@jbrowse/plugin-variants 3.1.0 → 3.3.0

package/dist/VariantFeatureWidget/VariantSampleGrid/VariantSampleGrid.js

@@ -3,30 +3,54 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = VariantSamples;
+exports.default = VariantSampleGrid;
 const jsx_runtime_1 = require("react/jsx-runtime");
 const react_1 = require("react");
 const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
+const ui_1 = require("@jbrowse/core/ui");
+const DataGridFlexContainer_1 = __importDefault(require("@jbrowse/core/ui/DataGridFlexContainer"));
+const ErrorBoundary_1 = require("@jbrowse/core/ui/ErrorBoundary");
 const util_1 = require("@jbrowse/core/util");
 const material_1 = require("@mui/material");
 const x_data_grid_1 = require("@mui/x-data-grid");
+const Checkbox2_1 = __importDefault(require("../Checkbox2"));
+const VariantGenotypeFrequencyTable_1 = __importDefault(require("./VariantGenotypeFrequencyTable"));
 const VariantSampleFilters_1 = __importDefault(require("./VariantSampleFilters"));
-function VariantSamples(props) {
+const util_2 = require("./util");
+const util_3 = require("../../VcfFeature/util");
+function VariantSampleGrid(props) {
     var _a;
     const { feature, descriptions = {} } = props;
     const [filter, setFilter] = (0, react_1.useState)({});
+    const [showOnlyGenotypeColumns, setShowOnlyGenotypeColumns] = (0, react_1.useState)(true);
+    const [showFilters, setShowFilters] = (0, react_1.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: `${(_a = val.GT) === null || _a === void 0 ? void 0 : _a[0]}`,
+                genotype: (0, util_3.makeSimpleAltString)(`${(_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], `${e[1]}`])),
-                sample: row[0],
-                id: row[0],
+                ...Object.fromEntries(Object.entries(val).map(([formatField, formatValue]) => [
+                    formatField,
+                    formatValue,
+                ])),
+                sample: key,
+                id: key,
             };
         })
             .filter(row => filters.length
@@ -39,9 +63,9 @@ function VariantSamples(props) {
             : true);
     }
     catch (e) {
+        console.error(e);
         error = e;
     }
-    const [checked, setChecked] = (0, react_1.useState)(false);
     const keys = ['sample', ...Object.keys(((_a = preFilteredRows[0]) === null || _a === void 0 ? void 0 : _a[1]) || {})];
     const widths = keys.map(e => (0, util_1.measureGridWidth)(rows.map(r => r[e])));
     const columns = keys.map((field, index) => {
@@ -52,16 +76,13 @@ function VariantSamples(props) {
             width: widths[index],
         });
     });
-    return !preFilteredRows.length ? null : ((0, jsx_runtime_1.jsxs)(BaseCard_1.default, { ...props, title: "Samples", children: [error ? (0, jsx_runtime_1.jsx)(material_1.Typography, { color: "error", children: `${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,
-                            },
-                        },
-                    } }) })] }));
+    const s1 = new Set(['sample', 'GT', 'genotype']);
+    const s2 = new Set(keys);
+    return !preFilteredRows.length ? null : ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(BaseCard_1.default, { ...props, title: "Genotype frequencies", children: (0, jsx_runtime_1.jsx)(ErrorBoundary_1.ErrorBoundary, { FallbackComponent: ui_1.ErrorMessage, children: (0, jsx_runtime_1.jsx)(VariantGenotypeFrequencyTable_1.default, { rows: rows }) }) }), (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)(Checkbox2_1.default, { label: "Show filters", checked: showFilters, onChange: event => {
+                            setShowFilters(event.target.checked);
+                        } }), (0, util_2.areSetsEqual)(s1, s2) ? null : ((0, jsx_runtime_1.jsx)(Checkbox2_1.default, { label: "Show only genotype columns", checked: showOnlyGenotypeColumns, onChange: event => {
+                            setShowOnlyGenotypeColumns(event.target.checked);
+                        } })), showFilters ? ((0, jsx_runtime_1.jsx)(VariantSampleFilters_1.default, { setFilter: setFilter, columns: columns, filter: filter })) : null, (0, jsx_runtime_1.jsx)(DataGridFlexContainer_1.default, { children: (0, jsx_runtime_1.jsx)(x_data_grid_1.DataGrid, { rows: rows, hideFooter: rows.length < 100, columns: showOnlyGenotypeColumns
+                                ? columns.filter(f => s1.has(f.field))
+                                : columns, rowHeight: 25, columnHeaderHeight: 35, showToolbar: true }) })] })] }));
 }

