@jbrowse/plugin-variants 3.0.0 → 3.0.2

package/esm/MultiLinearVariantMatrixDisplay/model.d.ts

@@ -82,7 +82,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     configuration: AnyConfigurationSchemaType;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearVariantMatrixDisplay">;
-    layout: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("../types").Source[], import("../types").Source[], import("../types").Source[]>, [undefined]>;
+    layout: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("../shared/types").Source[], import("../shared/types").Source[], import("../shared/types").Source[]>, [undefined]>;
     configuration: AnyConfigurationSchemaType;
     minorAlleleFrequencyFilter: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
     showSidebarLabelsSetting: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -236,27 +236,27 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     sourcesLoadingStopToken: string | undefined;
     featureUnderMouseVolatile: import("@jbrowse/core/util").Feature | undefined;
-    sourcesVolatile: import("../types").Source[] | undefined;
+    sourcesVolatile: import("../shared/types").Source[] | undefined;
     featuresVolatile: import("@jbrowse/core/util").Feature[] | undefined;
     hasPhased: boolean;
-    sampleInfo: undefined | Record<string, import("../types").SampleInfo>;
+    sampleInfo: undefined | Record<string, import("../shared/types").SampleInfo>;
     hoveredGenotype: string | undefined;
 } & {
     setRowHeight(arg: number): void;
     setHoveredGenotype(arg: string): void;
     setFeatures(f: import("@jbrowse/core/util").Feature[]): void;
-    setLayout(layout: import("../types").Source[]): void;
+    setLayout(layout: import("../shared/types").Source[]): void;
     clearLayout(): void;
     setSourcesLoading(str: string): void;
-    setSources(sources: import("../types").Source[]): void;
+    setSources(sources: import("../shared/types").Source[]): void;
     setMafFilter(arg: number): void;
     setShowSidebarLabels(arg: boolean): void;
     setPhasedMode(arg: string): void;
     setAutoHeight(arg: boolean): void;
     setHasPhased(arg: boolean): void;
-    setSampleInfo(arg: Record<string, import("../types").SampleInfo>): void;
+    setSampleInfo(arg: Record<string, import("../shared/types").SampleInfo>): void;
 } & {
-    readonly preSources: import("../types").Source[] | undefined;
+    readonly preSources: import("../shared/types").Source[] | undefined;
     readonly sources: {
         label: string;
         id: string;

package/esm/MultiLinearVariantMatrixDisplay/renderSvg.js

@@ -1,8 +1,8 @@
 import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
 import { getContainingView } from '@jbrowse/core/util';
 import { when } from 'mobx';
-import LegendBar from '../shared/LegendBar';
 import LinesConnectingMatrixToGenomicPosition from './components/LinesConnectingMatrixToGenomicPosition';
+import LegendBar from '../shared/components/LegendBar';
 export async function renderSvg(model, opts, superRenderSvg) {
     await when(() => !!model.regionCannotBeRenderedText);
     const { offsetPx } = getContainingView(model);

package/esm/MultiLinearVariantMatrixRenderer/LinearVariantMatrixRenderer.js

@@ -33,12 +33,12 @@ export default class LinearVariantMatrixRenderer extends BoxRendererType {
             ...results,
             ...res,
             features: new Map(),
-            simplifiedFeatures: mafs.map((s) => new SimpleFeature({
-                id: s.id(),
+            simplifiedFeatures: mafs.map(({ feature }) => new SimpleFeature({
+                id: feature.id(),
                 data: {
-                    start: s.get('start'),
-                    end: s.get('end'),
-                    refName: s.get('refName'),
+                    start: feature.get('start'),
+                    end: feature.get('end'),
+                    refName: feature.get('refName'),
                 },
             })),
             height,

package/esm/MultiLinearVariantMatrixRenderer/makeImageData.d.ts

@@ -4,7 +4,10 @@ export declare function makeImageData({ ctx, canvasWidth, canvasHeight, renderAr
     canvasWidth: number;
     canvasHeight: number;
     renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
-}): {
-    mafs: import("@jbrowse/core/util").Feature[];
+}): Promise<{
+    mafs: {
+        feature: import("@jbrowse/core/util").Feature;
+        mostFrequentAlt: string;
+    }[];
     arr: string[][];
-};
+}>;

