sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / chimeraslayercommand.cpp

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index d8e0952a8b9f89cd237946a27ea624f11fa42898..d16843c8d612fac2bde8c03db8e45ce68e869412 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);   
@@ -837,6 +834,11 @@ int ChimeraSlayerCommand::execute(){
                        }
                }
                
+        itTypes = outputTypes.find("count");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
+               }
+        
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }       
@@ -1626,7 +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);