void bsw2_extend_rght(const bsw2opt_t *opt, bwtsw2_t *b, uint8_t *query, int lq, uint8_t *pac, bwtint_t l_pac, uint8_t *_mem)
{
int i, matrix[25];
bwtint_t k;
uint8_t *target;
AlnParam par;
par.matrix = matrix;
__gen_ap(par, opt);
target = calloc(((lq + 1) / 2 * opt->a + opt->r) / opt->r + lq, 1);
for (i = 0; i < b->n; ++i) {
bsw2hit_t *p = b->hits + i;
int lt = ((lq - p->beg + 1) / 2 * opt->a + opt->r) / opt->r + lq;
int j, score;
path_t path;
if (p->l) continue;
for (k = p->k, j = 0; k < p->k + lt && k < l_pac; ++k)
target[j++] = pac[k>>2] >> (~k&3)*2 & 0x3;
lt = j;
score = aln_extend_core(target, lt, query + p->beg, lq - p->beg, &par, &path, 0, 1, _mem);
// if (score < p->G) fprintf(stderr, "[bsw2_extend_hits] %d < %d\n", score, p->G);
if (score >= p->G) {
p->G = score;
p->len = path.i;
p->end = path.j + p->beg;
}
}
free(target);
}
void bsw2_extend_left(const bsw2opt_t *opt, bwtsw2_t *b, uint8_t *_query, int lq, uint8_t *pac, uint32_t l_pac, int is_rev, uint8_t *_mem)
{
int i, matrix[25];
bwtint_t k;
uint8_t *target = 0, *query;
AlnParam par;
par.matrix = matrix;
__gen_ap(par, opt);
query = calloc(lq, 1);
// sort according to the descending order of query end
ks_introsort(hit, b->n, b->hits);
target = calloc(((lq + 1) / 2 * opt->a + opt->r) / opt->r + lq, 1);
// reverse _query
for (i = 0; i < lq; ++i) query[lq - i - 1] = _query[i];
// core loop
for (i = 0; i < b->n; ++i) {
bsw2hit_t *p = b->hits + i;
int lt = ((p->beg + 1) / 2 * opt->a + opt->r) / opt->r + lq;
int score, j;
path_t path;
p->n_seeds = 1;
if (p->l || p->k == 0) continue;
for (j = score = 0; j < i; ++j) {
bsw2hit_t *q = b->hits + j;
if (q->beg <= p->beg && q->k <= p->k && q->k + q->len >= p->k + p->len) {
if (q->n_seeds < (1<<14) - 2) ++q->n_seeds;
++score;
}
}
if (score) continue;
if (lt > p->k) lt = p->k;
if (is_rev) {
for (k = p->k - 1, j = 0; k > 0 && j < lt; --k) // FIXME: k=0 not considered!
target[j++] = __rpac(pac, l_pac, k);
} else {
for (k = p->k - 1, j = 0; k > 0 && j < lt; --k) // FIXME: k=0 not considered!
target[j++] = pac[k>>2] >> (~k&3)*2 & 0x3;
}
lt = j;
score = aln_extend_core(target, lt, query + lq - p->beg, p->beg, &par, &path, 0, p->G, _mem);
if (score > p->G) { // extensible
p->G = score;
p->len += path.i;
p->beg -= path.j;
p->k -= path.i;
}
}
free(query); free(target);
}
/* generate CIGAR array(s) in b->cigar[] */
static void gen_cigar(const bsw2opt_t *opt, int lq, uint8_t *seq[2], uint8_t *pac, bwtsw2_t *b)
{
uint8_t *target;
int i, matrix[25];
AlnParam par;
path_t *path;
par.matrix = matrix;
__gen_ap(par, opt);
i = ((lq + 1) / 2 * opt->a + opt->r) / opt->r + lq; // maximum possible target length
target = calloc(i, 1);
path = calloc(i + lq, sizeof(path_t));
// memory clean up for b
if (b->n < b->max) {
b->max = b->n;
b->hits = realloc(b->hits, b->n * sizeof(bsw2hit_t));
}
if (b->cigar) free(b->cigar);
if (b->n_cigar) free(b->n_cigar);
b->cigar = (uint32_t**)calloc(b->max, sizeof(void*));
b->n_cigar = (int*)calloc(b->max, sizeof(int));
// generate CIGAR
for (i = 0; i < b->n; ++i) {
bsw2hit_t *p = b->hits + i;
uint8_t *query;
uint32_t k;
int score, path_len, beg, end;
if (p->l) continue;
beg = (p->flag & 0x10)? lq - p->end : p->beg;
end = (p->flag & 0x10)? lq - p->beg : p->end;
query = seq[(p->flag & 0x10)? 1 : 0] + beg;
for (k = p->k; k < p->k + p->len; ++k) // in principle, no out-of-boundary here
target[k - p->k] = pac[k>>2] >> (~k&3)*2 & 0x3;