package/dist/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/dist/VariantFeatureWidget/VariantSampleGrid/types.js

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

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

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

package/dist/VariantFeatureWidget/VariantSampleGrid/util.js

@@ -0,0 +1,14 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.areSetsEqual = areSetsEqual;
+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/dist/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/dist/VariantRPC/MultiVariantClusterGenotypeMatrix.js

@@ -0,0 +1,30 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.MultiVariantClusterGenotypeMatrix = void 0;
+const RpcMethodTypeWithFiltersAndRenameRegions_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions"));
+const cluster_1 = require("@jbrowse/core/util/cluster");
+const getGenotypeMatrix_1 = require("./getGenotypeMatrix");
+class MultiVariantClusterGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions_1.default {
+    constructor() {
+        super(...arguments);
+        this.name = 'MultiVariantClusterGenotypeMatrix';
+    }
+    async execute(args, rpcDriverClassName) {
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const matrix = await (0, getGenotypeMatrix_1.getGenotypeMatrix)({
+            pluginManager: this.pluginManager,
+            args: deserializedArgs,
+        });
+        return (0, cluster_1.clusterData)({
+            data: Object.values(matrix),
+            stopToken: deserializedArgs.stopToken,
+            onProgress: progress => {
+                deserializedArgs.statusCallback(progress);
+            },
+        });
+    }
+}
+exports.MultiVariantClusterGenotypeMatrix = MultiVariantClusterGenotypeMatrix;

package/dist/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/dist/VariantRPC/MultiVariantGetGenotypeMatrix.js

@@ -4,70 +4,18 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 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 minorAlleleFrequencyUtils_1 = require("../shared/minorAlleleFrequencyUtils");
+const getGenotypeMatrix_1 = require("./getGenotypeMatrix");
 class MultiVariantGetGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions_1.default {
     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 (0, dataAdapterCache_1.getAdapter)(pm, sessionId, adapterConfig);
-        const dataAdapter = adapter.dataAdapter;
-        const feats = await (0, rxjs_1.firstValueFrom)(dataAdapter
-            .getFeaturesInMultipleRegions(regions, deserializedArgs)
-            .pipe((0, rxjs_1.toArray)()));
-        const genotypeFactor = new Set();
-        const mafs = (0, minorAlleleFrequencyUtils_1.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 (0, getGenotypeMatrix_1.getGenotypeMatrix)({
+            pluginManager: this.pluginManager,
+            args: await this.deserializeArguments(args, rpcDriverClassName),
+        });
     }
 }
 exports.MultiVariantGetGenotypeMatrix = MultiVariantGetGenotypeMatrix;

package/dist/VariantRPC/MultiVariantGetSimplifiedFeatures.d.ts

@@ -1,17 +1,9 @@
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import type { GetSimplifiedFeaturesArgs } 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 {
     name: string;
-    execute(args: {
-        adapterConfig: AnyConfigurationModel;
-        stopToken?: string;
-        sessionId: string;
-        headers?: Record<string, string>;
-        regions: Region[];
-        bpPerPx: number;
-    }, rpcDriverClassName: string): Promise<{
+    execute(args: GetSimplifiedFeaturesArgs, rpcDriverClassName: string): Promise<{
         hasPhased: boolean;
         sampleInfo: Record<string, SampleInfo>;
         features: {
@@ -20,6 +12,7 @@ export declare class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWith
                 start: number;
                 end: number;
                 refName: string;
+                name: any;
             };
         }[];
     }>;

