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Merge pull request #429 from chhylp123/hifiasm_dev_debug
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avoid misassemblies; better polyploidy graph
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@chhylp123
chhylp123 authored Mar 22, 2023
2 parents b763e1f + 86b7dd4 commit 00ad745
Showing 12 changed files with 1,929 additions and 77 deletions.
2 changes: 1 addition & 1 deletion CommandLines.cpp
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Original file line number Diff line number Diff line change
@@ -285,7 +285,7 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->min_path_drop_rate = 0.2;
asm_opt->max_path_drop_rate = 0.6;
asm_opt->hifi_pst_join = 1;
asm_opt->ul_pst_join = 0;
asm_opt->ul_pst_join = 1;
}

void destory_enzyme(enzyme* f)
2 changes: 1 addition & 1 deletion CommandLines.h
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Original file line number Diff line number Diff line change
@@ -5,7 +5,7 @@
#include <pthread.h>
#include <stdint.h>

#define HA_VERSION "0.19.2-r560"
#define HA_VERSION "0.19.2-r572"

#define VERBOSE 0

85 changes: 70 additions & 15 deletions Correct.cpp
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Original file line number Diff line number Diff line change
@@ -15216,8 +15216,10 @@ bit_extz_t *exz, overlap_region *aux_o, double e_rate, int64_t ql, int64_t tl, u
else ibeg = ov->qn;
iend = ov->tn;
assert(iend>=ibeg+1);
// fprintf(stderr, "\n***[M::%s::rid->%lu] utg%.6dl(%c), s::%u, e::%u, z::[%u, %u), ibeg::%ld, iend::%ld, ch_n::%ld\n",
// __func__, rid, (int32_t)z->y_id+1, "+-"[z->y_pos_strand], ov->qs, ov->qe, z->x_pos_s, z->x_pos_e+1, ibeg, iend, ch_n);
// if(z->x_id == 57 && z->y_id == 2175) {
// fprintf(stderr, "\n***[M::%s::rid->%lu] utg%.6dl(%c), s::%u, e::%u, z::[%u, %u), ibeg::%ld, iend::%ld, ch_n::%ld\n",
// __func__, rid, (int32_t)z->y_id+1, "+-"[z->y_pos_strand], ov->qs, ov->qe, z->x_pos_s, z->x_pos_e+1, ibeg, iend, ch_n);
// }
for (l = ibeg, i = ibeg + 1; i <= iend; i++) {
q[0] = q[1] = t[0] = t[1] = mode = -1; is_done = 0;
if(l >= 0) {
@@ -15243,14 +15245,14 @@ bit_extz_t *exz, overlap_region *aux_o, double e_rate, int64_t ql, int64_t tl, u
}

if(mode == 1 || mode == 2) adjust_ext_offset(&(q[0]), &(q[1]), &(t[0]), &(t[1]), ql, tl, 0, mode);
// if(aux_o->x_id == 29033 && aux_o->y_id == 21307) {
// if(z->x_id == 57 && z->y_id == 2175) {
// fprintf(stderr, "#[M::%s::] utg%.6dl(%c), q::[%ld, %ld), t::[%ld, %ld), mode::%ld\n",
// __func__, (int32_t)z->y_id+1, "+-"[z->y_pos_strand], q[0], q[1], t[0], t[1], mode);
// }
is_done = hc_aln_exz_adv(z, uref, hpc_g, rref, qstr, tu, q[0], q[1], t[0], t[1], mode, wl, exz, ql, e_rate,
MAX_SIN_L, MAX_SIN_E, FORCE_SIN_L, -1, aux_o);

// if(aux_o->x_id == 29033 && aux_o->y_id == 21307) {
// if(z->x_id == 57 && z->y_id == 2175) {
// fprintf(stderr, "-is_done::%ld[M::%s::] utg%.6dl(%c), q::[%ld, %ld), t::[%ld, %ld), mode::%ld\n",
// is_done, __func__, (int32_t)z->y_id+1, "+-"[z->y_pos_strand], q[0], q[1], t[0], t[1], mode);
// }
@@ -19123,11 +19125,40 @@ uint64_t gen_sub_ov_adv(const ul_idx_t *udb, overlap_region* o, double o_rate, u
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->x_id == 57 && z->y_id == 2175) {
// 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);
// i = z->shared_seed; pid = cl->list[i].readID;
// 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,
// "+-"[cl->list[i].strand]);
// }
// }



i = z->shared_seed; pid = cl->list[i].readID;
for (; i < cn && cl->list[i].readID == pid && cl->list[i].readID != ((uint32_t)(0x7fffffff)); i++);
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->x_id == 57 && z->y_id == 2175) {
// 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;
// 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,
// "+-"[cl->list[i].strand]);
// }
// }
return cn;
}