package/esm/MultiLinearVariantMatrixRenderer/makeImageData.js

@@ -1,50 +1,69 @@
-import { getColorAlleleCount, getColorPhased, getColorPhasedWithPhaseSet, } from '../shared/multiVariantColor';
-import { getFeaturesThatPassMinorAlleleFrequencyFilter } from '../util';
-const fudgeFactor = 0.6;
-const f2 = fudgeFactor / 2;
-function drawColorAlleleCount(alleles, ctx, x, y, w, h) {
-    ctx.fillStyle = getColorAlleleCount(alleles);
-    ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
-}
-function drawPhased(alleles, ctx, x, y, w, h, HP, PS) {
-    ctx.fillStyle =
-        PS !== undefined
-            ? getColorPhasedWithPhaseSet(alleles, HP, PS)
-            : getColorPhased(alleles, HP);
-    ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
-}
-export function makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs, }) {
-    var _a, _b;
+import { updateStatus } from '@jbrowse/core/util';
+import { f2 } from '../shared/constants';
+import { drawColorAlleleCount } from '../shared/drawAlleleCount';
+import { drawPhased } from '../shared/drawPhased';
+import { getFeaturesThatPassMinorAlleleFrequencyFilter } from '../shared/minorAlleleFrequencyUtils';
+export async function makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs, }) {
     const { renderingMode: renderingMode, minorAlleleFrequencyFilter, sources, features, } = renderArgs;
     const { statusCallback = () => { } } = renderArgs;
-    statusCallback('Drawing variant matrix');
     const h = canvasHeight / sources.length;
     const mafs = getFeaturesThatPassMinorAlleleFrequencyFilter(features.values(), minorAlleleFrequencyFilter);
     const arr = [];
     const m = mafs.length;
     const w = canvasWidth / m;
-    for (let i = 0; i < m; i++) {
-        const arr2 = [];
-        const f = mafs[i];
-        const hasPhaseSet = f.get('format').includes('PS');
-        if (hasPhaseSet) {
-            const samp = f.get('samples');
-            const x = (i / mafs.length) * canvasWidth;
-            const sln = sources.length;
-            for (let j = 0; j < sln; j++) {
-                const y = (j / sln) * canvasHeight;
-                const { name, HP } = sources[j];
-                const s = samp[name];
-                if (s) {
-                    const genotype = (_a = s.GT) === null || _a === void 0 ? void 0 : _a[0];
+    await updateStatus('Drawing variant matrix', statusCallback, () => {
+        var _a, _b;
+        for (let i = 0; i < m; i++) {
+            const arr2 = [];
+            const { feature, mostFrequentAlt } = mafs[i];
+            const hasPhaseSet = feature.get('format').includes('PS');
+            if (hasPhaseSet) {
+                const samp = feature.get('samples');
+                const x = (i / mafs.length) * canvasWidth;
+                const sln = sources.length;
+                for (let j = 0; j < sln; j++) {
+                    const y = (j / sln) * canvasHeight;
+                    const { name, HP } = sources[j];
+                    const s = samp[name];
+                    if (s) {
+                        const genotype = (_a = s.GT) === null || _a === void 0 ? void 0 : _a[0];
+                        if (genotype) {
+                            arr2.push(genotype);
+                            const isPhased = genotype.includes('|');
+                            if (renderingMode === 'phased') {
+                                if (isPhased) {
+                                    const PS = (_b = s.PS) === null || _b === void 0 ? void 0 : _b[0];
+                                    const alleles = genotype.split('|');
+                                    drawPhased(alleles, ctx, x, y, w, h, HP, PS);
+                                }
+                                else {
+                                    ctx.fillStyle = 'black';
+                                    ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
+                                }
+                            }
+                            else {
+                                const alleles = genotype.split(/[/|]/);
+                                drawColorAlleleCount(alleles, ctx, x, y, w, h, mostFrequentAlt);
+                            }
+                        }
+                    }
+                }
+            }
+            else {
+                const samp = feature.get('genotypes');
+                const x = (i / mafs.length) * canvasWidth;
+                const sln = sources.length;
+                for (let j = 0; j < sln; j++) {
+                    const y = (j / sln) * canvasHeight;
+                    const { name, HP } = sources[j];
+                    const genotype = samp[name];
                     if (genotype) {
                         arr2.push(genotype);
                         const isPhased = genotype.includes('|');
                         if (renderingMode === 'phased') {
                             if (isPhased) {
-                                const PS = (_b = s.PS) === null || _b === void 0 ? void 0 : _b[0];
                                 const alleles = genotype.split('|');
-                                drawPhased(alleles, ctx, x, y, w, h, HP, PS);
+                                drawPhased(alleles, ctx, x, y, w, h, HP);
                             }
                             else {
                                 ctx.fillStyle = 'black';
@@ -53,43 +72,14 @@ export function makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs, }) {
                         }
                         else {
                             const alleles = genotype.split(/[/|]/);
-                            drawColorAlleleCount(alleles, ctx, x, y, w, h);
+                            drawColorAlleleCount(alleles, ctx, x, y, w, h, mostFrequentAlt);
                         }
                     }
                 }
             }
+            arr.push(arr2);
         }
-        else {
-            const samp = f.get('genotypes');
-            const x = (i / mafs.length) * canvasWidth;
-            const sln = sources.length;
-            const arr2 = [];
-            for (let j = 0; j < sln; j++) {
-                const y = (j / sln) * canvasHeight;
-                const { name, HP } = sources[j];
-                const genotype = samp[name];
-                if (genotype) {
-                    arr2.push(genotype);
-                    const isPhased = genotype.includes('|');
-                    if (renderingMode === 'phased') {
-                        if (isPhased) {
-                            const alleles = genotype.split('|');
-                            drawPhased(alleles, ctx, x, y, w, h, HP);
-                        }
-                        else {
-                            ctx.fillStyle = 'black';
-                            ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
-                        }
-                    }
-                    else {
-                        const alleles = genotype.split(/[/|]/);
-                        drawColorAlleleCount(alleles, ctx, x, y, w, h);
-                    }
-                }
-            }
-        }
-        arr.push(arr2);
-    }
+    });
     return {
         mafs,
         arr,

