v0.1.0-alpha.15

Decoding-Us Navigator — v0.1.0-alpha.15 (prerelease)

⚡ CRAM files analyse in seconds, not hours

If your data is a .cram — most public datasets are, and so are many lab exports — every analysis that reads a region of your genome has been paying an enormous hidden cost. Reading one position took 21 seconds on chromosome 21 and nearly two minutes on chromosome 1. The same read from a .bam took four milliseconds.

Fixed. The measured difference on a real 30× genome:

	before	after
one position, chr21	20.9 s	8 ms
one position, chr1	116 s	113 ms
variant calling, one chromosome	over 96 minutes (abandoned)	44 seconds

The cause: every region query was decoding the entire chromosome and then throwing away everything outside the region you asked for, even though the file's own index says exactly which pieces to read. It now reads only those pieces. Nothing about your results changes — the records returned are byte-for-byte identical, which is tested against the previous behaviour on a real 11 GB file.

BAM files were never affected. This is why it went unnoticed: the reference genome we test against most is a BAM.

🧬 Neanderthal segments, rebuilt

Alpha.14 could show where Neanderthal DNA sits on your chromosomes. That feature was wrong, and this release replaces it.

Checked against an independent published callset for the same 20 people, the old version's tract locations matched no better than chance, and the amount it reported did not track the individual at all. It reproduced the right average for a population while telling you nothing about you. It was switched off, rebuilt on a different principle, and switched back on.

What changed. The old method looked for stretches of your genome with slightly more mutations than average — a technique designed for researchers who don't have Neanderthal genomes to compare against. We do have them. The new method asks the direct question: does this stretch of your DNA actually match an archaic genome? That turns out to be about thirty times more evidence per segment.

How well it works now, measured on whole genomes against the same independent callset:

	old	new
finds the same tracts as the reference	no better than chance	40–43 % of them
of what it reports, how much is corroborated	1.5 %	~46 %
does the amount track the individual?	no (r = −0.02)	yes (r = +0.71)

Every individual tested, across two continents, scores far above what random guessing would produce.

Compare this number only with people of similar ancestry. It is measured against the four archaic genomes that have been sequenced, and they resemble some ancestries more closely than others — so it under-counts East Asians relative to Europeans. The app says so on the card itself. This is a limitation of which ancient genomes exist, not something we can tune away.

Still deliberately withheld: which archaic lineage a segment came from. Neanderthal-versus-Denisovan attribution is not reliable enough to report, and reporting it would manufacture Denisovan findings for people who have none.

Needs whole-genome data and a completed variant-calling run. The card tells you if it can't proceed.

📦 Smaller download — about 55 MB less

	alpha.14	alpha.15
macOS .dmg	199 MB	142 MB
Windows -setup.exe	163 MB	109 MB
Linux .AppImage	186 MB	130 MB

Three large reference files that only the archaic-segment feature uses are now fetched on demand the first time you use it, rather than shipping with the app — the same treatment the chromosome painter's reference already had. If you never open that feature, you never download them.

Under the hood

• The Neanderthal marker count (the 23andMe-style headline number, and what Simple mode shows) is unaffected throughout. It is a different measurement on a different dataset and has been correct all along.
• Results cached from the previous archaic method are automatically recomputed rather than shown. The same applies if you analysed a single chromosome and later ran the whole genome — a case that previously kept showing the single-chromosome answer.
• navigator-analysis gains five diagnostic tools, and scripts/archaic-validation/ the harness that produced every number above, so the claims can be re-checked rather than taken on trust.

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

Full changelog: v0.1.0-alpha.14...v0.1.0-alpha.15