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#include <boost/program_options.hpp>
#include "../lib/headers.h"
#include "../lib/definitions.h"
#include "../lib/kindex.h"
#include "../lib/argument_parser.h"
AlignmentSettings globalAlignmentSettings;
mutex_map<std::string> fileLocks;
/**
* Main function that organizes the overall structure of the program.
* @param argc Number of arguments
* @param argv Argument array
* @return 0 on success, other numbers on error
*/
int main(int argc, const char* argv[]) {
// Program start output.
std::cout << std::endl << "________________________________________________________________________________" << std::endl << std::endl << "HiLive Index Builder v" << HiLive_VERSION_MAJOR << "." << HiLive_VERSION_MINOR <<
" - Build Index for Realtime Alignment of Illumina Reads" << std::endl << "________________________________________________________________________________" << std::endl << std::endl;
// Init argument parser
BuildIndexArgumentParser argumentParser(argc, argv);
// Parse command line arguments
int parser_returnStatus = argumentParser.parseCommandLineArguments();
// Successful execution of "help" or "license"
if ( parser_returnStatus == 1 ) {
exit(EXIT_SUCCESS);
}
// Parsing error
else if ( parser_returnStatus == -1 ) {
std::cout << "Parsing of command line options failed. For help, type 'hilive-build --help'." << std::endl;
exit(EXIT_FAILURE);
}
// Build index
std::cout << "Create FM-index from file " << argumentParser.fasta_name << " ..." << std::endl;
KixBuild* index = new KixBuild();
// create and save the index
switch( index->create_index(argumentParser.fasta_name, argumentParser.index_name, !argumentParser.do_not_convert_spaces, argumentParser.trim_ids) ) {
case 0: std::cerr << "Index was successfully built to file(s) " << argumentParser.index_name << std::endl; break;
case 1: std::cerr << "Reading input file failed (no sequences found)." << std::endl; break;
case 2: std::cerr << "Reading input file failed." << std::endl; break;
case 3: std::cerr << "Writing metadata to file(s) failed." << std::endl; break;
case 4: std::cerr << "Index building failed." << std::endl; break;
case 5: std::cerr << "Writing index to file " << argumentParser.index_name << " failed." << std::endl; break;
default: std::cerr << "Failed due to an unknown error." << std::endl; break;
}
delete index;
return EXIT_SUCCESS;
}
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