@jbrowse/plugin-alignments 1.7.0 → 1.7.1

package/dist/PileupRenderer/PileupRenderer.d.ts

@@ -1,125 +1,125 @@
-/// <reference types="react" />
-import BoxRendererType, { RenderArgs, RenderArgsSerialized, RenderArgsDeserialized as BoxRenderArgsDeserialized, RenderResults, ResultsSerialized, ResultsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
-import { Theme } from '@material-ui/core';
-import { Region, Feature } from '@jbrowse/core/util';
-import { BaseLayout } from '@jbrowse/core/util/layouts/BaseLayout';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { PileupLayoutSession, PileupLayoutSessionProps } from './PileupLayoutSession';
-export interface RenderArgsDeserialized extends BoxRenderArgsDeserialized {
-    colorBy?: {
-        type: string;
-        tag?: string;
-    };
-    colorTagMap?: Record<string, string>;
-    modificationTagMap?: Record<string, string>;
-    sortedBy?: {
-        type: string;
-        pos: number;
-        refName: string;
-        assemblyName: string;
-        tag?: string;
-    };
-    showSoftClip: boolean;
-    highResolutionScaling: number;
-}
-export interface RenderArgsDeserializedWithFeaturesAndLayout extends RenderArgsDeserialized {
-    features: Map<string, Feature>;
-    layout: BaseLayout<Feature>;
-    regionSequence?: string;
-}
-interface LayoutRecord {
-    feature: Feature;
-    leftPx: number;
-    rightPx: number;
-    topPx: number;
-    heightPx: number;
-}
-interface LayoutFeature {
-    heightPx: number;
-    topPx: number;
-    feature: Feature;
-}
-export default class PileupRenderer extends BoxRendererType {
-    supportsSVG: boolean;
-    getCharWidthHeight(ctx: CanvasRenderingContext2D): {
-        charWidth: number;
-        charHeight: number;
-    };
-    layoutFeature({ feature, layout, bpPerPx, region, showSoftClip, heightPx, displayMode, }: {
-        feature: Feature;
-        layout: BaseLayout<Feature>;
-        bpPerPx: number;
-        region: Region;
-        showSoftClip?: boolean;
-        heightPx: number;
-        displayMode: string;
-    }): LayoutRecord | null;
-    getExpandedRegion(region: Region, renderArgs: RenderArgsDeserialized): {
-        start: number;
-        end: number;
-        refName: string;
-        assemblyName: string;
-        reversed?: boolean | undefined;
-    };
-    colorByOrientation(feature: Feature, config: AnyConfigurationModel): string;
-    getOrientation(feature: Feature, config: AnyConfigurationModel): string;
-    colorByInsertSize(feature: Feature, _config: AnyConfigurationModel): string;
-    colorByStranded(feature: Feature, _config: AnyConfigurationModel): "color_rev_strand" | "color_fwd_strand" | "color_rev_missing_mate" | "color_fwd_missing_mate" | "color_rev_strand_not_proper" | "color_fwd_strand_not_proper" | "color_fwd_diff_chr" | "color_rev_diff_chr";
-    colorByPerBaseLettering(ctx: CanvasRenderingContext2D, feat: LayoutFeature, _config: AnyConfigurationModel, region: Region, bpPerPx: number, props: {
-        colorForBase: Record<string, string>;
-        contrastForBase: Record<string, string>;
-        charWidth: number;
-        charHeight: number;
-    }): void;
-    colorByPerBaseQuality(ctx: CanvasRenderingContext2D, feat: LayoutFeature, _config: AnyConfigurationModel, region: Region, bpPerPx: number): void;
-    colorByModifications(ctx: CanvasRenderingContext2D, layoutFeature: LayoutFeature, _config: AnyConfigurationModel, region: Region, bpPerPx: number, props: RenderArgsDeserializedWithFeaturesAndLayout): void;
-    colorByMethylation(ctx: CanvasRenderingContext2D, layoutFeature: LayoutFeature, _config: AnyConfigurationModel, region: Region, bpPerPx: number, props: RenderArgsDeserializedWithFeaturesAndLayout): void;
-    drawRect(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserialized): void;
-    drawAlignmentRect(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserializedWithFeaturesAndLayout & {
-        colorForBase: Record<string, string>;
-        contrastForBase: Record<string, string>;
-        charWidth: number;
-        charHeight: number;
-        defaultColor: boolean;
-    }): void;
-    drawMismatches(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserializedWithFeaturesAndLayout, opts: {
-        colorForBase: {
-            [key: string]: string;
-        };
-        contrastForBase: {
-            [key: string]: string;
-        };
-        mismatchAlpha?: boolean;
-        drawSNPs?: boolean;
-        drawIndels?: boolean;
-        minSubfeatureWidth: number;
-        largeInsertionIndicatorScale: number;
-        charWidth: number;
-        charHeight: number;
-    }): void;
-    drawSoftClipping(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserializedWithFeaturesAndLayout, config: AnyConfigurationModel, theme: Theme): void;
-    makeImageData(ctx: CanvasRenderingContext2D, layoutRecords: (LayoutFeature | null)[], props: RenderArgsDeserializedWithFeaturesAndLayout): Promise<void>;
-    layoutFeats(props: RenderArgsDeserializedWithFeaturesAndLayout): (LayoutRecord | null)[];
-    fetchSequence(renderProps: RenderArgsDeserialized): Promise<any>;
-    render(renderProps: RenderArgsDeserialized): Promise<{
-        features: Map<string, Feature>;
-        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
-        height: number;
-        width: number;
-        maxHeightReached: boolean;
-        reactElement: any;
-        imageData?: undefined;
-        html?: string | undefined;
-    } | {
-        features: Map<string, Feature>;
-        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
-        height: number;
-        width: number;
-        maxHeightReached: boolean;
-        imageData: any;
-        reactElement?: import("react").ReactElement<any, string | ((props: any) => import("react").ReactElement<any, any> | null) | (new (props: any) => import("react").Component<any, any, any>)> | undefined;
-        html?: string | undefined;
-    }>;
-    createSession(args: PileupLayoutSessionProps): PileupLayoutSession;
-}
