========= Changelog ========= [1.3.1] - 2026-03-05 ==================== 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`). Maintenance ----------- * 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``. [Unreleased] - 2026-02-12 ========================= Maintenance ----------- * Updated the documentation to clarify inputs, outputs, and parameters (:pr:`219`, :user:`gregorgorjanc`). [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: https://github.com/AlphaGenes/AlphaPeel/issues/113#issue-1935197000. * 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`).