Tsinfer

Latest version: v0.3.3

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0.4.0

**Features**

- `tsinfer` now supports inferring data from an `vcf-zarr` dataset. This allows users
to infer from VCFs via the optimised and parallel VCF parsing in `bio2zarr`.
- The `VariantData` class can be used to load the vcf-data and be used for inference.
- `vcf-zarr` `sample_ids` are inserted into individual metadata as `variant_data_sample_id`
if this key does not already exist.

**Breaking Changes**

- Remove the `uuid` field from SampleData. SampleData equality is now purely based
on data. ({pr}`748`, {user}`benjeffery`)

**Performance improvements**

- Reduce memory usage when running `match_samples` against large cohorts
containing sequences with substantial amounts of error.
({pr}`761`, {user}`jeromekelleher`)

- `truncate_ancestors` no longer requires loading all the ancestors into RAM.
({pr}`811`, {user}`benjeffery`)

- Reduce memory requirements of the `generate_ancestors` function by providing
the `genotype_encoding` ({pr}`809`) and `mmap_temp_dir` ({pr}`808`) options
({user}`jeromekelleher`).

- Increase parallelisation of `match_ancestors` by generating parallel groups from
their implied dependency graph. ({pr}`828`, {issue}`147`, {user}`benjeffery`)

0.4.0a2

0.4.0a1

0.3.3

**Fixes**
- Bug fix release for numpy 2 ({issue}`937`).

**Breaking Changes**
- A permissive json schema is now set on node table metadata
({issue}`416` {pr}`931`, {user}`hyanwong`).

0.3.2

**Features**

- `tsinfer` now supports numpy2 (and 1.XX) and python 3.12.

**Breaking Changes**

- tsinfer now requires Python 3.9 or later

0.3.1

- Bug fix release for a bad dependency specification.

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