added rarepercent and keepties parameters to the filter.shared command.

[mothur.git] / classifyseqscommand.cpp

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 89668d9e7bd122577d9be167f590a96a6aedbf22..8b6a77b4936b0095741747cb255e143a1cd78e64 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -258,7 +258,6 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
 
                        namefile = validParameter.validFile(parameters, "name", false);
                        if (namefile == "not found") { namefile = "";  }
-
                        else { 
                                m->splitAtDash(namefile, namefileNames);
                                
@@ -610,7 +609,7 @@ int ClassifySeqsCommand::execute(){
        try {
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
         
-        string outputMethodTag = method + ".";
+        string outputMethodTag = method;
                if(method == "wang"){   classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters, rand(), flip, writeShortcuts);     }
                else if(method == "knn"){       classify = new Knn(taxonomyFileName, templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, numWanted, rand());                               }
         else if(method == "zap"){      
@@ -782,7 +781,7 @@ int ClassifySeqsCommand::execute(){
                        }
 #endif
                        
-                       if (!m->isBlank(newaccnosFile)) { m->mothurOutEndLine(); m->mothurOut("[WARNING]: mothur suspects some of your sequences may be reversed, please check " + newaccnosFile + " for the list of the sequences."); m->mothurOutEndLine(); 
+                       if (!m->isBlank(newaccnosFile)) { m->mothurOutEndLine(); m->mothurOut("[WARNING]: mothur reversed some your sequences for a better classification.  If you would like to take a closer look, please check " + newaccnosFile + " for the list of the sequences."); m->mothurOutEndLine(); 
                 outputNames.push_back(newaccnosFile); outputTypes["accnos"].push_back(newaccnosFile);
             }else { m->mothurRemove(newaccnosFile); }
 
@@ -1044,6 +1043,9 @@ int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile,
                //Close all thread handles and free memory allocations.
                for(int i=0; i < pDataArray.size(); i++){
                        num += pDataArray[i]->count;
+            if (pDataArray[i]->count != pDataArray[i]->end) {
+                m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true; 
+            }
                        CloseHandle(hThreadArray[i]);
                        delete pDataArray[i];
                }