Rather than just die()ing, you could auto convert the file to the native format on load. That's something I do often in my scripts where I could be recieving files in DOS, Unix or Mac format.

open my $fh, '<', $filename or die "Can't open file. $!\n";
while (<$fh>){
  $_ =~ s/\cM\cJ|\cM|\cJ/\n/g;

  # do somthing with line

}
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Yeah, it does useless conversions on native format files, but the overhead is nearly negligible usually.