From e6cdac9ea9c14fbc967c13af8ca119d0086cd7e6 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Thu, 26 Dec 2019 10:06:58 -0500
Subject: [PATCH] fixed a few harmless warnings

---
 Overlaps.cpp | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/Overlaps.cpp b/Overlaps.cpp
index 08d27c3..e159cb0 100644
--- a/Overlaps.cpp
+++ b/Overlaps.cpp
@@ -104,6 +104,7 @@ uint64_t* source_index, long long listLen)
         source_i = (uint32_t)(source_index[i]);
         tmp = &(source_paf_list[source_n].buffer[source_i]);
 
+		ele.del = 0;
         ele.rev = tmp->rev;
         ele.qns = Get_tn((*tmp));
         ele.qns = ele.qns << 32;
@@ -445,6 +446,7 @@ void normalize_ma_hit_t(ma_hit_t_alloc* sources, long long num_sources)
             else
             {
                 ///must have this line
+				new_element.del = 0;
                 new_element.ml = 1;
                 new_element.no_l_indel = 1;
                 set_reverse_overlap(&new_element, &(sources[i].buffer[j]));
@@ -4685,7 +4687,7 @@ int asg_arc_del_too_short_overlaps(asg_t *g, long long dropLen, float drop_ratio
     double startTime = Get_T();
 
 	uint32_t v, v_max, v_maxLen, n_vtx = g->n_seq * 2, n_short = 0;
-    long long drop_ratio_Len;
+    long long drop_ratio_Len = 0;
     
     for (v = 0; v < n_vtx; ++v) 
     {
@@ -5741,7 +5743,7 @@ int asg_arc_del_tri_link(asg_t *g, int max_dist)
             
             if(f1 && f2)
             {
-                if((l1 <= min_thres) || (l2 <= min_thres))
+                if(l1 <= min_thres || l2 <= min_thres) // TODO: check this block: it is always false
                 {
                     continue;
                 } 
@@ -7607,6 +7609,7 @@ int asg_arc_del_orthology_multiple_way(asg_t *g, ma_hit_t_alloc* reverse_sources
         n_arc = get_real_length(g, v, NULL);
         if (n_arc < 2) continue;
         v_max = (uint32_t)-1;
+		v_maxLen = 0;
 
         for (i = 0, n_arc = 0; i < nv; i++)
         {