hic multiple rounds

Overlaps.h

@@ -1043,6 +1043,7 @@ typedef struct{
     double weight;
     uint32_t uID:31, del:1;
     uint64_t dis;
+	uint64_t occ;
     ///uint32_t enzyme;
 } hc_edge;
 

hic.cpp

@@ -1572,15 +1572,27 @@ void dfs_bubble(asg_t *g, kvec_t_u32_warp* stack, kvec_t_u32_warp* result, uint3
     }
 }
 
-
+void update_bub_b_s_idx(bubble_type* bub);
 void identify_bubbles(ma_ug_t* ug, bubble_type* bub, hc_links* link)
 {
     asg_cleanup(ug->g);
     if (!ug->g->is_symm) asg_symm(ug->g);
-    memset(bub, 0, sizeof(bubble_type));
     uint32_t v, n_vtx = ug->g->n_seq * 2, i, k, mode = (((uint32_t)-1)<<2);
+    uint32_t beg, sink, n, *a, n_occ;
     uint64_t pathLen, tLen;
     bub->ug = ug; 
+    for (i = 0, tLen = 1; i < ug->u.n; i++) tLen += ug->u.a[i].len;
+    bub->b_bub = bub->b_end_bub = bub->tangle_bub = bub->cross_bub = 0;
+
+    if(bub->round_id == 0)
+    {
+        buf_t b; memset(&b, 0, sizeof(buf_t)); b.a = (binfo_t*)calloc(n_vtx, sizeof(binfo_t));
+        kv_init(bub->list); kv_init(bub->num); kv_init(bub->pathLen);
+        kv_init(bub->b_s_idx); kv_malloc(bub->b_s_idx, ug->g->n_seq); 
+        bub->b_ug = NULL; kv_init(bub->chain_weight);
+        bub->b_s_idx.n = ug->g->n_seq;
+        memset(bub->b_s_idx.a, -1, bub->b_s_idx.n * sizeof(uint64_t));
+
         CALLOC(bub->index, n_vtx);
         for (i = 0; i < ug->g->n_seq; i++)
         {
@@ -1591,9 +1603,7 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, hc_links* link)
             } 
         }
 
-    kv_init(bub->list); kv_init(bub->num); kv_init(bub->pathLen);
+        
-    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;
 
         for (v = 0; v < n_vtx; ++v) 
         {
@@ -1615,6 +1625,7 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, hc_links* link)
             }
         }
 
+
         kvec_t_u32_warp stack, result;
         kv_init(stack.a); kv_init(result.a);
         for (v = 0; v < n_vtx; ++v) 
@@ -1671,7 +1682,7 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, hc_links* link)
         
         kv_push(uint32_t, bub->num, bub->list.n);
         free(b.a); free(b.S.a); free(b.T.a); free(b.b.a); free(b.e.a);
-    bub->f_bub = bub->num.n - 1; bub->b_bub = bub->b_end_bub = bub->tangle_bub = bub->cross_bub = 0; ///bub->s_bub = bub->num.n - 1;
+        bub->f_bub = bub->num.n - 1; ///bub->s_bub = bub->num.n - 1;
 
         for (i = 0; i < ug->g->n_seq; i++)
         {
@@ -1692,12 +1703,7 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, hc_links* link)
             }         
         }
 
-    kv_init(bub->b_s_idx);
-    kv_malloc(bub->b_s_idx, ug->g->n_seq); 
-    bub->b_s_idx.n = ug->g->n_seq;
-    memset(bub->b_s_idx.a, -1, bub->b_s_idx.n * sizeof(uint64_t));
 
-    uint32_t beg, sink, n, *a, n_occ;
         for (i = 0; i < bub->f_bub; i++)
         {
             get_bubbles(bub, i, &beg, &sink, &a, &n, &pathLen);
@@ -1762,7 +1768,21 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, hc_links* link)
                 }
             }
         }
-    bub->b_ug = NULL; kv_init(bub->chain_weight);
+
+    }
+    else
+    {
+        bub->num.n = bub->f_bub + 1; 
+        bub->pathLen.n = bub->f_bub;
+        bub->list.n = bub->num.a[bub->num.n-1];
+        update_bub_b_s_idx(bub);
+        bub->check_het = 0;
+        asg_destroy(bub->b_g); bub->b_g = NULL;
+        ma_ug_destroy(bub->b_ug); bub->b_ug = NULL;
+        kv_destroy(bub->chain_weight); kv_init(bub->chain_weight);
+    }
+    bub->b_g = NULL;
+    bub->b_ug = NULL;
     build_bub_graph(ug, bub);
 }
 
