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#ifndef BM_CMD_ARGS_H__INCLUDED__
#define BM_CMD_ARGS_H__INCLUDED__
inline
void show_help()
{
std::cerr
<< "BitMagic DNA k-mer build example (c) 2019" << std::endl
<< "-fa file-name -- input FASTA file" << std::endl
<< "-k size -- k-mer size (4,8,16,..24) " << std::endl
<< "-kd file-name -- k-mer dictionary file (output)" << std::endl
<< "-j number-of-threads -- number of parallel jobs to run" << std::endl
<< "-diag -- run diagnostics" << std::endl
<< "-timing -- collect timings" << std::endl
;
}
// cmd-line arguments parser
//
inline
int parse_args(int argc, char *argv[])
{
for (int i = 1; i < argc; ++i)
{
std::string arg = argv[i];
if ((arg == "-h") || (arg == "--help"))
{
show_help();
return 0;
}
if (arg == "-fa" || arg == "--fa")
{
if (i + 1 < argc)
{
ifa_name = argv[++i];
}
else
{
std::cerr << "Error: -fa requires file name" << std::endl;
return 1;
}
continue;
}
if (arg == "-kd" || arg == "--kd")
{
if (i + 1 < argc)
{
ikd_name = argv[++i];
}
else
{
std::cerr << "Error: -kd requires file name" << std::endl;
return 1;
}
continue;
}
if (arg == "-k" || arg == "--k")
{
if (i + 1 < argc)
{
std::string ksize_str = argv[++i];
if (ksize_str.empty())
{
std::cerr << "Error: -k requires size" << std::endl;
return 1;
}
ik_size = (unsigned)std::stoi(ksize_str);
if (ik_size < 2)
{
ik_size = 8;
}
if (ik_size > 24)
{
std::cerr << "Error: unsupported k-mer size (too big)" << std::endl;
return 1;
}
}
else
{
std::cerr << "Error: -k requires size" << std::endl;
return 1;
}
continue;
}
if (arg == "-j" || arg == "--j")
{
if (i + 1 < argc)
{
parallel_jobs = unsigned(::atoi(argv[++i]));
}
else
{
std::cerr << "Error: -j requires number of jobs" << std::endl;
return 1;
}
continue;
}
if (arg == "-diag" || arg == "--diag" || arg == "-d" || arg == "--d")
is_diag = true;
if (arg == "-timing" || arg == "--timing" || arg == "-t" || arg == "--t")
is_timing = true;
if (arg == "-bench" || arg == "--bench" || arg == "-b" || arg == "--b")
is_bench = true;
} // for i
return 0;
}
#endif
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