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// ==========================================================================
// RABEMA Read Alignment Benchmark
// ==========================================================================
// Copyright (C) 2010-1012 Manuel Holtgrewe, FU Berlin
//
// This program is free software: you can redistribute it and/or modify it
// under the terms of the GNU General Public License as published by the Free
// Software Foundation, either version 3 of the License, or (at your option)
// any later version.
//
// This program is distributed in the hope that it will be useful, but WITHOUT
// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
// FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
// more details.
//
// You should have received a copy of the GNU General Public License along
// with this program. If not, see <http://www.gnu.org/licenses/>.
//
// ==========================================================================
// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================
// Read mapper benchmark tool. This is the top level program that
// parses the command line parameters and then calls the main routine
// from the headers "build_gold_standard.h" and "evaluation.h". These
// headers contain the code for building the gold standard and
// comparing the read mapper results against the gold standard. They
// also contain the command line parsing code used here.
//
// Usage: rabema build_standard -o GOLD_STANDARD.gsi GENOME.fasta GOLD.sam
// rabema compare GENOME.fasta GOLD_STANDARD.gsi READ_MAPPER_OUTPUT.sam
// ==========================================================================
#include "rabema.h"
#include <iostream>
#include "evaluation.h"
#include "build_gold_standard.h"
/* Print global help. This function is called when the user specifies
a wrong simulation command.
*/
void printHelpGlobal()
{
std::cerr << "RABEMA - Read Alignment Benchmark" << std::endl
<< "(c) 2010 by Manuel Holtgrewe" << std::endl
<< std::endl
<< "Usage: rabema build_standard -o GOLD_STANDARD.gsi GENOME.fasta GOLD.sam" << std::endl
<< " rabema compare GENOME.fasta GOLD_STANDARD.gsi READ_MAPPER_OUTPUT.sam" << std::endl
<< std::endl
<< "Call with 'rabema COMMAND --help' to get detailed help." << std::endl;
}
int parseOptions(Options<Global> & options, const int argc, const char * argv[])
{
if (argc == 1 ||
(argc >= 2 && CharString(argv[1]) == "--help") ||
(argc >= 2 && CharString(argv[1]) == "-h"))
{
printHelpGlobal();
return 0;
}
else if (argc >= 2 && CharString(argv[1]) != "build_standard" && CharString(argv[1]) != "compare")
{
printHelpGlobal();
return 1;
}
if (CharString(argv[1]) == "build_standard")
{
options.selectedCommand = COMMAND_BUILD_STANDARD;
}
else if (CharString(argv[1]) == "compare")
{
options.selectedCommand = COMMAND_EVALUATE;
}
else
{
printHelpGlobal();
return 1;
}
return 0;
}
int main(int argc, char const ** argv)
{
Options<Global> globalOptions;
int ret = parseOptions(globalOptions, argc, argv);
if (ret)
return ret;
if (globalOptions.selectedCommand == COMMAND_BUILD_STANDARD)
{
CommandLineParser parser;
setUpCommandLineParser(parser, BuildGoldStandard());
Options<BuildGoldStandard> options;
int ret = parseCommandLineAndCheck(options, parser, argc, argv);
if (options.showHelp)
return 0;
if (ret != 0)
return ret;
return buildGoldStandard(options);
}
else if (globalOptions.selectedCommand == COMMAND_EVALUATE)
{
CommandLineParser parser;
setUpCommandLineParser(parser, EvaluateResults());
Options<EvaluateResults> options;
int ret = parseCommandLineAndCheck(options, parser, argc, argv);
if (options.showHelp)
return 0;
if (ret != 0)
return ret;
return evaluateReadMapperResult(options);
}
return 0;
}
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