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perl -we 'open $_, "<", shift or die for my($D, $Q); my $p = -1e9999; 
+my $s = -1e9999; my $x; while (my $q = <$Q>) { chomp($q); my $k = (sp
+lit " ", $q)[1]; $p <= $k or die "query not sorted"; $p = $k; while (
+$s < $p and defined(my $d = <$D>)) { (my($l), $x) = (split " ", $d)[2
+,0]; $s <= $l or die "db not sorted"; $s = $l; } my $z = $p == $s ? $
+x : "-"; print $q, "    ", $z, "\n"; }' file1.db file2.query

1190    31277    A > T    1    0    0    -
1190    31607    C > A    0    3    1    -
...
1190    32199    C > T    0    1    1    -
1190    32487    T > C    0    1    1    -
1190    32496    A > G    0    3    0    -