cigars.c

//YA HAGH
#include<cstdio>

const int READ_SIZE = 100;
int match_start[READ_SIZE] = {0, 4, 8, 13};
int match_index[READ_SIZE] = {2, 6, 9, 14};
int d[READ_SIZE][10];
char arr[READ_SIZE][10];
char tmp_cigar[READ_SIZE];
bool matched[READ_SIZE] = {1, 1, 1, 1};
int parts = 4;

char read[READ_SIZE] = "ACCCTAACCCGGA";
char ref[READ_SIZE] = "TTACCCGACCCGGA";

/*
char ref[READ_SIZE]="TT ACCC-GAC- CCGGA";
char read[READ_SIZE]=  "ACCC-TAAC-CCGGA";
*/
int smith_waterman(int part, char *cigar, int head) {
    const int off = 5;
    int i = 0, j = 0;
    for (i = off / 2; i < off; i++)
        d[0][i] = i - off / 2;

    fprintf(stderr, " : %d\n", match_index[part + 1] - match_index[part]);
    for (i = 1; i <= match_start[part + 1] - match_start[part]; i++) {
        for (j = 0; j < off; j++) {
            int real_off = j - off / 2;
            int ref_i = i + real_off;
            if (ref_i < 0)
                continue;
            if (ref_i == 0) {
                d[i][j] = i;
                continue;
            }

            d[i][j] = d[i - 1][j];
            arr[i][j] = 'm';
//			fprintf(stderr,"%c\n",ref[match_index[part]+ref_i-1]);
            if (ref[match_index[part] + ref_i - 1] != read[match_start[part] + i - 1]) {
                //			fprintf(stderr,"mismatched!\n");
                d[i][j]++;
            }
            if (j > 0 && (d[i][j] > d[i][j - 1] + 1)) {
                d[i][j] = d[i][j - 1] + 1;
                arr[i][j] = 'd';
            }
            if (j < off - 1 && (d[i][j] > d[i - 1][j + 1] + 1)) {
                d[i][j] = d[i - 1][j + 1] + 1;
                arr[i][j] = 'i';
            }
            fprintf(stderr, "i=%d, ref_i=%d, d=%d, arr=%c\n", i, ref_i, d[i][j], arr[i][j]);
        }
    }
    /* do ta tike darim mikhaym match konim,
       d[i][j]= read[match[start]] ta khode read[match[start]+i] ro ba
       ref[match[index]] ta khode ref[match[index]+ i + j
       */
    int cur_off = (match_index[part + 1] - match_index[part]) - (match_start[part + 1] - match_start[part]) + off / 2;
    int cur_i = match_start[part + 1] - match_start[part];
    /*	int best_d=d[match_start[part+1]-match_start[part]][0];

    	for (i=1; i<off; i++)
    	{
    			fprintf(stderr," ::: %d\n",d[match_start[part+1]-match_start[part]][i]);
    		if (d[match_start[part+1]-match_start[part]][i]<best_d)
    		{
    			best_d=d[match_start[part+1]-match_start[part]][i];
    			cur_off=i;
    		}
    	}
    */    fprintf(stderr, "curf off : %d\n", cur_off);

    fprintf(stderr, "d[ans] : %d\n", d[match_start[part + 1] - match_start[part]][cur_off]);
    int tail = 0;
    while (true) {
        int ref_i = cur_i + cur_off - off / 2;
        if (cur_i == 0) {
            for (j = 0; j < ref_i; j++)
                tmp_cigar[tail++] = 'd';
            break;
        }
        if (ref_i == 0) {

            fprintf(stderr, "heey %d %d\n", cur_i, cur_off);
            for (j = 0; j < cur_i; j++)
                tmp_cigar[tail++] = 'i';
            break;
        }
        tmp_cigar[tail++] = arr[cur_i][cur_off];
        if (arr[cur_i][cur_off] == 'i') {
            cur_off++;
            cur_i--;
        } else if (arr[cur_i][cur_off] == 'd') {
            cur_off--;
        } else if (arr[cur_i][cur_off] == 'm') {
            cur_i--;
        }
        fprintf(stderr, "bug %d %d\n", cur_i, cur_off);
        fprintf(stderr, "%c", tmp_cigar[tail - 1]);
    }
    tmp_cigar[tail] = 0;
    fprintf(stderr, "%s\n", tmp_cigar);
    int ct = 0;
    char last = tmp_cigar[tail - 1];
    for (i = tail - 1; i >= -1; i--) {

        fprintf(stderr, "-- %d\n", tail);

        if (i >= 0 && tmp_cigar[i] == last)
            ct++;
        else {
            head += snprintf(cigar + head, 4, "%d%c", ct, last);
            last = tmp_cigar[i];
            ct = 1;
        }
    }
    printf("%s\n", cigar);
    return head;
}
// -----+++++++
//*----***++++++
/*
char ref[READ_SIZE]="TT ACCC-GAC- CCGGA";
char read[READ_SIZE]=  "ACCC-TAAC-CCGGA";
*/
void build_cigar(char *cigar) {
    int i = 0;
    int head = 0;
    fprintf(stderr, "%d\n", parts);
    for (i = 0; i < parts - 1; i++) //TODO:check if reverse and if reversed check all the code
    {
        if (matched[i]) {
            /*			int shift=0;
            			if (i>0 && matched[i-1])
            				shift=(match_index[i] - match_index[i-1]) - (match_start[i]-match_start[i-1]);
            			fprintf(stderr,"shift = %d %d %d\n",shift,i,match_index[i]);
            			if (shift>0)
            				head+=snprintf(cigar+head,4,"%di",shift);
            			if (shift<0)
            				head+=snprintf(cigar+head,4,"%dd",-shift);*/
            int ref_len = match_index[i + 1] - match_index[i];
            int read_len = match_start[i + 1] - match_start[i];
            int min_len = ref_len;
            if (read_len < min_len)
                min_len = read_len;
            head += snprintf(cigar + head, 4, "%dm", min_len);
            if (ref_len < read_len)
                head += snprintf(cigar + head, 4, "%di", read_len - ref_len);
            if (ref_len > read_len)
                head += snprintf(cigar + head, 4, "%dd", ref_len - read_len);
        } else {
            head = smith_waterman(i, cigar, head);
        }
    }
}

int main() {
    char cigar[200];
    cigar[0] = 0;
    build_cigar(cigar);
    printf("%s\n", cigar);
    return 0;
}