added make.fastq command

[mothur.git] / makefastqcommand.h

diff --git a/makefastqcommand.h b/makefastqcommand.h
new file mode 100644 (file)
index 0000000..fd893ad
--- /dev/null
+++ b/makefastqcommand.h
@@ -0,0 +1,43 @@
+#ifndef MAKEFASTQCOMMAND_H
+#define MAKEFASTQCOMMAND_H
+
+/*
+ *  makefastqcommand.h
+ *  mothur
+ *
+ *  Created by westcott on 2/14/11.
+ *  Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "command.hpp"
+
+class MakeFastQCommand : public Command {
+       
+public:
+       
+       MakeFastQCommand(string);       
+       MakeFastQCommand();
+       ~MakeFastQCommand(){}
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
+       int execute();
+       void help();    
+       
+private:
+       
+       string fastafile, qualfile, outputDir;
+       bool abort;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
+       
+       string convertQual(vector<int>);
+       
+};
+
+#endif
+
+