BamTools::Constants Namespace Reference

Provides basic constants for handling BAM files. More...

Variables
const uint8_t	BAM_SIZEOF_INT = 4
const char *const	BAM_HEADER_MAGIC = "BAM\1"
const uint8_t	BAM_HEADER_MAGIC_LENGTH = 4
const uint8_t	BAM_CORE_SIZE = 32
const uint8_t	BAM_CORE_BUFFER_SIZE = 8
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 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)
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
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 = '*'
const char	GZIP_ID1 = 31
const char	GZIP_ID2 = 139
const char	CM_DEFLATE = 8
const char	FLG_FEXTRA = 4
const char	OS_UNKNOWN = 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
const char	SAM_COLON = ':'
const char	SAM_EQUAL = '='
const char	SAM_PERIOD = '.'
const char	SAM_STAR = '*'
const char	SAM_TAB = '\t'
const std::string	SAM_DIGITS = "0123456789"
const std::string	SAM_CURRENT_VERSION = "1.4"
const std::string	SAM_HD_BEGIN_TOKEN = "@HD"
const std::string	SAM_HD_VERSION_TAG = "VN"
const std::string	SAM_HD_SORTORDER_TAG = "SO"
const std::string	SAM_HD_GROUPORDER_TAG = "GO"
const std::string	SAM_SQ_BEGIN_TOKEN = "@SQ"
const std::string	SAM_SQ_ASSEMBLYID_TAG = "AS"
const std::string	SAM_SQ_CHECKSUM_TAG = "M5"
const std::string	SAM_SQ_LENGTH_TAG = "LN"
const std::string	SAM_SQ_NAME_TAG = "SN"
const std::string	SAM_SQ_SPECIES_TAG = "SP"
const std::string	SAM_SQ_URI_TAG = "UR"
const std::string	SAM_RG_BEGIN_TOKEN = "@RG"
const std::string	SAM_RG_DESCRIPTION_TAG = "DS"
const std::string	SAM_RG_FLOWORDER_TAG = "FO"
const std::string	SAM_RG_ID_TAG = "ID"
const std::string	SAM_RG_KEYSEQUENCE_TAG = "KS"
const std::string	SAM_RG_LIBRARY_TAG = "LB"
const std::string	SAM_RG_PLATFORMUNIT_TAG = "PU"
const std::string	SAM_RG_PREDICTEDINSERTSIZE_TAG = "PI"
const std::string	SAM_RG_PRODUCTIONDATE_TAG = "DT"
const std::string	SAM_RG_PROGRAM_TAG = "PG"
const std::string	SAM_RG_SAMPLE_TAG = "SM"
const std::string	SAM_RG_SEQCENTER_TAG = "CN"
const std::string	SAM_RG_SEQTECHNOLOGY_TAG = "PL"
const std::string	SAM_PG_BEGIN_TOKEN = "@PG"
const std::string	SAM_PG_COMMANDLINE_TAG = "CL"
const std::string	SAM_PG_ID_TAG = "ID"
const std::string	SAM_PG_NAME_TAG = "PN"
const std::string	SAM_PG_PREVIOUSPROGRAM_TAG = "PP"
const std::string	SAM_PG_VERSION_TAG = "VN"
const std::string	SAM_CO_BEGIN_TOKEN = "@CO"
const std::string	SAM_HD_SORTORDER_COORDINATE = "coordinate"
const std::string	SAM_HD_SORTORDER_QUERYNAME = "queryname"
const std::string	SAM_HD_SORTORDER_UNKNOWN = "unknown"
const std::string	SAM_HD_SORTORDER_UNSORTED = "unsorted"
const std::string	SAM_HD_GROUPORDER_NONE = "none"
const std::string	SAM_HD_GROUPORDER_QUERY = "query"
const std::string	SAM_HD_GROUPORDER_REFERENCE = "reference"
const unsigned int	SAM_SQ_LENGTH_MIN = 1
const unsigned int	SAM_SQ_LENGTH_MAX = 536870911
const std::string	SAM_RG_SEQTECHNOLOGY_CAPILLARY = "CAPILLARY"
const std::string	SAM_RG_SEQTECHNOLOGY_HELICOS = "HELICOS"
const std::string	SAM_RG_SEQTECHNOLOGY_ILLUMINA = "ILLUMINA"
const std::string	SAM_RG_SEQTECHNOLOGY_IONTORRENT = "IONTORRENT"
const std::string	SAM_RG_SEQTECHNOLOGY_LS454 = "LS454"
const std::string	SAM_RG_SEQTECHNOLOGY_PACBIO = "PACBIO"
const std::string	SAM_RG_SEQTECHNOLOGY_SOLID = "SOLID"