fixed phylo.diversity

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 0f4c89a28ce7ca2b01eae1de815bebfb78ff6a77..5aabeef9437bd9f5fdd90f6b785e52065afc3115 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -90,6 +90,8 @@ AlignCommand::AlignCommand(string option)  {
                                
                                //go through files and make sure they are good, if not, then disregard them
                                for (int i = 0; i < candidateFileNames.size(); i++) {
+                                       //candidateFileNames[i] = m->getFullPathName(candidateFileNames[i]);
+                                       
                                        if (inputDir != "") {
                                                string path = m->hasPath(candidateFileNames[i]);
                                                //if the user has not given a path then, add inputdir. else leave path alone.
@@ -348,7 +350,6 @@ int AlignCommand::execute(){
 #else
 
                vector<unsigned long int> positions = m->divideFile(candidateFileNames[s], processors);
-                               
                for (int i = 0; i < (positions.size()-1); i++) {
                        lines.push_back(new linePair(positions[i], positions[(i+1)]));
                }