@gmod/gff/dist/api.d.ts

read and write GFF3 data as streams

/// <reference types="node" />
import { Transform, TransformCallback, Readable, Writable } from 'stream';
import { StringDecoder as Decoder } from 'string_decoder';
import Parser from './parse';
import { GFF3Comment, GFF3Directive, GFF3Feature, GFF3FeatureLine, GFF3FeatureLineWithRefs, GFF3Sequence, GFF3Item } from './util';
export type { GFF3Comment, GFF3Directive, GFF3Feature, GFF3FeatureLine, GFF3FeatureLineWithRefs, GFF3Sequence, GFF3Item, };
/** Parser options */
export interface ParseOptions {
    /** Whether to resolve references to derives from features */
    disableDerivesFromReferences?: boolean;
    /** Text encoding of the input GFF3. default 'utf8' */
    encoding?: BufferEncoding;
    /** Whether to parse features, default true */
    parseFeatures?: boolean;
    /** Whether to parse directives, default false */
    parseDirectives?: boolean;
    /** Whether to parse comments, default false */
    parseComments?: boolean;
    /** Whether to parse sequences, default true */
    parseSequences?: boolean;
    /**
     * Parse all features, directives, comments, and sequences. Overrides other
     * parsing options. Default false.
     */
    parseAll?: boolean;
    /** Maximum number of GFF3 lines to buffer, default 1000 */
    bufferSize?: number;
}
declare class GFFTransform extends Transform {
    encoding: BufferEncoding;
    decoder: Decoder;
    textBuffer: string;
    parser: Parser;
    constructor(inputOptions?: ParseOptions);
    private _addLine;
    private _nextText;
    _transform(chunk: Buffer, _encoding: BufferEncoding, callback: TransformCallback): void;
    _flush(callback: TransformCallback): void;
}
/**
 * Parse a stream of text data into a stream of feature, directive, comment,
 * an sequence objects.
 *
 * @param options - Parsing options
 * @returns stream (in objectMode) of parsed items
 */
export declare function parseStream(options?: ParseOptions): GFFTransform;
/**
 * Synchronously parse a string containing GFF3 and return an array of the
 * parsed items.
 *
 * @param str - GFF3 string
 * @param inputOptions - Parsing options
 * @returns array of parsed features, directives, comments and/or sequences
 */
export declare function parseStringSync(str: string, inputOptions?: {
    disableDerivesFromReferences?: boolean;
    encoding?: BufferEncoding;
    bufferSize?: number;
} | undefined): (GFF3Feature | GFF3Sequence)[];
export declare function parseStringSync<T extends boolean>(str: string, inputOptions: {
    parseAll?: T;
    disableDerivesFromReferences?: boolean;
    encoding?: BufferEncoding;
    bufferSize?: number;
}): T extends true ? GFF3Item[] : never;
export declare function parseStringSync<F extends boolean>(str: string, inputOptions: {
    disableDerivesFromReferences?: boolean;
    parseFeatures: F;
    encoding?: BufferEncoding;
    bufferSize?: number;
}): F extends true ? (GFF3Feature | GFF3Sequence)[] : GFF3Sequence[];
export declare function parseStringSync<D extends boolean>(str: string, inputOptions: {
    disableDerivesFromReferences?: boolean;
    parseDirectives: D;
    encoding?: BufferEncoding;
    bufferSize?: number;
}): D extends true ? (GFF3Feature | GFF3Directive | GFF3Sequence)[] : (GFF3Feature | GFF3Sequence)[];
export declare function parseStringSync<C extends boolean>(str: string, inputOptions: {
    parseComments: C;
    encoding?: BufferEncoding;
    bufferSize?: number;
}): C extends true ? (GFF3Feature | GFF3Comment | GFF3Sequence)[] : (GFF3Feature | GFF3Sequence)[];
export declare function parseStringSync<S extends boolean>(str: string, inputOptions: {
    disableDerivesFromReferences?: boolean;
    parseSequences: S;
    encoding?: BufferEncoding;
    bufferSize?: number;
}): S extends true ? (GFF3Feature | GFF3Sequence)[] : GFF3Feature[];
export declare function parseStringSync<F extends boolean, D extends boolean>(str: string, inputOptions: {
