shhh.seqs and trim.flows modifications.

[mothur.git] / pipelinepdscommand.h

diff --git a/pipelinepdscommand.h b/pipelinepdscommand.h
index 8a8a195eef38c9787332c2b029c889f693c55639..289a909c9d6eef64f4ad2fe61d136592c51120b6 100644 (file)
--- a/pipelinepdscommand.h
+++ b/pipelinepdscommand.h
@@ -20,7 +20,7 @@ class PipelineCommand : public Command {
        
 public:
        PipelineCommand(string);
-       PipelineCommand() {}
+       PipelineCommand() { abort = true; calledHelp = true; }
        ~PipelineCommand();
        vector<string> getRequiredParameters();
        vector<string> getValidParameters();
@@ -43,7 +43,7 @@ private:
        void createPatsPipeline();
        bool parseCommand(string, string&, string&);
        bool checkForValidAndRequiredParameters(string, string, map<string, vector<string> >&);
-       bool fillInMothurMade(string&, map<string, vector<string> >);
+       bool fillInMothurMade(string&, map<string, vector<string> >&);
 };
 
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