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my @inInterval = map { $_->[1] } grep { $start <= $_->[0] and $_->[0] 
+<= $end } @SNPs;

open my $CG, "<", $cg_input or die "can't open $cg_input\n";
my @SNPs = map { [ (split /\t/)[3], $_ ] } <$CG>;
...
    close $OUT;
}
close($INTERVAL);