@jbrowse/plugin-variants 2.18.0 → 3.0.0

package/dist/VcfFeature/index.js

@@ -2,7 +2,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const util_1 = require("./util");
 function dataFromVariant(variant, parser) {
-    const { REF = '', ALT, POS, CHROM, ID } = variant;
+    const { FORMAT, REF = '', ALT, POS, CHROM, ID } = variant;
     const start = POS - 1;
     const [type, description] = (0, util_1.getSOTermAndDescription)(REF, ALT, parser);
     return {
@@ -13,6 +13,7 @@ function dataFromVariant(variant, parser) {
         type,
         name: ID === null || ID === void 0 ? void 0 : ID.join(','),
         aliases: ID && ID.length > 1 ? ID.slice(1) : undefined,
+        format: FORMAT,
     };
 }
 function getEnd(variant) {

package/dist/VcfFeature/util.js

@@ -51,10 +51,9 @@ function getSOTermAndDescription(ref, alt, parser) {
             return suffixes.length ? `${prefix} -> ${suffixes.join(',')}` : prefix;
         }));
     }
-    if (soTerms.size) {
-        return [[...soTerms].join(','), [...descriptions].join(',')];
-    }
-    return [];
+    return soTerms.size
+        ? [[...soTerms].join(','), [...descriptions].join(',')]
+        : [];
 }
 function getSOAndDescFromAltDefs(alt, parser) {
     if (typeof alt === 'string' && !alt.startsWith('<')) {

package/dist/VcfTabixAdapter/VcfTabixAdapter.js

@@ -6,24 +6,29 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const tabix_1 = require("@gmod/tabix");
 const vcf_1 = __importDefault(require("@gmod/vcf"));
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+const util_1 = require("@jbrowse/core/util");
 const io_1 = require("@jbrowse/core/util/io");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const VcfFeature_1 = __importDefault(require("../VcfFeature"));
 class VcfTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
-    async configurePre() {
-        const pm = this.pluginManager;
+    async configurePre(opts) {
+        const { statusCallback = () => { } } = opts || {};
         const vcfGzLocation = this.getConf('vcfGzLocation');
         const location = this.getConf(['index', 'location']);
         const indexType = this.getConf(['index', 'indexType']);
-        const filehandle = (0, io_1.openLocation)(vcfGzLocation, pm);
+        const filehandle = (0, io_1.openLocation)(vcfGzLocation, this.pluginManager);
         const isCSI = indexType === 'CSI';
         const vcf = new tabix_1.TabixIndexedFile({
             filehandle,
-            csiFilehandle: isCSI ? (0, io_1.openLocation)(location, pm) : undefined,
-            tbiFilehandle: !isCSI ? (0, io_1.openLocation)(location, pm) : undefined,
+            csiFilehandle: isCSI
+                ? (0, io_1.openLocation)(location, this.pluginManager)
+                : undefined,
+            tbiFilehandle: !isCSI
+                ? (0, io_1.openLocation)(location, this.pluginManager)
+                : undefined,
             chunkCacheSize: 50 * 2 ** 20,
         });
-        const header = await vcf.getHeader();
+        const header = await (0, util_1.updateStatus)('Downloading index', statusCallback, () => vcf.getHeader());
         return {
             vcf,
             parser: new vcf_1.default({ header }),
@@ -53,8 +58,9 @@ class VcfTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     getFeatures(query, opts = {}) {
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
             const { refName, start, end } = query;
+            const { statusCallback = () => { } } = opts;
             const { vcf, parser } = await this.configure();
-            await vcf.getLines(refName, start, end, {
+            await (0, util_1.updateStatus)('Downloading variants', statusCallback, () => vcf.getLines(refName, start, end, {
                 lineCallback: (line, fileOffset) => {
                     observer.next(new VcfFeature_1.default({
                         variant: parser.parseLine(line),
@@ -63,15 +69,35 @@ class VcfTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                     }));
                 },
                 ...opts,
-            });
+            }));
             observer.complete();
         }, opts.stopToken);
     }
     async getSources() {
-        const { parser } = await this.configure();
-        return parser.samples.map(name => ({
-            name,
-        }));
+        const conf = this.getConf('samplesTsvLocation');
+        if (conf.uri === '' || conf.uri === '/path/to/samples.tsv') {
+            const { parser } = await this.configure();
+            return parser.samples.map(name => ({
+                name,
+            }));
+        }
+        else {
+            const txt = await (0, util_1.fetchAndMaybeUnzipText)((0, io_1.openLocation)(conf, this.pluginManager));
+            const lines = txt.split(/\n|\r\n|\r/);
+            const header = lines[0].split('\t');
+            const { parser } = await this.configure();
+            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() { }
 }

