@jbrowse/plugin-variants 2.13.1 → 2.14.0

package/esm/ChordVariantDisplay/models/stateModelFactory.js

@@ -40,7 +40,9 @@ const stateModelFactory = (configSchema) => {
                 radius: view.radiusPx,
                 blockDefinitions: self.blockDefinitions,
                 config: self.configuration.renderer,
-                onChordClick: (arg) => self.onChordClick(arg),
+                onChordClick: (arg) => {
+                    self.onChordClick(arg);
+                },
             };
         },
     }));

package/esm/LinearVariantDisplay/model.d.ts

@@ -139,7 +139,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function;
+        onHorizontalScroll?: () => void;
         blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: import("react").FC<{

package/esm/StructuralVariantChordRenderer/Chord.js

@@ -29,6 +29,7 @@ const Chord = observer(function Chord({ feature, blocksForRefs, radius, config,
     let endBlock;
     const alt = (_a = feature.get('ALT')) === null || _a === void 0 ? void 0 : _a[0];
     const bnd = alt && parseBreakend(alt);
+    const startPos = feature.get('start');
     if (bnd) {
         // VCF BND
         const matePosition = bnd.MatePosition.split(':');
@@ -39,7 +40,7 @@ const Chord = observer(function Chord({ feature, blocksForRefs, radius, config,
         // VCF TRA
         const chr2 = (_c = (_b = feature.get('INFO')) === null || _b === void 0 ? void 0 : _b.CHR2) === null || _c === void 0 ? void 0 : _c[0];
         const end = (_e = (_d = feature.get('INFO')) === null || _d === void 0 ? void 0 : _d.END) === null || _e === void 0 ? void 0 : _e[0];
-        endPosition = parseInt(end, 10);
+        endPosition = Number.parseInt(end, 10);
         endBlock = blocksForRefs[chr2];
     }
     else if (svType === 'mate') {
@@ -49,8 +50,11 @@ const Chord = observer(function Chord({ feature, blocksForRefs, radius, config,
         endPosition = mate.start;
         endBlock = blocksForRefs[chr2];
     }
+    else {
+        console.warn('unknown sv type', svType);
+        endPosition = startPos + 1;
+    }
     if (endBlock) {
-        const startPos = feature.get('start');
         const startRadians = bpToRadians(startBlock, startPos);
         const endRadians = bpToRadians(endBlock, endPosition);
         const startXY = polarToCartesian(radius, startRadians);
@@ -63,9 +67,7 @@ const Chord = observer(function Chord({ feature, blocksForRefs, radius, config,
             feature,
         });
         return (React.createElement("path", { "data-testid": `chord-${feature.id()}`, cursor: "crosshair", fill: "none", d: ['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' '), ...getStrokeProps(hovered ? hoverStrokeColor : strokeColor), strokeWidth: hovered ? 3 : 1, onClick: evt => {
-                if (endBlock && startBlock) {
-                    onClick(feature, startBlock.region, endBlock.region, evt);
-                }
+                onClick(feature, startBlock.region, endBlock.region, evt);
             }, onMouseOver: () => {
                 if (!selected) {
                     setHovered(true);

package/esm/StructuralVariantChordRenderer/ReactComponent.d.ts

@@ -2,11 +2,11 @@ import React from 'react';
 import { Feature } from '@jbrowse/core/util';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import { Block, AnyRegion } from './Chord';
-declare const StructuralVariantChordsReactComponent: ({ features, config, displayModel, blockDefinitions, radius, bezierRadius, displayModel: { selectedFeatureId }, onChordClick, }: {
+declare const StructuralVariantChordsReactComponent: ({ features, config, displayModel, blockDefinitions, radius, bezierRadius, onChordClick, }: {
     features: Map<string, Feature>;
     radius: number;
     config: AnyConfigurationModel;
-    displayModel: {
+    displayModel?: {
         id: string;
         selectedFeatureId: string;
     };

