X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerauchimecommand.cpp;h=6f7ba106ead04e9ccd3b7b290dce4c3a55dabd20;hb=79a7d3273749b08d4f9f8dfe350c964ff0c4351e;hp=ae011906ded5c95b3aec8bfb57047e27ae42392b;hpb=e10c72304ee071c0c40e0218a06d89dc4731cbc2;p=mothur.git

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index ae01190..6f7ba10 100644
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -1452,15 +1452,21 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc
 			
 			string name = "";
 			string chimeraFlag = "";
-			in >> chimeraFlag >> name;
-			
-			//fix name if needed
-			if (templatefile == "self") { 
-				name = name.substr(0, name.length()-1); //rip off last /
-				name = name.substr(0, name.find_last_of('/'));
+			//in >> chimeraFlag >> name;
+			
+            string line = m->getline(in);
+            vector<string> pieces = m->splitWhiteSpace(line);
+            if (pieces.size() > 2) { 
+                name = pieces[1];
+                //fix name if needed
+                if (templatefile == "self") { 
+                    name = name.substr(0, name.length()-1); //rip off last /
+                    name = name.substr(0, name.find_last_of('/'));
+                }
+                
+                chimeraFlag = pieces[pieces.size()-1];
 			}
-			
-			for (int i = 0; i < 15; i++) {  in >> chimeraFlag; }
+			//for (int i = 0; i < 15; i++) {  in >> chimeraFlag; }
 			m->gobble(in);
 			
 			if (chimeraFlag == "Y") {  out << name << endl; numChimeras++; }