@jbrowse/plugin-alignments 2.16.1 → 2.18.0

package/dist/PileupRPC/methods/GetReducedFeatures.d.ts

@@ -1,11 +1,10 @@
-import { Region } from '@jbrowse/core/util';
-import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals';
 import PileupBaseRPC from '../base';
+import type { Region } from '@jbrowse/core/util';
 export default class PileupGetReducedFeatures extends PileupBaseRPC {
     name: string;
     execute(args: {
         adapterConfig: Record<string, unknown>;
-        signal?: RemoteAbortSignal;
+        stopToken?: string;
         headers?: Record<string, string>;
         regions: Region[];
         sessionId: string;
@@ -23,7 +22,7 @@ export default class PileupGetReducedFeatures extends PileupBaseRPC {
             pair_orientation: any;
             next_ref: any;
             next_pos: any;
-            clipPos: any;
+            clipPos: number;
             SA: any;
         }[][];
         stats: {

package/dist/PileupRPC/methods/GetReducedFeatures.js

@@ -5,13 +5,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
 const util_1 = require("@jbrowse/core/util");
-const operators_1 = require("rxjs/operators");
 const rxjs_1 = require("rxjs");
-// locals
-const util_2 = require("../util");
+const operators_1 = require("rxjs/operators");
+const MismatchParser_1 = require("../../MismatchParser");
 const base_1 = __importDefault(require("../base"));
-const util_3 = require("../../util");
-// specialized get features to return limited data about alignments
+const util_2 = require("../util");
 class PileupGetReducedFeatures extends base_1.default {
     constructor() {
         super(...arguments);
@@ -22,21 +20,24 @@ class PileupGetReducedFeatures extends base_1.default {
         const { adapterConfig, sessionId, regions } = des;
         const dataAdapter = (await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
         const featuresArray = await (0, rxjs_1.firstValueFrom)(dataAdapter.getFeaturesInMultipleRegions(regions, des).pipe((0, operators_1.toArray)()));
-        const reduced = (0, util_1.dedupe)(featuresArray.map(f => ({
-            id: f.id(),
-            refName: f.get('refName'),
-            name: f.get('name'),
-            start: f.get('start'),
-            strand: f.get('strand'),
-            end: f.get('end'),
-            flags: f.get('flags'),
-            tlen: f.get('template_length'),
-            pair_orientation: f.get('pair_orientation'),
-            next_ref: f.get('next_ref'),
-            next_pos: f.get('next_pos'),
-            clipPos: f.get('clipPos'),
-            SA: (0, util_3.getTag)(f, 'SA'),
-        })), f => f.id);
+        const reduced = (0, util_1.dedupe)(featuresArray.map(f => {
+            var _a;
+            return ({
+                id: f.id(),
+                refName: f.get('refName'),
+                name: f.get('name'),
+                start: f.get('start'),
+                strand: f.get('strand'),
+                end: f.get('end'),
+                flags: f.get('flags'),
+                tlen: f.get('template_length'),
+                pair_orientation: f.get('pair_orientation'),
+                next_ref: f.get('next_ref'),
+                next_pos: f.get('next_pos'),
+                clipPos: (0, MismatchParser_1.getClip)(f.get('CIGAR'), f.get('strand')),
+                SA: (_a = f.get('tags')) === null || _a === void 0 ? void 0 : _a.SA,
+            });
+        }), f => f.id);
         const filtered = (0, util_2.filterForPairs)(reduced);
         const stats = filtered.length ? (0, util_2.getInsertSizeStats)(filtered) : undefined;
         const chains = (0, util_1.groupBy)(reduced, f => f.name);