package/esm/StructuralVariantChordRenderer/ReactComponent.js

@@ -2,7 +2,8 @@ import React, { useMemo } from 'react';
 import { observer } from 'mobx-react';
 // locals
 import Chord from './Chord';
-const StructuralVariantChordsReactComponent = observer(function ({ features, config, displayModel, blockDefinitions, radius, bezierRadius, displayModel: { selectedFeatureId }, onChordClick, }) {
+const StructuralVariantChordsReactComponent = observer(function ({ features, config, displayModel, blockDefinitions, radius, bezierRadius, onChordClick, }) {
+    const { id, selectedFeatureId } = displayModel || {};
     // make a map of refName -> blockDefinition
     const blocksForRefsMemo = useMemo(() => {
         const blocksForRefs = {};
@@ -16,10 +17,6 @@ const StructuralVariantChordsReactComponent = observer(function ({ features, con
         }
         return blocksForRefs;
     }, [blockDefinitions]);
-    return (React.createElement("g", { id: `chords-${typeof jest !== 'undefined' ? 'test' : displayModel.id}`, "data-testid": "structuralVariantChordRenderer" }, [...features.values()].map(feature => {
-        const id = feature.id();
-        const selected = String(selectedFeatureId) === String(id);
-        return (React.createElement(Chord, { key: id, feature: feature, config: config, radius: radius, bezierRadius: bezierRadius, blocksForRefs: blocksForRefsMemo, selected: selected, onClick: onChordClick }));
-    })));
+    return (React.createElement("g", { "data-testid": "structuralVariantChordRenderer" }, [...features.values()].map(feature => (React.createElement(Chord, { key: feature.id(), feature: feature, config: config, radius: radius, bezierRadius: bezierRadius, blocksForRefs: blocksForRefsMemo, selected: String(selectedFeatureId) === String(id), onClick: onChordClick })))));
 });
 export default StructuralVariantChordsReactComponent;

package/esm/VariantFeatureWidget/AnnotGrid.js

@@ -6,6 +6,8 @@ export default function VariantAnnotPanel({ rows, columns, }) {
     const [checked, setChecked] = useState(false);
     const widths = columns.map(e => measureGridWidth(rows.map(r => r[e.field])));
     return rows.length ? (React.createElement("div", null,
-        React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: checked, onChange: event => setChecked(event.target.checked) }), label: React.createElement(Typography, { variant: "body2" }, "Show options") }),
+        React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: checked, onChange: event => {
+                    setChecked(event.target.checked);
+                } }), label: React.createElement(Typography, { variant: "body2" }, "Show options") }),
         React.createElement(DataGrid, { rowHeight: 25, rows: rows, columns: columns.map((c, i) => ({ ...c, width: widths[i] })), slots: { toolbar: checked ? GridToolbar : null } }))) : null;
 }

package/esm/VariantFeatureWidget/BreakendOptionDialog.js

@@ -25,8 +25,12 @@ const BreakendOptionDialog = observer(function ({ model, handleClose, feature, v
     const [mirror, setMirror] = useState(true);
     return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Breakpoint split view options" },
         React.createElement(DialogContent, null,
-            React.createElement(Checkbox2, { checked: copyTracks, onChange: event => setCopyTracks(event.target.checked), label: "Copy tracks into the new view" }),
-            React.createElement(Checkbox2, { checked: mirror, onChange: event => setMirror(event.target.checked), label: "Mirror tracks vertically in vertically stacked view" })),
+            React.createElement(Checkbox2, { checked: copyTracks, onChange: event => {
+                    setCopyTracks(event.target.checked);
+                }, label: "Copy tracks into the new view" }),
+            React.createElement(Checkbox2, { checked: mirror, onChange: event => {
+                    setMirror(event.target.checked);
+                }, label: "Mirror tracks vertically in vertically stacked view" })),
         React.createElement(DialogActions, null,
             React.createElement(Button, { onClick: () => {
                     const { view } = model;
@@ -59,6 +63,8 @@ const BreakendOptionDialog = observer(function ({ model, handleClose, feature, v
                     }
                     handleClose();
                 }, variant: "contained", color: "primary", autoFocus: true }, "OK"),
-            React.createElement(Button, { onClick: () => handleClose(), color: "secondary", variant: "contained" }, "Cancel"))));
+            React.createElement(Button, { onClick: () => {
+                    handleClose();
+                }, color: "secondary", variant: "contained" }, "Cancel"))));
 });
 export default BreakendOptionDialog;

