/usr/include/bamtools/api/BamConstants.h is in libbamtools-dev 2.4.1+dfsg-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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// 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 "api/api_global.h"
#include <cassert>
#include <string>
/*! \namespace BamTools::Constants
\brief Provides basic constants for handling BAM files.
*/
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;
// 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 = 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;
} // namespace Constants
//! \cond
// -------------------------
// 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(void) { 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(void) { 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(void) { 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(void) { 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(void) { 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(void) { 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(void) { 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(void) { 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(void) { return Constants::BAM_TAG_TYPE_STRING; }
};
//! \endcond
} // namespace BamTools
#endif // BAM_CONSTANTS_H
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