[XingerTang]

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).

• Add support for direct in-process AlphaPeel calls for accuracy benchmarking,
  profiling, and development workflows (:pr:292, :user:XingerTang, :user:gregorgorjanc).

• Add locus-based multi-threading options and benchmarking support for comparing
  family-wise and locus-wise thread settings (:pr:292, :user:XingerTang, :user:gregorgorjanc).

• Add switch-error rate and phasing-error rate calculation utilities for accuracy
  reporting (:issue:255, :pr:256, :user:XingerTang).

• Add controls for output rounding precision (:issue:271, :pr:272, :user:XingerTang).

• Add explicit output options for estimated genotype error probabilities,
  estimated sequence error probabilities, and recombination probabilities
  (:issue:252, :pr:268, :user:XingerTang).

Bug fixes

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

• Fix X chromosome peeling behaviour, including penetrance handling and default
  segregation probabilities (:issue:225, :pr:226, :user:AprilYUZhang).

• Fix the accuracy report test configuration file names
  (:issue:259, :pr:262, :user:XingerTang).

• Fix estimation of alternative allele probabilities when using up to two
  metafounders per individual (:issue:260, :pr:263, :user:RosCraddock).

Maintenance

• Updated the documentation for alt_allele_prob_file and estimation of
  phenotype penetrance probabilities (:pr:220, :user:RosCraddock).

• Update the alternative allele probability limits from [0.01, 0.99] to [0.001, 0.999]
  (:issue:185, :issue:276, :pr:277, :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).

• Update the tinyhouse submodule reference after metafounder updates
  (:issue:228, :pr:229, :user:RosCraddock).

• Remove obsolete repository files and make minor documentation and packaging
  refinements (:issue:233, :pr:234, :user:XingerTang).

• 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).

• Remove the ineffective IO multi-threading option
  (:issue:210, :issue:250, :pr:251, :user:XingerTang).

• Remove the sequence file requirement from the accuracy test runner
  (:issue:257, :pr:261, :user:AprilYUZhang).

• Refactor warning handling for clearer runtime messages
  (:issue:266, :pr:267, :user:XingerTang).

• Clarify documentation and help text for method selection, alternative allele
  probability output, and male X chromosome genotype probability formatting
  (:pr:275, :user:XingerTang).

• Clarify haplotype and penetrance input handling, remove the unsupported
  reference option, and update the tinyhouse submodule for renamed haplotype
  input messages (:issue:73, :issue:74, :issue:127, :issue:167,
  :issue:231, :pr:278, :user:XingerTang).

• Restructure the documentation to make file format documentation easier to navigate and cross-reference
  (:pr:283, :user:XingerTang, :user:gregorgorjanc).

• Remove unsupported PLINK IO functionality and its functional tests
  (:issue:286, :pr:291, :user:XingerTang).

• Rework the accuracy test and reporting scheme to produce clearer benchmark
  outputs, generation-wise metrics, switch-error metrics, runtime summaries,
  and visualization-ready reports (:pr:292, :user:XingerTang, :user:gregorgorjanc).

• Optimize memory use and runtime in the peeling implementation, including
  lower-memory data structures, streamlined array handling, and faster
  alternative allele probability updates (:pr:292, :user:XingerTang,
  :user:gregorgorjanc).

• Refactor code and documentation for clearer module-level reuse
  (:pr:292, :user:XingerTang, :user:gregorgorjanc).

• Add developer documentation for testing, benchmarking, memory profiling,
  runtime profiling, multi-thread profiling, and code-quality
  checks (:pr:292, :user:XingerTang, :user:gregorgorjanc).

• Update continuous-integration configuration and supported Python-version
  testing setup for the current development workflow (:pr:292, :user:XingerTang,
  :user:gregorgorjanc).

[gregorgorjanc]

Well done us! A lot of work has gone into this version.