added flow file to sort.seqs. added setName and setScores functions to Quality Scores...

[mothur.git] / trimflowscommand.cpp

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index 77dacfe711ea694d7d81cb7536fd15d14cb0ec97..f5ef635f6eb6e223e72e8f2e50f23eb041f447a5 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -295,7 +295,7 @@ int TrimFlowsCommand::execute(){
                                                        m->mothurRemove(barcodePrimerComboFileNames[i][j]);
                                                }
                                                else{
-                                                       output << barcodePrimerComboFileNames[i][j] << endl;
+                                                       output << m->getFullPathName(barcodePrimerComboFileNames[i][j]) << endl;
                                                        outputNames.push_back(barcodePrimerComboFileNames[i][j]);
                                                        outputTypes["flow"].push_back(barcodePrimerComboFileNames[i][j]);
                                                }
@@ -309,7 +309,7 @@ int TrimFlowsCommand::execute(){
                        flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "flow.files";
                        m->openOutputFile(flowFilesFileName, output);
                        
-                       output << trimFlowFileName << endl;
+                       output << m->getFullPathName(trimFlowFileName) << endl;
                        
                        output.close();
                }