void setOptions (CArgs &arg)
{
// File reading options
if (arg.Search("--file"))
{
par::file = arg.parameters[ arg.Index("--file") ];
if (par::pedfile != "null" or par::mapfile != "null") error ("Cannot specify a map or pedfile while using the --file option");
par::pedfile = par::file + ".ped";
par::mapfile = par::file + ".map";
arg.clinelist.push_back("--file");
arg.clinevalue.push_back(par::file);
}
if (arg.Search("--ped"))
{
if (par::file != "null") error ("Cannot specify --file and --ped at the same time");
par::pedfile = arg.parameters[ arg.Index("--ped") ];
arg.clinelist.push_back("--ped");
arg.clinevalue.push_back(par::pedfile);
}
if (arg.Search("--map"))
{
if (par::file != "null") error ("Cannot specify --file and --map at the same time");
par::mapfile = arg.parameters[ arg.Index("--map") ];
arg.clinelist.push_back("--map");
arg.clinevalue.push_back( par::mapfile );
}
if (arg.Search("--tfile"))
{
par::tfile = arg.parameters[ arg.Index("--tfile") ];
if (par::tpedfile != "null" or par::tfamfile != "null") error ("Cannot specify a tped file or tfam file while using the --tfile option");
par::tpedfile = par::tfile + ".tped";
par::tfamfile = par::tfile + ".tfam";
arg.clinelist.push_back("--tfile");
arg.clinevalue.push_back( par::tfile );
}
if (arg.Search("--tped"))
{
if (par::tfile != "null") error ("Cannot specify --tfile and --tped at the same time");
par::tpedfile = arg.parameters[ arg.Index("--tped") ];
arg.clinelist.push_back("--tped");
arg.clinevalue.push_back(par::tfamfile);
}
if (arg.Search("--tfam"))
{
if (par::tfile != "null") error ("Cannot specify --tfile and --tfam at the same time");
par::tfamfile = arg.parameters[ arg.Index("--tfam") ];
arg.clinelist.push_back("--tfam");
arg.clinevalue.push_back( par::tfamfile );
}
// if (arg.Search("--bfile"))
// {
// par::bfile = arg.parameters[ arg.Index("--bfile") ];
//
// if (par::bpedfile != "null" or par::bmapfile != "null") error ("Cannot specify a bped or bmap file separately when using --bfile option");
//
// par::bpedfile = par::bfile + ".bped";
// par::bmapfile = par::bfile + ".bmap";
// par::bfamfile = par::bfile + ".bfam";
//
// arg.clinelist.push_back("--bfile");
// arg.clinevalue.push_back(par::bfile);
// }
//
// if (arg.Search("--bped"))
// {
// if (par::bfile != "null") error ("Cannot specify --bfile and --bped at the same time");
//
// par::bpedfile = arg.parameters[ arg.Index("--bped") ];
//
// arg.clinelist.push_back("--bped");
// arg.clinevalue.push_back(par::bpedfile);
// }
//
// if (arg.Search("--bmap"))
// {
// if (par::bfile != "null") error ("Cannot specify --bfile and --bmap at the same time");
//
// par::bmapfile = arg.parameters[ arg.Index("--bmap") ];
//
// arg.clinelist.push_back("--bmap");
// arg.clinevalue.push_back(par::bmapfile);
// }
//
// if (arg.Search("--bfam"))
// {
// if (par::bfile != "null") error ("Cannot specify --bfile and --bfam at the same time");
// }
// File writing options
if (arg.Search("--recode"))
{
par::recode = true;
arg.clinelist.push_back("--recode");
arg.clinevalue.push_back(" ");
}
if (arg.Search("--transpose"))
{
par::transpose = true;
arg.clinelist.push_back("--transpose");
arg.clinevalue.push_back(" ");
}
if (arg.Search("--webduo"))
{
par::webduo = true;
arg.clinelist.push_back("--webduo");
arg.clinevalue.push_back(" ");
}
// if (arg.Search("--binary"))
// {
// par::binary = true;
//
// arg.clinelist.push_back("--binary");
// arg.clinevalue.push_back(" ");