-export type { RenderArgs, RenderArgsSerialized, RenderResults, ResultsSerialized, ResultsDeserialized, };
+/// <reference types="react" />
+import BoxRendererType, { RenderArgs, RenderArgsSerialized, RenderArgsDeserialized as BoxRenderArgsDeserialized, RenderResults, ResultsSerialized, ResultsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+import { Theme } from '@material-ui/core';
+import { Region, Feature } from '@jbrowse/core/util';
+import { BaseLayout } from '@jbrowse/core/util/layouts/BaseLayout';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { PileupLayoutSession, PileupLayoutSessionProps } from './PileupLayoutSession';
+export interface RenderArgsDeserialized extends BoxRenderArgsDeserialized {
+    colorBy?: {
+        type: string;
+        tag?: string;
+    };
+    colorTagMap?: Record<string, string>;
+    modificationTagMap?: Record<string, string>;
+    sortedBy?: {
+        type: string;
+        pos: number;
+        refName: string;
+        assemblyName: string;
+        tag?: string;
+    };
+    showSoftClip: boolean;
+    highResolutionScaling: number;
+}
+export interface RenderArgsDeserializedWithFeaturesAndLayout extends RenderArgsDeserialized {
+    features: Map<string, Feature>;
+    layout: BaseLayout<Feature>;
+    regionSequence?: string;
+}
+interface LayoutRecord {
+    feature: Feature;
+    leftPx: number;
+    rightPx: number;
+    topPx: number;
+    heightPx: number;
+}
+interface LayoutFeature {
+    heightPx: number;
+    topPx: number;
+    feature: Feature;
+}
+export default class PileupRenderer extends BoxRendererType {
+    supportsSVG: boolean;
+    getCharWidthHeight(ctx: CanvasRenderingContext2D): {
+        charWidth: number;
+        charHeight: number;
+    };
+    layoutFeature({ feature, layout, bpPerPx, region, showSoftClip, heightPx, displayMode, }: {
+        feature: Feature;
+        layout: BaseLayout<Feature>;
+        bpPerPx: number;
+        region: Region;
+        showSoftClip?: boolean;
+        heightPx: number;
+        displayMode: string;
+    }): LayoutRecord | null;
+    getExpandedRegion(region: Region, renderArgs: RenderArgsDeserialized): {
+        start: number;
+        end: number;
+        refName: string;
+        assemblyName: string;
+        reversed?: boolean | undefined;
+    };
+    colorByOrientation(feature: Feature, config: AnyConfigurationModel): string;
+    getOrientation(feature: Feature, config: AnyConfigurationModel): string;
+    colorByInsertSize(feature: Feature, _config: AnyConfigurationModel): string;
+    colorByStranded(feature: Feature, _config: AnyConfigurationModel): "color_rev_strand" | "color_fwd_strand" | "color_rev_missing_mate" | "color_fwd_missing_mate" | "color_rev_strand_not_proper" | "color_fwd_strand_not_proper" | "color_fwd_diff_chr" | "color_rev_diff_chr";
+    colorByPerBaseLettering(ctx: CanvasRenderingContext2D, feat: LayoutFeature, _config: AnyConfigurationModel, region: Region, bpPerPx: number, props: {
+        colorForBase: Record<string, string>;
+        contrastForBase: Record<string, string>;
+        charWidth: number;
+        charHeight: number;
+    }): void;
+    colorByPerBaseQuality(ctx: CanvasRenderingContext2D, feat: LayoutFeature, _config: AnyConfigurationModel, region: Region, bpPerPx: number): void;
+    colorByModifications(ctx: CanvasRenderingContext2D, layoutFeature: LayoutFeature, _config: AnyConfigurationModel, region: Region, bpPerPx: number, props: RenderArgsDeserializedWithFeaturesAndLayout): void;
+    colorByMethylation(ctx: CanvasRenderingContext2D, layoutFeature: LayoutFeature, _config: AnyConfigurationModel, region: Region, bpPerPx: number, props: RenderArgsDeserializedWithFeaturesAndLayout): void;
+    drawRect(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserialized): void;
+    drawAlignmentRect(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserializedWithFeaturesAndLayout & {
+        colorForBase: Record<string, string>;
+        contrastForBase: Record<string, string>;
+        charWidth: number;
+        charHeight: number;
+        defaultColor: boolean;
+    }): void;
+    drawMismatches(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserializedWithFeaturesAndLayout, opts: {
+        colorForBase: {
+            [key: string]: string;
+        };
+        contrastForBase: {
+            [key: string]: string;
+        };
+        mismatchAlpha?: boolean;
+        drawSNPs?: boolean;
+        drawIndels?: boolean;
+        minSubfeatureWidth: number;
+        largeInsertionIndicatorScale: number;
+        charWidth: number;
+        charHeight: number;
+    }): void;
+    drawSoftClipping(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserializedWithFeaturesAndLayout, config: AnyConfigurationModel, theme: Theme): void;
+    makeImageData(ctx: CanvasRenderingContext2D, layoutRecords: (LayoutFeature | null)[], props: RenderArgsDeserializedWithFeaturesAndLayout): Promise<void>;
+    layoutFeats(props: RenderArgsDeserializedWithFeaturesAndLayout): (LayoutRecord | null)[];
+    fetchSequence(renderProps: RenderArgsDeserialized): Promise<any>;
+    render(renderProps: RenderArgsDeserialized): Promise<{
+        features: Map<string, Feature>;
+        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
+        height: number;
+        width: number;
+        maxHeightReached: boolean;
+        reactElement: JSX.Element;
+        imageData?: undefined;
+        html?: string | undefined;
+    } | {
+        features: Map<string, Feature>;
+        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
+        height: number;
+        width: number;
+        maxHeightReached: boolean;
+        imageData: import("@jbrowse/core/util/offscreenCanvas/types").AbstractImageBitmap;
+        reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        html?: string | undefined;
+    }>;
+    createSession(args: PileupLayoutSessionProps): PileupLayoutSession;
+}
+export type { RenderArgs, RenderArgsSerialized, RenderResults, ResultsSerialized, ResultsDeserialized, };

