diff --git a/CHANGELOG.md b/CHANGELOG.md index 109dc3cd..5f5ddbed 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,10 +2,15 @@ ## [0.4.0a3] - ****-**-** +**Features** + +- Document that the `zarr-vcf` dataset can be either a path or an in-memory zarr group. + (feature introduced in {pr}`966`, documented in {pr}`974`, {user}`hyanwong`) + **Fixes** - Properly account for "N" as an unknown ancestral state, and ban "" from being - set as an ancestral state ({pr}`963`, {user}`hyanwong`)) + set as an ancestral state ({pr}`963`, {user}`hyanwong`) ## [0.4.0a2] - 2024-09-06 diff --git a/tsinfer/formats.py b/tsinfer/formats.py index 99d48064..c485d792 100644 --- a/tsinfer/formats.py +++ b/tsinfer/formats.py @@ -2308,8 +2308,10 @@ class VariantData(SampleData): the inference process will have ``inferred_ts.num_samples`` equal to double the number returned by ``VariantData.num_samples``. - :param str path: The path to the file containing the input dataset in VCF-Zarr - format. + :param Union(str, zarr.hierarchy.Group) path_or_zarr: The input dataset in + `VCF Zarr `_ format. + This can either a path to the Zarr dataset saved on disk, or the + Zarr object itself. :param Union(array, str) ancestral_state: A numpy array of strings specifying the ancestral states (alleles) used in inference. This must be the same length as the number of unmasked sites in the dataset. Alternatively, a single string