added consensus.seqs command

[mothur.git] / clustersplitcommand.cpp

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index 85a183aca409f65e3cb0e605d5ae777d10efe665..85c70f04127b4ae63ddf1f16f6e8adb2fea39e9c 100644 (file)
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -37,6 +37,7 @@ ClusterSplitCommand::ClusterSplitCommand(){
                outputTypes["list"] = tempOutNames;
                outputTypes["rabund"] = tempOutNames;
                outputTypes["sabund"] = tempOutNames;
+               outputTypes["column"] = tempOutNames;
        }
        catch(exception& e) {
                m->errorOut(e, "ClusterSplitCommand", "ClusterSplitCommand");
@@ -100,6 +101,7 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
                        outputTypes["list"] = tempOutNames;
                        outputTypes["rabund"] = tempOutNames;
                        outputTypes["sabund"] = tempOutNames;
+                       outputTypes["column"] = tempOutNames;
                        
                        globaldata->newRead();
                        
@@ -360,6 +362,10 @@ int ClusterSplitCommand::execute(){
                vector< map<string, string> > distName = split->getDistanceFiles();  //returns map of distance files -> namefile sorted by distance file size
                delete split;
                
+               //output a merged distance file
+               if (splitmethod == "fasta")             { createMergedDistanceFile(distName); }
+                       
+                               
                if (m->control_pressed) { return 0; }
                
                m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to split the distance file."); m->mothurOutEndLine();
@@ -1077,5 +1083,45 @@ vector<string> ClusterSplitCommand::cluster(vector< map<string, string> > distNa
 
 
 }
+//**********************************************************************************************************************
 
+int ClusterSplitCommand::createMergedDistanceFile(vector< map<string, string> > distNames) {
+       try{
+               
+#ifdef USE_MPI
+               int pid;
+               MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+               
+               if (pid != 0) {
+#endif
+               
+               string thisOutputDir = outputDir;
+               if (outputDir == "") { thisOutputDir = m->hasPath(fastafile); }
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "dist";
+               remove(outputFileName.c_str());
+               
+               
+               for (int i = 0; i < distNames.size(); i++) {
+                       if (m->control_pressed) {  return 0; }
+                       
+                       string thisDistFile = distNames[i].begin()->first;
+                       
+                       m->appendFiles(thisDistFile, outputFileName);
+               }       
+                       
+               outputTypes["column"].push_back(outputFileName); outputNames.push_back(outputFileName);
+                       
+#ifdef USE_MPI
+               }
+#endif
+                               
+                       
+               
+               
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ClusterSplitCommand", "createMergedDistanceFile");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************