forced rarefaction.single to output ending line for all groups. added subsample...

[mothur.git] / deuniqueseqscommand.cpp

diff --git a/deuniqueseqscommand.cpp b/deuniqueseqscommand.cpp
index aed53037c152ded2b13e00b1dfbf30ff739d341d..7481416f649ddad983877ab02cac08e5668316d1 100644 (file)
--- a/deuniqueseqscommand.cpp
+++ b/deuniqueseqscommand.cpp
@@ -114,7 +114,7 @@ DeUniqueSeqsCommand::DeUniqueSeqsCommand(string option)  {
                                fastaFile = m->getFastaFile(); 
                                if (fastaFile != "") { m->mothurOut("Using " + fastaFile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setFastaFile(fastaFile); }   
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  
@@ -128,7 +128,7 @@ DeUniqueSeqsCommand::DeUniqueSeqsCommand(string option)  {
                                nameFile = m->getNameFile(); 
                                if (nameFile != "") { m->mothurOut("Using " + nameFile + " as input file for the name parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current namefile and the name parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }
+                       }else { m->setNameFile(nameFile); }
                }
 
        }
@@ -155,14 +155,14 @@ int DeUniqueSeqsCommand::execute() {
                m->openOutputFile(outFastaFile, out);
                
                readNamesFile();
-               if (m->control_pressed) {  out.close(); outputTypes.clear(); remove(outFastaFile.c_str()); return 0; }
+               if (m->control_pressed) {  out.close(); outputTypes.clear(); m->mothurRemove(outFastaFile); return 0; }
                
                ifstream in;
                m->openInputFile(fastaFile, in);
                
                while (!in.eof()) {
                
-                       if (m->control_pressed) { in.close(); out.close(); outputTypes.clear(); remove(outFastaFile.c_str()); return 0; }
+                       if (m->control_pressed) { in.close(); out.close(); outputTypes.clear(); m->mothurRemove(outFastaFile); return 0; }
                        
                        Sequence seq(in); m->gobble(in);
                        
@@ -196,7 +196,7 @@ int DeUniqueSeqsCommand::execute() {
                        }
                }
                                
-               if (m->control_pressed) { outputTypes.clear(); remove(outFastaFile.c_str()); return 0; }
+               if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outFastaFile); return 0; }
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();