Revert to previous commit

[mothur.git] / makefastqcommand.h

diff --git a/makefastqcommand.h b/makefastqcommand.h
new file mode 100644 (file)
index 0000000..1c209aa
--- /dev/null
+++ b/makefastqcommand.h
@@ -0,0 +1,48 @@
+#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> setParameters();
+       string getCommandName()                 { return "make.fastq";                          }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Make.fastq"; }
+       string getDescription()         { return "creates a fastq file from a fasta and quality file"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+       
+private:
+       
+       string fastafile, qualfile, outputDir;
+       bool abort;
+       vector<string> outputNames;
+       
+       string convertQual(vector<int>);
+       
+};
+
+#endif
+
+