Reece Hart

Add examples of valid HGVS to documentation

7

For example, from the server test data: ``` va.transcriptEffects[0].hgvsAnnotation.toJsonDict() ``` gives ``` {u'genomic': u'1:g.46286_46288delTAT', u'protein': u'', u'transcript': u'n.46286_46288delTAT'} ``` I think we will ultimately defeat the utility of the GA4GH...

API accepts invalid HGVS and rejects valid HGVS

4

First: Thank you. Making data easily available is a great service to the community! # Issue MyVariant.info accepts invalid (MyVariant.info-specific) HGVS and does not accept valid HGVS. Since HGVS expressions...

Implement Genotypes

3

This issue is being split from #186, which was previously to implement Haplotypes and Genotypes.

Get feedback on documentation from new users

1

For this issue, we will gather input regarding the VRS documentation from new users. A hackathon is an ideal place for a team of users to review the documentation and...

Update validation suite for all classes

2

The validation suite (in `validation/`) is a language-neutral set of tests intended to be used by any group that implements VRS. These tests are used by vrs-python for testing. The...

Define how to refer to reverse complement sequences

1

Use cases: * Insert inverted sequence * Feature (gene, exon, intron, transcript) defined on rev comp

Imported from #201: Use cases for Gene locations. ## Use cases ### Gene-specified fusions - [BCR / ABL1 fusion](https://civicdb.org/events/genes/4/summary/variants/1/summary) - [KIAA1549 / BRAF fusion](https://civicdb.org/events/genes/5/summary/variants/618/summary/evidence/7148/summary#evidence) - [ALK fusions](https://ckb.jax.org/molecularProfile/showMolecularProfileByVariant?geneVariantId=2602) - [RET fusions](https://www.oncokb.org/gene/RET/Fusions)...

Implement support for transcript-based locations

10

Coordinates based on transcripts depend on the exon structure at least. Coding position requires also cds start and end. Proposal: Implement TranscriptLocation, à la HGVS, by creating a class that...

Write specification for representing translocations and fusions/junctions

31

VR needs to have a path for representing translocations. Allele is currently defined as a contiguous sequence change at a single location. Translocations and junctions are unlikely to fit in...

build UTA REST interface / refactor UTA client packaging

3

**Originally reported by Reece Hart (Bitbucket: [reece](http://bitbucket.org/reece), GitHub: [reece](http://github.com/reece)) in [biocommons/uta](https://bitbucket.org/biocommons/uta/) [#164](https://bitbucket.org/biocommons/uta/issue/164)** Migrated by [bitbucket-issue-migration](https://github.com/reece/bitbucket-issue-migration) on 2016-09-09 15:15:07 --- Data in UTA would be more accessible if it were accessible...