added mothurOutJustToScreen function and changed all counter outputs to use it.

[mothur.git] / chimeraslayercommand.cpp

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index fceef2180163f60e3c33cfecb7e861839c4bd1c7..e7003c4d88bfe40266dffcf0770e3037cb39f38f 100644 (file)
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -603,10 +603,7 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                        m->mothurConvert(temp, numwanted);
             
                        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);
                        
                        blastlocation = validParameter.validFile(parameters, "blastlocation", false);   
@@ -1631,7 +1628,7 @@ int ChimeraSlayerCommand::createProcessesGroups(string outputFName, string accno
                //Create processor worker threads.
                for(int i=1; i<processors; i++ ){
                        string extension = toString(i) + ".temp";
-                       slayerData* tempslayer = new slayerData(group2NameMap, hasCount, dups, (accnos + extension+".byCount"), (outputFName + extension), (fasta + extension), (accnos + extension), templatefile, search, blastlocation, trimera, trim, realign, m, breakUp[i], fileGroup, ksize, match, mismatch, window, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, divR, priority, i);
+                       slayerData* tempslayer = new slayerData(group2NameMap, hasCount, dups, (accnos + toString(i) +".byCount"), (outputFName + extension), (fasta + extension), (accnos + extension), templatefile, search, blastlocation, trimera, trim, realign, m, breakUp[i], fileGroup, ksize, match, mismatch, window, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, divR, priority, i);
                        pDataArray.push_back(tempslayer);
                        processIDS.push_back(i);
                        
@@ -1826,10 +1823,10 @@ int ChimeraSlayerCommand::driver(linePair filePos, string outputFName, string fi
                        
                        delete candidateSeq;
                        //report progress
-                       if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
+                       if((count) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n");             }
                }
                //report progress
-               if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
+               if((count) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count)+ "\n");              }
                
                int numNoParents = chimera->getNumNoParents();
                if (numNoParents == count) { m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors."); m->mothurOutEndLine(); } 
@@ -1976,10 +1973,10 @@ int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fil
                        delete candidateSeq;
                        
                        //report progress
-                       if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;        m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n");          }
+                       if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;                }
                }
                //report progress
-               if(num % 100 != 0){             cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n");  }
+               if(num % 100 != 0){             cout << "Processing sequence: " << num << endl;         }
                
                int numNoParents = chimera->getNumNoParents();
                if (numNoParents == num) { cout << "[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors." << endl; }