// ***************************************************************************
// bamtools_options.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ***************************************************************************
// bamtools_options.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Parses command line arguments and creates a help menu
// ---------------------------------------------------------------------------
// ---------------------------------------------------------------------------
// Parses command line arguments and creates a help menu
// ---------------------------------------------------------------------------
// The Mosaik suite's command line parser class: COptions
// (c) 2006 - 2009 Michael Str�mberg
// Marth Lab, Department of Biology, Boston College
// The Mosaik suite's command line parser class: COptions
// (c) 2006 - 2009 Michael Str�mberg
// Marth Lab, Department of Biology, Boston College
-// * Modified to fit BamTools code-style, otherwise code is same. (DB)
+// * Modified slightly to fit BamTools, otherwise code is same.
+// * (BamTools namespace, added stdin/stdout) (DB)
// ***************************************************************************
#ifndef BAMTOOLS_OPTIONS_H
#define BAMTOOLS_OPTIONS_H
// ***************************************************************************
#ifndef BAMTOOLS_OPTIONS_H
#define BAMTOOLS_OPTIONS_H
// parses the command line
static void Parse(int argc, char* argv[], int offset = 0);
// sets the program info
// parses the command line
static void Parse(int argc, char* argv[], int offset = 0);
// sets the program info
- static void SetProgramInfo(const std::string& programName, const std::string& description, const std::string& arguments);
+ static void SetProgramInfo(const std::string& programName,
+ const std::string& description,
+ const std::string& arguments);
// returns string representation of stdin
static const std::string& StandardIn(void);
// returns string representation of stdout
// returns string representation of stdin
static const std::string& StandardIn(void);
// returns string representation of stdout
// stores the options in a map
static std::map<std::string, OptionValue> m_optionsMap;
// string representation of stdin
// stores the options in a map
static std::map<std::string, OptionValue> m_optionsMap;
// string representation of stdin