Re: genomic locus

On Fri, Dec 15, 2017 at 10:49 PM, Gene Selkov <selkovjr(at)gmail(dot)com> wrote:
> Greetings everyone,

Привет !

>
> I need a data type to represent genomic positions, which will consist of a
> string and a pair of integers with interval logic and access methods. Sort
> of like my seg type, but more straightforward.

Why not use composite type ? For simple interval approach it's worked for us
(see attached hdate.sql). If you need to specify distribution
function, than it may be
worth to see orion project http://orion.cs.purdue.edu/index.html
6 years ago we was thinking about implementation special UNCERTAINTY data type
(http://www.sai.msu.su/~megera/postgres/talks/big_uncertain_data.pdf), but never
started :( It'd be nice if you start this very interesting for science project.

btw, now you can use range data type, check
https://wiki.postgresql.org/images/7/73/Range-types-pgopen-2012.pdf

>
> I noticed somebody took a good care of seg while I was away for the last 20
> years, and I am extremely grateful for that. I have been using it. In the
> meantime, things have changed and now I am almost clueless about how you
> deal with contributed modules and what steps I should take once I get it to
> work. Also, is it a good idea to clone and fix seg for this purpose, or is
> there a more appropriate template? Or maybe just building it from scratch
> will be a better idea?
>
> I have seen a lot of bit rot in other extensions (never contributed) that I
> have not maintained since 2009 and I now I am unable to fix some of them, so
> I wonder how much of old knowledge is still applicable. In other words, is
> what I see in new code just a change of macros or the change of principles?

nothing special, copy, modify, compile

>
> Thanks,
>
> --Gene