@jbrowse/plugin-alignments 2.18.0 → 3.0.1

package/dist/SNPCoverageRenderer/configSchema.d.ts

@@ -9,17 +9,17 @@ declare const SNPCoverageRenderer: import("@jbrowse/core/configuration/configura
         description: string;
         defaultValue: number;
     };
-    drawArcs: {
+    showArcs: {
         type: string;
         description: string;
         defaultValue: boolean;
     };
-    drawInterbaseCounts: {
+    showInterbaseCounts: {
         type: string;
         description: string;
         defaultValue: boolean;
     };
-    drawIndicators: {
+    showInterbaseIndicators: {
         type: string;
         description: string;
         defaultValue: boolean;

package/dist/SNPCoverageRenderer/configSchema.js

@@ -13,17 +13,17 @@ const SNPCoverageRenderer = (0, configuration_1.ConfigurationSchema)('SNPCoverag
         description: 'the proportion of reads containing a insertion/clip indicator',
         defaultValue: 0.4,
     },
-    drawArcs: {
+    showArcs: {
         type: 'boolean',
         description: 'Draw sashimi-style arcs for intron features',
         defaultValue: true,
     },
-    drawInterbaseCounts: {
+    showInterbaseCounts: {
         type: 'boolean',
         description: 'draw count "upsidedown histogram" of the interbase events that don\'t contribute to the coverage count so are not drawn in the normal histogram',
         defaultValue: true,
     },
-    drawIndicators: {
+    showInterbaseIndicators: {
         type: 'boolean',
         description: 'draw a triangular indicator where an event has been detected',
         defaultValue: true,

package/dist/SNPCoverageRenderer/makeImage.d.ts

@@ -0,0 +1,2 @@
+import type { RenderArgsDeserializedWithFeatures } from './types';
+export declare function makeImage(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): Promise<void>;

