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bug fixed for mask calculation

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chhylp123
2023-02-24 00:36:52 -05:00
parent 2b4b4f29e0
commit 04f660fd8c
3 changed files with 49 additions and 10 deletions
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Correct.cpp
+45 -8
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@@ -18617,7 +18617,18 @@ void ul_lalign(overlap_region_alloc* ol, Candidates_list *cl, const ul_idx_t *ur
if(ol->length <= 0) return;
} else {
// fprintf(stderr, "-[M::%s] on::%lu\n", __func__, ol->length);
if(ol->length <= 1) return;
if(ol->length <= 1) {
if(ol->length == 1) {
window_list *p;
z = &(ol->list[0]); z->w_list.n = 0;
kv_pushp(window_list, z->w_list, &p);
memset(p, 0, sizeof((*p)));
p->x_start = z->x_pos_s; p->x_end = z->x_pos_e+1; p->clen = 0;
z->align_length = z->overlapLen = z->x_pos_e+1-z->x_pos_s;
z->non_homopolymer_errors = 0;
}
return;
}
///coordinates for all intervals with cov > 1
copy_asg_arr(iidx, hap->snp_srt); copy_asg_arr(buf, v_idx->a); copy_asg_arr(buf1, (*stb));
// fprintf(stderr, "\n[M::%s] iidx_n::%ld\n", __func__, (int64_t)iidx.n);
@@ -21022,7 +21033,7 @@ bit_extz_t *exz, double e_rate, int64_t w_l, uint64_t ql, uint64_t rid, uint64_t
int64_t aux_n = aux_o->w_list.n;
// if(z->x_id == 29033 && z->y_id == 21307) {
// if(z->x_id == 77960 && z->y_id == 27340) {
// fprintf(stderr, "\n[M::%s]\tutg%.6u%c\txl::%u\tx::[%u,\t%u)\t%c\tutg%.6u%c\tyl::%u\ty::[%u,\t%u)\n",
// __func__,
// z->x_id+1, "lc"[udb->ug->u.a[z->x_id].circ], udb->ug->u.a[z->x_id].len, z->x_pos_s, z->x_pos_e+1,
@@ -21046,7 +21057,7 @@ bit_extz_t *exz, double e_rate, int64_t w_l, uint64_t ql, uint64_t rid, uint64_t
rechain_aln(z, cl, aux_o, i, w_l, udb, NULL, NULL, qstr, tu, exz, e_rate, ql, tl, khit, rid);
}
// if(z->x_id == 29033 && z->y_id == 21307) {
// if(z->x_id == 77960 && z->y_id == 27340) {
// fprintf(stderr, "\n[M::%s]\tutg%.6u%c\txl::%u\tx::[%u,\t%u)\t%c\tutg%.6u%c\tyl::%u\ty::[%u,\t%u)\n",
// __func__,
// z->x_id+1, "lc"[udb->ug->u.a[z->x_id].circ], udb->ug->u.a[z->x_id].len, z->x_pos_s, z->x_pos_e+1,
@@ -21086,7 +21097,7 @@ bit_extz_t *exz, double e_rate, int64_t w_l, uint64_t ql, uint64_t rid, uint64_t
}
z->non_homopolymer_errors = zerr;
// if(z->x_id == 29033 && z->y_id == 21307) {
// if(z->x_id == 77960 && z->y_id == 27340) {
// fprintf(stderr, "\n[M::%s]\tutg%.6u%c\txl::%u\tx::[%u,\t%u)\t%c\tutg%.6u%c\tyl::%u\ty::[%u,\t%u)\n",
// __func__,
// z->x_id+1, "lc"[udb->ug->u.a[z->x_id].circ], udb->ug->u.a[z->x_id].len, z->x_pos_s, z->x_pos_e+1,
@@ -21308,12 +21319,13 @@ void ug_lalign(overlap_region_alloc* ol, Candidates_list *cl, const ul_idx_t *ur
rr = gen_extend_err_exz(z, uref, NULL, NULL, in/**qu->seq**/, tu->seq, exz, NULL/**v_idx?v_idx->a.a:NULL**/, w.window_length, -1, err, (e_max+0.000001), &re);