package/dist/PileupRPC/methods/GetVisibleModifications.d.ts

@@ -1,14 +1,14 @@
-import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals';
-import { Region } from '@jbrowse/core/util';
 import PileupBaseRPC from '../base';
+import type { ModificationType } from '../../shared/types';
+import type { Region } from '@jbrowse/core/util';
 export default class PileupGetVisibleModifications extends PileupBaseRPC {
     name: string;
     execute(args: {
         adapterConfig: Record<string, unknown>;
-        signal?: RemoteAbortSignal;
+        stopToken?: string;
         headers?: Record<string, string>;
         regions: Region[];
         sessionId: string;
         tag: string;
-    }, rpcDriver: string): Promise<string[]>;
+    }, rpcDriver: string): Promise<ModificationType[]>;
 }

package/dist/PileupRPC/methods/GetVisibleModifications.js

@@ -4,12 +4,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
-const operators_1 = require("rxjs/operators");
 const rxjs_1 = require("rxjs");
-// locals
-const MismatchParser_1 = require("../../MismatchParser");
-const base_1 = __importDefault(require("../base"));
+const operators_1 = require("rxjs/operators");
+const ModificationParser_1 = require("../../ModificationParser");
 const util_1 = require("../../util");
+const base_1 = __importDefault(require("../base"));
 class PileupGetVisibleModifications extends base_1.default {
     constructor() {
         super(...arguments);
@@ -19,11 +18,15 @@ class PileupGetVisibleModifications extends base_1.default {
         const { adapterConfig, sessionId, regions } = await this.deserializeArguments(args, rpcDriver);
         const dataAdapter = (await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
         const featuresArray = await (0, rxjs_1.firstValueFrom)(dataAdapter.getFeaturesInMultipleRegions(regions).pipe((0, operators_1.toArray)()));
-        const uniqueValues = new Set();
+        const uniqueModifications = new Map();
         featuresArray.forEach(f => {
-            (0, MismatchParser_1.getModificationTypes)((0, util_1.getTagAlt)(f, 'MM', 'Mm') || '').forEach(t => uniqueValues.add(t));
+            for (const mod of (0, ModificationParser_1.getModTypes)((0, util_1.getTagAlt)(f, 'MM', 'Mm') || '')) {
+                if (!uniqueModifications.has(mod.type)) {
+                    uniqueModifications.set(mod.type, mod);
+                }
+            }
         });
-        return [...uniqueValues];
+        return [...uniqueModifications.values()];
     }
 }
 exports.default = PileupGetVisibleModifications;

package/dist/PileupRPC/util.d.ts

@@ -1,4 +1,4 @@
-import { ReducedFeature } from '../shared/fetchChains';
+import type { ReducedFeature } from '../shared/fetchChains';
 export declare function getInsertSizeStats(features: ReducedFeature[]): {
     upper: number;
     lower: number;

package/dist/PileupRenderer/PileupLayoutSession.d.ts

@@ -1,28 +1,29 @@
 import { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
-import GranularRectLayout from '@jbrowse/core/util/layouts/GranularRectLayout';
-import MultiLayout from '@jbrowse/core/util/layouts/MultiLayout';
+import type { FilterBy, SortedBy } from '../shared/types';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
+import type GranularRectLayout from '@jbrowse/core/util/layouts/GranularRectLayout';
+import type MultiLayout from '@jbrowse/core/util/layouts/MultiLayout';
 export interface PileupLayoutSessionProps {
     config: AnyConfigurationModel;
     bpPerPx: number;
     filters: SerializableFilterChain;
-    filterBy: unknown;
-    sortedBy: unknown;
-    showSoftClip: unknown;
+    filterBy: FilterBy;
+    sortedBy: SortedBy;
+    showSoftClip: boolean;
 }
 type MyMultiLayout = MultiLayout<GranularRectLayout<unknown>, unknown>;
 interface CachedPileupLayout {
     layout: MyMultiLayout;
     config: AnyConfigurationModel;
     filters?: SerializableFilterChain;
-    filterBy: unknown;
-    sortedBy: unknown;
+    filterBy?: FilterBy;
+    sortedBy?: SortedBy;
     showSoftClip: boolean;
 }
 export declare class PileupLayoutSession extends LayoutSession {
-    sortedBy: unknown;
-    filterBy: unknown;
+    sortedBy?: SortedBy;
+    filterBy?: FilterBy;
     showSoftClip: boolean;
     constructor(args: PileupLayoutSessionProps);
     cachedLayoutIsValid(cachedLayout: CachedPileupLayout): boolean;