package/dist/SNPCoverageRenderer/makeImage.js

@@ -0,0 +1,270 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.makeImage = makeImage;
+const configuration_1 = require("@jbrowse/core/configuration");
+const ui_1 = require("@jbrowse/core/ui");
+const util_1 = require("@jbrowse/core/util");
+const stopToken_1 = require("@jbrowse/core/util/stopToken");
+const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
+const util_2 = require("../shared/util");
+const INTERBASE_INDICATOR_WIDTH = 7;
+const INTERBASE_INDICATOR_HEIGHT = 4.5;
+const MINIMUM_INTERBASE_INDICATOR_READ_DEPTH = 7;
+const complementBase = {
+    C: 'G',
+    G: 'C',
+    A: 'T',
+    T: 'A',
+};
+const fudgeFactor = 0.6;
+async function makeImage(ctx, props) {
+    var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k;
+    const { features, regions, bpPerPx, colorBy, displayCrossHatches, visibleModifications = {}, scaleOpts, height: unadjustedHeight, theme: configTheme, config: cfg, ticks, stopToken, } = props;
+    const theme = (0, ui_1.createJBrowseTheme)(configTheme);
+    const region = regions[0];
+    const width = (region.end - region.start) / bpPerPx;
+    const offset = plugin_wiggle_1.YSCALEBAR_LABEL_OFFSET;
+    const height = unadjustedHeight - offset * 2;
+    const opts = { ...scaleOpts, range: [0, height] };
+    const viewScale = (0, plugin_wiggle_1.getScale)(opts);
+    const indicatorViewScale = (0, plugin_wiggle_1.getScale)({
+        ...opts,
+        range: [0, height / 2],
+        scaleType: 'linear',
+    });
+    const originY = (0, plugin_wiggle_1.getOrigin)(scaleOpts.scaleType);
+    const originLinear = (0, plugin_wiggle_1.getOrigin)('linear');
+    const indicatorThreshold = (0, configuration_1.readConfObject)(cfg, 'indicatorThreshold');
+    const showInterbaseCounts = (0, configuration_1.readConfObject)(cfg, 'showInterbaseCounts');
+    const showArcs = (0, configuration_1.readConfObject)(cfg, 'showArcs');
+    const showInterbaseIndicators = (0, configuration_1.readConfObject)(cfg, 'showInterbaseIndicators');
+    const toY = (n) => height - (viewScale(n) || 0) + offset;
+    const toHeight = (n) => toY(originY) - toY(n);
+    const toY2 = (n) => height - (indicatorViewScale(n) || 0) + offset;
+    const toHeight2 = (n) => toY2(originLinear) - toY2(n);
+    const { bases } = theme.palette;
+    const colorForBase = {
+        A: bases.A.main,
+        C: bases.C.main,
+        G: bases.G.main,
+        T: bases.T.main,
+        insertion: 'purple',
+        softclip: 'blue',
+        hardclip: 'red',
+        total: (0, configuration_1.readConfObject)(cfg, 'color'),
+        mod_NONE: 'blue',
+        cpg_meth: 'red',
+        cpg_unmeth: 'blue',
+    };
+    const feats = [...features.values()];
+    ctx.fillStyle = colorForBase.total;
+    let start = performance.now();
+    for (const feature of feats) {
+        if (feature.get('type') === 'skip') {
+            continue;
+        }
+        const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
+        const w = rightPx - leftPx + fudgeFactor;
+        const score = feature.get('score');
+        ctx.fillRect(leftPx, toY(score), w, toHeight(score));
+        if (performance.now() - start > 400) {
+            (0, stopToken_1.checkStopToken)(stopToken);
+            start = performance.now();
+        }
+    }
+    let prevTotal = 0;
+    const extraHorizontallyFlippedOffset = region.reversed ? 1 / bpPerPx : 0;
+    const drawingModifications = colorBy.type === 'modifications';
+    const drawingMethylation = colorBy.type === 'methylation';
+    const isolatedModification = (_a = colorBy.modifications) === null || _a === void 0 ? void 0 : _a.isolatedModification;
+    start = performance.now();
+    for (const feature of feats) {
+        const now = performance.now();
+        if (now - start > 400) {
+            (0, stopToken_1.checkStopToken)(stopToken);
+        }
+        if (feature.get('type') === 'skip') {
+            continue;
+        }
+        const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
+        const snpinfo = feature.get('snpinfo');
+        const w = Math.max(rightPx - leftPx, 1);
+        const score0 = feature.get('score');
+        if (drawingModifications) {
+            let curr = 0;
+            const refbase = (_b = snpinfo.refbase) === null || _b === void 0 ? void 0 : _b.toUpperCase();