package/dist/PileupRenderer/components/PileupRendering.d.ts

@@ -1,23 +1,23 @@
-import { Region } from '@jbrowse/core/util/types';
-import React from 'react';
-import type { BaseLinearDisplayModel } from '@jbrowse/plugin-linear-genome-view';
-declare function PileupRendering(props: {
-    blockKey: string;
-    displayModel: BaseLinearDisplayModel;
-    width: number;
-    height: number;
-    regions: Region[];
-    bpPerPx: number;
-    sortedBy?: {
-        type: string;
-        pos: number;
-        refName: string;
-    };
-    colorBy?: {
-        type: string;
-        tag?: string;
-    };
-    onMouseMove?: (event: React.MouseEvent, featureId: string | undefined) => void;
-}): JSX.Element;
-declare const _default: typeof PileupRendering;
-export default _default;
+import { Region } from '@jbrowse/core/util/types';
+import React from 'react';
+import type { BaseLinearDisplayModel } from '@jbrowse/plugin-linear-genome-view';
+declare function PileupRendering(props: {
+    blockKey: string;
+    displayModel: BaseLinearDisplayModel;
+    width: number;
+    height: number;
+    regions: Region[];
+    bpPerPx: number;
+    sortedBy?: {
+        type: string;
+        pos: number;
+        refName: string;
+    };
+    colorBy?: {
+        type: string;
+        tag?: string;
+    };
+    onMouseMove?: (event: React.MouseEvent, featureId: string | undefined) => void;
+}): JSX.Element;
+declare const _default: typeof PileupRendering;
+export default _default;

package/dist/PileupRenderer/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/PileupRenderer/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/PileupRenderer/sortUtil.d.ts

