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chhylp123
2025-03-14 01:40:21 -04:00
parent a96191560e
commit b3b18ab1d0
4 changed files with 246 additions and 29 deletions
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Correct.cpp
+103 -17
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@@ -17423,11 +17423,11 @@ bit_extz_t *exz, overlap_region *aux_o, double e_rate, int64_t ql, int64_t tl, u
void hc_ovlp_base_direct(overlap_region *z, k_mer_hit *ch_a, int64_t ch_n, int64_t wl, All_reads *rref, char* qstr, UC_Read *tu,
bit_extz_t *exz, overlap_region *aux_o, double e_rate, int64_t ql, int64_t tl, uint64_t rid)
bit_extz_t *exz, overlap_region *aux_o, double e_rate, int64_t ql, int64_t tl, uint64_t rid, int64_t pre_mode)
{
int64_t i, l, mode, q[2], t[2], qr, tr, is_done, zn;
int64_t i, l, mode, q[2], t[2], qr, tr, is_done, zn, si, ei;
if(z->non_homopolymer_errors == 0 && z->w_list.n) {
if((pre_mode < 0) && (z->non_homopolymer_errors == 0) && (z->w_list.n)) {
zn = z->w_list.n;
for (i = 1; i < zn; i++) {
if((z->w_list.a[i].error == 0 && z->w_list.a[i-1].error == 0) && (z->w_list.a[i].x_start == z->w_list.a[i-1].x_end + 1) &&
@@ -17461,7 +17461,16 @@ bit_extz_t *exz, overlap_region *aux_o, double e_rate, int64_t ql, int64_t tl, u
}
}
for (l = -1, i = 0; i <= ch_n; i++) {
si = 0; ei = ch_n;
if(pre_mode == 0) {
si = 1; ei = ch_n - 1;
} else if(pre_mode == 1) {
si = 1;
} else if(pre_mode == 2) {
ei = ch_n - 1;
}
for (l = si - 1, i = si; i <= ei; i++) {
q[0] = q[1] = t[0] = t[1] = mode = -1; is_done = 0;
if(l >= 0) {
q[0] = ch_a[l].self_offset; t[0] = ch_a[l].offset;
@@ -17702,7 +17711,7 @@ All_reads *rref, char* qstr, UC_Read *tu, bit_extz_t *exz, double e_rate, int64_
// idx.qs, idx.qe, idx.ts, idx.te, idx.qn, idx.tn);
// }
// ovlp_base_aln(z, ch_a, ch_n, &idx, wl, uref, hpc_g, rref, qstr, tu, exz, aux_o, e_rate, ql, tl, (uint64_t)-1);
hc_ovlp_base_direct(z, ch_a, ch_n, wl, rref, qstr, tu, exz, aux_o, e_rate, ql, tl, (uint64_t)-1);
hc_ovlp_base_direct(z, ch_a, ch_n, wl, rref, qstr, tu, exz, aux_o, e_rate, ql, tl, (uint64_t)-1, mode);
an = aux_o->w_list.n; q[0] = q[1] = t[0] = t[1] = 0; todo = 0;
// if(z->x_id == 29033 && z->y_id == 21307) {
// fprintf(stderr, "[M::%s]\tan::%ld\n", __func__, an);
@@ -17820,11 +17829,17 @@ uint64_t gen_hc_fast_cigar0(overlap_region *z, Candidates_list *cl, uint64_t wl,
aux_o->x_pos_s = z->x_pos_s; aux_o->x_pos_e = z->x_pos_e;
aux_o->y_pos_s = z->y_pos_s; aux_o->y_pos_e = z->y_pos_e;
hc_ovlp_base_direct(z, ch_a, ch_n, wl, rref, qstr, tu, exz, aux_o, e_rate, ql, tl, rid);
hc_ovlp_base_direct(z, ch_a, ch_n, wl, rref, qstr, tu, exz, aux_o, e_rate, ql, tl, rid, -1);
int64_t aux_n = aux_o->w_list.n;
for (i = 0; i < aux_n; i++) {
// if(z->y_id == 30129) {
// fprintf(stderr, "[aln::-i->%ld::ql->%d] q::[%d, %d), t::[%d, %d), err::%d, clen::%u, mode::%d\n", i,
// aux_o->w_list.a[i].x_end+1-aux_o->w_list.a[i].x_start,
// aux_o->w_list.a[i].x_start, aux_o->w_list.a[i].x_end+1,
// aux_o->w_list.a[i].y_start, aux_o->w_list.a[i].y_end+1,
// aux_o->w_list.a[i].error, aux_o->w_list.a[i].clen, aux_o->w_list.a[i].error_threshold);
// }
if(!(is_ualn_win(aux_o->w_list.a[i]))) continue;
// if((aux_o->w_list.a[i].x_end+1-aux_o->w_list.a[i].x_start) <= FORCE_CNS_L) {
