X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=shhhseqscommand.cpp;h=5c6359ec58bb776ce9a050a132e8409e60cf197b;hb=2c97dd48b8e27ee0a6a86c7a082f4c504c3357c6;hp=6a339b880eb54eedaa7be7af3c297ed0089beb10;hpb=0ca63a8165baa0afa459e644ebe140ba496d5ba0;p=mothur.git

diff --git a/shhhseqscommand.cpp b/shhhseqscommand.cpp
index 6a339b8..5c6359e 100644
--- a/shhhseqscommand.cpp
+++ b/shhhseqscommand.cpp
@@ -161,10 +161,16 @@ ShhhSeqsCommand::ShhhSeqsCommand(string option) {
 			
 			string temp	= validParameter.validFile(parameters, "sigma", false);		if(temp == "not found"){	temp = "0.01"; }
 			m->mothurConvert(temp, sigma); 
-			
+			sigma = 1/sigma;
+            
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
 			m->mothurConvert(temp, processors);
+			
+			if (namefile == "") {
+				vector<string> files; files.push_back(fastafile);
+				parser.getNameFile(files);
+			}
 		}
 	}
 	catch(exception& e) {
@@ -358,7 +364,7 @@ vector<string> ShhhSeqsCommand::createProcessesGroups(SequenceParser& parser, st
 			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) {
@@ -689,14 +695,15 @@ int ShhhSeqsCommand::deconvoluteResults(string fastaFile, string nameFile){
 		string inputString = "fasta=" + fastaFile + ", name=" + nameFile;
 		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(); 
 		
 		string newnameFile = filenames["name"][0];