v1.3.0

[1.3.0] - 2026-02-05

New features

• Allow phenotype input, currently only works for one phenotype and one genotype/locus,
  currently still experimental (:pr:195, :user:RosCraddock, :user:XingerTang).

  • Added pheno_file file with phenotypes for phenotyped individuals.

  • Added pheno_penetrance_file file with user-provided phenotype error rates
    for the phenotypes, that is, the conditional probability of each phenotype
    given the genotype. TODO: Rename to pheno_error_prob_file

  • Added pheno_prob to output the phenotype probabilities of individuals.

  • Added update_pheno_penetrance_file to re-estimate the phenotype penetrance
    after each peeling cycle following Kinghorn (2003).

• Allow X chromosome input,
  currently still experimental (:pr:198, :user:AprilYuZhang, :user:XingerTang).

  • Move X chromosome flag sex_chrom to x_chr.

  • Update the X chromosome related peeling functions.

• Add mutation rate input (:pr:198, :user:AprilYuZhang, :user:XingerTang).

  • Added mutation_rate to allow user-provided mutation rate.

Add map file input (:pr:208, :user:XingerTang, :user:gregorgorjanc).

- Modified ``map_file`` to enable map file input for non-hybrid mode.

Bug fixes

• Fix minor bug in simulation code for accuracy tests
  (:issue:181, :pr:208, :user:XingerTang, :user:gregorgorjanc).

• Fix bug in the example code and the corresponding accuracy check code
  (:issue:205, :issue:206, :pr:208, :user:XingerTang, :user:gregorgorjanc).

• Fix tinyhouse bug of incorrectly classified founders
  (:issue:118, :pr:208, :user:XingerTang, :user:gregorgorjanc, :user:augustusgrant).

• Fix map file bug for non-ascending order input
  (:issue:155, :pr:208, :user:XingerTang, :user:gregorgorjanc).

• Fix minor typo in the .gitattributes file name
  (:issue:30, :pr:208, :user:XingerTang, :user:gregorgorjanc).

• Fix the bug that ignores the first locus while calculating the accuracy in the accuracy test
  (:pr:208, :user:XingerTang, :user:gregorgorjanc).

Maintenance

• Update the documentation and tests for the phenotype file input
  (:pr:195, :user:RosCraddock, :user:XingerTang).

• Add docstrings for main peeling functions
  (:pr:195, :user:RosCraddock, :user:XingerTang).

• Add changelog (:pr:195, :user:RosCraddock, :user:XingerTang).

• Update the documentation and tests for the X chromosome peeling
  (:pr:198, :pr:201, :user:AprilYuZhang, :user:XingerTang).

• Update the documentation for mutation rate
  (:pr:198, :user:AprilYuZhang, :user:XingerTang).

• Move changelog to documentation; add algorithm section, add a simple example, and
  update installation instructions in the documentation
  (:pr:208, :user:XingerTang, :user:gregorgorjanc).