@jbrowse/plugin-variants 3.1.0 → 3.3.0

package/esm/MultiLinearVariantRenderer/makeImageData.js

@@ -1,53 +1,93 @@
-import { featureSpanPx } from '@jbrowse/core/util';
+import { featureSpanPx, forEachWithStopTokenCheck } from '@jbrowse/core/util';
+import { checkStopToken } from '@jbrowse/core/util/stopToken';
 import RBush from 'rbush';
 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 { scrollTop, minorAlleleFrequencyFilter, sources, rowHeight, features, regions, bpPerPx, renderingMode, stopToken, lengthCutoffFilter, referenceDrawingMode, } = props;
     const region = regions[0];
-    const mafs = getFeaturesThatPassMinorAlleleFrequencyFilter(features.values(), minorAlleleFrequencyFilter);
+    checkStopToken(stopToken);
+    const mafs = getFeaturesThatPassMinorAlleleFrequencyFilter({
+        stopToken,
+        features: features.values(),
+        minorAlleleFrequencyFilter,
+        lengthCutoffFilter,
+    });
+    checkStopToken(stopToken);
     const rbush = new RBush();
-    for (const { mostFrequentAlt, feature } of mafs) {
+    forEachWithStopTokenCheck(mafs, stopToken, ({ mostFrequentAlt, feature }) => {
         const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
         const w = Math.max(Math.round(rightPx - leftPx), 2);
         const samp = feature.get('genotypes');
         let y = -scrollTop;
         const s = sources.length;
-        for (let j = 0; j < s; j++) {
-            const { name, HP } = sources[j];
-            const genotype = samp[name];
-            const x = Math.floor(leftPx);
-            const h = Math.max(rowHeight, 1);
-            if (genotype) {
-                rbush.insert({
-                    minX: x - f2,
-                    maxX: x + w + f2,
-                    minY: y - f2,
-                    maxY: y + h + f2,
-                    genotype,
-                });
-                const isPhased = genotype.includes('|');
-                if (renderingMode === 'phased') {
+        if (renderingMode === 'phased') {
+            for (let j = 0; j < s; j++) {
+                const { name, HP } = sources[j];
+                const genotype = samp[name];
+                const x = Math.floor(leftPx);
+                const h = Math.max(rowHeight, 1);
+                if (genotype) {
+                    const isPhased = genotype.includes('|');
                     if (isPhased) {
                         const alleles = genotype.split('|');
-                        drawPhased(alleles, ctx, x, y, w, h, HP);
+                        if (drawPhased(alleles, ctx, x, y, w, h, HP, undefined, referenceDrawingMode === 'draw')) {
+                            rbush.insert({
+                                minX: x,
+                                maxX: x + w,
+                                minY: y,
+                                maxY: y + h,
+                                genotype,
+                                name,
+                                featureId: feature.id(),
+                            });
+                        }
                     }
                     else {
                         ctx.fillStyle = 'black';
                         ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
                     }
                 }
-                else {
+                y += rowHeight;
+            }
+        }
+        else {
+            for (let j = 0; j < s; j++) {
+                const { name } = sources[j];
+                const genotype = samp[name];
+                const x = Math.floor(leftPx);
+                const h = Math.max(rowHeight, 1);
+                if (genotype) {
                     const alleles = genotype.split(/[/|]/);
-                    drawColorAlleleCount(alleles, ctx, x, y, w, h, mostFrequentAlt);
+                    if (drawColorAlleleCount(alleles, ctx, x, y, w, h, mostFrequentAlt, referenceDrawingMode === 'draw', feature.get('type'), feature.get('strand'), 0.75)) {
+                        rbush.insert({
+                            minX: x,
+                            maxX: x + w,
+                            minY: y,
+                            maxY: y + h,
+                            genotype,
+                            name,
+                            featureId: feature.id(),
+                        });
+                    }
                 }
+                y += rowHeight;
             }
-            y += rowHeight;
         }
-    }
+    });
     return {
         rbush: rbush.toJSON(),
+        featureGenotypeMap: Object.fromEntries(mafs.map(({ feature }) => [
+            feature.id(),
+            {
+                alt: feature.get('ALT'),
+                ref: feature.get('REF'),
+                name: feature.get('name'),
+                description: feature.get('description'),
+                length: feature.get('end') - feature.get('start'),
+            },
+        ])),
     };
 }

