v0.1.0-alpha.10

Decoding-Us Navigator — v0.1.0-alpha.10 (prerelease)

✨ Ancient ancestry is back — rebuilt properly

In alpha.9 we turned ancient ancestry off because the old reference data was unusable and the numbers couldn't be trusted. It now returns, rebuilt from the ground up on a real method and a real ancient-genome reference.

• A genuine admixture model. We replaced the old "which single population are you?" classifier with qpAdm (f4-statistics), the same approach used in the population-genetics literature. It answers the right question: what mixture of ancient sources are you? — reported as Hunter-Gatherer (WHG) / Early European Farmer (EEF) / Steppe.
• Real ancient references. The estimate is anchored to the AADR 1240K ancient-genome panel, using a source/outgroup configuration drawn from Patterson et al. 2022 (Nature).
• It's validated. Our estimator reproduces the published admixtools2 package, the same person gets the same answer from a chip and from a WGS (stable to ~0.3% — the failure that sank the old version), and genotyping agreement is 99.84%.

Deep ancestry is off by default until you build your autosomal consensus (on the Autosomal tab); the app will tell you when it's ready. You can run it from Simple mode, the Advanced view, or the deep-ancestry CLI command.

Improved

• Ancient ancestry now works on all three references. Like modern ancestry, deep ancestry runs on GRCh37, GRCh38, and CHM13/T2T alignments — and on chip data — not just CHM13.
• Progressive consensus. Your autosomal consensus now builds up incrementally as you import data, instead of being recomputed from scratch each time. Batch imports fold in the panel sites as they go, so deep ancestry is ready sooner.
• Ancestry cards redesigned. Modern and ancient breakdowns now sit side by side instead of stacked, populations are shown with friendly names (e.g. "British", "NW European"), and every chart is a clean pie — the odd hollow wedge is gone.
• Faster. Deep ancestry went from 3+ hours to about 100 seconds, and it now picks your best sample by callable/alignment quality rather than raw depth.
• The reference download now explains itself — the app tells you which genome it's fetching and why.

Diagnostics for the "Assign Y haplogroup fails" report (#20)

We have not been able to reproduce the macOS failure in #20 on any of our own Macs, and the reporter still hits it after rebuilding the CRAM index with samtools index — so the cause is not yet known. This build adds instrumentation to pin down the failure mode the next time it happens, plus fixes for the adjacent problems that were making any such failure hard to read.

• A failed alignment command now opens a diagnostic modal with a "Copy report" button that probes each participating file separately and names the actual file at fault — distinguishing the three look-alike macOS failures: file missing (ENOENT), Unix permission bits (EACCES), and the OS privacy layer (EPERM/TCC). Previously all of these collapsed into one generic I/O error pointing at the .cram.
• New navigator doctor --file <path> CLI command prints the same pasteable diagnosis for any alignment, even one that can't be imported.
• The .crai index is now built automatically before every random-access command, and CRAM index-build failures name the real cause instead of guessing — ruling those out as candidates.
• Batch analysis preflights each sample once, reporting a single actionable line naming the real file instead of repeating a misattributed error per step.

If you hit #20, please try alpha.10 and paste the Copy report output (or navigator doctor --file <your.cram>) into the issue — that report is what we need to identify the failure.

Fixed

• The modern ancestry card no longer accidentally shows the ancient breakdown.
• Cancel actually stops a running analysis now.
• Structural variants are called on CRAM, not only BAM.

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Prerelease build. Installers below: macOS .dmg (universal), Windows -setup.exe, Linux .AppImage / .deb. Verify against SHA256SUMS.

What's Changed

• Fix/20 alignment preflight diagnosis by @JamesKane in #21
• Wip/ancient ancestry rebuild by @JamesKane in #22
• Progressive autosomal consensus + panel batch mode by @JamesKane in #23
• Fix ancestry cards: modern donor regression, pie charts, friendly names by @JamesKane in #24

Full Changelog: v0.1.0-alpha.9...v0.1.0-alpha.10