@@ -4353,8 +4373,8 @@ void weight_edges(ha_ug_index* idx, kvec_pe_hit* hits, hc_links* link, bubble_ty
         weight = 1;
         /*******************************for distance debug************************************/
 
-        e1->weight += weight;
+        e1->weight += weight; e1->occ++;
-        e2->weight += weight;
+        e2->weight += weight; e2->occ++;
     }
 }
 
@@ -6944,9 +6964,6 @@ void get_forward_distance(uint32_t src, uint32_t dest, asg_t *sg, hc_links* link
     if(e == NULL) return;
     uint32_t v, j;
     uint64_t d[2], db[2], q_u, min, min_i, min_b;
-    // fprintf(stderr, "\nsrc-utg%.6ul\tdest-utg%.6ul\n", src+1, dest+1);
-    // fprintf(stderr, "%s\t%s\tdis(%lu)\n", e->dis == (uint64_t)-1? "unreach pre": "**reach pre", 
-    //                                             ((e->dis>>2)&1)?"back":"forw", e->dis>>3);
     e->dis = (uint64_t)-1;
 
     for (v = ((uint64_t)(src)<<1); v < ((uint64_t)(src+1)<<1); v++)
@@ -6978,6 +6995,8 @@ void get_forward_distance(uint32_t src, uint32_t dest, asg_t *sg, hc_links* link
     //                                             ((e->dis>>2)&1)?"back":"forw", e->dis>>3);
 }
 
+///void get_trans_rate(ha_ug_index* idx, kvec_pe_hit* hits, hc_links* link, bubble_type* bub)
+
 void init_hic_p(ha_ug_index* idx, kvec_pe_hit* hits, hc_links* link, bubble_type* bub, kvec_hc_edge* back_hc_edge, MT* M)
 {
     uint64_t k, i, m, beg, end, t_d, r_idx, f_idx, b_size, med = (uint64_t)-1, uID;
@@ -6986,6 +7005,18 @@ void init_hic_p(ha_ug_index* idx, kvec_pe_hit* hits, hc_links* link, bubble_type
     kv_init(buf);
     kv_init(buf_idx);
 
+    if(bub->round_id > 0)
+    {
+        for (i = 0; i < link->a.n; i++)
+        {
+            for (k = 0; k < link->a.a[i].e.n; k++)
+            {
+                link->a.a[i].e.a[k].dis = (uint64_t)-1;
+            }
+        }
+        fill_utg_distance_multi(idx, link, M, bub);
+    }
+
     buf.n = 0;
     for (i = 0; i < bub->f_bub; i++)
     {
@@ -7204,6 +7235,7 @@ void init_hic_p(ha_ug_index* idx, kvec_pe_hit* hits, hc_links* link, bubble_type
             if(link->a.a[i].e.a[k].del) continue;
             link->a.a[i].e.a[m] = link->a.a[i].e.a[k];
             link->a.a[i].e.a[m].weight = 0;
+            link->a.a[i].e.a[m].occ = 0;
             m++;
         }
         link->a.a[i].e.n = m;
@@ -10426,7 +10458,7 @@ uint32_t phasing_improvement(H_partition* h, G_partition* g_p, ha_ug_index* idx,
         update_partition_flag(h, g_p, idx->link, i);
     }
 
-    print_phase_group(g_p, bub, "Small");
+    ///print_phase_group(g_p, bub, "Small");
     // double w0 = 0, w1 = 0;
     // uint32_t *h0, h0_n, *h1, h1_n;
     // get_phased_block(g_p, NULL, 2973, NULL, NULL, &h0, &h0_n, &h1, &h1_n, NULL, NULL);
@@ -10705,6 +10737,24 @@ void print_bubble_chain(bubble_type* bub)
     }
 }
 
