@jbrowse/plugin-alignments 1.7.0 → 1.7.1

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts

@@ -1,6 +1,6 @@
-/// <reference types="react" />
-declare function AlignmentFeatureDetails(props: {
-    model: any;
-}): JSX.Element;
-declare const _default: typeof AlignmentFeatureDetails;
-export default _default;
+/// <reference types="react" />
+declare function AlignmentFeatureDetails(props: {
+    model: any;
+}): JSX.Element;
+declare const _default: typeof AlignmentFeatureDetails;
+export default _default;

package/dist/AlignmentsFeatureDetail/index.d.ts

@@ -1,13 +1,13 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
-    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    type: import("mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
-    featureData: import("mobx-state-tree").IType<any, any, any>;
-    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-}, {
-    setFeatureData(data: unknown): void;
-    clearFeatureData(): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export default function register(pluginManager: PluginManager): void;
-export { configSchema };
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
+    featureData: import("mobx-state-tree").IType<any, any, any>;
+    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+}, {
+    setFeatureData(data: unknown): void;
+    clearFeatureData(): void;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export default function register(pluginManager: PluginManager): void;
+export { configSchema };

package/dist/AlignmentsTrack/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-export default function register(pluginManager: PluginManager): void;
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function register(pluginManager: PluginManager): void;

package/dist/BamAdapter/BamAdapter.d.ts

@@ -1,30 +1,40 @@
-import { BamFile } from '@gmod/bam';
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-export default class BamAdapter extends BaseFeatureDataAdapter {
-    private samHeader?;
-    private setupP?;
-    protected configured?: Promise<{
-        bam: BamFile;
-        sequenceAdapter?: BaseFeatureDataAdapter;
-    }>;
-    protected configure(): Promise<{
-        bam: BamFile;
-        sequenceAdapter?: BaseFeatureDataAdapter | undefined;
-    }>;
-    getHeader(opts?: BaseOptions): Promise<any>;
-    private setupPre;
-    private setup;
-    getRefNames(opts?: BaseOptions): Promise<string[]>;
-    private seqFetch;
-    getFeatures(region: Region & {
-        originalRefName?: string;
-    }, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats | {
-        bytes: number;
-        fetchSizeLimit: any;
-    }>;
-    freeResources(): void;
-    refIdToName(refId: number): string | undefined;
-}
+import { BamFile } from '@gmod/bam';
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Region } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+export default class BamAdapter extends BaseFeatureDataAdapter {
+    private samHeader?;
+    private setupP?;
+    protected configured?: Promise<{
+        bam: BamFile;
+        sequenceAdapter?: BaseFeatureDataAdapter;
+    }>;
+    protected configure(): Promise<{
+        bam: BamFile;
+        sequenceAdapter?: BaseFeatureDataAdapter | undefined;
+    }>;
+    getHeader(opts?: BaseOptions): Promise<any>;
+    private setupPre;
+    private setup;
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    private seqFetch;
+    getFeatures(region: Region & {
+        originalRefName?: string;
+    }, opts?: BaseOptions & {
+        filterBy: {
+            flagInclude: number;
+            flagExclude: number;
+            tagFilter: {
+                tag: string;
+                value: unknown;
+            };
+            name: string;
+        };
+    }): import("rxjs").Observable<Feature>;
+    estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats | {
+        bytes: number;
+        fetchSizeLimit: any;
+    }>;
+    freeResources(): void;
+    refIdToName(refId: number): string | undefined;
+}

