while (<$in_file>) {
    chomp;

    if (/^SAMPLE/) {
        my ( $placeholder, @coords ) = split /,/;
        foreach my $coord (@coords) {
            push @snp_bins, int( $coord / 100_000 );
        }
    }

    else {
        my ( $id, @snps ) = split /,/;
        foreach my $snp (@snps) {    # (@snps[0..$#snps-1]
            $snp =~ s/$snp/$snp,/    # put commas back in (preserve csv format)
        }

        foreach my $index ( 0 .. $#snp_bins ) {
			if ( $snps[$index] ) {
            push( @{ $data{$id}[ $snp_bins[$index] ] }, $snps[$index] );  # see note [1]
		    }

			else {                   # replace 'undef' elements with flag data
				my @ones_array;
				foreach ( 1 .. 100) {
					push @ones_array, "1 1,";
				}
				push( @{ $data{$id}[ $snp_bins[$index] ] }, @ones_array )
			}
        }
    }
}

##</code><code>##

if ( $snps[$index] )