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ont simplex support

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chhylp123
2024-11-27 13:27:13 -05:00
parent 80fa5ed436
commit 676385cf8e
10 changed files with 896 additions and 88 deletions
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Correct.cpp
+108 -2
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@@ -24531,7 +24531,108 @@ void reassign_gaps(overlap_region *z, overlap_region *aux, char* qstr, int64_t q
// }
}
void gen_hc_r_alin(overlap_region_alloc* ol, Candidates_list *cl, All_reads *rref, UC_Read* qu, UC_Read* tu, bit_extz_t *exz, overlap_region *aux_o, double e_rate, int64_t wl, int64_t rid, int64_t khit, int64_t move_gap, asg16_v* buf)
uint32_t is_ovlp_debug(int64_t s, int64_t e, int64_t ws, int64_t we, int64_t op)
{
int64_t os, oe, ovlp;
os = MAX(s, ws); oe = MIN(e, we);
ovlp = ((oe>os)? (oe-os):0);
if(op != 2) {
return (!!ovlp);
} else {
if(ws >= s && we <= e) return 1;
}
return 0;
}
uint32_t inline ff_tend(overlap_region *z, int64_t wn, int64_t dn, double dr, double er, int64_t min_err)
{
int64_t k, zwn = z->w_list.n, err, mm, qi, ci, cn, ql, ws, we, zs, ze, s, e, os, oe, ovlp; bit_extz_t ez; uint32_t cl; uint16_t c;
zs = z->x_pos_s; ze = z->x_pos_e + 1; ql = ze - zs;
if(ql < wn) return 0; if(dn > (ql*dr)) dn = ql*dr; if(dn < wn) return 0; if(ql < dn) return 0;
s = zs; e = zs + dn;
// if(z->y_id == 27) fprintf(stderr, "-a-[M::%s] tid::%u\t%.*s\tz::[%ld,%ld)\ti::[%ld,%ld)\n", __func__, z->y_id, (int)Get_NAME_LENGTH(R_INF, z->y_id), Get_NAME(R_INF, z->y_id), zs, ze, s, e);
for (k = err = mm = 0, qi = zs; (k < zwn) && (z->w_list.a[k].x_start < e); k++) {
// if(z->y_id == 27) fprintf(stderr, "-a-[M::%s] tid::%u\t%.*s\tw::[%d,%d)\terr::%d\n", __func__, z->y_id, (int)Get_NAME_LENGTH(R_INF, z->y_id), Get_NAME(R_INF, z->y_id), z->w_list.a[k].x_start, z->w_list.a[k].x_end + 1, z->w_list.a[k].error);
if(!(is_ualn_win(z->w_list.a[k]))) {
set_bit_extz_t(ez, (*z), k);
ci = 0; cn = ez.cigar.n; qi = ez.ts; //ti = ez.ps;
while (ci < cn && qi < e) {
ws = qi;
ci = pop_trace(&(ez.cigar), ci, &c, &cl);
if(c!=2) qi += cl;
// if(c!=3) ti += cl;
we = qi;
if(c == 0) {
os = MAX(s, ws); oe = MIN(e, we);
ovlp = ((oe>os)? (oe-os):0); mm += ovlp;
} else {
err += cl;
}
// assert(is_ovlp_debug(s, e, ws, we, c));
if((err > min_err) && ((mm + err) > wn) && (err > ((mm + err)*er))) {
// fprintf(stderr, "-0-[M::%s] tid::%u\t%.*s\tmm::%ld\terr::%ld\tdn::%ld\twn::%ld\tdif::%f\n", __func__, z->y_id, (int)Get_NAME_LENGTH(R_INF, z->y_id), Get_NAME(R_INF, z->y_id), mm, err, dn, wn, er);
return 1;
}
}
} else {
ws = z->w_list.a[k].x_start; we = z->w_list.a[k].x_end + 1;
err += we - ws;
// assert(is_ovlp_debug(s, e, ws, we, -1));
if((err > min_err) && ((mm + err) > wn) && (err > ((mm + err)*er))) {
// fprintf(stderr, "-1-[M::%s] tid::%u\t%.*s\tmm::%ld\terr::%ld\tdn::%ld\twn::%ld\tdif::%f\n", __func__, z->y_id, (int)Get_NAME_LENGTH(R_INF, z->y_id), Get_NAME(R_INF, z->y_id), mm, err, dn, wn, er);
return 1;
}
}
}
s = ze - dn; e = ze;
for (k = zwn - 1, err = mm = 0, qi = ze; (k >= 0) && ((z->w_list.a[k].x_end + 1) > s); k--) {
if(!(is_ualn_win(z->w_list.a[k]))) {
set_bit_extz_t(ez, (*z), k);
ci = ((int64_t)ez.cigar.n) - 1; qi = ez.te + 1; //ti = ez.pe + 1;
while (ci >= 0 && qi > s) {
we = qi;
