Merge remote-tracking branch 'mothur/master'

[mothur.git] / makecontigscommand.cpp

diff --git a/makecontigscommand.cpp b/makecontigscommand.cpp
index 523edd5e8ba1fd00f1bf5050a380b43e1549ee4f..691d706ab00efa8823412753b72f08e5198873b1 100644 (file)
--- a/makecontigscommand.cpp
+++ b/makecontigscommand.cpp
@@ -38,8 +38,8 @@ string MakeContigsCommand::getHelpString(){
                string helpString = "";
                helpString += "The make.contigs command reads a forward fastq file and a reverse fastq file and outputs new fasta and quality files.\n";
                helpString += "The make.contigs command parameters are ffastq, rfastq, align, match, mismatch, gapopen, gapextend and processors.\n";
-               helpString += "The ffastq and rfastq parameter is required.\n";
-               helpString += "The align parameter allows you to specify the alignment method to use.  Your options are: gotoh, needleman, blast and noalign. The default is needleman.\n";
+               helpString += "The ffastq and rfastq parameters are required.\n";
+               helpString += "The align parameter allows you to specify the alignment method to use.  Your options are: gotoh and needleman. The default is needleman.\n";
                helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n";
                helpString += "The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n";
                helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n";
@@ -56,7 +56,28 @@ string MakeContigsCommand::getHelpString(){
                exit(1);
        }
 }
-
+//**********************************************************************************************************************
+string MakeContigsCommand::getOutputFileNameTag(string type, string inputName=""){     
+       try {
+        string outputFileName = "";
+               map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "fasta")             {   outputFileName =  "contigs.fasta";         }
+            else if (type == "qfile")        {   outputFileName =  "contigs.qual";          }
+            else if (type == "mismatch")     {   outputFileName =  "contigs.mismatch";      }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "MakeContigsCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 MakeContigsCommand::MakeContigsCommand(){      
        try {
@@ -189,9 +210,9 @@ int MakeContigsCommand::execute(){
     
         if (m->control_pressed) { return 0; }
         
-        string outFastaFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "contigs.fasta";
-        string outQualFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "contigs.qual";
-        string outMisMatchFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "contigs.mismatches";
+        string outFastaFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + getOutputFileNameTag("fasta");
+        string outQualFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + getOutputFileNameTag("qfile");
+        string outMisMatchFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + getOutputFileNameTag("mismatch");
         outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
         outputNames.push_back(outQualFile); outputTypes["qfile"].push_back(outQualFile);
         outputNames.push_back(outMisMatchFile); outputTypes["mismatch"].push_back(outMisMatchFile);