added parse.fastaq command, added permute option to venn command, fixed bug with...

[mothur.git] / chimeracheckcommand.cpp

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index 18554399e43220b596723a745142b49d2d8c123e..c8761b9bd51ea60fed4e9f5bc1636a8b0afb1987 100644 (file)
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -217,6 +217,7 @@ int ChimeraCheckCommand::execute(){
 
                        if (m->control_pressed) { delete chimera;       return 0;       }
                        
+                       if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]);  }//if user entered a file with a path then preserve it
                        string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i]))  + "chimeracheck.chimeras";
                        outputNames.push_back(outputFileName);