	BamTools::Constants::Z_DEFAULT_MEM_LEVEL = 8
const uint8_t	BamTools::Constants::BGZF_BLOCK_HEADER_LENGTH = 18
const uint8_t	BamTools::Constants::BGZF_BLOCK_FOOTER_LENGTH = 8
const uint32_t	BamTools::Constants::BGZF_MAX_BLOCK_SIZE = 65536
const uint32_t	BamTools::Constants::BGZF_DEFAULT_BLOCK_SIZE = 65536