Revert to previous commit

[mothur.git] / parsefastaqcommand.h

diff --git a/parsefastaqcommand.h b/parsefastaqcommand.h
new file mode 100644 (file)
index 0000000..6feabce
--- /dev/null
+++ b/parsefastaqcommand.h
@@ -0,0 +1,44 @@
+#ifndef PARSEFASTAQCOMMAND_H
+#define PARSEFASTAQCOMMAND_H
+
+/*
+ *  parsefastaqcommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 9/30/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "command.hpp"
+
+class ParseFastaQCommand : public Command {
+
+public:
+       ParseFastaQCommand(string);
+       ParseFastaQCommand();
+       ~ParseFastaQCommand() {}
+       
+       vector<string> setParameters();
+       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()); }          
+private:
+
+       vector<string> outputNames;     
+       string outputDir, fastaQFile;
+       bool abort, fasta, qual;
+       
+       vector<int> convertQual(string);
+};
+
+#endif
+
+