BamTools 2.5.2
Variables
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 int BAM_ALIGNMENT_SUPPLEMENTARY = 0x0800
 
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 = 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
 
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"
 

Detailed Description

Provides basic constants for handling BAM files.

Variable Documentation

◆ BAM_ALIGNMENT_DUPLICATE

const int BamTools::Constants::BAM_ALIGNMENT_DUPLICATE = 0x0400

◆ BAM_ALIGNMENT_MATE_REVERSE_STRAND

const int BamTools::Constants::BAM_ALIGNMENT_MATE_REVERSE_STRAND = 0x0020

◆ BAM_ALIGNMENT_MATE_UNMAPPED

const int BamTools::Constants::BAM_ALIGNMENT_MATE_UNMAPPED = 0x0008

◆ BAM_ALIGNMENT_PAIRED

const int BamTools::Constants::BAM_ALIGNMENT_PAIRED = 0x0001

◆ BAM_ALIGNMENT_PROPER_PAIR

const int BamTools::Constants::BAM_ALIGNMENT_PROPER_PAIR = 0x0002

◆ BAM_ALIGNMENT_QC_FAILED

const int BamTools::Constants::BAM_ALIGNMENT_QC_FAILED = 0x0200

◆ BAM_ALIGNMENT_READ_1

const int BamTools::Constants::BAM_ALIGNMENT_READ_1 = 0x0040

◆ BAM_ALIGNMENT_READ_2

const int BamTools::Constants::BAM_ALIGNMENT_READ_2 = 0x0080

◆ BAM_ALIGNMENT_REVERSE_STRAND

const int BamTools::Constants::BAM_ALIGNMENT_REVERSE_STRAND = 0x0010

◆ BAM_ALIGNMENT_SECONDARY

const int BamTools::Constants::BAM_ALIGNMENT_SECONDARY = 0x0100

◆ BAM_ALIGNMENT_SUPPLEMENTARY

const int BamTools::Constants::BAM_ALIGNMENT_SUPPLEMENTARY = 0x0800

◆ BAM_ALIGNMENT_UNMAPPED

const int BamTools::Constants::BAM_ALIGNMENT_UNMAPPED = 0x0004

◆ BAM_BASECODE_A

const uint8_t BamTools::Constants::BAM_BASECODE_A = 1

◆ BAM_BASECODE_B

const uint8_t BamTools::Constants::BAM_BASECODE_B = 14

◆ BAM_BASECODE_C

const uint8_t BamTools::Constants::BAM_BASECODE_C = 2

◆ BAM_BASECODE_D

const uint8_t BamTools::Constants::BAM_BASECODE_D = 13

◆ BAM_BASECODE_EQUAL

const uint8_t BamTools::Constants::BAM_BASECODE_EQUAL = 0

◆ BAM_BASECODE_G

const uint8_t BamTools::Constants::BAM_BASECODE_G = 4

◆ BAM_BASECODE_H

const uint8_t BamTools::Constants::BAM_BASECODE_H = 11

◆ BAM_BASECODE_K

const uint8_t BamTools::Constants::BAM_BASECODE_K = 12

◆ BAM_BASECODE_M

const uint8_t BamTools::Constants::BAM_BASECODE_M = 3

◆ BAM_BASECODE_N

const uint8_t BamTools::Constants::BAM_BASECODE_N = 15

◆ BAM_BASECODE_R

const uint8_t BamTools::Constants::BAM_BASECODE_R = 5

◆ BAM_BASECODE_S

const uint8_t BamTools::Constants::BAM_BASECODE_S = 6

◆ BAM_BASECODE_T

const uint8_t BamTools::Constants::BAM_BASECODE_T = 8

◆ BAM_BASECODE_V

const uint8_t BamTools::Constants::BAM_BASECODE_V = 7

◆ BAM_BASECODE_W

const uint8_t BamTools::Constants::BAM_BASECODE_W = 9

◆ BAM_BASECODE_Y

const uint8_t BamTools::Constants::BAM_BASECODE_Y = 10

◆ BAM_CIGAR_DEL

const uint8_t BamTools::Constants::BAM_CIGAR_DEL = 2

◆ BAM_CIGAR_DEL_CHAR

const char BamTools::Constants::BAM_CIGAR_DEL_CHAR = 'D'

