BamTools
2.5.1
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BamConstants.h File Reference
#include <cassert>
#include <string>
#include "
api/api_global.h
"
Go to the source code of this file.
Namespaces
BamTools::Constants
Provides basic constants for handling BAM files.
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 int
BamTools::Constants::SUPPLEMENTARY
= 0x0800
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
= static_cast<char>(139)
const char
BamTools::Constants::CM_DEFLATE
= 8
const char
BamTools::Constants::FLG_FEXTRA
= 4
const char
BamTools::Constants::OS_UNKNOWN
= static_cast<char>(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
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