added parse.fastaq command, added permute option to venn command, fixed bug with...

[mothur.git] / parsefastaqcommand.h

diff --git a/parsefastaqcommand.h b/parsefastaqcommand.h
new file mode 100644 (file)
index 0000000..0710775
--- /dev/null
+++ b/parsefastaqcommand.h
@@ -0,0 +1,35 @@
+#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();
+       int execute();
+       void help();    
+       
+private:
+
+       vector<string> outputNames;     
+       string outputDir, fastaQFile;
+       bool abort;
+       
+       vector<int> convertQual(string);
+};
+
+#endif
+
+