package/esm/MultiLinearVariantMatrixRenderer/types.d.ts

@@ -1,4 +1,4 @@
-import type { Source } from '../types';
+import type { Source } from '../shared/types';
 import type { RenderArgsDeserialized as BoxRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
 import type { Feature } from '@jbrowse/core/util';
 export interface RenderArgsDeserialized extends BoxRenderArgsDeserialized {
@@ -12,4 +12,5 @@ export interface RenderArgsDeserializedWithFeaturesAndLayout extends RenderArgsD
     sources: Source[];
     features: Map<string, Feature>;
     renderingMode: string;
+    statusCallback?: (arg: string) => void;
 }

package/esm/MultiLinearVariantRenderer/MultiVariantRendering.d.ts

@@ -1,5 +1,5 @@
 import RBush from 'rbush';
-import type { Source } from '../types';
+import type { Source } from '../shared/types';
 import type { Feature } from '@jbrowse/core/util';
 import type { Region } from '@jbrowse/core/util/types';
 declare const MultiVariantRendering: (props: {

package/esm/MultiLinearVariantRenderer/components/MultiVariantRendering.d.ts

@@ -0,0 +1,22 @@
+import RBush from 'rbush';
+import type { Source } from '../../shared/types';
+import type { Feature } from '@jbrowse/core/util';
+import type { Region } from '@jbrowse/core/util/types';
+declare const MultiVariantRendering: (props: {
+    regions: Region[];
+    features: Map<string, Feature>;
+    bpPerPx: number;
+    width: number;
+    height: number;
+    sources: Source[];
+    scrollTop: number;
+    totalHeight: number;
+    rbush: RBush<{
+        genotype: string;
+    }>;
+    displayModel: any;
+    onMouseLeave?: (event: React.MouseEvent) => void;
+    onMouseMove?: (event: React.MouseEvent, arg?: Feature) => void;
+    onFeatureClick?: (event: React.MouseEvent, arg?: Feature) => void;
+}) => import("react/jsx-runtime").JSX.Element;
+export default MultiVariantRendering;