package/esm/MultiLinearVariantRenderer/types.d.ts

@@ -16,4 +16,5 @@ export interface MultiRenderArgsDeserialized extends RenderArgsDeserializedWithF
     rowHeight: number;
     scrollTop: number;
     minorAlleleFrequencyFilter: number;
+    lengthCutoffFilter: number;
 }

package/esm/SplitVcfTabixAdapter/configSchema.js

@@ -17,9 +17,11 @@ const SplitVcfTabixAdapter = ConfigurationSchema('SplitVcfTabixAdapter', {
         type: 'fileLocation',
         defaultValue: {
             uri: '/path/to/samples.tsv',
-            description: 'tsv with header like name\tpopulation\tetc. where the first column is required, and is the sample names',
+            description: 'tsv with header like "name\tpopulation\tetc" where the first column is required, and corresponds to the sample names in the VCF files',
             locationType: 'UriLocation',
         },
     },
-}, { explicitlyTyped: true });
+}, {
+    explicitlyTyped: true,
+});
 export default SplitVcfTabixAdapter;

package/esm/VariantFeatureWidget/AltFormatter.d.ts

@@ -0,0 +1,4 @@
+export default function AltFormatter({ value, ref, }: {
+    value: string;
+    ref: string;
+}): string | import("react/jsx-runtime").JSX.Element;

package/esm/VariantFeatureWidget/AltFormatter.js

@@ -0,0 +1,10 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { useState } from 'react';
+import { getMinimalDesc } from '../VcfFeature/util';
+export default function AltFormatter({ value, ref, }) {
+    const [show, setShow] = useState(false);
+    const alt = getMinimalDesc(ref, value);
+    return alt !== value ? (_jsxs("div", { children: [_jsx("button", { onClick: () => {
+                    setShow(!show);
+                }, children: show ? 'Show simplified ALT' : 'Show raw ALT' }), ' ', show ? value : getMinimalDesc(ref, value)] })) : (value);
+}

package/esm/VariantFeatureWidget/Checkbox2.js

@@ -1,12 +1,5 @@
 import { jsx as _jsx } from "react/jsx-runtime";
-import { Checkbox, FormControlLabel } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
-const useStyles = makeStyles()({
-    block: {
-        display: 'block',
-    },
-});
+import { Checkbox, FormControlLabel, Typography } from '@mui/material';
 export default function Checkbox2({ checked, disabled, label, onChange, }) {
-    const { classes } = useStyles();
-    return (_jsx(FormControlLabel, { disabled: disabled, className: classes.block, control: _jsx(Checkbox, { checked: checked, onChange: onChange }), label: label }));
+    return (_jsx(FormControlLabel, { disabled: disabled, control: _jsx(Checkbox, { checked: checked, onChange: onChange }), label: _jsx(Typography, { variant: "body2", children: label }) }));
 }

package/esm/VariantFeatureWidget/Formatter.d.ts

@@ -0,0 +1,3 @@
+export default function Formatter({ value }: {
+    value: unknown;
+}): import("react/jsx-runtime").JSX.Element;

package/esm/VariantFeatureWidget/Formatter.js

@@ -0,0 +1,17 @@
+import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
+import { useState } from 'react';
+import copy from 'copy-to-clipboard';
+export default function Formatter({ value }) {
+    const [show, setShow] = useState(false);
+    const [copied, setCopied] = useState(false);
+    const display = String(value);
+    return display.length > 100 ? (_jsxs(_Fragment, { children: [_jsx("button", { type: "button", onClick: () => {
+                    copy(display);
+                    setCopied(true);
+                    setTimeout(() => {
+                        setCopied(false);
+                    }, 700);
+                }, children: copied ? 'Copied to clipboard' : 'Copy' }), _jsx("button", { type: "button", onClick: () => {
+                    setShow(val => !val);
+                }, children: show ? 'Show less' : 'Show more' }), _jsx("div", { children: show ? display : `${display.slice(0, 100)}...` })] })) : (_jsx("div", { children: display }));
+}

package/esm/VariantFeatureWidget/{VariantConsequenceDataGridWrapper.js → VariantConsequence/VariantConsequenceDataGridWrapper.js}

