added merge.taxsummary command. added column format to dist.shared.

[mothur.git] / clustersplitcommand.cpp

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index ac5e75536fa44ff36341795b3cbecf7226061c6f..92f0e486898f80b2c6f85bb984a5b7662bc18340 100644 (file)
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -439,6 +439,8 @@ int ClusterSplitCommand::execute(){
                vector< map<string, string> > distName = split->getDistanceFiles();  //returns map of distance files -> namefile sorted by distance file size
                delete split;
                
+        if (m->debug) { m->mothurOut("[DEBUG]: distName.size() = " + toString(distName.size()) + ".\n"); }
+                
                //output a merged distance file
                if (splitmethod == "fasta")             { createMergedDistanceFile(distName); }
                        
@@ -447,11 +449,9 @@ int ClusterSplitCommand::execute(){
                
                m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to split the distance file."); m->mothurOutEndLine();
                estart = time(NULL);
-                
+              
         if (!runCluster) { 
-#ifdef USE_MPI
-    }
-#endif 
+
                 m->mothurOutEndLine();
                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                 for (int i = 0; i < distName.size(); i++) {    m->mothurOut(distName[i].begin()->first); m->mothurOutEndLine(); m->mothurOut(distName[i].begin()->second); m->mothurOutEndLine();      }
@@ -459,7 +459,7 @@ int ClusterSplitCommand::execute(){
                 return 0;
                 
         }
-                
+   
                //****************** break up files between processes and cluster each file set ******************************//
        #ifdef USE_MPI
                        ////you are process 0 from above////
@@ -818,10 +818,10 @@ int ClusterSplitCommand::mergeLists(vector<string> listNames, map<float, int> us
                
         map<string, string> variables; 
         variables["[filename]"] = fileroot;
-        if (countfile != "") { variables["[tag2]"] = "unique_list"; }
         variables["[clustertag]"] = tag;
         string sabundFileName = getOutputFileName("sabund", variables);
         string rabundFileName = getOutputFileName("rabund", variables);
+        if (countfile != "") { variables["[tag2]"] = "unique_list"; }
         string listFileName = getOutputFileName("list", variables);
         
         if (countfile == "") {
@@ -947,7 +947,7 @@ vector<string>  ClusterSplitCommand::createProcesses(vector< map<string, string>
             if ((processToAssign-1) == 1) { m->mothurOut(distName[i].begin()->first + "\n"); }
         }
         
-        //not lets reverse the order of ever other process, so we balance big files running with little ones
+        //now lets reverse the order of ever other process, so we balance big files running with little ones
         for (int i = 0; i < processors; i++) {
             //cout << i << endl;
             int remainder = ((i+1) % processors);