Nick Watts

Allow alternate rate limit notifications

1

Allow a callable to be passed to `wait_on_rate_limit_notify` so that a rate limit notice can trigger actions other than logging a warning.

Hail should support quote-escaped quotes.

7

Some delimited text processors use quotes to escape quotes so that the string `a"b` is rendered as `a""b`. Moreover an individual entry of the delimited text is itself wrapped in...

`hailctl dataproc` can pass through gcloud configurations specified with `--configuration` to the `gcloud dataproc` commands that it runs. However, that argument is often not respected for other `gcloud` commands that...

String split behavior inconsistent with Python

4

Hail version: 0.2.55-0d4ce0df2457 The behavior of the second parameter to [StringExpression's split method](https://hail.is/docs/0.2/hail.expr.StringExpression.html#hail.expr.StringExpression.split) is determined by its Java implementation and differs from Python [string's split method](https://docs.python.org/3/library/stdtypes.html#str.split). > The limit parameter...

Support custom session names in `--keywords` expression

3

**How would this feature be useful?** Currently, providing a `--keywords` argument that is not a valid expression causes Nox to crash with a SyntaxError. ``` $ nox -k 'foo:bar' Traceback...

Document how to use gnomAD API

1

Include some examples: - Fetch variant data - Fetch gene data - Selecting dataset

Many components render differently based on the current dataset. Check for conditionals such as `datasetId.startsWith('gnomad_r3')`. Ideally, instead of checking the dataset ID directly, abstract checks into functions in [dataset-metadata](https://github.com/broadinstitute/gnomad-browser/tree/main/dataset-metadata). For...

Update version of VEP used in ClinVar data pipeline

1

When starting a Dataproc cluster for the GRCh38 ClinVar data pipeline ([deploy/docs/UpdateClinvarVariants.md](https://github.com/broadinstitute/gnomad-browser/blob/main/deploy/docs/UpdateClinvarVariants.md)), use the same VEP init script and configuration as used to annotate v4.

See instructions in [reads/README.md](https://github.com/broadinstitute/gnomad-browser/tree/main/reads#adding-reads-for-a-dataset). Since v4 will use a different version of VEP than v3, the transcripts track in the IGV.js viewer will also need to be updated. - [reads/README.md#reference-data](https://github.com/broadinstitute/gnomad-browser/tree/main/reads#reference-data)...

Replace references to v3 with updated information about v4 in [about](https://github.com/broadinstitute/gnomad-browser/tree/main/browser/about) and [help](https://github.com/broadinstitute/gnomad-browser/tree/main/browser/help) content.