modified freq parameter be a percentage of numSeqs, added catchall command - not...

[mothur.git] / collectcommand.cpp

diff --git a/collectcommand.cpp b/collectcommand.cpp
index cf8ba10e8e43054304c42892cbfb9c2014a8da1f..1e2bf2fcd42e771e2b84e7f2d3f93abd2171a15a 100644 (file)
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -86,7 +86,7 @@ CollectCommand::CollectCommand(string option)  {
                        splitAtDash(calc, Estimators);
 
                        string temp;
-                       temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
+                       temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "0.10"; }
                        convert(temp, freq); 
                        
                        temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
@@ -110,6 +110,7 @@ void CollectCommand::help(){
                m->mothurOut("The collect.single command can be executed after a successful cluster command.  It will use the .list file from the output of the cluster.\n");
                m->mothurOut("The collect.single command parameters are label, freq, calc and abund.  No parameters are required. \n");
                m->mothurOut("The collect.single command should be in the following format: \n");
+               m->mothurOut("The freq parameter is used indicate when to output your data.  It is a percentage of the number of sequences.  By default it is set to 0.10, meaning 10%. \n");
                m->mothurOut("collect.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n");
                m->mothurOut("Example collect(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-chao-ace-jack).\n");
                m->mothurOut("The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson.\n");