z->is_match = 0;///must be here;
// if(sid == 7 && z->y_id == 135) {
// fprintf(stderr, "===utg%.6u%c\t%u\t%u\t%u\t%c\tutg%.6u%c\t%u\t%u\t%u\talign_length::%u\terr::%f\trr::%f\twn::%u\n",
// if(z->x_id == 77960 && z->y_id == 27340) {
// fprintf(stderr, "+utg%.6u%c\t%u\t%u\t%u\t%c\tutg%.6u%c\t%u\t%u\t%u\talign_length::%u\terr::%f\trr::%f\twn::%u\tk::%lu\ti::%lu\n",
// z->x_id+1, "lc"[uref->ug->u.a[z->x_id].circ], uref->ug->u.a[z->x_id].len,
// z->x_pos_s, z->x_pos_e+1, "+-"[z->y_pos_strand],
// z->y_id+1, "lc"[uref->ug->u.a[z->y_id].circ], uref->ug->u.a[z->y_id].len,
// z->y_pos_s, z->y_pos_e+1, z->align_length, err, rr, (uint32_t)z->w_list.n/**gen_nkhits(cl, z)**/);
// z->y_pos_s, z->y_pos_e+1, z->align_length, err, rr, (uint32_t)z->w_list.n/**gen_nkhits(cl, z)**/,
// k, i);
// }
if (rr <= err) {
if(k != i) {
@@ -21327,18 +21339,39 @@ void ug_lalign(overlap_region_alloc* ol, Candidates_list *cl, const ul_idx_t *ur
}
ol->length = k;
// if(sid == 77960) {
// fprintf(stderr, "+utg%.6ld%c\tol->length::%lu\n", sid+1, "lc"[uref->ug->u.a[sid].circ], ol->length);
// }
if(ol->length <= 0) return;
} else {
if(ol->length <= 1) return;
// if(ol->length <= 1) return;
if(ol->length <= 0) return;
if(qu) {
resize_UC_Read(qu, ql); qu->length = ql; memcpy(qu->seq, qstr, ql); in = qu->seq;
}
for (i = k = 0; i < ol->length; i++) {
z = &(ol->list[i]);
// if(z->x_id == 77960 && z->y_id == 27340) {
// fprintf(stderr, "-1-utg%.6u%c\t%u\t%u\t%u\t%c\tutg%.6u%c\t%u\t%u\t%u\talign_length::%u\terr::%f\twn::%u\tk::%lu\ti::%lu\n",
// z->x_id+1, "lc"[uref->ug->u.a[z->x_id].circ], uref->ug->u.a[z->x_id].len,
// z->x_pos_s, z->x_pos_e+1, "+-"[z->y_pos_strand],
// z->y_id+1, "lc"[uref->ug->u.a[z->y_id].circ], uref->ug->u.a[z->y_id].len,
// z->y_pos_s, z->y_pos_e+1, z->align_length, err, (uint32_t)z->w_list.n/**gen_nkhits(cl, z)**/,
// k, i);
// }
if(!ul_raw_aln(z, cl, uref, in/**qu->seq**/, tu, exz, err, wl, ql, sid, khit, aux_o)) {
z->is_match = 0;
continue;
}
// if(z->x_id == 77960 && z->y_id == 27340) {
// fprintf(stderr, "-2-utg%.6u%c\t%u\t%u\t%u\t%c\tutg%.6u%c\t%u\t%u\t%u\talign_length::%u\terr::%f\twn::%u\tk::%lu\ti::%lu\n",
// z->x_id+1, "lc"[uref->ug->u.a[z->x_id].circ], uref->ug->u.a[z->x_id].len,
// z->x_pos_s, z->x_pos_e+1, "+-"[z->y_pos_strand],
// z->y_id+1, "lc"[uref->ug->u.a[z->y_id].circ], uref->ug->u.a[z->y_id].len,
// z->y_pos_s, z->y_pos_e+1, z->align_length, err, (uint32_t)z->w_list.n/**gen_nkhits(cl, z)**/,
// k, i);
// }
if(k != i) {
t = ol->list[k];
ol->list[k] = ol->list[i];
@@ -21348,5 +21381,9 @@ void ug_lalign(overlap_region_alloc* ol, Candidates_list *cl, const ul_idx_t *ur
k++;
}
ol->length = k;
// if(sid == 77960) {
// fprintf(stderr, "-utg%.6ld%c\tol->length::%lu\n", sid+1, "lc"[uref->ug->u.a[sid].circ], ol->length);
// }
}
}