working on current change

[mothur.git] / seqerrorcommand.cpp

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 6ce944ef21189948519310e372907580d8ac1400..564e412ea95f1421b1d3cc72761c2ac98fe61c44 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -164,6 +164,7 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                                else {  m->mothurOut("You have no current fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }
                        else if (queryFileName == "not open") { abort = true; } 
+                       else { m->setFastaFile(queryFileName); }
                        
                        referenceFileName = validParameter.validFile(parameters, "reference", true);
                        if (referenceFileName == "not found") { m->mothurOut("reference is a required parameter for the seq.error command."); m->mothurOutEndLine(); abort = true; }
@@ -174,11 +175,13 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                        namesFileName = validParameter.validFile(parameters, "name", true);
                        if(namesFileName == "not found"){       namesFileName = "";     }
                        else if (namesFileName == "not open") { namesFileName = ""; abort = true; }     
+                       else { m->setNameFile(namesFileName); }
                        
                        qualFileName = validParameter.validFile(parameters, "qfile", true);
                        if(qualFileName == "not found"){        qualFileName = "";      }
                        else if (qualFileName == "not open") { qualFileName = ""; abort = true; }       
-
+                       else { m->setQualFile(qualFileName); }
+                       
                        reportFileName = validParameter.validFile(parameters, "report", true);
                        if(reportFileName == "not found"){      reportFileName = "";    }
                        else if (reportFileName == "not open") { reportFileName = ""; abort = true; }