diff --git a/wrap/FileWriter.cpp b/wrap/FileWriter.cpp
index 38abf2488..03339a7f0 100644
--- a/wrap/FileWriter.cpp
+++ b/wrap/FileWriter.cpp
@@ -35,7 +35,7 @@ void FileWriter::emit(bool add_header, bool force_overwrite) const {
 	// Only write a file if it is new, an update, or overwrite is forced
 	string new_contents = oss.str();
 	if (force_overwrite || !file_exists || existing_contents != new_contents) {
-		ofstream ofs(filename_.c_str());
+		ofstream ofs(filename_.c_str(), ios::binary); // Binary to use LF line endings instead of CRLF
 		if (!ofs) throw CantOpenFile(filename_);
 
 		// header
diff --git a/wrap/utilities.cpp b/wrap/utilities.cpp
index 9c5d93c76..6eb47c55d 100644
--- a/wrap/utilities.cpp
+++ b/wrap/utilities.cpp
@@ -29,7 +29,7 @@ using namespace std;
 
 /* ************************************************************************* */
 string file_contents(const string& filename, bool skipheader) {
-  ifstream ifs(filename.c_str());
+  ifstream ifs(filename.c_str(), ios::binary); // Do not do LF/CRLF translation - we always write in binary mode too
   if(!ifs) throw CantOpenFile(filename);
 
   // read file into stringstream