@@ -1,8 +1,8 @@
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-interface SortObject {
-    pos: number;
-    type: string;
-    tag?: string;
-}
-export declare const sortFeature: (features: Map<string, Feature>, sortedBy: SortObject) => Map<string, Feature>;
-export {};
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+interface SortObject {
+    pos: number;
+    type: string;
+    tag?: string;
+}
+export declare const sortFeature: (features: Map<string, Feature>, sortedBy: SortObject) => Map<string, Feature>;
+export {};

package/dist/SNPCoverageAdapter/SNPCoverageAdapter.d.ts

@@ -1,71 +1,67 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { AugmentedRegion as Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
-interface SNPCoverageOptions extends BaseOptions {
-    filters?: SerializableFilterChain;
-}
-export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
-    protected configure(): Promise<{
-        subadapter: BaseFeatureDataAdapter;
-        sequenceAdapter: BaseFeatureDataAdapter | undefined;
-    }>;
-    fetchSequence(region: Region): Promise<any>;
-    getFeatures(region: Region, opts?: SNPCoverageOptions): import("rxjs").Observable<Feature>;
-    estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
-    getRefNames(opts?: BaseOptions): Promise<string[]>;
-    freeResources(): void;
-    generateCoverageBins(features: Feature[], region: Region, opts: {
-        bpPerPx?: number;
-        colorBy?: {
-            type: string;
-            tag?: string;
-        };
-    }): Promise<{
-        bins: {
-            total: number;
-            lowqual: {
-                total: number;
-                strands: {
-                    [key: string]: number;
-                };
-            };
-            cov: {
-                total: number;
-                strands: {
-                    [key: string]: number;
-                };
-            };
-            delskips: {
-                total: number;
-                strands: {
-                    [key: string]: number;
-                };
-            };
-            noncov: {
-                total: number;
-                strands: {
-                    [key: string]: number;
-                };
-            };
-            ref: {
-                total: number;
-                strands: {
-                    [key: string]: number;
-                };
-            };
-        }[];
-        skipmap: {
-            [key: string]: {
-                score: number;
-                feature: unknown;
-                start: number;
-                end: number;
-                strand: number;
-                xs: string;
-            };
-        };
-    }>;
-}
-declare const capabilities: string[];
-export { capabilities };
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { AugmentedRegion as Region } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
+    protected configure(): Promise<{
+        subadapter: BaseFeatureDataAdapter;
+        sequenceAdapter: BaseFeatureDataAdapter | undefined;
+    }>;
+    fetchSequence(region: Region): Promise<any>;
+    getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    freeResources(): void;
+    generateCoverageBins(features: Feature[], region: Region, opts: {
+        bpPerPx?: number;
+        colorBy?: {
+            type: string;
+            tag?: string;
+        };
+    }): Promise<{
+        bins: {
+            total: number;
+            lowqual: {
+                total: number;
+                strands: {
+                    [key: string]: number;
+                };
+            };
+            cov: {
+                total: number;
+                strands: {
+                    [key: string]: number;
+                };
+            };
+            delskips: {
+                total: number;
+                strands: {
+                    [key: string]: number;
+                };
+            };
+            noncov: {
+                total: number;
+                strands: {
+                    [key: string]: number;
+                };
+            };
+            ref: {
+                total: number;
+                strands: {
+                    [key: string]: number;
+                };
+            };
+        }[];
+        skipmap: {
+            [key: string]: {
+                score: number;
+                feature: unknown;
+                start: number;
+                end: number;
+                strand: number;
+                xs: string;
+            };
+        };
+    }>;
+}
+declare const capabilities: string[];
+export { capabilities };

package/dist/SNPCoverageAdapter/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/SNPCoverageAdapter/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/SNPCoverageRenderer/SNPCoverageRenderer.d.ts

