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// ==========================================================================
// Gustaf
// ==========================================================================
// Copyright (c) 2011-2026, Kathrin Trappe, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of Knut Reinert or the FU Berlin nor the names of
// its contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
//
// ==========================================================================
// Author: Kathrin Trappe <ktrappe@inf.fu-berlin.de>
// ==========================================================================
#include <seqan/basic.h>
#include <seqan/sequence.h>
#include "../stellar/stellar.h"
#include "msplazer_parse_options.h"
#include "msplazer.h"
#include "msplazer_main.h"
using namespace seqan2;
// Program entry point
int main(int argc, char const ** argv)
{
double start = sysTime();
// command line parsing
ArgumentParser parser("gustaf");
// Stellar Options
StellarOptions stellarOptions = StellarOptions();
// MSplazer Options
MSplazerOptions msplazerOptions = MSplazerOptions();
// New Argument Parser
_setupArgumentParser(parser);
// _setParser(parser);
ArgumentParser::ParseResult res = parse(parser, argc, argv);
if (res != ArgumentParser::PARSE_OK)
return res == ArgumentParser::PARSE_ERROR;
if (!_parseOptions(parser, stellarOptions, msplazerOptions))
return 1;
_writeFileNames(stellarOptions);
_writeParams(msplazerOptions);
// msplazer wrapper function
msplazer(stellarOptions, msplazerOptions);
// ///////////////////////////////////////////////////////////////////
// Fragmentstore
// Usage via fragmentStore
/*Stellar can now handle FragmentStore input which is based on an Index using a StringSet based on
Owner<ConcatDirect<>>. However, StellarMatch positions are wrong when processing multiple reads
(i.e. after read 1). Maybe bc. of consecutive positions due to the ConcatDirect format?
*/
/*
FragmentStore<void> fragments;
bool success = loadReads(fragments, queryFilename);
if(!success)
cout << "Unable to open file from " << queryFilename << endl;
for(unsigned i = 0; i < length(fragments.readSeqStore); ++i)
cout << "Read " << i << " : " << fragments.readSeqStore[i] << endl;
*/
std::cout << "TIME all " << (sysTime() - start) << "s" << std::endl;
return 0;
}
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