open (ALIGNED, "<:encoding(UTF-8)", "${filename}.txt") or die "Can't open aligned file for reading: $!";
open (ALIGNED_MOD, ">:encoding(UTF-8)", "${filename}_mod.txt") or die "Can't open file for writing: $!";

if ($delete_dupes eq "y") {

	my %seen;		# hash that contains uique records (hash lookups are faster than array lookups)
	my $key;		# key to be put in hash
	while (<ALIGNED>) {
		/^([^\t]*\t[^\t]*)/;	# only watch first two fields
		chomp ($key = $1);		# only watch first two fields
		print ALIGNED_MOD $_ if (! $seen{ $key }++); # add to hash, and if new, print to file
	}

	my $unfiltered_number = $.;
	my $filtered_number = keys %seen;
	print "\n\n-------------------------------------------------";
	print "\n\nSegment numbers before and after filtering out dupes: $unfiltered_number -> $filtered_number\n";
	print LOG "\nFiltered out dupes: $unfiltered_number -> $filtered_number";

	undef %seen; # free up memory

	close ALIGNED;
	close ALIGNED_MOD;
	rename ("${filename}_mod.txt", "${filename}.txt") or die "Can't rename file: $!";
}