jean — Molecular Biology & Genomics

adopt_trace_calls

Replace a Sanger read's own base calls with TraceTuner's, on the trace that is open, so the rest of the editor works from the re-called read: its sequence, its consensus, its verification against a reference, and every export. The signal is untouched — this is the same electropherogram with a second opinion about where the bases are — and every coordinate already on the read is carried across the peaks it sits on, so a trim window, a hand-corrected call and an annotation all follow. Reports what moved and what could not be placed. Use call_bases_from_trace instead to ASK what the re-call says without changing the read.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`mode`	No	which reading to adopt. `rescore` keeps the instrument's bases and only re-measures their confidence; `denovo` derives the bases from the signal and can return a different read LENGTH; `het` and `mix` derive them and write a two-base IUB code where a second allele is present, differing only in whether the two are assumed equal in amount.	rescore
`table`	No	the instrument and polymer the quality scale was calibrated on. There is no universal default: a base scores differently under a different table.	3730pop7
`_files`	No	The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
`_subject`	No	The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
`min_ratio`	No	for `het` and `mix` only: how tall a second peak must be, as a fraction of the called one, to be called as a second allele. Ignored by the other two modes. Only applies when mode is het or mix.

Output Schema

TableJSON Schema

Name	Required	Description
`bases`	Yes	how many bases the read carries after the adoption
`sequence`	Yes	the read the document now carries, trimmed and with manual calls applied
`basesBefore`	Yes	how many it carried before it, so a gate can see the read change length
`everythingPlaced`	Yes	false when any annotation end sat on a call the new reading does not make, so it was placed at its nearest neighbor. Wire it into a gate before trusting a boundary

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 20, 2026

TDQS

A4.3/5.0

Behavior5/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations only say readOnlyHint=false and destructiveHint=false; the description goes far beyond that by disclosing that the signal is untouched, that existing coordinates (trims, hand corrections, annotations) are carried across the peaks, that sequence/consensus/verification/exports all follow, and that it reports what moved and what could not be placed.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The mutating action is front-loaded in the first clause, and every sentence carries real information (what changes, what does not, what to use instead). It is dense with em-dash asides and runs slightly long for the amount an agent must retain.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

An output schema exists, so return values need not be spelled out, and the description still flags that it reports moved/unplaceable calls. The mutation semantics and sibling routing are covered; the only gap is how a trace comes to be 'open' (load_trace/list_traces) and whether the change is persisted.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100% and the mode/table/min_ratio parameters are fully documented in the schema itself (including when min_ratio is ignored). The description adds no parameter-level meaning beyond that, so the baseline 3 applies.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb and resource ('Replace a Sanger read's own base calls with TraceTuner's, on the trace that is open') and names the scope of consequences. It explicitly separates itself from the sibling call_bases_from_trace, so an agent can pick between them without opening either schema.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Includes a precondition ('on the trace that is open') and an explicit alternative with its selection condition: use call_bases_from_trace to ASK what the re-call says without changing the read. No exclusion is given for the adjacent call_mixed_bases_from_trace, which overlaps with the het/mix modes, so this is clear but not complete.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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