package/dist/PileupRenderer/PileupLayoutSession.js

@@ -4,12 +4,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.PileupLayoutSession = void 0;
-const fast_deep_equal_1 = __importDefault(require("fast-deep-equal"));
-const BoxRendererType_1 = require("@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType");
 const configuration_1 = require("@jbrowse/core/configuration");
-// The pileup layout session adds
-// - sorting and revealing soft clip changes the layout of pileup renderer
-// - extra conditions to see if cached layout is valid
+const BoxRendererType_1 = require("@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType");
+const fast_deep_equal_1 = __importDefault(require("fast-deep-equal"));
 class PileupLayoutSession extends BoxRendererType_1.LayoutSession {
     constructor(args) {
         super(args);

package/dist/PileupRenderer/PileupRenderer.d.ts

@@ -1,37 +1,16 @@
-import BoxRendererType, { RenderArgsDeserialized as BoxRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
-import { Feature, Region } from '@jbrowse/core/util';
-import { BaseLayout } from '@jbrowse/core/util/layouts/BaseLayout';
-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;
-}
+import BoxRendererType from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+import { PileupLayoutSession } from './PileupLayoutSession';
+import type { PileupLayoutSessionProps } from './PileupLayoutSession';
+import type { RenderArgsDeserialized } from './types';
+import type { Region } from '@jbrowse/core/util';
 export default class PileupRenderer extends BoxRendererType {
     supportsSVG: boolean;
-    fetchSequence(renderProps: RenderArgsDeserialized): Promise<any>;
+    fetchSequence(renderProps: RenderArgsDeserialized, region: Region): Promise<any>;
     getExpandedRegion(region: Region, renderArgs: RenderArgsDeserialized): {
         start: number;
         end: number;
-        refName: string;
         reversed?: boolean | undefined;
+        refName: string;
         assemblyName: string;
     };
     render(renderProps: RenderArgsDeserialized): Promise<{
@@ -40,6 +19,7 @@ export default class PileupRenderer extends BoxRendererType {
         height: number;
         width: number;
         maxHeightReached: boolean;
+        containsNoTransferables: boolean;
         canvasRecordedData: any;
         reactElement?: import("react").ReactElement;
         html?: string;
@@ -49,6 +29,7 @@ export default class PileupRenderer extends BoxRendererType {
         height: number;
         width: number;
         maxHeightReached: boolean;
+        containsNoTransferables: boolean;
         reactElement: React.JSX.Element;
         html?: string;
     } | {
@@ -57,10 +38,11 @@ export default class PileupRenderer extends BoxRendererType {
         height: number;
         width: number;
         maxHeightReached: boolean;
+        containsNoTransferables: boolean;
         imageData: any;
         reactElement?: import("react").ReactElement;
         html?: string;
     }>;
     createSession(args: PileupLayoutSessionProps): PileupLayoutSession;
 }
-export { type RenderArgs, type RenderResults, type RenderArgsSerialized, type ResultsSerialized, type ResultsDeserialized, } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+export type { RenderArgs, RenderArgsSerialized, RenderResults, ResultsDeserialized, ResultsSerialized, } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';

