diff --git a/Overlaps.h b/Overlaps.h
index 4a8a961..8a661cd 100644
--- a/Overlaps.h
+++ b/Overlaps.h
@@ -710,302 +710,11 @@ uint32_t stops_threshold, buf_t* b)
 #define UNAVAILABLE (uint32_t)-1
 #define PLOID 0
 #define NON_PLOID 1
-#define DIFF_HAP_RATE 0.75
+// #define DIFF_HAP_RATE 0.75
 #define TRIO_DROP_THRES 0.9
 #define TRIO_DROP_LENGTH_THRES 0.8
 #define MAX_STOP_RATE 0.6
 #define TANGLE_MISSED_THRES 0.6
-///if ug == NULL, nsg should be equal to read_sg
-inline uint32_t check_different_haps(asg_t *nsg, ma_ug_t *ug, asg_t *read_sg, 
-uint32_t v_0, uint32_t v_1, ma_hit_t_alloc* reverse_sources, buf_t* b_0, buf_t* b_1, 
-R_to_U* ruIndex, uint32_t min_edge_length, uint32_t stops_threshold)
-{
-	uint32_t vEnd, qn, tn, j, is_Unitig, uId;
-	long long ELen_0, ELen_1, tmp, max_stop_nodeLen, max_stop_baseLen;
-
-	b_0->b.n = b_1->b.n = 0;
-	if(get_unitig(nsg, ug, v_0, &vEnd, &ELen_0, &tmp, &max_stop_nodeLen, &max_stop_baseLen, 
-	stops_threshold, b_0) == LOOP)
-	{
-		return UNAVAILABLE;
-	}
-	if(get_unitig(nsg, ug, v_1, &vEnd, &ELen_1, &tmp, &max_stop_nodeLen, &max_stop_baseLen, 
-	stops_threshold, b_1) == LOOP)
-	{
-		return UNAVAILABLE;
-	}
-	if(ELen_0<=min_edge_length || ELen_1<=min_edge_length) return UNAVAILABLE;
-
-	rIdContig b_max, b_min;
-	b_max.b_0 = b_min.b_0 = NULL;
-	b_max.offset = b_max.readI = b_max.untigI = 0;
-	b_min.offset = b_min.readI = b_min.untigI = 0;
-
-	if(ELen_0<=ELen_1)
-	{
-        b_min.b_0 = b_0;
-        b_max.b_0 = b_1;
-    }
-    else
-    {
-        b_min.b_0 = b_1;
-        b_max.b_0 = b_0;
-    }
-
-	uint32_t max_count = 0, min_count = 0;
-	ma_utg_t *node_min = NULL, *node_max = NULL;
-	if(ug != NULL)
-	{
-		/*****************************label all unitigs****************************************/
-		for (b_max.untigI = 0; b_max.untigI < b_max.b_0->b.n; b_max.untigI++)
-		{
-			node_max = &(ug->u.a[b_max.b_0->b.a[b_max.untigI]>>1]);
-			///each read
-			for (b_max.readI = 0; b_max.readI < node_max->n; b_max.readI++)
-			{
-				qn = (node_max->a[b_max.readI]>>33);
-				set_R_to_U(ruIndex, qn, (b_max.b_0->b.a[b_max.untigI]>>1), 1, &(read_sg->seq[qn].c));
-			}
-		}
-		/*****************************label all unitigs****************************************/
-
-		///each unitig
-		for (b_min.untigI = 0; b_min.untigI < b_min.b_0->b.n; b_min.untigI++)
-		{
-			
-			node_min = &(ug->u.a[(b_min.b_0->b.a[b_min.untigI]>>1)]);
-
-			///each read
-			for (b_min.readI = 0; b_min.readI < node_min->n; b_min.readI++)
-        	{
-				qn = node_min->a[b_min.readI]>>33;
-
-				/************************BUG: don't forget****************************/
-				if(reverse_sources[qn].length > 0) min_count++;
-				///if(reverse_sources[qn].length >= 0) min_count++;
-				/************************BUG: don't forget****************************/
-				for (j = 0; j < (long long)reverse_sources[qn].length; j++)
-				{
-					tn = Get_tn(reverse_sources[qn].buffer[j]);
-					if(read_sg->seq[tn].del == 1)
-					{
-						get_R_to_U(ruIndex, tn, &tn, &is_Unitig);
-						if(tn == (uint32_t)-1 || is_Unitig == 1 || read_sg->seq[tn].del == 1) continue;
-					}
-
-					get_R_to_U(ruIndex, tn, &uId, &is_Unitig);
-					if(uId!=(uint32_t)-1 && is_Unitig == 1)
-					{