+            const { nonmods, mods, snps, ref } = snpinfo;
+            for (const m of Object.keys(nonmods).sort().reverse()) {
+                const mod = visibleModifications[m.replace('nonmod_', '')] ||
+                    visibleModifications[m.replace('mod_', '')];
+                if (!mod) {
+                    console.warn(`${m} not known yet`);
+                    continue;
+                }
+                if (isolatedModification && mod.type !== isolatedModification) {
+                    continue;
+                }
+                const cmp = complementBase[mod.base];
+                const detectable = mod.base === 'N'
+                    ? score0
+                    : (((_c = snps[mod.base]) === null || _c === void 0 ? void 0 : _c.entryDepth) || 0) +
+                        (((_d = snps[cmp]) === null || _d === void 0 ? void 0 : _d.entryDepth) || 0) +
+                        (refbase === mod.base ? ref['1'] : 0) +
+                        (refbase === cmp ? ref['-1'] : 0);
+                const modifiable = mod.base === 'N'
+                    ? score0
+                    : (((_e = snps[mod.base]) === null || _e === void 0 ? void 0 : _e.entryDepth) || 0) +
+                        (((_f = snps[cmp]) === null || _f === void 0 ? void 0 : _f.entryDepth) || 0) +
+                        (refbase === mod.base ? ref.entryDepth : 0) +
+                        (refbase === cmp ? ref.entryDepth : 0);
+                const { entryDepth, avgProbability = 0 } = snpinfo.nonmods[m];
+                const modFraction = (modifiable / score0) * (entryDepth / detectable);
+                const nonModColor = 'blue';
+                const c = (0, util_2.alphaColor)(nonModColor, avgProbability);
+                const height = toHeight(score0);
+                const bottom = toY(score0) + height;
+                ctx.fillStyle = c;
+                ctx.fillRect(Math.round(leftPx), bottom - (curr + modFraction * height), w, modFraction * height);
+                curr += modFraction * height;
+            }
+            for (const m of Object.keys(mods).sort().reverse()) {
+                const mod = visibleModifications[m.replace('mod_', '')];
+                if (!mod) {
+                    console.warn(`${m} not known yet`);
+                    continue;
+                }
+                if (isolatedModification && mod.type !== isolatedModification) {
+                    continue;
+                }
+                const cmp = complementBase[mod.base];
+                const detectable = mod.base === 'N'
+                    ? score0
+                    : (((_g = snps[mod.base]) === null || _g === void 0 ? void 0 : _g.entryDepth) || 0) +
+                        (((_h = snps[cmp]) === null || _h === void 0 ? void 0 : _h.entryDepth) || 0) +
+                        (refbase === mod.base ? ref['1'] : 0) +
+                        (refbase === cmp ? ref['-1'] : 0);
+                const modifiable = mod.base === 'N'
+                    ? score0
+                    : (((_j = snps[mod.base]) === null || _j === void 0 ? void 0 : _j.entryDepth) || 0) +
+                        (((_k = snps[cmp]) === null || _k === void 0 ? void 0 : _k.entryDepth) || 0) +
+                        (refbase === mod.base ? ref.entryDepth : 0) +
+                        (refbase === cmp ? ref.entryDepth : 0);
+                const { entryDepth, avgProbability = 0 } = mods[m];
+                const modFraction = (modifiable / score0) * (entryDepth / detectable);
+                const baseColor = mod.color || 'black';
+                const c = (0, util_2.alphaColor)(baseColor, avgProbability);
+                const height = toHeight(score0);
+                const bottom = toY(score0) + height;
+                ctx.fillStyle = c;
+                ctx.fillRect(Math.round(leftPx), bottom - (curr + modFraction * height), w, modFraction * height);
+                curr += modFraction * height;
+            }
+        }
+        else if (drawingMethylation) {
+            const { depth, nonmods, mods } = snpinfo;
+            let curr = 0;
+            for (const base of Object.keys(mods).sort().reverse()) {
+                const { entryDepth } = mods[base];
+                const height = toHeight(score0);
+                const bottom = toY(score0) + height;
