File: alphabet.cpp

package info (click to toggle)
bowtie2 2.4.2-2
  • links: PTS, VCS
  • area: main
  • in suites: bullseye, sid
  • size: 27,104 kB
  • sloc: cpp: 60,331; perl: 7,540; sh: 1,111; python: 949; makefile: 520; ansic: 122
file content (244 lines) | stat: -rw-r--r-- 8,457 bytes parent folder | download | duplicates (2)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
/*
 * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
 *
 * This file is part of Bowtie 2.
 *
 * Bowtie 2 is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * Bowtie 2 is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with Bowtie 2.  If not, see <http://www.gnu.org/licenses/>.
 */

#include <stdint.h>
#include <cassert>
#include <string>
#include "alphabet.h"

using namespace std;

/**
 * Mapping from ASCII characters to DNA categories:
 *
 * 0 = invalid - error
 * 1 = DNA
 * 2 = IUPAC (ambiguous DNA)
 * 3 = not an error, but unmatchable; alignments containing this
 *     character are invalid
 */
uint8_t asc2dnacat[] = {
	/*   0 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/*  16 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/*  32 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 0, 0,
	       /*                                        - */
	/*  48 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/*  64 */ 0, 1, 2, 1, 2, 0, 0, 1, 2, 0, 0, 2, 0, 2, 2, 0,
	       /*    A  B  C  D        G  H        K     M  N */
	/*  80 */ 0, 0, 2, 2, 1, 0, 2, 2, 2, 2, 0, 0, 0, 0, 0, 0,
	       /*       R  S  T     V  W  X  Y */
	/*  96 */ 0, 1, 2, 1, 2, 0, 0, 1, 2, 0, 0, 2, 0, 2, 2, 0,
	       /*    a  b  c  d        g  h        k     m  n */
	/* 112 */ 0, 0, 2, 2, 1, 0, 2, 2, 2, 2, 0, 0, 0, 0, 0, 0,
	       /*       r  s  t     v  w  x  y */
	/* 128 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/* 144 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/* 160 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/* 176 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/* 192 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/* 208 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/* 224 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/* 240 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
};

// 5-bit pop count
int mask2popcnt[] = {
	0, 1, 1, 2, 1, 2, 2, 3,
	1, 2, 2, 3, 2, 3, 3, 4,
	1, 2, 2, 3, 2, 3, 3, 4,
	2, 3, 3, 4, 3, 4, 4, 5
};

/**
 * Mapping from masks to ASCII characters for ambiguous nucleotides.
 */
char mask2dna[] = {
	'?', // 0
	'A', // 1
	'C', // 2
	'M', // 3
	'G', // 4
	'R', // 5
	'S', // 6
	'V', // 7
	'T', // 8
	'W', // 9
	'Y', // 10
	'H', // 11
	'K', // 12
	'D', // 13
	'B', // 14
	'N', // 15 (inclusive N)
	'N'  // 16 (exclusive N)
};

/**
 * Mapping from ASCII characters for ambiguous nucleotides into masks:
 */
uint8_t asc2dnamask[] = {
	/*   0 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/*  16 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/*  32 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/*  48 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/*  64 */ 0, 1,14, 2,13, 0, 0, 4,11, 0, 0,12, 0, 3,15, 0,
	       /*    A  B  C  D        G  H        K     M  N */
	/*  80 */ 0, 0, 5, 6, 8, 0, 7, 9, 0,10, 0, 0, 0, 0, 0, 0,
	       /*       R  S  T     V  W     Y */
	/*  96 */ 0, 1,14, 2,13, 0, 0, 4,11, 0, 0,12, 0, 3,15, 0,
	       /*    a  b  c  d        g  h        k     m  n */
	/* 112 */ 0, 0, 5, 6, 8, 0, 7, 9, 0,10, 0, 0, 0, 0, 0, 0,
	       /*       r  s  t     v  w     y */
	/* 128 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/* 144 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/* 160 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/* 176 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/* 192 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/* 208 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/* 224 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/* 240 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
};

