@jbrowse/plugin-alignments 3.7.0 → 4.0.1

package/dist/PileupRenderer/PileupLayoutSession.js

@@ -1,35 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.PileupLayoutSession = void 0;
-const LayoutSession_1 = require("@jbrowse/core/pluggableElementTypes/renderers/LayoutSession");
-const fast_deep_equal_1 = __importDefault(require("fast-deep-equal"));
-class PileupLayoutSession extends LayoutSession_1.LayoutSession {
-    constructor(props) {
-        super(props);
-        this.props = props;
-    }
-    update(props) {
-        super.update(props);
-        this.props = props;
-        return this;
-    }
-    cachedLayoutIsValid(cachedLayout) {
-        return (super.cachedLayoutIsValid(cachedLayout) &&
-            this.props.showSoftClip === cachedLayout.props.showSoftClip &&
-            (0, fast_deep_equal_1.default)(this.props.sortedBy, cachedLayout.props.sortedBy) &&
-            (0, fast_deep_equal_1.default)(this.props.filterBy, cachedLayout.props.filterBy));
-    }
-    get layout() {
-        if (!this.cachedLayout || !this.cachedLayoutIsValid(this.cachedLayout)) {
-            this.cachedLayout = {
-                layout: this.makeLayout(),
-                props: this.props,
-            };
-        }
-        return this.cachedLayout.layout;
-    }
-}
-exports.PileupLayoutSession = PileupLayoutSession;

package/dist/PileupRenderer/PileupRenderer.d.ts

@@ -1,53 +0,0 @@
-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, region: Region): Promise<any>;
-    getExpandedRegion(region: Region, renderArgs: RenderArgsDeserialized): {
-        start: number;
-        end: number;
-        refName: string;
-        reversed?: boolean | undefined;
-        assemblyName: string;
-    };
-    render(renderProps: RenderArgsDeserialized): Promise<{
-        features: Map<any, any>;
-        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
-        height: number;
-        width: number;
-        maxHeightReached: boolean;
-        containsNoTransferables: boolean;
-        flatbush: ArrayBufferLike;
-        items: import("./types").FlatbushItem[];
-        canvasRecordedData: Record<string, unknown>;
-        reactElement?: React.ReactElement;
-        html?: string;
-    } | {
-        features: Map<any, any>;
-        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
-        height: number;
-        width: number;
-        maxHeightReached: boolean;
-        containsNoTransferables: boolean;
-        flatbush: ArrayBufferLike;
-        items: import("./types").FlatbushItem[];
-        imageData: any;
-        reactElement?: React.ReactElement;
-        html?: string;
-    } | {
-        features: Map<any, any>;
-        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
-        height: number;
-        width: number;
-        maxHeightReached: boolean;
-        containsNoTransferables: boolean;
-        flatbush: ArrayBufferLike;
-        items: import("./types").FlatbushItem[];
-        reactElement: React.ReactElement;
-        html?: string;
-    }>;
-    createLayoutSession(args: PileupLayoutSessionProps): PileupLayoutSession;
-}

package/dist/PileupRenderer/PileupRenderer.js

@@ -1,126 +0,0 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || (function () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __setModuleDefault(result, mod);
-        return result;
-    };
-})();
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-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");
-const util_2 = require("../util");
-const layoutFeatures_1 = require("./layoutFeatures");
-class PileupRenderer extends BoxRendererType_1.default {
-    constructor() {
-        super(...arguments);
-        this.supportsSVG = true;
-    }
-    async fetchSequence(renderProps, region) {
-        const { sessionId, adapterConfig } = renderProps;
-        const { sequenceAdapter } = adapterConfig;
-        if (!sequenceAdapter) {
-            return undefined;
-        }
-        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;
-        const { start, end } = region;
-        const maxClippingSize = (0, configuration_1.readConfObject)(config, 'maxClippingSize');
-        const bpExpansion = showSoftClip ? Math.round(maxClippingSize) : 0;
-        return {
-            ...region,
-            start: Math.floor(Math.max(start - bpExpansion, 0)),
-            end: Math.ceil(end + bpExpansion),
-        };
-    }
-    async render(renderProps) {
-        const features = await this.getFeatures(renderProps);
-        const layout = this.createLayoutInWorker(renderProps);
-        const { statusCallback = () => { }, colorBy, regions, bpPerPx } = renderProps;
-        const region = regions[0];
-        const width = (region.end - region.start) / bpPerPx;
-        const { layoutRecords, height } = await (0, util_1.updateStatus)('Creating layout', statusCallback, () => (0, layoutFeatures_1.layoutFeats)({
-            ...renderProps,
-            features,
-            layout,
-        }));
-        const res = await (0, util_1.updateStatus)('Rendering alignments', statusCallback, async () => {
-            const regionSequence = (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation' && features.size
-                ? await this.fetchSequence(renderProps, region)
-                : undefined;
-            const { makeImageData } = await Promise.resolve().then(() => __importStar(require('./makeImageData')));
-            return (0, util_1.renderToAbstractCanvas)(width, height, renderProps, ctx => makeImageData({
-                ctx,
-                layoutRecords,
-                canvasWidth: width,
-                renderArgs: {
-                    ...renderProps,
-                    layout,
-                    features,
-                    regionSequence,
-                },
-            }));
-        });
-        const results = await super.render({
-            ...renderProps,
-            ...res,
-            features,
-            layout,
-            height,
-            width,
-        });
-        return {
-            ...results,
-            ...res,
-            features: new Map(),
-            layout,
-            height,
-            width,
-            maxHeightReached: layout.maxHeightReached,
-            containsNoTransferables: true,
-        };
-    }
-    createLayoutSession(args) {
-        return new PileupLayoutSession_1.PileupLayoutSession(args);
-    }
-}
-exports.default = PileupRenderer;

