some changes while testing 1.9

[mothur.git] / mgclustercommand.cpp

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index 6d5acb2386ad0ccd836ee41d2d8f5b24c5e4048e..6eb9c7d72f99590ec22b2f4b8aa758057a7f24f2 100644 (file)
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -538,12 +538,12 @@ ListVector* MGClusterCommand::mergeOPFs(map<string, int> binInfo, float dist){
 void MGClusterCommand::sortHclusterFiles(string unsortedDist, string unsortedOverlap) {
        try {
                //sort distFile
-               string sortedDistFile = sortFile(unsortedDist);
+               string sortedDistFile = sortFile(unsortedDist, outputDir);
                remove(unsortedDist.c_str());  //delete unsorted file
                distFile = sortedDistFile;
                
                //sort overlap file
-               string sortedOverlapFile = sortFile(unsortedOverlap);
+               string sortedOverlapFile = sortFile(unsortedOverlap, outputDir);
                remove(unsortedOverlap.c_str());  //delete unsorted file
                overlapFile = sortedOverlapFile;
        }