added sets to amova and homova commands. added oligos to make.contigs. added metadat...

[mothur.git] / chimerauchimecommand.cpp

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index ae011906ded5c95b3aec8bfb57047e27ae42392b..6f7ba106ead04e9ccd3b7b290dce4c3a55dabd20 100644 (file)
--- 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++; }