@jbrowse/plugin-variants 2.18.0 → 3.0.0

package/dist/VariantFeatureWidget/VariantFeatureWidget.js

@@ -15,68 +15,79 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importStar(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const vcf_1 = require("@gmod/vcf");
 const FeatureDetails_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails"));
 const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
-const VariantAnnotationTable_1 = __importDefault(require("./VariantAnnotationTable"));
 const VariantSampleGrid_1 = __importDefault(require("./VariantSampleGrid"));
 const variantFieldDescriptions_1 = require("./variantFieldDescriptions");
 const LaunchBreakendPanel = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./LaunchBreakendPanel'))));
+const VariantConsequenceDataGrid = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./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;
     const annFields = ((_d = (_c = annDesc === null || annDesc === void 0 ? void 0 : annDesc.match(/.*Functional annotations:'(.*)'$/)) === null || _c === void 0 ? void 0 : _c[1]) === null || _d === void 0 ? void 0 : _d.split('|')) || [];
     const ann = ((_e = feature.INFO) === null || _e === void 0 ? void 0 : _e.ANN) || [];
-    return (react_1.default.createElement(VariantAnnotationTable_1.default, { fields: annFields, data: ann, title: "Variant ANN field" }));
+    return ((0, jsx_runtime_1.jsx)(VariantConsequenceDataGrid, { fields: annFields, data: ann, title: "Variant ANN field" }));
 }
 function CsqPanel({ descriptions, feature, }) {
     var _a, _b, _c, _d, _e;
     const csqDescription = (_b = (_a = descriptions === null || descriptions === void 0 ? void 0 : descriptions.INFO) === null || _a === void 0 ? void 0 : _a.CSQ) === null || _b === void 0 ? void 0 : _b.Description;
     const csqFields = ((_d = (_c = csqDescription === null || csqDescription === void 0 ? void 0 : csqDescription.match(/.*Format: (.*)/)) === null || _c === void 0 ? void 0 : _c[1]) === null || _d === void 0 ? void 0 : _d.split('|')) || [];
     const csq = ((_e = feature.INFO) === null || _e === void 0 ? void 0 : _e.CSQ) || [];
-    return (react_1.default.createElement(VariantAnnotationTable_1.default, { fields: csqFields, data: csq, title: "Variant CSQ field" }));
+    return ((0, jsx_runtime_1.jsx)(VariantConsequenceDataGrid, { fields: csqFields, data: csq, title: "Variant CSQ field" }));
+}
+function LaunchBreakendWidgetArea({ model, }) {
+    const { featureData } = model;
+    const feat = JSON.parse(JSON.stringify(featureData));
+    const { type = '' } = feat;
+    return type === 'breakend' ? ((0, jsx_runtime_1.jsx)(LaunchBreakendPanel, { feature: feat, locStrings: feat.ALT.map((alt) => { var _a; return ((_a = (0, vcf_1.parseBreakend)(alt)) === null || _a === void 0 ? void 0 : _a.MatePosition) || ''; }), model: model })) : type === 'translocation' ? ((0, jsx_runtime_1.jsx)(LaunchBreakendPanel, { feature: feat, model: model, locStrings: [`${feat.INFO.CHR2[0]}:${feat.INFO.END}`] })) : type === 'paired_feature' ? ((0, jsx_runtime_1.jsx)(LaunchBreakendPanel, { feature: feat, model: model, locStrings: [`${feat.mate.refName}:${feat.mate.start}`] })) : type.includes('inversion') ||
+        type.includes('deletion') ||
+        type.includes('duplication') ||
+        type.includes('cnv') ||
+        type.includes('sv') ? ((0, jsx_runtime_1.jsx)(LaunchBreakendPanel, { feature: {
+            uniqueId: 'random',
+            refName: feat.refName,
