Gideon Dresdner <gideond@gmail.com> writes: > I've created a small dump of my database that recreates the problem. I hope > that this will help recreate the problem. It is attached. I'd be happy to > hear if there is an easier way of doing this.
Ah. Now that I see the database schema, the problem is here:
regression=# \d vcf ... chr | smallint | ...
So "chr" is smallint in one table and integer in the other. That means the parser translates qcregions.chr = vcf.chr using the int42eq operator instead of int4eq --- and nobody's ever taught btree_gist about crosstype operators. So the clause simply isn't considered indexable with this index. If you change the query to "qcregions.chr = vcf.chr::int" then all is well.
Personally I'd just change vcf.chr to integer --- it's not even saving you any space, with that table schema, because the next column has to be int-aligned anyway.
