Data::Data(std::string datapath,int nthreads)
{
nSites = 0;
nIndiv = 0;
this->datapath = datapath;
this->nthreads = nthreads;
if( pio_open( &plink_file, datapath.c_str() ) != PIO_OK )
{
std::cerr << "[Data::getsize] Error opening plink files " << datapath << ".[bed/bim/fam] "
<< std::endl << std::endl
<< "This error means that libplinkio (https://github.com/mfranberg/libplinkio) "
<< "cannot read the dataset correctly."
<< std::endl << std::endl
<< "Make sure that plink can process the dataset without non-standard input "
<< "options such as `--allow-extra-chr` which indicates that the data "
<< "contains unrecognized chromosome codes."
<< std::endl << std::endl
<< "For example, check that `plink --bfile datapath --freq` runs without errors."
<< std::endl << std::endl;
exit(1);
}
if( !pio_one_locus_per_row( &plink_file ) )
{
std::cerr << "[Data::getsize] bed2diffs requires plink files [bed/bim/fam] in SNP-major mode" << std::endl;
exit(1);
}
}
Data::Data(std::string datapath,int nthreads)
{
nSites = 0;
nIndiv = 0;
this->datapath = datapath;
this->nthreads = nthreads;
if( pio_open( &plink_file, datapath.c_str() ) != PIO_OK )
{
std::cerr << "[Data::getsize] Error opening plink files " << datapath << ".[bed/bim/fam]" << std::endl;
exit(1);
}
if( !pio_one_locus_per_row( &plink_file ) )
{
std::cerr << "[Data::getsize] This program requires plink files [bed/bim/fam] in SNP-major mode" << std::endl;
exit(1);
}
}