package/esm/VariantFeatureWidget/BreakendPanel.js

@@ -8,7 +8,9 @@ function LocStringList({ locStrings, model, }) {
     const session = getSession(model);
     return (React.createElement("div", null,
         React.createElement(Typography, null, "Link to linear view of breakend endpoints"),
-        React.createElement("ul", null, locStrings.map((locString, index) => (React.createElement("li", { key: `${locString}-${index}` },
+        React.createElement("ul", null, locStrings.map((locString, index) => (
+        /* biome-ignore lint/suspicious/noArrayIndexKey: */
+        React.createElement("li", { key: `${locString}-${index}` },
             React.createElement(Link, { href: "#", onClick: event => {
                     var _a;
                     event.preventDefault();
@@ -32,7 +34,7 @@ function LaunchBreakpointSplitViewPanel({ locStrings, model, feature, viewType,
     const simpleFeature = new SimpleFeature(feature);
     return (React.createElement("div", null,
         React.createElement(Typography, null, "Launch split views with breakend source and target"),
-        React.createElement("ul", null, locStrings.map(locString => (React.createElement("li", { key: `${JSON.stringify(locString)}` },
+        React.createElement("ul", null, locStrings.map(locString => (React.createElement("li", { key: JSON.stringify(locString) },
             React.createElement(Link, { href: "#", onClick: event => {
                     event.preventDefault();
                     session.queueDialog(handleClose => [

package/esm/VariantFeatureWidget/VariantAnnotationTable.js

@@ -6,5 +6,5 @@ export default function VariantAnnotationTable({ data, fields, title, }) {
         React.createElement(AnnotGrid, { rows: data.map((elt, id) => ({
                 id,
                 ...Object.fromEntries(elt.split('|').map((e, i) => [fields[i], e])),
-            })) || [], columns: fields.map(c => ({ field: c })) }))) : null;
+            })), columns: fields.map(c => ({ field: c })) }))) : null;
 }

package/esm/VariantFeatureWidget/VariantFeatureWidget.js

@@ -9,17 +9,17 @@ import BreakendPanel from './BreakendPanel';
 import VariantAnnotationTable from './VariantAnnotationTable';
 import { variantFieldDescriptions } from './variantFieldDescriptions';
 function AnnPanel({ descriptions, feature, }) {
-    var _a, _b, _c, _d;
+    var _a, _b, _c, _d, _e;
     const annDesc = (_b = (_a = descriptions === null || descriptions === void 0 ? void 0 : descriptions.INFO) === null || _a === void 0 ? void 0 : _a.ANN) === null || _b === void 0 ? void 0 : _b.Description;
-    const annFields = ((_c = annDesc === null || annDesc === void 0 ? void 0 : annDesc.match(/.*Functional annotations:'(.*)'$/)) === null || _c === void 0 ? void 0 : _c[1].split('|')) || [];
-    const ann = ((_d = feature.INFO) === null || _d === void 0 ? void 0 : _d.ANN) || [];
+    const annFields = ((_d = (_c = annDesc === null || annDesc === void 0 ? void 0 : annDesc.match(/.*Functional annotations:'(.*)'$/)) === null || _c === void 0 ? void 0 : _c[1]) === null || _d === void 0 ? void 0 : _d.split('|')) || [];
+    const ann = ((_e = feature.INFO) === null || _e === void 0 ? void 0 : _e.ANN) || [];
     return (React.createElement(VariantAnnotationTable, { fields: annFields, data: ann, title: "Variant ANN field" }));
 }
 function CsqPanel({ descriptions, feature, }) {
-    var _a, _b, _c, _d;
+    var _a, _b, _c, _d, _e;
     const csqDescription = (_b = (_a = descriptions === null || descriptions === void 0 ? void 0 : descriptions.INFO) === null || _a === void 0 ? void 0 : _a.CSQ) === null || _b === void 0 ? void 0 : _b.Description;
-    const csqFields = ((_c = csqDescription === null || csqDescription === void 0 ? void 0 : csqDescription.match(/.*Format: (.*)/)) === null || _c === void 0 ? void 0 : _c[1].split('|')) || [];
-    const csq = ((_d = feature.INFO) === null || _d === void 0 ? void 0 : _d.CSQ) || [];
+    const csqFields = ((_d = (_c = csqDescription === null || csqDescription === void 0 ? void 0 : csqDescription.match(/.*Format: (.*)/)) === null || _c === void 0 ? void 0 : _c[1]) === null || _d === void 0 ? void 0 : _d.split('|')) || [];
+    const csq = ((_e = feature.INFO) === null || _e === void 0 ? void 0 : _e.CSQ) || [];
     return (React.createElement(VariantAnnotationTable, { fields: csqFields, data: csq, title: "Variant CSQ field" }));
 }
 const VariantFeatureWidget = observer(function (props) {

