Fix seg fault when memorymapped handles files that end exactly at the…

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soedinglab · Nov 23, 2022 · 712f288 · 712f288
1 parent 19dce03
commit 712f288
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Showing 2 changed files with 6 additions and 3 deletions.
diff --git 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
@@ -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);