added adjustDots function to pcr.seqs, keeps sequences aligned in case where primers...

[mothur.git] / setdircommand.cpp

diff --git a/setdircommand.cpp b/setdircommand.cpp
index b0d12b87bc49f4d3b6e9cae63558ba622b199701..4536d9516688fe6db1d9c10e709e789c40abe93c 100644 (file)
--- a/setdircommand.cpp
+++ b/setdircommand.cpp
@@ -12,12 +12,12 @@
 //**********************************************************************************************************************
 vector<string> SetDirectoryCommand::setParameters(){   
        try {
-               CommandParameter ptempdefault("tempdefault", "String", "", "", "", "", "",false,false); parameters.push_back(ptempdefault);
-        CommandParameter pdebug("debug", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pdebug);
-               CommandParameter pinput("input", "String", "", "", "", "", "",false,false); parameters.push_back(pinput);
-               CommandParameter poutput("output", "String", "", "", "", "", "",false,false); parameters.push_back(poutput);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter ptempdefault("tempdefault", "String", "", "", "", "", "","",false,false); parameters.push_back(ptempdefault);
+        CommandParameter pdebug("debug", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pdebug);
+               CommandParameter pinput("input", "String", "", "", "", "", "","",false,false,true); parameters.push_back(pinput);
+               CommandParameter poutput("output", "String", "", "", "", "", "","",false,false,true); parameters.push_back(poutput);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -92,6 +92,8 @@ SetDirectoryCommand::SetDirectoryCommand(string option)  {
                        if (temp == "not found") {  debug = false;  nodebug=true; }
             else {  debug = m->isTrue(temp); }
             m->debug = debug;
+            
+            if (debug) { m->mothurOut("Setting [DEBUG] flag.\n"); }
                                
                        if ((input == "") && (output == "") && (tempdefault == "") && nodebug) {        
                                m->mothurOut("You must provide either an input, output, tempdefault or debug for the set.outdir command."); m->mothurOutEndLine(); abort = true;