if (abs $atob > 1  &&  
    abs $btoc > 1  &&  
    abs $atoc > 1     ) {

    print OUTFILE "DIFF > 1 all three\n";
    $matrixflags[$row - 4][$i] = 1;
    $matrixflags[$row - 3][$i] = 1; 
    $matrixflags[$row - 2][$i] = 1;
}

elsif (abs $atob > 1  &&
       abs $btoc < 1  &&
       abs $atoc > 1    ) {

    print OUTFILE "DIFFA > 1 $atob  $atoc $btoc\n";
    $matrixflags[$row - 4][$i] = 1;
    $matrixflags[$row - 3][$i] = 0;
    $matrixflags[$row - 2][$i] = 0;
}
elsif ( ... ) { ... }