// fprintf(stderr, "[aln::-i->%ld::ql->%d] q::[%d, %d), t::[%d, %d), err::%d, clen::%u, mode::%d\n", i,
@@ -19761,7 +19776,7 @@ inline uint64_t set_cgid(ul_ov_t *z, uint64_t *ia, uint64_t *iak, uint64_t ian,
}
///need to print some examples for double check
uint64_t is_get_group(ul_ov_t *a, uint64_t *ga, uint64_t *ia, uint64_t gi, uint64_t tn)
uint64_t is_get_group(ul_ov_t *a/**, uint64_t an, uint64_t rid**/, uint64_t *ga, uint64_t *ia, uint64_t gi, uint64_t tn)
{
// fprintf(stderr, "+[M::%s] gi::%lu\n", __func__, gi);
uint64_t k = ga[gi]>>32;
@@ -19771,7 +19786,10 @@ uint64_t is_get_group(ul_ov_t *a, uint64_t *ga, uint64_t *ia, uint64_t gi, uint6
// fprintf(stderr, "-[M::%s] k::%lu\n", __func__, k);
// }
for (k = ga[gi]>>32; (k != ((uint64_t)-1)) && (a[k].tn != tn); k = ia[k]);
if((k != ((uint32_t)-1)) && (a[k].tn == tn)) return 0;
// if((k != ((uint32_t)-1)) && (k >= an)) {
// fprintf(stderr, "-[M::%s] rid::%lu, an::%lu, k::%lu\n", __func__, rid, an, k);
// }
if((k != ((uint64_t)-1)) && (a[k].tn == tn)) return 0;
return 1;
}
@@ -19867,12 +19885,13 @@ int64_t rphase_lidel_cc(overlap_region_alloc* oa, ul_ov_t *a, int64_t an, double
ol = (a[k].qe - a[k].qs) * len_st; if(ol < len_w) ol = len_w;
if((a[k].qe - a[k].qs) < ol) continue;
mk = -1; msw = -1;
for (z = k + 1; (z < an) && (a[z].qs < a[k].qe); z++) {
for (z = 0/**k + 1**/; (z < an) && (a[z].qs < a[k].qe); z++) {
if(a[z].sec < c_sz) continue;
if(a[z].ts == ((uint32_t)-1)) continue;
if(z == k) continue;
sw = cal_lindel_dd(&(a[k]), &(a[z]), len_st, len_w, err_dif, c_sz);
if(sw < 0) continue;
if((sw > msw) && (is_get_group(a, ca, ia, a[z].ts, a[k].tn))) {
if((sw > msw) && (is_get_group(a, /**an, rid,**/ ca, ia, a[z].ts, a[k].tn))) {
mk = a[z].ts; msw = sw;
}
}
@@ -22979,7 +22998,7 @@ int64_t return_t_chain(overlap_region *z, Candidates_list *cl)
{
int64_t i, cn = cl->length, scn; uint64_t pid; k_mer_hit *ca;
// if(z->y_id == 4378833 || z->y_id == 4378837) {
// if(z->y_id == 30129) {
// fprintf(stderr, "\n-0-[M::%s]\tutg%.6ul\tx::[%u,\t%u)\t%c\tutg%.6ul\ty::[%u,\t%u)\n",
// __func__, z->x_id+1, z->x_pos_s, z->x_pos_e+1,
// "+-"[z->y_pos_strand], z->y_id+1, z->y_pos_s, z->y_pos_e+1);
@@ -22998,14 +23017,14 @@ int64_t return_t_chain(overlap_region *z, Candidates_list *cl)
scn = i - z->shared_seed; ca = cl->list+z->shared_seed;
i = lchain_refine(ca, scn, ca, &(cl->chainDP), 50, 5000, 512, 16); cn = i;
for (; i < scn; i++) ca[i].readID = ((uint32_t)(0x7fffffff));
// if(z->y_id == 30129) fprintf(stderr, "\n-a-[M::%s]\tcn::%ld\n", __func__, cn);
// if(z->y_id == 4378833 || z->y_id == 4378837) {
// if(z->y_id == 30129) {
// fprintf(stderr, "\n-1-[M::%s]\tutg%.6ul\tx::[%u,\t%u)\t%c\tutg%.6ul\ty::[%u,\t%u)\n",
// __func__, z->x_id+1, z->x_pos_s, z->x_pos_e+1,
// "+-"[z->y_pos_strand], z->y_id+1, z->y_pos_s, z->y_pos_e+1);
// i = z->shared_seed; pid = cl->list[i].readID;
// i = z->shared_seed; pid = cl->list[i].readID; cn = cl->length;
// for (; i < cn && cl->list[i].readID == pid && cl->list[i].readID != ((uint32_t)(0x7fffffff)); i++) {
// fprintf(stderr, "i::%ld[M::%s]\treadID::%u\tself_offset::%u\toffset::%u\t%c\n",
// i, __func__, cl->list[i].readID, cl->list[i].self_offset, cl->list[i].offset,
