DNAconsts.cpp

/* sdm: simple demultiplexer
Copyright (C) 2013  Falk Hildebrand
email: Falk.Hildebrand@gmail.com

This program 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.

 This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.
*/

#include "DNAconsts.h"

char DNA_trans[256];
short DNA_amb[256];//to count amb chars
short DNA_IUPAC[256 * 256];
short NT_POS[256];

bool canonicalDNA(char x) {
	return (DNA_amb[(int)x]==0);
	
	//no longer needed
	if (x == 'A' || x == 'G' || x == 'C' || x == 'T') {
		return true;
	}
	if (x == 'a' || x == 'g' || x == 'c' || x == 't') {
		return true;
	}
	return false;
}
void ini_DNAconstants() {
//static char* DNA_trans[256] = "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX";	
    //DNA_trans.resize(256,'X');
    
    
    memset(DNA_trans, 'N', 256);
    DNA_trans['A'] = 'T';
    DNA_trans['T'] = 'A';
    DNA_trans['C'] = 'G';
    DNA_trans['G'] = 'C';
    DNA_trans['a'] = 'T';
    DNA_trans['t'] = 'A';
    DNA_trans['c'] = 'G';
    DNA_trans['g'] = 'C';

    DNA_trans['W'] = 'W';
    DNA_trans['w'] = 'W';
    DNA_trans['S'] = 'S';
    DNA_trans['s'] = 'S';
    DNA_trans['M'] = 'K';
    DNA_trans['m'] = 'K';
    DNA_trans['K'] = 'M';
    DNA_trans['k'] = 'M';
    
    DNA_trans['R'] = 'Y';
    DNA_trans['r'] = 'Y';
    DNA_trans['Y'] = 'R';
    DNA_trans['y'] = 'R';
    DNA_trans['B'] = 'V';
    DNA_trans['b'] = 'V';
    DNA_trans['D'] = 'H';
    DNA_trans['d'] = 'H';

    DNA_trans['H'] = 'D';
    DNA_trans['h'] = 'D';
    DNA_trans['V'] = 'B';
    DNA_trans['v'] = 'B';
 
    //memset(DNA_amb, unsigned int(1), 256);
	for (int i = 0; i < 256; i++) {
		DNA_amb[i] = 1;
	}
    
    DNA_amb['A'] = 0;
    DNA_amb['T'] = 0;
    DNA_amb['C'] = 0;
    DNA_amb['G'] = 0;
    DNA_amb['a'] = 0;
    DNA_amb['t'] = 0;
    DNA_amb['c'] = 0;
    DNA_amb['g'] = 0;
    
    for (int i = 0; i < 256; i++) {
        NT_POS[i] = 5;
    }
//    memset(NT_POS, 5, 256);
    
    NT_POS['A'] = 0;
    NT_POS['T'] = 1;
    NT_POS['G'] = 2;
    NT_POS['C'] = 3;
    NT_POS['N'] = 4;
    NT_POS['a'] = 0;
    NT_POS['t'] = 1;
    NT_POS['g'] = 2;
    NT_POS['c'] = 3;
    NT_POS['n'] = 4;
    
    for ( int i = 0; i < 256 * 256; i++ ) { DNA_IUPAC[i] = 1;  }
    
    //memset(DNA_IUPAC, 1, 1 << 16);
    
    // ?  Don't you want to iterate the whole DNA space (which comprises 15 elements)
    // For each char in the DNA space mapping with N is a hit.
    for (int i = 0; i < 14; i++) {
        DNA_IUPAC[256 * DNA_SPACE[i] + 'N'] = 0;
        DNA_IUPAC[256 * 'N' + DNA_SPACE[i]] = 0;
    }
    
