BamTools  2.5.1
BamConstants.h
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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 // ***************************************************************************
9 
10 #ifndef BAM_CONSTANTS_H
11 #define BAM_CONSTANTS_H
12 
13 #include <cassert>
14 #include <string>
15 #include "api/api_global.h"
16 
21 namespace BamTools {
22 namespace Constants {
23 
24 const uint8_t BAM_SIZEOF_INT = 4;
25 
26 // header magic number
27 const char* const BAM_HEADER_MAGIC = "BAM\1";
28 const uint8_t BAM_HEADER_MAGIC_LENGTH = 4;
29 
30 // BAM alignment core size
31 const uint8_t BAM_CORE_SIZE = 32;
32 const uint8_t BAM_CORE_BUFFER_SIZE = 8;
33 
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;
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;
46 const int SUPPLEMENTARY = 0x0800; // Additional patch by tiddit package
47 
48 // CIGAR constants
49 const char* const BAM_CIGAR_LOOKUP = "MIDNSHP=X";
50 const uint8_t BAM_CIGAR_MATCH = 0;
51 const uint8_t BAM_CIGAR_INS = 1;
52 const uint8_t BAM_CIGAR_DEL = 2;
53 const uint8_t BAM_CIGAR_REFSKIP = 3;
54 const uint8_t BAM_CIGAR_SOFTCLIP = 4;
55 const uint8_t BAM_CIGAR_HARDCLIP = 5;
56 const uint8_t BAM_CIGAR_PAD = 6;
57 const uint8_t BAM_CIGAR_SEQMATCH = 7;
58 const uint8_t BAM_CIGAR_MISMATCH = 8;
59 
60 const char BAM_CIGAR_MATCH_CHAR = 'M';
61 const char BAM_CIGAR_INS_CHAR = 'I';
62 const char BAM_CIGAR_DEL_CHAR = 'D';
63 const char BAM_CIGAR_REFSKIP_CHAR = 'N';
64 const char BAM_CIGAR_SOFTCLIP_CHAR = 'S';
65 const char BAM_CIGAR_HARDCLIP_CHAR = 'H';
66 const char BAM_CIGAR_PAD_CHAR = 'P';
67 const char BAM_CIGAR_SEQMATCH_CHAR = '=';
68 const char BAM_CIGAR_MISMATCH_CHAR = 'X';
69 
70 const int BAM_CIGAR_SHIFT = 4;
71 const int BAM_CIGAR_MASK = ((1 << BAM_CIGAR_SHIFT) - 1);
72 
73 // BAM tag types & sizes
74 const char BAM_TAG_TYPE_ASCII = 'A';
75 const char BAM_TAG_TYPE_INT8 = 'c';
76 const char BAM_TAG_TYPE_UINT8 = 'C';
77 const char BAM_TAG_TYPE_INT16 = 's';
78 const char BAM_TAG_TYPE_UINT16 = 'S';
79 const char BAM_TAG_TYPE_INT32 = 'i';
80 const char BAM_TAG_TYPE_UINT32 = 'I';
81 const char BAM_TAG_TYPE_FLOAT = 'f';
82 const char BAM_TAG_TYPE_STRING = 'Z';
83 const char BAM_TAG_TYPE_HEX = 'H';
84 const char BAM_TAG_TYPE_ARRAY = 'B';
85 
86 const uint8_t BAM_TAG_TAGSIZE = 2;
87 const uint8_t BAM_TAG_TYPESIZE = 1;
88 const uint8_t BAM_TAG_ARRAYBASE_SIZE = 8;
89 
90 // DNA bases
91 const char* const BAM_DNA_LOOKUP = "=ACMGRSVTWYHKDBN";
92 const uint8_t BAM_BASECODE_EQUAL = 0;
93 const uint8_t BAM_BASECODE_A = 1;
94 const uint8_t BAM_BASECODE_C = 2;
95 const uint8_t BAM_BASECODE_M = 3;
96 const uint8_t BAM_BASECODE_G = 4;
97 const uint8_t BAM_BASECODE_R = 5;
98 const uint8_t BAM_BASECODE_S = 6;
99 const uint8_t BAM_BASECODE_V = 7;
100 const uint8_t BAM_BASECODE_T = 8;
101 const uint8_t BAM_BASECODE_W = 9;
102 const uint8_t BAM_BASECODE_Y = 10;
103 const uint8_t BAM_BASECODE_H = 11;
104 const uint8_t BAM_BASECODE_K = 12;
105 const uint8_t BAM_BASECODE_D = 13;
106 const uint8_t BAM_BASECODE_B = 14;
107 const uint8_t BAM_BASECODE_N = 15;
108 
109 const char BAM_DNA_EQUAL = '=';
110 const char BAM_DNA_A = 'A';
111 const char BAM_DNA_C = 'C';
112 const char BAM_DNA_M = 'M';
113 const char BAM_DNA_G = 'G';