package/dist/BamAdapter/BamSlightlyLazyFeature.d.ts

@@ -1,33 +1,33 @@
-/// <reference types="node" />
-import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
-import { BamRecord } from '@gmod/bam';
-import BamAdapter from './BamAdapter';
-export default class BamSlightlyLazyFeature implements Feature {
-    private record;
-    private adapter;
-    private ref?;
-    constructor(record: BamRecord, adapter: BamAdapter, ref?: string | undefined);
-    _get_name(): any;
-    _get_type(): string;
-    _get_score(): number;
-    _get_flags(): string;
-    _get_strand(): number;
-    _get_pair_orientation(): string | null | undefined;
-    _get_next_seq_id(): number;
-    _get_seq_id(): number;
-    _get_next_refName(): string | undefined;
-    _get_next_segment_position(): string | undefined;
-    _get_seq(): string;
-    qualRaw(): Buffer | undefined;
-    set(): void;
-    tags(): string[];
-    id(): string;
-    get(field: string): any;
-    _get_refName(): string | undefined;
-    parent(): undefined;
-    children(): undefined;
-    pairedFeature(): boolean;
-    toJSON(): SimpleFeatureSerialized;
-    _get_mismatches(): import("./MismatchParser").Mismatch[];
-    _get_clipPos(): number;
-}
+/// <reference types="node" />
+import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
+import { BamRecord } from '@gmod/bam';
+import BamAdapter from './BamAdapter';
+export default class BamSlightlyLazyFeature implements Feature {
+    private record;
+    private adapter;
+    private ref?;
+    constructor(record: BamRecord, adapter: BamAdapter, ref?: string | undefined);
+    _get_name(): any;
+    _get_type(): string;
+    _get_score(): number;
+    _get_flags(): string;
+    _get_strand(): number;
+    _get_pair_orientation(): string | null | undefined;
+    _get_next_seq_id(): number;
+    _get_seq_id(): number;
+    _get_next_refName(): string | undefined;
+    _get_next_segment_position(): string | undefined;
+    _get_seq(): string;
+    qualRaw(): Buffer | undefined;
+    set(): void;
+    tags(): string[];
+    id(): string;
+    get(field: string): any;
+    _get_refName(): string | undefined;
+    parent(): undefined;
+    children(): undefined;
+    pairedFeature(): boolean;
+    toJSON(): SimpleFeatureSerialized;
+    _get_mismatches(): import("./MismatchParser").Mismatch[];
+    _get_clipPos(): number;
+}

package/dist/BamAdapter/MismatchParser.d.ts

@@ -1,28 +1,28 @@
-/// <reference types="node" />
-export interface Mismatch {
-    qual?: number;
-    start: number;
-    length: number;
-    type: string;
-    base: string;
-    altbase?: string;
-    seq?: string;
-    cliplen?: number;
-}
-export declare function parseCigar(cigar: string): string[];
-export declare function cigarToMismatches(ops: string[], seq: string, ref?: string, qual?: Buffer): Mismatch[];
-/**
- * parse a SAM MD tag to find mismatching bases of the template versus the reference
- * @returns array of mismatches and their positions
- */
-export declare function mdToMismatches(mdstring: string, ops: string[], cigarMismatches: Mismatch[], seq: string, qual?: Buffer): Mismatch[];
-export declare function getMismatches(cigar: string, md: string, seq: string, ref?: string, qual?: Buffer): Mismatch[];
-export declare function getNextRefPos(cigarOps: string[], positions: number[]): Generator<number, void, unknown>;
-export declare function getModificationPositions(mm: string, fseq: string, fstrand: number): ({
-    type: string;
-    positions: number[];
-} | {
-    type: string;
-    positions: never[];
-})[];
-export declare function getModificationTypes(mm: string): string[];
+/// <reference types="node" />
+export interface Mismatch {
+    qual?: number;
+    start: number;
+    length: number;
+    type: string;
+    base: string;
+    altbase?: string;
+    seq?: string;
+    cliplen?: number;
+}
+export declare function parseCigar(cigar: string): string[];
+export declare function cigarToMismatches(ops: string[], seq: string, ref?: string, qual?: Buffer): Mismatch[];
+/**
+ * parse a SAM MD tag to find mismatching bases of the template versus the reference
+ * @returns array of mismatches and their positions
+ */
+export declare function mdToMismatches(mdstring: string, ops: string[], cigarMismatches: Mismatch[], seq: string, qual?: Buffer): Mismatch[];
+export declare function getMismatches(cigar: string, md: string, seq: string, ref?: string, qual?: Buffer): Mismatch[];
+export declare function getNextRefPos(cigarOps: string[], positions: number[]): Generator<number, void, unknown>;
+export declare function getModificationPositions(mm: string, fseq: string, fstrand: number): ({
+    type: string;
+    positions: number[];
+} | {
+    type: string;
+    positions: never[];
+})[];
+export declare function getModificationTypes(mm: string): string[];

