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@jeromekelleher jeromekelleher released this 18 Dec 16:05
· 459 commits to main since this release
0.2.0
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Learn about vigilant mode.

Major feature release, including some incompatible file format and API updates.

New features:

  • Mismatch and recombination parameters can now be specified via the recombination_rate and mismatch_ratio arguments in the Python API.

  • Missing data can be accomodated in SampleData using the tskit.MISSING_DATA value in input genotypes. Missing data will be imputed in the output tree sequence.

  • Metadata schemas for population, individual, site and tree sequence metadata can now we be specified in the SampleData format. These will be included in the final tree sequence and allow for automatic decoding of JSON metadata.

  • Map non-inference sites onto the tree by using the tskit map_mutations parsimony method. This allows us to support sites with > 2 alleles.

  • Historical (non-contemporaneous) samples can now be accommodated in inference, assuming that the true dates of ancestors have been set, by using the concept of "proxy samples". This is done via the new function AncestorData.insert_proxy_samples(), then setting the new parameter force_sample_times=True when matching samples.

  • The default tree sequence returned after inference when simplify=True retains unary nodes (i.e. simplify is done with keep_unary=True.

Breaking changes:

  • The ancestors tree sequence now contains the real alleles and not 0/1 values as before.

  • Times for undated sites now use frequencies (0..1), not as counts (1..num_samples), and are now stored as -inf, then calculated on the fly in the variants() iterator.

  • The SampleData file no longer accepts the inference argument to add_site. This functionality has been replaced by the exclude_positions argument to the infer and generate_ancestors functions.

  • The SampleData format is now at version 5, and older versions cannot be read. Users should rerun their data ingest pipelines.

  • Users can specify variant ages, via sample_data.add_sites(... , time=user_time). If not None, this overrides the default time position of an ancestor, otherwise ancestors are ordered in time by using the frequency of the derived variant (#143).

  • Change "age" to "time" to match tskit/msprime notation, and to avoid confusion with the age since birth of an individual (#149). Together with the 2 changes below, this addition bumped the file format to 3.0.

  • Add the ability to record user-specified times for individuals, and therefore the samples contained in them (currently ignored during inference). Times are added using sample_data.add_individual(... , time=user_time) (#190).

  • Change tsinfer.UNKNOWN_ALLELE to tskit.MISSING_DATA for marking unknown regions of ancestral haplotypes (#188) . This also involves changing the allele storage to a signed int from np.uint8 which matches the tskit v0.2 format for allele storage (see tskit-dev/tskit#144).

Bugfixes:

  • Individuals and populations in the SampleData file are kept in the returned tree sequence, even if they are not referenced by any sample. The individual and population ids are therefore guaranteed to stay the same between the sample data file and the inferred tree sequence. (:pr:348)
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