Reece Hart

The `jsonld.compact()` example in README.rst raises an exception during json decoding. If this example was intended to be a template for how to call `compact()` (i.e., not a working example),...

implement support for repeats

5

Originally reported by: **Reece Hart (Bitbucket: [reece](http://bitbucket.org/reece), GitHub: [reece](http://github.com/reece))** ---------------------------------------- See comments in hgvs.pymeta. http://www.hgvs.org/mutnomen/recs-DNA.html#var Lots of gotchas: * reported as start position w/seq, or interval without seq. e.g., g.123TG[4],...

Converge variant models for all sequence types

3

This issue provides a place to collect ideas and comments regarding variant modeling, and particularly a single model that represents all variant and sequence types as coherently as possible. ##...

implement method to identify/describe transcripts regions for variant

1

Originally reported by: **Reece Hart (Bitbucket: [reece](http://bitbucket.org/reece), GitHub: [reece](http://github.com/reece))** ---------------------------------------- e.g., given c. variant, return something like "exon 3", "intron 2", "exon 1..2", "5' UTR", {'exons': [1,2,3]}. This needs a...

Implement caching for doctests

3

Some doctests appears to evade caching. Investigate why and re-enable. Until then, they've been disabled in pytest.ini

Investigate replacing psycopg2 with asyncpg

5

[asyncpg](http://magic.io/blog/asyncpg-1m-rows-from-postgres-to-python/) is a pure-python python library with support for asyncio. In principle, this would obviate libpq (see #199).

See how https://pypi.org/project/promise/ handles test dependencies. Migrate to that instead of the home-grown etc/develop.reqs stuff. Much better!

Code cleanup for 2.0 release

1

This issue collects changes to consider for the next major release. See also the [2.0 milestone](https://github.com/biocommons/hgvs/issues?q=is%3Aissue%20state%3Aopen%20milestone%3A2.0) Issues will be made for any changes that we commit to. Ideas: - [...

move SequenceVariant.fill_ref() to separate module

5

SequenceVariants have a fill_ref method that requires a data provider instance. This violates the intention to have the classes be data models with intrinsic methods only (i.e., methods that operate...

With #437, transcript coordinates may now be outside of the transcript bounds. Absolute numbers (e.g., `n.-5 and n.500 for a tx w/length