package/dist/VariantRPC/MultiVariantGetSimplifiedFeatures.js

@@ -6,6 +6,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.MultiVariantGetSimplifiedFeatures = void 0;
 const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
 const RpcMethodTypeWithFiltersAndRenameRegions_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions"));
+const util_1 = require("@jbrowse/core/util");
 const rxjs_1 = require("rxjs");
 const minorAlleleFrequencyUtils_1 = require("../shared/minorAlleleFrequencyUtils");
 class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenameRegions_1.default {
@@ -14,18 +15,21 @@ class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenam
         this.name = 'MultiVariantGetSimplifiedFeatures';
     }
     async execute(args, rpcDriverClassName) {
-        var _a, _b;
-        const pm = this.pluginManager;
         const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
-        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 features = (0, minorAlleleFrequencyUtils_1.getFeaturesThatPassMinorAlleleFrequencyFilter)(feats, minorAlleleFrequencyFilter);
+        const { lengthCutoffFilter, minorAlleleFrequencyFilter, regions, adapterConfig, stopToken, sessionId, } = deserializedArgs;
+        const { dataAdapter } = await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig);
+        const features = (0, minorAlleleFrequencyUtils_1.getFeaturesThatPassMinorAlleleFrequencyFilter)({
+            minorAlleleFrequencyFilter,
+            lengthCutoffFilter,
+            stopToken,
+            features: await (0, rxjs_1.firstValueFrom)(dataAdapter
+                .getFeaturesInMultipleRegions(regions, deserializedArgs)
+                .pipe((0, rxjs_1.toArray)())),
+        });
         const sampleInfo = {};
         let hasPhased = false;
-        for (const { feature } of features) {
+        (0, util_1.forEachWithStopTokenCheck)(features, stopToken, ({ feature }) => {
+            var _a, _b;
             const samp = feature.get('genotypes');
             for (const [key, val] of Object.entries(samp)) {
                 const isPhased = val.includes('|');
@@ -35,7 +39,7 @@ class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenam
                     isPhased: ((_b = sampleInfo[key]) === null || _b === void 0 ? void 0 : _b.isPhased) || isPhased,
                 };
             }
-        }
+        });
         return {
             hasPhased,
             sampleInfo,
@@ -45,6 +49,7 @@ class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenam
                     start: feature.get('start'),
                     end: feature.get('end'),
                     refName: feature.get('refName'),
+                    name: feature.get('name'),
                 },
             })),
         };

package/dist/VariantRPC/getGenotypeMatrix.d.ts

@@ -0,0 +1,6 @@
+import type { GetGenotypeMatrixArgs } from './types';
+import type PluginManager from '@jbrowse/core/PluginManager';
+export declare function getGenotypeMatrix({ pluginManager, args, }: {
+    pluginManager: PluginManager;
+    args: GetGenotypeMatrixArgs;
+}): Promise<Record<string, number[]>>;

package/dist/VariantRPC/getGenotypeMatrix.js

@@ -0,0 +1,60 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getGenotypeMatrix = getGenotypeMatrix;
+const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
+const util_1 = require("@jbrowse/core/util");
+const rxjs_1 = require("rxjs");
+const minorAlleleFrequencyUtils_1 = require("../shared/minorAlleleFrequencyUtils");
+async function getGenotypeMatrix({ pluginManager, args, }) {
+    const { sources, minorAlleleFrequencyFilter, regions, adapterConfig, sessionId, lengthCutoffFilter, stopToken, } = args;
+    const adapter = await (0, dataAdapterCache_1.getAdapter)(pluginManager, sessionId, adapterConfig);
+    const dataAdapter = adapter.dataAdapter;
+    const genotypeFactor = new Set();
+    const mafs = (0, minorAlleleFrequencyUtils_1.getFeaturesThatPassMinorAlleleFrequencyFilter)({
+        minorAlleleFrequencyFilter,
+        lengthCutoffFilter,
+        stopToken,
+        features: await (0, rxjs_1.firstValueFrom)(dataAdapter.getFeaturesInMultipleRegions(regions, args).pipe((0, rxjs_1.toArray)())),
+    });
+    for (const { alleleCounts } of mafs) {
+        for (const alt of alleleCounts.keys()) {
+            genotypeFactor.add(alt);
+        }
+    }
+    const rows = {};
+    (0, util_1.forEachWithStopTokenCheck)(mafs, stopToken, ({ feature }) => {
+        const genotypes = feature.get('genotypes');
+        for (const { name } of sources) {
+            if (!rows[name]) {
+                rows[name] = [];
+            }
+            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].push(genotypeStatus);
+        }
+    });
+    return rows;
+}