package/esm/VariantFeatureWidget/VariantSampleGrid.js

@@ -6,7 +6,9 @@ import { measureGridWidth } from '@jbrowse/core/util';
 function SampleFilters({ columns, filter, setFilter, }) {
     return (React.createElement(React.Fragment, null,
         React.createElement(Typography, null, "These filters can use a plain text search or regex style query, e.g. in the genotype field, entering 1 will query for all genotypes that include the first alternate allele e.g. 0|1 or 1|1, entering [1-9]\\d* will find any non-zero allele e.g. 0|2 or 2/33"),
-        columns.map(({ field }) => (React.createElement(TextField, { key: `filter-${field}`, placeholder: `Filter ${field}`, value: filter[field] || '', onChange: event => setFilter({ ...filter, [field]: event.target.value }) })))));
+        columns.map(({ field }) => (React.createElement(TextField, { key: `filter-${field}`, placeholder: `Filter ${field}`, value: filter[field] || '', onChange: event => {
+                setFilter({ ...filter, [field]: event.target.value });
+            } })))));
 }
 export default function VariantSamples(props) {
     var _a;
@@ -33,7 +35,7 @@ export default function VariantSamples(props) {
             ? filters.every(key => {
                 const currFilter = filter[key];
                 return currFilter
-                    ? row[key].match(new RegExp(currFilter, 'i'))
+                    ? new RegExp(currFilter, 'i').exec(row[key])
                     : true;
             })
             : true);
@@ -56,7 +58,9 @@ export default function VariantSamples(props) {
     // https://github.com/mui-org/material-ui-x/issues/1197
     return !preFilteredRows.length ? null : (React.createElement(BaseCard, { ...props, title: "Samples" },
         error ? React.createElement(Typography, { color: "error" }, `${error}`) : null,
-        React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: checked, onChange: event => setChecked(event.target.checked) }), label: React.createElement(Typography, { variant: "body2" }, "Show options") }),
+        React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: checked, onChange: event => {
+                    setChecked(event.target.checked);
+                } }), label: React.createElement(Typography, { variant: "body2" }, "Show options") }),
         checked ? (React.createElement(SampleFilters, { setFilter: setFilter, columns: columns, filter: filter })) : null,
         React.createElement(DataGrid, { autoHeight: true, rows: rows, hideFooter: rows.length < 100, columns: columns, disableRowSelectionOnClick: true, rowHeight: 25, columnHeaderHeight: 35, disableColumnMenu: true, slots: { toolbar: checked ? GridToolbar : null }, slotProps: {
                 toolbar: {

package/esm/VcfAdapter/VcfAdapter.d.ts

@@ -1,24 +1,28 @@
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { Region, Feature } from '@jbrowse/core/util';
 import IntervalTree from '@flatten-js/interval-tree';
-import VcfFeature from '../VcfFeature';
+type StatusCallback = (arg: string) => void;
 export default class VcfAdapter extends BaseFeatureDataAdapter {
-    static capabilities: string[];
-    protected vcfFeatures?: Promise<{
+    calculatedIntervalTreeMap: Record<string, IntervalTree>;
+    vcfFeatures?: Promise<{
         header: string;
-        intervalTree: Record<string, IntervalTree<VcfFeature>>;
+        intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree>;
     }>;
+    static capabilities: string[];
     getHeader(): Promise<string>;
     getMetadata(): Promise<any>;
-    setupP(): Promise<{
+    setupP(opts?: BaseOptions): Promise<{
         header: string;
-        intervalTree: Record<string, IntervalTree<VcfFeature>>;
+        intervalTreeMap: {
+            [k: string]: (sc?: (arg: string) => void) => IntervalTree<any>;
+        };
     }>;
     setup(): Promise<{
         header: string;
-        intervalTree: Record<string, IntervalTree<VcfFeature>>;
+        intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree>;
     }>;
     getRefNames(_?: BaseOptions): Promise<string[]>;
     getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     freeResources(): void;
 }
+export {};