+            start: feat.start,
+            end: feat.start + 1,
+            mate: {
+                refName: feat.refName,
+                start: feat.end,
+                end: feat.end + 1,
+            },
+        }, model: model, locStrings: [`${feat.refName}:${feat.end}`] })) : null;
 }
 const VariantFeatureWidget = (0, mobx_react_1.observer)(function (props) {
     const { model } = props;
     const { featureData, descriptions } = model;
     const feat = JSON.parse(JSON.stringify(featureData));
-    const { samples, ALT, type = '', ...rest } = feat;
-    return (react_1.default.createElement(material_1.Paper, { "data-testid": "variant-side-drawer" },
-        react_1.default.createElement(FeatureDetails_1.default, { feature: rest, descriptions: { ...variantFieldDescriptions_1.variantFieldDescriptions, ...descriptions }, ...props }),
-        react_1.default.createElement(CsqPanel, { feature: rest, descriptions: descriptions }),
-        react_1.default.createElement(AnnPanel, { feature: rest, descriptions: descriptions }),
-        react_1.default.createElement(react_1.Suspense, { fallback: null },
-            type === 'breakend' ? (react_1.default.createElement(LaunchBreakendPanel, { feature: feat, locStrings: feat.ALT.map((alt) => { var _a; return ((_a = (0, vcf_1.parseBreakend)(alt)) === null || _a === void 0 ? void 0 : _a.MatePosition) || ''; }), model: model })) : null,
-            type === 'translocation' ? (react_1.default.createElement(LaunchBreakendPanel, { feature: feat, model: model, locStrings: [`${feat.INFO.CHR2[0]}:${feat.INFO.END}`] })) : null,
-            type === 'paired_feature' ? (react_1.default.createElement(LaunchBreakendPanel, { feature: feat, model: model, locStrings: [`${feat.mate.refName}:${feat.mate.start}`] })) : null,
-            type.includes('inversion') ||
-                type.includes('deletion') ||
-                type.includes('duplication') ||
-                type.includes('cnv') ||
-                type.includes('sv') ? (react_1.default.createElement(LaunchBreakendPanel, { feature: {
-                    uniqueId: 'random',
-                    refName: feat.refName,
-                    start: feat.start,
-                    end: feat.start + 1,
-                    mate: {
-                        refName: feat.refName,
-                        start: feat.end,
-                        end: feat.end + 1,
-                    },
-                }, model: model, locStrings: [`${feat.refName}:${feat.end}`] })) : null),
-        react_1.default.createElement(VariantSampleGrid_1.default, { feature: feat, ...props, descriptions: descriptions })));
+    const { samples, ALT, ...rest } = feat;
+    return ((0, jsx_runtime_1.jsxs)(material_1.Paper, { "data-testid": "variant-side-drawer", children: [(0, jsx_runtime_1.jsx)(FeatureDetails_1.default, { feature: rest, descriptions: {
+                    ...variantFieldDescriptions_1.variantFieldDescriptions,
+                    ...descriptions,
+                }, ...props }), (0, jsx_runtime_1.jsxs)(react_1.Suspense, { fallback: null, children: [(0, jsx_runtime_1.jsx)(CsqPanel, { feature: rest, descriptions: descriptions }), (0, jsx_runtime_1.jsx)(AnnPanel, { feature: rest, descriptions: descriptions }), (0, jsx_runtime_1.jsx)(LaunchBreakendWidgetArea, { model: model })] }), (0, jsx_runtime_1.jsx)(VariantSampleGrid_1.default, { feature: feat, ...props, descriptions: descriptions })] }));
 });
 exports.default = VariantFeatureWidget;

