added dups parameter to chimera.uchime. working on make.contigs command.

[mothur.git] / mgclustercommand.cpp

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index a845e0bfe080782b2b12d2f1a634925781578d70..1861aa5b5d8c19f547ed90e3ec57866a3b53ecd2 100644 (file)
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -13,8 +13,8 @@
 vector<string> MGClusterCommand::setParameters(){      
        try {
                CommandParameter pblast("blast", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pblast);
-               CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
-        CommandParameter pcount("count", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pcount);
+               CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName",false,false); parameters.push_back(pname);
+               CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pcount);
                CommandParameter plength("length", "Number", "", "5", "", "", "",false,false); parameters.push_back(plength);
                CommandParameter ppenalty("penalty", "Number", "", "0.10", "", "", "",false,false); parameters.push_back(ppenalty);
                CommandParameter pcutoff("cutoff", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pcutoff);
@@ -147,6 +147,14 @@ MGClusterCommand::MGClusterCommand(string option) {
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["name"] = inputDir + it->second;             }
                                }
+                
+                it = parameters.find("count");
+                               //user has given a template file
+                               if(it != parameters.end()){ 
+                                       path = m->hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["count"] = inputDir + it->second;            }
+                               }
                        }
 
                        
@@ -268,7 +276,9 @@ int MGClusterCommand::execute(){
                
         string sabundFileName = fileroot+ tag + "." + getOutputFileNameTag("sabund");
         string rabundFileName = fileroot+ tag + "." + getOutputFileNameTag("rabund");
-        string listFileName = fileroot+ tag + "." + getOutputFileNameTag("list");
+        string listFileName = fileroot+ tag + ".";
+        if (countfile != "") { listFileName += "unique_"; }
+        listFileName += getOutputFileNameTag("list");
         
         if (countfile == "") {
             m->openOutputFile(sabundFileName,  sabundFile);
@@ -287,7 +297,7 @@ int MGClusterCommand::execute(){
                
                if (!hclusterWanted) {
                        //get distmatrix and overlap
-                       SparseMatrix* distMatrix = read->getDistMatrix();
+                       SparseDistanceMatrix* distMatrix = read->getDistMatrix();
                        overlapMatrix = read->getOverlapMatrix(); //already sorted by read 
                        delete read;