ci = pop_trace_back(&(ez.cigar), ci, &c, &cl);
if(c!=2) qi -= cl;
// if(c!=3) ti += cl;
ws = qi;
if(c == 0) {
os = MAX(s, ws); oe = MIN(e, we);
ovlp = ((oe>os)? (oe-os):0); mm += ovlp;
} else {
err += cl;
}
// assert(is_ovlp_debug(s, e, ws, we, c));
if((err > min_err) && ((mm + err) > wn) && (err > ((mm + err)*er))) {
// fprintf(stderr, "-2-[M::%s] tid::%u\t%.*s\tmm::%ld\terr::%ld\tdn::%ld\twn::%ld\tdif::%f\n", __func__, z->y_id, (int)Get_NAME_LENGTH(R_INF, z->y_id), Get_NAME(R_INF, z->y_id), mm, err, dn, wn, er);
return 1;
}
}
} else {
ws = z->w_list.a[k].x_start; we = z->w_list.a[k].x_end + 1;
err += we - ws;
// assert(is_ovlp_debug(s, e, ws, we, -1));
if((err > min_err) && ((mm + err) > wn) && (err > ((mm + err)*er))) {
// fprintf(stderr, "-3-[M::%s] tid::%u\t%.*s\tmm::%ld\terr::%ld\tdn::%ld\twn::%ld\tdif::%f\n", __func__, z->y_id, (int)Get_NAME_LENGTH(R_INF, z->y_id), Get_NAME(R_INF, z->y_id), mm, err, dn, wn, er);
return 1;
}
}
}
return 0;
}
void gen_hc_r_alin(overlap_region_alloc* ol, Candidates_list *cl, All_reads *rref, UC_Read* qu, UC_Read* tu, bit_extz_t *exz, overlap_region *aux_o, double e_rate, int64_t wl, int64_t rid, int64_t khit, int64_t move_gap, asg16_v* buf, uint8_t chem_drop)
{
uint64_t i, bs, k, ql = qu->length; Window_Pool w; double err, e_max, rr; int64_t re;
overlap_region t; overlap_region *z; //asg64_v iidx, buf, buf1;
@@ -24565,6 +24666,9 @@ void gen_hc_r_alin(overlap_region_alloc* ol, Candidates_list *cl, All_reads *rre
if(!gen_hc_fast_cigar(z, cl, rref, w.window_length, qu->seq, tu, exz, aux_o, e_rate, ql, rid, khit, &re)) continue;
if(chem_drop && ff_tend(z, 384, 2000, 0.1, (((e_rate*10)<0.36)?(e_rate*10):(0.36)), 128)) continue;
// if(z->x_id == 3196 && z->y_id == 3199) fprintf(stderr, "-1-[M::%s] tid::%u\t%.*s\trr::%f\tre::%ld\n", __func__, z->y_id, (int)Get_NAME_LENGTH(R_INF, z->y_id), Get_NAME(R_INF, z->y_id), rr, re);
reassign_gaps(z, aux_o, qu->seq, ql, NULL, -1, rref, tu, buf);
@@ -24586,7 +24690,7 @@ void gen_hc_r_alin(overlap_region_alloc* ol, Candidates_list *cl, All_reads *rre
}
void gen_hc_r_alin_nec(overlap_region_alloc* ol, Candidates_list *cl, All_reads *rref, UC_Read* qu, UC_Read* tu, bit_extz_t *exz, overlap_region *aux_o, double e_rate, int64_t wl, int64_t rid, int64_t khit, int64_t move_gap, asg16_v* buf)
void gen_hc_r_alin_nec(overlap_region_alloc* ol, Candidates_list *cl, All_reads *rref, UC_Read* qu, UC_Read* tu, bit_extz_t *exz, overlap_region *aux_o, double e_rate, int64_t wl, int64_t rid, int64_t khit, int64_t move_gap, asg16_v* buf, uint8_t chem_drop)
{
uint64_t i, bs, k, ql = qu->length; Window_Pool w; double err, e_max, rr; int64_t re;
overlap_region t; overlap_region *z; //asg64_v iidx, buf, buf1;
@@ -24628,6 +24732,8 @@ void gen_hc_r_alin_nec(overlap_region_alloc* ol, Candidates_list *cl, All_reads
if(!gen_hc_fast_cigar(z, cl, rref, w.window_length, qu->seq, tu, exz, aux_o, e_rate, ql, rid, khit, &re)) continue;
if(chem_drop && ff_tend(z, 384, 2000, 0.1, (((e_rate*10)<0.36)?(e_rate*10):(0.36)), 128)) continue;
// if(z->x_id == 3196 && z->y_id == 3199) fprintf(stderr, "-1-[M::%s] tid::%u\t%.*s\trr::%f\tre::%ld\n", __func__, z->y_id, (int)Get_NAME_LENGTH(R_INF, z->y_id), Get_NAME(R_INF, z->y_id), rr, re);
///debug for memory
// snprintf(NULL, 0, "dwn::%u\tdcn::%u", (uint32_t)aux_o->w_list.n, (uint32_t)aux_o->w_list.c.n);