package/dist/BamAdapter/configSchema.d.ts

@@ -1,2 +1,2 @@
-declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default _default;
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/dist/BamAdapter/index.d.ts

@@ -1,3 +1,3 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/dist/CramAdapter/CramAdapter.d.ts

@@ -1,43 +1,52 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-import CramSlightlyLazyFeature from './CramSlightlyLazyFeature';
-interface Header {
-    idToName?: string[];
-    nameToId?: Record<string, number>;
-    readGroups?: number[];
-}
-export default class CramAdapter extends BaseFeatureDataAdapter {
-    samHeader: Header;
-    private setupP?;
-    private seqIdToRefName;
-    private seqIdToOriginalRefName;
-    configure(): Promise<{
-        cram: any;
-        sequenceAdapter: BaseFeatureDataAdapter | import("@jbrowse/core/data_adapters/BaseAdapter").BaseSequenceAdapter;
-    }>;
-    getHeader(opts?: BaseOptions): Promise<any>;
-    private seqFetch;
-    private setupPre;
-    private setup;
-    getRefNames(opts?: BaseOptions): Promise<string[]>;
-    refNameToId(refName: string): number | undefined;
-    refIdToName(refId: number): string | undefined;
-    refIdToOriginalName(refId: number): string;
-    getFeatures(region: Region & {
-        originalRefName?: string;
-    }, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
-    cramRecordToFeature(record: unknown): CramSlightlyLazyFeature;
-    estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<{
-        bytes: any;
-        fetchSizeLimit: any;
-    }>;
-    /**
-     * get the approximate number of bytes queried from the file for the given
-     * query regions
-     * @param regions - list of query regions
-     */
-    private bytesForRegions;
-}
-export {};
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Region, Feature } from '@jbrowse/core/util';
+import CramSlightlyLazyFeature from './CramSlightlyLazyFeature';
+interface Header {
+    idToName?: string[];
+    nameToId?: Record<string, number>;
+    readGroups?: number[];
+}
+export default class CramAdapter extends BaseFeatureDataAdapter {
+    samHeader: Header;
+    private setupP?;
+    private seqIdToRefName;
+    private seqIdToOriginalRefName;
+    configure(): Promise<{
+        cram: any;
+        sequenceAdapter: BaseFeatureDataAdapter | import("@jbrowse/core/data_adapters/BaseAdapter").BaseSequenceAdapter;
+    }>;
+    getHeader(opts?: BaseOptions): Promise<any>;
+    private seqFetch;
+    private setupPre;
+    private setup;
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    refNameToId(refName: string): number | undefined;
+    refIdToName(refId: number): string | undefined;
+    refIdToOriginalName(refId: number): string;
+    getFeatures(region: Region & {
+        originalRefName?: string;
+    }, opts?: BaseOptions & {
+        filterBy: {
+            flagInclude: number;
+            flagExclude: number;
+            tagFilter: {
+                tag: string;
+                value: unknown;
+            };
+            name: string;
+        };
+    }): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+    cramRecordToFeature(record: unknown): CramSlightlyLazyFeature;
+    estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<{
+        bytes: any;
+        fetchSizeLimit: any;
+    }>;
+    /**
+     * get the approximate number of bytes queried from the file for the given
+     * query regions
+     * @param regions - list of query regions
+     */
+    private bytesForRegions;
+}
+export {};