package/dist/VariantFeatureWidget/VariantSampleFilters.d.ts

@@ -0,0 +1,9 @@
+type Filters = Record<string, string>;
+export default function SampleFilters({ columns, filter, setFilter, }: {
+    columns: {
+        field: string;
+    }[];
+    filter: Filters;
+    setFilter: (arg: Filters) => void;
+}): import("react/jsx-runtime").JSX.Element;
+export {};

package/dist/VariantFeatureWidget/VariantSampleFilters.js

@@ -0,0 +1,10 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = SampleFilters;
+const jsx_runtime_1 = require("react/jsx-runtime");
+const material_1 = require("@mui/material");
+function SampleFilters({ columns, filter, setFilter, }) {
+    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "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 }) => ((0, jsx_runtime_1.jsx)(material_1.TextField, { placeholder: `Filter ${field}`, value: filter[field] || '', onChange: event => {
+                    setFilter({ ...filter, [field]: event.target.value });
+                } }, `filter-${field}`)))] }));
+}

package/dist/VariantFeatureWidget/VariantSampleGrid.d.ts

@@ -1,10 +1,12 @@
-import React from 'react';
 import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
+interface FormatRecord {
+    Description?: string;
+}
+interface Descriptions {
+    FORMAT?: Record<string, FormatRecord>;
+}
 export default function VariantSamples(props: {
     feature: SimpleFeatureSerialized;
-    descriptions?: {
-        FORMAT?: Record<string, {
-            Description?: string;
-        }>;
-    } | null;
-}): React.JSX.Element | null;
+    descriptions?: Descriptions | null;
+}): import("react/jsx-runtime").JSX.Element | null;
+export {};

package/dist/VariantFeatureWidget/VariantSampleGrid.js

@@ -1,44 +1,16 @@
 "use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = VariantSamples;
-const react_1 = __importStar(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
 const util_1 = require("@jbrowse/core/util");
 const material_1 = require("@mui/material");
 const x_data_grid_1 = require("@mui/x-data-grid");
-function SampleFilters({ columns, filter, setFilter, }) {
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement(material_1.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_1.default.createElement(material_1.TextField, { key: `filter-${field}`, placeholder: `Filter ${field}`, value: filter[field] || '', onChange: event => {
-                setFilter({ ...filter, [field]: event.target.value });
-            } })))));
-}
+const VariantSampleFilters_1 = __importDefault(require("./VariantSampleFilters"));
 function VariantSamples(props) {
     var _a;
     const { feature, descriptions = {} } = props;
@@ -80,18 +52,16 @@ function VariantSamples(props) {
             width: widths[index],
         });
     });
-    return !preFilteredRows.length ? null : (react_1.default.createElement(BaseCard_1.default, { ...props, title: "Samples" },
-        error ? react_1.default.createElement(material_1.Typography, { color: "error" }, `${error}`) : null,
-        react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: checked, onChange: event => {
-                    setChecked(event.target.checked);
-                } }), label: react_1.default.createElement(material_1.Typography, { variant: "body2" }, "Show options") }),
-        checked ? (react_1.default.createElement(SampleFilters, { setFilter: setFilter, columns: columns, filter: filter })) : null,
-        react_1.default.createElement("div", { style: { display: 'flex', flexDirection: 'column' } },
-            react_1.default.createElement(x_data_grid_1.DataGrid, { rows: rows, hideFooter: rows.length < 100, columns: columns, disableRowSelectionOnClick: true, rowHeight: 25, columnHeaderHeight: 35, disableColumnMenu: true, slots: { toolbar: checked ? x_data_grid_1.GridToolbar : null }, slotProps: {
-                    toolbar: {
-                        printOptions: {
-                            disableToolbarButton: true,
+    return !preFilteredRows.length ? null : ((0, jsx_runtime_1.jsxs)(BaseCard_1.default, { ...props, title: "Samples", children: [error ? (0, jsx_runtime_1.jsx)(material_1.Typography, { color: "error", children: `${error}` }) : null, (0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { control: (0, jsx_runtime_1.jsx)(material_1.Checkbox, { checked: checked, onChange: event => {
+                        setChecked(event.target.checked);
+                    } }), label: (0, jsx_runtime_1.jsx)(material_1.Typography, { variant: "body2", children: "Show options" }) }), checked ? ((0, jsx_runtime_1.jsx)(VariantSampleFilters_1.default, { setFilter: setFilter, columns: columns, filter: filter })) : null, (0, jsx_runtime_1.jsx)("div", { style: {
+                    display: 'flex',
+                    flexDirection: 'column',
+                }, children: (0, jsx_runtime_1.jsx)(x_data_grid_1.DataGrid, { rows: rows, hideFooter: rows.length < 100, columns: columns, disableRowSelectionOnClick: true, rowHeight: 25, columnHeaderHeight: 35, disableColumnMenu: true, slots: { toolbar: checked ? x_data_grid_1.GridToolbar : null }, slotProps: {
+                        toolbar: {
+                            printOptions: {
+                                disableToolbarButton: true,
+                            },
                         },
-                    },
-                } }))));
+                    } }) })] }));
 }

