#!usr/bin/perl -w
open IN,"<$ARGV[0]" or die "cannot open the file $!";
open OUT,">$ARGV[1]" or die "cannot open the file $!";
$count=0; %filter=();@list=();
print scalar <IN> for 1..5;
while(<IN>)
{
    chomp;
    @tmp=split("\t",$_);
    $tmp[9]=~s/^chr//;
    @array=split/\||\:/,$tmp[9];
    if($array[-1] eq "-")
    {
        if($tmp[13] eq $array[0]&&(($tmp[15]<=($array[4]+999850)&&$tmp[15]>=($array[4]-150))||($tmp[16]>=($array[4]-150)&&$tmp[16]<=($array[4]+999850))))
        {
            $filter{$tmp[9]}=1;
            print "$_\n";
            $count++;
        }
        else
        {
            push @list,$tmp[9];
        }
    }
    else
    {
        if($tmp[13] eq $array[0]&&(($tmp[15]<=($array[2]+999850)&&$tmp[15]>=($array[2]-150))||($tmp[16]>=($array[2]-150)&&$tmp[16]<=($array[2]+999850))))
        {
            $filter{$tmp[9]}=1;
            print "$_\n";
            $count++;
        }
        else
        {
            push @list,$tmp[9];
        }
    }
}
foreach $i(@list)
{
    if(!exists $filter{$i})
    {
        print OUT "chr","$i\n"
    }
}
print "$count\n";
close IN;
close OUT;