package/dist/PileupRenderer/PileupRenderer.js

@@ -26,12 +26,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const BoxRendererType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType"));
-const util_1 = require("@jbrowse/core/util");
 const configuration_1 = require("@jbrowse/core/configuration");
 const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
+const BoxRendererType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType"));
+const util_1 = require("@jbrowse/core/util");
 const PileupLayoutSession_1 = require("./PileupLayoutSession");
-// locals
 const util_2 = require("../util");
 const layoutFeatures_1 = require("./layoutFeatures");
 class PileupRenderer extends BoxRendererType_1.default {
@@ -39,16 +38,18 @@ class PileupRenderer extends BoxRendererType_1.default {
         super(...arguments);
         this.supportsSVG = true;
     }
-    async fetchSequence(renderProps) {
-        const { sessionId, regions, adapterConfig } = renderProps;
+    async fetchSequence(renderProps, region) {
+        const { sessionId, adapterConfig } = renderProps;
         const { sequenceAdapter } = adapterConfig;
         if (!sequenceAdapter) {
             return undefined;
         }
-        const pm = this.pluginManager;
-        const { dataAdapter } = await (0, dataAdapterCache_1.getAdapter)(pm, sessionId, sequenceAdapter);
-        const region = regions[0];
-        return (0, util_2.fetchSequence)(region, dataAdapter);
+        const { dataAdapter } = await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, sequenceAdapter);
+        return (0, util_2.fetchSequence)({
+            ...region,
+            start: Math.max(0, region.start - 1),
+            end: region.end + 1,
+        }, dataAdapter);
     }
     getExpandedRegion(region, renderArgs) {
         const { config, showSoftClip } = renderArgs;
@@ -56,35 +57,30 @@ class PileupRenderer extends BoxRendererType_1.default {
         const maxClippingSize = (0, configuration_1.readConfObject)(config, 'maxClippingSize');
         const bpExpansion = showSoftClip ? Math.round(maxClippingSize) : 0;
         return {
-            // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
             ...region,
             start: Math.floor(Math.max(start - bpExpansion, 0)),
             end: Math.ceil(end + bpExpansion),
         };
     }
     async render(renderProps) {
-        var _a;
         const features = await this.getFeatures(renderProps);
         const layout = this.createLayoutInWorker(renderProps);
-        const { regions, bpPerPx } = renderProps;
+        const { colorBy, regions, bpPerPx } = renderProps;
         const region = regions[0];
-        const layoutRecords = (0, layoutFeatures_1.layoutFeats)({
+        const regionSequence = (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation' && features.size
+            ? await this.fetchSequence(renderProps, region)
+            : undefined;
+        const { layoutRecords, height } = (0, layoutFeatures_1.layoutFeats)({
             ...renderProps,
             features,
             layout,
         });
-        // only need reference sequence if there are features and only for some
-        // cases
-        const regionSequence = features.size && (0, util_2.shouldFetchReferenceSequence)((_a = renderProps.colorBy) === null || _a === void 0 ? void 0 : _a.type)
-            ? await this.fetchSequence(renderProps)
-            : undefined;
         const width = (region.end - region.start) / bpPerPx;
-        const height = Math.max(layout.getTotalHeight(), 1);
         const { makeImageData } = await Promise.resolve().then(() => __importStar(require('./makeImageData')));
         const res = await (0, util_1.renderToAbstractCanvas)(width, height, renderProps, ctx => {
             makeImageData({
                 ctx,
-                layoutRecords: layoutRecords.filter(util_1.notEmpty),
+                layoutRecords,
                 canvasWidth: width,
                 renderArgs: {
                     ...renderProps,
@@ -111,6 +107,7 @@ class PileupRenderer extends BoxRendererType_1.default {
             height,
             width,
             maxHeightReached: layout.maxHeightReached,
+            containsNoTransferables: true,
         };
     }
     createSession(args) {

package/dist/PileupRenderer/colorBy.d.ts

@@ -1,5 +1,5 @@
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { Feature } from '@jbrowse/core/util';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Feature } from '@jbrowse/core/util';
 export declare function colorByInsertSize(feature: Feature): string;
 export declare function colorByMappingQuality(feature: Feature): string;
 export declare function colorByStrand(feature: Feature): "#EC8B8B" | "#8F8FD8";

