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done contain clean

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chhylp123
2022-10-27 17:05:46 -04:00
parent df3e0eeaa3
commit 249bee7304
7 changed files with 1312 additions and 85 deletions
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Correct.cpp
+67 -45
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@@ -3449,7 +3449,7 @@ inline void recalcate_window_advance(overlap_region_alloc* overlap_list, All_rea
///debug_scan_cigar(&(overlap_list->list[j]));
///only calculate cigar for high quality overlaps
if ((rref && (overlap_length*OVERLAP_THRESHOLD_FILTER <= z->align_length)) ||
if ((rref && (overlap_length*OVERLAP_THRESHOLD_HIFI_FILTER <= z->align_length)) ||
(uref && (overlap_length*(1-e_rate) <= z->align_length))) {
a_nw = z->w_list.n;
// int64_t tt = 0;
@@ -4178,7 +4178,7 @@ inline void refine_ed_aln(overlap_region_alloc* overlap_list, All_reads *rref, c
}
}
mm_ws = z->x_pos_s; mm_aln = mm_we+1-mm_ws;
if(!simi_pass(ovl, mm_aln, uref?1:0, OVERLAP_THRESHOLD_FILTER, NULL)) continue;
if(!simi_pass(ovl, mm_aln, uref?1:0, OVERLAP_THRESHOLD_NOSI_FILTER, NULL)) continue;
if(nw > 0 && w_idx[0] != (uint64_t)-1) mm_ws = z->w_list.a[w_idx[0]].x_end+1;
for (i = 1; i < nw; i++) { //utilize the the start pos of next window in backward
@@ -4215,13 +4215,13 @@ inline void refine_ed_aln(overlap_region_alloc* overlap_list, All_reads *rref, c
}
total_y_end = p->y_start - 1;
}
if(!simi_pass(ovl, mm_aln, uref?1:0, OVERLAP_THRESHOLD_FILTER, NULL)) break;
if(!simi_pass(ovl, mm_aln, uref?1:0, OVERLAP_THRESHOLD_NOSI_FILTER, NULL)) break;
}
if(w_idx[i] != (uint64_t)-1) mm_ws = z->w_list.a[w_idx[i]].x_end+1;
}
if(i < nw) continue;
if(uref && simi_pass(ovl, z->align_length, uref?1:0, OVERLAP_THRESHOLD_FILTER, NULL)) {
if(uref && simi_pass(ovl, z->align_length, uref?1:0, OVERLAP_THRESHOLD_NOSI_FILTER, NULL)) {
z->is_match = 3; overlap_list->mapped_overlaps_length += z->align_length;
///sort for set_herror_win
if(!is_srt) radix_sort_window_list_xs_srt(z->w_list.a, z->w_list.a + z->w_list.n);
@@ -4245,7 +4245,7 @@ inline void refine_ed_aln(overlap_region_alloc* overlap_list, All_reads *rref, c
///debug_scan_cigar(&(overlap_list->list[j]));
///only calculate cigar for high quality overlaps
// int64_t tt = 0;
if(simi_pass(ovl, z->align_length, 0, OVERLAP_THRESHOLD_FILTER, &e_rate)) {
if(simi_pass(ovl, z->align_length, 0, OVERLAP_THRESHOLD_NOSI_FILTER, &e_rate)) {
a_nw = z->w_list.n;
for (i = 0, is_srt = 1; i < a_nw; i++) {
p = &(z->w_list.a[i]);
@@ -4298,26 +4298,6 @@ inline void refine_ed_aln(overlap_region_alloc* overlap_list, All_reads *rref, c
}
}
double test_err_rate(overlap_region *z, const ul_idx_t *uref, hpc_t *hpc_g, All_reads *rref, UC_Read* g_read,
char* qstr, char *tstr, char *tstr_1, Correct_dumy* dumy, kvec_t_u64_warp* v_idx, int64_t block_s, double e_rate)
{
int64_t ovl = z->x_pos_e+1-z->x_pos_s, a_nw = z->w_list.n, i; double error_rate;
window_list *p; int64_t y_id = z->y_id, y_strand = z->y_pos_strand;
if(!simi_pass(ovl, z->align_length, 0, OVERLAP_THRESHOLD_FILTER, &e_rate)) return DBL_MAX;
