added getline function to mothur and modified places where we use getline to use...

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 5af8e959a6caa3edd98a33a21fa680bd5815d2dc..2fda2529176bb263070c055965e74eaac732faf4 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -197,7 +197,7 @@ int AlignCommand::execute(){
                        
                        string input;
                        while(!inFASTA.eof()){
-                               getline(inFASTA, input);
+                               input = getline(inFASTA);
                                if (input.length() != 0) {
                                        if(input[0] == '>'){    int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);       }
                                }