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while (<$fh>) {
   # If the file contained lines ending with CRLF, $_ ends with LF
   # If the file contained lines ending with LF,   $_ ends with LF
   chomp;  # Removes LF
}

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while (<$fh>) {
   # If the file contained lines ending with CRLF, $_ ends with CRLF
   # If the file contained lines ending with LF,   $_ ends with LF
   s/\r?\n\z//;  # Removes CRLF or LF
}