for (i = 0; i < a_nw; i++) {
p = &(z->w_list.a[i]);
///check if the cigar of this window has been got
if(p->clen == 0) {
gen_backtrace_adv(p, z, rref, hpc_g, uref, qstr, tstr, tstr_1, dumy, y_strand, y_id);
assert(p->error != -1);
} else {
p->y_end -= p->extra_begin;
}
}
error_rate = non_trim_error_rate(z, rref, uref, v_idx, dumy, g_read, e_rate, block_s);
return error_rate;
}
uint32_t align_ul_ed_post(overlap_region *z, const ul_idx_t *uref, hpc_t *hpc_g, char* qstr, char *tstr, char *tstr_1,
Correct_dumy* dumy, double e_rate, int64_t w_l, double ovlp_cut, void *km);
@@ -4332,10 +4312,10 @@ inline void refine_ed_aln_test(overlap_region_alloc* overlap_list, All_reads *rr
for (j = 0; j < on; ++j) {
z = &(overlap_list->list[j]); ovl = z->x_pos_e+1-z->x_pos_s;
if(!align_ul_ed_post(z, uref, NULL, g_read->seq, dumy->overlap_region, dumy->overlap_region_fix,
dumy, e_rate, block_s, OVERLAP_THRESHOLD_FILTER, NULL)) {
dumy, e_rate, block_s, OVERLAP_THRESHOLD_NOSI_FILTER, NULL)) {
continue;
}
if(uref && simi_pass(ovl, z->align_length, uref?1:0, OVERLAP_THRESHOLD_FILTER, NULL)) {
if(uref && simi_pass(ovl, z->align_length, uref?1:0, OVERLAP_THRESHOLD_NOSI_FILTER, NULL)) {
z->is_match = 3; overlap_list->mapped_overlaps_length += z->align_length;
}
}
@@ -16503,6 +16483,9 @@ int64_t extract_subov(int64_t ts, int64_t te, overlap_region *o, double o_rate,
if(!ovlp) continue;
salnl += ovlp;
}
// if(o->y_id == 700) {
// fprintf(stderr, "[M::%s] raw_t::[%ld, %ld), raw_q::[%ld, %ld), salnl::%ld\n", __func__, ts, te, qs, qe, salnl);
// }
if((((qe-qs)*o_rate)<=salnl) && (salnl > 0)) return 1;
else return 0;
}
@@ -18166,10 +18149,21 @@ uint64_t rid, rtrace_t *tc, ul_ov_t *res)
// }
}
void prt_aln_w(overlap_region *o)
{
uint64_t k;
for (k = 0; k < o->w_list.n; k++) {
fprintf(stderr, "[M::%s::aln->%u] q::[%d, %d), t::[%d, %d), err::%d\n",
__func__, ((o->w_list.a[k].y_end != -1) && (!(is_ualn_win(o->w_list.a[k])))),
o->w_list.a[k].x_start, o->w_list.a[k].x_end+1,
o->w_list.a[k].y_start, o->w_list.a[k].y_end+1, o->w_list.a[k].error);
}
}
///[ts, te) -> this is the reverse coordinates of t, not the original coordinates of t
int64_t extract_subov_cigar(const ul_idx_t *uref, char* qstr, UC_Read *tu, bit_extz_t *exz,
int64_t ts0, int64_t te0, overlap_region *o, double o_rate, int64_t *in_k, int64_t ql,
double e_rate, uint64_t rid, rtrace_t *trace, ul_ov_t *res)
double e_rate, uint64_t rid, uint64_t dbg_id, rtrace_t *trace, ul_ov_t *res)
{
int64_t rev = o->y_pos_strand, t[2], q[2], k = 0, wts, wte, ii[2];
int64_t wn = o->w_list.n, os, oe, ovlp, salnl = 0;
@@ -18196,14 +18190,22 @@ double e_rate, uint64_t rid, rtrace_t *trace, ul_ov_t *res)
if(k > ii[1]) ii[1] = k;
salnl += ovlp;
}
// if(dbg_id == 5525) {
// prt_aln_w(o);
// fprintf(stderr, "[M::%s::aln->%ld] ii::[%ld, %ld), q_aln0::[%d, %d), t0::[%ld, %ld)\n",
// __func__, salnl, ii[0], ii[1]+1, o->w_list.a[ii[0]].x_start, o->w_list.a[ii[0]].x_end+1,
// ts0, te0);
// }
if((!salnl) || (ii[0] == INT32_MAX) || (ii[1] < 0)) return 0;
if((ii[0] == ii[1]) && (is_ualn_win(o->w_list.a[ii[0]]))) return 0;
//[ii[0], ii[1]]
win_boundary_offset(o->w_list.a, o->w_list.n, ii[0], ts0, ql, &(q[0]), &(t[0]));