package/esm/MultiLinearVariantRenderer/components/MultiVariantRendering.js

@@ -0,0 +1,47 @@
+import { jsx as _jsx } from "react/jsx-runtime";
+import { useMemo, useRef } from 'react';
+import { PrerenderedCanvas } from '@jbrowse/core/ui';
+import { observer } from 'mobx-react';
+import RBush from 'rbush';
+const MultiVariantRendering = observer(function (props) {
+    const { totalHeight, scrollTop } = props;
+    const { rbush, displayModel } = props;
+    const ref = useRef(null);
+    const rbush2 = useMemo(() => new RBush().fromJSON(rbush), [rbush]);
+    function getFeatureUnderMouse(eventClientX, eventClientY) {
+        var _a;
+        let offsetX = 0;
+        let offsetY = 0;
+        if (ref.current) {
+            const r = ref.current.getBoundingClientRect();
+            offsetX = eventClientX - r.left;
+            offsetY = eventClientY - r.top;
+        }
+        const ret = rbush2.search({
+            minX: offsetX,
+            maxX: offsetX + 3,
+            minY: offsetY,
+            maxY: offsetY + 3,
+        });
+        return (_a = ret[0]) === null || _a === void 0 ? void 0 : _a.genotype;
+    }
+    return (_jsx("div", { ref: ref, onMouseMove: e => {
+            var _a;
+            return (_a = displayModel.setHoveredGenotype) === null || _a === void 0 ? void 0 : _a.call(displayModel, getFeatureUnderMouse(e.clientX, e.clientY));
+        }, onMouseLeave: () => {
+            var _a;
+            (_a = displayModel.setHoveredGenotype) === null || _a === void 0 ? void 0 : _a.call(displayModel, undefined);
+        }, onMouseOut: () => {
+            var _a;
+            (_a = displayModel.setHoveredGenotype) === null || _a === void 0 ? void 0 : _a.call(displayModel, undefined);
+        }, style: {
+            overflow: 'visible',
+            position: 'relative',
+            height: totalHeight,
+        }, children: _jsx(PrerenderedCanvas, { ...props, style: {
+                position: 'absolute',
+                left: 0,
+                top: scrollTop,
+            } }) }));
+});
+export default MultiVariantRendering;

package/esm/MultiLinearVariantRenderer/index.js

@@ -1,5 +1,5 @@
 import MultiVariantRenderer from './MultiVariantRenderer';
-import ReactComponent from './MultiVariantRendering';
+import ReactComponent from './components/MultiVariantRendering';
 import configSchema from './configSchema';
 export default function MultiVariantRendererF(pluginManager) {
     pluginManager.addRendererType(() => {