package/dist/VariantFeatureWidget/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };

package/dist/VariantFeatureWidget/types.d.ts

@@ -0,0 +1,16 @@
+export interface Descriptions {
+    INFO?: {
+        ANN?: {
+            Description?: string;
+        };
+        CSQ?: {
+            Description?: string;
+        };
+    };
+}
+export interface ReducedFeature {
+    INFO?: {
+        ANN?: string[];
+        CSQ?: string[];
+    };
+}

package/dist/VariantFeatureWidget/types.js

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

package/dist/VariantRPC/MultiVariantGetGenotypeMatrix.js

@@ -7,6 +7,7 @@ exports.MultiVariantGetGenotypeMatrix = void 0;
 const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
 const RpcMethodTypeWithFiltersAndRenameRegions_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions"));
 const rxjs_1 = require("rxjs");
+const util_1 = require("../util");
 class MultiVariantGetGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions_1.default {
     constructor() {
         super(...arguments);
@@ -15,39 +16,18 @@ class MultiVariantGetGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameReg
     async execute(args, rpcDriverClassName) {
         const pm = this.pluginManager;
         const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
-        const { sources, mafFilter, regions, adapterConfig, sessionId } = deserializedArgs;
+        const { sources, minorAlleleFrequencyFilter, regions, adapterConfig, sessionId, } = deserializedArgs;
         const adapter = await (0, dataAdapterCache_1.getAdapter)(pm, sessionId, adapterConfig);
         const dataAdapter = adapter.dataAdapter;
         const region = regions[0];
         const feats = await (0, rxjs_1.firstValueFrom)(dataAdapter.getFeatures(region, deserializedArgs).pipe((0, rxjs_1.toArray)()));
         const genotypeFactor = new Set();
-        const mafs = [];
+        const mafs = (0, util_1.getFeaturesThatPassMinorAlleleFrequencyFilter)(feats, minorAlleleFrequencyFilter);
         for (const feat of feats) {
-            let c = 0;
-            let c2 = 0;
             const samp = feat.get('genotypes');
-            if (feat.get('end') - feat.get('start') <= 10) {
-                for (const { name } of sources) {
-                    const s = samp[name];
-                    genotypeFactor.add(s);
-                    if (s === '0|0' || s === './.') {
-                        c2++;
-                    }
-                    else if (s === '1|0' || s === '0|1') {
-                        c++;
-                    }
-                    else if (s === '1|1') {
-                        c++;
-                        c2++;
-                    }
-                    else {
-                        c++;
-                    }
-                }
-                if (c / sources.length > mafFilter &&
-                    c2 / sources.length < 1 - mafFilter) {
-                    mafs.push(feat);
-                }
+            for (const { name } of sources) {
+                const s = samp[name];
+                genotypeFactor.add(s);
             }
         }
         const genotypeFactorMap = Object.fromEntries([...genotypeFactor].map((type, idx) => [type, idx]));
@@ -56,7 +36,10 @@ class MultiVariantGetGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameReg
             const samp = feat.get('genotypes');
             for (const { name } of sources) {
                 if (!rows[name]) {
-                    rows[name] = { name, genotypes: [] };
+                    rows[name] = {
+                        name,
+                        genotypes: [],
+                    };
                 }
                 rows[name].genotypes.push(genotypeFactorMap[samp[name]]);
             }