114 const char BAM_DNA_R = 'R';
115 const char BAM_DNA_S = 'S';
116 const char BAM_DNA_V = 'V';
117 const char BAM_DNA_T = 'T';
118 const char BAM_DNA_W = 'W';
119 const char BAM_DNA_Y = 'Y';
120 const char BAM_DNA_H = 'H';
121 const char BAM_DNA_K = 'K';
122 const char BAM_DNA_D = 'D';
123 const char BAM_DNA_B = 'B';
124 const char BAM_DNA_N = 'N';
125 const char BAM_DNA_DEL = '-';
126 const char BAM_DNA_PAD = '*';
127 
128 // zlib & BGZF constants
129 const char GZIP_ID1 = 31;
130 const char GZIP_ID2 = static_cast<char>(139);
131 const char CM_DEFLATE = 8;
132 const char FLG_FEXTRA = 4;
133 const char OS_UNKNOWN = static_cast<char>(255);
134 const char BGZF_XLEN = 6;
135 const char BGZF_ID1 = 66;
136 const char BGZF_ID2 = 67;
137 const char BGZF_LEN = 2;
138 
139 const int8_t GZIP_WINDOW_BITS = -15;
140 const int8_t Z_DEFAULT_MEM_LEVEL = 8;
141 const uint8_t BGZF_BLOCK_HEADER_LENGTH = 18;
142 const uint8_t BGZF_BLOCK_FOOTER_LENGTH = 8;
143 const uint32_t BGZF_MAX_BLOCK_SIZE = 65536;
144 const uint32_t BGZF_DEFAULT_BLOCK_SIZE = 65536;
145 
146 } // namespace Constants
147 
149 // -------------------------
150 // tag-type helper structs
151 // -------------------------
152 
153 // fail on any types not specified below
154 template <typename T>
155 struct TagTypeHelper
156 {
157  static bool CanConvertFrom(const char)
158  {
159  assert(false);
160  return false;
161  }
162  static bool CanConvertTo(const char)
163  {
164  assert(false);
165  return false;
166  }
167  static char TypeCode()
168  {
169  assert(false);
170  return 0;
171  }
172 };
173 
174 template <>
175 struct TagTypeHelper<uint8_t>
176 {
177  static bool CanConvertFrom(const char c)
178  {
180  }
181  static bool CanConvertTo(const char c)
182  {
185  }
186 
187  static char TypeCode()
188  {
190  }
191 };
192 
193 template <>
194 struct TagTypeHelper<int8_t>
195 {
196  static bool CanConvertFrom(const char c)
197  {
199  }
200  static bool CanConvertTo(const char c)
201  {
204  }
205  static char TypeCode()
206  {
208  }
209 };
210 
211 template <>
212 struct TagTypeHelper<uint16_t>
213 {
214  static bool CanConvertFrom(const char c)
215  {
218  }
219  static bool CanConvertTo(const char c)
220  {
222  }
223  static char TypeCode()
224  {
226  }
227 };
228 
229 template <>
230 struct TagTypeHelper<int16_t>
231 {
232  static bool CanConvertFrom(const char c)
233  {
236  }
237  static bool CanConvertTo(const char c)
238  {
240  }
241  static char TypeCode()
242  {
244  }
245 };
246 
247 template <>
248 struct TagTypeHelper<uint32_t>
249 {
250  static bool CanConvertFrom(const char c)
251  {
254  }
255  static bool CanConvertTo(const char c)
256  {
257  return (c == Constants::BAM_TAG_TYPE_UINT32);
258  }
259  static char TypeCode()
260  {
262  }
263 };
264 
265 template <>
266 struct TagTypeHelper<int32_t>
267 {
268  static bool CanConvertFrom(const char c)
269  {
272  }
273  static bool CanConvertTo(const char c)
274  {
275  return (c == Constants::BAM_TAG_TYPE_INT32);
276  }
277  static char TypeCode()
278  {
280  }
281 };
282 
283 template <>
284 struct TagTypeHelper<float>
285 {
286  static bool CanConvertFrom(const char c)
287  {
292  }
293  static bool CanConvertTo(const char c)
294  {
295  return (c == Constants::BAM_TAG_TYPE_FLOAT);