package/esm/VcfAdapter/VcfAdapter.js

@@ -1,4 +1,5 @@
 import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { updateStatus, isGzip } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import IntervalTree from '@flatten-js/interval-tree';
@@ -6,66 +7,84 @@ import { unzip } from '@gmod/bgzf-filehandle';
 import VCF from '@gmod/vcf';
 // local
 import VcfFeature from '../VcfFeature';
-const readVcf = (f) => {
-    const header = [];
-    const rest = [];
-    f.split(/\n|\r\n|\r/)
-        .map(f => f.trim())
-        .filter(f => !!f)
-        .forEach(line => {
-        if (line.startsWith('#')) {
-            header.push(line);
-        }
-        else if (line) {
-            rest.push(line);
-        }
-    });
-    return { header: header.join('\n'), lines: rest };
-};
-function isGzip(buf) {
-    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
-}
 class VcfAdapter extends BaseFeatureDataAdapter {
+    constructor() {
+        super(...arguments);
+        this.calculatedIntervalTreeMap = {};
+    }
     async getHeader() {
         const { header } = await this.setup();
         return header;
     }
     async getMetadata() {
         const { header } = await this.setup();
-        const parser = new VCF({ header: header });
+        const parser = new VCF({ header });
         return parser.getMetadata();
     }
-    // converts lines into an interval tree
-    async setupP() {
-        const pm = this.pluginManager;
-        const buf = await openLocation(this.getConf('vcfLocation'), pm).readFile();
-        const buffer = isGzip(buf) ? await unzip(buf) : buf;
-        // 512MB  max chrome string length is 512MB
-        if (buffer.length > 536870888) {
-            throw new Error('Data exceeds maximum string length (512MB)');
-        }
-        const str = new TextDecoder().decode(buffer);
-        const { header, lines } = readVcf(str);
-        const intervalTree = {};
-        const parser = new VCF({ header });
-        let idx = 0;
-        for (const line of lines) {
-            const f = new VcfFeature({
-                variant: parser.parseLine(line),
-                parser,
-                id: `${this.id}-${idx++}`,
-            });
-            const key = f.get('refName');
-            if (!intervalTree[key]) {
-                intervalTree[key] = new IntervalTree();
+    async setupP(opts) {
+        const { statusCallback = () => { } } = opts || {};
+        const buf = (await openLocation(this.getConf('vcfLocation'), this.pluginManager).readFile(opts));
+        const buffer = isGzip(buf)
+            ? await updateStatus('Unzipping', statusCallback, () => unzip(buf))
+            : buf;
+        const headerLines = [];
+        const featureMap = {};
+        let blockStart = 0;
+        const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
+        let i = 0;
+        while (blockStart < buffer.length) {
+            const n = buffer.indexOf('\n', blockStart);
+            // could be a non-newline ended file, so slice to end of file if n===-1
+            const b = n === -1 ? buffer.slice(blockStart) : buffer.slice(blockStart, n);
+            const line = ((decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString()).trim();
+            if (line) {
+                if (line.startsWith('#')) {
+                    headerLines.push(line);
+                }
+                else {
+                    const ret = line.indexOf('\t');
+                    const refName = line.slice(0, ret);
+                    if (!featureMap[refName]) {
+                        featureMap[refName] = [];
+                    }
+                    featureMap[refName].push(line);
+                }
             }
-            intervalTree[key].insert([f.get('start'), f.get('end')], f);
+            if (i++ % 10000 === 0) {
+                statusCallback(`Loading ${Math.floor(blockStart / 1000000).toLocaleString('en-US')}/${Math.floor(buffer.length / 1000000).toLocaleString('en-US')} MB`);
+            }
+            blockStart = n + 1;
         }
-        return { header, intervalTree };
+        const header = headerLines.join('\n');
+        const parser = new VCF({ header });
+        const intervalTreeMap = Object.fromEntries(Object.entries(featureMap).map(([refName, lines]) => [
+            refName,
+            (sc) => {
+                if (!this.calculatedIntervalTreeMap[refName]) {
+                    sc === null || sc === void 0 ? void 0 : sc('Parsing VCF data');
+                    let idx = 0;
+                    const intervalTree = new IntervalTree();
+                    for (const line of lines) {
+                        const f = new VcfFeature({
+                            variant: parser.parseLine(line),
+                            parser,
+                            id: `${this.id}-${refName}-${idx++}`,
+                        });
+                        intervalTree.insert([f.get('start'), f.get('end')], f);
+                    }
+                    this.calculatedIntervalTreeMap[refName] = intervalTree;
+                }
+                return this.calculatedIntervalTreeMap[refName];
+            },
+        ]));
+        return {
+            header,
+            intervalTreeMap,
+        };
     }
     async setup() {
         if (!this.vcfFeatures) {
-            this.vcfFeatures = this.setupP().catch(e => {
+            this.vcfFeatures = this.setupP().catch((e) => {
                 this.vcfFeatures = undefined;
                 throw e;
             });
@@ -73,16 +92,16 @@ class VcfAdapter extends BaseFeatureDataAdapter {
         return this.vcfFeatures;
     }
     async getRefNames(_ = {}) {
-        const { intervalTree } = await this.setup();
-        return Object.keys(intervalTree);
+        const { intervalTreeMap } = await this.setup();
+        return Object.keys(intervalTreeMap);
     }
     getFeatures(region, opts = {}) {
         return ObservableCreate(async (observer) => {
             var _a;
             try {
                 const { start, end, refName } = region;
-                const { intervalTree } = await this.setup();
-                (_a = intervalTree[refName]) === null || _a === void 0 ? void 0 : _a.search([start, end]).forEach((f) => {
+                const { intervalTreeMap } = await this.setup();
+                (_a = intervalTreeMap[refName]) === null || _a === void 0 ? void 0 : _a.call(intervalTreeMap, opts.statusCallback).search([start, end]).forEach(f => {
                     observer.next(f);
                 });
                 observer.complete();

