Skip to content

Latest commit

 

History

History
96 lines (63 loc) · 3.17 KB

CHANGELOG.rst

File metadata and controls

96 lines (63 loc) · 3.17 KB
Raw

[0.2.0] - XXXX-XX-XX

Breaking changes:

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

[0.1.5] - 2019-09-25

Breaking changes:

  • Bumped SampleData file format version to 2.0, then to 3.0 as a result of the additions below. Older SampleData files will not be readable and must be regenerated.
  • 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). This addition bumped the file format to 2.0
  • 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). Together with the changes above and below, this addition bumped the file format to 3.0.
  • 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). Together with the 2 changes above, this addition bumped the file format to 3.0.

New features:

  • Map non-inference sites onto the tree by using the built-in tskit map_mutatations method. With further work, this should allow triallelic sites to be mapped (#185)
  • The default tree sequence returned after inference when simplify=True retains unary nodes (i.e. simplify is done with keep_unary=True. This tends to result in better compression.

[0.1.4] - 2018-12-12

Bugfix release.

  • Fix issue caused by upstream changes in numcodecs (#136).

[0.1.3] - 2018-11-02

Release corresponding to code used in the preprint.

[0.1.2] - 2018-06-18

Minor update to take advantage of msprime 0.6.0's Population and Individual objects and fix various bugs.

Breaking changes:

  • Bumped SampleData file format version to 1.0 because of the addition of individuals and populations. Older SampleData files will not be readable and must be regenerated.
  • Changed the order of the alleles and genotypes arguments to SampleData.add_site.

New features:

  • Sample and individual metadata now handled correctly.
  • Added --no-simplify option to CLI and simplify=True option to infer function.
  • Better handling of missing files (raises correct exceptions).
  • tsinfer list now presents basic information for .trees files.

Bug fixes:

  • Degenerate examples with zero inference sites are now rooted (#44)
  • Simplify=False results in tree sequence with correct sample nodes.