added chimera.uchime

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index abd699eff98156435de11ad2f3cf891b09ffa76e..891b77b63a082c43002d337986ba258e8f88ee0f 100644 (file)
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -380,11 +380,12 @@ int ChimeraUchimeCommand::execute(){
                        
                        if (m->control_pressed) {  for (int j = 0; j < outputNames.size(); j++) {       remove(outputNames[j].c_str()); }  return 0;    }
                        
+                       int numSeqs = 0;
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-                       if(processors == 1){ driver(outputFileName, fastaFileNames[s], accnosFileName); }
-                       else{   createProcesses(outputFileName, fastaFileNames[s], accnosFileName); }
+                       if(processors == 1){ numSeqs = driver(outputFileName, fastaFileNames[s], accnosFileName); }
+                       else{   numSeqs = createProcesses(outputFileName, fastaFileNames[s], accnosFileName); }
 #else
-                       driver(outputFileName, fastaFileNames[s], accnosFileName);
+                       numSeqs = driver(outputFileName, fastaFileNames[s], accnosFileName);
 #endif
                        if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) {        remove(outputNames[j].c_str()); } return 0; }
 
@@ -392,7 +393,7 @@ int ChimeraUchimeCommand::execute(){
                        outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
                        outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName);
                        
-                       m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check your sequences.");      m->mothurOutEndLine();
+                       m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
                }
                
                //set accnos file as new current accnosfile
@@ -454,7 +455,7 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc
                
                char** uchimeParameters;
                uchimeParameters = new char*[cPara.size()];
-               for (int i = 0; i < cPara.size(); i++) {  uchimeParameters[i] = cPara[i]; cout << cPara[i]; } cout << endl;
+               for (int i = 0; i < cPara.size(); i++) {  uchimeParameters[i] = cPara[i];  } 
                int numArgs = cPara.size();
                
                uchime_main(numArgs, uchimeParameters);