working on testing for 1.13

[mothur.git] / degapseqscommand.cpp

diff --git a/degapseqscommand.cpp b/degapseqscommand.cpp
index 6a9c25eb74d240404b16f2677ec30b047781a159..e475727cb68dd0a28c27ffb64f699a9e633229f8 100644 (file)
--- a/degapseqscommand.cpp
+++ b/degapseqscommand.cpp
@@ -131,7 +131,9 @@ int DegapSeqsCommand::execute(){
                        m->openInputFile(fastaFileNames[s], inFASTA);
                        
                        ofstream outFASTA;
-                       string degapFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "ng.fasta";
+                       string tempOutputDir = outputDir;
+                       if (outputDir == "") { tempOutputDir = m->hasPath(fastaFileNames[s]); }
+                       string degapFile = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "ng.fasta";
                        m->openOutputFile(degapFile, outFASTA);
                        
                        while(!inFASTA.eof()){