package/dist/VcfTabixAdapter/configSchema.d.ts

@@ -20,5 +20,13 @@ declare const VcfTabixAdapter: import("@jbrowse/core/configuration/configuration
             };
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    samplesTsvLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            description: string;
+            locationType: string;
+        };
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default VcfTabixAdapter;

package/dist/VcfTabixAdapter/configSchema.js

@@ -22,5 +22,13 @@ const VcfTabixAdapter = (0, configuration_1.ConfigurationSchema)('VcfTabixAdapte
             },
         },
     }),
+    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 = VcfTabixAdapter;

package/dist/VcfTabixAdapter/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/extensionPoints.js

@@ -1,51 +1,39 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = ExtensionPointsF;
+const util_1 = require("@jbrowse/core/util");
 const tracks_1 = require("@jbrowse/core/util/tracks");
 function ExtensionPointsF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
         return (file, index, adapterHint) => {
-            const regexGuess = /\.vcf\.b?gz$/i;
-            const adapterName = 'VcfTabixAdapter';
             const fileName = (0, tracks_1.getFileName)(file);
             const indexName = index && (0, tracks_1.getFileName)(index);
-            const obj = {
-                type: adapterName,
-                vcfGzLocation: file,
-                index: {
-                    location: index || (0, tracks_1.makeIndex)(file, '.tbi'),
-                    indexType: (0, tracks_1.makeIndexType)(indexName, 'CSI', 'TBI'),
-                },
-            };
-            if (regexGuess.test(fileName) && !adapterHint) {
-                return obj;
+            if ((0, util_1.testAdapter)(fileName, /\.vcf\.b?gz$/i, adapterHint, 'VcfTabixAdapter')) {
+                return {
+                    type: 'VcfTabixAdapter',
+                    vcfGzLocation: file,
+                    index: {
+                        location: index || (0, tracks_1.makeIndex)(file, '.tbi'),
+                        indexType: (0, tracks_1.makeIndexType)(indexName, 'CSI', 'TBI'),
+                    },
+                };
+            }
+            else if ((0, util_1.testAdapter)(fileName, /\.vcf(\.gz)?$/i, adapterHint, 'VcfAdapter')) {
+                return {
+                    type: 'VcfAdapter',
+                    vcfLocation: file,
+                };
             }
-            if (adapterHint === adapterName) {
-                return obj;
+            else {
+                return adapterGuesser(file, index, adapterHint);
             }
-            return adapterGuesser(file, index, adapterHint);
         };
     });
     pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
         return (adapterName) => {
-            if (adapterName === 'VcfTabixAdapter' || adapterName === 'VcfAdapter') {
-                return 'VariantTrack';
-            }
-            return trackTypeGuesser(adapterName);
-        };
-    });
-    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-        return (file, index, adapterHint) => {
-            const regexGuess = /\.vcf$/i;
-            const adapterName = 'VcfAdapter';
-            const fileName = (0, tracks_1.getFileName)(file);
-            if (regexGuess.test(fileName) || adapterHint === adapterName) {
-                return {
-                    type: adapterName,
-                    vcfLocation: file,
-                };
-            }
-            return adapterGuesser(file, index, adapterHint);
+            return ['VcfTabixAdapter', 'VcfAdapter'].includes(adapterName)
+                ? 'VariantTrack'
+                : trackTypeGuesser(adapterName);
         };
     });
 }

