1 // ***************************************************************************
2 // BamConstants.h (c) 2011 Derek Barnett
3 // Marth Lab, Department of Biology, Boston College
4 // ---------------------------------------------------------------------------
5 // Last modified: 16 October 2011 (DB)
6 // ---------------------------------------------------------------------------
7 // Provides basic constants for handling BAM files.
8 // ***************************************************************************
10 #ifndef BAM_CONSTANTS_H
11 #define BAM_CONSTANTS_H
13 #include "api/api_global.h"
17 /*! \namespace BamTools::Constants
18 \brief Provides basic constants for handling BAM files.
24 const uint8_t BAM_SIZEOF_INT = 4;
26 // header magic number
27 const char* const BAM_HEADER_MAGIC = "BAM\1";
28 const uint8_t BAM_HEADER_MAGIC_LENGTH = 4;
30 // BAM alignment core size
31 const uint8_t BAM_CORE_SIZE = 32;
32 const uint8_t BAM_CORE_BUFFER_SIZE = 8;
34 // BAM alignment flags
35 const int BAM_ALIGNMENT_PAIRED = 0x0001;
36 const int BAM_ALIGNMENT_PROPER_PAIR = 0x0002;
37 const int BAM_ALIGNMENT_UNMAPPED = 0x0004;
38 const int BAM_ALIGNMENT_MATE_UNMAPPED = 0x0008;
39 const int BAM_ALIGNMENT_REVERSE_STRAND = 0x0010;
40 const int BAM_ALIGNMENT_MATE_REVERSE_STRAND = 0x0020;
41 const int BAM_ALIGNMENT_READ_1 = 0x0040;
42 const int BAM_ALIGNMENT_READ_2 = 0x0080;
43 const int BAM_ALIGNMENT_SECONDARY = 0x0100;
44 const int BAM_ALIGNMENT_QC_FAILED = 0x0200;
45 const int BAM_ALIGNMENT_DUPLICATE = 0x0400;
48 const char* const BAM_CIGAR_LOOKUP = "MIDNSHP=X";
49 const uint8_t BAM_CIGAR_MATCH = 0;
50 const uint8_t BAM_CIGAR_INS = 1;
51 const uint8_t BAM_CIGAR_DEL = 2;
52 const uint8_t BAM_CIGAR_REFSKIP = 3;
53 const uint8_t BAM_CIGAR_SOFTCLIP = 4;
54 const uint8_t BAM_CIGAR_HARDCLIP = 5;
55 const uint8_t BAM_CIGAR_PAD = 6;
56 const uint8_t BAM_CIGAR_SEQMATCH = 7;
57 const uint8_t BAM_CIGAR_MISMATCH = 8;
59 const char BAM_CIGAR_MATCH_CHAR = 'M';
60 const char BAM_CIGAR_INS_CHAR = 'I';
61 const char BAM_CIGAR_DEL_CHAR = 'D';
62 const char BAM_CIGAR_REFSKIP_CHAR = 'N';
63 const char BAM_CIGAR_SOFTCLIP_CHAR = 'S';
64 const char BAM_CIGAR_HARDCLIP_CHAR = 'H';
65 const char BAM_CIGAR_PAD_CHAR = 'P';
66 const char BAM_CIGAR_SEQMATCH_CHAR = '=';
67 const char BAM_CIGAR_MISMATCH_CHAR = 'X';
69 const int BAM_CIGAR_SHIFT = 4;
70 const int BAM_CIGAR_MASK = ((1 << BAM_CIGAR_SHIFT) - 1);
72 // BAM tag types & sizes
73 const char BAM_TAG_TYPE_ASCII = 'A';
74 const char BAM_TAG_TYPE_INT8 = 'c';
75 const char BAM_TAG_TYPE_UINT8 = 'C';
76 const char BAM_TAG_TYPE_INT16 = 's';
77 const char BAM_TAG_TYPE_UINT16 = 'S';
78 const char BAM_TAG_TYPE_INT32 = 'i';
79 const char BAM_TAG_TYPE_UINT32 = 'I';
80 const char BAM_TAG_TYPE_FLOAT = 'f';
81 const char BAM_TAG_TYPE_STRING = 'Z';
82 const char BAM_TAG_TYPE_HEX = 'H';
83 const char BAM_TAG_TYPE_ARRAY = 'B';
85 const uint8_t BAM_TAG_TAGSIZE = 2;
86 const uint8_t BAM_TAG_TYPESIZE = 1;
87 const uint8_t BAM_TAG_ARRAYBASE_SIZE = 8;
