Hi!
Problem 1. What is a union of ‘1:6000-7000’ and ‘X:10000-20000’? Intuitively, it
should be NULL, however, I am not sure the method allows for that; it was
developed for objects living in the same metric space. I have mechanistically
reproduce the indexing methods of seg, but the resulting index is broken. All
queries against an indexed table return a null result.
You can use fixed-size signature for string part (contig?) of locus, it will
help to find that string part by equlity or intersection of need it. Signature
of inner key should be bitwise-ORed of all child keys. Looking on query example,
seems, you need to build signature tree and, if signature is the same of two
key, take into account start-end range.
Problem 2. While the intersection (overlap, &c.) of any two loci produces
obvious results, non-intersection does not. When I query for all loci not
overlapping ‘1:6000-7000’, I expect to find all non-overlapping loci on contig
1. I don’t want the query to return anything from other contigs, because it is
obvious that features on different contigs do not overlap. I may be able to fix
that by making separate functions for non-overlaps and adding a constraint to
them, but that seems like a kludge.
Seems like you have two different non-overlap operation...
Problem 3 (alternative to 1). I realize that any clustering can help build an
efficient index, no matter how bizarre. So I could, for example, ignore the
contigs altogether and build a single index tree, using only position
co-ordinates and pretending that all positions are on the same contig; the
question then is whether and how such lossy index will affect the ordering of
query results. Can I use a separate function for ordering? I have yet to make an
experiment. Not that this would be equivalent to indexing the attributes of a
composite type separately (if I understood it correctly).
Ordering and GiST aren't very close things :) You can try to have a look to
KNN-search feature of GiST. https://www.pgcon.org/2010/schedule/events/227.en.html
--
Teodor Sigaev E-mail: teo...@sigaev.ru
WWW: http://www.sigaev.ru/
