working on pam

[mothur.git] / chimeraperseuscommand.cpp

diff --git a/chimeraperseuscommand.cpp b/chimeraperseuscommand.cpp
index 842a65ee22fd54c730143cbed94f91688dba8006..0547802198960198d9d2a063bc498e79f04bfe33 100644 (file)
--- a/chimeraperseuscommand.cpp
+++ b/chimeraperseuscommand.cpp
@@ -469,10 +469,7 @@ ChimeraPerseusCommand::ChimeraPerseusCommand(string option)  {
                        m->mothurConvert(temp, beta);
             
                        temp = validParameter.validFile(parameters, "dereplicate", false);      
-                       if (temp == "not found") { 
-                               if (groupfile != "")    {  temp = "false";                                      }
-                               else                    {  temp = "true";       }
-                       }
+                       if (temp == "not found") { temp = "false";                      }
                        dups = m->isTrue(temp);
                }
        }
@@ -519,7 +516,7 @@ int ChimeraPerseusCommand::execute(){
             
             if (hasCount) {
                 CountTable* ct = new CountTable();
-                ct->readTable(nameFile);
+                ct->readTable(nameFile, true, false);
                 
                 if (ct->hasGroupInfo()) {
                     cparser = new SequenceCountParser(fastaFileNames[s], *ct);
@@ -537,7 +534,7 @@ int ChimeraPerseusCommand::execute(){
                     
                     if(processors == 1)        {       numSeqs = driverGroups(outputFileName, accnosFileName, newCountFile, 0, groups.size(), groups);
                         if (dups) {
-                            CountTable c; c.readTable(nameFile);
+                            CountTable c; c.readTable(nameFile, true, false);
                             if (!m->isBlank(newCountFile)) {
                                 ifstream in2;
                                 m->openInputFile(newCountFile, in2);
@@ -562,7 +559,7 @@ int ChimeraPerseusCommand::execute(){
                         numChimeras = deconvoluteResults(uniqueNames, outputFileName, accnosFileName);
                     }else {
                         set<string> doNotRemove;
-                        CountTable c; c.readTable(newCountFile);
+                        CountTable c; c.readTable(newCountFile, true, true);
                         vector<string> namesInTable = c.getNamesOfSeqs();
                         for (int i = 0; i < namesInTable.size(); i++) {
                             int temp = c.getNumSeqs(namesInTable[i]);
@@ -1049,10 +1046,10 @@ int ChimeraPerseusCommand::driver(string chimeraFileName, vector<seqData>& seque
                        }
        
                        //report progress
-                       if((i+1) % 100 == 0){   m->mothurOut("Processing sequence: " + toString(i+1) + "\n");           }
+                       if((i+1) % 100 == 0){   m->mothurOutJustToScreen("Processing sequence: " + toString(i+1) + "\n");               }
                }
                
-               if((numSeqs) % 100 != 0){       m->mothurOut("Processing sequence: " + toString(numSeqs) + "\n");               }
+               if((numSeqs) % 100 != 0){       m->mothurOutJustToScreen("Processing sequence: " + toString(numSeqs) + "\n");           }
                
                chimeraFile.close();
                accnosFile.close();
@@ -1073,7 +1070,7 @@ int ChimeraPerseusCommand::createProcessesGroups(string outputFName, string accn
                int num = 0;
                
         CountTable newCount;
-        if (hasCount && dups) { newCount.readTable(name); }
+        if (hasCount && dups) { newCount.readTable(name, true, false); }
         
                //sanity check
                if (groups.size() < processors) { processors = groups.size(); }