LINE 1: I:\HDL\HHDL_chr4.txt (location and name of the data file)
LINE 2: I:\HDL\Result_chr4 (location and name of the result file: This file will be created when run the program)
LINE 3: 100 (maximum number of iteration in Newton-Raphson method) 
        10e-5 (convergence criterion)
        50 (one half of the maximum number of categories of Y without invoking rounding.
            If the maximum number of categories in Y is more than 2x50, Y is rounded to 
            have 2x50 categories in computing SPORT-d and SPORT-p)
LINE 4: 1265 (Total number of variables in your data)  
        1 (dimension of the phenotype or quantitative trait) 
        1 (dimension of SNPs in the model)
        2 (dimension of confounders, two refers to gender and age in the example)             
LINE 5: 2 (location of the phenotype in the dataset, 2 means the second variable) 
LINE 6: 1 (location of the dichotomized phenotype in the dataset, 1 means the first variable)
LINE 7: 5 (location of the first SNP in the dataset, 5 means the fifth variable. Note the program              
            assumes that all other SNPs are lining after the first SNP until the last variable) 
LINE 8: 3 4 (locations of the two confounders in the dataset, 3 4 means the third and fourth variables) 
LINE 9: -9 (the value used to indicate a missing value)
LINE 10 and BEYOND are ignored.