Fixes bug with cluster method agc

Improper size notation was causing vsearch to ignore it

source/commands/chimerauchimecommand.cpp

@@ -675,7 +675,7 @@ int ChimeraUchimeCommand::execute(){
 				if (error == 1) { for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	}  return 0; }
 				if (seqs.size() != nameMapCount.size()) { m->mothurOut( "The number of sequences in your fastafile does not match the number of sequences in your namefile, aborting."); m->mothurOutEndLine(); for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	}  return 0; }
 				
-                m->printVsearchFile(nameMapCount, newFasta, "ab");
+                m->printVsearchFile(nameMapCount, newFasta, "/ab=", "/");
 				fastaFileNames[s] = newFasta;
 			}
 			

source/commands/chimeravsearchcommand.cpp

@@ -627,7 +627,7 @@ int ChimeraVsearchCommand::execute(){
                 if (error == 1) { for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	}  return 0; }
                 if (seqs.size() != nameMapCount.size()) { m->mothurOut( "The number of sequences in your fastafile does not match the number of sequences in your namefile, aborting."); m->mothurOutEndLine(); for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	}  return 0; }
                 
-                m->printVsearchFile(nameMapCount, newFasta);
+                m->printVsearchFile(nameMapCount, newFasta, ";size=", ";");
                 fastaFileNames[s] = newFasta;
             }
             

source/commands/clustercommand.cpp

@@ -563,6 +563,8 @@ int ClusterCommand::vsearchDriver(string inputFile, string ucClusteredFile, stri
         for (int i = 0; i < vsearchParameters.size(); i++) {    commandString += toString(vsearchParameters[i]) + " "; }
  
         //cout << "commandString = " << commandString << endl;
+        //exit(1);
+        
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
         commandString = "\"" + commandString + "\"";

source/mothurout.cpp

@@ -4873,7 +4873,7 @@ int MothurOut::min(int A, int B){
     }
 }
 //**********************************************************************************************************************
-int MothurOut::printVsearchFile(vector<seqPriorityNode>& nameMapCount, string filename, string tag){
+int MothurOut::printVsearchFile(vector<seqPriorityNode>& nameMapCount, string filename, string tag, string tag2){
     try {
         
         sort(nameMapCount.begin(), nameMapCount.end(), compareSeqPriorityNodes);
@@ -4884,7 +4884,7 @@ int MothurOut::printVsearchFile(vector<seqPriorityNode>& nameMapCount, string fi
         //print new file in order of
         for (int i = 0; i < nameMapCount.size(); i++) {
             if (control_pressed) {break;}
-            out << ">" << nameMapCount[i].name  << "/" + tag + "=" << nameMapCount[i].numIdentical << "/" << endl << nameMapCount[i].seq << endl;
+            out << ">" << nameMapCount[i].name  << tag << nameMapCount[i].numIdentical << tag2 << endl << nameMapCount[i].seq << endl;
         }
         out.close();
         

source/mothurout.h

@@ -140,7 +140,7 @@ class MothurOut {
 		int readNames(string, map<string, vector<string> >&);
 		int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
 		int mothurRemove(string);
-        int printVsearchFile(vector<seqPriorityNode>&, string, string); //sorts and prints by abundance adding /ab=xxx/
+        int printVsearchFile(vector<seqPriorityNode>&, string, string, string); //sorts and prints by abundance adding /ab=xxx/
         bool mothurConvert(char, int&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
 		bool mothurConvert(string, int&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
         bool mothurConvert(string, intDist&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.

source/vsearchfileparser.cpp

@@ -111,7 +111,7 @@ string VsearchFileParser::createVsearchFasta(string inputFile){
         }
         in.close();
         
-        m->printVsearchFile(seqs, vsearchFasta, "size");
+        m->printVsearchFile(seqs, vsearchFasta, ";size=", ";");
         
         return vsearchFasta;
     }
@@ -226,7 +226,7 @@ int VsearchFileParser::createListFile(string inputFile, string listFile, string
 string VsearchFileParser::removeAbundances(string seqName){
     try {
         
-        int pos = seqName.find_last_of("/", seqName.length()-2); //don't look at the last /
+        int pos = seqName.find_last_of(";", seqName.length()-2); //don't look at the last /
         if (pos != string::npos) { seqName = seqName.substr(0, pos); }
         
         return seqName;