X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=preclustercommand.cpp;h=f2fbc80088b1adf2927ee78d5b1e02fbf9691cb1;hb=9aa36ad8297141ef9fcab04fea10e96d2fed26fe;hp=8e4f3274a490679c85f992f8584605c877c84850;hpb=d6c0a11d1cecfac18b323285e7ffadb7f58e848f;p=mothur.git

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index 8e4f327..f2fbc80 100644
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -217,17 +217,19 @@ int PreClusterCommand::execute(){
 			m->mothurOutEndLine(); 
 			m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
 			m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine(); 
-			
+			m->mothurCalling = true;
+            
 			Command* uniqueCommand = new DeconvoluteCommand(inputString);
 			uniqueCommand->execute();
 			
 			map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
 			
 			delete uniqueCommand;
-			
+			m->mothurCalling = false;
 			m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
 			
 			m->renameFile(filenames["fasta"][0], newFastaFile);
+            m->renameFile(filenames["name"][0], newNamesFile);
 			
 			m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run pre.cluster."); m->mothurOutEndLine(); 
 				
@@ -302,7 +304,7 @@ int PreClusterCommand::createProcessesGroups(SequenceParser* parser, string newF
 			lines.push_back(linePair(startIndex, endIndex));
 		}
 		
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)		
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)		
 		
 		//loop through and create all the processes you want
 		while (process != processors) {
@@ -553,6 +555,7 @@ int PreClusterCommand::readFASTA(){
 		//inNames.close();
         
         if (lengths.size() > 1) { m->control_pressed = true; m->mothurOut("[ERROR]: your sequences are not all the same length. pre.cluster requires sequences to be aligned."); m->mothurOutEndLine(); }
+        else if (lengths.size() == 1) { length = *(lengths.begin()); }
         
 		return alignSeqs.size();
 	}
@@ -598,6 +601,7 @@ int PreClusterCommand::loadSeqs(map<string, string>& thisName, vector<Sequence>&
 		}
 		
         if (lengths.size() > 1) { error = true; m->mothurOut("[ERROR]: your sequences are not all the same length. pre.cluster requires sequences to be aligned."); m->mothurOutEndLine(); }
+        else if (lengths.size() == 1) { length = *(lengths.begin()); }
         
 		//sanity check
 		if (error) { m->control_pressed = true; }