No comment on the NL problem really, except that reading is usually not a problem in Perl - you have to be more careful if writing files for distribution to *nix or WinDOS. If you are looking at making your code more robust, I would second the previous recommendations on file handling - remember FH style globs are global.

You might even consider using IO::File which IMHO has an easy peasy and pretty interface, and automatically closes in a kernel resource friendly manner!

use IO::File;

my $fh = IO::File->new($filename, "r")
  or die "unable to open $filename: $!";
 
for my $line ( $fh->getlines() ) {
  chomp $line;
  print "[$line]\n";
}
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I would also add the comment that your two subs duplicate each other - why not just have one? Or if you really like having the two names then...

sub load_primers {
  return _loadIndex( @_);
}

sub load_parents {
  return _loadIndex( @_);
}
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and move all the code into _loadIndex();

$0.02