some changes on qFinderDMM

[mothur.git] / createdatabasecommand.cpp

diff --git a/createdatabasecommand.cpp b/createdatabasecommand.cpp
index 58799e7a33e840580654d006b7a085ec02e7c5f5..235682bfec8fdfc36c43ed25fb78ffd06eef1b4f 100644 (file)
--- a/createdatabasecommand.cpp
+++ b/createdatabasecommand.cpp
@@ -298,7 +298,7 @@ int CreateDatabaseCommand::execute(){
             }
             repNames = tempRepNames;
         }else {
-            ct.readTable(countfile, true);
+            ct.readTable(countfile, true, false);
             numUniqueNamesFile = ct.getNumUniqueSeqs();
             nameMap = ct.getNameMap();
         }
@@ -380,8 +380,8 @@ int CreateDatabaseCommand::execute(){
                 if (countfile == "") {
                     sort(binNames.begin(), binNames.end());
                     bin = "";
-                    for (int i = 0; i < binNames.size()-1; i++) {
-                        bin += binNames[i] + ',';
+                    for (int j = 0; j < binNames.size()-1; j++) {
+                        bin += binNames[j] + ',';
                     }
                     bin += binNames[binNames.size()-1];
                     map<string, string>::iterator it = repNames.find(bin);
@@ -506,7 +506,7 @@ int CreateDatabaseCommand::findIndex(vector<string>& otuLabels, string label){
        try {
         int index = -1;
         for (int i = 0; i < otuLabels.size(); i++) {
-            if (otuLabels[i] == label) { index = i; break; }
+            if (m->isLabelEquivalent(otuLabels[i],label)) { index = i; break; }
         }
                return index;
     }
@@ -743,7 +743,7 @@ vector<SharedRAbundVector*> CreateDatabaseCommand::getShared(){
         return lookup;
     }
        catch(exception& e) {
-               m->errorOut(e, "CreateDatabaseCommand", "getList");
+               m->errorOut(e, "CreateDatabaseCommand", "getShared");
                exit(1);
        }
 }