◆ BAM_CIGAR_HARDCLIP

const uint8_t BamTools::Constants::BAM_CIGAR_HARDCLIP = 5

◆ BAM_CIGAR_HARDCLIP_CHAR

const char BamTools::Constants::BAM_CIGAR_HARDCLIP_CHAR = 'H'

◆ BAM_CIGAR_INS

const uint8_t BamTools::Constants::BAM_CIGAR_INS = 1

◆ BAM_CIGAR_INS_CHAR

const char BamTools::Constants::BAM_CIGAR_INS_CHAR = 'I'

◆ BAM_CIGAR_LOOKUP

const char* const BamTools::Constants::BAM_CIGAR_LOOKUP = "MIDNSHP=X"

◆ BAM_CIGAR_MASK

const int BamTools::Constants::BAM_CIGAR_MASK = ((1 << BAM_CIGAR_SHIFT) - 1)

◆ BAM_CIGAR_MATCH

const uint8_t BamTools::Constants::BAM_CIGAR_MATCH = 0

◆ BAM_CIGAR_MATCH_CHAR

const char BamTools::Constants::BAM_CIGAR_MATCH_CHAR = 'M'

◆ BAM_CIGAR_MISMATCH

const uint8_t BamTools::Constants::BAM_CIGAR_MISMATCH = 8

◆ BAM_CIGAR_MISMATCH_CHAR

const char BamTools::Constants::BAM_CIGAR_MISMATCH_CHAR = 'X'

◆ BAM_CIGAR_PAD

const uint8_t BamTools::Constants::BAM_CIGAR_PAD = 6

◆ BAM_CIGAR_PAD_CHAR

const char BamTools::Constants::BAM_CIGAR_PAD_CHAR = 'P'

◆ BAM_CIGAR_REFSKIP

const uint8_t BamTools::Constants::BAM_CIGAR_REFSKIP = 3

◆ BAM_CIGAR_REFSKIP_CHAR

const char BamTools::Constants::BAM_CIGAR_REFSKIP_CHAR = 'N'

◆ BAM_CIGAR_SEQMATCH

const uint8_t BamTools::Constants::BAM_CIGAR_SEQMATCH = 7

◆ BAM_CIGAR_SEQMATCH_CHAR

const char BamTools::Constants::BAM_CIGAR_SEQMATCH_CHAR = '='

◆ BAM_CIGAR_SHIFT

const int BamTools::Constants::BAM_CIGAR_SHIFT = 4

◆ BAM_CIGAR_SOFTCLIP

const uint8_t BamTools::Constants::BAM_CIGAR_SOFTCLIP = 4

◆ BAM_CIGAR_SOFTCLIP_CHAR

const char BamTools::Constants::BAM_CIGAR_SOFTCLIP_CHAR = 'S'

◆ BAM_CORE_BUFFER_SIZE

const uint8_t BamTools::Constants::BAM_CORE_BUFFER_SIZE = 8

◆ BAM_CORE_SIZE

const uint8_t BamTools::Constants::BAM_CORE_SIZE = 32

◆ BAM_DNA_A

const char BamTools::Constants::BAM_DNA_A = 'A'

◆ BAM_DNA_B

const char BamTools::Constants::BAM_DNA_B = 'B'

◆ BAM_DNA_C

const char BamTools::Constants::BAM_DNA_C = 'C'

◆ BAM_DNA_D

const char BamTools::Constants::BAM_DNA_D = 'D'

◆ BAM_DNA_DEL

const char BamTools::Constants::BAM_DNA_DEL = '-'

◆ BAM_DNA_EQUAL

const char BamTools::Constants::BAM_DNA_EQUAL = '='

◆ BAM_DNA_G

const char BamTools::Constants::BAM_DNA_G = 'G'

◆ BAM_DNA_H

const char BamTools::Constants::BAM_DNA_H = 'H'

◆ BAM_DNA_K

const char BamTools::Constants::BAM_DNA_K = 'K'

◆ BAM_DNA_LOOKUP

const char* const BamTools::Constants::BAM_DNA_LOOKUP = "=ACMGRSVTWYHKDBN"

◆ BAM_DNA_M

const char BamTools::Constants::BAM_DNA_M = 'M'

◆ BAM_DNA_N

const char BamTools::Constants::BAM_DNA_N = 'N'