-						max_count++;
-						break;
-					}
-				}
-			}
-		}
-		/*****************************label all unitigs****************************************/
-		for (b_max.untigI = 0; b_max.untigI < b_max.b_0->b.n; b_max.untigI++)
-		{
-			node_max = &(ug->u.a[b_max.b_0->b.a[b_max.untigI]>>1]);
-			///each read
-			for (b_max.readI = 0; b_max.readI < node_max->n; b_max.readI++)
-			{
-				qn = (node_max->a[b_max.readI]>>33);
-				ruIndex->index[qn] = (uint32_t)-1;
-			}
-		}
-		/*****************************label all unitigs****************************************/
-	}
-	else
-	{
-		/*****************************label all reads****************************************/
-		for (b_max.untigI = 0; b_max.untigI < b_max.b_0->b.n; b_max.untigI++)
-		{
-			qn = (b_max.b_0->b.a[b_max.untigI]>>1);
-			set_R_to_U(ruIndex, qn, 1, 1, &(read_sg->seq[qn].c));
-		}
-		/*****************************label all reads****************************************/
-
-		///each read
-		for (b_min.untigI = 0; b_min.untigI < b_min.b_0->b.n; b_min.untigI++)
-		{
-			qn = (b_min.b_0->b.a[b_min.untigI]>>1);
-
-			/************************BUG: don't forget****************************/
-			if(reverse_sources[qn].length > 0) min_count++;
-			///if(reverse_sources[qn].length >= 0) min_count++;
-			/************************BUG: don't forget****************************/
-
-			for (j = 0; j < (long long)reverse_sources[qn].length; j++)
-        	{
-            	tn = Get_tn(reverse_sources[qn].buffer[j]);
-				if(nsg->seq[tn].del == 1)
-				{
-					get_R_to_U(ruIndex, tn, &tn, &is_Unitig);
-					if(tn == (uint32_t)-1 || is_Unitig == 1 || nsg->seq[tn].del == 1) continue;
-				}
-
-
-				get_R_to_U(ruIndex, tn, &uId, &is_Unitig);
-				if(uId!=(uint32_t)-1 && is_Unitig == 1)
-				{
-					max_count++;
-					break;
-				}
-			}
-		}
-
-		/*****************************label all reads****************************************/
-		for (b_max.untigI = 0; b_max.untigI < b_max.b_0->b.n; b_max.untigI++)
-		{
-			qn = (b_max.b_0->b.a[b_max.untigI]>>1);
-			ruIndex->index[qn] = (uint32_t)-1;
-		}
-		/*****************************label all reads****************************************/
-	}
-
-	// if(((v_0==7707) && (v_1==26867))||((v_1==7707) && (v_0==26867)))
-	// {
-	// 	fprintf(stderr, "******\nv_0>>1: %u, v_0&1: %u, ELen_0: %u\n", v_0>>1, v_0&1, (uint32_t)ELen_0);
-	// 	fprintf(stderr, "v_1>>1: %u, v_1&1: %u, ELen_1: %u\n", v_1>>1, v_1&1, (uint32_t)ELen_1);
-	// 	fprintf(stderr, "min_count: %u, max_count: %u, DIFF_HAP_RATE: %f\n\n", 
-	// 	min_count, max_count, DIFF_HAP_RATE);
-	// }
-	
-	if(min_count == 0) return UNAVAILABLE;
-	if(max_count > min_count*DIFF_HAP_RATE) return PLOID;
-	return NON_PLOID;
-}
-
-inline uint32_t check_different_haps_naive(asg_t *nsg, ma_ug_t *ug, asg_t *read_sg, 
-uint32_t v_0, uint32_t v_1, ma_hit_t_alloc* reverse_sources, buf_t* b_0, buf_t* b_1, 
-R_to_U* ruIndex, uint32_t min_edge_length, uint32_t stops_threshold)
-{
-	uint32_t vEnd, qn, tn, j, is_Unitig;
-	long long ELen_0, ELen_1, tmp, max_stop_nodeLen, max_stop_baseLen;
-
-	b_0->b.n = b_1->b.n = 0;
-	if(get_unitig(nsg, ug, v_0, &vEnd, &ELen_0, &tmp, &max_stop_nodeLen, &max_stop_baseLen, 
-	stops_threshold, b_0) == LOOP)
-	{
-		return UNAVAILABLE;