    disableDerivesFromReferences?: boolean;
    parseFeatures: F;
    parseDirectives: D;
    encoding?: BufferEncoding;
    bufferSize?: number;
}): F extends true ? D extends true ? (GFF3Feature | GFF3Directive | GFF3Sequence)[] : (GFF3Feature | GFF3Sequence)[] : D extends true ? (GFF3Directive | GFF3Sequence)[] : GFF3Sequence[];
export declare function parseStringSync<F extends boolean, C extends boolean>(str: string, inputOptions: {
    disableDerivesFromReferences?: boolean;
    parseFeatures: F;
    parseComments: C;
    encoding?: BufferEncoding;
    bufferSize?: number;
}): F extends true ? C extends true ? (GFF3Feature | GFF3Comment | GFF3Sequence)[] : (GFF3Feature | GFF3Sequence)[] : C extends true ? (GFF3Comment | GFF3Sequence)[] : GFF3Sequence[];
export declare function parseStringSync<F extends boolean, S extends boolean>(str: string, inputOptions: {
    disableDerivesFromReferences?: boolean;
    parseFeatures: F;
    parseSequences: S;
    encoding?: BufferEncoding;
    bufferSize?: number;
}): F extends true ? S extends true ? (GFF3Feature | GFF3Sequence)[] : GFF3Feature[] : S extends true ? GFF3Sequence[] : [];
export declare function parseStringSync<D extends boolean, C extends boolean>(str: string, inputOptions: {
    disableDerivesFromReferences?: boolean;
    parseDirectives: D;
    parseComments: C;
    encoding?: BufferEncoding;
    bufferSize?: number;
}): D extends true ? C extends true ? (GFF3Feature | GFF3Directive | GFF3Comment | GFF3Sequence)[] : (GFF3Feature | GFF3Directive | GFF3Sequence)[] : C extends true ? (GFF3Feature | GFF3Comment | GFF3Sequence)[] : (GFF3Feature | GFF3Sequence)[];
export declare function parseStringSync<D extends boolean, S extends boolean>(str: string, inputOptions: {
    disableDerivesFromReferences?: boolean;
    parseDirectives: D;
    parseSequences: S;
    encoding?: BufferEncoding;
    bufferSize?: number;
}): D extends true ? S extends true ? (GFF3Feature | GFF3Directive | GFF3Sequence)[] : (GFF3Feature | GFF3Directive)[] : S extends true ? (GFF3Feature | GFF3Sequence)[] : GFF3Feature[];
export declare function parseStringSync<C extends boolean, S extends boolean>(str: string, inputOptions: {
    disableDerivesFromReferences?: boolean;
    parseComments: C;
    parseSequences: S;
    encoding?: BufferEncoding;
    bufferSize?: number;
}): C extends true ? S extends true ? (GFF3Feature | GFF3Comment | GFF3Sequence)[] : (GFF3Feature | GFF3Comment)[] : S extends true ? (GFF3Feature | GFF3Sequence)[] : GFF3Feature[];
export declare function parseStringSync<F extends boolean, D extends boolean, C extends boolean>(str: string, inputOptions: {
    disableDerivesFromReferences?: boolean;
    parseFeatures: F;
    parseDirectives: D;
    parseComments: C;
    encoding?: BufferEncoding;
    bufferSize?: number;
}): F extends true ? D extends true ? C extends true ? GFF3Item[] : (GFF3Feature | GFF3Directive | GFF3Sequence)[] : C extends true ? (GFF3Feature | GFF3Comment | GFF3Sequence)[] : (GFF3Feature | GFF3Sequence)[] : D extends true ? C extends true ? (GFF3Directive | GFF3Comment | GFF3Sequence)[] : (GFF3Directive | GFF3Sequence)[] : C extends true ? (GFF3Comment | GFF3Sequence)[] : GFF3Sequence[];
export declare function parseStringSync<F extends boolean, D extends boolean, S extends boolean>(str: string, inputOptions: {
    disableDerivesFromReferences?: boolean;
    parseFeatures: F;
    parseDirectives: D;
    parseSequences: S;
    encoding?: BufferEncoding;
    bufferSize?: number;
}): F extends true ? D extends true ? S extends true ? (GFF3Feature | GFF3Directive | GFF3Sequence)[] : (GFF3Feature | GFF3Directive)[] : S extends true ? (GFF3Feature | GFF3Sequence)[] : GFF3Feature[] : D extends true ? S extends true ? (GFF3Directive | GFF3Sequence)[] : GFF3Directive[] : S extends true ? GFF3Sequence[] : [];
export declare function parseStringSync<F extends boolean, C extends boolean, S extends boolean>(str: string, inputOptions: {