+                ctx.fillStyle = colorForBase[base] || 'black';
+                ctx.fillRect(Math.round(leftPx), bottom - ((entryDepth + curr) / depth) * height, w, (entryDepth / depth) * height);
+                curr += entryDepth;
+            }
+            for (const base of Object.keys(nonmods).sort().reverse()) {
+                const { entryDepth } = nonmods[base];
+                const height = toHeight(score0);
+                const bottom = toY(score0) + height;
+                ctx.fillStyle = colorForBase[base] || 'black';
+                ctx.fillRect(Math.round(leftPx), bottom - ((entryDepth + curr) / depth) * height, w, (entryDepth / depth) * height);
+                curr += entryDepth;
+            }
+        }
+        else {
+            const { depth, snps } = snpinfo;
+            let curr = 0;
+            for (const base of Object.keys(snps).sort().reverse()) {
+                const { entryDepth } = snps[base];
+                const height = toHeight(score0);
+                const bottom = toY(score0) + height;
+                ctx.fillStyle = colorForBase[base] || 'black';
+                ctx.fillRect(Math.round(leftPx), bottom - ((entryDepth + curr) / depth) * height, w, (entryDepth / depth) * height);
+                curr += entryDepth;
+            }
+        }
+        const interbaseEvents = Object.keys(snpinfo.noncov);
+        if (showInterbaseCounts) {
+            let curr = 0;
+            for (const base of interbaseEvents) {
+                const { entryDepth } = snpinfo.noncov[base];
+                const r = 0.6;
+                ctx.fillStyle = colorForBase[base];
+                ctx.fillRect(leftPx - r + extraHorizontallyFlippedOffset, INTERBASE_INDICATOR_HEIGHT + toHeight2(curr), r * 2, toHeight2(entryDepth));
+                curr += entryDepth;
+            }
+        }
+        if (showInterbaseIndicators) {
+            let accum = 0;
+            let max = 0;
+            let maxBase = '';
+            for (const base of interbaseEvents) {
+                const { entryDepth } = snpinfo.noncov[base];
+                accum += entryDepth;
+                if (entryDepth > max) {
+                    max = entryDepth;
+                    maxBase = base;
+                }
+            }
+            const indicatorComparatorScore = Math.max(score0, prevTotal);
+            if (accum > indicatorComparatorScore * indicatorThreshold &&
+                indicatorComparatorScore > MINIMUM_INTERBASE_INDICATOR_READ_DEPTH) {
+                ctx.fillStyle = colorForBase[maxBase];
+                ctx.beginPath();
+                const l = leftPx + extraHorizontallyFlippedOffset;
+                ctx.moveTo(l - INTERBASE_INDICATOR_WIDTH / 2, 0);
+                ctx.lineTo(l + INTERBASE_INDICATOR_WIDTH / 2, 0);
+                ctx.lineTo(l, INTERBASE_INDICATOR_HEIGHT);
+                ctx.fill();
+            }
+        }
+        prevTotal = score0;
+    }
+    if (showArcs) {
+        for (const f of feats) {
+            if (f.get('type') !== 'skip') {
+                continue;
+            }
+            const s = f.get('start');
+            const e = f.get('end');
+            const [left, right] = (0, util_1.bpSpanPx)(s, e, region, bpPerPx);
+            ctx.beginPath();
+            const effectiveStrand = f.get('effectiveStrand');
+            const pos = 'rgba(255,200,200,0.7)';
+            const neg = 'rgba(200,200,255,0.7)';
+            const neutral = 'rgba(200,200,200,0.7)';
+            if (effectiveStrand === 1) {
+                ctx.strokeStyle = pos;
+            }
+            else if (effectiveStrand === -1) {
+                ctx.strokeStyle = neg;
+            }
+            else {
+                ctx.strokeStyle = neutral;
+            }
+            ctx.lineWidth = Math.log(f.get('score') + 1);
+            ctx.moveTo(left, height - offset * 2);
+            ctx.bezierCurveTo(left, 0, right, 0, right, height - offset * 2);
+            ctx.stroke();
+        }
+    }
+    if (displayCrossHatches) {
+        ctx.lineWidth = 1;
+        ctx.strokeStyle = 'rgba(140,140,140,0.8)';
+        for (const tick of ticks.values) {
+            ctx.beginPath();
+            ctx.moveTo(0, Math.round(toY(tick)));
+            ctx.lineTo(width, Math.round(toY(tick)));
+            ctx.stroke();
+        }
+    }
+}