win_boundary_offset(o->w_list.a, o->w_list.n, ii[1], te0-1, ql, &(q[1]), &(t[1]));
q[1]++; t[1]++;
// fprintf(stderr, "\n[M::%s::aln->%ld] ii::[%ld, %ld), q::[%ld, %ld), t::[%ld, %ld)\n",
// __func__, salnl, ii[0], ii[1]+1, q[0], q[1], t[0], t[1]);
// if(dbg_id == 5525) {
// fprintf(stderr, "[M::%s::aln->%ld] ii::[%ld, %ld), q::[%ld, %ld), t::[%ld, %ld)\n",
// __func__, salnl, ii[0], ii[1]+1, q[0], q[1], t[0], t[1]);
// }
if(salnl < ((t[1]-t[0])*o_rate)) return 0;
gen_raln(uref, qstr, tu, o, exz, ii[0], ii[1]+1, ts0, te0, ql, o->y_id, rev, e_rate, rid, trace, res);
@@ -18238,8 +18240,8 @@ uint64_t sid, uint64_t oid, kv_rtrace_t *trace, kv_ul_ov_t *res)
if(e <= ts) continue;
if(s >= te) break;
t[0] = (rev?(u->len-e):(s)); t[1] = (rev?(u->len-s):(e));
if(extract_subov_cigar(udb, qstr, tu, exz, t[0], t[1], o, o_rate, &k, ql, e_rate, sid, &tz, &z)) {
tz.oid = oid;
if(extract_subov_cigar(udb, qstr, tu, exz, t[0], t[1], o, o_rate, &k, ql, e_rate, sid, rid, &tz, &z)) {
tz.oid = oid;
z.ts -= t[0]; z.te -= t[0];
z.rev = ((o->y_pos_strand == ((u->a[i]>>32)&1))?0:1);
if(z.rev) {
@@ -18257,8 +18259,9 @@ uint64_t sid, uint64_t oid, kv_rtrace_t *trace, kv_ul_ov_t *res)
kv_push(rtrace_t, *trace, tz);
// fprintf(stderr, "+[M::%s::rid->%lu::rev->%lu] utg_t::[%ld, %ld), ql::%ld\n",
// __func__, rid, rev, t[0], t[1], ql);
// fprintf(stderr, "+[M::%s::rid->%u::%c] q::[%u, %u), ql::%ld, t::[%u, %u), tl::%lu, err::%u\n",
// __func__, z.tn, "+-"[z.rev], z.qs, z.qe, ql, z.ts, z.te, Get_READ_LENGTH(R_INF, z.tn), z.sec);
// fprintf(stderr, "+[M::%s::%.*s::%c] q::[%u, %u), ql::%ld, t::[%u, %u), tl::%lu, err::%u\n",
// __func__, (int)Get_NAME_LENGTH(R_INF, z.tn), Get_NAME(R_INF, z.tn),
// "+-"[z.rev], z.qs, z.qe, ql, z.ts, z.te, Get_READ_LENGTH(R_INF, z.tn), z.sec);
}
}
} else {
@@ -18267,10 +18270,10 @@ uint64_t sid, uint64_t oid, kv_rtrace_t *trace, kv_ul_ov_t *res)
if(e <= ts) continue;
if(s >= te) break;
t[0] = (rev?(u->len-e):(s)); t[1] = (rev?(u->len-s):(e));
if(extract_subov_cigar(udb, qstr, tu, exz, t[0], t[1], o, o_rate, &k, ql, e_rate, sid, &tz, &z)) {
if(extract_subov_cigar(udb, qstr, tu, exz, t[0], t[1], o, o_rate, &k, ql, e_rate, sid, rid, &tz, &z)) {
tz.oid = oid;
z.ts -= t[0]; z.te -= t[0];
z.rev = ((o->y_pos_strand == ((u->a[i]>>32)&1))?0:1);
z.rev = ((o->y_pos_strand == (ct_a[i].x&1))?0:1);
if(z.rev) {
t[0] = z.ts; t[1] = z.te;
z.ts = Get_READ_LENGTH(R_INF, rid) - t[1];
@@ -18286,8 +18289,9 @@ uint64_t sid, uint64_t oid, kv_rtrace_t *trace, kv_ul_ov_t *res)
kv_push(rtrace_t, *trace, tz);
// fprintf(stderr, "-[M::%s::rid->%lu::rev->%lu] utg_t::[%ld, %ld), ql::%ld\n",
// __func__, rid, rev, t[0], t[1], ql);
// fprintf(stderr, "-[M::%s::rid->%u::%c] q::[%u, %u), ql::%ld, t::[%u, %u), tl::%lu, err::%u\n",
// __func__, z.tn, "+-"[z.rev], z.qs, z.qe, ql, z.ts, z.te, Get_READ_LENGTH(R_INF, z.tn), z.sec);
// fprintf(stderr, "-[M::%s::%.*s::%c] q::[%u, %u), ql::%ld, t::[%u, %u), tl::%lu, err::%u\n",
// __func__, (int)Get_NAME_LENGTH(R_INF, z.tn), Get_NAME(R_INF, z.tn),
// "+-"[z.rev], z.qs, z.qe, ql, z.ts, z.te, Get_READ_LENGTH(R_INF, z.tn), z.sec);
