/**
 * @fileoverview Shared genotype-call pull logic — the async-search machinery
 * (`POST /search/calls` → poll → page-walk) and the `CallRow` schema extracted
 * from `brapi-find-genotype-calls.tool.ts` so that `brapi_export_genotype_matrix`
 * can reuse the same pull infrastructure without duplicating it.
 *
 * This module owns: the `CallRowSchema`, `CallFormatting` type, and the
 * `collectCalls` / `consumePage` helpers. It does NOT contain `spillCalls` or
 * any tool-level concerns — those stay in the consuming tool files.
 *
 * @module mcp-server/tools/shared/genotype-calls
 */
import { type Context, z } from '@cyanheads/mcp-ts-core';
import type { BrapiClient } from '../../../services/brapi-client/index.js';
import type { RegisteredServer } from '../../../services/server-registry/types.js';
export declare const CallRowSchema: z.ZodObject<{
    callSetDbId: z.ZodOptional<z.ZodNullable<z.ZodString>>;
    callSetName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
    variantDbId: z.ZodOptional<z.ZodNullable<z.ZodString>>;
    variantName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
    variantSetDbId: z.ZodOptional<z.ZodNullable<z.ZodString>>;
    genotype: z.ZodOptional<z.ZodNullable<z.ZodObject<{
        values: z.ZodOptional<z.ZodNullable<z.ZodArray<z.ZodString>>>;
    }, z.core.$loose>>>;
    genotypeValue: z.ZodOptional<z.ZodNullable<z.ZodString>>;
    phaseSet: z.ZodOptional<z.ZodNullable<z.ZodString>>;
}, z.core.$loose>;
export type CallRow = z.infer<typeof CallRowSchema>;
export interface CallFormatting {
    expandHomozygotes?: boolean | null;
    sepPhased?: string | null;
    sepUnphased?: string | null;
    unknownString?: string | null;
}
export interface CollectCallsInput {
    body: Record<string, unknown>;
    client: BrapiClient;
    connection: RegisteredServer;
    ctx: Context;
    maxCalls: number;
    warnings: string[];
}
export interface CollectCallsResult {
    callFormatting: CallFormatting;
    rows: CallRow[];
    truncated: boolean;
}
/**
 * Build the POST /search/calls body from named filter params. Handles both the
 * singular `variantSetDbId` convenience and the plural `variantSetDbIds` array,
 * merging and deduplicating them.
 */
export declare function buildCallsSearchBody(input: {
    variantSetDbId?: string | undefined;
    variantSetDbIds?: string[] | undefined;
    germplasmDbIds?: string[] | undefined;
    callSetDbIds?: string[] | undefined;
    variantDbIds?: string[] | undefined;
    callFormat?: string | undefined;
}): Record<string, unknown>;
/**
 * Pull all genotype call pages for a given search body, capping at `maxCalls`.
 * Uses BrAPI's async-search pattern: `POST /search/calls` → `GET /search/calls/{id}`
 * with 202-retry. Pages are collected until all results are fetched or `maxCalls`
 * is reached.
 */
export declare function collectCalls(input: CollectCallsInput): Promise<CollectCallsResult>;
/**
 * Extract call rows and `callFormatting` hints from one BrAPI envelope page.
 * Mutates `rows` in-place; invokes `setCallFormatting` when formatting hints
 * are present so the caller can merge across pages.
 */
export declare function consumePage(envelope: Awaited<ReturnType<BrapiClient['get']>>, rows: CallRow[], setCallFormatting: (f: CallFormatting) => void): void;
/**
 * Render the genotype string for one call row given the server's callFormatting
 * hints. Prefers `genotype.values` joined with the appropriate separator;
 * falls back to `genotypeValue`; returns the `unknownString` (or ".") when
 * no data is available.
 */
export declare function renderGenotypeString(row: CallRow, callFormatting: CallFormatting, phased?: boolean): string;
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