Dan King

### What happened? In particular, VDS is doubly sparse: 1. Sparse columns. Reference blocks are a form of run-length compression of homozygous reference calls. 2. Sparse alleles. Local alleles is...

### What happened? See discussion at https://atgu.slack.com/archives/CRA2TKTV0/p1699911268906349 The default behavior of assuming all the samples are unrelated is probably the wrong default. We might want to force the user to...

### What happened? How can we achieve this? ### Version 0.2.126 ### Relevant log output _No response_

### What happened? ``` =================================== FAILURES =================================== _______________ ServiceTests.test_python_job_incorrect_signature _______________ self = def setUp(self): # https://stackoverflow.com/questions/42332030/pytest-monkeypatch-setattr-inside-of-test-class-method self.monkeypatch = MonkeyPatch() self.backend = ServiceBackend() remote_tmpdir = get_remote_tmpdir('hailtop_test_batch_service_tests') if not remote_tmpdir.endswith('/'): remote_tmpdir +=...

### What happened? Ben W reports that he can reliably cause a batch worker VM to become non-responsive, triggering the driver to kill the VM, and the job to get...

AFAICT, it's currently required to specify exactly one authentication type in `fs.gs.auth.type`. This is fine for clusters, but annoying for non-expert users who go back and forth between local prototyping...

documentation on how to force all tests in one session to use the same event loop appears to not force fixtures into the same event loop

4

I checked in all the files referenced below into this repo: https://github.com/danking/pytest-asyncio-confusion ``` pytest==7.4.3 pytest-asyncio==0.23.3 ``` Simple test file: ```python3 import pytest import asyncio @pytest.fixture(scope='session') async def foo(): yield asyncio.get_running_loop()...

What does `.` mean for an `A`, `R`, or `G` indexed field?

6

Hey all, I'm trying to pin down exactly what `.` means for an `A`, `R` or `G` indexed field. In particular does `.` mean: 1. This field is missing. 2....

[query] Hail should provide `hl.saige` in both QoS and QoB

3

### What happened? [SAIGE](https://github.com/weizhouUMICH/SAIGE) and its competitor [REGENIE](https://rgcgithub.github.io/regenie/) are the standard bearers for modern GWAS. Hail should expose SAIGE within the Hail Query language. The interface should roughly match `hl.linear_regression_rows`....

[datasets] Lily & Ruchit want to contribute updated dbNSFP and EVE tables to the annotation database & datasets API.

2

### What happened? https://hail.zulipchat.com/#narrow/stream/127634-Feature-Requests/topic/Adding.20to.20Hail.20annotation.20database/near/397575602 We need a Hail team member to write up how to contribute to the annotation database and then help them do that. Patrick Cummings was the...