#!/usr/bin/perl
use warnings;
use strict;
use Data::Dumper;

#link to input file from command line - 2 arguments or error displayed; Set to respective variables
@ARGV == 2 or die "Invalid number or arguments. Please re-run program and supply as arguments: \n1) the filter file and \n2) the input file.";
my ($filter_file, $input_file) = @ARGV;

open (FILTER,"$filter_file");
my @filter;

<FILTER>; # read one line from the file [HEADERS]

while (<FILTER>)
{ # read other lines
	chomp; # remove "\n" from the end of the line
	push @filter,[(split /\t/,$_)]; # create an array of the line by splitting it by <TAB>, make a reference of it and push the reference to the @filter array
	close $filter_file if eof;
}


@filter = sort { $a->[5] <=> $b->[5] } @filter; # sort the array 

#PRINTS REFERENCES TO ARRAY FROM LEAST TO GREATEST REGARDING 'ORDER' COLUMN
print Dumper \@filter; #### For Debugging Purposes
my $num_elements = (@filter-1); #Number of elements in array - will be used to control loop when comparisons take place later in code