package/esm/MultiLinearVariantRenderer/makeImageData.js

@@ -1,23 +1,15 @@
 import { featureSpanPx } from '@jbrowse/core/util';
 import RBush from 'rbush';
-import { getColorAlleleCount, getColorPhased, } from '../shared/multiVariantColor';
-import { getFeaturesThatPassMinorAlleleFrequencyFilter } from '../util';
-const fudgeFactor = 0.6;
-const f2 = fudgeFactor / 2;
-function drawColorAlleleCount(alleles, ctx, x, y, w, h) {
-    ctx.fillStyle = getColorAlleleCount(alleles);
-    ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
-}
-function drawPhased(alleles, ctx, x, y, w, h, HP) {
-    ctx.fillStyle = getColorPhased(alleles, HP);
-    ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
-}
+import { f2 } from '../shared/constants';
+import { drawColorAlleleCount } from '../shared/drawAlleleCount';
+import { drawPhased } from '../shared/drawPhased';
+import { getFeaturesThatPassMinorAlleleFrequencyFilter } from '../shared/minorAlleleFrequencyUtils';
 export async function makeImageData(ctx, props) {
     const { scrollTop, minorAlleleFrequencyFilter, sources, rowHeight, features, regions, bpPerPx, renderingMode, } = props;
     const region = regions[0];
     const mafs = getFeaturesThatPassMinorAlleleFrequencyFilter(features.values(), minorAlleleFrequencyFilter);
     const rbush = new RBush();
-    for (const feature of mafs) {
+    for (const { mostFrequentAlt, feature } of mafs) {
         const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
         const w = Math.max(Math.round(rightPx - leftPx), 2);
         const samp = feature.get('genotypes');
@@ -49,7 +41,7 @@ export async function makeImageData(ctx, props) {
                 }
                 else {
                     const alleles = genotype.split(/[/|]/);
-                    drawColorAlleleCount(alleles, ctx, x, y, w, h);
+                    drawColorAlleleCount(alleles, ctx, x, y, w, h, mostFrequentAlt);
                 }
             }
             y += rowHeight;

package/esm/MultiLinearVariantRenderer/types.d.ts

@@ -1,4 +1,4 @@
-import type { Source } from '../types';
+import type { Source } from '../shared/types';
 import type { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
 import type { Feature } from '@jbrowse/core/util';
 import type { ThemeOptions } from '@mui/material';

package/esm/MultiVariantBaseRenderer.d.ts

@@ -1,15 +1,15 @@
 import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
-import type { Source } from './types';
-import type { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+import type { Source } from './shared/types';
+import type { RenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
 import type { Feature } from '@jbrowse/core/util';
 import type { ThemeOptions } from '@mui/material';
-export interface RenderArgsDeserialized extends FeatureRenderArgsDeserialized {
+export interface RenderArgs extends RenderArgsDeserialized {
     bpPerPx: number;
     height: number;
     highResolutionScaling: number;
     themeOptions: ThemeOptions;
 }
-export interface RenderArgsDeserializedWithFeatures extends RenderArgsDeserialized {
+export interface RenderArgsDeserializedWithFeatures extends RenderArgs {
     features: Map<string, Feature>;
 }
 export interface MultiRenderArgsDeserialized extends RenderArgsDeserializedWithFeatures {
@@ -17,7 +17,7 @@ export interface MultiRenderArgsDeserialized extends RenderArgsDeserializedWithF
 }
 export default abstract class MultiVariantBaseRenderer extends FeatureRendererType {
     supportsSVG: boolean;
-    render(renderProps: RenderArgsDeserialized): Promise<{
+    render(renderProps: RenderArgs): Promise<{
         features: Map<string, Feature>;
         height: number;
         width: number;

package/esm/VariantRPC/MultiVariantGetGenotypeMatrix.js

@@ -1,7 +1,7 @@
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
 import { firstValueFrom, toArray } from 'rxjs';
-import { getFeaturesThatPassMinorAlleleFrequencyFilter } from '../util';
+import { getFeaturesThatPassMinorAlleleFrequencyFilter } from '../shared/minorAlleleFrequencyUtils';
 export class MultiVariantGetGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
     constructor() {
         super(...arguments);
@@ -26,8 +26,8 @@ export class MultiVariantGetGenotypeMatrix extends RpcMethodTypeWithFiltersAndRe
         }
         const genotypeFactorMap = Object.fromEntries([...genotypeFactor].map((type, idx) => [type, idx]));
         const rows = {};
-        for (const feat of mafs) {
-            const samp = feat.get('genotypes');
+        for (const { feature } of mafs) {
+            const samp = feature.get('genotypes');
             for (const { name } of sources) {
                 if (!rows[name]) {
                     rows[name] = {

package/esm/VariantRPC/MultiVariantGetSimplifiedFeatures.d.ts

@@ -1,5 +1,5 @@
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
-import type { SampleInfo } from '../types';
+import type { SampleInfo } from '../shared/types';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { Region } from '@jbrowse/core/util';
 export declare class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenameRegions {

package/esm/VariantRPC/MultiVariantGetSimplifiedFeatures.js

@@ -1,7 +1,7 @@
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
 import { firstValueFrom, toArray } from 'rxjs';
-import { getFeaturesThatPassMinorAlleleFrequencyFilter } from '../util';
+import { getFeaturesThatPassMinorAlleleFrequencyFilter } from '../shared/minorAlleleFrequencyUtils';
 export class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenameRegions {
     constructor() {
         super(...arguments);
@@ -19,8 +19,8 @@ export class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersA
         const features = getFeaturesThatPassMinorAlleleFrequencyFilter(feats, minorAlleleFrequencyFilter);
         const sampleInfo = {};
         let hasPhased = false;
-        for (const f of features) {
-            const samp = f.get('genotypes');
+        for (const { feature } of features) {
+            const samp = feature.get('genotypes');
             for (const [key, val] of Object.entries(samp)) {
                 const isPhased = val.includes('|');
                 hasPhased || (hasPhased = isPhased);
@@ -33,12 +33,12 @@ export class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersA
         return {
             hasPhased,
             sampleInfo,
-            features: features.map(f => ({
-                id: f.id(),
+            features: features.map(({ feature }) => ({
+                id: feature.id(),
                 data: {
-                    start: f.get('start'),
-                    end: f.get('end'),
-                    refName: f.get('refName'),
+                    start: feature.get('start'),
+                    end: feature.get('end'),
+                    refName: feature.get('refName'),
                 },
             })),
         };

package/esm/VcfTabixAdapter/VcfTabixAdapter.d.ts

@@ -7,13 +7,16 @@ import type { NoAssemblyRegion } from '@jbrowse/core/util/types';
 export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
     private configured?;
     private configurePre;
-    protected configure(): Promise<{
+    protected configurePre2(): Promise<{
+        vcf: TabixIndexedFile;
+        parser: VcfParser;
+    }>;
+    configure(opts?: BaseOptions): Promise<{
         vcf: TabixIndexedFile;
         parser: VcfParser;
     }>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
-    getHeader(): Promise<string>;
-    getMetadata(): Promise<any>;
+    getHeader(opts?: BaseOptions): Promise<string>;
     getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     getSources(): Promise<{
         name: string;

package/esm/VcfTabixAdapter/VcfTabixAdapter.js

@@ -6,8 +6,7 @@ import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import VcfFeature from '../VcfFeature';
 export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
-    async configurePre(opts) {
-        const { statusCallback = () => { } } = opts || {};
+    async configurePre(_opts) {
         const vcfGzLocation = this.getConf('vcfGzLocation');
         const location = this.getConf(['index', 'location']);
         const indexType = this.getConf(['index', 'indexType']);
@@ -23,13 +22,14 @@ export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
                 : undefined,
             chunkCacheSize: 50 * 2 ** 20,
         });
-        const header = await updateStatus('Downloading index', statusCallback, () => vcf.getHeader());
         return {
             vcf,
-            parser: new VcfParser({ header }),
+            parser: new VcfParser({
+                header: await vcf.getHeader(),
+            }),
         };
     }
-    async configure() {
+    async configurePre2() {
         if (!this.configured) {
             this.configured = this.configurePre().catch((e) => {
                 this.configured = undefined;
@@ -38,23 +38,23 @@ export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
         }
         return this.configured;
     }
+    async configure(opts) {
+        const { statusCallback = () => { } } = opts || {};
+        return updateStatus('Downloading index', statusCallback, () => this.configurePre2());
+    }
     async getRefNames(opts = {}) {
-        const { vcf } = await this.configure();
+        const { vcf } = await this.configure(opts);
         return vcf.getReferenceSequenceNames(opts);
     }
-    async getHeader() {
-        const { vcf } = await this.configure();
+    async getHeader(opts) {
+        const { vcf } = await this.configure(opts);
         return vcf.getHeader();
     }
-    async getMetadata() {
-        const { parser } = await this.configure();
-        return parser.getMetadata();
-    }
     getFeatures(query, opts = {}) {
         return ObservableCreate(async (observer) => {
             const { refName, start, end } = query;
             const { statusCallback = () => { } } = opts;
-            const { vcf, parser } = await this.configure();
+            const { vcf, parser } = await this.configure(opts);
             await updateStatus('Downloading variants', statusCallback, () => vcf.getLines(refName, start, end, {
                 lineCallback: (line, fileOffset) => {
                     observer.next(new VcfFeature({

