added processors to pre.cluster for mac and windows. Fixed bug in reNameFile function...

[mothur.git] / chopseqscommand.cpp

diff --git a/chopseqscommand.cpp b/chopseqscommand.cpp
index cbc55ef56e4deb762db35e23899127ebd224e255..e2b0fa46fc28bb6fd6be1af8a085e409a9a8b4df 100644 (file)
--- a/chopseqscommand.cpp
+++ b/chopseqscommand.cpp
@@ -73,6 +73,7 @@ ChopSeqsCommand::ChopSeqsCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -114,7 +115,7 @@ ChopSeqsCommand::ChopSeqsCommand(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"){  outputDir = m->hasPath(fastafile);      }
@@ -164,7 +165,7 @@ int ChopSeqsCommand::execute(){
                        
                        Sequence seq(in);
                        
-                       if (m->control_pressed) { outputTypes.clear(); in.close(); out.close(); outAcc.close(); remove(outputFileName.c_str()); remove(outputFileNameAccnos.c_str()); return 0;  }
+                       if (m->control_pressed) { outputTypes.clear(); in.close(); out.close(); outAcc.close(); m->mothurRemove(outputFileName); m->mothurRemove(outputFileNameAccnos); return 0;  }
                        
                        if (seq.getName() != "") {
                                string newSeqString = getChopped(seq);
@@ -187,7 +188,7 @@ int ChopSeqsCommand::execute(){
                m->mothurOut(outputFileName); m->mothurOutEndLine();    outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
                
                if (wroteAccnos) { m->mothurOut(outputFileNameAccnos); m->mothurOutEndLine(); outputNames.push_back(outputFileNameAccnos); outputTypes["accnos"].push_back(outputFileNameAccnos); }
-               else {  remove(outputFileNameAccnos.c_str());  }
+               else {  m->mothurRemove(outputFileNameAccnos);  }
                
                m->mothurOutEndLine();