open(FILE, "<$ARGV[0]") || die "$!";
count_bases(20);
count_bases(30);
...
sub count_bases {
seek FILE, 0, SEEK_SET; #reset file pointer
my $min_quality = shift;

foreach $line (<FILE>) #main loop
{ 
  my @tmp_ar = split("\t", $line);
  ... 
  #make comparisons and put #s in hash 
}

##</code><code>##

count_bases(20, $ARGV[1]);
count_bases(30, $ARGV[1]);
...
sub count_bases {
my $min_quality = shift;

while(<>)
{ 
  my @tmp_ar = split();
  ... 
  #make comparisons and put #s in hash 
}