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C:\>perl -c ag2gen.pl
"my" variable $i masks earlier declaration in same statement at ag2gen
+.pl line 1391.
...
"my" variable $j masks earlier declaration in same statement at ag2gen
+.pl line 1394.
syntax error at ag2gen.pl line 1389, near "2]"
ag2gen.pl had compilation errors.

1389: for my $i (0..@test_order-2])
1390: {
...
1392:   {
1393:     unless ( ( $test_order[$i] eq $test_order[$j] )
1394:       or exists($test_order{"$test_order[$i]\t$test_order[$j]"} 
+) )