#!/usr/bin/perl
use warnings;
use strict;
use v5.14;

die "need two arguments (i.e. chr cont) at invocation" unless @ARGV == 2;

chomp( my $chr_num = shift );
chomp( my $cont    = shift );

open my $out_file, ">", "chr${chr_num}_exome_snps_processed_${cont}_STATS"
  or die "Can't open output file: $!\n";

# Get a list of individuals (will be hash keys later):
open my $in_file, "<", "chr${chr_num}_exome_snps_processed_$cont"
  or die "Can't open input file: $!\n";

my @individuals;
my %data;

while (<$in_file>) {
    chomp;
    my @snp_bins;
    if (/^SAMPLE/) {
        my ( $placeholder, @coords ) = split /,/;
        foreach my $coord (@coords) {
            push @snp_bins, int( $coord / 100_000 );
        }
    }
    else {
        my ( $id, @snps ) = split /,/;
        push @individuals, $id;
        foreach my $individual (@individuals) {
            foreach my $snp (@snps) {
                $data{$individual}[ [ shift @snp_bins ] ] = $snp;
            }

        }

    }
}

close $in_file;

##</code><code>##

## Sample of data file. Each file has hundreds of thousands of columns and hundreds of rows
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