X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerauchimecommand.cpp;h=3d23a7693818f329ff6ac53cca560998c8a9fc95;hb=c48d91112209b841444923670dca5454da0e2a4d;hp=cb155eb2e53c3b8ba47c4ed36aa495efaef4460a;hpb=e946299389ed49b4afc4262a4e8070ee3d804769;p=mothur.git

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index cb155eb..3d23a76 100644
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -564,10 +564,7 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
             
             
 			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);
 
 			
@@ -774,6 +771,7 @@ int ChimeraUchimeCommand::execute(){
                         }
                         out2.close();
                         c.printTable(newCountFile);
+                        outputNames.push_back(newCountFile); outputTypes["count"].push_back(newCountFile);
                     }
                 }
                 
@@ -819,6 +817,11 @@ int ChimeraUchimeCommand::execute(){
 		if (itTypes != outputTypes.end()) {
 			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
 		}
+        
+        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();
@@ -839,10 +842,6 @@ int ChimeraUchimeCommand::deconvoluteResults(map<string, string>& uniqueNames, s
 		map<string, string>::iterator itUnique;
 		int total = 0;
 		
-		//edit accnos file
-		ifstream in2; 
-		m->openInputFile(accnosFileName, in2);
-		
 		ofstream out2;
 		m->openOutputFile(accnosFileName+".temp", out2);
 		
@@ -852,27 +851,32 @@ int ChimeraUchimeCommand::deconvoluteResults(map<string, string>& uniqueNames, s
 		set<string> chimerasInFile;
 		set<string>::iterator itChimeras;
 
-		
-		while (!in2.eof()) {
-			if (m->control_pressed) { in2.close(); out2.close(); m->mothurRemove(outputFileName); m->mothurRemove((accnosFileName+".temp")); return 0; }
-			
-			in2 >> name; m->gobble(in2);
-			
-			//find unique name
-			itUnique = uniqueNames.find(name);
-			
-			if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing accnos results. Cannot find " + name + "."); m->mothurOutEndLine(); m->control_pressed = true; }
-			else {
-				itChimeras = chimerasInFile.find((itUnique->second));
-				
-				if (itChimeras == chimerasInFile.end()) {
-					out2 << itUnique->second << endl;
-					chimerasInFile.insert((itUnique->second));
-					total++;
-				}
-			}
-		}
-		in2.close();
+        if (!m->isBlank(accnosFileName)) {
+            //edit accnos file
+            ifstream in2;
+            m->openInputFile(accnosFileName, in2);
+            
+            while (!in2.eof()) {
+                if (m->control_pressed) { in2.close(); out2.close(); m->mothurRemove(outputFileName); m->mothurRemove((accnosFileName+".temp")); return 0; }
+                
+                in2 >> name; m->gobble(in2);
+                
+                //find unique name
+                itUnique = uniqueNames.find(name);
+                
+                if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing accnos results. Cannot find " + name + "."); m->mothurOutEndLine(); m->control_pressed = true; }
+                else {
+                    itChimeras = chimerasInFile.find((itUnique->second));
+                    
+                    if (itChimeras == chimerasInFile.end()) {
+                        out2 << itUnique->second << endl;
+                        chimerasInFile.insert((itUnique->second));
+                        total++;
+                    }
+                }
+            }
+            in2.close();
+        }
 		out2.close();
 		
 		m->mothurRemove(accnosFileName);
@@ -1181,6 +1185,7 @@ int ChimeraUchimeCommand::driverGroups(string outputFName, string filename, stri
 		int totalSeqs = 0;
 		int numChimeras = 0;
         
+        
         ofstream outCountList;
         if (hasCount && dups) { m->openOutputFile(countlist, outCountList); }