@@ -1,20 +1,20 @@
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-import { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
-import { ScaleOpts, WiggleBaseRenderer } from '@jbrowse/plugin-wiggle';
-export interface RenderArgsDeserialized extends FeatureRenderArgsDeserialized {
-    bpPerPx: number;
-    height: number;
-    highResolutionScaling: number;
-    scaleOpts: ScaleOpts;
-}
-export interface RenderArgsDeserializedWithFeatures extends RenderArgsDeserialized {
-    features: Map<string, Feature>;
-    ticks: {
-        values: number[];
-    };
-    displayCrossHatches: boolean;
-    modificationTagMap?: Record<string, string>;
-}
-export default class SNPCoverageRenderer extends WiggleBaseRenderer {
-    draw(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): void;
-}
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+import { ScaleOpts, WiggleBaseRenderer } from '@jbrowse/plugin-wiggle';
+export interface RenderArgsDeserialized extends FeatureRenderArgsDeserialized {
+    bpPerPx: number;
+    height: number;
+    highResolutionScaling: number;
+    scaleOpts: ScaleOpts;
+}
+export interface RenderArgsDeserializedWithFeatures extends RenderArgsDeserialized {
+    features: Map<string, Feature>;
+    ticks: {
+        values: number[];
+    };
+    displayCrossHatches: boolean;
+    modificationTagMap?: Record<string, string>;
+}
+export default class SNPCoverageRenderer extends WiggleBaseRenderer {
+    draw(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): void;
+}

package/dist/SNPCoverageRenderer/configSchema.d.ts

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

package/dist/SNPCoverageRenderer/index.d.ts

@@ -1,3 +1,3 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default function register(pluginManager: PluginManager): void;
+import PluginManager from '@jbrowse/core/PluginManager';
+export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default function register(pluginManager: PluginManager): void;

package/dist/index.d.ts

@@ -1,10 +1,10 @@
-import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
-import * as MismatchParser from './BamAdapter/MismatchParser';
-import { LinearPileupDisplayModel } from './LinearPileupDisplay/model';
-export { MismatchParser };
-export type { LinearPileupDisplayModel };
-export default class AlignmentsPlugin extends Plugin {
-    name: string;
-    install(pluginManager: PluginManager): void;
-}
+import Plugin from '@jbrowse/core/Plugin';
+import PluginManager from '@jbrowse/core/PluginManager';
+import * as MismatchParser from './BamAdapter/MismatchParser';
+import { LinearPileupDisplayModel } from './LinearPileupDisplay/model';
+export { MismatchParser };
+export type { LinearPileupDisplayModel };
+export default class AlignmentsPlugin extends Plugin {
+    name: string;
+    install(pluginManager: PluginManager): void;
+}

package/dist/shared.d.ts

@@ -1,25 +1,25 @@
-import { BlockSet } from '@jbrowse/core/util/blockTypes';
-import { IAnyStateTreeNode } from 'mobx-state-tree';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
-export declare function getUniqueTagValues(self: IAnyStateTreeNode & {
-    adapterConfig: AnyConfigurationModel;
-}, colorScheme: {
-    type: string;
-    tag?: string;
-}, blocks: BlockSet, opts?: {
-    headers?: Record<string, string>;
-    signal?: AbortSignal;
-    filters?: string[];
-}): Promise<string[]>;
-export declare function getUniqueModificationValues(self: IAnyStateTreeNode & {
-    parentTrack: IAnyStateTreeNode & {
-        configuration: AnyConfigurationModel;
-    };
-}, adapterConfig: AnyConfigurationModel, colorScheme: {
-    type: string;
-    tag?: string;
-}, blocks: BlockSet, opts?: {
-    headers?: Record<string, string>;
-    signal?: AbortSignal;
-    filters?: string[];
-}): Promise<string[]>;
+import { BlockSet } from '@jbrowse/core/util/blockTypes';
+import { IAnyStateTreeNode } from 'mobx-state-tree';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+export declare function getUniqueTagValues(self: IAnyStateTreeNode & {
+    adapterConfig: AnyConfigurationModel;
+}, colorScheme: {
+    type: string;
+    tag?: string;
+}, blocks: BlockSet, opts?: {
+    headers?: Record<string, string>;
+    signal?: AbortSignal;
+    filters?: string[];
+}): Promise<string[]>;
+export declare function getUniqueModificationValues(self: IAnyStateTreeNode & {
+    parentTrack: IAnyStateTreeNode & {
+        configuration: AnyConfigurationModel;
+    };
+}, adapterConfig: AnyConfigurationModel, colorScheme: {
+    type: string;
+    tag?: string;
+}, blocks: BlockSet, opts?: {
+    headers?: Record<string, string>;
+    signal?: AbortSignal;
+    filters?: string[];
+}): Promise<string[]>;