package/dist/SNPCoverageRenderer/types.d.ts

@@ -0,0 +1,19 @@
+import type { ColorBy, ModificationTypeWithColor } from '../shared/types';
+import type { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+import type { Feature } from '@jbrowse/core/util';
+import type { ScaleOpts } 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;
+    visibleModifications?: Record<string, ModificationTypeWithColor>;
+    colorBy: ColorBy;
+}

package/dist/SNPCoverageRenderer/types.js

@@ -0,0 +1,2 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });

package/dist/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+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 };
 };

package/dist/shared/components/BaseDisplayComponent.d.ts

@@ -1,8 +1,7 @@
-import React from 'react';
 import type { LinearReadArcsDisplayModel } from '../../LinearReadArcsDisplay/model';
 import type { LinearReadCloudDisplayModel } from '../../LinearReadCloudDisplay/model';
 declare const BaseDisplayComponent: ({ model, children, }: {
     model: LinearReadArcsDisplayModel | LinearReadCloudDisplayModel;
     children?: React.ReactNode;
-}) => React.JSX.Element | null;
+}) => import("react/jsx-runtime").JSX.Element | null;
 export default BaseDisplayComponent;

package/dist/shared/components/BaseDisplayComponent.js

@@ -1,9 +1,6 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importDefault(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
 const ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("@jbrowse/core/util");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
@@ -25,27 +22,23 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
 }));
 const BlockError = (0, mobx_react_1.observer)(function ({ model, }) {
     const { error } = model;
-    return (react_1.default.createElement(plugin_linear_genome_view_1.BlockMsg, { message: `${error}`, severity: "error", action: react_1.default.createElement(material_1.Tooltip, { title: "Reload" },
-            react_1.default.createElement(material_1.Button, { "data-testid": "reload_button", onClick: () => {
+    return ((0, jsx_runtime_1.jsx)(plugin_linear_genome_view_1.BlockMsg, { message: `${error}`, severity: "error", action: (0, jsx_runtime_1.jsx)(material_1.Tooltip, { title: "Reload", children: (0, jsx_runtime_1.jsx)(material_1.Button, { "data-testid": "reload_button", onClick: () => {
                     model.reload();
-                } }, "Reload")) }));
+                }, children: "Reload" }) }) }));
 });
 const BaseDisplayComponent = (0, mobx_react_1.observer)(function ({ model, children, }) {
     const { error, regionTooLarge } = model;
-    return error ? (react_1.default.createElement(BlockError, { model: model })) : regionTooLarge ? (model.regionCannotBeRendered()) : (react_1.default.createElement(DataDisplay, { model: model }, children));
+    return error ? ((0, jsx_runtime_1.jsx)(BlockError, { model: model })) : regionTooLarge ? (model.regionCannotBeRendered()) : ((0, jsx_runtime_1.jsx)(DataDisplay, { model: model, children: children }));
 });
 const DataDisplay = (0, mobx_react_1.observer)(function ({ model, children, }) {
     const { drawn, loading } = model;
     const view = (0, util_1.getContainingView)(model);
     const left = (model.lastDrawnOffsetPx || 0) - view.offsetPx;
-    return (react_1.default.createElement("div", { "data-testid": `drawn-${drawn}` },
-        react_1.default.createElement("div", { style: { position: 'absolute', left } }, children),
-        left !== 0 || loading ? react_1.default.createElement(LoadingBar, { model: model }) : null));
+    return ((0, jsx_runtime_1.jsxs)("div", { "data-testid": `drawn-${drawn}`, children: [(0, jsx_runtime_1.jsx)("div", { style: { position: 'absolute', left }, children: children }), left !== 0 || loading ? (0, jsx_runtime_1.jsx)(LoadingBar, { model: model }) : null] }));
 });
 const LoadingBar = (0, mobx_react_1.observer)(function ({ model, }) {
     const { classes } = useStyles();
     const { message } = model;
-    return (react_1.default.createElement("div", { className: classes.loading },
-        react_1.default.createElement(ui_1.LoadingEllipses, { message: message })));
+    return ((0, jsx_runtime_1.jsx)("div", { className: classes.loading, children: (0, jsx_runtime_1.jsx)(ui_1.LoadingEllipses, { message: message }) }));
 });
 exports.default = BaseDisplayComponent;

package/dist/shared/components/FilterByTagDialog.d.ts

@@ -1,4 +1,3 @@
-import React from 'react';
 import type { FilterBy } from '../types';
 declare const FilterByTagDialog: (props: {
     model: {
@@ -6,5 +5,5 @@ declare const FilterByTagDialog: (props: {
         setFilterBy: (arg: FilterBy) => void;
     };
     handleClose: () => void;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default FilterByTagDialog;

