Yes, the is_dos_format() is smashing $_ in your grep block. The easy fix is to either local()ize $_ in the function or use a different variable in your while loop: 
sub is_dos_format {
  local $_;

  ...
}

# or

sub is_dos_format {
  ...
  while (my $line = <RJA>) {
  ...
}

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Jeff japhy Pinyan, P.L., P.M., P.O.D, X.S.: Perl, regex, and perl hacker
How can we ever be the sold short or the cheated, we who for every service have long ago been overpaid? ~~ Meister Eckhart

In reply to Re: grep and find file weirdness by japhy
in thread grep and find file weirdness by reasonablekeith

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