package/dist/VariantRPC/MultiVariantGetSimplifiedFeatures.d.ts

@@ -1,4 +1,5 @@
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import type { SampleInfo } from '../types';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { Region } from '@jbrowse/core/util';
 export declare class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenameRegions {
@@ -11,11 +12,15 @@ export declare class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWith
         regions: Region[];
         bpPerPx: number;
     }, rpcDriverClassName: string): Promise<{
-        id: string;
-        data: {
-            start: number;
-            end: number;
-            refName: string;
-        };
-    }[]>;
+        hasPhased: boolean;
+        sampleInfo: Record<string, SampleInfo>;
+        features: {
+            id: string;
+            data: {
+                start: number;
+                end: number;
+                refName: string;
+            };
+        }[];
+    }>;
 }

package/dist/VariantRPC/MultiVariantGetSimplifiedFeatures.js

@@ -7,57 +7,47 @@ exports.MultiVariantGetSimplifiedFeatures = void 0;
 const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
 const RpcMethodTypeWithFiltersAndRenameRegions_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions"));
 const rxjs_1 = require("rxjs");
+const util_1 = require("../util");
 class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenameRegions_1.default {
     constructor() {
         super(...arguments);
         this.name = 'MultiVariantGetSimplifiedFeatures';
     }
     async execute(args, rpcDriverClassName) {
+        var _a, _b;
         const pm = this.pluginManager;
         const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
-        const { mafFilter, sources, regions, adapterConfig, sessionId } = deserializedArgs;
+        const { minorAlleleFrequencyFilter, regions, adapterConfig, sessionId } = deserializedArgs;
         const { dataAdapter } = await (0, dataAdapterCache_1.getAdapter)(pm, sessionId, adapterConfig);
         const feats = await (0, rxjs_1.firstValueFrom)(dataAdapter
             .getFeaturesInMultipleRegions(regions, deserializedArgs)
             .pipe((0, rxjs_1.toArray)()));
-        const genotypeFactor = new Set();
-        const mafs = [];
-        for (const feat of feats) {
-            let c = 0;
-            let c2 = 0;
-            const samp = feat.get('genotypes');
-            if (feat.get('end') - feat.get('start') <= 10) {
-                for (const { name } of sources) {
-                    const s = samp[name];
-                    genotypeFactor.add(s);
-                    if (s === '0|0' || s === './.') {
-                        c2++;
-                    }
-                    else if (s === '1|0' || s === '0|1') {
-                        c++;
-                    }
-                    else if (s === '1|1') {
-                        c++;
-                        c2++;
-                    }
-                    else {
-                        c++;
-                    }
-                }
-                if (c / sources.length > mafFilter &&
-                    c2 / sources.length < 1 - mafFilter) {
-                    mafs.push(feat);
-                }
+        const features = (0, util_1.getFeaturesThatPassMinorAlleleFrequencyFilter)(feats, minorAlleleFrequencyFilter);
+        const sampleInfo = {};
+        let hasPhased = false;
+        for (const f of features) {
+            const samp = f.get('genotypes');
+            for (const [key, val] of Object.entries(samp)) {
+                const isPhased = val.includes('|');
+                hasPhased || (hasPhased = isPhased);
+                sampleInfo[key] = {
+                    maxPloidy: Math.max(((_a = sampleInfo[key]) === null || _a === void 0 ? void 0 : _a.maxPloidy) || 0, val.split('|').length),
+                    isPhased: ((_b = sampleInfo[key]) === null || _b === void 0 ? void 0 : _b.isPhased) || isPhased,
+                };
             }
         }
-        return mafs.map(f => ({
-            id: f.id(),
-            data: {
-                start: f.get('start'),
-                end: f.get('end'),
-                refName: f.get('refName'),
-            },
-        }));
+        return {
+            hasPhased,
+            sampleInfo,
+            features: features.map(f => ({
+                id: f.id(),
+                data: {
+                    start: f.get('start'),
+                    end: f.get('end'),
+                    refName: f.get('refName'),
+                },
+            })),
+        };
     }
 }
 exports.MultiVariantGetSimplifiedFeatures = MultiVariantGetSimplifiedFeatures;

