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TEagle v3.2.1

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@tunabirgun tunabirgun released this 30 Jul 11:25
· 14 commits to main since this release
v3.2.1
94da0a3

A fix release. No new feature — one scientific-correctness fix and a set of robustness and documentation corrections surfaced by a full review of 3.2.0.

Classification — a reported target-site duplication can change

Structural detection runs before the superfamily is known, so it selected the longest exact repeat flanking the element. A coincidental longer repeat in an AT-rich flank could outrank the diagnostic short duplication — a Tc1/mariner element's 2 bp TA in particular — which then read as incongruent (discrediting genuinely complete termini) and exported the wrong duplication coordinates.

Once the superfamily is resolved, the duplication is now re-detected with its literature target-site length preferred. The correction is monotonic: it can only shorten a coincidental repeat to the diagnostic length when that length genuinely flanks the element, never lengthen or fabricate one. Effect on real specimens: none for a bare pasted element (no flanks, no duplication to reassess); a change is possible only for a flanked element of a superfamily with a literature target-site length whose insertion happens to sit in a coincidental longer exact repeat.

Reliability and connectivity

  • Adding a custom organism no longer races on its store. Two concurrent resolves could each read the assembly store and the second write clobber the first — an organism the app reported as added would silently vanish. The read-modify-write is now serialised.
  • The "Add" control is disabled for the duration of its network resolve. Only the text field was disabled before, so a double-click or Enter-then-click queued duplicate NCBI lookups; a single-flight guard now survives a manager close/reopen.
  • The "Resolving… against NCBI" status shows as a Notice, not an Error — it had inherited the default error styling (an Error-titled, focus-stealing dialog) for a routine in-progress message.

Documentation

  • Report: corrected the mariner Mos1 benchmark accession (M14653 → X78906, the record actually benchmarked) and removed an unsubstantiated Tam3 specimen.
  • app/README.md: provenance cross-reference pointed at the wrong panel (05 → 07); the superfamily list predated the 3.2.0 panel growth (now includes ERV, DIRS, CACTA, MULE and IS4-like/piggyBac); XLSX was missing from the table-export formats.
  • The LTR congruent-TSD evidence sentence was rewritten to state the observed length; the DNA "no attributable expected length" case now reads neutrally instead of implying congruence.
  • Every figure recaptured at 3.2.1 — the app renders its version in the header badge and provenance card, so figures go stale on any bump.

Installer SHA256 B5731FE1D7036B9BFC9979205EA0FEC2E4546AFDC3EFD9F27CAE1405D779393A. Frozen-bundle self-test passes (primer3 2.3.0 · ViennaRNA optional, not bundled · pyhmmer 0.12.1 · HMM 57f2b7881f35, 30 profiles).

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