package/dist/PileupRenderer/colorBy.d.ts

@@ -1,7 +0,0 @@
-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";
-export declare function colorByOrientation(feature: Feature, config: AnyConfigurationModel): string;
-export declare function colorByStrandedRnaSeq(feature: Feature): string;

package/dist/PileupRenderer/colorBy.js

@@ -1,61 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.colorByInsertSize = colorByInsertSize;
-exports.colorByMappingQuality = colorByMappingQuality;
-exports.colorByStrand = colorByStrand;
-exports.colorByOrientation = colorByOrientation;
-exports.colorByStrandedRnaSeq = colorByStrandedRnaSeq;
-const configuration_1 = require("@jbrowse/core/configuration");
-const color_1 = require("../shared/color");
-const util_1 = require("../util");
-function colorByInsertSize(feature) {
-    return feature.get('is_paired') &&
-        feature.get('refName') !== feature.get('next_ref')
-        ? '#555'
-        : `hsl(${Math.abs(feature.get('template_length')) / 10},50%,50%)`;
-}
-function colorByMappingQuality(feature) {
-    return `hsl(${feature.get('score')},50%,50%)`;
-}
-function getOrientation(feature, config) {
-    const orientationType = (0, configuration_1.readConfObject)(config, 'orientationType');
-    const type = util_1.orientationTypes[orientationType];
-    const orientation = type[feature.get('pair_orientation')];
-    return {
-        LR: 'color_pair_lr',
-        RR: 'color_pair_rr',
-        RL: 'color_pair_rl',
-        LL: 'color_pair_ll',
-    }[orientation];
-}
-function colorByStrand(feature) {
-    return feature.get('strand') === -1 ? '#8F8FD8' : '#EC8B8B';
-}
-function colorByOrientation(feature, config) {
-    return color_1.fillColor[getOrientation(feature, config) || 'color_nostrand'];
-}
-function getStranded(feature) {
-    const flags = feature.get('flags');
-    const strand = feature.get('strand');
-    if (flags & 1) {
-        const flipper = flags & 64 ? -1 : 1;
-        if (flags & 2) {
-            return strand * flipper === 1 ? 'color_rev_strand' : 'color_fwd_strand';
-        }
-        if (flags & 8) {
-            return strand * flipper === 1
-                ? 'color_rev_missing_mate'
-                : 'color_fwd_missing_mate';
-        }
-        if (feature.get('refName') === feature.get('next_ref')) {
-            return strand * flipper === 1
-                ? 'color_rev_strand_not_proper'
-                : 'color_fwd_strand_not_proper';
-        }
-        return strand === 1 ? 'color_fwd_diff_chr' : 'color_rev_diff_chr';
-    }
-    return 'color_unknown';
-}
-function colorByStrandedRnaSeq(feature) {
-    return color_1.fillColor[getStranded(feature)];
-}

