added code to format fast files for uchime. started work on sff.multiple command

[mothur.git] / subsamplecommand.cpp

diff --git a/subsamplecommand.cpp b/subsamplecommand.cpp
index 35441013919fbfe55452532e735b5bd1d7673f2f..8c5761d7209df23b3a8127475772e3d80b89967e 100644 (file)
--- a/subsamplecommand.cpp
+++ b/subsamplecommand.cpp
@@ -569,8 +569,8 @@ int SubSampleCommand::getSubSampleFasta() {
                        delete uniqueCommand;
                        m->mothurCalling = false;
             
-            m->renameFile(filenames["name"][0], outputNameFileName);
-            m->renameFile(filenames["fasta"][0], outputFileName);
+            m->renameFile(filenames["name"][0], outputNameFileName); 
+            m->renameFile(filenames["fasta"][0], outputFileName);  
             
                        outputTypes["name"].push_back(outputNameFileName);  outputNames.push_back(outputNameFileName);
 
@@ -808,7 +808,7 @@ int SubSampleCommand::processShared(vector<SharedRAbundVector*>& thislookup) {
                
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + thislookup[0]->getLabel() + getOutputFileNameTag("shared", sharedfile);        
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + thislookup[0]->getLabel() + "." +getOutputFileNameTag("shared", sharedfile);        
         SubSample sample;
         vector<string> subsampledLabels = sample.getSample(thislookup, size);