@@ -2,16 +2,14 @@ import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { useState } from 'react';
 import { measureGridWidth } from '@jbrowse/core/util';
 import { Checkbox, FormControlLabel, Typography } from '@mui/material';
-import { DataGrid, GridToolbar } from '@mui/x-data-grid';
+import { DataGrid } from '@mui/x-data-grid';
 export default function VariantConsequenceDataGridWrapper({ rows, columns, }) {
     const [checked, setChecked] = useState(false);
     const widths = columns.map(e => measureGridWidth(rows.map(r => r[e.field])));
-    return rows.length ? (_jsxs("div", { children: [_jsx(FormControlLabel, { control: _jsx(Checkbox, { checked: checked, onChange: event => {
+    return rows.length ? (_jsxs("div", { children: [_jsx(FormControlLabel, { label: _jsx(Typography, { variant: "body2", children: "Show options" }), control: _jsx(Checkbox, { checked: checked, onChange: event => {
                         setChecked(event.target.checked);
-                    } }), label: _jsx(Typography, { variant: "body2", children: "Show options" }) }), _jsx(DataGrid, { rowHeight: 25, rows: rows, columns: columns.map((c, i) => ({
+                    } }) }), _jsx(DataGrid, { rowHeight: 25, hideFooter: rows.length < 100, rows: rows, showToolbar: checked, columns: columns.map((c, i) => ({
                     ...c,
                     width: widths[i],
-                })), slots: {
-                    toolbar: checked ? GridToolbar : null,
-                } })] })) : null;
+                })) })] })) : null;
 }

package/esm/VariantFeatureWidget/VariantFeatureWidget.js

@@ -4,10 +4,12 @@ import { parseBreakend } from '@gmod/vcf';
 import FeatureDetails from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails';
 import { Paper } from '@mui/material';
 import { observer } from 'mobx-react';
+import AltFormatter from './AltFormatter';
+import Formatter from './Formatter';
 import VariantSampleGrid from './VariantSampleGrid/VariantSampleGrid';
 import { variantFieldDescriptions } from './variantFieldDescriptions';
 const LaunchBreakendPanel = lazy(() => import('./LaunchBreakendPanel/LaunchBreakendPanel'));
-const VariantConsequenceDataGrid = lazy(() => import('./VariantConsequenceDataGrid'));
+const VariantConsequenceDataGrid = lazy(() => import('./VariantConsequence/VariantConsequenceDataGrid'));
 function AnnPanel({ descriptions, feature, }) {
     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;
@@ -46,10 +48,13 @@ const VariantFeatureWidget = observer(function (props) {
     const { model } = props;
     const { featureData, descriptions } = model;
     const feat = JSON.parse(JSON.stringify(featureData));
-    const { samples, ALT, ...rest } = feat;
+    const { samples, ...rest } = feat;
+    const { REF } = rest;
     return (_jsxs(Paper, { "data-testid": "variant-side-drawer", children: [_jsx(FeatureDetails, { feature: rest, descriptions: {
                     ...variantFieldDescriptions,
                     ...descriptions,
+                }, formatter: (value, key) => {
+                    return key === 'ALT' ? (_jsx(AltFormatter, { value: `${value}`, ref: REF })) : (_jsx(Formatter, { value: value }));
                 }, ...props }), _jsxs(Suspense, { fallback: null, children: [_jsx(CsqPanel, { feature: rest, descriptions: descriptions }), _jsx(AnnPanel, { feature: rest, descriptions: descriptions }), _jsx(LaunchBreakendWidgetArea, { model: model })] }), _jsx(VariantSampleGrid, { feature: feat, ...props, descriptions: descriptions })] }));
 });
 export default VariantFeatureWidget;

package/esm/VariantFeatureWidget/VariantSampleGrid/VariantGenotypeFrequencyTable.d.ts

