added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / parsefastaqcommand.h

diff --git a/parsefastaqcommand.h b/parsefastaqcommand.h
index fe77cf08f34e3760734fb7b70568c4db09d603a2..6feabce848c09c21b2e276df8361ac4d78667f22 100644 (file)
--- a/parsefastaqcommand.h
+++ b/parsefastaqcommand.h
@@ -24,6 +24,9 @@ public:
        string getCommandName()                 { return "parse.fastq";         }
        string getCommandCategory()             { return "Sequence Processing"; }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Parse.fastq"; }
+       string getDescription()         { return "reads a fastq file and creates a fasta and quality file"; }
+
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }          
@@ -31,7 +34,7 @@ private:
 
        vector<string> outputNames;     
        string outputDir, fastaQFile;
-       bool abort;
+       bool abort, fasta, qual;
        
        vector<int> convertQual(string);
 };