1 // ***************************************************************************
2 // BamConstants.h (c) 2011 Derek Barnett
3 // Marth Lab, Department of Biology, Boston College
4 // All rights reserved.
5 // ---------------------------------------------------------------------------
6 // Last modified: 19 April 2011 (DB)
7 // ---------------------------------------------------------------------------
8 // Provides basic constants for handling BAM files.
9 // ***************************************************************************
11 #ifndef BAM_CONSTANTS_H
12 #define BAM_CONSTANTS_H
16 /*! \namespace BamTools::Constants
17 \brief Provides basic constants for handling BAM files.
23 const int BAM_SIZEOF_INT = 4;
25 // header magic number
26 const char* const BAM_HEADER_MAGIC = "BAM\1";
27 const unsigned int BAM_HEADER_MAGIC_LENGTH = 4;
29 // BAM alignment core size
30 const int BAM_CORE_SIZE = 32;
31 const int BAM_CORE_BUFFER_SIZE = 8;
33 // BAM alignment flags
34 const int BAM_ALIGNMENT_PAIRED = 0x0001;
35 const int BAM_ALIGNMENT_PROPER_PAIR = 0x0002;
36 const int BAM_ALIGNMENT_UNMAPPED = 0x0004;
37 const int BAM_ALIGNMENT_MATE_UNMAPPED = 0x0008;
38 const int BAM_ALIGNMENT_REVERSE_STRAND = 0x0010;
39 const int BAM_ALIGNMENT_MATE_REVERSE_STRAND = 0x0020;
40 const int BAM_ALIGNMENT_READ_1 = 0x0040;
41 const int BAM_ALIGNMENT_READ_2 = 0x0080;
42 const int BAM_ALIGNMENT_SECONDARY = 0x0100;
43 const int BAM_ALIGNMENT_QC_FAILED = 0x0200;
44 const int BAM_ALIGNMENT_DUPLICATE = 0x0400;
47 const char* const BAM_CIGAR_LOOKUP = "MIDNSHP=X";
48 const int BAM_CIGAR_MATCH = 0;
49 const int BAM_CIGAR_INS = 1;
50 const int BAM_CIGAR_DEL = 2;
51 const int BAM_CIGAR_REFSKIP = 3;
52 const int BAM_CIGAR_SOFTCLIP = 4;
53 const int BAM_CIGAR_HARDCLIP = 5;
54 const int BAM_CIGAR_PAD = 6;
55 const int BAM_CIGAR_SEQMATCH = 7;
56 const int BAM_CIGAR_MISMATCH = 8;
58 const char BAM_CIGAR_MATCH_CHAR = 'M';
59 const char BAM_CIGAR_INS_CHAR = 'I';
60 const char BAM_CIGAR_DEL_CHAR = 'D';
61 const char BAM_CIGAR_REFSKIP_CHAR = 'N';
62 const char BAM_CIGAR_SOFTCLIP_CHAR = 'S';
63 const char BAM_CIGAR_HARDCLIP_CHAR = 'H';
64 const char BAM_CIGAR_PAD_CHAR = 'P';
65 const char BAM_CIGAR_SEQMATCH_CHAR = '=';
66 const char BAM_CIGAR_MISMATCH_CHAR = 'X';
68 const int BAM_CIGAR_SHIFT = 4;
69 const int BAM_CIGAR_MASK = ((1 << BAM_CIGAR_SHIFT) - 1);
72 const char BAM_TAG_TYPE_ASCII = 'A';
73 const char BAM_TAG_TYPE_UINT8 = 'c';
74 const char BAM_TAG_TYPE_INT8 = 'C';
75 const char BAM_TAG_TYPE_UINT16 = 's';
76 const char BAM_TAG_TYPE_INT16 = 'S';
77 const char BAM_TAG_TYPE_UINT32 = 'i';
78 const char BAM_TAG_TYPE_INT32 = 'I';
79 const char BAM_TAG_TYPE_FLOAT = 'f';
80 const char BAM_TAG_TYPE_STRING = 'Z';
81 const char BAM_TAG_TYPE_HEX = 'H';
82 const char BAM_TAG_TYPE_ARRAY = 'B';
84 const size_t BAM_TAG_TAGSIZE = 2;
85 const size_t BAM_TAG_TYPESIZE = 1;
86 const int BAM_TAG_ARRAYBASE_SIZE = 8;
89 const char* const BAM_DNA_LOOKUP = "=ACMGRSVTWYHKDBN";
90 const unsigned char BAM_BASECODE_EQUAL = 0;
91 const unsigned char BAM_BASECODE_A = 1;
92 const unsigned char BAM_BASECODE_C = 2;
93 const unsigned char BAM_BASECODE_G = 4;
94 const unsigned char BAM_BASECODE_T = 8;
95 const unsigned char BAM_BASECODE_N = 15;
97 const char BAM_DNA_EQUAL = '=';
98 const char BAM_DNA_A = 'A';
99 const char BAM_DNA_C = 'C';
100 const char BAM_DNA_G = 'G';
101 const char BAM_DNA_T = 'T';
102 const char BAM_DNA_N = 'N';
103 const char BAM_DNA_DEL = '-';
104 const char BAM_DNA_PAD = '*';
107 const int GZIP_ID1 = 31;
108 const int GZIP_ID2 = 139;
109 const int CM_DEFLATE = 8;
110 const int FLG_FEXTRA = 4;
111 const int OS_UNKNOWN = 255;
112 const int BGZF_XLEN = 6;
113 const int BGZF_ID1 = 66;
114 const int BGZF_ID2 = 67;
115 const int BGZF_LEN = 2;
116 const int GZIP_WINDOW_BITS = -15;
117 const int Z_DEFAULT_MEM_LEVEL = 8;
120 const int BGZF_BLOCK_HEADER_LENGTH = 18;
121 const int BGZF_BLOCK_FOOTER_LENGTH = 8;
122 const int BGZF_MAX_BLOCK_SIZE = 65536;
123 const int BGZF_DEFAULT_BLOCK_SIZE = 65536;
125 } // namespace Constants
126 } // namespace BamTools
128 #endif // BAM_CONSTANTS_H