From 281c7ed77ba176f8f3de3d2b9063452068439444 Mon Sep 17 00:00:00 2001
From: Anton Korobeynikov <anton@korobeynikov.info>
Date: Tue, 19 Aug 2025 22:44:31 -0700
Subject: [PATCH] Fix invalid memory use

---
 ext/src/ssw/ssw_cpp.cpp                                       | 4 ++--
 .../modules/simplification/topological_edge_conditions.hpp    | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/ext/src/ssw/ssw_cpp.cpp b/ext/src/ssw/ssw_cpp.cpp
index 21dde2a12f..e76c758cb7 100644
--- a/ext/src/ssw/ssw_cpp.cpp
+++ b/ext/src/ssw/ssw_cpp.cpp
@@ -126,8 +126,8 @@ int CalculateNumberMismatch(
     int8_t const *query,
     const int& query_len) {
 
-  ref   += al->ref_begin;
-  query += al->query_begin;
+  ref   += (al->ref_begin > 0 ? al->ref_begin : 0);
+  query += (al->query_begin > 0 ? al->query_begin : 0);
   int mismatch_length = 0;
 
   std::vector<uint32_t> new_cigar;
diff --git a/src/common/modules/simplification/topological_edge_conditions.hpp b/src/common/modules/simplification/topological_edge_conditions.hpp
index 5aeff4820c..a1bb183753 100644
--- a/src/common/modules/simplification/topological_edge_conditions.hpp
+++ b/src/common/modules/simplification/topological_edge_conditions.hpp
@@ -63,7 +63,7 @@ UniquePathLengthLowerBound(const Graph &g, size_t min_length) {
 template<class Graph>
 EdgePredicate<Graph>
 UniqueIncomingPathLengthLowerBound(const Graph &g, size_t min_length) {
-    return [&] (typename Graph::EdgeId e) {
+    return [&g, min_length] (typename Graph::EdgeId e) {
         typename Graph::VertexId v = g.EdgeStart(e);
         return g.CheckUniqueIncomingEdge(v) &&
                 UniquePathLengthLowerBound(g, min_length)(g.GetUniqueIncomingEdge(v));