package/esm/getMultiVariantFeaturesAutorun.d.ts

@@ -1,4 +1,4 @@
-import type { SampleInfo, Source } from './types';
+import type { SampleInfo, Source } from './shared/types';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { Feature } from '@jbrowse/core/util';
 export declare function getMultiVariantFeaturesAutorun(self: {

package/esm/getMultiVariantSourcesAutorun.d.ts

@@ -1,4 +1,4 @@
-import type { Source } from './types';
+import type { Source } from './shared/types';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 export declare function getMultiVariantSourcesAutorun(self: {
     configuration: AnyConfigurationModel;

package/esm/shared/MultiVariantBaseModel.d.ts

@@ -1,4 +1,4 @@
-import type { SampleInfo, Source } from '../types';
+import type { SampleInfo, Source } from '../shared/types';
 import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import type { Feature } from '@jbrowse/core/util';
 import type { Instance } from 'mobx-state-tree';

package/esm/shared/MultiVariantBaseModel.js

@@ -9,10 +9,10 @@ import SplitscreenIcon from '@mui/icons-material/Splitscreen';
 import VisibilityIcon from '@mui/icons-material/Visibility';
 import deepEqual from 'fast-deep-equal';
 import { types } from 'mobx-state-tree';
-const SetColorDialog = lazy(() => import('../shared/SetColorDialog'));
-const MAFFilterDialog = lazy(() => import('../shared/MAFFilterDialog'));
-const ClusterDialog = lazy(() => import('../shared/ClusterDialog'));
-const SetRowHeightDialog = lazy(() => import('../shared/SetRowHeightDialog'));
+const SetColorDialog = lazy(() => import('./components/SetColorDialog'));
+const MAFFilterDialog = lazy(() => import('./components/MAFFilterDialog'));
+const ClusterDialog = lazy(() => import('./components/ClusterDialog'));
+const SetRowHeightDialog = lazy(() => import('./components/SetRowHeightDialog'));
 export default function MultiVariantBaseModelF(configSchema) {
     return types
         .compose('LinearVariantMatrixDisplay', linearBareDisplayStateModelFactory(configSchema), types.model({

package/esm/shared/{SourcesGridHeader.js → components/SourcesGridHeader.js}

@@ -6,7 +6,7 @@ import KeyboardArrowUpIcon from '@mui/icons-material/KeyboardArrowUp';
 import KeyboardDoubleArrowDownIcon from '@mui/icons-material/KeyboardDoubleArrowDown';
 import KeyboardDoubleArrowUpIcon from '@mui/icons-material/KeyboardDoubleArrowUp';
 import { Button } from '@mui/material';
-import { moveDown, moveUp } from './util';
+import { moveDown, moveUp } from '../sourcesGridUtils';
 export default function SourcesGridHeader({ selected, onChange, rows, showTips, }) {
     const [anchorEl, setAnchorEl] = useState(null);
     const [widgetColor, setWidgetColor] = useState('blue');

package/esm/shared/constants.d.ts

@@ -0,0 +1,2 @@
+export declare const fudgeFactor = 0.6;
+export declare const f2: number;

package/esm/shared/constants.js

@@ -0,0 +1,2 @@
+export const fudgeFactor = 0.6;
+export const f2 = fudgeFactor / 2;

package/esm/shared/drawAlleleCount.d.ts

@@ -0,0 +1 @@
+export declare function drawColorAlleleCount(alleles: string[], ctx: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, mostFrequentAlt: string): void;