editing_plate_quantify

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Quantify a whole plate of edited samples against ONE untreated control trace and return a single sortable table — the plate-scale form of sanger_indel_spectrum, base_edit_quant and sanger_knockin_quant, chosen with `mode`. Each sample gives one row keyed by its id, carrying the headline number for that mode (edited fraction / editing at the target base / intended knock-in percentage), the fit-quality numbers behind it (R², or the background n and noise floor for base mode), and fitAdequate — the single-sample tool's own gate verdict on that row, so the plate cannot drift from the per-well answer. Failure is isolated per well: a sample whose read is short, mismatched or unfittable becomes a failed ROW with its error message and the other 95 still come back, while an error about the control trace, the mode or the work ceilings throws, because it is wrong for every row. Duplicate sample ids are suffixed (against the whole plate, so the suffix never lands on another well's name) rather than merged. Arguments are strict: an argument belonging to another mode, an unknown argument, an out-of-range limit, and an `offset` override (which is a property of one pair of reads, not of a plate) are all rejected rather than ignored or clamped, because at plate scale a substituted setting rewrites every row identically and nothing in the table looks odd. Returns the rows in input order, a tally, and a CSV. Comparing two wells' percentages is only meaningful when both rows are fitAdequate, which is why the plate summary is computed over those rows alone. PREDICTED, NOT MEASURED. None is published for this implementation, and being a batch does not soften that: each row is exactly the claim the corresponding single-sample tool makes. What every row instead reports is what it rests on — R² for the indel and knock-in modes, the background n, sd and noise floor for base mode — plus fitAdequate, which is the single-sample tool's OWN gate verdict on that row rather than a threshold re-invented here. Recovery of known synthetic mixtures is deliberately NOT offered as validation: it tests the arithmetic and the plate plumbing, not whether the model fits a real capillary trace, and for a knock-in with novel inserted bases it is circular, because a synthetic trace is built from the same idealised peaks the basis assumes. Quoting it would be the mistake rbs_predict made when it shipped a calibration residual as held-out skill. Valid for: One control read and a set of edited reads that are all the SAME amplicon, chemistry and primer as that control, with each read extending well past the edit site. COMPARING TWO WELLS' PERCENTAGES IS ONLY MEANINGFUL WHEN BOTH ROWS ARE fitAdequate: a percentage from a badly fitting well is not a smaller number than one from a well that fitted, it is a different kind of statement, and the plate summary here is therefore computed over the adequate rows only. Ranking wells also assumes they differ only in the variable under test — the same control is subtracted from all of them, so a well whose read started 30 bases later or whose reaction was dirty carries that difference into its number. Mode-specific limits carry over unchanged: indel mode is blind to substitutions, base mode is blind to indels and its percentages run low by roughly the crosstalk fraction, and knock-in mode cannot separate an intended pure deletion from an NHEJ deletion of the same length at the same site.