// creat Chan's hull
void
shape_build_hull(shape_t* shape) {
assert(shape!= NULL);
points_v hull;
kv_init(hull);
kv_copy(point_t, hull, shape->points);
uint32_t s = chanhull(hull.a, hull.n);
uint32_t l = hull.n-s;
// copy part of points vector
kv_resize(point_t, shape->hull, l+1);
shape->hull.n = l+1;
// memcpy(shape->hull.a, hull.a+s, sizeof(point_t)*l);
// shape->hull.a[l] = *(hull.a+s);
// revert point direction
for(uint32_t i=0; i<=l;i++) {
shape->hull.a[l-i] = hull.a[s+i%l];
}
kv_destroy(hull);
}
static aln_v align_read(const kseq_t *read,
const kseq_v targets,
const align_config_t *conf)
{
kseq_t *r;
const int32_t read_len = read->seq.l;
aln_v result;
kv_init(result);
kv_resize(aln_t, result, kv_size(targets));
uint8_t *read_num = calloc(read_len, sizeof(uint8_t));
for(size_t k = 0; k < read_len; ++k)
read_num[k] = conf->table[(int)read->seq.s[k]];
// Align to each target
kswq_t *qry = NULL;
for(size_t j = 0; j < kv_size(targets); j++) {
// Encode target
r = &kv_A(targets, j);
uint8_t *ref_num = calloc(r->seq.l, sizeof(uint8_t));
for(size_t k = 0; k < r->seq.l; ++k)
ref_num[k] = conf->table[(int)r->seq.s[k]];
aln_t aln;
aln.target_idx = j;
aln.loc = ksw_align(read_len, read_num,
r->seq.l, ref_num,
conf->m,
conf->mat,
conf->gap_o,
conf->gap_e,
KSW_XSTART,
&qry);
ksw_global(aln.loc.qe - aln.loc.qb + 1,
&read_num[aln.loc.qb],
aln.loc.te - aln.loc.tb + 1,
&ref_num[aln.loc.tb],
conf->m,
conf->mat,
conf->gap_o,
conf->gap_e,
50, /* TODO: Magic number - band width */
&aln.n_cigar,
&aln.cigar);
aln.nm = 0;
size_t qi = aln.loc.qb, ri = aln.loc.tb;
for(size_t k = 0; k < aln.n_cigar; k++) {
const int32_t oplen = bam_cigar_oplen(aln.cigar[k]),
optype = bam_cigar_type(aln.cigar[k]);
if(optype & 3) { // consumes both - check for mismatches
for(size_t j = 0; j < oplen; j++) {
if(UNLIKELY(read_num[qi + j] != ref_num[ri + j]))
aln.nm++;
}
} else {
aln.nm += oplen;
}
if(optype & 1) qi += oplen;
if(optype & 2) ri += oplen;
}
kv_push(aln_t, result, aln);
free(ref_num);
}
free(qry);
free(read_num);
ks_introsort(dec_score, kv_size(result), result.a);
return result;
}
static aln_v align_read(const kseq_t *read, const kseq_v targets,
const size_t n_extra_targets,
const kseq_v *extra_targets,
const align_config_t *conf) {
kseq_t *r;
const int32_t read_len = read->seq.l;
aln_v result;
kv_init(result);
kv_resize(aln_t, result, kv_size(targets));
uint8_t *read_num = calloc(read_len, sizeof(uint8_t));
for (int k = 0; k < read_len; ++k)
read_num[k] = conf->table[(int)read->seq.s[k]];
// Align to each target
kswq_t *qry = NULL;
int min_score = -1000;
int max_score = 0;
for (size_t j = 0; j < kv_size(targets); j++) {
// Encode target
r = &kv_A(targets, j);
aln_t aln =
align_read_against_one(r, read_len, read_num, &qry, conf, min_score);
if (aln.cigar != NULL) {
max_score = aln.loc.score > max_score ? aln.loc.score : max_score;
min_score = (aln.loc.score - conf->max_drop) > min_score
? (aln.loc.score - conf->max_drop)
: min_score;
kv_push(aln_t, result, aln);
}
}
/* If no alignments to the first set of targets reached the minimum score,
* abort.
*/
if (max_score < conf->min_score) {
// kv_size returns the n field of a kvec_t, which is a size_t.
for (size_t i = 0; i < kv_size(result); i++)
free(kv_A(result, i).cigar);
kv_size(result) = 0;
free(qry);
free(read_num);
return result;
}
drop_low_scores(&result, 0, conf->max_drop);
// Extra references - qe points to the exact end of the sequence
int qend = kv_A(result, 0).loc.qe + 1;
int read_len_trunc = read_len - qend;
uint8_t *read_num_trunc = read_num + qend;
free(qry);
qry = NULL;
if (read_len_trunc > 2) {
for (size_t i = 0; i < n_extra_targets; i++) {
const size_t idx = n_extra_targets - i - 1;
min_score = -1000;
const size_t init_count = kv_size(result);
for (size_t j = 0; j < kv_size(extra_targets[idx]); j++) {
r = &kv_A(extra_targets[idx], j);
aln_t aln = align_read_against_one(r, read_len_trunc, read_num_trunc,
&qry, conf, min_score);
if (aln.cigar != NULL) {
min_score = (aln.loc.score - conf->max_drop) > min_score
? (aln.loc.score - conf->max_drop)
: min_score;
aln.loc.qb += qend;
aln.loc.qe += qend;
kv_push(aln_t, result, aln);
}
}
drop_low_scores(&result, init_count, conf->max_drop);
/* Truncate */
const int alen =
kv_A(result, init_count).loc.qe - kv_A(result, init_count).loc.qb;
read_len_trunc = read_len_trunc - alen;
free(qry);
qry = NULL;
}
}
free(qry);
free(read_num);
return result;
}
