fix missed ug when bubble popping

Overlaps.cpp

@@ -12712,104 +12712,6 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex, int max_hang, int min_ovlp, kvec_asg_a
     /*******************************for debug************************************/
 }
 
-void hic_clean(asg_t* read_g)
-{
-    uint32_t n_vtx, v, u;
-    uint64_t i, k, k_i, tLen, v_occ, u_occ, utg_occ;
-    double bub_rate = 0.1;
-    ma_ug_t *ug = NULL;
-    ug = ma_ug_gen_primary(read_g, PRIMARY_LABLE);
-    n_vtx = ug->g->n_seq * 2;
-    buf_t b; memset(&b, 0, sizeof(buf_t)); b.a = (binfo_t*)calloc(n_vtx, sizeof(binfo_t));
-    ///for (i = 0, tLen = 1; i < ug->u.n; i++) tLen += ug->u.a[i].len;
-    tLen = get_bub_pop_max_dist_advance(ug->g, &b);
-    uint8_t* bs_flag = (uint8_t*)calloc(n_vtx, 1);
-    kvec_t(uint32_t) ax;
-    kv_init(ax);
-    for (v = 0; v < ug->g->n_seq; ++v) 
-    {
-        if(ug->g->seq[v].del) continue;
-        ug->g->seq[v].c = PRIMARY_LABLE;
-        EvaluateLen(ug->u, v) = ug->u.a[v].n;
-    }
-
-
-    for (v = 0; v < n_vtx; ++v) 
-    {
-        if(ug->g->seq[v>>1].del) continue;
-        if(asg_arc_n(ug->g, v) < 2) continue;
-        if(bs_flag[v] != 0) continue;
-        if(asg_bub_pop1_primary_trio(ug->g, NULL, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 0, NULL, NULL, NULL, 0, 0))
-        {
-            //beg is v, end is b.S.a[0]
-            //note b.b include end, does not include beg
-            for (i = 0; i < b.b.n; i++)
-            {
-                if(b.b.a[i]==v || b.b.a[i]==b.S.a[0]) continue;
-                bs_flag[b.b.a[i]] = bs_flag[b.b.a[i]^1] = 1;
-            }
-            bs_flag[v] = 2; bs_flag[b.S.a[0]^1] = 3;
-        }
-    }
-
-
-    for (v = 0; v < n_vtx; ++v) 
-    {
-        if(bs_flag[v] !=2) continue;
-        if(asg_bub_pop1_primary_trio(ug->g, NULL, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 0, NULL, NULL, NULL, 0, 0))
-        {
-            //note b.b include end, does not include beg
-            for (i = v_occ = ax.n = 0; i < b.b.n; i++)
-            {
-                if(b.b.a[i]==v || b.b.a[i]==b.S.a[0]) continue;
-                v_occ += ug->u.a[b.b.a[i]>>1].n;
-                kv_push(uint32_t, ax, b.b.a[i]>>1);
-            }
-
-            for (i = 0; i < ax.n; i++)
-            {
-                for (k = 0; k < 2; k++)
-                {
-                    u = (ax.a[i]<<1) + k;
-                    if(asg_arc_n(ug->g, u) < 2) continue;
-                    if(asg_bub_pop1_primary_trio(ug->g, NULL, u, tLen, &b, (uint32_t)-1, (uint32_t)-1, 0, NULL, NULL, NULL, 0, 0))
-                    {
-                        for (k_i = u_occ = utg_occ = 0; k_i < b.b.n; k_i++)
-                        {
-                            if(b.b.a[k_i]==u || b.b.a[k_i]==b.S.a[0]) continue;
-                            u_occ += ug->u.a[b.b.a[k_i]>>1].n;
-                            utg_occ++;
-                        }
-
-                        if(u_occ >= v_occ*bub_rate) continue;
-                        if(u_occ > 3) continue;
-                        if(utg_occ > 2) continue;
-                        asg_bub_pop1_primary_trio(ug->g, NULL, u, tLen, &b, (uint32_t)-1, (uint32_t)-1, 1, NULL, NULL, NULL, 0, 0);
-                    }
-                }
-            }
-        }
-    }
-
-    ma_utg_t* m = NULL;
-    for (v = 0; v < ug->g->n_seq; ++v) 
-    {
-        if(ug->g->seq[v].del) continue;
-        if(ug->g->seq[v].c != ALTER_LABLE) continue;
-        m = &(ug->u.a[v]);
-        if(m->m == 0) continue;
-        for (k = 0; k < m->n; k++)
-        {
-            asg_seq_del(read_g, m->a[k]>>33);
-        }
-    }
-
-    asg_cleanup(read_g);
-    free(b.a); free(b.S.a); free(b.T.a); free(b.b.a); free(b.e.a); free(bs_flag);
-    ma_ug_destroy(ug);
-    kv_destroy(ax);
-}
-
 void write_trans_chain(trans_chain* t_ch, const char *fn)
 {
     char *buf = (char*)calloc(strlen(fn) + 25, 1);
@@ -12899,7 +12801,6 @@ long long tipsLen, float tip_drop_ratio, long long stops_threshold,
 R_to_U* ruIndex, float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp, 
 long long gap_fuzz, bub_label_t* b_mask_t)
 { 
-    hic_clean(sg);
     ug_opt_t opt; memset(&opt, 0, sizeof(opt));
     opt.coverage_cut = coverage_cut;
     opt.sources = sources;
@@ -13675,8 +13576,6 @@ long long tipsLen, float tip_drop_ratio, long long stops_threshold,
 R_to_U* ruIndex, float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp, 
 bub_label_t* b_mask_t)
 { 
-    hic_clean(sg);
-
     kvec_asg_arc_t_warp new_rtg_edges;
     kv_init(new_rtg_edges.a);
     ma_ug_t *ug = NULL;
@@ -29782,7 +29681,7 @@ void flat_bubbles(asg_t *sg, uint8_t* r_het)
             if(bs_flag[v] == 1) continue;
             if(bs_flag[v] == 0) bs_flag[v] = 1;
 
