working on current change

[mothur.git] / sffinfocommand.cpp

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 765dc78e68a2ac12034853c008055b87d58abc03..77af9e647be61a96ba83bf4929156aa7554633e8 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -283,7 +283,7 @@ SffInfoCommand::SffInfoCommand(string option)  {
                        }
                        
                        if ((sfftxtFilename == "") && (filenames.size() == 0)) {  
-                               //if there is a current fasta file, use it
+                               //if there is a current sff file, use it
                                string filename = m->getSFFFile(); 
                                if (filename != "") { filenames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the sff parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("[ERROR]: you must provide a valid sff or sfftxt file."); m->mothurOutEndLine(); abort=true;  }
@@ -901,13 +901,20 @@ int SffInfoCommand::parseSffTxt() {
                //output file names
                ofstream outFasta, outQual, outFlow;
                string outFastaFileName, outQualFileName;
-               string outFlowFileName = outputDir + m->getRootName(m->getSimpleName(sfftxtFilename)) + "flow";
+               string fileRoot = m->getRootName(m->getSimpleName(sfftxtFilename));
+               if (fileRoot.length() > 0) {
+                       //rip off last .
+                       fileRoot = fileRoot.substr(0, fileRoot.length()-1);
+                       fileRoot = m->getRootName(fileRoot);
+               }
+               
+               string outFlowFileName = outputDir + fileRoot + "flow";
                if (trim) {
-                       outFastaFileName = outputDir + m->getRootName(m->getSimpleName(sfftxtFilename)) + "fasta";
-                       outQualFileName = outputDir + m->getRootName(m->getSimpleName(sfftxtFilename)) + "qual";
+                       outFastaFileName = outputDir + fileRoot + "fasta";
+                       outQualFileName = outputDir + fileRoot + "qual";
                }else{
-                       outFastaFileName = outputDir + m->getRootName(m->getSimpleName(sfftxtFilename)) + "raw.fasta";
-                       outQualFileName = outputDir + m->getRootName(m->getSimpleName(sfftxtFilename)) + "raw.qual";
+                       outFastaFileName = outputDir + fileRoot + "raw.fasta";
+                       outQualFileName = outputDir + fileRoot + "raw.qual";
                }
                
                if (fasta)      { m->openOutputFile(outFastaFileName, outFasta);        outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }