Jerome Kelleher
Jerome Kelleher
It would be useful if vcf_to_zarr wrote some debugging information to the Python log. It's a bit of a black box at the moment trying to figure out what's happening...
I'm not finding any documentation how to do something like: ``` ds = sg.load_dataset(ds_path) ds = sg.count_variant_alleles(ds) # Don't overwrite the whole thing, just write out the new variables so...
There doesn't seem to be any link between variables, and how they are computed either in the documentation, or in error messages. For example, I want to get ``variant_allele_frequency`` which...
In #2823 we added support for the genetic_relatedness_matrix function as a follow-up usage of ``divergence_matrix`` using sample sets. This doesn't work when the sample_sets have a length > 1. It's...
It would be handy to have a ``mid`` property on the Interval class, much like we have ``span`` at the moment. This would be ``self.left + (self.right - self.left) /...
The documentation for IBD is quite sparse and preliminary. When we have implemented MRCA IBD (#2896) we should flesh it out.
The MRCA definition of IBD is useful in some cases, and it would be good for us to support it. From an API perspective, I think all that we need...
Numpy 2.0 is about to land, and might have some consequences for us at the C level. Notes on [C API changes](https://numpy.org/devdocs/numpy_2_0_migration_guide.html#c-api-changes) More importantly, [oldest-supported-numpy](https://github.com/scipy/oldest-supported-numpy) is being deprecated, so we...
Numpy 2.0 is about to drop: https://github.com/numpy/numpy/issues/24300 - [migration guide](https://numpy.org/devdocs/numpy_2_0_migration_guide.html) There is a ruff plugin which can check this as [lint](https://numpy.org/devdocs/numpy_2_0_migration_guide.html#ruff-plugin) This might be a motivation to switch to ruff...
Currently undocumented. See also #2889 Also note the parallelism, this needs some explanation.