@@ -0,0 +1,4 @@
+import type { VariantSampleGridRow } from './types';
+export default function VariantGenotypeFrequencyTable({ rows, }: {
+    rows: VariantSampleGridRow[];
+}): import("react/jsx-runtime").JSX.Element;

package/esm/VariantFeatureWidget/VariantSampleGrid/VariantGenotypeFrequencyTable.js

@@ -0,0 +1,74 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { useState } from 'react';
+import DataGridFlexContainer from '@jbrowse/core/ui/DataGridFlexContainer';
+import { measureGridWidth } from '@jbrowse/core/util';
+import { Checkbox, FormControlLabel, Typography } from '@mui/material';
+import { DataGrid } from '@mui/x-data-grid';
+function toP(n) {
+    return n.toPrecision(3);
+}
+export default function VariantGenotypeFrequencyTable({ rows, }) {
+    const [useCounts, setUseCounts] = useState(false);
+    const summary = {};
+    if (!useCounts) {
+        for (const row of rows) {
+            const gt = row.GT;
+            if (!summary[gt]) {
+                summary[gt] = {
+                    count: 0,
+                    GT: row.GT,
+                    genotype: row.genotype,
+                };
+            }
+            summary[gt].count++;
+        }
+    }
+    else {
+        for (const row of rows) {
+            const alleleCounts = {};
+            const alleles = row.GT.split(/[/|]/);
+            for (const allele of alleles) {
+                alleleCounts[allele] = (alleleCounts[allele] || 0) + 1;
+            }
+            const key = Object.entries(alleleCounts)
+                .map(([key, val]) => `${key}:${val}`)
+                .join(';');
+            if (!summary[key]) {
+                summary[key] = {
+                    count: 0,
+                    GT: key,
+                    genotype: row.genotype,
+                };
+            }
+            summary[key].count++;
+        }
+    }
+    const gridRows = Object.entries(summary).map(([key, val]) => ({
+        id: key,
+        ...val,
+        count: `${val.count} / ${rows.length}`,
+        frequency: `${toP((val.count / rows.length) * 100)}%`,
+    }));
+    const keys = gridRows[0] ? Object.keys(gridRows[0]) : [];
+    const widths = keys.map(e => measureGridWidth(gridRows.map(r => `${r[e]}`)));
+    return (_jsxs("div", { children: [_jsx(FormControlLabel, { control: _jsx(Checkbox, { checked: useCounts }), label: _jsx(Typography, { variant: "body2", children: "Use allele counts instead of exact GT" }), onChange: (_, checked) => {
+                    setUseCounts(checked);
+                } }), _jsx(DataGridFlexContainer, { children: _jsx(DataGrid, { rows: gridRows, hideFooter: true, rowHeight: 25, columnHeaderHeight: 35, columns: [
+                        {
+                            field: 'GT',
+                            width: widths[0],
+                        },
+                        {
+                            field: 'count',
+                            width: widths[1],
+                        },
+                        {
+                            field: 'frequency',
+                            width: widths[2],
+                        },
+                        {
+                            field: 'genotype',
+                            width: widths[3],
+                        },
+                    ] }) })] }));
+}

package/esm/VariantFeatureWidget/VariantSampleGrid/VariantSampleGrid.d.ts

@@ -1,12 +1,6 @@
+import type { VariantFieldDescriptions } from './types';
 import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
-interface FormatRecord {
-    Description?: string;
-}
-interface Descriptions {
-    FORMAT?: Record<string, FormatRecord>;
-}
-export default function VariantSamples(props: {
+export default function VariantSampleGrid(props: {
     feature: SimpleFeatureSerialized;
-    descriptions?: Descriptions | null;
+    descriptions?: VariantFieldDescriptions | null;
 }): import("react/jsx-runtime").JSX.Element | null;
-export {};

