From 2726494a626d667d796e305c2da5da6badbceca0 Mon Sep 17 00:00:00 2001
From: Mohamed Abuelanin <abuelanin@users.noreply.github.com>
Date: Mon, 5 Mar 2018 00:37:33 +0200
Subject: [PATCH 1/2] Update match function

---
 src/KmerIndex.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/KmerIndex.cpp b/src/KmerIndex.cpp
index 4f9316b9..5342a47b 100644
--- a/src/KmerIndex.cpp
+++ b/src/KmerIndex.cpp
@@ -1096,7 +1096,7 @@ void KmerIndex::match(const char *s, int l, std::vector<std::pair<KmerEntry, int
           auto search2 = kmap.find(rep2);
           bool found2 = false;
           int  found2pos = pos+dist;
-          if (search2 == kmap.end()) {
+          if (search2 != kmap.end()) {
             found2=true;
             found2pos = pos;
           } else if (val.contig == search2->second.contig) {

From 08d486c8fce6351d4b99edf19bc38e1cd4aa42c3 Mon Sep 17 00:00:00 2001
From: Mohamed Abuelanin <abuelanin@users.noreply.github.com>
Date: Mon, 5 Mar 2018 16:06:35 +0200
Subject: [PATCH 2/2] Update kmerindex::match function

---
 src/KmerIndex.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/KmerIndex.cpp b/src/KmerIndex.cpp
index 5342a47b..bed5905c 100644
--- a/src/KmerIndex.cpp
+++ b/src/KmerIndex.cpp
@@ -1099,6 +1099,7 @@ void KmerIndex::match(const char *s, int l, std::vector<std::pair<KmerEntry, int
           if (search2 != kmap.end()) {
             found2=true;
             found2pos = pos;
+            v.push_back({search2->second, kit2->second});
           } else if (val.contig == search2->second.contig) {
             found2=true;
             found2pos = pos+dist;