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v3.18.0 — the coverage level is in the vector now
DEFAULT_CSTAR = 0.20 is one number stretched over seven loci that attain very different coverage, and a vsig:div block computed at it is fully populated and entirely plausible. Nothing said it was a guess.
Added: vsig:qc:-:cstar_fallback_frac — the share of a sample's present loci whose coverage level came from the flat fallback rather than from a measurement. Same channel and shape as the V/J fallback fractions one block over.
Measured on 40 synthetic TRB samples of 400–4,000 clonotypes, median absolute shift against the bulk-RNA-seq measured level (C* = 0.1072), in log10 Hill units:
| coverage level | 1D_c |
0D_c |
2D_c |
clonality |
|---|---|---|---|---|
flat fallback C* = 0.20 |
0.2684 | 0.2765 | 0.2575 | 0.4575 |
amplicon C* = 0.4080 |
0.5755 | 0.6030 | 0.5432 | 1.0329 |
0.2684 in log10 is a factor of 1.86 on the Shannon diversity. 40/40 samples estimable in both, so none of it shows up as a hole.
Changed: cstar takes None and takes a partial dict. A locus the dict does not cover establishes no level — vsig:div:* are holes, mask:*:estimable is 0, one warning names the loci. That path used to raise KeyError, so the shipped amplicon reference (TRA and TRB only) died on the first B-cell locus. vdjtools signature --cstar none reaches the same path.
Tier widths move by one: core 153, standard 689, full 1404; the vsig half 161. Only the nuisance preset gains the column (74) — classify, transfer, compact, bcell, geometry and statistics are unchanged.
Full notes in CHANGELOG.md.