◆ BAM_DNA_PAD

const char BamTools::Constants::BAM_DNA_PAD = '*'

◆ BAM_DNA_R

const char BamTools::Constants::BAM_DNA_R = 'R'

◆ BAM_DNA_S

const char BamTools::Constants::BAM_DNA_S = 'S'

◆ BAM_DNA_T

const char BamTools::Constants::BAM_DNA_T = 'T'

◆ BAM_DNA_V

const char BamTools::Constants::BAM_DNA_V = 'V'

◆ BAM_DNA_W

const char BamTools::Constants::BAM_DNA_W = 'W'

◆ BAM_DNA_Y

const char BamTools::Constants::BAM_DNA_Y = 'Y'

◆ BAM_HEADER_MAGIC

const char* const BamTools::Constants::BAM_HEADER_MAGIC = "BAM\1"

◆ BAM_HEADER_MAGIC_LENGTH

const uint8_t BamTools::Constants::BAM_HEADER_MAGIC_LENGTH = 4

◆ BAM_SIZEOF_INT

const uint8_t BamTools::Constants::BAM_SIZEOF_INT = 4

◆ BAM_TAG_ARRAYBASE_SIZE

const uint8_t BamTools::Constants::BAM_TAG_ARRAYBASE_SIZE = 8

◆ BAM_TAG_TAGSIZE

const uint8_t BamTools::Constants::BAM_TAG_TAGSIZE = 2

◆ BAM_TAG_TYPE_ARRAY

const char BamTools::Constants::BAM_TAG_TYPE_ARRAY = 'B'

◆ BAM_TAG_TYPE_ASCII

const char BamTools::Constants::BAM_TAG_TYPE_ASCII = 'A'

◆ BAM_TAG_TYPE_FLOAT

const char BamTools::Constants::BAM_TAG_TYPE_FLOAT = 'f'

◆ BAM_TAG_TYPE_HEX

const char BamTools::Constants::BAM_TAG_TYPE_HEX = 'H'

◆ BAM_TAG_TYPE_INT16

const char BamTools::Constants::BAM_TAG_TYPE_INT16 = 's'

◆ BAM_TAG_TYPE_INT32

const char BamTools::Constants::BAM_TAG_TYPE_INT32 = 'i'

◆ BAM_TAG_TYPE_INT8

const char BamTools::Constants::BAM_TAG_TYPE_INT8 = 'c'

◆ BAM_TAG_TYPE_STRING

const char BamTools::Constants::BAM_TAG_TYPE_STRING = 'Z'

◆ BAM_TAG_TYPE_UINT16

const char BamTools::Constants::BAM_TAG_TYPE_UINT16 = 'S'

◆ BAM_TAG_TYPE_UINT32

const char BamTools::Constants::BAM_TAG_TYPE_UINT32 = 'I'

◆ BAM_TAG_TYPE_UINT8

const char BamTools::Constants::BAM_TAG_TYPE_UINT8 = 'C'

◆ BAM_TAG_TYPESIZE

const uint8_t BamTools::Constants::BAM_TAG_TYPESIZE = 1

◆ BGZF_BLOCK_FOOTER_LENGTH

const uint8_t BamTools::Constants::BGZF_BLOCK_FOOTER_LENGTH = 8

◆ BGZF_BLOCK_HEADER_LENGTH

const uint8_t BamTools::Constants::BGZF_BLOCK_HEADER_LENGTH = 18

◆ BGZF_DEFAULT_BLOCK_SIZE

const uint32_t BamTools::Constants::BGZF_DEFAULT_BLOCK_SIZE = 65536

◆ BGZF_ID1

const char BamTools::Constants::BGZF_ID1 = 66

◆ BGZF_ID2

const char BamTools::Constants::BGZF_ID2 = 67

◆ BGZF_LEN

const char BamTools::Constants::BGZF_LEN = 2

◆ BGZF_MAX_BLOCK_SIZE

const uint32_t BamTools::Constants::BGZF_MAX_BLOCK_SIZE = 65536

◆ BGZF_XLEN

const char BamTools::Constants::BGZF_XLEN = 6

◆ CM_DEFLATE

const char BamTools::Constants::CM_DEFLATE = 8

◆ FLG_FEXTRA

const char BamTools::Constants::FLG_FEXTRA = 4

◆ GZIP_ID1

const char BamTools::Constants::GZIP_ID1 = 31

◆ GZIP_ID2

const char BamTools::Constants::GZIP_ID2 = static_cast<char>(139)