    // Iterate over A C G T N (DNA_SPACE)
    for (int i = 0; i < 5; i++) {
        // initialize MAP where A C G T N + B H D or V is a hit
        DNA_IUPAC[256 * DNA_SPACE[i] + 'B'] = 0;
        DNA_IUPAC[256 * DNA_SPACE[i] + 'H'] = 0;
        DNA_IUPAC[256 * DNA_SPACE[i] + 'D'] = 0;
        DNA_IUPAC[256 * DNA_SPACE[i] + 'V'] = 0;
        
        DNA_IUPAC[256 * 'B' + DNA_SPACE[i]] = 0;
        DNA_IUPAC[256 * 'H' + DNA_SPACE[i]] = 0;
        DNA_IUPAC[256 * 'D' + DNA_SPACE[i]] = 0;
        DNA_IUPAC[256 * 'V' + DNA_SPACE[i]] = 0;
    }
    
    // Why would you manually set to one? You set everything to one before. (68)
    DNA_IUPAC[256 * 'A' + 'B'] = 1;
    DNA_IUPAC[256 * 'B' + 'A'] = 1;
    DNA_IUPAC[256 * 'C' + 'D'] = 1;
    DNA_IUPAC[256 * 'D' + 'C'] = 1;
    DNA_IUPAC[256 * 'G' + 'H'] = 1;
    DNA_IUPAC[256 * 'H' + 'G'] = 1;
    DNA_IUPAC[256 * 'T' + 'V'] = 1;
    DNA_IUPAC[256 * 'V' + 'T'] = 1;
    
    //
    DNA_IUPAC['R' + 256 * 'A'] = 0;
    DNA_IUPAC[256 * 'R' + 'A'] = 0;
    DNA_IUPAC['R' + 256 * 'G'] = 0;
    DNA_IUPAC[256 * 'R' + 'G'] = 0;
    DNA_IUPAC['M' + 256 * 'C'] = 0;
    DNA_IUPAC[256 * 'M' + 'C'] = 0;
    DNA_IUPAC['M' + 256 * 'A'] = 0;
    DNA_IUPAC[256 * 'M' + 'A'] = 0;
    DNA_IUPAC['Y' + 256 * 'C'] = 0;
    DNA_IUPAC[256 * 'Y' + 'C'] = 0;
    DNA_IUPAC['Y' + 256 * 'T'] = 0;
    DNA_IUPAC[256 * 'Y' + 'T'] = 0;
    DNA_IUPAC['K' + 256 * 'G'] = 0;
    DNA_IUPAC[256 * 'K' + 'G'] = 0;
    DNA_IUPAC['K' + 256 * 'T'] = 0;
    DNA_IUPAC[256 * 'K' + 'T'] = 0;
    DNA_IUPAC['W' + 256 * 'A'] = 0;
    DNA_IUPAC[256 * 'W' + 'A'] = 0;
    DNA_IUPAC['W' + 256 * 'T'] = 0;
    DNA_IUPAC[256 * 'W' + 'T'] = 0;
    DNA_IUPAC['S' + 256 * 'C'] = 0;
    DNA_IUPAC[256 * 'S' + 'C'] = 0;
    DNA_IUPAC['S' + 256 * 'G'] = 0;
    DNA_IUPAC[256 * 'S' + 'G'] = 0;
    
    DNA_IUPAC['A' + 256 * 'A'] = 0;
    DNA_IUPAC[256 * 'A' + 'A'] = 0;
    DNA_IUPAC['T' + 256 * 'T'] = 0;
    DNA_IUPAC[256 * 'T' + 'T'] = 0;
    DNA_IUPAC['G' + 256 * 'G'] = 0;
    DNA_IUPAC[256 * 'G' + 'G'] = 0;
    DNA_IUPAC['C' + 256 * 'C'] = 0;
    DNA_IUPAC[256 * 'C' + 'C'] = 0;
    //DEBUG
    
    //fake use to surpress compiler warnings
    //if (sdm_version == 0.f){ cout << "too low version" << sdm_status; }
    //if (strcmp(sdm_status, "XX")){ cout << "Some"; }
    
}