X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clustersplitcommand.cpp;h=270ea6208d8ead0683d8cf46fb8d7a417469c243;hb=372fb21ea66ced432b109225851a1b80ef0491a3;hp=92f0e486898f80b2c6f85bb984a5b7662bc18340;hpb=01d5a60fc5f396339acf529151fa8186ee7c1a41;p=mothur.git

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index 92f0e48..270ea62 100644
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -442,8 +442,7 @@ int ClusterSplitCommand::execute(){
         if (m->debug) { m->mothurOut("[DEBUG]: distName.size() = " + toString(distName.size()) + ".\n"); }
                 
 		//output a merged distance file
-		if (splitmethod == "fasta")		{ createMergedDistanceFile(distName); }
-			
+		//if (splitmethod == "fasta")		{ createMergedDistanceFile(distName); }
 				
 		if (m->control_pressed) { return 0; }
 		
@@ -844,9 +843,12 @@ int ClusterSplitCommand::mergeLists(vector<string> listNames, map<float, int> us
 			if (itLabel->first == -1) { thisLabel = "unique"; }
 			else { thisLabel = toString(itLabel->first,  length-1);  } 
 			
-			outList << thisLabel << '\t' << itLabel->second << '\t';
+			//outList << thisLabel << '\t' << itLabel->second << '\t';
             
             RAbundVector* rabund = NULL;
+            ListVector completeList;
+            completeList.setLabel(thisLabel);
+            
             if (countfile == "") {
                 rabund = new RAbundVector();
                 rabund->setLabel(thisLabel);
@@ -855,7 +857,8 @@ int ClusterSplitCommand::mergeLists(vector<string> listNames, map<float, int> us
 			//add in singletons
 			if (listSingle != NULL) {
 				for (int j = 0; j < listSingle->getNumBins(); j++) {
-					outList << listSingle->get(j) << '\t';
+					//outList << listSingle->get(j) << '\t';
+                    completeList.push_back(listSingle->get(j));
 					if (countfile == "") { rabund->push_back(m->getNumNames(listSingle->get(j))); }
 				}
 			}
@@ -872,7 +875,8 @@ int ClusterSplitCommand::mergeLists(vector<string> listNames, map<float, int> us
 				if (list == NULL) { m->mothurOut("Error merging listvectors in file " + listNames[k]); m->mothurOutEndLine();  }	
 				else {		
 					for (int j = 0; j < list->getNumBins(); j++) {
-						outList << list->get(j) << '\t';
+						//outList << list->get(j) << '\t';
+                        completeList.push_back(list->get(j));
 						if (countfile == "") { rabund->push_back(m->getNumNames(list->get(j))); }
 					}
 					delete list;
@@ -885,7 +889,8 @@ int ClusterSplitCommand::mergeLists(vector<string> listNames, map<float, int> us
                 sabund.print(outSabund);
                 rabund->print(outRabund);
             }
-			outList << endl;
+			//outList << endl;
+            completeList.print(outList);
 			
 			if (rabund != NULL) { delete rabund; }
 		}
@@ -1169,7 +1174,7 @@ string ClusterSplitCommand::clusterClassicFile(string thisDistFile, string thisN
             cluster->readPhylipFile(thisDistFile, nameMap);
 		}else if (countfile != "") {
             ct = new CountTable();
-            ct->readTable(thisNamefile);
+            ct->readTable(thisNamefile, false);
             cluster->readPhylipFile(thisDistFile, ct);
         }
         tag = cluster->getTag();
@@ -1297,7 +1302,7 @@ string ClusterSplitCommand::clusterFile(string thisDistFile, string thisNamefile
             read->read(nameMap);
 		}else if (countfile != "") {
             ct = new CountTable();
-            ct->readTable(thisNamefile);
+            ct->readTable(thisNamefile, false);
             read->read(ct);
         }else { read->read(nameMap); }