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

@@ -1,19 +0,0 @@
-import type { ColorBy, FilterBy, SortedBy } from '../../shared/types';
-import type { FlatbushItem } from '../types';
-import type { Region } from '@jbrowse/core/util/types';
-import type { BaseLinearDisplayModel } from '@jbrowse/plugin-linear-genome-view';
-declare const PileupRendering: (props: {
-    blockKey: string;
-    displayModel?: BaseLinearDisplayModel;
-    width: number;
-    height: number;
-    regions: Region[];
-    bpPerPx: number;
-    sortedBy?: SortedBy;
-    colorBy?: ColorBy;
-    filterBy?: FilterBy;
-    items: FlatbushItem[];
-    flatbush: any;
-    onMouseMove?: (event: React.MouseEvent, featureId?: string, extra?: string) => void;
-}) => import("react/jsx-runtime").JSX.Element;
-export default PileupRendering;

package/dist/PileupRenderer/components/PileupRendering.js

@@ -1,152 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const ui_1 = require("@jbrowse/core/ui");
-const util_1 = require("@jbrowse/core/util");
-const flatbush_1 = __importDefault(require("@jbrowse/core/util/flatbush"));
-const mobx_react_1 = require("mobx-react");
-const PileupRendering = (0, mobx_react_1.observer)(function (props) {
-    var _a;
-    const { onMouseMove, blockKey, displayModel, width, height, regions, bpPerPx, sortedBy, colorBy, filterBy, flatbush, items, } = props;
-    const flatbush2 = (0, react_1.useMemo)(() => flatbush_1.default.from(flatbush), [flatbush]);
-    const { selectedFeatureId, featureIdUnderMouse, contextMenuFeature } = displayModel || {};
-    const [firstRender, setFirstRender] = (0, react_1.useState)(false);
-    (0, react_1.useEffect)(() => {
-        setFirstRender(true);
-    }, []);
-    const region = regions[0];
-    const ref = (0, react_1.useRef)(null);
-    const [mouseIsDown, setMouseIsDown] = (0, react_1.useState)(false);
-    const [movedDuringLastMouseDown, setMovedDuringLastMouseDown] = (0, react_1.useState)(false);
-    const selectedRect = selectedFeatureId
-        ? displayModel === null || displayModel === void 0 ? void 0 : displayModel.getFeatureByID(blockKey, selectedFeatureId)
-        : undefined;
-    const highlightedFeature = featureIdUnderMouse || (contextMenuFeature === null || contextMenuFeature === void 0 ? void 0 : contextMenuFeature.id());
-    const highlightedRect = highlightedFeature
-        ? displayModel === null || displayModel === void 0 ? void 0 : displayModel.getFeatureByID(blockKey, highlightedFeature)
-        : undefined;
-    function makeRect(r, offset = 2) {
-        const [leftBp, topPx, rightBp, bottomPx] = r;
-        const [leftPx, rightPx] = (0, util_1.bpSpanPx)(leftBp, rightBp, region, bpPerPx);
-        const rectTop = Math.round(topPx);
-        const rectHeight = Math.round(bottomPx - topPx);
-        return {
-            left: leftPx - offset,
-            top: rectTop - offset,
-            width: rightPx - leftPx,
-            height: rectHeight,
-        };
-    }
-    const selected = selectedRect ? makeRect(selectedRect) : undefined;
-    const highlight = highlightedRect ? makeRect(highlightedRect, 0) : undefined;
-    function onMouseDown(event) {
-        setMouseIsDown(true);
-        setMovedDuringLastMouseDown(false);
-        callMouseHandler('MouseDown', event);
-    }
-    function onMouseEnter(event) {
-        callMouseHandler('MouseEnter', event);
-    }
-    function onMouseOut(event) {
-        callMouseHandler('MouseOut', event);
-        callMouseHandler('MouseLeave', event);
-    }
-    function onMouseOver(event) {
-        callMouseHandler('MouseOver', event);
-    }
-    function onMouseUp(event) {
-        setMouseIsDown(false);
-        callMouseHandler('MouseUp', event);
-    }
-    function onClick(event) {
-        if (!movedDuringLastMouseDown) {
-            callMouseHandler('Click', event);
-        }
-    }
