X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimeraslayercommand.cpp;h=d16843c8d612fac2bde8c03db8e45ce68e869412;hp=d8e0952a8b9f89cd237946a27ea624f11fa42898;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=859e3a473a3e63e0060c49be70b80f9289253da2

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index d8e0952..d16843c 100644
--- 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);