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, @RosCraddock, @gregorgorjanc, @XingerTang).

• Add a version option to the command line interface (PR #237, @XingerTang).

Bug fixes

• Fix bug for subsetting snps with map file input (PR #241, @XingerTang).

Maintenance

• Update the alternative allele probability limits from [0.01, 0.99] to [0.001, 0.999] (Issue #185, Issue #276, PR #227, @RosCraddock, @XingerTang, @gregorgorjanc).

• Renaming of command line arguments, changing of input format, and corresponding documentation and test updates (Issue #221, PR #219 ,:pr:222, @RosCraddock, @gregorgorjanc, @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, @gregorgorjanc).

• Add collaboration guidelines to the documentation (PR #224, @XingerTang, @RosCraddock, @AprilYuZhang, @gregorgorjanc).

• Updated the documentation to add more techincal instructions for developers and contributors (PR #237, @XingerTang).

• Round up threshold for output file names (PR #246, @XingerTang).

• Update help messages for command line arguments (PR #246, @XingerTang).

• Rename option mutation_rate to mut_prob for consistency with other options (PR #246, @XingerTang).

• Add explanation of no_phase_founder option in the documentation (PR #246, @XingerTang).

• Add explanation of rec_length option in the documentation (PR #246, @XingerTang).

• Add explanation of file format for the seg_map_file in the documentation (PR #246, @XingerTang).

• Remove extra empty lines in the genotype probabilities output file (PR #246, @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, @RosCraddock, @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, @AprilYuZhang, @XingerTang).

  • Move X chromosome flag sex_chrom to x_chr.

  • Update the X chromosome related peeling functions.

• Add mutation rate input (PR #198, @AprilYuZhang, @XingerTang).

  • Added mutation_rate to allow user-provided mutation rate.

• Add map file input (PR #208, @XingerTang, @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, @XingerTang, @gregorgorjanc).

• Fix bug in the example code and the corresponding accuracy check code (Issue #205, Issue #206, PR #208, @XingerTang, @gregorgorjanc).

• Fix tinyhouse bug of incorrectly classified founders (Issue #118, PR #208, @XingerTang, @gregorgorjanc, @augustusgrant).

• Fix map file bug for non-ascending order input (Issue #155, PR #208, @XingerTang, @gregorgorjanc).

• Fix minor typo in the .gitattributes file name (Issue #30, PR #208, @XingerTang, @gregorgorjanc).

• Fix the bug that ignores the first locus while calculating the accuracy in the accuracy test (PR #208, @XingerTang, @gregorgorjanc).

Maintenance

• Update the documentation and tests for the phenotype file input (PR #195, @RosCraddock, @XingerTang).

• Add docstrings for main peeling functions (PR #195, @RosCraddock, @XingerTang).

• Add changelog (PR #195, @RosCraddock, @XingerTang).

• Update the documentation and tests for the X chromosome peeling (PR #198, PR #201, @AprilYuZhang, @XingerTang).

• Update the documentation for mutation rate (PR #198, @AprilYuZhang, @XingerTang).

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

[1.2.0] - 2025-03-21

New features

• Allow metafounders, defined as “MF_”, in the pedigree file input (PR #175, @RosCraddock, @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, @RosCraddock).

Maintenance

• User-warnings and documentation updates for metafounder implementation and estimation of alternative allele frequency (PR #152, PR #175, PR #182, @RosCraddock, @XingerTang).

• Functional and accuracy tests for metafounder implementation (PR #156, PR #182, @XingerTang, @RosCraddock).

• Updated reference to tinyhouse (PR #177, @XingerTang).

[1.1.6] - 2024-10-22

New features

• Addition of map file input for non-hybrid mode (PR #154, @XingerTang).

Bug fixes

• Resolved bug to produce output file with -hap and -geno (PR #157, @AprilYUZhang).

Maintenance

• Set default hap and geno threshold as 1/3 when calling genotypes (PR #157, @AprilYUZhang).

[1.1.5] - 2023-12-01

New features

• Addition of output options: geno, and hap_threshold (PR #119, @AprilYuZhang).

Maintenance

• Updates in option and file names (PR #105, PR #115, PR #122, @XingerTang, @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: https://github.com/AlphaGenes/AlphaPeel/issues/113#issue-1935197000.

• Updates the documentation and help functions (PR #88, PR #119, @XingerTang, @AprilYuZhang).

• Updates to accuracy and functional tests for new option names (PR #126, PR #130, PR #131, @XingerTang).

[1.1.4] - 2023-08-25

New features / additions

• Implementation of functional and accuracy testing with pytest (PR #53, @XingerTang).

• Implementation of pre-commit code formatting with Black and Flake8 (PR #40, @XingerTang).

• Implementation of cross-platform tests workflow with GitHub actions (PR #59, @XingerTang).

• Added instructions on how to contribute to AlphaPeel (PR #27, PR #31, @XingerTang).

Bug fixes

• Fixed bug on the loading of submodule (PR #22, @XingerTang).

Maintenance

• Update theme for the HTML documentation (PR #38, @XingerTang).

• Modified the URL for installation (PR #11, @XingerTang).