package/dist/PileupRenderer/colorBy.js

@@ -37,27 +37,21 @@ function colorByOrientation(feature, config) {
 function getStranded(feature) {
     const flags = feature.get('flags');
     const strand = feature.get('strand');
-    // is paired
     if (flags & 1) {
-        // first-of-pair?
         const flipper = flags & 64 ? -1 : 1;
-        // proper pairing
         if (flags & 2) {
             return strand * flipper === 1 ? 'color_rev_strand' : 'color_fwd_strand';
         }
-        // mate missing, separate color
         if (flags & 8) {
             return strand * flipper === 1
                 ? 'color_rev_missing_mate'
                 : 'color_fwd_missing_mate';
         }
-        // same chrom without proper pairing gets separate color
         if (feature.get('refName') === feature.get('next_ref')) {
             return strand * flipper === 1
                 ? 'color_rev_strand_not_proper'
                 : 'color_fwd_strand_not_proper';
         }
-        // abberant chrom
         return strand === 1 ? 'color_fwd_diff_chr' : 'color_rev_diff_chr';
     }
     return 'color_unknown';

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

@@ -1,5 +1,5 @@
 import React from 'react';
-import { Region } from '@jbrowse/core/util/types';
+import type { Region } from '@jbrowse/core/util/types';
 import type { BaseLinearDisplayModel } from '@jbrowse/plugin-linear-genome-view';
 declare const PileupRendering: (props: {
     blockKey: string;

package/dist/PileupRenderer/components/PileupRendering.js

@@ -106,9 +106,7 @@ const PileupRendering = (0, mobx_react_1.observer)(function (props) {
         onMouseMove === null || onMouseMove === void 0 ? void 0 : onMouseMove(event, displayModel === null || displayModel === void 0 ? void 0 : displayModel.getFeatureOverlapping(blockKey, clientBp, offsetY));
     }
     function callMouseHandler(handlerName, event) {
-        // @ts-expect-error
         const featureHandler = props[`onFeature${handlerName}`];
-        // @ts-expect-error
         const canvasHandler = props[`on${handlerName}`];
         if (featureHandler && featureIdUnderMouse) {
             featureHandler(event, featureIdUnderMouse);
@@ -118,7 +116,6 @@ const PileupRendering = (0, mobx_react_1.observer)(function (props) {
         }
     }
     const canvasWidth = Math.ceil(width);
-    // need to call this in render so we get the right observer behavior
     return (react_1.default.createElement("div", { ref: ref, "data-testid": [
             'pileup-overlay',
             sortedBy === null || sortedBy === void 0 ? void 0 : sortedBy.type,

package/dist/PileupRenderer/configSchema.d.ts

@@ -1,84 +1,53 @@
 declare const PileupRenderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     * default magenta here is used to detect the user has not customized this
-     */
     color: {
         type: string;
         description: string;
         defaultValue: string;
         contextVariable: string[];
     };
-    /**
-     * #slot
-     */
     orientationType: {
         type: string;
         model: import("mobx-state-tree").ISimpleType<string>;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     */
     displayMode: {
         type: string;
         model: import("mobx-state-tree").ISimpleType<string>;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     minSubfeatureWidth: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
     maxHeight: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
     maxClippingSize: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
     height: {
         type: string;
         description: string;
         defaultValue: number;
         contextVariable: string[];
     };
-    /**
-     * #slot
-     */
     noSpacing: {
         type: string;
         description: string;
         defaultValue: boolean;
     };
-    /**
-     * #slot
-     */
     largeInsertionIndicatorScale: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
     mismatchAlpha: {
         type: string;
         defaultValue: boolean;

