X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifyotucommand.cpp;h=ec22de8b35762adf92e2a3b750198dcbb91f0396;hb=e339f9008daa7d37c9a9034829565620a6abe783;hp=f36631a0590725867dffc402f74fd73af6168e20;hpb=74dc92cf53df65fd8b14d8eaf35489bbecbccac6;p=mothur.git

diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index f36631a..ec22de8 100644
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -182,7 +182,7 @@ ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
 			else if (refTaxonomy == "not open") { abort = true; }
 	
 			namefile = validParameter.validFile(parameters, "name", true);
-			if (namefile == "not open") { abort = true; }	
+			if (namefile == "not open") { namefile = ""; abort = true; }	
 			else if (namefile == "not found") { namefile = ""; }
 			else { m->setNameFile(namefile); }
 			
@@ -206,7 +206,7 @@ ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
 			if ((basis != "otu") && (basis != "sequence")) { m->mothurOut("Invalid option for basis. basis options are otu and sequence, using otu."); m->mothurOutEndLine(); }
 			
 			string temp = validParameter.validFile(parameters, "cutoff", false);			if (temp == "not found") { temp = "51"; }
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 			
 			temp = validParameter.validFile(parameters, "probs", false);					if (temp == "not found"){	temp = "true";			}
 			probs = m->isTrue(temp);
@@ -214,6 +214,11 @@ ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
 			
 			if ((cutoff < 51) || (cutoff > 100)) { m->mothurOut("cutoff must be above 50, and no greater than 100."); m->mothurOutEndLine(); abort = true;  }
 			
+			if (namefile == ""){
+				vector<string> files; files.push_back(taxfile);
+				parser.getNameFile(files);
+			}
+			
 		}
 	}
 	catch(exception& e) {
@@ -470,6 +475,9 @@ vector<string> ClassifyOtuCommand::findConsensusTaxonomy(int bin, ListVector* th
 				}
 				
 			}
+            
+            //phylotree adds an extra unknown so we want to remove that
+            if (bestChild.name == "unknown") { bestChildSize--; }
 				
 			//is this taxonomy above cutoff
 			int consensusConfidence = ceil((bestChildSize / (float) size) * 100);