int main(int argc, char **argv) {
byte_vector B;
vector C;
comp_matrix O;
comp_vector S, Scomp, R, Rcomp;
if (argc!=3) {
printf("Syntax:\n\t%s input_dir nucleotides\n", argv[0]);
return 1;
}
timevars();
initReplaceTable(argv[2]);
tic("Loading data structures from input directory");
readUIntVector(&C, argv[1], "C");
readCompMatrix(&O, argv[1], "O");
readCharVector(&B, argv[1], "B");
readUIntCompVector(&S, argv[1], "S");
readUIntCompVector(&Scomp, argv[1], "Scomp");
readUIntCompVector(&R, argv[1], "R");
readUIntCompVector(&Rcomp, argv[1], "Rcomp");
toc();
for (unsigned int i=0; i<S.n; i++) {
if (getScompValue(i, &Scomp, &C, &O) != S.vector[i]) {
printf("S diferent!\n");
}
if (getRcompValue(i, &Rcomp, &C, &O) != R.vector[i]) {
printf("R diferent!\n");
}
}
printf("Memory frees\n");
free(B.vector);
free(S.vector);
free(Scomp.vector);
free(R.vector);
free(Rcomp.vector);
return 0;
}
int write_results(results_list *r_list, exome* ex, comp_vector *S, comp_vector *Si, vector *C, comp_matrix *O, comp_matrix *Oi, char *mapping, int nW, int type, FILE *fp) {
result *r;
unsigned int index, key;
int enW;
int found=0;
char search[MAXLINE+1];
char mask[MAXLINE+1];
int direction;
search[0] = '\0';
strncat(search, mapping, nW);
for (size_t i=0;i<r_list->num_results; i++) { //TODO: Cigar code
r = &r_list->list[i];
mask[0] = '\0';
strncat(mask, init_mask, nW);
mask[nW] = '\0';
//enW = nW;
enW = r->end - r->start + 1; //Partial results
for (int rr=0; rr<r->num_mismatches; rr++) {
if (r->err_kind[rr]==DELETION)
enW--;
else if (r->err_kind[rr]==INSERTION)
enW++;
if (r->err_kind[rr]==DELETION)
mask[r->err_pos[rr]] = 'D';
else if (r->err_kind[rr]==MISMATCH)
mask[r->err_pos[rr]] = 'M';
else if (r->err_kind[rr]==INSERTION)
mask[r->err_pos[rr]] = 'I';
}
//printf("%lu %lu -> %d\n", r->k, r->l, r->err_kind[0]);
//printf("%d %d %d\n", r->start, r->pos, r->end);
//printf("\n");
//TODO: Añadir calculo de la mascara
for (size_t j=r->k; j<=r->l; j++) {
if (type) {
direction = r->dir;
} else {
direction = !r->dir;
}
if (S->ratio==1) {
if (direction)
key = Si->siz - Si->vector[j] - enW - 1;
else
key = S->vector[j];
} else {
if (direction)
key = Si->siz - getScompValue(j, Si, C, Oi) - enW -1;
else
key = getScompValue(j, S, C, O);
}
index = binsearch(ex->offset, ex->size, key);
if(key + enW <= ex->offset[index]) {
found = 1;
//printf("%lu\n", r_list->read_index);
fprintf(fp, "read_%u\t%c\t%s %u %s %s\n", r_list->read_index, plusminus[type], ex->chromosome + (index-1)*IDMAX, ex->start[index-1] + (key - ex->offset[index-1]), search, search /*mask*/);
//printf("read_%u\t%c\t%s %u %s %s\n", r_list->read_index, plusminus[type], ex->chromosome + (index-1)*IDMAX, ex->start[index-1] + (key - ex->offset[index-1]), search, mask);
}
}
}
return found;
}
