Avoiding side effects

[Anders Wirzenius <anders@no.email.thanks.invalid>]

Another thread about functions and side effects triggered me to
ask advice how to solve a specific problem without using side effects.

Problem:
Two files A and B containing one code per line (actually a
material number). I want to have the difference between those
files (A-B), i.e. remove those lines in A that are mentioned in
B.
B may contain codes that are not present in A.
A and B contain up to 1.5 million lines each.

My solution:
I sort the files alphabetically and remove possible duplicates
(Unix commands sort and uniq).
I create two functions, Strip and Advance.
function Strip (Remove_This : in String) return String
   -- Displays rows until row > Remove_This.
function Advance (Candidate : in String) return String
   --  Advance in file until row > Candidate.
The main program is then merely a loop where I alternate between
advancing lines in the two files until the row in the file is
greater than the value to compare against:
...
loop
   Trans_String := To_Unbounded_String (Strip (To_String
    (Trans_String)));
   Trans_String := To_Unbounded_String (Advance (To_String
    (Trans_String)));
end loop;
The problem is how to deal with the situation when I reach the
end of the file. 
I have done it using a side effect:
EOF_Reached     : Boolean := False;
loop
   Trans_String...
   exit when EOF_Reached;
   Trans_String...
   exit when EOF_Reached;
end loop;
--  Display possible tail of file A.
EOF_Reached is set to True in the functions Strip and Advance as
a side effect.

Is there a better way without using the side effect EOF_Reached?

-- 
Anders