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.
To rebuild the database:
- create a database
- run from the commandline `$ psql database-name < 1000genomes-schema.sql`
- run this within a psql REPL ` #\copy public.qcregions FROM
'/tmp/1000genomes-qcregions.tsv' DELIMITER ' ' CSV;` (where the
delimiter is a tab)
- similarly run this within a psql REPL, `#\copy public.vcf FROM
'/tmp/1000genomes-vcf.tsv' DELIMITER ' ' CSV;`
To see that the GIST index is not being hit, try running the following
query:
EXPLAIN SELECT * FROM vcf
WHERE EXISTS (SELECT region FROM qcregions
WHERE qcregions.chr = vcf.chr
AND vcf.pos <@ qcregions.region);
The actual query I am trying to run is:
EXPLAIN SELECT * FROM vcf
WHERE EXISTS (SELECT region FROM qcregions
WHERE qcregions.chr = vcf.chr
AND qcregions.type = 'include'
AND vcf.pos <@ qcregions.region);
Let me know what else I can try,
Gideon.
On Wed, Aug 12, 2015 at 11:07 AM Gideon Dresdner <gide...@gmail.com> wrote:
> What's a good way for me to create a self-contained test case. AFAIU the
> only way to make these test cases more self-contained would be to inline
> the second table and its index. How do you create an index to an inlined
> table of values?
>
> Or perhaps I could send over a dump of a subset of the data?
>
> Yes, I am fairly sure that I am running 9.4.4:
>
> $ psql --version
> psql (PostgreSQL) 9.4.4
>
> # select version();
> version
>
>
> -----------------------------------------------------------------------------------
> PostgreSQL 9.4.4 on x86_64-unknown-linux-gnu, compiled by gcc (GCC)
> 5.1.0, 64-bit
> (1 row)
>
> Thanks for the help,
> Gideon.
>
> On Tue, Aug 11, 2015 at 10:23 PM Tom Lane <t...@sss.pgh.pa.us> wrote:
>
>> Gideon Dresdner <gide...@gmail.com> writes:
>> > I had a discussion on IRC today with RhodiumToad regarding optimizing a
>> > specific query. We didn't manage to figure out how to get postgres to
>> hit a
>> > GIST index.
>>
>> FWIW, I couldn't reproduce the described behavior. Can you provide a
>> self-contained test case? Are you sure your server is 9.4.4?
>>
>> regards, tom lane
>>
>
1000genomes-dump.tar.gz
Description: application/gzip
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