    disableDerivesFromReferences?: boolean;
    parseFeatures: F;
    parseComments: C;
    parseSequences: S;
    encoding?: BufferEncoding;
    bufferSize?: number;
}): F extends true ? C extends true ? S extends true ? (GFF3Feature | GFF3Comment | GFF3Sequence)[] : (GFF3Feature | GFF3Comment)[] : S extends true ? (GFF3Feature | GFF3Sequence)[] : GFF3Feature[] : C extends true ? S extends true ? (GFF3Comment | GFF3Sequence)[] : GFF3Comment[] : S extends true ? GFF3Sequence[] : [];
export declare function parseStringSync<D extends boolean, C extends boolean, S extends boolean>(str: string, inputOptions: {
    disableDerivesFromReferences?: boolean;
    parseFeatures: D;
    parseComments: C;
    parseSequences: S;
    encoding?: BufferEncoding;
    bufferSize?: number;
}): D extends true ? C extends true ? S extends true ? GFF3Item[] : (GFF3Feature | GFF3Directive | GFF3Comment)[] : S extends true ? (GFF3Feature | GFF3Directive | GFF3Sequence)[] : (GFF3Feature | GFF3Directive)[] : C extends true ? S extends true ? (GFF3Feature | GFF3Comment | GFF3Sequence)[] : (GFF3Feature | GFF3Comment)[] : S extends true ? (GFF3Feature | GFF3Sequence)[] : GFF3Feature[];
export declare function parseStringSync<F extends boolean, D extends boolean, C extends boolean, S extends boolean>(str: string, inputOptions: {
    disableDerivesFromReferences?: boolean;
    parseFeatures: F;
    parseDirectives: D;
    parseComments: C;
    parseSequences: S;
    encoding?: BufferEncoding;
    bufferSize?: number;
}): F extends true ? D extends true ? C extends true ? S extends true ? GFF3Item[] : (GFF3Feature | GFF3Directive | GFF3Comment)[] : S extends true ? (GFF3Feature | GFF3Directive | GFF3Sequence)[] : (GFF3Feature | GFF3Directive)[] : C extends true ? S extends true ? (GFF3Feature | GFF3Comment | GFF3Sequence)[] : (GFF3Feature | GFF3Comment)[] : S extends true ? (GFF3Feature | GFF3Sequence)[] : GFF3Feature[] : D extends true ? C extends true ? S extends true ? (GFF3Directive | GFF3Comment | GFF3Sequence)[] : (GFF3Directive | GFF3Comment)[] : S extends true ? (GFF3Directive | GFF3Sequence)[] : GFF3Directive[] : C extends true ? S extends true ? (GFF3Comment | GFF3Sequence)[] : GFF3Comment[] : S extends true ? GFF3Sequence[] : [];
/**
 * Format an array of GFF3 items (features,directives,comments) into string of
 * GFF3. Does not insert synchronization (###) marks.
 *
 * @param items - Array of features, directives, comments and/or sequences
 * @returns the formatted GFF3
 */
export declare function formatSync(items: GFF3Item[]): string;
interface FormatOptions {
    minSyncLines?: number;
    insertVersionDirective?: boolean;
    encoding?: BufferEncoding;
}
declare class FormattingTransform extends Transform {
    linesSinceLastSyncMark: number;
    haveWeEmittedData: boolean;
    fastaMode: boolean;
    minLinesBetweenSyncMarks: number;
    insertVersionDirective: boolean;
    constructor(options?: FormatOptions);
    _transform(chunk: GFF3Item[], _encoding: BufferEncoding, callback: TransformCallback): void;
}
/**
 * Format a stream of features, directives, comments and/or sequences into a
 * stream of GFF3 text.
 *
 * Inserts synchronization (###) marks automatically.
 *
 * @param options - parser options
 */
export declare function formatStream(options?: FormatOptions): FormattingTransform;
/**
 * Format a stream of features, directives, comments and/or sequences into a
 * GFF3 file and write it to the filesystem.

 * Inserts synchronization (###) marks and a ##gff-version
 * directive automatically (if one is not already present).
 *
 * @param stream - the stream to write to the file
 * @param filename - the file path to write to
 * @param options - parser options
 * @returns promise for null that resolves when the stream has been written
 */
export declare function formatFile(stream: Readable, writeStream: Writable, options?: FormatOptions): Promise<null>;