bugs for 1.5

diff --git a/engine.cpp b/engine.cpp
index e5898036e2e4ebd5ddea0af89735ed7efacdf924..0a0f5a0ce7f0f4f0a120509e2c3d5c0e51471ecb 100644 (file)
--- a/engine.cpp
+++ b/engine.cpp
@@ -119,10 +119,7 @@ bool BatchEngine::getInput(){
                while(quitCommandCalled == 0){
        
                        if (inputBatchFile.eof()) { input = "quit()"; }
-                       else { getline(inputBatchFile, input); }
-       //cout << "input = ";           
-       //for (int i = 0; i < input.size();  i++) {  cout << input[i];  if ((input[i] == '\n') || (input[i] == '\r')) {  char c = input[i]; cout << "line feed = " << c << endl; } }
-       //cout << endl;         
+                       else { input = getline(inputBatchFile); }
                        
                        if (input[0] != '#') {
                                

diff --git a/fileoutput.cpp b/fileoutput.cpp
index df1bfecfc0de7e3183ace1e826ef9d536f9dc5c3..63130a83ba6c850bc8db4ea720ba51a15d80ff81 100644 (file)
--- a/fileoutput.cpp
+++ b/fileoutput.cpp
@@ -409,7 +409,7 @@ void SharedOneColumnFile::output(int nSeqs, vector<double> data){
                        }
                        if(counter != 0){               
                                string inputBuffer;
-                               inputBuffer = getline(inFile);
+                               getline(inFile, inputBuffer);
 
                                outFile <<  inputBuffer << setprecision(2) << '\t' << dataOutput << endl;
                        }