package/esm/VcfFeature/index.d.ts

@@ -36,7 +36,7 @@ export default class VCFFeature implements Feature {
         ALT: string[];
         CHROM: string;
         INFO: any;
-        ID: string[];
+        ID?: string[];
     }): FeatureData;
     toJSON(): any;
 }

package/esm/VcfFeature/index.js

@@ -1,14 +1,12 @@
 // locals
 import { getSOTermAndDescription } from './util';
 export default class VCFFeature {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     constructor(args) {
         this.variant = args.variant;
         this.parser = args.parser;
         this.data = this.dataFromVariant(this.variant);
         this._id = args.id;
     }
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     get(field) {
         var _a;
         return field === 'samples'
@@ -32,8 +30,8 @@ export default class VCFFeature {
         const { REF, ALT, POS, CHROM, INFO, ID } = variant;
         const start = POS - 1;
         const [type, description] = getSOTermAndDescription(REF, ALT, this.parser);
-        const isTRA = ALT === null || ALT === void 0 ? void 0 : ALT.some(f => f === '<TRA>');
-        const isSymbolic = ALT === null || ALT === void 0 ? void 0 : ALT.some(f => f.includes('<'));
+        const isTRA = ALT.includes('<TRA>');
+        const isSymbolic = ALT.some(f => f.includes('<'));
         return {
             refName: CHROM,
             start,
@@ -41,10 +39,9 @@ export default class VCFFeature {
             description,
             type,
             name: ID === null || ID === void 0 ? void 0 : ID.join(','),
-            aliases: ID && ID.length > 1 ? variant.ID.slice(1) : undefined,
+            aliases: ID && ID.length > 1 ? ID.slice(1) : undefined,
         };
     }
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     toJSON() {
         return {
             uniqueId: this._id,

package/esm/VcfFeature/util.d.ts

@@ -2,6 +2,6 @@ import VCF from '@gmod/vcf';
 /**
  * Get a sequence ontology (SO) term that describes the variant type
  */
-export declare function getSOTermAndDescription(ref: string, alt: string[], parser: VCF): string[];
+export declare function getSOTermAndDescription(ref: string, alt: string[] | undefined, parser: VCF): string[];
 export declare function getSOAndDescFromAltDefs(alt: string, parser: VCF): string[];
 export declare function getSOAndDescByExamination(ref: string, alt: string): string[];

