added abundance and sample parameters to get.coremicrobiome command.

[mothur.git] / shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 89d78288639e6cca3e8eebca34dd01174c3963da..49e2faa03c1cd2eb74ea502ee5952c0512678644 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -152,11 +152,11 @@ ShhherCommand::ShhherCommand(string option) {
                 string thisoutputDir = m->hasPath(flowFilesFileName); //if user entered a file with a path then preserve it
                 
                                //flow.files = 9 character offset
-                               compositeFASTAFileName = thisoutputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.fasta";
+                               compositeFASTAFileName = thisoutputDir + m->getRootName(m->getSimpleName(flowFilesFileName)) + "shhh.fasta";
                                m->openOutputFile(compositeFASTAFileName, temp);
                                temp.close();
                                
-                               compositeNamesFileName = thisoutputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.names";
+                               compositeNamesFileName = thisoutputDir + m->getRootName(m->getSimpleName(flowFilesFileName)) + "shhh.names";
                                m->openOutputFile(compositeNamesFileName, temp);
                                temp.close();
                        }