simultaneously reducing both memory usage and runtime for a query

Hi everyone,

I've been trying to reduce both memory usage and runtime for a query. An
issue I have encountered is that I can drastically reduce both runtime and
memory usage by splitting up the query into two pieces and gluing them
together outside PostgreSQL. However, I'm unable to get similar results
inside PostgreSQL. I have tried different variations of the same query,
but either the memory or the runtime blows up. I wonder if I'm missing
something. In any case, feedback would be helpful. Details of my attempts
at optimization are at

http://bulldog.duhs.duke.edu/~faheem/snppy/opt.pdf

See particularly Section 1 - Background and Discussion.

If you want a text version, see

http://bulldog.duhs.duke.edu/~faheem/snppy/opt.tex

For background see

http://bulldog.duhs.duke.edu/~faheem/snppy/diag.pdf (text version
http://bulldog.duhs.duke.edu/~faheem/snppy/diag.tex) and
http://bulldog.duhs.duke.edu/~faheem/snppy/snppy.pdf

Please CC any replies to me at the above email address. Thanks.

                                                      Regards, Faheem.