Reece Hart

require points or ranges as appropriate for edit type

6

Originally reported by: **Reece Hart (Bitbucket: [reece](http://bitbucket.org/reece), GitHub: [reece](http://github.com/reece))** ---------------------------------------- The parser decomposes PosEdits into Positions and Edits. Positions are modeled as Intervals with start and end. Point positions are...

RFC: Develop plan to replace Parsley

6

We currently use [parsley](http://parsley.readthedocs.io/en/latest/) to parse HGVS expressions. Parsley was last released in 2015. The most recent commit on github is 2017. The project appears to be defunct, which presents...

untangle lru_cache and persistent cache

5

The current lru_cache code is complicated because it mixes several intentions. Let's untangle them. The two goals are 1) in-memory memoization layer to reduce remote data fetches; 2) persistent caching...

Implement personalis variant tests

3

See * https://docs.google.com/presentation/d/1QEzzH_tkMAIdImKxCRFVI6yifyBWy1IxCe0esnjWo-w/edit#slide=id.p * https://github.com/personalis/hgvslib * https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-016-0396-7 The relevant functionality is likely covered already, but it's worth having them explicitly covered using exactly the variants in their test set.

support uncertain ranges

7

Originally reported by: **Reece Hart (Bitbucket: [reece](http://bitbucket.org/reece), GitHub: [reece](http://github.com/reece))** ---------------------------------------- Indefinite positions such as g.123_(450_456)del are not currently supported ---------------------------------------- - Bitbucket: https://bitbucket.org/biocommons/hgvs/issue/225

p_to_* reverse translation methods

1

Originally reported by: **Brian Craft (Bitbucket: [brian_craft_](http://bitbucket.org/brian_craft_), GitHub: Unknown)** ---------------------------------------- Mapping protein to other coords would be useful. ---------------------------------------- - Bitbucket: https://bitbucket.org/biocommons/hgvs/issue/265

Clarify semantics of NARefAlt and AARefAlt

1

Originally reported by: **Reece Hart (Bitbucket: [reece](http://bitbucket.org/reece), GitHub: [reece](http://github.com/reece))** ---------------------------------------- hgvs has two core classes, NARefAlt and AARefAlt that are used to represent SNVs, insertions, deletions, and indels. Although these...

hgvs 1.0.0rc1: ``` In [44]: var_c = hp.parse_hgvs_variant("NM_000088.3:c.591_593inv") In [46]: am37.c_to_p(var_c) ... NotImplementedError: c to p translation unsupported for NM_000088.3:c.591_593inv type ```

Originally reported by: **Reece Hart (Bitbucket: [reece](http://bitbucket.org/reece), GitHub: [reece](http://github.com/reece))** ---------------------------------------- Tests in the hgvs package are pretty broad, but we should also create thorough comparison tests (based on ClinVar or...

Selenocysteine not correctly handled by c_to_p

3

@veenaraj reported that NC_000001.10:g.26139280T>G is projected by VEP to ENSP00000363434:p.Sec428Gly. hgvs gives NP_065184.2:p.?. N.B.: c.1384 should map to p.462. I've not confirmed the VEP output. Regardless of whether there's a...