package/dist/shared/components/FilterByTagDialog.js

@@ -1,29 +1,7 @@
 "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 (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importStar(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const ui_1 = require("@jbrowse/core/ui");
 const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
@@ -53,24 +31,20 @@ const flagNames = [
 ];
 function Bitmask(props) {
     const { flag = 0, setFlag } = props;
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement(material_1.TextField, { type: "number", value: flag, onChange: event => {
-                setFlag(+event.target.value);
-            } }),
-        flagNames.map((name, index) => {
-            const val = flag & (1 << index);
-            const key = `${name}_${val}`;
-            return (react_1.default.createElement("div", { key: key },
-                react_1.default.createElement("input", { type: "checkbox", checked: Boolean(val), onChange: event => {
-                        if (event.target.checked) {
-                            setFlag(flag | (1 << index));
-                        }
-                        else {
-                            setFlag(flag & ~(1 << index));
-                        }
-                    } }),
-                react_1.default.createElement("label", { htmlFor: key }, name)));
-        })));
+    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(material_1.TextField, { type: "number", value: flag, onChange: event => {
+                    setFlag(+event.target.value);
+                } }), flagNames.map((name, index) => {
+                const val = flag & (1 << index);
+                const key = `${name}_${val}`;
+                return ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)("input", { type: "checkbox", checked: Boolean(val), onChange: event => {
+                                if (event.target.checked) {
+                                    setFlag(flag | (1 << index));
+                                }
+                                else {
+                                    setFlag(flag & ~(1 << index));
+                                }
+                            } }), (0, jsx_runtime_1.jsx)("label", { htmlFor: key, children: name })] }, key));
+            })] }));
 }
 const FilterByTagDialog = (0, mobx_react_1.observer)(function (props) {
     var _a, _b;
@@ -84,55 +58,31 @@ const FilterByTagDialog = (0, mobx_react_1.observer)(function (props) {
     const [readName, setReadName] = (0, react_1.useState)(filterBy.readName || '');
     const validTag = /^[A-Za-z][A-Za-z0-9]$/.exec(tag);
     const site = 'https://broadinstitute.github.io/picard/explain-flags.html';
-    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Filter options" },
-        react_1.default.createElement(material_1.DialogContent, null,
-            react_1.default.createElement(material_1.Typography, null,
-                "Set filter bitmask options. Refer to ",
-                react_1.default.createElement(material_1.Link, { href: site }, site),
-                ' ',
-                "for details"),
-            react_1.default.createElement(material_1.Paper, { className: classes.paper, variant: "outlined" },
-                react_1.default.createElement("div", { style: { display: 'flex' } },
-                    react_1.default.createElement("div", null,
-                        react_1.default.createElement(material_1.Typography, null, "Read must have ALL these flags"),
-                        react_1.default.createElement(Bitmask, { flag: flagInclude, setFlag: setFlagInclude })),
-                    react_1.default.createElement("div", null,
-                        react_1.default.createElement(material_1.Typography, null, "Read must have NONE of these flags"),
-                        react_1.default.createElement(Bitmask, { flag: flagExclude, setFlag: setFlagExclude })))),
-            react_1.default.createElement(material_1.Paper, { className: classes.paper, variant: "outlined" },
-                react_1.default.createElement(material_1.Typography, null, "Filter by tag name and value. Use * in the value field to get all reads containing any value for that tag. Example: filter tag name SA with value * to get all split/supplementary reads. Other examples include HP for haplotype, or RG for read group"),
-                react_1.default.createElement(material_1.TextField, { className: classes.field, value: tag, onChange: event => {
-                        setTag(event.target.value);
-                    }, placeholder: "Enter tag name", error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '', slotProps: {
-                        htmlInput: {
-                            maxLength: 2,
-                        },
-                    } }),
-                react_1.default.createElement(material_1.TextField, { className: classes.field, value: tagValue, onChange: event => {
-                        setTagValue(event.target.value);
-                    }, placeholder: "Enter tag value" })),
-            react_1.default.createElement(material_1.Paper, { className: classes.paper, variant: "outlined" },
