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TEagle v3.1.0

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@tunabirgun tunabirgun released this 26 Jul 10:06
· 17 commits to main since this release
v3.1.0
7ea9e03

Classification — displayed completeness tiers can change

The Class II (DNA transposon) branch of the completeness assessment now derives its tier from a real present/missing ledger instead of asserting intact / autonomous-consistent whenever a transposase and a TIR pair merely co-occur. A TIR pair now counts only if its arms bracket the transposase — an inverted repeat elsewhere in the record is not that element's termini (Wicker 2007).

Effect on real specimens: none. Tc1, Activator Ac, hobo, mariner Mos1 and Tam3 all keep intact / autonomous-consistent, and the 22-specimen retroelement panel is untouched. What changes is the case the previous logic got wrong — a non-enclosing TIR pair now reads partial (transposase present), as do 5′/3′-truncated copies and internal fragments.

The tier vocabulary is unchanged, and every existing hedge — including the "scoped to the tested Pfam domain panel" caveat — is preserved verbatim. classify() only receives structural and domain evidence, so it still cannot see record-level truncation; the new evidence line says so in hedged terms rather than implying otherwise.

Figures

  • GAG #7A7A7A → #6438FC. The old grey sat only 5.63 CAM02-UCS from the #888 unknown-domain fallback — and since both are achromatic, colour-vision-deficiency simulation moved that separation by 0.00. A named GAG domain looked unnamed. The new hue was chosen for the best worst-case CVD separation (18.41) while clearing 3:1 contrast against both the dark and light track backgrounds.

Documentation

  • Every figure recaptured at 3.1.0 — the app renders its version in the header badge and provenance card, so figures go stale on any bump.
  • Two manual figures produced by neither capture harness are now regenerated, and the orphan sweep covers report/manual_figures/ (it previously audited only docs/img/).
  • README installer size corrected: 40 MiB is the download; 148 MiB was the unpacked bundle.

Installer SHA256 FE66DFA25EA9901F04D2B2228580695E91711BE842E89604DFF9BE8CFCB463AD. Frozen-bundle selftest passes (primer3 2.3.0 · ViennaRNA 2.7.2 · pyhmmer 0.12.1 · HMM 197579b7a891, 21 profiles).

Assets 4
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