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[pull] main from AlphaGenes:main - #3

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AlphaGenes:main

Aug 7, 2026

Merged

[pull] main from AlphaGenes:main#3
pull[bot] merged 88 commits into
HighlanderLab:mainfrom
AlphaGenes:main

Commits on Jan 4, 2026
- Two dif MF
  RosCraddock
  committed
  32bab25
Commits on Feb 11, 2026
- Merge pull request #4 from RosCraddock/feat_pheno_info
  XingerTang
  authored
  142fd5b
Commits on Mar 2, 2026
- Added an x_chr example #199
  
  gregorgorjanc
  authored and
  XingerTang
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  364a3bc
Commits on Mar 3, 2026
- reset the defalt seg probs#199
  AprilYUZhang
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  3f46cfd
- fix the probability of geno and so on #199 #215 #225
  AprilYUZhang
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Commits on Mar 9, 2026
- Metafounders, alt_allele_prob, and name changes
  RosCraddock
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  29af0dc
- Merge remote-tracking branch 'RosCraddock/feat_pheno_info' into upstream/devel AlphaGenes/AlphaPeel#222
  XingerTang
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Commits on Mar 10, 2026
- update tinyhouse reference
  
  RosCraddock
  authored and
  XingerTang
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  0412048
Commits on Mar 17, 2026
- Apply suggestion from @AprilYUZhang
  AprilYUZhang
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  228574c
Commits on Mar 19, 2026
- Minor refinements AlphaGenes/AlphaPeel#233
  
  XingerTang
  authored and
  gregorgorjanc
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Commits on Mar 26, 2026
- Merge remote-tracking branch 'upstream/devel' into feat/issue-225-improve-xchr-function
  AprilYUZhang
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Commits on Apr 2, 2026
- Improve technical instruction AlphaGenes/AlphaPeel#230\n Add -version flag AlphaGenes/AlphaPeel#204
  XingerTang
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  bff0801
Commits on Apr 17, 2026
- Fix AlphaGenes/AlphaPeel#238
  XingerTang
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Commits on Apr 21, 2026
- fix/issue-244-code-cleanup AlphaGenes#244
  XingerTang
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  32d0f30
Commits on Apr 22, 2026
- Fix AlphaGenes/AlphaPeel#250 remove multi-io option
  XingerTang
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  5313505
Commits on Apr 30, 2026
- Add SER and PER AlphaGenes/AlphaPeel#255
  XingerTang
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Commits on May 7, 2026
Commits on May 18, 2026
- remove sequence file#257
  
  AprilYUZhang
  authored and
  XingerTang
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  1dc52cc
- Fix accuracy report table AlphaGenes/AlphaPeel#259
  XingerTang
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  69955c4
Commits on May 20, 2026
- Fix issue #260
  
  RosCraddock
  authored and
  XingerTang
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  7a8f305
Commits on May 21, 2026
- Fix issue 266 warnings
  XingerTang
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  674ae6b
Commits on May 26, 2026
- Fix issue 252 params output
  XingerTang
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  ef61eab
Commits on May 29, 2026
- Add option for output rounding digits AlphaGenes/AlphaPeel#271
  XingerTang
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  76085a3
Commits on Jun 1, 2026
- Update documentation and help message
  XingerTang
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  667f063
Commits on Jun 2, 2026
- Extending MAF limits per issue #276
  