package/esm/VcfFeature/util.js

@@ -35,10 +35,12 @@ export function getSOTermAndDescription(ref, alt, parser) {
     // Combine descriptions like ["SNV G -> A", "SNV G -> T"] to ["SNV G -> A,T"]
     if (descriptions.size > 1) {
         const descs = [...descriptions];
-        const prefixes = new Set(descs.map(desc => {
+        const prefixes = new Set(descs
+            .map(desc => {
             const prefix = desc.split('->');
             return prefix[1] ? prefix[0] : desc;
-        }));
+        })
+            .filter((f) => !!f));
         descriptions = new Set([...prefixes]
             .map(r => r.trim())
             .map(prefix => {
@@ -83,43 +85,43 @@ export function getSOAndDescByExamination(ref, alt) {
     if (bnd) {
         return ['breakend', alt];
     }
-    else if (ref.length === 1 && alt.length === 1) {
+    if (ref.length === 1 && alt.length === 1) {
         return ['SNV', makeDescriptionString('SNV', ref, alt)];
     }
-    else if (alt === '<INS>') {
+    if (alt === '<INS>') {
         return ['insertion', alt];
     }
-    else if (alt === '<DEL>') {
+    if (alt === '<DEL>') {
         return ['deletion', alt];
     }
-    else if (alt === '<INV>') {
+    if (alt === '<INV>') {
         return ['inversion', alt];
     }
-    else if (alt === '<TRA>') {
+    if (alt === '<TRA>') {
         return ['translocation', alt];
     }
-    else if (alt.includes('<')) {
+    if (alt.includes('<')) {
         return ['sv', alt];
     }
-    else if (ref.length === alt.length) {
+    if (ref.length === alt.length) {
         return ref.split('').reverse().join('') === alt
             ? ['inversion', makeDescriptionString('inversion', ref, alt)]
             : ['substitution', makeDescriptionString('substitution', ref, alt)];
     }
-    else if (ref.length <= alt.length) {
+    if (ref.length <= alt.length) {
         const len = alt.length - ref.length;
         const lena = len.toLocaleString('en-US');
         return [
             'insertion',
-            len > 5 ? lena + 'bp INS' : makeDescriptionString('insertion', ref, alt),
+            len > 5 ? `${lena}bp INS` : makeDescriptionString('insertion', ref, alt),
         ];
     }
-    else if (ref.length > alt.length) {
+    if (ref.length > alt.length) {
         const len = ref.length - alt.length;
         const lena = len.toLocaleString('en-US');
         return [
             'deletion',
-            len > 5 ? lena + 'bp DEL' : makeDescriptionString('deletion', ref, alt),
+            len > 5 ? `${lena}bp DEL` : makeDescriptionString('deletion', ref, alt),
         ];
     }
     return ['indel', makeDescriptionString('indel', ref, alt)];

package/esm/VcfTabixAdapter/VcfTabixAdapter.js

@@ -28,7 +28,7 @@ export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
     }
     async configure() {
         if (!this.configured) {
-            this.configured = this.configurePre().catch(e => {
+            this.configured = this.configurePre().catch((e) => {
                 this.configured = undefined;
                 throw e;
             });

package/esm/extensionPoints.js

@@ -17,7 +17,7 @@ export default function ExtensionPointsF(pluginManager) {
             if (regexGuess.test(fileName) && !adapterHint) {
                 return obj;
             }
-            else if (adapterHint === adapterName) {
+            if (adapterHint === adapterName) {
                 return obj;
             }
             return adapterGuesser(file, index, adapterHint);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "2.13.1",
+  "version": "2.14.0",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -24,7 +24,7 @@
   ],
   "scripts": {
     "build": "npm-run-all build:*",
-    "test": "cd ../..; jest plugins/variants",
+    "test": "cd ../..; jest --passWithNoTests plugins/variants",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build && yarn useDist",
     "postpack": "yarn useSrc",
@@ -62,5 +62,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "fcebca71cc1d066654603e1a9accfa6c6d4f764d"
+  "gitHead": "9fb8231d932db40adf0a283081765431756c66ff"
 }