From 03193ff423c9526ff6525040cab60ff715d8cc48 Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Mon, 3 Aug 2009 12:17:33 +0000
Subject: [PATCH] bugs for 1.5

---
 engine.cpp     | 5 +----
 fileoutput.cpp | 2 +-
 2 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/engine.cpp b/engine.cpp
index e589803..0a0f5a0 100644
--- 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 df1bfec..63130a8 100644
--- 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;
 			}
-- 
2.39.2