package/dist/CramAdapter/CramSlightlyLazyFeature.d.ts

@@ -1,49 +1,49 @@
-import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
-import CramAdapter from './CramAdapter';
-export interface Mismatch {
-    qual?: number;
-    start: number;
-    length: number;
-    type: string;
-    base: string;
-    altbase?: string;
-    seq?: string;
-    cliplen?: number;
-}
-export default class CramSlightlyLazyFeature implements Feature {
-    private record;
-    private _store;
-    constructor(record: any, _store: CramAdapter);
-    _get_name(): any;
-    _get_start(): number;
-    _get_end(): number;
-    _get_cram_read_features(): any;
-    _get_type(): string;
-    _get_score(): any;
-    _get_flags(): any;
-    _get_strand(): 1 | -1;
-    _read_group_id(): number | undefined;
-    _get_qual(): any;
-    qualRaw(): any;
-    _get_seq_id(): string | undefined;
-    _get_refName(): string | undefined;
-    _get_is_paired(): boolean;
-    _get_pair_orientation(): any;
-    _get_template_length(): any;
-    _get_next_seq_id(): string | undefined;
-    _get_next_pos(): any;
-    _get_next_segment_position(): string | undefined;
-    _get_tags(): any;
-    _get_seq(): any;
-    _get_CIGAR(): string;
-    tags(): string[];
-    id(): string;
-    get(field: string): any;
-    parent(): undefined | Feature;
-    children(): undefined | Feature[];
-    set(): void;
-    pairedFeature(): boolean;
-    _get_clipPos(): any;
-    toJSON(): SimpleFeatureSerialized;
-    _get_mismatches(): Mismatch[];
-}
+import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
+import CramAdapter from './CramAdapter';
+export interface Mismatch {
+    qual?: number;
+    start: number;
+    length: number;
+    type: string;
+    base: string;
+    altbase?: string;
+    seq?: string;
+    cliplen?: number;
+}
+export default class CramSlightlyLazyFeature implements Feature {
+    private record;
+    private _store;
+    constructor(record: any, _store: CramAdapter);
+    _get_name(): any;
+    _get_start(): number;
+    _get_end(): number;
+    _get_cram_read_features(): any;
+    _get_type(): string;
+    _get_score(): any;
+    _get_flags(): any;
+    _get_strand(): 1 | -1;
+    _read_group_id(): number | undefined;
+    _get_qual(): any;
+    qualRaw(): any;
+    _get_seq_id(): string | undefined;
+    _get_refName(): string | undefined;
+    _get_is_paired(): boolean;
+    _get_pair_orientation(): any;
+    _get_template_length(): any;
+    _get_next_seq_id(): string | undefined;
+    _get_next_pos(): any;
+    _get_next_segment_position(): string | undefined;
+    _get_tags(): any;
+    _get_seq(): any;
+    _get_CIGAR(): string;
+    tags(): string[];
+    id(): string;
+    get(field: string): any;
+    parent(): undefined | Feature;
+    children(): undefined | Feature[];
+    set(): void;
+    pairedFeature(): boolean;
+    _get_clipPos(): any;
+    toJSON(): SimpleFeatureSerialized;
+    _get_mismatches(): Mismatch[];
+}

