for v0.14-hic

Overlaps.cpp

@@ -286,8 +286,6 @@ void asg_cleanup(asg_t *g)
 
 
 
-
-
 // delete multi-arcs
 /**
  * remove edges like:   v has two out-edges to w
@@ -7886,12 +7884,6 @@ add_unitig:
 	return ug;
 }
 
-
-
-
-
-
-
 ma_ug_t *ma_ug_gen_primary(asg_t *g, uint8_t flag)
 {
     asg_cleanup(g);
@@ -24705,7 +24697,7 @@ long long bubble_dist, int read_graph, int write)
         &R_INF, output_file_name);
     }
 
-    ///debug_info_of_specfic_read("m64062_190803_042216/177341795/ccs", sources, reverse_sources, -1, "beg");
+    ///debug_info_of_specfic_read("m64011_190830_220126/31720629/ccs", sources, reverse_sources, -1, "beg");
 
     if (!(asm_opt.flag & HA_F_BAN_ASSEMBLY))
     {

Overlaps.h

@@ -395,7 +395,8 @@ typedef struct {
 }kvec_asg_arc_t_warp;
 
 void sort_kvec_t_u64_warp(kvec_t_u64_warp* u_vecs, uint32_t is_descend);
-
+int asg_arc_del_multi(asg_t *g);
+int asg_arc_del_asymm(asg_t *g);
 
 typedef struct {
 	uint32_t q_pos;
@@ -1095,7 +1096,6 @@ asg_t* copy_read_graph(asg_t *src);
 ma_ug_t *ma_ug_gen(asg_t *g);
 void ma_ug_destroy(ma_ug_t *ug);
 
-
 inline int inter_interval(int a_s, int a_e, int b_s, int b_e, int* i_s, int* i_e)
 {
     if(a_s > b_e || b_s > a_e) return 0;

hic.h

@@ -27,12 +27,10 @@ typedef struct {
     kvec_t(uint32_t) num;
     kvec_t(uint64_t) pathLen;
     kvec_t(uint64_t) b_s_idx;
-    uint64_t s_bub, f_bub, b_bub;
+    uint64_t s_bub, f_bub, b_bub, b_end_bub, tangle_bub, cross_bub;
     uint32_t check_het;
     asg_t *b_g;
-    uint32_t *b_g_index; 
     ma_ug_t* b_ug;
-    uint32_t *b_ug_index; 
     kvec_t(chain_w_type) chain_weight;
 } bubble_type;
 #define P_het(B) ((B).num.n)