/**
 * Set the category for all IUPAC codes.  By default they're in
 * category 2 (IUPAC), but sometimes we'd like to put them in category
 * 3 (unmatchable), for example.
 */
void setIupacsCat(uint8_t cat) {
	assert(cat < 4);
	asc2dnacat[(int)'B'] = asc2dnacat[(int)'b'] =
	asc2dnacat[(int)'D'] = asc2dnacat[(int)'d'] =
	asc2dnacat[(int)'H'] = asc2dnacat[(int)'h'] =
	asc2dnacat[(int)'K'] = asc2dnacat[(int)'k'] =
	asc2dnacat[(int)'M'] = asc2dnacat[(int)'m'] =
	asc2dnacat[(int)'N'] = asc2dnacat[(int)'n'] =
	asc2dnacat[(int)'R'] = asc2dnacat[(int)'r'] =
	asc2dnacat[(int)'S'] = asc2dnacat[(int)'s'] =
	asc2dnacat[(int)'V'] = asc2dnacat[(int)'v'] =
	asc2dnacat[(int)'W'] = asc2dnacat[(int)'w'] =
	asc2dnacat[(int)'X'] = asc2dnacat[(int)'x'] =
	asc2dnacat[(int)'Y'] = asc2dnacat[(int)'y'] = cat;
}

/// For converting from ASCII to the Dna5 code where A=0, C=1, G=2,
/// T=3, N=4
/// According to the manual all the other characters, including
/// IUPAC codes are being converted to N
uint8_t asc2dna[] = {
	/*   0 */ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
	/*  16 */ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
	/*  32 */ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
	/*                                               - */
	/*  48 */ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
	/*  64 */ 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
	       /*    A  B  C  D        G  H        K     M  N */
	/*  80 */ 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
	       /*       R  S  T  U  V  W     Y */
	/*  96 */ 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
	       /*    a  b  c  d        g  h        k     m  n */
	/* 112 */ 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
	       /*       r  s  t  u  v  w     y */
	/* 128 */ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
	/* 144 */ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
	/* 160 */ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
	/* 176 */ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
	/* 192 */ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
	/* 208 */ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
	/* 224 */ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
	/* 240 */ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
};

/// For converting from ASCII to the Dna5 code where A=0, C=1, G=2,
/// T=3, N=4
uint8_t asc2col[] = {
	/*   0 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/*  16 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/*  32 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 4, 0,
	       /*                                        -  . */
	/*  48 */ 0, 1, 2, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	       /* 0  1  2  3 */
	/*  64 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/*  80 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/*  96 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/* 112 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/* 128 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/* 144 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/* 160 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/* 176 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/* 192 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/* 208 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/* 224 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	/* 240 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
};

/**
 * Convert a pair of nucleotides to a color.
 */
uint8_t dinuc2color[5][5] = {
	/* A */ {0, 1, 2, 3, 4},
	/* C */ {1, 0, 3, 2, 4},
	/* G */ {2, 3, 0, 1, 4},
	/* T */ {3, 2, 1, 0, 4},
	/* N */ {4, 4, 4, 4, 4}
};

/// Convert bit encoded DNA char to its complement
int dnacomp[5] = {
	3, 2, 1, 0, 4
};

const char *iupacs = "!ACMGRSVTWYHKDBN!acmgrsvtwyhkdbn";

signed char mask2iupac[16] = {
	-1,
	'A', // 0001
	'C', // 0010
	'M', // 0011
	'G', // 0100
	'R', // 0101
	'S', // 0110
	'V', // 0111
	'T', // 1000
	'W', // 1001
	'Y', // 1010
	'H', // 1011
	'K', // 1100
	'D', // 1101
	'B', // 1110
	'N', // 1111
};

int maskcomp[16] = {
	0,  // 0000 (!) -> 0000 (!)
	8,  // 0001 (A) -> 1000 (T)
	4,  // 0010 (C) -> 0100 (G)
	12, // 0011 (M) -> 1100 (K)
	2,  // 0100 (G) -> 0010 (C)
	10, // 0101 (R) -> 1010 (Y)
	6,  // 0110 (S) -> 0110 (S)
	14, // 0111 (V) -> 1110 (B)
	1,  // 1000 (T) -> 0001 (A)
	9,  // 1001 (W) -> 1001 (W)
	5,  // 1010 (Y) -> 0101 (R)
	13, // 1011 (H) -> 1101 (D)
	3,  // 1100 (K) -> 0011 (M)
	11, // 1101 (D) -> 1011 (H)
	7,  // 1110 (B) -> 0111 (V)
	15, // 1111 (N) -> 1111 (N)
};