import type PluginManager from '@jbrowse/core/PluginManager';
import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
import type { LastStopTokenCheck, Region } from '@jbrowse/core/util';
export type LDMetric = 'r2' | 'dprime';
export interface FilterStats {
    totalVariants: number;
    passedVariants: number;
    filteredByMaf: number;
    filteredByLength: number;
    filteredByMultiallelic: number;
    filteredByHwe: number;
    filteredByCallRate: number;
}
export interface RecombinationData {
    values: Float32Array;
    positions: number[];
}
export interface LDMatrixResult {
    snps: {
        id: string;
        refName: string;
        start: number;
        end: number;
    }[];
    ldValues: Float32Array;
    metric: LDMetric;
    filterStats: FilterStats;
    recombination: RecombinationData;
}
export declare function getLDMatrix({ pluginManager, args, }: {
    pluginManager: PluginManager;
    args: {
        adapterConfig: AnyConfigurationModel;
        stopTokenCheck?: LastStopTokenCheck;
        sessionId: string;
        headers?: Record<string, string>;
        regions: Region[];
        bpPerPx: number;
        minorAlleleFrequencyFilter: number;
        lengthCutoffFilter: number;
        hweFilterThreshold?: number;
        callRateFilter?: number;
        jexlFilters?: string[];
        ldMetric?: LDMetric;
        signedLD?: boolean;
    };
}): Promise<LDMatrixResult>;