X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=aligncommand.cpp;h=2fda2529176bb263070c055965e74eaac732faf4;hp=5af8e959a6caa3edd98a33a21fa680bd5815d2dc;hb=5ff964d3871ce86f59fec3052f9c25e872f22c42;hpb=28d65de5f06f5b033109a3b8bbb6d3c4060914d3

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 5af8e95..2fda252 100644
--- 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);	}
 				}