added pcr.seqs command. fixed bug in rarefacftion.single that caused parsing error...

[mothur.git] / filterseqscommand.cpp

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index 93e18e82f374c9fa5bad6a90f6fc2ff56e20246a..a7d42b331bc3044de372c030175da4663f9e3a9c 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -125,7 +125,12 @@ FilterSeqsCommand::FilterSeqsCommand(string option)  {
                        fasta = validParameter.validFile(parameters, "fasta", false);
                        if (fasta == "not found") {                             
                                fasta = m->getFastaFile(); 
-                               if (fasta != "") { fastafileNames.push_back(fasta);  m->mothurOut("Using " + fasta + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+                               if (fasta != "") { 
+                    fastafileNames.push_back(fasta);  
+                    m->mothurOut("Using " + fasta + " as input file for the fasta parameter."); m->mothurOutEndLine();
+                    string simpleName = m->getSimpleName(fasta);
+                    filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
+                }
                                else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }
                        else {