working on current change

[mothur.git] / reversecommand.cpp

diff --git a/reversecommand.cpp b/reversecommand.cpp
index 17924c9669b6b5338d15824b2920410fcf305af4..ea2ddeb8e718b44363409f0b332827feec41d6a9 100644 (file)
--- a/reversecommand.cpp
+++ b/reversecommand.cpp
@@ -113,11 +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(); }