changelog.rst

Changelog

[Unreleased] - 2026-04-??

New features

• Allow a founding individual to have two different metafounders, e.g., one for the paternal lineage and one for the maternal lineage (:pr:`222`, :user:`RosCraddock`, :user:`gregorgorjanc`, :user:`XingerTang`).
• Add a version option to the command line interface (:pr:`237`, :user:`XingerTang`).

Bug fixes

• Fix bug for subsetting snps with map file input (:pr:`241`, :user:`XingerTang`).

Maintenance

• Update the alternative allele probability limits from [0.01, 0.99] to [0.001, 0.999] (:issue:`185`, :issue:`276`, :pr:`227`, :user:`RosCraddock`, :user:`XingerTang`, :user:`gregorgorjanc`).

• Renaming of command line arguments, changing of input format, and corresponding documentation and test updates (:issue:`221`, :pr:`219` ,:pr:222, :user:`RosCraddock`, :user:`gregorgorjanc`, :user:`XingerTang`).

  • est_alt_allele_prob to est_start_alt_allele_prob.
  • update_alt_allele_prob to est_alt_allele_prob.
  • pheno_penetrance_file to phenotype_penetrance_prob_file.
  • update_pheno_penetrance to est_pheno_penetrance_file.
  • Reformatted the alt_allele_prob_file input to match the outputted alt_allele_prob_file.

• Updated the documentation to clarify inputs, outputs, and parameters (:pr:`219`, :user:`gregorgorjanc`).

• Add collaboration guidelines to the documentation (:pr:`224`, :user:`XingerTang`, :user:`RosCraddock`, :user:`AprilYuZhang`, :user:`gregorgorjanc`).

• Updated the documentation to add more techincal instructions for developers and contributors (:pr:`237`, :user:`XingerTang`).

• Round up threshold for output file names (:pr:`246`, :user:`XingerTang`).

• Update help messages for command line arguments (:pr:`246`, :user:`XingerTang`).

• Rename option mutation_rate to mut_prob for consistency with other options (:pr:`246`, :user:`XingerTang`).

• Add explanation of no_phase_founder option in the documentation (:pr:`246`, :user:`XingerTang`).

• Add explanation of rec_length option in the documentation (:pr:`246`, :user:`XingerTang`).

• Add explanation of file format for the seg_map_file in the documentation (:pr:`246`, :user:`XingerTang`).

• Remove extra empty lines in the genotype probabilities output file (:pr:`246`, :user:`XingerTang`).

[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.
  • 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`).

[1.2.0] - 2025-03-21

New features

• Allow metafounders, defined as “MF_”, in the pedigree file input (:pr:`175`, :user:`RosCraddock`, :user:`XingerTang`)>

  • Added alt_allele_prob_file for user-inputted alternative allele frequencies for each metafounder and loci. For now, these are restricted to be between 0.01 and 0.99.
  • Added main_metafounder to allow user to assign the default metafounder to use where a metafounder has not been assigned to a founder in the pedigree.
  • Added update_alt_allele_prob to allow the base alternative allele frequencies to be updated after each peeling cycle based on the mean of the founders within the assigned metafounder

Bug fixes

• Fixed bug due to setuptools package being updated for all wheel file naming to follow binary distribution specification (i.e., all lower case) and updated documentation (:pr:`182`, :user:`RosCraddock`).

Maintenance

• User-warnings and documentation updates for metafounder implementation and estimation of alternative allele frequency (:pr:`152`, :pr:`175`, :pr:`182`, :user:`RosCraddock`, :user:`XingerTang`).
• Functional and accuracy tests for metafounder implementation (:pr:`156`, :pr:`182`, :user:`XingerTang`, :user:`RosCraddock`).
• Updated reference to tinyhouse (:pr:`177`, :user:`XingerTang`).

[1.1.6] - 2024-10-22

New features

• Addition of map file input for non-hybrid mode (:pr:`154`, :user:`XingerTang`).

Bug fixes

• Resolved bug to produce output file with -hap and -geno (:pr:`157`, :user:`AprilYUZhang`).

Maintenance

• Set default hap and geno threshold as 1/3 when calling genotypes (:pr:`157`, :user:`AprilYUZhang`).

[1.1.5] - 2023-12-01

New features

• Addition of output options: geno, and hap_threshold (:pr:`119`, :user:`AprilYuZhang`).

Maintenance

• Updates in option and file names (:pr:`105`, :pr:`115`, :pr:`122`, :user:`XingerTang`, :user:`AprilYuZhang`), the major ones include:

  • no_dosages to no_dosage,
  • calling_threshold to geno_threshold,
  • call_phase to hap,
  • haps to phased_geno_prob,
  • pedigree to ped_file,
  • genotypes to geno_file,
  • and more, for all changes please visit: AlphaGenes#113 (comment).

• Updates the documentation and help functions (:pr:`88`, :pr:`119`, :user:`XingerTang`, :user:`AprilYuZhang`).

• Updates to accuracy and functional tests for new option names (:pr:`126`, :pr:`130`, :pr:`131`, :user:`XingerTang`).

[1.1.4] - 2023-08-25

New features / additions

• Implementation of functional and accuracy testing with pytest (:pr:`53`, :user:`XingerTang`).
• Implementation of pre-commit code formatting with Black and Flake8 (:pr:`40`, :user:`XingerTang`).
• Implementation of cross-platform tests workflow with GitHub actions (:pr:`59`, :user:`XingerTang`).
• Added instructions on how to contribute to AlphaPeel (:pr:`27`, :pr:`31`, :user:`XingerTang`).

Bug fixes

• Fixed bug on the loading of submodule (:pr:`22`, :user:`XingerTang`).

Maintenance

• Update theme for the HTML documentation (:pr:`38`, :user:`XingerTang`).
• Modified the URL for installation (:pr:`11`, :user:`XingerTang`).