Kyle Ferriter

support stdin in vcf annotator

1

https://pysam.readthedocs.io/en/latest/usage.html#using-streams https://github.com/ga4gh/vrs-python/blob/main/src/ga4gh/vrs/extras/annotator/vcf.py#L209

Clarify definition of SEQREPO_ROOT_DIR

3

seqrepo makes heavy use of the concept of a "root dir" or "data dir" and refers to it in code as SEQREPO_ROOT_DIR. This is analogous to other database "data dir"s,...

Update `psycopg2` to `psycopg` (and make optional)

1

**Is your feature request related to a problem? Please describe.** Applications which require `biocommons.hgvs` must build `psycopg2`. This also requires installing a C compiler and libpq. **Describe the solution you'd...

Same-as-reference Alleles should have a ReferenceLengthExpression state

4

``` 2. Compare the two Allele sequences, if: a. both are empty, the input Allele is a reference Allele. Return a new Allele with: 1. the `location` from the input...

Add seqrepo and vrs-python docker scripts and github action

1

I think this needs to be tested a little bit more on my fork to ensure the multi-stage build is indeed reusing the cached layers This supersedes https://github.com/ga4gh/vrs-python/pull/555. TODO: also...

Add additional input/output methods to the `vrs-annotate` CLI

1

User should be able to pass in a newline delimited file/stream of HGVS and SPDI expressions and receive newline delimited Allele JSON records (JSONL) as an output file/stream. Consider also...

Remove vcf annotator healthcheck

3

Close #530

Create `examples` folder with markdown file pointing to different use cases, e.g. https://github.com/gks-anvil Maybe include a slim example like: https://github.com/ga4gh/vrs-python/blob/feature/vrs-in-a-box/vrs-in-a-box/VrsVcfAnnotator.wdl @ahwagner