use strict;
use warnings;

##</code><code>##

Global symbol "$count" requires explicit package name at test.pl line 13.
Global symbol "@line" requires explicit package name at test.pl line 15.
Global symbol "@line" requires explicit package name at test.pl line 19.
Global symbol "@line" requires explicit package name at test.pl line 25.
test.pl had compilation errors.

##</code><code>##

...
my (@line, $count);

while (<$fhConditions>)
{
    push @line, $_;
    $count++;
}

for (my $i = 0; $i < $count; $i++)
{
	my @pos = $line[$i] =~ /chr[0-9]\s+(.+?)\s/g;
	...