#!/usr/bin/env perl
use Modern::Perl;

my %data;                 # HoAoA holding final data structure
my @indexes;              # array of indexes into %data based on coordinates

my $header_line = <DATA>; # some of these steps could be combined;
chomp $header_line;       # including them for clarity
my @headers = split ',', $header_line;
shift @headers; # throw away SAMPLE
for my $n (@headers){
    my $x = $n/100_000;
    my $y = $n % 100_000;
    push @indexes, [ $x, $y ];
}

while(<DATA>){
    chomp;
    my( $id, @bits ) = split ',';
    for my $i (0..@bits-1){
        $data{$id}[$indexes[$i][0]][$indexes[$i][1]] = $bits[$i];
    }
}
say "Expecting 0 0: ", $data{HG00553}[162][87365];
say "Expecting 1 1: ", $data{HG00638}[162][87851];

__DATA__
SAMPLE,16287215,16287226,16287365,16287649,16287784,16287851,16287912
HG00553,0 0,0 0,0 0,0 0,0 0,0 0,0 0
HG00554,0 0,0 0,0 0,0 0,0 0,0 0,0 0
HG00637,0 0,0 0,0 0,0 0,0 0,0 0,0 0
HG00638,0 0,0 0,0 0,0 0,0 0,1 1,0 0
HG00640,0 0,0 0,0 0,0 0,0 0,1 1,0 0