fixed bug in sffinfo when ~ was used in the sff filename. fixed issue in shhh.flows...

[mothur.git] / shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 5bcd7d843a18829793afcc9660af7b7667385c4b..be410d9d9f4ecec2fc885a239c9ba57b5f409e89 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -150,14 +150,21 @@ ShhherCommand::ShhherCommand(string option) {
                        else{
                                ofstream temp;
                 
-                string thisoutputDir = m->hasPath(flowFilesFileName); //if user entered a file with a path then preserve it
+                string thisoutputDir = outputDir;
+                if (outputDir == "") {  thisoutputDir =  m->hasPath(flowFilesFileName); } //if user entered a file with a path then preserve it
                 
-                               //flow.files = 9 character offset
-                               compositeFASTAFileName = thisoutputDir + m->getRootName(m->getSimpleName(flowFilesFileName)) + "shhh.fasta";
+                               //we want to rip off .files, and also .flow if its there
+                string fileroot = m->getRootName(m->getSimpleName(flowFilesFileName));
+                if (fileroot[fileroot.length()-1] == '.') {  fileroot = fileroot.substr(0, fileroot.length()-1); } //rip off dot
+                string extension = m->getExtension(fileroot);
+                if (extension == ".flow") { fileroot = m->getRootName(fileroot);  }
+                else { fileroot += "."; } //add back if needed
+                
+                               compositeFASTAFileName = thisoutputDir + fileroot + "shhh.fasta";
                                m->openOutputFile(compositeFASTAFileName, temp);
                                temp.close();
                                
-                               compositeNamesFileName = thisoutputDir + m->getRootName(m->getSimpleName(flowFilesFileName)) + "shhh.names";
+                               compositeNamesFileName = thisoutputDir + fileroot + "shhh.names";
                                m->openOutputFile(compositeNamesFileName, temp);
                                temp.close();
                        }