package/dist/VcfAdapter/VcfAdapter.d.ts

@@ -1,4 +1,5 @@
 import IntervalTree from '@flatten-js/interval-tree';
+import VcfParser from '@gmod/vcf';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { Feature, Region } from '@jbrowse/core/util';
@@ -7,6 +8,7 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
     calculatedIntervalTreeMap: Record<string, IntervalTree>;
     vcfFeatures?: Promise<{
         header: string;
+        parser: VcfParser;
         intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree>;
     }>;
     static capabilities: string[];
@@ -14,16 +16,21 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
     getMetadata(): Promise<any>;
     setupP(opts?: BaseOptions): Promise<{
         header: string;
+        parser: VcfParser;
         intervalTreeMap: {
             [k: string]: (sc?: (arg: string) => void) => IntervalTree<any>;
         };
     }>;
     setup(): Promise<{
         header: string;
+        parser: VcfParser;
         intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree>;
     }>;
     getRefNames(_?: BaseOptions): Promise<string[]>;
     getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    getSources(): Promise<{
+        name: string;
+    }[]>;
     freeResources(): void;
 }
 export {};

package/dist/VcfAdapter/VcfAdapter.js

@@ -20,8 +20,7 @@ class VcfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         return header;
     }
     async getMetadata() {
-        const { header } = await this.setup();
-        const parser = new vcf_1.default({ header });
+        const { parser } = await this.setup();
         return parser.getMetadata();
     }
     async setupP(opts) {
@@ -34,7 +33,7 @@ class VcfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         const decoder = new TextDecoder('utf8');
         let i = 0;
         while (blockStart < buffer.length) {
-            const n = buffer.indexOf('\n', blockStart);
+            const n = buffer.indexOf(10, blockStart);
             const b = n === -1 ? buffer.subarray(blockStart) : buffer.subarray(blockStart, n);
             const line = decoder.decode(b).trim();
             if (line) {
@@ -79,6 +78,7 @@ class VcfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         ]));
         return {
             header,
+            parser,
             intervalTreeMap,
         };
     }
@@ -111,6 +111,32 @@ class VcfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             }
         }, opts.stopToken);
     }
+    async getSources() {
+        const conf = this.getConf('samplesTsvLocation');
+        if (conf.uri === '' || conf.uri === '/path/to/samples.tsv') {
+            const { parser } = await this.setup();
+            return parser.samples.map(name => ({
+                name,
+            }));
+        }
+        else {
+            const txt = await (0, io_1.openLocation)(conf).readFile('utf8');
+            const lines = txt.split(/\n|\r\n|\r/);
+            const header = lines[0].split('\t');
+            const { parser } = await this.setup();
+            const s = new Set(parser.samples);
+            return lines
+                .slice(1)
+                .map(line => {
+                const cols = line.split('\t');
+                return {
+                    name: cols[0],
+                    ...Object.fromEntries(cols.slice(1).map((c, idx) => [header[idx + 1], c])),
+                };
+            })
+                .filter(f => s.has(f.name));
+        }
+    }
     freeResources() { }
 }
 VcfAdapter.capabilities = ['getFeatures', 'getRefNames'];

package/dist/VcfAdapter/configSchema.d.ts

@@ -6,5 +6,13 @@ declare const VcfAdapter: import("@jbrowse/core/configuration/configurationSchem
             locationType: string;
         };
     };
+    samplesTsvLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            description: string;
+            locationType: string;
+        };
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default VcfAdapter;

package/dist/VcfAdapter/configSchema.js

@@ -5,7 +5,18 @@ function x() { }
 const VcfAdapter = (0, configuration_1.ConfigurationSchema)('VcfAdapter', {
     vcfLocation: {
         type: 'fileLocation',
-        defaultValue: { uri: '/path/to/my.vcf', locationType: 'UriLocation' },
+        defaultValue: {
+            uri: '/path/to/my.vcf',
+            locationType: 'UriLocation',
+        },
+    },
+    samplesTsvLocation: {
+        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',
+            locationType: 'UriLocation',
+        },
     },
 }, { explicitlyTyped: true });
 exports.default = VcfAdapter;

package/dist/VcfAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };