// Receive an alignment file, run chaining and output a chain file
void CompTool::run_chaining(const string file, ofstream& ofs, const int near_dist, const bool forward){
// Count alignments
ifstream ifs;
ifs.open(file.c_str());
if(!ifs.is_open()) {cout << "File not found\n> " << file << endl; exit(1);}
string line;
int num_alignment = 0;
getline(ifs, line); // Skip header
while(getline(ifs, line)) num_alignment++;
ifs.close();
// Load alignments
ifs.open(file.c_str());
getline(ifs, line); // Skip header
Alignment* alignments = new Alignment[num_alignment];
// TODO: Parse kmer-size from header and calculate end positions of matches
int* buf = new int[5];
for(int i = 0; i < num_alignment; i++){
for(int j = 0; j < 5; j++){
ifs >> buf[j];
}
alignments[i].set(buf);
}
delete[] buf;
// Run chaining
Chaining chaining(alignments, num_alignment, near_dist);
chaining.run();
chaining.output_major_chains(ofs);
}
void bsw2_chain_filter(const bsw2opt_t *opt, int len, bwtsw2_t *b[2])
{
hsaip_t *z[2], *chain[2];
int i, j, k, n[2], m[2];
char *flag;
// initialization
n[0] = b[0]->n; n[1] = b[1]->n;
z[0] = (hsaip_t*)calloc(n[0] + n[1], sizeof(hsaip_t));
z[1] = z[0] + n[0];
chain[0] = (hsaip_t*)calloc(n[0] + n[1], sizeof(hsaip_t));
for (k = j = 0; k < 2; ++k) {
for (i = 0; i < b[k]->n; ++i) {
bsw2hit_t *p = b[k]->hits + i;
hsaip_t *q = z[k] + i;
q->flag = k; q->idx = i;
q->tbeg = p->k; q->tend = p->k + p->len;
q->chain = -1;
q->qbeg = p->beg; q->qend = p->end;
}
}
// chaining
m[0] = chaining(opt, 0, n[0], z[0], chain[0]);
chain[1] = chain[0] + m[0];
m[1] = chaining(opt, m[0], n[1], z[1], chain[1]);
// change query coordinate on the reverse strand
for (k = 0; k < m[1]; ++k) {
hsaip_t *p = chain[1] + k;
int tmp = p->qbeg;
p->qbeg = len - p->qend; p->qend = len - tmp;
}
// filtering
flag = (char*)calloc(m[0] + m[1], 1);
ks_introsort(hsaip, m[0] + m[1], chain[0]);
for (k = 1; k < m[0] + m[1]; ++k) {
hsaip_t *p = chain[0] + k;
for (j = 0; j < k; ++j) {
hsaip_t *q = chain[0] + j;
if (flag[q->idx]) continue;
if (q->qend >= p->qend && q->chain > p->chain * opt->t_seeds * 2) {
flag[p->idx] = 1;
break;
}
}
}
for (k = 0; k < n[0] + n[1]; ++k) {
hsaip_t *p = z[0] + k;
if (flag[p->chain])
b[p->flag]->hits[p->idx].G = 0;
}
free(flag);
// squeeze out filtered elements in b[2]
for (k = 0; k < 2; ++k) {
for (j = i = 0; j < n[k]; ++j) {
bsw2hit_t *p = b[k]->hits + j;
if (p->G) {
if (i != j) b[k]->hits[i++] = *p;
else ++i;
}
}
b[k]->n = i;
}
// free
free(z[0]); free(chain[0]);
}