import type { Mismatch } from '../shared/types';
import type { Feature } from '@jbrowse/core/util';
export declare function parseCigar(cigar?: string): string[];
export declare function getMismatches(cigar?: string, md?: string, seq?: string, ref?: string, qual?: Uint8Array): Mismatch[];
export declare function getOrientedCigar(flip: boolean, cigar: string[]): string[];
export declare function getOrientedMismatches(flip: boolean, cigar: string): Mismatch[];
export declare function getLengthOnRef(cigar: string): number;
export declare function getLength(cigar: string): number;
export declare function getLengthSansClipping(cigar: string): number;
export declare function getClip(cigar: string, strand: number): number;
export declare function getTag(feature: Feature, tag: string): any;
export declare function featurizeSA(SA: string | undefined, id: string, strand: number, readName: string, normalize?: boolean): {
    refName: string;
    start: number;
    end: number;
    seqLength: number;
    clipPos: number;
    CIGAR: string;
    strand: number;
    uniqueId: string;
    mate: {
        start: number;
        end: number;
        refName: string;
    };
}[];
export { getNextRefPos } from './getNextRefPos';