-    function onMouseLeave(event) {
-        callMouseHandler('MouseOut', event);
-        callMouseHandler('MouseLeave', event);
-    }
-    function onContextMenu(event) {
-        callMouseHandler('ContextMenu', event);
-    }
-    function mouseMove(event) {
-        if (!ref.current) {
-            return;
-        }
-        if (mouseIsDown) {
-            setMovedDuringLastMouseDown(true);
-        }
-        const rect = ref.current.getBoundingClientRect();
-        const offsetX = event.clientX - rect.left;
-        const offsetY = event.clientY - rect.top;
-        const px = region.reversed ? width - offsetX : offsetX;
-        const clientBp = region.start + bpPerPx * px;
-        const search = flatbush2.search(offsetX, offsetY, offsetX + 1, offsetY + 1);
-        const item = search.length ? items[search[0]] : undefined;
-        const label = item
-            ? item.type === 'insertion'
-                ? `Insertion: ${item.seq}`
-                : item.type === 'deletion'
-                    ? `Deletion: ${item.seq}bp`
-                    : item.type === 'modification'
-                        ? item.seq
-                        : `Mismatch: ${item.seq}`
-            : undefined;
-        onMouseMove === null || onMouseMove === void 0 ? void 0 : onMouseMove(event, displayModel === null || displayModel === void 0 ? void 0 : displayModel.getFeatureOverlapping(blockKey, clientBp, offsetY), label);
-    }
-    function callMouseHandler(handlerName, event) {
-        const featureHandler = props[`onFeature${handlerName}`];
-        const canvasHandler = props[`on${handlerName}`];
-        if (featureHandler && featureIdUnderMouse) {
-            featureHandler(event, featureIdUnderMouse);
-        }
-        else if (canvasHandler) {
-            canvasHandler(event, featureIdUnderMouse);
-        }
-    }
-    const canvasWidth = Math.ceil(width);
-    return ((0, jsx_runtime_1.jsxs)("div", { ref: ref, "data-testid": [
-            'pileup-overlay',
-            sortedBy === null || sortedBy === void 0 ? void 0 : sortedBy.type,
-            colorBy === null || colorBy === void 0 ? void 0 : colorBy.type,
-            colorBy === null || colorBy === void 0 ? void 0 : colorBy.tag,
-            (_a = filterBy === null || filterBy === void 0 ? void 0 : filterBy.tagFilter) === null || _a === void 0 ? void 0 : _a.tag,
-        ]
-            .filter(f => !!f)
-            .join('-'), style: { position: 'relative', width: canvasWidth, height }, onMouseDown: event => {
-            onMouseDown(event);
-        }, onMouseEnter: event => {
-            onMouseEnter(event);
-        }, onMouseOut: event => {
-            onMouseOut(event);
-        }, onMouseOver: event => {
-            onMouseOver(event);
-        }, onMouseUp: event => {
-            onMouseUp(event);
-        }, onMouseLeave: event => {
-            onMouseLeave(event);
-        }, onMouseMove: event => {
-            mouseMove(event);
-        }, onClick: event => {
-            onClick(event);
-        }, onContextMenu: event => {
-            onContextMenu(event);
-        }, onFocus: () => { }, onBlur: () => { }, children: [(0, jsx_runtime_1.jsx)(ui_1.PrerenderedCanvas, { ...props, style: { position: 'absolute', left: 0, top: 0 } }), firstRender && highlight ? ((0, jsx_runtime_1.jsx)("div", { style: {
-                    position: 'absolute',
-                    backgroundColor: '#0003',
-                    pointerEvents: 'none',
-                    ...highlight,
-                } })) : null, firstRender && selected ? ((0, jsx_runtime_1.jsx)("div", { style: {
-                    position: 'absolute',
-                    border: '2px solid #00b8ff',
-                    boxSizing: 'content-box',
-                    pointerEvents: 'none',
-                    ...selected,
-                } })) : null] }));
-});
-exports.default = PileupRendering;