-	} 
-	if(get_unitig(nsg, ug, v_1, &vEnd, &ELen_1, &tmp, &max_stop_nodeLen, &max_stop_baseLen, 
-	stops_threshold, b_1) == LOOP)
-	{
-		return UNAVAILABLE;
-	}
-
-	if(ELen_0<=min_edge_length || ELen_1<=min_edge_length) return UNAVAILABLE;
-
-	rIdContig b_max, b_min;
-	b_max.b_0 = b_min.b_0 = NULL;
-	b_max.offset = b_max.readI = b_max.untigI = 0;
-	b_min.offset = b_min.readI = b_min.untigI = 0;
-
-	if(ELen_0<=ELen_1)
-	{
-        b_min.b_0 = b_0;
-        b_max.b_0 = b_1;
-    }
-    else
-    {
-        b_min.b_0 = b_1;
-        b_max.b_0 = b_0;
-    }
-
-	uint32_t max_count = 0, min_count = 0;
-	ma_utg_t *node_min = NULL, *node_max = NULL;
-
-	if(ug != NULL)
-	{
-		///each unitig
-		for (b_min.untigI = 0; b_min.untigI < b_min.b_0->b.n; b_min.untigI++)
-		{
-			
-			node_min = &(ug->u.a[(b_min.b_0->b.a[b_min.untigI]>>1)]);
-
-			///each read
-			for (b_min.readI = 0; b_min.readI < node_min->n; b_min.readI++)
-        	{
-				qn = node_min->a[b_min.readI]>>33;
-
-				if(reverse_sources[qn].length > 0) min_count++;
-				for (j = 0; j < (long long)reverse_sources[qn].length; j++)
-				{
-					tn = Get_tn(reverse_sources[qn].buffer[j]);
-					if(read_sg->seq[tn].del == 1)
-					{
-						get_R_to_U(ruIndex, tn, &tn, &is_Unitig);
-						if(tn == (uint32_t)-1 || is_Unitig == 1 || read_sg->seq[tn].del == 1) continue;
-					}
-
-					///each unitig
-					for (b_max.untigI = 0; b_max.untigI < b_max.b_0->b.n; b_max.untigI++)
-					{
-						node_max = &(ug->u.a[b_max.b_0->b.a[b_max.untigI]>>1]);
-						///each read
-						for (b_max.readI = 0; b_max.readI < node_max->n; b_max.readI++)
-						{
-							if(tn == (node_max->a[b_max.readI]>>33))
-							{
-								max_count++;
-								goto end_check_different_haps_ug;
-							}
-						}
-					}
-				}
-
-				end_check_different_haps_ug:;
-			}
-		}
-	}
-	else
-	{
-		///each read
-		for (b_min.untigI = 0; b_min.untigI < b_min.b_0->b.n; b_min.untigI++)
-		{
-			qn = (b_min.b_0->b.a[b_min.untigI]>>1);
-
-			if(reverse_sources[qn].length > 0) min_count++;
-
-			for (j = 0; j < (long long)reverse_sources[qn].length; j++)
-        	{
-            	tn = Get_tn(reverse_sources[qn].buffer[j]);
-				if(nsg->seq[tn].del == 1)
-				{
-					get_R_to_U(ruIndex, tn, &tn, &is_Unitig);
-					if(tn == (uint32_t)-1 || is_Unitig == 1 || nsg->seq[tn].del == 1) continue;
-				}
-
-				///each read
-				for (b_max.untigI = 0; b_max.untigI < b_max.b_0->b.n; b_max.untigI++)
-                {
-					if((b_max.b_0->b.a[b_max.untigI]>>1) == tn)
-					{
-						max_count++;
-						goto end_check_different_haps_non_ug;
-					}
-				}
-			}
-
-			end_check_different_haps_non_ug:;
-		}
-	}
-
-	// if(((v_0==7707) && (v_1==26867))||((v_1==7707) && (v_0==26867)))
-	// {
-	// 	fprintf(stderr, "******\nv_0>>1: %u, v_0&1: %u, ELen_0: %u\n", v_0>>1, v_0&1, (uint32_t)ELen_0);
-	// 	fprintf(stderr, "v_1>>1: %u, v_1&1: %u, ELen_1: %u\n", v_1>>1, v_1&1, (uint32_t)ELen_1);
-	// 	fprintf(stderr, "min_count: %u, max_count: %u, DIFF_HAP_RATE: %f\n\n", 
-	// 	min_count, max_count, DIFF_HAP_RATE);
-	// }
-	
-	if(min_count == 0) return UNAVAILABLE;
-	if(max_count > min_count*DIFF_HAP_RATE) return PLOID;
-	return NON_PLOID;
-}
-
-
 
 typedef struct {
 	uint32_t father_occ;