-            if(asg_bub_pop1_primary_trio(ug->g, NULL, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 0, NULL, NULL, NULL, 0, 0))
+            if(asg_bub_pop1_primary_trio(ug->g, ug, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 0, NULL, NULL, NULL, 0, 0))
             {
                 //note b.b include end, does not include beg
                 for (i = path = 0; i < b.b.n; i++)
@@ -29871,7 +29770,7 @@ void flat_bubbles(asg_t *sg, uint8_t* r_het)
 
                 if(is_het_b > path && is_het_s > path && (is_het_b+is_het_s)>(path<<2))
                 {
-                    asg_bub_pop1_primary_trio(ug->g, NULL, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 1, NULL, NULL, NULL, 0, 0);
+                    asg_bub_pop1_primary_trio(ug->g, ug, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 1, NULL, NULL, NULL, 0, 0);
                     n_pop++;
                 }
             }
@@ -29962,7 +29861,7 @@ void flat_bubbles_advance(asg_t *sg, ma_hit_t_alloc* sources, R_to_U* ruIndex, u
             if(bs_flag[v] == 1) continue;
             if(bs_flag[v] == 0) bs_flag[v] = 1;
 
-            if(asg_bub_pop1_primary_trio(ug->g, NULL, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 0, NULL, NULL, NULL, 0, 0))
+            if(asg_bub_pop1_primary_trio(ug->g, ug, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 0, NULL, NULL, NULL, 0, 0))
             {
                 bs_flag[v] = 2; bs_flag[b.S.a[0]^1] = 2;
                 //note b.b include end, does not include beg
@@ -30015,7 +29914,7 @@ void flat_bubbles_advance(asg_t *sg, ma_hit_t_alloc* sources, R_to_U* ruIndex, u
                 if((C_bases/R_bases) <= het_thres)
                 {
                     fprintf(stderr, "s-utg%.6ul\te-utg%.6ul\tC_bases:%lu\tR_bases:%lu\n", (v>>1)+1, (b.S.a[0]>>1)+1, C_bases, R_bases);
-                    asg_bub_pop1_primary_trio(ug->g, NULL, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 1, NULL, NULL, NULL, 0, 0);
+                    asg_bub_pop1_primary_trio(ug->g, ug, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 1, NULL, NULL, NULL, 0, 0);
                     n_pop++;
                 }
                 

hic.cpp

@@ -2344,7 +2344,7 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *r_het_flag, kv_u_t
         for (v = 0; v < n_vtx; ++v) 
         {
             if((bub->index[v]&(uint32_t)3) !=2) continue;
-            if(asg_bub_pop1_primary_trio(ug->g, NULL, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 0, &pathLen, NULL, NULL, 0, 0))
+            if(asg_bub_pop1_primary_trio(ug->g, ug, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 0, &pathLen, NULL, NULL, 0, 0))
             {   
                 //note b.b include end, does not include beg
                 i = b.b.n + 1;
@@ -2376,7 +2376,7 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *r_het_flag, kv_u_t
             if((bub->num.a[k]>>31) == 0) bub->s_bub++;
             v = (bub->num.a[k]<<1)>>1;
             bub->num.a[k] = bub->list.n;
-            if(asg_bub_pop1_primary_trio(ug->g, NULL, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 0, &pathLen, NULL, NULL, 0, 0))
+            if(asg_bub_pop1_primary_trio(ug->g, ug, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 0, &pathLen, NULL, NULL, 0, 0))
             {
                 kv_push(uint64_t, bub->pathLen, pathLen);
                 //beg is v, end is b.S.a[0]