296  }
297  static char TypeCode()
298  {
300  }
301 };
302 
303 template <>
304 struct TagTypeHelper<std::string>
305 {
306  static bool CanConvertFrom(const char c)
307  {
309  }
310  static bool CanConvertTo(const char c)
311  {
313  }
314  static char TypeCode()
315  {
317  }
318 };
319 
321 
322 } // namespace BamTools
323 
324 #endif // BAM_CONSTANTS_H
const int BAM_ALIGNMENT_UNMAPPED
Definition: BamConstants.h:37
const char BAM_TAG_TYPE_UINT8
Definition: BamConstants.h:76
const char CM_DEFLATE
Definition: BamConstants.h:131
const uint8_t BAM_BASECODE_S
Definition: BamConstants.h:98
const char BAM_DNA_N
Definition: BamConstants.h:124
const uint8_t BAM_CIGAR_MISMATCH
Definition: BamConstants.h:58
const char BAM_DNA_H
Definition: BamConstants.h:120
const char BAM_TAG_TYPE_HEX
Definition: BamConstants.h:83
const uint32_t BGZF_DEFAULT_BLOCK_SIZE
Definition: BamConstants.h:144
const char BAM_TAG_TYPE_INT32
Definition: BamConstants.h:79
const char BAM_DNA_D
Definition: BamConstants.h:122
const char BAM_TAG_TYPE_ASCII
Definition: BamConstants.h:74
const char BAM_DNA_V
Definition: BamConstants.h:116
const uint8_t BAM_BASECODE_M
Definition: BamConstants.h:95
const int BAM_CIGAR_SHIFT
Definition: BamConstants.h:70
const char BAM_DNA_T
Definition: BamConstants.h:117
const uint8_t BAM_CIGAR_REFSKIP
Definition: BamConstants.h:53
const uint8_t BAM_CIGAR_SEQMATCH
Definition: BamConstants.h:57
const uint8_t BAM_CIGAR_PAD
Definition: BamConstants.h:56
const uint8_t BGZF_BLOCK_FOOTER_LENGTH
Definition: BamConstants.h:142
const char BAM_CIGAR_INS_CHAR
Definition: BamConstants.h:61
const int BAM_ALIGNMENT_DUPLICATE
Definition: BamConstants.h:45
const char BAM_DNA_G
Definition: BamConstants.h:113
const char BAM_DNA_B
Definition: BamConstants.h:123
const uint8_t BAM_BASECODE_N
Definition: BamConstants.h:107
const char BGZF_XLEN
Definition: BamConstants.h:134
const char BAM_CIGAR_SEQMATCH_CHAR
Definition: BamConstants.h:67
const int BAM_ALIGNMENT_PAIRED
Definition: BamConstants.h:35
const uint8_t BAM_BASECODE_C
Definition: BamConstants.h:94
const char BGZF_LEN
Definition: BamConstants.h:137
const char BAM_CIGAR_MATCH_CHAR
Definition: BamConstants.h:60
const uint8_t BAM_BASECODE_B
Definition: BamConstants.h:106
const char BAM_DNA_DEL
Definition: BamConstants.h:125
const uint8_t BAM_BASECODE_T
Definition: BamConstants.h:100
const char BAM_CIGAR_SOFTCLIP_CHAR
Definition: BamConstants.h:64
const uint8_t BAM_TAG_TAGSIZE
Definition: BamConstants.h:86
const char *const BAM_HEADER_MAGIC
Definition: BamConstants.h:27
const uint8_t BAM_CORE_BUFFER_SIZE
Definition: BamConstants.h:32
const uint8_t BAM_BASECODE_W
Definition: BamConstants.h:101
const char BAM_TAG_TYPE_ARRAY
Definition: BamConstants.h:84
const int BAM_ALIGNMENT_SECONDARY
Definition: BamConstants.h:43
const uint8_t BAM_CIGAR_INS
Definition: BamConstants.h:51
const char BAM_DNA_R
Definition: BamConstants.h:114
const char BAM_DNA_K
Definition: BamConstants.h:121
const char *const BAM_CIGAR_LOOKUP
Definition: BamConstants.h:49
const char BAM_TAG_TYPE_FLOAT
Definition: BamConstants.h:81
const uint8_t BAM_BASECODE_V
Definition: BamConstants.h:99
const char BAM_TAG_TYPE_UINT32
Definition: BamConstants.h:80
const uint8_t BAM_CORE_SIZE
