added check to make sure shhh.flows child processes finish properly. added subsamplin...

[mothur.git] / reversecommand.cpp

diff --git a/reversecommand.cpp b/reversecommand.cpp
index 0a2e9380ebd71a5deae50725d3b36c2d10b52c4e..c664ad7548b52f8966c799749f382d31169f564d 100644 (file)
--- a/reversecommand.cpp
+++ b/reversecommand.cpp
@@ -66,6 +66,7 @@ ReverseSeqsCommand::ReverseSeqsCommand(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();
@@ -112,11 +113,13 @@ ReverseSeqsCommand::ReverseSeqsCommand(string option)  {
                        fastaFileName = validParameter.validFile(parameters, "fasta", true);
                        if (fastaFileName == "not open") { abort = true; }
                        else if (fastaFileName == "not found") { fastaFileName = "";}// m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true;  }    
+                       else { m->setFastaFile(fastaFileName); }
                        
                        qualFileName = validParameter.validFile(parameters, "qfile", true);
                        if (qualFileName == "not open") { abort = true; }
                        else if (qualFileName == "not found") { qualFileName = ""; }//m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true;  }      
-
+                       else { m->setQualFile(qualFileName); }
+                       
                        if((fastaFileName == "") && (qualFileName == "")){
                                fastaFileName = m->getFastaFile(); 
                                if (fastaFileName != "") {  m->mothurOut("Using " + fastaFileName + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
@@ -163,7 +166,7 @@ int ReverseSeqsCommand::execute(){
                        m->openOutputFile(fastaReverseFileName, outFASTA);
                        
                        while(!inFASTA.eof()){
-                               if (m->control_pressed) {  inFASTA.close();  outFASTA.close(); remove(fastaReverseFileName.c_str()); return 0; }
+                               if (m->control_pressed) {  inFASTA.close();  outFASTA.close(); m->mothurRemove(fastaReverseFileName); return 0; }
                                 
                                Sequence currSeq(inFASTA);  m->gobble(inFASTA);
                                if (currSeq.getName() != "") {
@@ -191,7 +194,7 @@ int ReverseSeqsCommand::execute(){
                        m->openOutputFile(qualReverseFileName, outQual);
 
                        while(!inQual.eof()){
-                               if (m->control_pressed) {  inQual.close();  outQual.close(); remove(qualReverseFileName.c_str()); return 0; }
+                               if (m->control_pressed) {  inQual.close();  outQual.close(); m->mothurRemove(qualReverseFileName); return 0; }
                                currQual = QualityScores(inQual);  m->gobble(inQual);
                                currQual.flipQScores(); 
                                currQual.printQScores(outQual);
@@ -201,7 +204,7 @@ int ReverseSeqsCommand::execute(){
                        outputNames.push_back(qualReverseFileName); outputTypes["qfile"].push_back(qualReverseFileName);
                }
                
-               if (m->control_pressed) {  remove(qualReverseFileName.c_str()); remove(fastaReverseFileName.c_str()); return 0; }
+               if (m->control_pressed) {  m->mothurRemove(qualReverseFileName); m->mothurRemove(fastaReverseFileName); return 0; }
                
                //set fasta file as new current fastafile
                string current = "";