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phasing speedup

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chhylp123
2026-04-11 22:33:18 -04:00
parent 815d709fb9
commit ba8627fb23
13 changed files with 1055 additions and 186 deletions
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56
Process_Read.cpp
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@@ -1843,6 +1843,62 @@ void retrieve_u_seq(UC_Read* i_r, char* i_s, ma_utg_t *u, uint8_t strand, int64_
}
}
void retrieve_u_seq_fast(UC_Read* i_r, char* i_s, ma_utg_t *u, uint8_t strand, int64_t s, int64_t l, void *km)
{
if(u->m == 0 || u->n == 0) return;
if(l < 0) l = u->len;
char *r = NULL, *a = NULL;
int64_t e = s + l, ssp, sep, rs, re, des_i;
uint64_t k, rId, ori, r_l;
if(i_r) {
i_r->length = l; i_r->RID = 0;
if(i_r->length > i_r->size) {
i_r->size = i_r->length;
if(!km) REALLOC(i_r->seq, i_r->size);
else KREALLOC(km, i_r->seq, i_r->size);
// i_r->seq = (char*)realloc(i_r->seq,sizeof(char)*(i_r->size));
}
r = i_r->seq;
}
if(i_s) r = i_s;
if(u->s) {
memcpy(r, u->s + s, l * sizeof((*(u->s))));
} else {
if(strand == 1) {
sep = u->len - s;
ssp = u->len - e;
s = ssp; e = sep;
}
for (k = l = des_i = 0; k < u->n; k++) {
rId = u->a[k]>>33;
ori = u->a[k]>>32&1;
r_l = (uint32_t)u->a[k];
if(r_l == 0) continue;
ssp = l; sep = l + r_l;
l += r_l;
if(sep <= s) continue;
if(ssp >= e) break;
rs = MAX(ssp, s); re = MIN(sep, e);
a = r + des_i; des_i += re - rs;
recover_UC_Read_sub_region(a, rs-ssp, re-rs, ori, &R_INF, rId);
}
}
if(strand == 1) {
char t;
re = (e - s);
l = re>>1;
for (k = 0; k < (uint64_t)l; k++) {
des_i = re - k - 1;
t = r[des_i];
r[des_i] = RC_CHAR(r[k]);
r[k] = RC_CHAR(t);
}
if(re&1) r[l] = RC_CHAR(r[l]);
}
}
uint32_t retrieve_u_cov(const ul_idx_t *ul, uint64_t id, uint8_t strand, uint64_t pos, uint8_t dir, int64_t *pi)
{
uint64_t *a = ul->cc->interval.a + ul->cc->idx[id], cc = 0, ff = 0;