ktmeaton/ncov-recombinant: v0.7.0 - Recursive Recombinants
Bibliographic record
Abstract
Notes This is a minor release aimed towards a <code>nextclade</code> dataset upgrade from <code>2022-10-27</code> to <code>2023-01-09</code> which adds nomenclature for newly designated recombinants <code>XBH</code> - <code>XBP</code>. This release also adds initial support for the detection of "recursive recombination" including <code>XBL</code> and <code>XBN</code> which are recombinants of <code>XBB</code>. A comprehensive test summary report can be downloaded directly with: ncov-recombinant_v0.6.1_v0.7.0.zip or viewed at the following link once the release is complete. Documentation Issue #24: Create documentation on Read The Docs Dataset Issue #210: Handle numeric strain names. Resources Issue #185: Simplify creation of the pango-lineage nomenclature phylogeny to use the lineage_notes.txt file and the pango_aliasor library. sc2rf Issue #195: Add bypass to intermission allele ratio for edge cases. Issue #204: Add special handling for XBB sequenced with ARTIC v4.1 and dropout regions. Issue #205: Add new column <code>parents_conflict</code> to indicate whether the reported lineages from covSPECTRUM conflict with the reported parental clades from `sc2rf. Issue #213: Add <code>XBK</code> to auto-pass lineages. Issue #222: Add new parameter <code>--gisaid-access-key</code> to <code>sc2rf</code> and <code>sc2rf_recombinants</code>. Issue #229: Fix bug where auto-pass lineages are missing when exclude_negatives is set to true. Issue #231: Fix bug where 'null' lineages in covSPECTRUM caused error in <code>sc2rf</code> postprocess. The order of the <code>postprocessing.py</code> was rearranged to have more comprehensive details for auto-pass lineages. Add <code>XAN</code> to auto-pass lineages. Plot Issue #209: Restrict the palette for <code>rbd_level</code> to the range of <code>0:12</code>. Issue #218: Fix bug concerning data fragmentation with large numbers of sequences. Issue #221: Remove parameter <code>--singletons</code> in favor of <code>--min-cluster-size</code> to control cluster size in plots. Issue #224: Fix bug where plot crashed with extremely large datasets. Combine <code>plot</code> and <code>plot_historical</code> into one snakemake rule. Also at custom pattern <code>plot_NX</code> (ex. <code>plot_N10</code>) to adjust min cluster size. Report Combine <code>report</code> and <code>report_historical</code> into one snakemake rule. Validate Issue #225: Fix bug where false negatives passed validation because the status column wasn't checked. Designated Lineages Issue #217: <code>XBB.1.5</code> Issue #196: <code>XBF</code> Issue #206: <code>XBG</code> Issue #196: <code>XBH</code> Issue #199: <code>XBJ</code> Issue #213: <code>XBK</code> Issue #219: <code>XBL</code> Issue #215: <code>XBM</code> Issue #197: <code>XBN</code> Proposed Lineages Issue #203: <code>proposed1305</code> Issue #208: <code>proposed1340</code> Issue #212: <code>proposed1425</code> Issue #214: <code>proposed1440</code> Issue #216: <code>proposed1444</code> Issue #220: <code>proposed1576</code> Commits <code>c279f1e4</code> docs: add changelog for v0.7.0 <code>2964b4a1</code> docs: update notes to include 1576 proposed issue <code>fdc874ab</code> docs: add test summary package for v0.7.0 <code>3f3d4438</code> docs: update docs v0.7.0 <code>78696b36</code> script: add bug fix to sc2rf postprocess for #231 <code>403777a0</code> script: lint plotting script <code>2a09c783</code> script: fix sc2rf postprocess bug in duplicate removal <code>d44d5f90</code> data: add XBP to controls-gisaid <code>4293439c</code> profile: add controls-gisaid to virusseq builds <code>91d6fb89</code> defaults: update nextclade dataset to 2023-02-01 <code>630b2cd5</code> resources: update <code>49e6f598</code> profile: add virusseq profile <code>7e586d1d</code> script: add extra logic for auto-passing lineages <code>0ebe5e9c</code> script: fix bug in report where it didn't check that plots existed <code>25b2f243</code> docs: update developers guide <code>914d933f</code> defaults: add XBN to controls-gisaid and validation <code>8eaf08a9</code> data: restore controls-gisaid strain list <code>fa123009</code> script: defragment plot for 218 <code>5f24f695</code> dataset: update controls-gisaid strain list <code>efc5aab7</code> defaults: update validation to fix XBH dropout See CHANGELOG.md for additional commits.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.004 | 0.011 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; both teacher heads agree on what is shown here.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".