$in1=$ARGV[0];
$in2=$ARGV[1];
$in3=$ARGV[2];
$out1=$ARGV[3];

if (scalar @ARGV != 4){
die " Wrong command\n\n";
}

open(OUT,">$outfile");

open (IN1,"$in1");
while (<IN1>){
if ($_ !~ /^\expr/ && $_ !~ /^expr/){
if ($_ =~ /expr/){
if(cond){$some_count++;}
}
}
}
close IN1;
undef (@_);undef ($_);undef ($in1);

$per_reads_aligned = ($reads_aligned/$total_reads)*100;

my %hash1 = ();
open (IN2,"$in2");
while (<IN2>){
chomp ($_);
$hash1{$_} = 1;
}

$count2=keys(%hash1);
close IN2;

undef ($in2);
undef (@_);
undef ($_);

open (IN3,"$in3");
while (<IN3>){
if ($_ =~ /expr/){
$var1=$1;$var2=$2;$var3=$3;$var4=$4;

if($var1 ne "N" && $var1 ne "S"){
$hhkey1=$var2."_".$var4;
if (exists $hash1{$hhkey1}){
$count3++;
if($var3 >= 5){$count5++;}
if($var3 >= 10){$count6++;}
if($var3 >= 15){$count7++;}
if($var3 >= 20){$count8++;}
}
}
}
}
close IN3;

undef ($in3);
undef (@_);
undef ($_);
undef (%hash1);

## Some calculation and print to outfile

close OUT;