import type { Mismatch } from '../shared/types';
import type { CramRecord } from '@gmod/cram';
type ReadFeatures = CramRecord['readFeatures'];
export declare function readFeaturesToMismatches(readFeatures: ReadFeatures, start: number, qual?: number[] | null): Mismatch[];
export declare function readFeaturesToCIGAR(readFeatures: ReadFeatures, alignmentStart: number, readLen: number, refRegion?: {
    seq: string;
    start: number;
}): string;
export {};