cluster.split fix

[mothur.git] / summarysharedcommand.cpp

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index 5df448fc45c43656b56e8d0a54e42f089c16adf9..956e0805ee7a20ff5266cf4eba67632dbec7d722 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -229,13 +229,14 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
 void SummarySharedCommand::help(){
        try {
                m->mothurOut("The summary.shared command can only be executed after a successful read.otu command.\n");
-               m->mothurOut("The summary.shared command parameters are label, calc and all.  No parameters are required.\n");
+               m->mothurOut("The summary.shared command parameters are label, calc, distance and all.  No parameters are required.\n");
                m->mothurOut("The summary.shared command should be in the following format: \n");
                m->mothurOut("summary.shared(label=yourLabel, calc=yourEstimators, groups=yourGroups).\n");
                m->mothurOut("Example summary.shared(label=unique-.01-.03, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n");
                validCalculator->printCalc("sharedsummary", cout);
                m->mothurOut("The default value for calc is sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan\n");
                m->mothurOut("The default value for groups is all the groups in your groupfile.\n");
+               m->mothurOut("The distance parameter allows you to indicate you would like a distance file created for each calculator for each label, default=f.\n");
                m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
                m->mothurOut("The all parameter is used to specify if you want the estimate of all your groups together.  This estimate can only be made for sharedsobs and sharedchao calculators. The default is false.\n");
                m->mothurOut("If you use sharedchao and run into memory issues, set all to false. \n");
@@ -507,7 +508,11 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
                                                        }
                                                        
                                                        exit(0);
-                                               }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+                                               }else { 
+                                                       m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
+                                                       for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+                                                       exit(0);
+                                               }
                                        }
                                        
                                        //parent do your part