package/dist/VariantRPC/types.d.ts

@@ -0,0 +1,36 @@
+import type { Source } from '../shared/types';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Region } from '@jbrowse/core/util';
+export interface GetGenotypeMatrixArgs {
+    sources: Source[];
+    minorAlleleFrequencyFilter: number;
+    adapterConfig: AnyConfigurationModel;
+    stopToken?: string;
+    sessionId: string;
+    headers?: Record<string, string>;
+    regions: Region[];
+    bpPerPx: number;
+    lengthCutoffFilter: number;
+}
+export interface GetSimplifiedFeaturesArgs {
+    adapterConfig: AnyConfigurationModel;
+    stopToken?: string;
+    sessionId: string;
+    headers?: Record<string, string>;
+    regions: Region[];
+    bpPerPx: number;
+    minorAlleleFrequencyFilter: number;
+    lengthCutoffFilter: number;
+}
+export interface ClusterGenotypeMatrixArgs {
+    adapterConfig: AnyConfigurationModel;
+    stopToken?: string;
+    statusCallback: (arg: string) => void;
+    sessionId: string;
+    headers?: Record<string, string>;
+    regions: Region[];
+    bpPerPx: number;
+    sources: Source[];
+    minorAlleleFrequencyFilter: number;
+    lengthCutoffFilter: number;
+}

package/dist/VariantRPC/types.js

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

package/dist/VcfAdapter/VcfAdapter.js

@@ -50,7 +50,7 @@ class VcfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 }
             }
             if (i++ % 10000 === 0) {
-                statusCallback(`Loading ${Math.floor(blockStart / 1000000).toLocaleString('en-US')}/${Math.floor(buffer.length / 1000000).toLocaleString('en-US')} MB`);
+                statusCallback(`Loading ${(0, util_1.getProgressDisplayStr)(blockStart, buffer.length)}`);
             }
             blockStart = n + 1;
         }
@@ -101,9 +101,12 @@ class VcfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             try {
                 const { start, end, refName } = region;
                 const { intervalTreeMap } = await this.setup();
-                (_a = intervalTreeMap[refName]) === null || _a === void 0 ? void 0 : _a.call(intervalTreeMap, opts.statusCallback).search([start, end]).forEach(f => {
+                for (const f of ((_a = intervalTreeMap[refName]) === null || _a === void 0 ? void 0 : _a.call(intervalTreeMap, opts.statusCallback).search([
+                    start,
+                    end,
+                ])) || []) {
                     observer.next(f);
-                });
+                }
                 observer.complete();
             }
             catch (e) {

package/dist/VcfFeature/index.js

@@ -12,7 +12,6 @@ function dataFromVariant(variant, parser) {
         description,
         type,
         name: ID === null || ID === void 0 ? void 0 : ID.join(','),
-        aliases: ID && ID.length > 1 ? ID.slice(1) : undefined,
     };
 }
 function getEnd(variant) {

package/dist/VcfFeature/util.d.ts

@@ -2,3 +2,5 @@ import type VCF from '@gmod/vcf';
 export declare function getSOTermAndDescription(ref: string, alt: string[] | undefined, parser: VCF): string[];
 export declare function getSOAndDescFromAltDefs(alt: string, parser: VCF): string[];
 export declare function getSOAndDescByExamination(ref: string, alt: string): string[];
+export declare function getMinimalDesc(ref: string, alt: string): string;
+export declare function makeSimpleAltString(genotype: string, ref: string, alt: string[]): string;