package/dist/PileupRenderer/configSchema.js

@@ -2,33 +2,20 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
 const mobx_state_tree_1 = require("mobx-state-tree");
-/**
- * #config PileupRenderer
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const PileupRenderer = (0, configuration_1.ConfigurationSchema)('PileupRenderer', {
-    /**
-     * #slot
-     * default magenta here is used to detect the user has not customized this
-     */
     color: {
         type: 'color',
         description: 'the color of each feature in a pileup alignment',
         defaultValue: '#f0f',
         contextVariable: ['feature'],
     },
-    /**
-     * #slot
-     */
     orientationType: {
         type: 'stringEnum',
         model: mobx_state_tree_1.types.enumeration('orientationType', ['fr', 'rf', 'ff']),
         defaultValue: 'fr',
         description: 'read sequencer orientation. fr is normal "reads pointing at each other ---> <--- while some other sequencers can use other options',
     },
-    /**
-     * #slot
-     */
     displayMode: {
         type: 'stringEnum',
         model: mobx_state_tree_1.types.enumeration('displayMode', [
@@ -39,58 +26,37 @@ const PileupRenderer = (0, configuration_1.ConfigurationSchema)('PileupRenderer'
         description: 'Alternative display modes',
         defaultValue: 'normal',
     },
-    /**
-     * #slot
-     */
     minSubfeatureWidth: {
         type: 'number',
         description: 'the minimum width in px for a pileup mismatch feature. use for increasing/decreasing mismatch marker widths when zoomed out, e.g. 0 or 1',
         defaultValue: 1,
     },
-    /**
-     * #slot
-     */
     maxHeight: {
         type: 'integer',
         description: 'the maximum height to be used in a pileup rendering',
         defaultValue: 1200,
     },
-    /**
-     * #slot
-     */
     maxClippingSize: {
         type: 'integer',
         description: 'the max clip size to be used in a pileup rendering',
         defaultValue: 10000,
     },
-    /**
-     * #slot
-     */
     height: {
         type: 'number',
         description: 'the height of each feature in a pileup alignment',
         defaultValue: 7,
         contextVariable: ['feature'],
     },
-    /**
-     * #slot
-     */
     noSpacing: {
         type: 'boolean',
         description: 'remove spacing between features',
         defaultValue: false,
     },
-    /**
-     * #slot
-     */
     largeInsertionIndicatorScale: {
         type: 'number',
         description: 'scale at which to draw the large insertion indicators (bp/pixel)',
         defaultValue: 10,
     },
-    /**
-     * #slot
-     */
     mismatchAlpha: {
         type: 'boolean',
         defaultValue: false,

package/dist/PileupRenderer/getAlignmentShapeColor.d.ts

@@ -1,5 +1,5 @@
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { Feature } from '@jbrowse/core/util';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Feature } from '@jbrowse/core/util';
 export declare function getAlignmentShapeColor({ colorType, tag, feature, config, defaultColor, colorTagMap, }: {
     colorType: string;
     tag: string;

package/dist/PileupRenderer/getAlignmentShapeColor.js

@@ -2,11 +2,9 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.getAlignmentShapeColor = getAlignmentShapeColor;
 const configuration_1 = require("@jbrowse/core/configuration");
-const color_1 = require("../shared/color");
 const colorBy_1 = require("./colorBy");
+const color_1 = require("../shared/color");
 function getAlignmentShapeColor({ colorType, tag, feature, config, defaultColor, colorTagMap, }) {
-    // first pass for simple color changes that change the color of the
-    // alignment
     switch (colorType) {
         case 'insertSize':
             return (0, colorBy_1.colorByInsertSize)(feature);
@@ -54,9 +52,6 @@ function getAlignmentShapeColor({ colorType, tag, feature, config, defaultColor,
             break;
         case 'modifications':
         case 'methylation':
-            // this coloring is similar to igv.js, and is helpful to color negative
-            // strand reads differently because their c-g will be flipped (e.g. g-c
-            // read right to left)
             return feature.get('flags') & 16 ? '#c8dcc8' : '#c8c8c8';
         default:
             return defaultColor

package/dist/PileupRenderer/index.d.ts

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