◆ GZIP_WINDOW_BITS

const int8_t BamTools::Constants::GZIP_WINDOW_BITS = -15

◆ OS_UNKNOWN

const char BamTools::Constants::OS_UNKNOWN = static_cast<char>(255)

◆ SAM_CO_BEGIN_TOKEN

const std::string BamTools::Constants::SAM_CO_BEGIN_TOKEN = "@CO"

◆ SAM_COLON

const char BamTools::Constants::SAM_COLON = ':'

◆ SAM_CURRENT_VERSION

const std::string BamTools::Constants::SAM_CURRENT_VERSION = "1.4"

◆ SAM_DIGITS

const std::string BamTools::Constants::SAM_DIGITS = "0123456789"

◆ SAM_EQUAL

const char BamTools::Constants::SAM_EQUAL = '='

◆ SAM_HD_BEGIN_TOKEN

const std::string BamTools::Constants::SAM_HD_BEGIN_TOKEN = "@HD"

◆ SAM_HD_GROUPORDER_NONE

const std::string BamTools::Constants::SAM_HD_GROUPORDER_NONE = "none"

◆ SAM_HD_GROUPORDER_QUERY

const std::string BamTools::Constants::SAM_HD_GROUPORDER_QUERY = "query"

◆ SAM_HD_GROUPORDER_REFERENCE

const std::string BamTools::Constants::SAM_HD_GROUPORDER_REFERENCE = "reference"

◆ SAM_HD_GROUPORDER_TAG

const std::string BamTools::Constants::SAM_HD_GROUPORDER_TAG = "GO"

◆ SAM_HD_SORTORDER_COORDINATE

const std::string BamTools::Constants::SAM_HD_SORTORDER_COORDINATE = "coordinate"

◆ SAM_HD_SORTORDER_QUERYNAME

const std::string BamTools::Constants::SAM_HD_SORTORDER_QUERYNAME = "queryname"

◆ SAM_HD_SORTORDER_TAG

const std::string BamTools::Constants::SAM_HD_SORTORDER_TAG = "SO"

◆ SAM_HD_SORTORDER_UNKNOWN

const std::string BamTools::Constants::SAM_HD_SORTORDER_UNKNOWN = "unknown"

◆ SAM_HD_SORTORDER_UNSORTED

const std::string BamTools::Constants::SAM_HD_SORTORDER_UNSORTED = "unsorted"

◆ SAM_HD_VERSION_TAG

const std::string BamTools::Constants::SAM_HD_VERSION_TAG = "VN"

◆ SAM_PERIOD

const char BamTools::Constants::SAM_PERIOD = '.'

◆ SAM_PG_BEGIN_TOKEN

const std::string BamTools::Constants::SAM_PG_BEGIN_TOKEN = "@PG"

◆ SAM_PG_COMMANDLINE_TAG

const std::string BamTools::Constants::SAM_PG_COMMANDLINE_TAG = "CL"

◆ SAM_PG_ID_TAG

const std::string BamTools::Constants::SAM_PG_ID_TAG = "ID"

◆ SAM_PG_NAME_TAG

const std::string BamTools::Constants::SAM_PG_NAME_TAG = "PN"

◆ SAM_PG_PREVIOUSPROGRAM_TAG

const std::string BamTools::Constants::SAM_PG_PREVIOUSPROGRAM_TAG = "PP"

◆ SAM_PG_VERSION_TAG

const std::string BamTools::Constants::SAM_PG_VERSION_TAG = "VN"

◆ SAM_RG_BEGIN_TOKEN

const std::string BamTools::Constants::SAM_RG_BEGIN_TOKEN = "@RG"

◆ SAM_RG_DESCRIPTION_TAG

const std::string BamTools::Constants::SAM_RG_DESCRIPTION_TAG = "DS"

◆ SAM_RG_FLOWORDER_TAG

const std::string BamTools::Constants::SAM_RG_FLOWORDER_TAG = "FO"

◆ SAM_RG_ID_TAG

const std::string BamTools::Constants::SAM_RG_ID_TAG = "ID"

◆ SAM_RG_KEYSEQUENCE_TAG

const std::string BamTools::Constants::SAM_RG_KEYSEQUENCE_TAG = "KS"