package/esm/VariantFeatureWidget/VariantSampleGrid/VariantSampleGrid.js

@@ -1,26 +1,50 @@
-import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
 import { useState } from 'react';
 import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
+import { ErrorMessage } from '@jbrowse/core/ui';
+import DataGridFlexContainer from '@jbrowse/core/ui/DataGridFlexContainer';
+import { ErrorBoundary } from '@jbrowse/core/ui/ErrorBoundary';
 import { measureGridWidth } from '@jbrowse/core/util';
-import { Checkbox, FormControlLabel, Typography } from '@mui/material';
-import { DataGrid, GridToolbar } from '@mui/x-data-grid';
+import { Typography } from '@mui/material';
+import { DataGrid } from '@mui/x-data-grid';
+import Checkbox2 from '../Checkbox2';
+import VariantGenotypeFrequencyTable from './VariantGenotypeFrequencyTable';
 import SampleFilters from './VariantSampleFilters';
-export default function VariantSamples(props) {
+import { areSetsEqual } from './util';
+import { makeSimpleAltString } from '../../VcfFeature/util';
+export default function VariantSampleGrid(props) {
     var _a;
     const { feature, descriptions = {} } = props;
     const [filter, setFilter] = useState({});
+    const [showOnlyGenotypeColumns, setShowOnlyGenotypeColumns] = useState(true);
+    const [showFilters, setShowFilters] = useState(false);
     const samples = (feature.samples || {});
-    const preFilteredRows = Object.entries(samples);
+    const ALT = feature.ALT;
+    const REF = feature.REF;
+    const preFilteredRows = Object.entries(samples).map(([key, val]) => {
+        var _a, _b;
+        return [
+            key,
+            {
+                ...val,
+                GT: `${(_a = val.GT) === null || _a === void 0 ? void 0 : _a[0]}`,
+                genotype: makeSimpleAltString(`${(_b = val.GT) === null || _b === void 0 ? void 0 : _b[0]}`, REF, ALT),
+            },
+        ];
+    });
     let error;
     let rows = [];
     const filters = Object.keys(filter);
     try {
         rows = preFilteredRows
-            .map(row => {
+            .map(([key, val]) => {
             return {
-                ...Object.fromEntries(Object.entries(row[1]).map(e => [e[0], `${e[1]}`])),
-                sample: row[0],
-                id: row[0],
+                ...Object.fromEntries(Object.entries(val).map(([formatField, formatValue]) => [
+                    formatField,
+                    formatValue,
+                ])),
+                sample: key,
+                id: key,
             };
         })
             .filter(row => filters.length
@@ -33,9 +57,9 @@ export default function VariantSamples(props) {
             : true);
     }
     catch (e) {
+        console.error(e);
         error = e;
     }
-    const [checked, setChecked] = useState(false);
     const keys = ['sample', ...Object.keys(((_a = preFilteredRows[0]) === null || _a === void 0 ? void 0 : _a[1]) || {})];
     const widths = keys.map(e => measureGridWidth(rows.map(r => r[e])));
     const columns = keys.map((field, index) => {
@@ -46,16 +70,13 @@ export default function VariantSamples(props) {
             width: widths[index],
         });
     });
-    return !preFilteredRows.length ? null : (_jsxs(BaseCard, { ...props, title: "Samples", children: [error ? _jsx(Typography, { color: "error", children: `${error}` }) : null, _jsx(FormControlLabel, { control: _jsx(Checkbox, { checked: checked, onChange: event => {
-                        setChecked(event.target.checked);
-                    } }), label: _jsx(Typography, { variant: "body2", children: "Show options" }) }), checked ? (_jsx(SampleFilters, { setFilter: setFilter, columns: columns, filter: filter })) : null, _jsx("div", { style: {
-                    display: 'flex',
-                    flexDirection: 'column',
-                }, children: _jsx(DataGrid, { rows: rows, hideFooter: rows.length < 100, columns: columns, disableRowSelectionOnClick: true, rowHeight: 25, columnHeaderHeight: 35, disableColumnMenu: true, slots: { toolbar: checked ? GridToolbar : null }, slotProps: {
-                        toolbar: {
-                            printOptions: {
-                                disableToolbarButton: true,
-                            },
-                        },
-                    } }) })] }));
+    const s1 = new Set(['sample', 'GT', 'genotype']);
+    const s2 = new Set(keys);
+    return !preFilteredRows.length ? null : (_jsxs(_Fragment, { children: [_jsx(BaseCard, { ...props, title: "Genotype frequencies", children: _jsx(ErrorBoundary, { FallbackComponent: ErrorMessage, children: _jsx(VariantGenotypeFrequencyTable, { rows: rows }) }) }), _jsxs(BaseCard, { ...props, title: "Samples", children: [error ? _jsx(Typography, { color: "error", children: `${error}` }) : null, _jsx(Checkbox2, { label: "Show filters", checked: showFilters, onChange: event => {
+                            setShowFilters(event.target.checked);
+                        } }), areSetsEqual(s1, s2) ? null : (_jsx(Checkbox2, { label: "Show only genotype columns", checked: showOnlyGenotypeColumns, onChange: event => {
+                            setShowOnlyGenotypeColumns(event.target.checked);
+                        } })), showFilters ? (_jsx(SampleFilters, { setFilter: setFilter, columns: columns, filter: filter })) : null, _jsx(DataGridFlexContainer, { children: _jsx(DataGrid, { rows: rows, hideFooter: rows.length < 100, columns: showOnlyGenotypeColumns
+                                ? columns.filter(f => s1.has(f.field))
+                                : columns, rowHeight: 25, columnHeaderHeight: 35, showToolbar: true }) })] })] }));
 }

