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use strict;
use warnings;

Global symbol "$count" requires explicit package name at test.pl line 
+13.
Global symbol "@line" requires explicit package name at test.pl line 1
+5.
Global symbol "@line" requires explicit package name at test.pl line 1
+9.
Global symbol "@line" requires explicit package name at test.pl line 2
+5.
test.pl had compilation errors.

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