+// ***************************************************************************
+// BamConstants.h (c) 2011 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// ---------------------------------------------------------------------------
+// Last modified: 4 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 int BAM_SIZEOF_INT = 4;
// header magic number
-const char* const BAM_HEADER_MAGIC = "BAM\001";
-const unsigned int BAM_HEADER_MAGIC_SIZE = 4;
+const char* const BAM_HEADER_MAGIC = "BAM\1";
+const unsigned int BAM_HEADER_MAGIC_LENGTH = 4;
// BAM alignment core size
const int BAM_CORE_SIZE = 32;
+const int BAM_CORE_BUFFER_SIZE = 8;
// BAM alignment flags
-const int BAM_ALIGNMENT_PAIRED = 1;
-const int BAM_ALIGNMENT_PROPER_PAIR = 2;
-const int BAM_ALIGNMENT_UNMAPPED = 4;
-const int BAM_ALIGNMENT_MATE_UNMAPPED = 8;
-const int BAM_ALIGNMENT_REVERSE_STRAND = 16;
-const int BAM_ALIGNMENT_MATE_REVERSE_STRAND = 32;
-const int BAM_ALIGNMENT_READ_1 = 64;
-const int BAM_ALIGNMENT_READ_2 = 128;
-const int BAM_ALIGNMENT_SECONDARY = 256;
-const int BAM_ALIGNMENT_QC_FAILED = 512;
-const int BAM_ALIGNMENT_DUPLICATE = 1024;
+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";
+const char* const BAM_CIGAR_LOOKUP = "MIDNSHP=X";
const int BAM_CIGAR_MATCH = 0;
const int BAM_CIGAR_INS = 1;
const int BAM_CIGAR_DEL = 2;
const int BAM_CIGAR_SOFTCLIP = 4;
const int BAM_CIGAR_HARDCLIP = 5;
const int BAM_CIGAR_PAD = 6;
+const int BAM_CIGAR_SEQMATCH = 7;
+const int 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
+const char BAM_TAG_TYPE_ASCII = 'A';
+const char BAM_TAG_TYPE_UINT8 = 'c';
+const char BAM_TAG_TYPE_INT8 = 'C';
+const char BAM_TAG_TYPE_UINT16 = 's';
+const char BAM_TAG_TYPE_INT16 = 'S';
+const char BAM_TAG_TYPE_UINT32 = 'i';
+const char BAM_TAG_TYPE_INT32 = '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 size_t BAM_TAG_TAGSIZE = 2;
+const size_t BAM_TAG_TYPESIZE = 1;
+const int BAM_TAG_ARRAYBASE_SIZE = 8;
+
// DNA bases
const char* const BAM_DNA_LOOKUP = "=ACMGRSVTWYHKDBN";
+const unsigned char BAM_BASECODE_EQUAL = 0;
+const unsigned char BAM_BASECODE_A = 1;
+const unsigned char BAM_BASECODE_C = 2;
+const unsigned char BAM_BASECODE_G = 4;
+const unsigned char BAM_BASECODE_T = 8;
+const unsigned char 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_G = 'G';
+const char BAM_DNA_T = 'T';
+const char BAM_DNA_N = 'N';
+const char BAM_DNA_DEL = '-';
+const char BAM_DNA_PAD = '*';
+
+// zlib constants
+const int GZIP_ID1 = 31;
+const int GZIP_ID2 = 139;
+const int CM_DEFLATE = 8;
+const int FLG_FEXTRA = 4;
+const int OS_UNKNOWN = 255;
+const int BGZF_XLEN = 6;
+const int BGZF_ID1 = 66;
+const int BGZF_ID2 = 67;
+const int BGZF_LEN = 2;
+const int GZIP_WINDOW_BITS = -15;
+const int Z_DEFAULT_MEM_LEVEL = 8;
+
+// BZGF constants
+const int BGZF_BLOCK_HEADER_LENGTH = 18;
+const int BGZF_BLOCK_FOOTER_LENGTH = 8;
+const int BGZF_MAX_BLOCK_SIZE = 65536;
+const int BGZF_DEFAULT_BLOCK_SIZE = 65536;
} // namespace Constants
+
+// -------------------------
+// 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 CanCovnertFrom(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; }
+};
+
} // namespace BamTools
#endif // BAM_CONSTANTS_H
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