#!/usr/bin/perl
=head2 SYNOPSIS

	Description: Add the additional read counts (from the cross-mapping reads) to the uniquely mapped read count.
             
=head2 AUTHOR

	Kang Zhang  Email:  demut@foxmail.com
	
=cut
#known read counts
open IN,"<$ARGV[0]" or die;

#added read counts:
open ADD,"<$ARGV[1]" or die;

while(<ADD>){
	chomp;
	my @arr=split;
	if($arr[2]%2 == 1){
		$arr[2]--;
	}
	$add{$arr[0]}=$arr[2]/2;
	$add{$arr[1]}=$arr[2]/2;
}

while(<IN>){
	next if (/^#/);
	next if (/^Geneid/);
	chomp;
	my @arr=split;
	my $count=$arr[6];
	my $added=$count+$add{$arr[0]};
	print "$arr[0]\t$arr[5]\t$added\n";
}