package/esm/VariantFeatureWidget/VariantSampleGrid/types.d.ts

@@ -0,0 +1,21 @@
+export interface FrequencyTableEntry {
+    count: number;
+    GT: string;
+    genotype: string | undefined;
+}
+export type FrequencyTable = Record<string, FrequencyTableEntry>;
+export interface VariantSampleGridRow {
+    sample: string;
+    id: string;
+    GT: string;
+    [key: string]: string;
+}
+export type InfoFields = Record<string, unknown[]>;
+export type Filters = Record<string, string>;
+interface FormatRecord {
+    Description?: string;
+}
+export interface VariantFieldDescriptions {
+    FORMAT?: Record<string, FormatRecord>;
+}
+export {};

package/esm/VariantFeatureWidget/VariantSampleGrid/types.js

@@ -0,0 +1 @@
+export {};

package/esm/VariantFeatureWidget/VariantSampleGrid/util.d.ts

@@ -0,0 +1 @@
+export declare function areSetsEqual<T>(set1: Set<T>, set2: Set<T>): boolean;

package/esm/VariantFeatureWidget/VariantSampleGrid/util.js

@@ -0,0 +1,11 @@
+export function areSetsEqual(set1, set2) {
+    if (set1.size !== set2.size) {
+        return false;
+    }
+    for (const item of set1) {
+        if (!set2.has(item)) {
+            return false;
+        }
+    }
+    return true;
+}

package/esm/VariantRPC/MultiVariantClusterGenotypeMatrix.d.ts

@@ -0,0 +1,14 @@
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import type { ClusterGenotypeMatrixArgs } from './types';
+export declare class MultiVariantClusterGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
+    name: string;
+    execute(args: ClusterGenotypeMatrixArgs, rpcDriverClassName: string): Promise<{
+        clusters: {
+            height: number;
+            indexes: number[];
+        } | undefined;
+        distances: number[][];
+        order: number[];
+        clustersGivenK: number[][][];
+    }>;
+}