}
}
}
@@ -18366,9 +18370,13 @@ kv_rtrace_t *trace, uint64_t ql, uint64_t rid, uint64_t oid, uint64_t khit, over
} else {
ol = z->x_pos_e+1-z->x_pos_s; aln_ol = z->align_length;
if(aln_ol <= min_ovlp) return 0;
// fprintf(stderr, "+[M::%s::aln_ol->%lu] utg%.6dl(%c), align::%u, q::[%u, %u), t::[%u, %u), ql::%lu\n", __func__, aln_ol,
// (int32_t)z->y_id + 1, "+-"[z->y_pos_strand], z->align_length,
// z->x_pos_s, z->x_pos_e+1, z->y_pos_s, z->y_pos_e+1, ql);
// if(z->y_id == 700) {
// fprintf(stderr, "+[M::%s::aln_ol->%lu::o_rate->%f] utg%.6dl(%c), align::%u, q::[%u, %u), t::[%u, %u), ql::%lu\n",
// __func__, aln_ol, o_rate,
// (int32_t)z->y_id + 1, "+-"[z->y_pos_strand], z->align_length,
// z->x_pos_s, z->x_pos_e+1, z->y_pos_s, z->y_pos_e+1, ql);
// print_aln_windows(z);
// }
rln_0 = rln->n;
if((ol*o_rate) <= aln_ol) {
kv_pushp(ul_ov_t, *rln, &p); memset(p, 0, sizeof(*p));
@@ -18385,6 +18393,13 @@ kv_rtrace_t *trace, uint64_t ql, uint64_t rid, uint64_t oid, uint64_t khit, over
if(rln->n <= rln_0) return 0;
radix_sort_ul_ov_srt_qs1(rln->a+rln_0, rln->a+rln->n);
// if(z->y_id == 700) {
// for (k = 0; k < rln->n; k++) {
// p = &(rln->a[k]);
// fprintf(stderr, "+[M::%s::k->%lu] candidate_q::[%u, %u)\n", __func__, k, p->qs, p->qe);
// }
// }
for (k = mm = rln_0, p = NULL; k < rln->n; k++) {
if((!p) || (rln->a[k].qs >= p->qe)) p = NULL;
if(p) {
@@ -18396,6 +18411,12 @@ kv_rtrace_t *trace, uint64_t ql, uint64_t rid, uint64_t oid, uint64_t khit, over
}
}
rln->n = mm;
// if(z->y_id == 700) {
// for (k = 0; k < rln->n; k++) {
// p = &(rln->a[k]);
// fprintf(stderr, "-[M::%s::k->%lu] candidate_q::[%u, %u)\n", __func__, k, p->qs, p->qe);
// }
// }
return_t_chain(z, cl);
cigar_gen_by_chain_adv_local(z, cl, rln->a+rln_0, rln->n-rln_0, w_l, udb, NULL, NULL, qstr, tu, exz, aux_o, e_rate, ql, rid, khit);
@@ -18468,7 +18489,7 @@ void ul_rid_lalign_adv(overlap_region_alloc* ol, Candidates_list *cl, const ul_i
for (i = k = 0; i < ol->length; i++) {
z = &(ol->list[i]); z->shared_seed = z->non_homopolymer_errors;///for index
if(!ul_local_aln(z, cl, uref, qu->seq, tu, exz, err, w.window_length,
1000, OVERLAP_THRESHOLD_FILTER, NULL, NULL, NULL, ql, sid, i, khit, NULL)) {
1000, OVERLAP_THRESHOLD_NOSI_FILTER, NULL, NULL, NULL, ql, sid, i, khit, NULL)) {
continue;
}
if(k != i) {
@@ -18483,10 +18504,11 @@ void ul_rid_lalign_adv(overlap_region_alloc* ol, Candidates_list *cl, const ul_i
} else {
for (i = cln->n = trace->n = 0; i < ol->length; i++) {
z = &(ol->list[i]); z->shared_seed = z->non_homopolymer_errors;///for index
// fprintf(stderr, "[M::%s] i::%ld, aln_l::%u, q::[%u, %u)\n", __func__, i, z->align_length,
// z->x_pos_s, z->x_pos_e+1);
// fprintf(stderr, "[M::%s::utg%.6dl(%c)] i::%ld, aln_l::%u, q::[%u, %u), ql::%u\n", __func__,
// (int32_t)z->y_id + 1, "+-"[z->y_pos_strand], i, z->align_length,
// z->x_pos_s, z->x_pos_e+1, z->x_pos_e+1-z->x_pos_s);
ul_local_aln(z, cl, uref, qu->seq, tu, exz, err, w.window_length, 1000,
OVERLAP_THRESHOLD_FILTER, aln, cln, trace, ql, sid, i, khit, aux_o);
OVERLAP_THRESHOLD_NOSI_FILTER, aln, cln, trace, ql, sid, i, khit, aux_o);
}
///contained reads