From 712f28879bb7a8b34da6adc470531c77964d3955 Mon Sep 17 00:00:00 2001
From: Ruoshi Zhang <rosyzhang9701@gmail.com>
Date: Tue, 11 Jan 2022 14:43:26 +0100
Subject: [PATCH] Fix seg fault when memorymapped handles files that end
 exactly at the end of page

---
 src/util/convertalignments.cpp | 6 ++++--
 src/util/gff2db.cpp            | 3 ++-
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/src/util/convertalignments.cpp b/src/util/convertalignments.cpp
index 79e38e04d..f0d889309 100644
--- a/src/util/convertalignments.cpp
+++ b/src/util/convertalignments.cpp
@@ -102,8 +102,9 @@ std::map<unsigned int, unsigned int> readKeyToSet(const std::string& file) {
 
     MemoryMapped lookup(file, MemoryMapped::WholeFile, MemoryMapped::SequentialScan);
     char* data = (char *) lookup.getData();
+    char* end = data + lookup.mappedSize();
     const char* entry[255];
-    while (*data != '\0') {
+    while (data < end && *data != '\0') {
         const size_t columns = Util::getWordsOfLine(data, entry, 255);
         if (columns < 3) {
             Debug(Debug::WARNING) << "Not enough columns in lookup file " << file << "\n";
@@ -125,8 +126,9 @@ std::map<unsigned int, std::string> readSetToSource(const std::string& file) {
 
     MemoryMapped source(file, MemoryMapped::WholeFile, MemoryMapped::SequentialScan);
     char* data = (char *) source.getData();
+    char* end = data + source.mappedSize();
     const char* entry[255];
-    while (*data != '\0') {
+    while (data < end && *data != '\0') {
         const size_t columns = Util::getWordsOfLine(data, entry, 255);
         if (columns < 2) {
             Debug(Debug::WARNING) << "Not enough columns in lookup file " << file << "\n";
diff --git a/src/util/gff2db.cpp b/src/util/gff2db.cpp
index 92daa0bba..6266e08f7 100644
--- a/src/util/gff2db.cpp
+++ b/src/util/gff2db.cpp
@@ -84,8 +84,9 @@ int gff2db(int argc, const char **argv, const Command &command) {
                 EXIT(EXIT_FAILURE);
             }
             char *data = (char *) file.getData();
+            char* end = data + file.mappedSize();
             size_t idx = 0;
-            while (*data != '\0') {
+            while (data < end && *data != '\0') {
                 // line is a comment or empty
                 if (*data == '#' || *data == '\n') {
                     data = Util::skipLine(data);