package/esm/VariantRPC/MultiVariantClusterGenotypeMatrix.js

@@ -0,0 +1,23 @@
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import { clusterData } from '@jbrowse/core/util/cluster';
+import { getGenotypeMatrix } from './getGenotypeMatrix';
+export class MultiVariantClusterGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
+    constructor() {
+        super(...arguments);
+        this.name = 'MultiVariantClusterGenotypeMatrix';
+    }
+    async execute(args, rpcDriverClassName) {
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const matrix = await getGenotypeMatrix({
+            pluginManager: this.pluginManager,
+            args: deserializedArgs,
+        });
+        return clusterData({
+            data: Object.values(matrix),
+            stopToken: deserializedArgs.stopToken,
+            onProgress: progress => {
+                deserializedArgs.statusCallback(progress);
+            },
+        });
+    }
+}

package/esm/VariantRPC/MultiVariantGetGenotypeMatrix.d.ts

@@ -1,17 +1,6 @@
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { Region } from '@jbrowse/core/util';
+import type { GetGenotypeMatrixArgs } from './types';
 export declare class MultiVariantGetGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
     name: string;
-    execute(args: {
-        adapterConfig: AnyConfigurationModel;
-        stopToken?: string;
-        sessionId: string;
-        headers?: Record<string, string>;
-        regions: Region[];
-        bpPerPx: number;
-    }, rpcDriverClassName: string): Promise<Record<string, {
-        name: string;
-        genotypes: string[];
-    }>>;
+    execute(args: GetGenotypeMatrixArgs, rpcDriverClassName: string): Promise<Record<string, number[]>>;
 }

package/esm/VariantRPC/MultiVariantGetGenotypeMatrix.js

@@ -1,66 +1,14 @@
-import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
-import { firstValueFrom, toArray } from 'rxjs';
-import { getFeaturesThatPassMinorAlleleFrequencyFilter } from '../shared/minorAlleleFrequencyUtils';
+import { getGenotypeMatrix } from './getGenotypeMatrix';
 export class MultiVariantGetGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
     constructor() {
         super(...arguments);
         this.name = 'MultiVariantGetGenotypeMatrix';
     }
     async execute(args, rpcDriverClassName) {
-        const pm = this.pluginManager;
-        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
-        const { sources, minorAlleleFrequencyFilter, regions, adapterConfig, sessionId, } = deserializedArgs;
-        const adapter = await getAdapter(pm, sessionId, adapterConfig);
-        const dataAdapter = adapter.dataAdapter;
-        const feats = await firstValueFrom(dataAdapter
-            .getFeaturesInMultipleRegions(regions, deserializedArgs)
-            .pipe(toArray()));
-        const genotypeFactor = new Set();
-        const mafs = getFeaturesThatPassMinorAlleleFrequencyFilter(feats, minorAlleleFrequencyFilter);
-        for (const { alleleCounts } of mafs) {
-            for (const alt of alleleCounts.keys()) {
-                genotypeFactor.add(alt);
-            }
-        }
-        const rows = {};
-        for (const { feature } of mafs) {
-            const genotypes = feature.get('genotypes');
-            for (const { name } of sources) {
-                if (!rows[name]) {
-                    rows[name] = {
-                        name,
-                        genotypes: [],
-                    };
-                }
-                const val = genotypes[name];
-                const alleles = val.split(/[/|]/);
-                let genotypeStatus = '0';
-                let nonRefCount = 0;
-                let uncalledCount = 0;
-                for (const l of alleles) {
-                    if (l === '.') {
-                        uncalledCount++;
-                    }
-                    else if (l !== '0') {
-                        nonRefCount++;
-                    }
-                }
-                if (uncalledCount === alleles.length) {
-                    genotypeStatus = '-1';
-                }
-                else if (nonRefCount === 0) {
-                    genotypeStatus = '0';
-                }
-                else if (nonRefCount === alleles.length) {
-                    genotypeStatus = '2';
-                }
-                else {
-                    genotypeStatus = '1';
-                }
-                rows[name].genotypes.push(genotypeStatus);
-            }
-        }
-        return rows;
+        return getGenotypeMatrix({
+            pluginManager: this.pluginManager,
+            args: await this.deserializeArguments(args, rpcDriverClassName),
+        });
     }
 }