sgkit

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Hi I realize that the `save_dataset` function doesn't return the delayed object. For instance, if ran with `compute=False`: https://github.com/sgkit-dev/sgkit/blob/eef911e87d1aad47cb139170bcda1b82f220114f/sgkit/io/dataset.py#L71 running `save_dataset` with `compute=False` has use cases for example - visualizing...

rajwanir

The best way to append samples to a dataset?

2

Hi, I am working with array datasets and wish to concatenate samples across multiple zarr stores (>100). Since these are genotyping array datasets, they only differ in sample dimension. Everything...

rajwanir

Diversity calculations on windowed datasets generate lots of unmanaged memory

10

When working on a reasonably large dataset (7TiB Zarr store), I noticed that diversity calculations, in particular windowed ones, generate lots of unmanaged memory. The `call_genotype` data portion is 280GiB...

percyfal

Part of #908 This is still a draft as there are a couple of things that might need more attention before merging.

tomwhite

Add separate function for Watterson's theta

3

sgkit-allel has functionality to [calculate Watterson's theta](https://scikit-allel.readthedocs.io/en/stable/stats/diversity.html#allel.watterson_theta) but in sgkit it is calculated implicitly in [Tajima's D function](https://github.com/sgkit-dev/sgkit/blob/54c8abe49a91fab43cc905d1ed5190397c5af8b7/sgkit/stats/popgen.py#L476). For some applications direct access to Watterson's theta would be of practical...

percyfal

`import sgkit` takes ~1.5s

7

For tools using the CLI this amount of delay feels excessive. Around 1s of this time is performing imports. Here's the import flame graph: (0.1s on `xarray.tutorial`?!?)  I assume...

benjeffery

Update Development Status classifier in setup.cfg

1

Currently it is [`Development Status :: 3 - Alpha`](https://github.com/pystatgen/sgkit/blob/main/setup.cfg#L13), should we change it to [Beta or Production/Stable](https://pypi.org/classifiers/), or perhaps remove entirely?

tomwhite

While trying to insall sgkit in Guix I had an error with the three submodules not being found. This can be fixed by specifying the submodules in the pyproject.toml here...

alxsimon

Dead link

2

Hi Link ```https://storage.googleapis.com/sgkit-data/tutorial/1kg.vcf.bgz``` referenced in [gwas_tutorial](https://sgkit-dev.github.io/sgkit/latest/examples/gwas_tutorial.html) is no longer accessible. Thanks

mattlyonofh

Remove (c)bgen dependency for unpack_variables?

5

Hi! Thanks for creating sgkit. Very useful package. We are using it for performing calculations on a dataset that was converted from bgen. For reading, our code uses something like...

jpfeuffer