90 const char* const BAM_DNA_LOOKUP = "=ACMGRSVTWYHKDBN";
91 const uint8_t BAM_BASECODE_EQUAL = 0;
92 const uint8_t BAM_BASECODE_A = 1;
93 const uint8_t BAM_BASECODE_C = 2;
94 const uint8_t BAM_BASECODE_M = 3;
95 const uint8_t BAM_BASECODE_G = 4;
96 const uint8_t BAM_BASECODE_R = 5;
97 const uint8_t BAM_BASECODE_S = 6;
98 const uint8_t BAM_BASECODE_V = 7;
99 const uint8_t BAM_BASECODE_T = 8;
100 const uint8_t BAM_BASECODE_W = 9;
101 const uint8_t BAM_BASECODE_Y = 10;
102 const uint8_t BAM_BASECODE_H = 11;
103 const uint8_t BAM_BASECODE_K = 12;
104 const uint8_t BAM_BASECODE_D = 13;
105 const uint8_t BAM_BASECODE_B = 14;
106 const uint8_t BAM_BASECODE_N = 15;
108 const char BAM_DNA_EQUAL = '=';
109 const char BAM_DNA_A = 'A';
110 const char BAM_DNA_C = 'C';
111 const char BAM_DNA_M = 'M';
112 const char BAM_DNA_G = 'G';
113 const char BAM_DNA_R = 'R';
114 const char BAM_DNA_S = 'S';
115 const char BAM_DNA_V = 'V';
116 const char BAM_DNA_T = 'T';
117 const char BAM_DNA_W = 'W';
118 const char BAM_DNA_Y = 'Y';
119 const char BAM_DNA_H = 'H';
120 const char BAM_DNA_K = 'K';
121 const char BAM_DNA_D = 'D';
122 const char BAM_DNA_B = 'B';
123 const char BAM_DNA_N = 'N';
124 const char BAM_DNA_DEL = '-';
125 const char BAM_DNA_PAD = '*';
127 // zlib & BGZF constants
128 const char GZIP_ID1 = 31;
129 const char GZIP_ID2 = 139;
130 const char CM_DEFLATE = 8;
131 const char FLG_FEXTRA = 4;
132 const char OS_UNKNOWN = 255;
133 const char BGZF_XLEN = 6;
134 const char BGZF_ID1 = 66;
135 const char BGZF_ID2 = 67;
136 const char BGZF_LEN = 2;
138 const int8_t GZIP_WINDOW_BITS = -15;
139 const int8_t Z_DEFAULT_MEM_LEVEL = 8;
140 const uint8_t BGZF_BLOCK_HEADER_LENGTH = 18;
141 const uint8_t BGZF_BLOCK_FOOTER_LENGTH = 8;
142 const uint32_t BGZF_MAX_BLOCK_SIZE = 65536;
143 const uint32_t BGZF_DEFAULT_BLOCK_SIZE = 65536;
145 } // namespace Constants
148 // -------------------------
149 // tag-type helper structs
150 // -------------------------
152 // fail on any types not specified below
154 struct TagTypeHelper {
155 static bool CanConvertFrom(const char) { assert(false); return false; }
156 static bool CanConvertTo(const char) { assert(false); return false; }
157 static char TypeCode(void) { assert(false); return 0; }
161 struct TagTypeHelper<uint8_t> {
162 static bool CanConvertFrom(const char c) {
163 return ( c == Constants::BAM_TAG_TYPE_ASCII ||
164 c == Constants::BAM_TAG_TYPE_UINT8 );
166 static bool CanConvertTo(const char c) {
167 return ( c == Constants::BAM_TAG_TYPE_ASCII ||
168 c == Constants::BAM_TAG_TYPE_UINT8 ||
169 c == Constants::BAM_TAG_TYPE_UINT16 ||
170 c == Constants::BAM_TAG_TYPE_UINT32 );
173 static char TypeCode(void) { return Constants::BAM_TAG_TYPE_UINT8; }
177 struct TagTypeHelper<int8_t> {
178 static bool CanConvertFrom(const char c) {
179 return ( c == Constants::BAM_TAG_TYPE_ASCII ||
180 c == Constants::BAM_TAG_TYPE_INT8 );
182 static bool CanConvertTo(const char c) {
183 return ( c == Constants::BAM_TAG_TYPE_ASCII ||