// }
if (arg.Search("--genome"))
{
par::genome = true;
par::genomefile = arg.parameters[ arg.Index("--genome") ];
arg.clinelist.push_back("--genome");
arg.clinevalue.push_back(" ");
}
if (arg.Search("--out"))
{
par::outfile = arg.parameters[ arg.Index("--out") ];
arg.clinelist.push_back("--out");
arg.clinevalue.push_back(par::outfile);
}
// // Analysis options
// if (arg.Search("--findblocks"))
// {
// par::findblocks = true;
//
// arg.clinelist.push_back("--findblocks");
// arg.clinevalue.push_back(" ");
// }
//
// if (arg.Search("--makeucsc"))
// {
// par::makeucsc = true;
//
// arg.clinelist.push_back("--makeucsc");
// arg.clinevalue.push_back(" ");
// }
if (arg.Search("--map3"))
{
par::map3 = true;
arg.clinelist.push_back("--map3");
arg.clinevalue.push_back(" ");
}
if (arg.Search("--silent"))
{
par::verbose = false;
arg.clinelist.push_back("--silent");
arg.clinevalue.push_back(" ");
}
if (arg.Search("--version"))
{
par::version = true;
arg.clinelist.push_back("--version");
arg.clinevalue.push_back(" ");
}
if (arg.Search("--counts"))
{
par::counts = true;
arg.clinelist.push_back("--counts");
arg.clinevalue.push_back(" ");
}
if (arg.Search("--summary"))
{
par::summary = true;
arg.clinelist.push_back("--summary");
arg.clinevalue.push_back(" ");
}
if (arg.Search("--specified"))
{
par::specified = true;
arg.clinelist.push_back("--specified");
arg.clinevalue.push_back(" ");
}
if (arg.Search("--calculated"))
{
par::calculated = true;
arg.clinelist.push_back("--calculated");
arg.clinevalue.push_back(" ");
}
if (arg.Search("--conflicting"))
{
par::conflicting = true;
arg.clinelist.push_back("--conflicting");
arg.clinevalue.push_back(" ");
}
// Help data
if (arg.Search("--help") or arg.Search("-h") or arg.parametercount == 1)
{
cout << ("\n"
"snpduo --file <fileroot> Specify .ped and .map files\n"
" --ped <ped file> Specify .ped file name (requires --map)\n"
" --map <map file> Specify .map file name\n"
" --tfile <fileroot> Specify .tfam and .tped files\n"
" --tped <tped file> Specify .tped file name (requires --tfam)\n"
" --tfam <tfam file> Specify .tfam file name\n"
" --genome <filename> Specify a PLINK .genome file for input\n"
" **Warning: Cannot get expected relationships from this file\n"
"\n"
" --out <fileroot> Specify the root name for output files\n"
"\n"
" --counts Prints IBS 0,1,2 and 2* (AB->AB) counts to .count file\n"
" --summary Prints counts + Mean and Standard Deviation of IBS to .summary file\n"
" --specified Prints relationships specified in input to .specified file\n"
" --calculated Prints calculated relationships from Mean and SD to .theoretical file\n"
" --conflicting Prints comparisons where specified relationship is different from calculated\n"
" relationship to .conflicting file\n"
// "\n"
// " --findblocks Find IBS blocks\n"
// " --makeucsc Turn blocks into UCSC track (.bed)\n"
"\n"
" --map3 Specifies no genetic distance column\n"
"\n"
" --recode Recodes data into ped/map files when used alone\n"
" --transpose When used with --recode outputs a tped/tfam files\n"
" --webduo When used with --recode outputs file compatible with\n"
" the web version of SNPduo (Custom format)\n"
" **Warning: Uses A/B coding but will NOT be the same\n"
" as the platform's A/B coding scheme. Only for Web SNPduo!\n"
"\n"
" --silent No messages printed to screen\n"
" --version Print version information and exit\n"
"\n"
" --help / -h Invokes this help menu\n");
shutdown();
}
}
