Major update to BamTools version 1.0

[bamtools.git] / src / api / BamConstants.h

diff --git a/src/api/BamConstants.h b/src/api/BamConstants.h
index 5bf03f9aa7258285b97983e53af7cd8ab33a43ed..6a97980b400298593733a370cb91239de8d2c4a6 100644 (file)
--- a/src/api/BamConstants.h
+++ b/src/api/BamConstants.h
@@ -3,17 +3,22 @@
 
 #include <string>
 
+/*! \namespace BamTools::Constants
+    \brief Contains most of the constants used throughout BamTools.
+*/
+
 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;
@@ -38,11 +43,68 @@ const int BAM_CIGAR_SOFTCLIP = 4;
 const int BAM_CIGAR_HARDCLIP = 5;
 const int BAM_CIGAR_PAD      = 6;
 
+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 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 size_t BAM_TAG_TAGSIZE  = 2;
+const size_t BAM_TAG_TYPESIZE = 1;
+
 // 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
 } // namespace BamTools