score = aln_global_core(target, p->len, query, end - beg, &par, path, &path_len);
b->cigar[i] = aln_path2cigar32(path, path_len, &b->n_cigar[i]);
if (beg != 0 || end < lq) { // write soft clipping
b->cigar[i] = realloc(b->cigar[i], 4 * (b->n_cigar[i] + 2));
if (beg != 0) {
memmove(b->cigar[i] + 1, b->cigar[i], b->n_cigar[i] * 4);
b->cigar[i][0] = beg<<4 | 4;
++b->n_cigar[i];
}
if (end < lq) {
b->cigar[i][b->n_cigar[i]] = (lq - end)<<4 | 4;
++b->n_cigar[i];
}
}
}
free(target); free(path);
}
/* generate CIGAR array(s) in b->cigar[] */
static void gen_cigar(const bsw2opt_t *opt, int lq, uint8_t *seq[2], const uint8_t *pac, bwtsw2_t *b, const char *name)
{
uint8_t *target;
int i, matrix[25];
AlnParam par;
path_t *path;
par.matrix = matrix;
__gen_ap(par, opt);
i = ((lq + 1) / 2 * opt->a + opt->r) / opt->r + lq; // maximum possible target length
target = calloc(i, 1);
path = calloc(i + lq, sizeof(path_t));
// generate CIGAR
for (i = 0; i < b->n; ++i) {
bsw2hit_t *p = b->hits + i;
bsw2aux_t *q = b->aux + i;
uint8_t *query;
bwtint_t k;
int path_len, beg, end;
if (p->l) continue;
beg = (p->flag & 0x10)? lq - p->end : p->beg;
end = (p->flag & 0x10)? lq - p->beg : p->end;
query = seq[(p->flag & 0x10)? 1 : 0] + beg;
for (k = p->k; k < p->k + p->len; ++k) // in principle, no out-of-boundary here
target[k - p->k] = pac[k>>2] >> (~k&3)*2 & 0x3;
aln_global_core(target, p->len, query, end - beg, &par, path, &path_len);
q->cigar = aln_path2cigar32(path, path_len, &q->n_cigar);
#if 0
if (name && score != p->G) { // debugging only
int j, glen = 0;
for (j = 0; j < q->n_cigar; ++j)
if ((q->cigar[j]&0xf) == 1 || (q->cigar[j]&0xf) == 2)
glen += q->cigar[j]>>4;
fprintf(stderr, "[E::%s] %s - unequal score: %d != %d; (qlen, aqlen, arlen, glen, bw) = (%d, %d, %d, %d, %d)\n",
__func__, name, score, p->G, lq, end - beg, p->len, glen, opt->bw);
}
#endif
if (beg != 0 || end < lq) { // write soft clipping
q->cigar = realloc(q->cigar, 4 * (q->n_cigar + 2));
if (beg != 0) {
memmove(q->cigar + 1, q->cigar, q->n_cigar * 4);
q->cigar[0] = beg<<4 | 4;
++q->n_cigar;
}
if (end < lq) {
q->cigar[q->n_cigar] = (lq - end)<<4 | 4;
++q->n_cigar;
}
}
}
/* generate CIGAR array(s) in b->cigar[] */
static void gen_cigar(const bsw2opt_t *opt, int lq, uint8_t *seq[2], const uint8_t *pac, bwtsw2_t *b)
{
uint8_t *target;
int i, matrix[25];
AlnParam par;
path_t *path;
par.matrix = matrix;
__gen_ap(par, opt);
i = ((lq + 1) / 2 * opt->a + opt->r) / opt->r + lq; // maximum possible target length
target = calloc(i, 1);
path = calloc(i + lq, sizeof(path_t));
// generate CIGAR
for (i = 0; i < b->n; ++i) {
bsw2hit_t *p = b->hits + i;
bsw2aux_t *q = b->aux + i;
uint8_t *query;
bwtint_t k;
int score, path_len, beg, end;
if (p->l) continue;
beg = (p->flag & 0x10)? lq - p->end : p->beg;
end = (p->flag & 0x10)? lq - p->beg : p->end;
query = seq[(p->flag & 0x10)? 1 : 0] + beg;
for (k = p->k; k < p->k + p->len; ++k) // in principle, no out-of-boundary here
target[k - p->k] = pac[k>>2] >> (~k&3)*2 & 0x3;
score = aln_global_core(target, p->len, query, end - beg, &par, path, &path_len);
q->cigar = aln_path2cigar32(path, path_len, &q->n_cigar);
if (beg != 0 || end < lq) { // write soft clipping
q->cigar = realloc(q->cigar, 4 * (q->n_cigar + 2));
if (beg != 0) {
memmove(q->cigar + 1, q->cigar, q->n_cigar * 4);
q->cigar[0] = beg<<4 | 4;
++q->n_cigar;
}
if (end < lq) {
q->cigar[q->n_cigar] = (lq - end)<<4 | 4;
++q->n_cigar;
}
}
}
free(target); free(path);
}
