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.

Input 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

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

A3.7/5.0

Behavior4/5

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

Annotations only say readOnlyHint=false and destructiveHint=false; the description adds real value by spelling out blast radius — the replaced calls propagate to sequence, consensus, reference verification and every export. It does not discuss reversibility or whether the original calls can be recovered (restore_trace_file_calls exists as a sibling), which is the one behavioral gap for an overwriting operation.

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?

A single front-loaded sentence with the mutation stated first and consequences after the colon. Slightly long, but each clause conveys a distinct downstream effect rather than repeating the schema.

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 and annotations cover the safety profile, so the description needn't explain return values; it does supply the propagation context an agent needs to decide to call it. The remaining gap is the absence of any undo/reversibility note for a tool whose name and text both say 'Replace'.

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 fields already carry rich inline semantics (including length changes in denovo and allele assumptions in het/mix). The tool description adds nothing about parameters, so the baseline 3 applies.

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

Purpose4/5

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

Specific verb and object: 'Replace a Sanger read's own base calls with TraceTuner's, on the trace that is open.' It also states the scope of effect (sequence, consensus, reference verification, exports). It does not name the sibling it differs from, e.g. call_bases_from_trace or restore_trace_file_calls, so an agent must infer the distinction from the 'open trace' scoping.

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

Usage Guidelines3/5

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

Usage is implied: adopt TraceTuner calls when you want the rest of the editor to work from the re-called read. There are no explicit when-not conditions, no prerequisite that a trace be loaded/open, and no pointer to restore_trace_file_calls as the way back, even though the word 'Replace' implies an undo path exists.

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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