  RosCraddock
  authored and
  XingerTang
  committed
  06bdbb1
Commits on Jun 12, 2026
- Update input options -phased_geno_prob, -hap_file, remove -reference
  XingerTang
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  86248a4
Commits on Jul 1, 2026
- Issue AlphaGenes/AlphaPeel#280 file formats
  XingerTang
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  f7b9a0e
Commits on Jul 3, 2026
- Fix issue AlphaGenes/AlphaPeel#286 remove plink io
  XingerTang
  committed
  9ab959c
Commits on Aug 7, 2026
- Refactoring functional tests
  XingerTang
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  72c4af8
- Fix pytest warnings
  XingerTang
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  a686e29
- Simplify accuracy test report
  XingerTang
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  277091d
- Proper hybrid test
  XingerTang
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  5a954ff
- Update test workflow
  XingerTang
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  5f0463a
- Shorten the list of Python versions
  XingerTang
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  623030e
- Update flake8 configuration
  XingerTang
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  8823ee1
- Test older version Python with older OS images
  XingerTang
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  582733a
- Python 3.6 is not well-supported
  XingerTang
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  ca0c758
- Update requirement
  XingerTang
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  8127d10
- Limit support to python >= 3.8
  XingerTang
  committed
  8602a4f
- Fix rounding for alt_allele_prob output
  XingerTang
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  819a905
- Ignore first two rows of seg files & special case for hap file of x_chr output
  XingerTang
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  d00c440
- Add gen-wise abs_diff and correct_rate output of seg_prob
  XingerTang
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  7cd10ee
- Refactor utils.py
  XingerTang
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  e51cacc
- Add SER and relevant metrics for hap
  XingerTang
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  9743ce2
- Add runtime and visualization
  XingerTang
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  ff8df9a
- Add SER and relevant metrics for hap
  XingerTang
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  6c98360
- Ignore uncalled hap & update docs on accu report
  XingerTang
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  d789707
- Refactor argument reassignment
  XingerTang
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  19d930c
- Regrouped the argument option parser
  XingerTang
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  b31081a
- Remove unused functions
  XingerTang
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  6eef1d7
- Remove commented code
  XingerTang
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  505154a
- Remove peelingInfo maf and PointSeg for memory optimisation
  XingerTang
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  be97756
- Remove peelingInfo genotyped
  XingerTang
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  29ee4a3
- Reduce 4 family terms to 2
  XingerTang
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  56088d4
- Optimise integer types
  XingerTang
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  ba7ad66
- Minor updates
  XingerTang
  committed
  ca4adc2
- Reordering array slicing for efficiency
  XingerTang
  committed
  95a5598
- Change variable name from penetranceState to penetranceProb
  XingerTang
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  81fe458
- Optimise MAF updates
  XingerTang
  committed
  c1b400a
- Refactor peeling code for runtime optimisation
  XingerTang
  committed
  28ca700
- Refactoring IO and XChr related code
  XingerTang
  committed
  bf593ba
- Renaming variables in snake_case style for naming consistency
  XingerTang
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  3578ec5
- Clean up docstring and comments
  XingerTang
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  3115821
- Fix mismatched
  XingerTang
  committed
  290dc2d
- update pheno_penetrance_prob_file related message
  XingerTang
  committed
  6d3dee5
- Update peeling_updates based on Pylint suggestions
  XingerTang
  committed
  8cb2984
- Refactor peeling_io and version based on Pylint suggestions
  XingerTang
  committed
  a78fb9c
- Refactor peeling based on Pylint suggestions
  XingerTang
  committed
  61bde9f
- Finish refactoring of peeling/ based on the Pylint suggestions
  XingerTang
  committed
  a9a903e
- Update pyproject
  XingerTang
  committed
  383a216
- Refactor tinypeel.py based on Pylint suggestions
  XingerTang
  committed
  b5e5e3f
- locus-parallel first draft
  XingerTang
  committed
  841d583
- Finalise locus-based multi-threading
  XingerTang
  committed
  dd9d84d
- Update doc for the multi-thread options
  XingerTang
  committed
  326b020
- Update docs
  XingerTang
  committed
  8e34661
- Update and add new sections for testing_and_profiling docs
  XingerTang
  committed
  8d7f542
- Add profiling instruction & multi-thread test
  XingerTang
  committed
  b29d7fb
- Pylint test code
  XingerTang
  committed
  f65436c
- Fix Github runner warnings
  XingerTang
  committed
  17ac314
- Fix GitHub runner warning 2
  XingerTang
  committed
  b0c1190
- Pylint conftest.py
  XingerTang
  committed
  3c6a8be
- Pylint all files
  XingerTang
  committed
  74c3a83
- Update Changelog
  XingerTang
  committed
  d435acb
- Bumped version to 1.4.0
  XingerTang
  committed
  f5bf2c1
- Update pyproject.toml and changelog
  XingerTang
  committed
  a539a54
- Release v1.4.0
  XingerTang
  authored
  d6bb908

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