package/dist/CramAdapter/CramTestAdapters.d.ts

@@ -1,29 +1,29 @@
-import { GenericFilehandle } from 'generic-filehandle';
-import { Observable } from 'rxjs';
-import SimpleFeature from '@jbrowse/core/util/simpleFeature';
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-export declare function parseSmallFasta(text: string): {
-    id: string;
-    description: string;
-    sequence: string;
-}[];
-declare type FileHandle = GenericFilehandle;
-export declare class FetchableSmallFasta {
-    data: Promise<ReturnType<typeof parseSmallFasta>>;
-    constructor(filehandle: FileHandle);
-    fetch(id: number, start: number, end: number): Promise<string>;
-    getSequenceList(): Promise<string[]>;
-}
-export declare class SequenceAdapter extends BaseFeatureDataAdapter {
-    fasta: FetchableSmallFasta;
-    refNames: string[];
-    constructor(filehandle: FileHandle);
-    getRefNames(): Promise<string[]>;
-    getFeatures({ refName, start, end, }: {
-        refName: string;
-        start: number;
-        end: number;
-    }): Observable<SimpleFeature>;
-    freeResources(): void;
-}
-export {};
+import { GenericFilehandle } from 'generic-filehandle';
+import { Observable } from 'rxjs';
+import SimpleFeature from '@jbrowse/core/util/simpleFeature';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+export declare function parseSmallFasta(text: string): {
+    id: string;
+    description: string;
+    sequence: string;
+}[];
+declare type FileHandle = GenericFilehandle;
+export declare class FetchableSmallFasta {
+    data: Promise<ReturnType<typeof parseSmallFasta>>;
+    constructor(filehandle: FileHandle);
+    fetch(id: number, start: number, end: number): Promise<string>;
+    getSequenceList(): Promise<string[]>;
+}
+export declare class SequenceAdapter extends BaseFeatureDataAdapter {
+    fasta: FetchableSmallFasta;
+    refNames: string[];
+    constructor(filehandle: FileHandle);
+    getRefNames(): Promise<string[]>;
+    getFeatures({ refName, start, end, }: {
+        refName: string;
+        start: number;
+        end: number;
+    }): Observable<SimpleFeature>;
+    freeResources(): void;
+}
+export {};

package/dist/CramAdapter/configSchema.d.ts

@@ -1,3 +1,3 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default _default;
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/dist/CramAdapter/index.d.ts

@@ -1,3 +1,3 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/dist/HtsgetBamAdapter/HtsgetBamAdapter.d.ts

@@ -1,9 +1,9 @@
-import { BamFile } from '@gmod/bam';
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import BamAdapter from '../BamAdapter/BamAdapter';
-export default class HtsgetBamAdapter extends BamAdapter {
-    protected configure(): Promise<{
-        bam: BamFile;
-        sequenceAdapter?: BaseFeatureDataAdapter | undefined;
-    }>;
-}
+import { BamFile } from '@gmod/bam';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import BamAdapter from '../BamAdapter/BamAdapter';
+export default class HtsgetBamAdapter extends BamAdapter {
+    protected configure(): Promise<{
+        bam: BamFile;
+        sequenceAdapter?: BaseFeatureDataAdapter | undefined;
+    }>;
+}

package/dist/HtsgetBamAdapter/configSchema.d.ts

@@ -1,2 +1,2 @@
-declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default _default;
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/dist/HtsgetBamAdapter/index.d.ts

@@ -1,3 +1,3 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts

@@ -1,7 +1,7 @@
-/// <reference types="react" />
-import { AlignmentsDisplayModel } from '../models/model';
-declare function AlignmentsDisplay({ model }: {
-    model: AlignmentsDisplayModel;
-}): JSX.Element;
-declare const _default: typeof AlignmentsDisplay;
-export default _default;
+/// <reference types="react" />
+import { AlignmentsDisplayModel } from '../models/model';
+declare function AlignmentsDisplay({ model }: {
+    model: AlignmentsDisplayModel;
+}): JSX.Element;
+declare const _default: typeof AlignmentsDisplay;
+export default _default;

package/dist/LinearAlignmentsDisplay/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-export default function (pluginManager: PluginManager): void;
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function (pluginManager: PluginManager): void;

package/dist/LinearAlignmentsDisplay/models/configSchema.d.ts

@@ -1,4 +1,4 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-declare const configModelFactory: (pluginManager: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export declare type AlignmentsConfigModel = ReturnType<typeof configModelFactory>;
-export default configModelFactory;
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const configModelFactory: (pluginManager: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export declare type AlignmentsConfigModel = ReturnType<typeof configModelFactory>;
+export default configModelFactory;