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@github-actions github-actions released this 22 Jul 12:51
v0.1.0-alpha.11
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Decoding-Us Navigator — v0.1.0-alpha.11 (prerelease)

✨ Bring your own caller — Navigator won't overwrite it

If you run an established variant-calling workflow (GATK4, or a 1240K pipeline), Navigator now treats your calls as authoritative and stops re-deriving them behind your back.

  • The overwrite bug is fixed. Previously, re-running analysis could silently replace an imported Y or mtDNA haplogroup with Navigator's own call — most visibly on ancient-DNA samples, where post-mortem damage made the internal call worse yet it still won. Imported (external) and internal calls now coexist; the internal caller never overwrites yours, and on damaged DNA it doesn't dilute your placement either.
  • A "Prefer external caller" setting (Preferences → on by default). When on, an imported GATK4 / 1240K call wins, and Navigator skips re-walking that alignment. Turn it off to always run the internal caller.

✨ Autosomal ancestry from your own call set — no CRAM decode

You can now feed Navigator's ancestry and IBD directly from an external autosomal call set, instead of having it re-genotype your alignment. Just import the file (or navigator ingest), and it folds into your autosomal consensus — driving modern, fine, and deep (qpAdm) ancestry and IBD.

  • Supported formats: a 1240K EIGENSTRAT call set (Reich-lab / pileupCaller), a GATK4 gVCF, or a genotyped VCF (e.g. bcftools mpileup over the 1240K sites) — anything that lists genotypes at panel sites.
  • No CRAM decode. A ~1.15M-site call set resolves in under a minute, versus re-walking the whole alignment.
  • Validated on real data. From an external 1240K VCF, deep ancestry came out within 0.2% of genotyping the CRAM directly (EEF / Steppe / WHG all matched) — the external call set is a stand-in for the alignment, not an approximation.

Fixed — the panel no longer needs building (#26)

  • Ancestry/IBD panels download themselves. Building the autosomal consensus used to fail with "IBD panel asset not found — build it with panelbuild ibd-panel" if your install didn't ship the panel. The panels (and the qpAdm/fine assets) now download automatically from the assets release the first time a feature needs them, the same way reference genomes do — you never run panelbuild.

Fixed — settings corruption and a surprise genome download (#26)

  • Saving reference settings could corrupt them. Because settings were written one row at a time from concurrent tasks, saving the References table could scramble reference_sources.json — which then silently discarded your custom local-reference path and made the app re-download the default genome (e.g. GRCh37 even with hs37d5.fa set). Config files are now written atomically, in a single save, so this can't happen.
  • An invalid config is reported, not ignored. If your config file is ever unreadable, Navigator now tells you it's falling back to auto-download instead of dropping your overrides in silence.

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

Full changelog: v0.1.0-alpha.10...v0.1.0-alpha.11

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