package/dist/getMultiVariantFeaturesAutorun.d.ts

@@ -1,19 +1,16 @@
+import type { SampleInfo, Source } from './types';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { Feature } from '@jbrowse/core/util';
-export interface Source {
-    name: string;
-    color?: string;
-    group?: string;
-    [key: string]: string | undefined;
-}
 export declare function getMultiVariantFeaturesAutorun(self: {
     configuration: AnyConfigurationModel;
     adapterConfig: AnyConfigurationModel;
     sources?: Source[];
-    mafFilter: number;
+    minorAlleleFrequencyFilter: number;
     statsReadyAndRegionNotTooLarge: boolean;
     adapterProps: () => Record<string, unknown>;
     setError: (error: unknown) => void;
     setFeatures: (f: Feature[]) => void;
     setMessage: (str: string) => void;
+    setHasPhased: (arg: boolean) => void;
+    setSampleInfo: (arg: Record<string, SampleInfo>) => void;
 }): void;

package/dist/getMultiVariantFeaturesAutorun.js

@@ -14,25 +14,26 @@ function getMultiVariantFeaturesAutorun(self) {
                 return;
             }
             const { rpcManager } = (0, util_1.getSession)(self);
-            const { sources, mafFilter, adapterConfig } = self;
-            if (!sources) {
-                return;
-            }
-            const sessionId = (0, tracks_1.getRpcSessionId)(self);
-            const features = (await rpcManager.call(sessionId, 'MultiVariantGetSimplifiedFeatures', {
-                regions: view.dynamicBlocks.contentBlocks,
-                sources,
-                mafFilter,
-                sessionId,
-                adapterConfig,
-            }));
-            if ((0, mobx_state_tree_1.isAlive)(self)) {
-                self.setFeatures(features.map(f => new util_1.SimpleFeature(f)));
+            const { sources, minorAlleleFrequencyFilter, adapterConfig } = self;
+            if (sources) {
+                const sessionId = (0, tracks_1.getRpcSessionId)(self);
+                const { sampleInfo, hasPhased, features } = (await rpcManager.call(sessionId, 'MultiVariantGetSimplifiedFeatures', {
+                    regions: view.dynamicBlocks.contentBlocks,
+                    sources,
+                    minorAlleleFrequencyFilter,
+                    sessionId,
+                    adapterConfig,
+                }));
+                if ((0, mobx_state_tree_1.isAlive)(self)) {
+                    self.setHasPhased(hasPhased);
+                    self.setSampleInfo(sampleInfo);
+                    self.setFeatures(features.map(f => new util_1.SimpleFeature(f)));
+                }
             }
         }
         catch (e) {
+            console.error(e);
             if (!(0, aborting_1.isAbortException)(e) && (0, mobx_state_tree_1.isAlive)(self)) {
-                console.error(e);
                 (0, util_1.getSession)(self).notifyError(`${e}`, e);
             }
         }

package/dist/getMultiVariantSourcesAutorun.d.ts

@@ -1,10 +1,5 @@
+import type { Source } from './types';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-export interface Source {
-    name: string;
-    color?: string;
-    group?: string;
-    [key: string]: string | undefined;
-}
 export declare function getMultiVariantSourcesAutorun(self: {
     configuration: AnyConfigurationModel;
     adapterConfig: AnyConfigurationModel;

package/dist/shared/BulkEditPanel.d.ts

@@ -1,6 +1,5 @@
-import React from 'react';
-import { type Source } from '../util';
-export default function BulkEditPanel({ setCurrLayout, currLayout, }: {
+import type { Source } from '../types';
+export default function BulkEditPanel({ onClose, currLayout, }: {
     currLayout: Source[];
-    setCurrLayout: (arg: Source[]) => void;
-}): React.JSX.Element;
+    onClose: (arg?: Source[]) => void;
+}): import("react/jsx-runtime").JSX.Element;