-                react_1.default.createElement(material_1.Typography, null, "Filter by read name"),
-                react_1.default.createElement(material_1.TextField, { className: classes.field, value: readName, onChange: event => {
-                        setReadName(event.target.value);
-                    }, placeholder: "Enter read name" })),
-            react_1.default.createElement(material_1.DialogActions, null,
-                react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", autoFocus: true, type: "submit", onClick: () => {
-                        model.setFilterBy({
-                            flagInclude,
-                            flagExclude,
-                            readName,
-                            tagFilter: tag !== ''
-                                ? {
-                                    tag,
-                                    value: tagValue,
-                                }
-                                : undefined,
-                        });
-                        handleClose();
-                    } }, "Submit"),
-                react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
-                        handleClose();
-                    } }, "Cancel")))));
+    return ((0, jsx_runtime_1.jsx)(ui_1.Dialog, { open: true, onClose: handleClose, title: "Filter options", children: (0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [(0, jsx_runtime_1.jsxs)(material_1.Typography, { children: ["Set filter bitmask options. Refer to ", (0, jsx_runtime_1.jsx)(material_1.Link, { href: site, children: site }), ' ', "for details"] }), (0, jsx_runtime_1.jsx)(material_1.Paper, { className: classes.paper, variant: "outlined", children: (0, jsx_runtime_1.jsxs)("div", { style: { display: 'flex' }, children: [(0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Read must have ALL these flags" }), (0, jsx_runtime_1.jsx)(Bitmask, { flag: flagInclude, setFlag: setFlagInclude })] }), (0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Read must have NONE of these flags" }), (0, jsx_runtime_1.jsx)(Bitmask, { flag: flagExclude, setFlag: setFlagExclude })] })] }) }), (0, jsx_runtime_1.jsxs)(material_1.Paper, { className: classes.paper, variant: "outlined", children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Filter by tag name and value. Use * in the value field to get all reads containing any value for that tag. Example: filter tag name SA with value * to get all split/supplementary reads. Other examples include HP for haplotype, or RG for read group" }), (0, jsx_runtime_1.jsx)(material_1.TextField, { className: classes.field, value: tag, onChange: event => {
+                                setTag(event.target.value);
+                            }, placeholder: "Enter tag name", error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '', slotProps: {
+                                htmlInput: {
+                                    maxLength: 2,
+                                },
+                            } }), (0, jsx_runtime_1.jsx)(material_1.TextField, { className: classes.field, value: tagValue, onChange: event => {
+                                setTagValue(event.target.value);
+                            }, placeholder: "Enter tag value" })] }), (0, jsx_runtime_1.jsxs)(material_1.Paper, { className: classes.paper, variant: "outlined", children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Filter by read name" }), (0, jsx_runtime_1.jsx)(material_1.TextField, { className: classes.field, value: readName, onChange: event => {
+                                setReadName(event.target.value);
+                            }, placeholder: "Enter read name" })] }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "primary", autoFocus: true, type: "submit", onClick: () => {
+                                model.setFilterBy({
+                                    flagInclude,
+                                    flagExclude,
+                                    readName,
+                                    tagFilter: tag !== ''
+                                        ? {
+                                            tag,
+                                            value: tagValue,
+                                        }
+                                        : undefined,
+                                });
+                                handleClose();
+                            }, children: "Submit" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
+                                handleClose();
+                            }, children: "Cancel" })] })] }) }));
 });
 exports.default = FilterByTagDialog;

package/dist/shared/renderSvgUtil.d.ts

@@ -1,7 +1,6 @@
-import React from 'react';
 export declare function renderSvg<T extends {
     id: string;
     height: number;
 }>(self: T, opts: {
     rasterizeLayers?: boolean;
-}, cb: (model: T, ctx: CanvasRenderingContext2D, width: number, height: number) => void): Promise<React.JSX.Element | undefined>;
+}, cb: (model: T, ctx: CanvasRenderingContext2D, width: number, height: number) => void): Promise<import("react/jsx-runtime").JSX.Element | undefined>;