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/*
* 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";
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)
};
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