package/dist/PileupRenderer/configSchema.d.ts

@@ -1,62 +0,0 @@
-declare const PileupRenderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    color: {
-        type: string;
-        description: string;
-        defaultValue: string;
-        contextVariable: string[];
-    };
-    orientationType: {
-        type: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
-        defaultValue: string;
-        description: string;
-    };
-    displayMode: {
-        type: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
-        description: string;
-        defaultValue: string;
-    };
-    minSubfeatureWidth: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-    hideSmallIndels: {
-        type: string;
-        description: string;
-        defaultValue: boolean;
-    };
-    maxHeight: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-    maxClippingSize: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-    height: {
-        type: string;
-        description: string;
-        defaultValue: number;
-        contextVariable: string[];
-    };
-    noSpacing: {
-        type: string;
-        description: string;
-        defaultValue: boolean;
-    };
-    largeInsertionIndicatorScale: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-    mismatchAlpha: {
-        type: string;
-        defaultValue: boolean;
-        description: string;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default PileupRenderer;

package/dist/PileupRenderer/configSchema.js

@@ -1,71 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-const mobx_state_tree_1 = require("mobx-state-tree");
-function x() { }
-const PileupRenderer = (0, configuration_1.ConfigurationSchema)('PileupRenderer', {
-    color: {
-        type: 'color',
-        description: 'the color of each feature in a pileup alignment',
-        defaultValue: '#f0f',
-        contextVariable: ['feature'],
-    },
-    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',
-    },
-    displayMode: {
-        type: 'stringEnum',
-        model: mobx_state_tree_1.types.enumeration('displayMode', [
-            'normal',
-            'compact',
-            'collapse',
-        ]),
-        description: 'Alternative display modes',
-        defaultValue: 'normal',
-    },
-    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,
-    },
-    hideSmallIndels: {
-        type: 'boolean',
-        description: 'Hides small indels, sometimes occurring in long read sequencing',
-        defaultValue: false,
-    },
-    maxHeight: {
-        type: 'integer',
-        description: 'the maximum height to be used in a pileup rendering',
-        defaultValue: 1200,
-    },
-    maxClippingSize: {
-        type: 'integer',
-        description: 'the max clip size to be used in a pileup rendering',
-        defaultValue: 10000,
-    },
-    height: {
-        type: 'number',
-        description: 'the height of each feature in a pileup alignment',
-        defaultValue: 7,
-        contextVariable: ['feature'],
-    },
-    noSpacing: {
-        type: 'boolean',
-        description: 'remove spacing between features',
-        defaultValue: false,
-    },
-    largeInsertionIndicatorScale: {
-        type: 'number',
-        description: 'scale at which to draw the large insertion indicators (bp/pixel)',
-        defaultValue: 10,
-    },
-    mismatchAlpha: {
-        type: 'boolean',
-        defaultValue: false,
-        description: 'Fade low quality mismatches',
-    },
-}, { explicitlyTyped: true });
-exports.default = PileupRenderer;

package/dist/PileupRenderer/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function register(pluginManager: PluginManager): void;

package/dist/PileupRenderer/index.js

@@ -1,20 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = register;
-const PileupRenderer_1 = __importDefault(require("./PileupRenderer"));
-const PileupRendering_1 = __importDefault(require("./components/PileupRendering"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-function register(pluginManager) {
-    pluginManager.addRendererType(() => {
-        return new PileupRenderer_1.default({
-            name: 'PileupRenderer',
-            displayName: 'Pileup renderer',
-            ReactComponent: PileupRendering_1.default,
-            configSchema: configSchema_1.default,
-            pluginManager,
-        });
-    });
-}

package/dist/PileupRenderer/layoutFeature.d.ts

@@ -1,18 +0,0 @@
-import type { Feature, Region } from '@jbrowse/core/util';
-import type { BaseLayout } from '@jbrowse/core/util/layouts';
-export interface LayoutRecord {
-    feature: Feature;
-    leftPx: number;
-    rightPx: number;
-    topPx: number;
-    heightPx: number;
-}
-export declare function 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;

package/dist/PileupRenderer/layoutFeature.js

@@ -1,42 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.layoutFeature = layoutFeature;
-const util_1 = require("@jbrowse/core/util");
-function layoutFeature({ feature, layout, bpPerPx, region, showSoftClip, heightPx, displayMode, }) {
-    let expansionBefore = 0;
-    let expansionAfter = 0;
-    if (showSoftClip) {
-        const mismatches = feature.get('mismatches');
-        const seq = feature.get('seq');
-        if (seq) {
-            for (const { type, start, cliplen = 0 } of mismatches) {
-                if (type === 'softclip') {
-                    if (start === 0) {
-                        expansionBefore = cliplen;
-                    }
-                    else {
-                        expansionAfter = cliplen;
-                    }
-                }
-            }
-        }
-    }
-    const [leftPx, rightPx] = (0, util_1.bpSpanPx)(feature.get('start') - expansionBefore, feature.get('end') + expansionAfter, region, bpPerPx);
-    if (displayMode === 'compact') {
-        heightPx /= 3;
-    }
-    if (feature.get('refName') !== region.refName) {
-        throw new Error(`feature ${feature.id()} is not on the current region's reference sequence ${region.refName}`);
-    }
-    const topPx = layout.addRect(feature.id(), feature.get('start') - expansionBefore, feature.get('end') + expansionAfter, heightPx, feature);
-    if (topPx === null) {
-        return null;
-    }
-    return {
-        feature,
-        leftPx,
-        rightPx,
-        topPx: displayMode === 'collapse' ? 0 : topPx,
-        heightPx,
-    };
-}