◆ SAM_RG_LIBRARY_TAG

const std::string BamTools::Constants::SAM_RG_LIBRARY_TAG = "LB"

◆ SAM_RG_PLATFORMUNIT_TAG

const std::string BamTools::Constants::SAM_RG_PLATFORMUNIT_TAG = "PU"

◆ SAM_RG_PREDICTEDINSERTSIZE_TAG

const std::string BamTools::Constants::SAM_RG_PREDICTEDINSERTSIZE_TAG = "PI"

◆ SAM_RG_PRODUCTIONDATE_TAG

const std::string BamTools::Constants::SAM_RG_PRODUCTIONDATE_TAG = "DT"

◆ SAM_RG_PROGRAM_TAG

const std::string BamTools::Constants::SAM_RG_PROGRAM_TAG = "PG"

◆ SAM_RG_SAMPLE_TAG

const std::string BamTools::Constants::SAM_RG_SAMPLE_TAG = "SM"

◆ SAM_RG_SEQCENTER_TAG

const std::string BamTools::Constants::SAM_RG_SEQCENTER_TAG = "CN"

◆ SAM_RG_SEQTECHNOLOGY_CAPILLARY

const std::string BamTools::Constants::SAM_RG_SEQTECHNOLOGY_CAPILLARY = "CAPILLARY"

◆ SAM_RG_SEQTECHNOLOGY_HELICOS

const std::string BamTools::Constants::SAM_RG_SEQTECHNOLOGY_HELICOS = "HELICOS"

◆ SAM_RG_SEQTECHNOLOGY_ILLUMINA

const std::string BamTools::Constants::SAM_RG_SEQTECHNOLOGY_ILLUMINA = "ILLUMINA"

◆ SAM_RG_SEQTECHNOLOGY_IONTORRENT

const std::string BamTools::Constants::SAM_RG_SEQTECHNOLOGY_IONTORRENT = "IONTORRENT"

◆ SAM_RG_SEQTECHNOLOGY_LS454

const std::string BamTools::Constants::SAM_RG_SEQTECHNOLOGY_LS454 = "LS454"

◆ SAM_RG_SEQTECHNOLOGY_PACBIO

const std::string BamTools::Constants::SAM_RG_SEQTECHNOLOGY_PACBIO = "PACBIO"

◆ SAM_RG_SEQTECHNOLOGY_SOLID

const std::string BamTools::Constants::SAM_RG_SEQTECHNOLOGY_SOLID = "SOLID"

◆ SAM_RG_SEQTECHNOLOGY_TAG

const std::string BamTools::Constants::SAM_RG_SEQTECHNOLOGY_TAG = "PL"

◆ SAM_SQ_ASSEMBLYID_TAG

const std::string BamTools::Constants::SAM_SQ_ASSEMBLYID_TAG = "AS"

◆ SAM_SQ_BEGIN_TOKEN

const std::string BamTools::Constants::SAM_SQ_BEGIN_TOKEN = "@SQ"

◆ SAM_SQ_CHECKSUM_TAG

const std::string BamTools::Constants::SAM_SQ_CHECKSUM_TAG = "M5"

◆ SAM_SQ_LENGTH_MAX

const unsigned int BamTools::Constants::SAM_SQ_LENGTH_MAX = 536870911

◆ SAM_SQ_LENGTH_MIN

const unsigned int BamTools::Constants::SAM_SQ_LENGTH_MIN = 1

◆ SAM_SQ_LENGTH_TAG

const std::string BamTools::Constants::SAM_SQ_LENGTH_TAG = "LN"

◆ SAM_SQ_NAME_TAG

const std::string BamTools::Constants::SAM_SQ_NAME_TAG = "SN"

◆ SAM_SQ_SPECIES_TAG

const std::string BamTools::Constants::SAM_SQ_SPECIES_TAG = "SP"

◆ SAM_SQ_URI_TAG

const std::string BamTools::Constants::SAM_SQ_URI_TAG = "UR"

◆ SAM_STAR

const char BamTools::Constants::SAM_STAR = '*'

◆ SAM_TAB

const char BamTools::Constants::SAM_TAB = '\t'

◆ Z_DEFAULT_MEM_LEVEL

const int8_t BamTools::Constants::Z_DEFAULT_MEM_LEVEL = 8