cluster.split command

[mothur.git] / hclustercommand.cpp

diff --git a/hclustercommand.cpp b/hclustercommand.cpp
index d9a14d9b5979636dba434733a132d35c25de8568..dc14e1670c5221599dd14929dd6d08fde6c6b766 100644 (file)
--- a/hclustercommand.cpp
+++ b/hclustercommand.cpp
@@ -21,7 +21,7 @@ HClusterCommand::HClusterCommand(string option)  {
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"cutoff","precision","method","phylip","column","name","sorted","showabund","timing","outputdir","inputdir"};
+                       string Array[] =  {"cutoff","hard","precision","method","phylip","column","name","sorted","showabund","timing","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -104,10 +104,13 @@ HClusterCommand::HClusterCommand(string option)  {
                        length = temp.length();
                        convert(temp, precision); 
                        
+                       temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "F"; }
+                       hard = isTrue(temp);
+                       
                        temp = validParameter.validFile(parameters, "cutoff", false);
                        if (temp == "not found") { temp = "10"; }
                        convert(temp, cutoff); 
-                       cutoff += (5 / (precision * 10.0));
+                       if (!hard) {  cutoff += (5 / (precision * 10.0));  }
                        
                        method = validParameter.validFile(parameters, "method", false);
                        if (method == "not found") { method = "furthest"; }
@@ -189,7 +192,7 @@ int HClusterCommand::execute(){
                time_t estart = time(NULL);
                
                if (!sorted) {
-                       read = new ReadCluster(distfile, cutoff);       
+                       read = new ReadCluster(distfile, cutoff, outputDir, true);      
                        read->setFormat(format);
                        read->read(globaldata->nameMap);