@@ -21017,6 +21048,20 @@ bit_extz_t *exz, double e_rate, int64_t w_l, uint64_t ql, uint64_t rid, uint64_t
tl = udb->ug->u.a[id].len;
for (i = ch_idx; i < cl->length && cl->list[i].readID == cl->list[ch_idx].readID; i++); ch_n = i-ch_idx;

// if(z->x_id == 57 && z->y_id == 2175) {
// 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)\tch_idx::%ld\tch_n::%ld\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,
// "+-"[z->y_pos_strand],
// z->y_id+1, "lc"[udb->ug->u.a[z->y_id].circ], udb->ug->u.a[z->y_id].len, z->y_pos_s, z->y_pos_e+1,
// ch_idx, ch_n);
// for (i = ch_idx; i < cl->length && cl->list[i].readID == cl->list[ch_idx].readID; 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,
// "+-"[cl->list[i].strand]);
// }
// }

// on = fusion_chain_ovlp(z, ch_a, ch_n, ov, on, wl, ql, tl);
aux_o->w_list.n = aux_o->w_list.c.n = 0;
aux_o->y_id = z->y_id; aux_o->y_pos_strand = z->y_pos_strand;
@@ -21033,8 +21078,8 @@ 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 == 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",
// if(z->x_id == 57 && z->y_id == 2175) {
// fprintf(stderr, "\n-0-[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,
// "+-"[z->y_pos_strand],
@@ -21057,8 +21102,8 @@ 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 == 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",
// if(z->x_id == 57 && z->y_id == 2175) {
// fprintf(stderr, "\n-1-[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,
// "+-"[z->y_pos_strand],
@@ -21085,6 +21130,7 @@ bit_extz_t *exz, double e_rate, int64_t w_l, uint64_t ql, uint64_t rid, uint64_t

///update z by aux_o
update_overlap_region(z, aux_o, ql, tl);
assert((z->x_pos_e>=z->x_pos_s) && (z->y_pos_e>=z->y_pos_s));

int64_t zwn = z->w_list.n, zerr = 0, zlen = z->x_pos_e+1-z->x_pos_s;
for (i = 0; i < zwn; i++) {
@@ -21097,8 +21143,8 @@ 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 == 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",
// if(z->x_id == 57 && z->y_id == 2175) {
// fprintf(stderr, "\n-2-[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,
// "+-"[z->y_pos_strand],
@@ -21114,6 +21160,15 @@ bit_extz_t *exz, double e_rate, int64_t w_l, uint64_t ql, uint64_t rid, uint64_t
// fprintf(stderr, "\n");
// }

// if(z->x_id == 57 && z->y_id == 2175) {
// fprintf(stderr, "\n-3-[M::%s]\tutg%.6u%c\txl::%u\tx::[%u,\t%u)\t%c\tutg%.6u%c\tyl::%u\ty::[%u,\t%u)\tzerr::%ld\tzlen::%ld\te_rate::%f\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,
// "+-"[z->y_pos_strand],
// z->y_id+1, "lc"[udb->ug->u.a[z->y_id].circ], udb->ug->u.a[z->y_id].len, z->y_pos_s, z->y_pos_e+1,
// zerr, zlen, e_rate);
// }

if(zerr >= zlen) return 0;
if(zerr <= 0 && zlen > 0) return 1;
if(zerr > (zlen*e_rate)) return 0;
@@ -21319,7 +21374,7 @@ 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(z->x_id == 77960 && z->y_id == 27340) {
// if(z->x_id == 57 && z->y_id == 2175) {
// 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],
@@ -21339,7 +21394,7 @@ void ug_lalign(overlap_region_alloc* ol, Candidates_list *cl, const ul_idx_t *ur
}

ol->length = k;
// if(sid == 77960) {
// if(sid == 57) {
// 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;
@@ -21351,7 +21406,7 @@ void ug_lalign(overlap_region_alloc* ol, Candidates_list *cl, const ul_idx_t *ur
}
for (i = k = 0; i < ol->length; i++) {
z = &(ol->list[i]);
// if(z->x_id == 77960 && z->y_id == 27340) {
// if(z->x_id == 57 && z->y_id == 2175) {
// 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],
@@ -21364,7 +21419,7 @@ void ug_lalign(overlap_region_alloc* ol, Candidates_list *cl, const ul_idx_t *ur
continue;
}

// if(z->x_id == 77960 && z->y_id == 27340) {
// if(z->x_id == 57 && z->y_id == 2175) {
// 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],
@@ -21382,7 +21437,7 @@ void ug_lalign(overlap_region_alloc* ol, Candidates_list *cl, const ul_idx_t *ur
}
ol->length = k;

// if(sid == 77960) {
// if(sid == 57) {
// fprintf(stderr, "-utg%.6ld%c\tol->length::%lu\n", sid+1, "lc"[uref->ug->u.a[sid].circ], ol->length);
// }
}
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