pio_status_t
pio_transpose(const char *plink_file_prefix, const char *transposed_file_prefix)
{
struct pio_file_t plink_file;
if( pio_open( &plink_file, plink_file_prefix ) != PIO_OK )
{
return PIO_ERROR;
}
char *bed_path = concatenate( plink_file_prefix, ".bed" );
char *transposed_bed_path = concatenate( transposed_file_prefix, ".bed" );
pio_status_t status = bed_transpose( bed_path, transposed_bed_path, pio_num_loci( &plink_file ), pio_num_samples( &plink_file ) );
if( status == PIO_OK )
{
char *fam_path = concatenate( plink_file_prefix, ".fam" );
char *transposed_fam_path = concatenate( transposed_file_prefix, ".fam" );
file_copy( fam_path, transposed_fam_path );
free( fam_path );
free( transposed_fam_path );
char *bim_path = concatenate( plink_file_prefix, ".bim" );
char *transposed_bim_path = concatenate( transposed_file_prefix, ".bim" );
file_copy( bim_path, transposed_bim_path );
free( bim_path );
free( transposed_bim_path );
}
pio_close( &plink_file );
free( bed_path );
free( transposed_bed_path );
return status;
}
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);
}
}
void key_drv_thread(KEY2_DRIVER_INFO* drv_info)
{
unsigned int i, mask;
unsigned char button_ticks[KEY_COUNT];
unsigned int new_keys;
CHandle keyrd_hnd;
pio_open(&keyrd_hnd, &drv_info->pins);
for(i=0; i<KEY_COUNT; i++)
button_ticks[i] = 0;
btns_pressed = 0;
for(;;)
{
// scan keyboard every 5ms while some key is pressed
do
{
tsk_sleep(KEY_POLLING_TIME-4);
keyrd_hnd.tsk_read(&new_keys, 4);
mask = 1;
for(i=0; i<KEY_COUNT; i++)
{
if (new_keys & drv_info->key_codes[i])
{
button_ticks[i] = 0;
if (mask & btns_pressed)
{
btns_pressed ^= mask;
key_post(KEY_UP_CODE+i);
}
} else
{//button pressed
button_ticks[i]++;
if(mask & btns_pressed)
{ //button hold?
if (button_ticks[i] > (KEY_REPEAT_TIME/KEY_POLLING_TIME))
{
button_ticks[i] = 0;
key_post(KEY_REPEAT_CODE+i);
}
} else
if (button_ticks[i] > (KEY_DEBOUNCE_TIME/KEY_POLLING_TIME))
{
button_ticks[i] = 0;
btns_pressed |= mask;
key_post(KEY_DOWN_CODE+i);
}
}
mask <<=1;
}
} while(new_keys ^ drv_info->pins.mask);
//wait for any key...
keyrd_hnd.tsk_read_locked(&new_keys, 4);
}
}