@@ -25532,7 +25551,70 @@ uint32_t inline ff_tend(overlap_region *z, int64_t wn, int64_t dn, double dr, do
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)
uint32_t inline ff_lunalign(overlap_region *z, double erate, double gap_rate, int64_t max_gap)
{
if((z->w_list.n == 1) && (!(is_ualn_win(z->w_list.a[0])))
&& (z->w_list.a[0].x_start == ((int64_t)z->x_pos_s)) && (z->w_list.a[0].x_end == ((int64_t)z->x_pos_e))
&& (z->w_list.a[0].y_start == ((int64_t)z->y_pos_s)) && (z->w_list.a[0].y_end == ((int64_t)z->y_pos_e))) {
return 1;
}
int64_t k, zwn = z->w_list.n, zq, zt, wq, wt, tot_e, tot_g, ql, tl;
// fprintf(stderr, "[M::%s]\n", __func__);
zq = z->x_pos_s; zt = z->y_pos_s; tot_e = tot_g = 0;
for (k = 0; k < zwn; k++) {
// fprintf(stderr, "[M::%s]\twk::%ld\tq::[%d, %d)\tt::[%d, %d)\terr::%d\n", __func__,
// k, z->w_list.a[k].x_start, z->w_list.a[k].x_end + 1, z->w_list.a[k].y_start, z->w_list.a[k].y_end + 1, z->w_list.a[k].error);
if(is_ualn_win(z->w_list.a[k])) continue;
wq = z->w_list.a[k].x_start;
wt = z->w_list.a[k].y_start;
if(wq != zq) tot_g += ((wq>=zq)?(wq-zq):(zq-wq));
if(wt != zt) tot_g += ((wt>=zt)?(wt-zt):(zt-wt));
zq = z->w_list.a[k].x_end + 1;
zt = z->w_list.a[k].y_end + 1;
tot_e += z->w_list.a[k].error;
// fprintf(stderr, "[M::%s]\twk::%ld\tq::[%d, %d)\tt::[%d, %d)\terr::%d\n", __func__,
// k, z->w_list.a[k].x_start, z->w_list.a[k].x_end + 1, z->w_list.a[k].y_start, z->w_list.a[k].y_end + 1, z->w_list.a[k].error);
}
wq = z->x_pos_e + 1;
wt = z->y_pos_e + 1;
if(wq != zq) tot_g += ((wq>=zq)?(wq-zq):(zq-wq));
if(wt != zt) tot_g += ((wt>=zt)?(wt-zt):(zt-wt));
// fprintf(stderr, "[M::%s]\t%.*s(id::%u)\tq::[%u, %u)\t%.*s(id::%u)\tt::[%u, %u)\tre::%ld\trg::%ld\n", __func__, (int)Get_NAME_LENGTH(R_INF, z->x_id), Get_NAME(R_INF, z->x_id), z->x_id, z->x_pos_s, z->x_pos_e + 1,
// (int)Get_NAME_LENGTH(R_INF, z->y_id), Get_NAME(R_INF, z->y_id), z->y_id, z->y_pos_s, z->y_pos_e + 1, tot_e, tot_g);
if(!tot_g) return 1;
// fprintf(stderr, "-0-[M::%s]\n", __func__);
if(tot_g > max_gap) return 0;
// fprintf(stderr, "-1-[M::%s]\n", __func__);
ql = z->x_pos_e + 1 - z->x_pos_s;
tl = z->y_pos_e + 1 - z->y_pos_s;
if((tot_g > (ql*gap_rate)) || (tot_g > (tl*gap_rate))) return 0;
// fprintf(stderr, "-2-[M::%s]\n", __func__);
tot_e += tot_g;
if((tot_e > (ql*erate)) || (tot_e > (tl*erate))) return 0;
// fprintf(stderr, "-3-[M::%s]\n", __func__);
return 1;
}
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, double align_gap_rate, int64_t align_gap_max)
{
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;
@@ -25566,6 +25648,8 @@ 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((align_gap_max >= 0) && (!ff_lunalign(z, err, align_gap_rate, align_gap_max))) continue;
if(chem_drop && ff_tend(z, 384, 2000, 0.1, (((e_rate*10)<0.36)?(e_rate*10):(0.36)), 128)) continue;
@@ -25590,7 +25674,7 @@ 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, uint8_t chem_drop)
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, double align_gap_rate, int64_t align_gap_max)
{
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;
@@ -25632,6 +25716,8 @@ 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((align_gap_max >= 0) && (!ff_lunalign(z, err, align_gap_rate, align_gap_max))) 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);