184 c == Constants::BAM_TAG_TYPE_INT8 ||
185 c == Constants::BAM_TAG_TYPE_INT16 ||
186 c == Constants::BAM_TAG_TYPE_INT32 );
188 static char TypeCode(void) { return Constants::BAM_TAG_TYPE_INT8; }
192 struct TagTypeHelper<uint16_t> {
193 static bool CanConvertFrom(const char c) {
194 return ( c == Constants::BAM_TAG_TYPE_ASCII ||
195 c == Constants::BAM_TAG_TYPE_UINT8 ||
196 c == Constants::BAM_TAG_TYPE_UINT16 );
198 static bool CanConvertTo(const char c) {
199 return ( c == Constants::BAM_TAG_TYPE_UINT16 ||
200 c == Constants::BAM_TAG_TYPE_UINT32);
202 static char TypeCode(void) { return Constants::BAM_TAG_TYPE_UINT16; }
206 struct TagTypeHelper<int16_t> {
207 static bool CanConvertFrom(const char c) {
208 return ( c == Constants::BAM_TAG_TYPE_ASCII ||
209 c == Constants::BAM_TAG_TYPE_INT8 ||
210 c == Constants::BAM_TAG_TYPE_INT16 );
212 static bool CanConvertTo(const char c) {
213 return ( c == Constants::BAM_TAG_TYPE_INT16 ||
214 c == Constants::BAM_TAG_TYPE_INT32);
216 static char TypeCode(void) { return Constants::BAM_TAG_TYPE_INT16; }
220 struct TagTypeHelper<uint32_t> {
221 static bool CanConvertFrom(const char c) {
222 return ( c == Constants::BAM_TAG_TYPE_ASCII ||
223 c == Constants::BAM_TAG_TYPE_UINT8 ||
224 c == Constants::BAM_TAG_TYPE_UINT16 ||
225 c == Constants::BAM_TAG_TYPE_UINT32 );
227 static bool CanConvertTo(const char c) {
228 return ( c == Constants::BAM_TAG_TYPE_UINT32 );
230 static char TypeCode(void) { return Constants::BAM_TAG_TYPE_UINT32; }
234 struct TagTypeHelper<int32_t> {
235 static bool CanConvertFrom(const char c) {
236 return ( c == Constants::BAM_TAG_TYPE_ASCII ||
237 c == Constants::BAM_TAG_TYPE_INT8 ||
238 c == Constants::BAM_TAG_TYPE_INT16 ||
239 c == Constants::BAM_TAG_TYPE_INT32 );
241 static bool CanConvertTo(const char c) {
242 return ( c == Constants::BAM_TAG_TYPE_INT32 );
244 static char TypeCode(void) { return Constants::BAM_TAG_TYPE_INT32; }
248 struct TagTypeHelper<float> {
249 static bool CanConvertFrom(const char c) {
250 return ( c == Constants::BAM_TAG_TYPE_ASCII ||
251 c == Constants::BAM_TAG_TYPE_UINT8 ||
252 c == Constants::BAM_TAG_TYPE_INT8 ||
253 c == Constants::BAM_TAG_TYPE_UINT16 ||
254 c == Constants::BAM_TAG_TYPE_INT16 ||
255 c == Constants::BAM_TAG_TYPE_UINT32 ||
256 c == Constants::BAM_TAG_TYPE_INT32 ||
257 c == Constants::BAM_TAG_TYPE_FLOAT);
259 static bool CanConvertTo(const char c) {
260 return ( c == Constants::BAM_TAG_TYPE_FLOAT );
262 static char TypeCode(void) { return Constants::BAM_TAG_TYPE_FLOAT; }
266 struct TagTypeHelper<std::string> {
267 static bool CanConvertFrom(const char c) {
268 return ( c == Constants::BAM_TAG_TYPE_HEX ||
269 c == Constants::BAM_TAG_TYPE_STRING );
271 static bool CanConvertTo(const char c) {
272 return ( c == Constants::BAM_TAG_TYPE_HEX ||
273 c == Constants::BAM_TAG_TYPE_STRING );
275 static char TypeCode(void) { return Constants::BAM_TAG_TYPE_STRING; }
280 } // namespace BamTools
282 #endif // BAM_CONSTANTS_H