Definition: BamConstants.h:31
const uint8_t BAM_BASECODE_EQUAL
Definition: BamConstants.h:92
const char BAM_DNA_A
Definition: BamConstants.h:110
const int BAM_ALIGNMENT_QC_FAILED
Definition: BamConstants.h:44
const char FLG_FEXTRA
Definition: BamConstants.h:132
const uint8_t BAM_CIGAR_DEL
Definition: BamConstants.h:52
const int8_t Z_DEFAULT_MEM_LEVEL
Definition: BamConstants.h:140
const char BAM_TAG_TYPE_STRING
Definition: BamConstants.h:82
const char BAM_CIGAR_MISMATCH_CHAR
Definition: BamConstants.h:68
const char *const BAM_DNA_LOOKUP
Definition: BamConstants.h:91
const char BAM_DNA_S
Definition: BamConstants.h:115
const uint32_t BGZF_MAX_BLOCK_SIZE
Definition: BamConstants.h:143
const char BAM_CIGAR_PAD_CHAR
Definition: BamConstants.h:66
const int SUPPLEMENTARY
Definition: BamConstants.h:46
const uint8_t BGZF_BLOCK_HEADER_LENGTH
Definition: BamConstants.h:141
const char BAM_TAG_TYPE_INT8
Definition: BamConstants.h:75
const int BAM_CIGAR_MASK
Definition: BamConstants.h:71
const int BAM_ALIGNMENT_READ_1
Definition: BamConstants.h:41
const char BGZF_ID1
Definition: BamConstants.h:135
const int BAM_ALIGNMENT_REVERSE_STRAND
Definition: BamConstants.h:39
const char BAM_DNA_C
Definition: BamConstants.h:111
const uint8_t BAM_BASECODE_K
Definition: BamConstants.h:104
const char BAM_TAG_TYPE_UINT16
Definition: BamConstants.h:78
const uint8_t BAM_HEADER_MAGIC_LENGTH
Definition: BamConstants.h:28
const int BAM_ALIGNMENT_READ_2
Definition: BamConstants.h:42
const char BAM_TAG_TYPE_INT16
Definition: BamConstants.h:77
const uint8_t BAM_BASECODE_Y
Definition: BamConstants.h:102
const uint8_t BAM_CIGAR_MATCH
Definition: BamConstants.h:50
const uint8_t BAM_SIZEOF_INT
Definition: BamConstants.h:24
const uint8_t BAM_BASECODE_D
Definition: BamConstants.h:105
const char BGZF_ID2
Definition: BamConstants.h:136
const char BAM_CIGAR_DEL_CHAR
Definition: BamConstants.h:62
const int BAM_ALIGNMENT_MATE_REVERSE_STRAND
Definition: BamConstants.h:40
const char BAM_DNA_M
Definition: BamConstants.h:112
const int8_t GZIP_WINDOW_BITS
Definition: BamConstants.h:139
const char BAM_DNA_PAD
Definition: BamConstants.h:126
const uint8_t BAM_BASECODE_A
Definition: BamConstants.h:93
const int BAM_ALIGNMENT_PROPER_PAIR
Definition: BamConstants.h:36
const uint8_t BAM_TAG_TYPESIZE
Definition: BamConstants.h:87
const char BAM_DNA_W
Definition: BamConstants.h:118
const uint8_t BAM_CIGAR_SOFTCLIP
Definition: BamConstants.h:54
const char OS_UNKNOWN
Definition: BamConstants.h:133
const char BAM_CIGAR_REFSKIP_CHAR
Definition: BamConstants.h:63
const uint8_t BAM_BASECODE_G
Definition: BamConstants.h:96
const char BAM_DNA_EQUAL
Definition: BamConstants.h:109
const int BAM_ALIGNMENT_MATE_UNMAPPED
Definition: BamConstants.h:38
const char BAM_CIGAR_HARDCLIP_CHAR
Definition: BamConstants.h:65
const char GZIP_ID1
Definition: BamConstants.h:129
const uint8_t BAM_BASECODE_H
Definition: BamConstants.h:103
const char GZIP_ID2
Definition: BamConstants.h:130
const uint8_t BAM_BASECODE_R
Definition: BamConstants.h:97
const char BAM_DNA_Y
Definition: BamConstants.h:119
const uint8_t BAM_CIGAR_HARDCLIP
Definition: BamConstants.h:55
const uint8_t BAM_TAG_ARRAYBASE_SIZE
Definition: BamConstants.h:88
Contains all BamTools classes & methods.
Definition: Sort.h:24