#include <stdlib.h>
#include <stdio.h>
#include <plinkio/plinkio.h>

int
main(int argc, char *argv[])
{   
    struct pio_file_t plink_file;
    snp_t *snp_buffer;
    int sample_id;
    int locus_id;

    if( pio_open( &plink_file, "/path/to/plink_file" ) != PIO_OK )
    {
        printf( "Error: Could not open %s\n", argv[ 1 ] );
        return EXIT_FAILURE;
    }

    if( !pio_one_locus_per_row( &plink_file ) )
    {
        printf( "This script requires that snps are rows and samples columns.\n" );
        return EXIT_FAILURE;
    }

    locus_id = 0;
    snp_buffer = (snp_t *) malloc( pio_row_size( &plink_file ) );
    while( pio_next_row( &plink_file, snp_buffer ) == PIO_OK )
    {
        for( sample_id = 0; sample_id < pio_num_samples( &plink_file ); sample_id++)
        {
            struct pio_sample_t *sample = pio_get_sample( &plink_file, sample_id );
            struct pio_locus_t *locus = pio_get_locus( &plink_file, locus_id );
            printf( "Individual %s has genotype %d for snp %s.\n", sample->iid, snp_buffer[ sample_id ], locus->name );
        }

        locus_id++;
    }

    free( snp_buffer );
    pio_close( &plink_file );
    
    return EXIT_SUCCESS;
}

/**
 * Data structure that contains the PLINK information about a sample (individual).
 */
struct pio_sample_t
{
    /**
     * An internal reference id, so that we can read them in order.
     */
    size_t pio_id;

    /**
     * Family identifier.
     */
    char *fid;

    /**
     * Plink individual identifier.
     */
    char *iid;

    /**
     * Plink individual identifier of father, 0 if none.
     */
    char *father_iid;

    /**
     * Plink individual identifier of mother, 0 if none.
     */
    char *mother_iid;

    /**
     * The sex of the individual.
     */
    enum sex_t sex;

    /**
     * Affection of the individuals, case, control or unkown. Control
     * is always 0 and case always 1.
     */
    enum affection_t affection;

    /**
     * A continuous phenotype of the individual.
     */
    float phenotype;
};

/**
 * Data structure that contains the PLINK information about a locus (SNP).
 */
struct pio_locus_t
{
    /**
     * An internal reference id, so that we can read them in order.
     */
    size_t pio_id;

    /**
     * Chromosome number starting from 1.
     */
    unsigned char chromosome;

    /**
     * Name of the SNP.
     */
    char *name;

    /**
     * Genetic position of the SNP.
     */
    float position;

    /**
     * Base pair position of the SNP.
     */
    long long bp_position;

    /**
     * First allele.
     */
    char *allele1;

    /**
     * Second allele.
     */
    char *allele2;
};