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Releases: bennettek99-spec/Archaic-DNA-processing-pipeline

Release list

v0.7.0 — source contrast, Oceania transect, admixture dating

v0.7.0 — source contrast, Oceania transect, admixture dating Latest
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@bennettek99-spec bennettek99-spec released this 16 Aug 21:43
v0.7.0
b08244b

Highlights

  • Neanderthal source contrast (archaic-pipeline neanderthal-source): Altai-vs-Vindija affinity across 10,954 Eurasian ancients; detection limit 0.0098 in D_VA (13% of signal), now backed by a two-way subsample power analysis showing archaic genomes (sites), not cohort size, bind the SE.
  • Oceania time transect: Remote Oceania Denisovan affinity tracks Papuan-related influx over 3,000 years; Guam/Marianas control stays flat.
  • Admixture dating (archaic-admixture-date): AADR-native Moorjani-style ancestry-covariance decay with Ranis/Zlatý kůň exploratory primary analysis.
  • Repo layout: scripts/docs flatten; upstream phase intermediates untracked; CI checkout@7 / setup-python@7; tomli ≥2.4.1.

Install

pip install git+https://github.com/bennettek99-spec/Archaic-DNA-processing-pipeline.git@v0.7.0

See CHANGELOG.md for the full entry. Zenodo DOI appears after the GitHub→Zenodo archive completes (if the integration is enabled).

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v0.6.0 — repository, documentation, and reproducibility

v0.6.0 — repository, documentation, and reproducibility

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@bennettek99-spec bennettek99-spec released this 17 Jul 20:38
v0.6.0
d86d77c
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Archaic DNA Processing Pipeline v0.6.0

This release makes the public repository match the maturity and scientific boundaries of the pipeline.

Highlights

  • focused README plus structured setup, methods, study/report, and data-policy documentation
  • canonical MIT license with the retained PRJEB10597 BAM exception documented by accession, MD5, SHA-256, and evidence limits
  • corrected distinction between calculated Neanderthal percentages, relative Denisovan affinity, and literature-derived combined-ancestry context
  • portable public provenance with machine-specific paths removed
  • community files, issue and pull-request templates, Dependabot, and private vulnerability reporting
  • CI across Python 3.10-3.12, a 50% coverage floor, package builds, documentation/version/BAM provenance checks, and a Windows smoke job

Validation

  • 56 tests passed locally with 58.57% coverage
  • all five GitHub checks passed, including Windows smoke
  • pyflakes, repository documentation checks, package builds, and diff checks passed

The five published Sima de los Huesos BAM files remain in the repository by design and were not removed or rewritten.

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