+void reset_H_partition(H_partition* hap, uint32_t is_init)
+{
+    if(!is_init)
+    {
+        hap->n = 0;
+        free(hap->lock);
+        free(hap->hap);
+        hap->m[0] = hap->m[1] = hap->m[2] = (uint32_t)-1;
+        hap->label = hap->label_add = hap->label_shift = (uint32_t)-1;
+        destory_G_partition(&(hap->g_p)); memset(&(hap->g_p), 0, sizeof(G_partition));
+        destory_G_partition(&(hap->group_g_p)); memset(&(hap->group_g_p), 0, sizeof(G_partition));
+        kv_destroy(hap->label_buffer); kv_init(hap->label_buffer);
+        kv_destroy(hap->b.vis); kv_init(hap->b.vis); memset(&(hap->b), 0, sizeof(block_phase_type));
+    }
+
+    memset(hap, 0, sizeof(H_partition));
+}
+
 
 int hic_short_align(const char *fn1, const char *fn2, ha_ug_index* idx)
 {
@@ -10726,11 +10776,6 @@ int hic_short_align(const char *fn1, const char *fn2, ha_ug_index* idx)
     kv_init(sl.hits.a);
     fprintf(stderr, "u.n: %d, uID_bits: %lu, pos_bits: %lu\n", (uint32_t)idx->ug->u.n, idx->uID_bits, idx->pos_bits);
     
-    bubble_type bub;
-    identify_bubbles(idx->ug, &bub, idx->link);
-    ///print_bubbles(idx->ug, &bub, sl.hits.a.n?&sl.hits:NULL, idx->link, idx);
-    fprintf(stderr, "bub.f_bub: %lu, bub.s_bub: %lu, bub.b_bub: %lu\n", bub.f_bub, bub.s_bub, bub.b_bub);
-
     if(!load_hc_hits(&sl.hits, asm_opt.output_file_name))
     {
         /*******************************for debug************************************/
@@ -10749,29 +10794,36 @@ int hic_short_align(const char *fn1, const char *fn2, ha_ug_index* idx)
         write_hc_hits(&sl.hits, asm_opt.output_file_name);
     }
 
-    ///print_hits(idx, &sl.hits, fn1);
+    H_partition hap;
     MT M;
     init_MT(&M, idx->ug->g->n_seq<<1);
-
+    bubble_type bub; 
+    memset(&bub, 0, sizeof(bubble_type));
+    bub.round_id = 0; bub.n_round = 2;
+    for (bub.round_id = 0; bub.round_id < bub.n_round; bub.round_id++)
+    {
+        identify_bubbles(idx->ug, &bub, idx->link);
+        if(bub.round_id == 0)
+        {
             collect_hc_links(sl.idx, &sl.hits, idx->link, &bub, &M);
             collect_hc_reverse_links(idx->link, idx->ug, &bub);
-    
+        }
-    
         init_hic_p((ha_ug_index*)sl.idx, &sl.hits, idx->link, &bub, &back_hc_edge, &M);
         ///init_hic_p_new((ha_ug_index*)sl.idx, &sl.hits, idx->link, &bub, &back_hc_edge, &M);
-    destory_MT(&M);
+        reset_H_partition(&hap, (bub.round_id == 0? 1 : 0));
-
-    H_partition hap;
         init_contig_partition(&hap, idx, &bub);
-
         phasing_improvement(&hap, &(hap.g_p), idx, &bub);
         label_unitigs(&hap, idx->ug);
+    }
+    destory_MT(&M);
 
-    print_debug_bubble_graph(&bub, idx->ug, asm_opt.output_file_name);
+    ///print_bubbles(idx->ug, &bub, sl.hits.a.n?&sl.hits:NULL, idx->link, idx);
+    ///print_hits(idx, &sl.hits, fn1);
     
-    print_bubble_chain(&bub);
 
-    print_hc_links(idx->link, 0, &hap);
+    // print_debug_bubble_graph(&bub, idx->ug, asm_opt.output_file_name);
+    // print_bubble_chain(&bub);
+    // print_hc_links(idx->link, 0, &hap);
     
     ///print_contig_partition(&hap, "final");
 

hic.h

@@ -21,7 +21,7 @@ typedef struct {
 }chain_w_type;
 
 typedef struct {
-    uint32_t* index;
+    uint32_t* index, round_id, n_round;
     ma_ug_t* ug;
     kvec_t(uint32_t) list;
     kvec_t(uint32_t) num;