working on dereplicate=t issue in chimera.slayer and chimera.perseus, added appendFil...

[mothur.git] / chimerauchimecommand.cpp

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index cb155eb2e53c3b8ba47c4ed36aa495efaef4460a..1d7e252cb702f58138ae0e756460bb98273b8908 100644 (file)
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -774,6 +774,7 @@ int ChimeraUchimeCommand::execute(){
                         }
                         out2.close();
                         c.printTable(newCountFile);
+                        outputNames.push_back(newCountFile); outputTypes["count"].push_back(newCountFile);
                     }
                 }
                 
@@ -839,10 +840,6 @@ 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 +849,32 @@ 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 +1183,7 @@ int ChimeraUchimeCommand::driverGroups(string outputFName, string filename, stri
                int totalSeqs = 0;
                int numChimeras = 0;
         
+        
         ofstream outCountList;
         if (hasCount && dups) { m->openOutputFile(countlist, outCountList); }