package/dist/shared/BulkEditPanel.js

@@ -1,30 +1,8 @@
 "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;
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = BulkEditPanel;
-const react_1 = __importStar(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const ui_1 = require("@jbrowse/core/ui");
 const material_1 = require("@mui/material");
 const mui_1 = require("tss-react/mui");
@@ -33,71 +11,74 @@ const useStyles = (0, mui_1.makeStyles)()({
         fontFamily: 'Courier New',
     },
 });
-function BulkEditPanel({ setCurrLayout, currLayout, }) {
+function BulkEditPanel({ onClose, currLayout, }) {
     const { classes } = useStyles();
     const [val, setVal] = (0, react_1.useState)('');
     const [error, setError] = (0, react_1.useState)();
-    return (react_1.default.createElement("div", null,
-        react_1.default.createElement(material_1.Typography, null, "Paste CSV or TSV. If a header column is present. First line is a header. If a column called \"name\" is present, it uses that to connect to IDs in the table, otherwise it uses the first column no."),
-        react_1.default.createElement(material_1.TextField, { variant: "outlined", multiline: true, minRows: 5, placeholder: 'name,population\nHG00098,GBR\nHG00101,GBR\nHG00459,CHS\n...', maxRows: 10, fullWidth: true, value: val, onChange: event => {
-                setVal(event.target.value);
-            }, slotProps: {
-                input: {
-                    classes: {
-                        input: classes.textAreaFont,
-                    },
-                },
-            } }),
-        react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => {
-                const lines = val
-                    .split('\n')
-                    .map(f => f.trim())
-                    .filter(f => !!f);
-                const fields = lines[0].split(/[,\t]/gm);
-                if (fields.includes('name')) {
-                    setError('');
-                    const oldLayout = currLayout.map(record => [record.name, record]);
-                    const newData = Object.fromEntries(lines.slice(1).map(line => {
-                        const cols = line.split(/[,\t]/gm);
-                        const newRecord = Object.fromEntries(cols.map((col, idx) => [fields[idx], col]));
-                        return [
-                            newRecord.name,
-                            { ...newRecord, ...oldLayout[newRecord.name] },
-                        ];
-                    }));
-                    setCurrLayout(currLayout.map(record => ({
-                        ...record,
-                        ...newData[record.name],
-                    })));
-                }
-                else {
-                    setError(new Error('No "name" column found on line 1'));
-                }
-            } }, "Update rows"),
-        react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => {
-                const lines = val
-                    .split('\n')
-                    .map(f => f.trim())
-                    .filter(f => !!f);
-                const fields = lines[0].split(/[,\t]/gm);
-                if (fields.includes('name')) {
-                    setError('');
-                    const oldLayout = currLayout.map(record => [record.name, record]);
-                    const newData = Object.fromEntries(lines.slice(1).map(line => {
-                        const cols = line.split(/[,\t]/gm);
-                        const newRecord = Object.fromEntries(cols.map((col, idx) => [fields[idx], col]));
-                        return [
-                            newRecord.name,
-                            { ...newRecord, ...oldLayout[newRecord.name] },
-                        ];
-                    }));
-                    setCurrLayout(currLayout.map(record => ({
-                        ...newData[record.name],
-                    })));
-                }
-                else {
-                    setError(new Error('No "name" column found on line 1'));
-                }
-            } }, "Replace rows"),
-        error ? react_1.default.createElement(ui_1.ErrorMessage, { error: error }) : null));
+    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Paste CSV or TSV. If a header column is present. First line is a header. If a column called \"name\" is present, it uses that to connect to IDs in the table, otherwise it uses the first column no." }), error ? (0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error }) : null, (0, jsx_runtime_1.jsx)(material_1.TextField, { variant: "outlined", multiline: true, minRows: 5, placeholder: 'name,population\nHG00098,GBR\nHG00101,GBR\nHG00459,CHS\n...', maxRows: 10, fullWidth: true, value: val, onChange: event => {
+                            setVal(event.target.value);
+                        }, slotProps: {
+                            input: {
+                                classes: {
+                                    input: classes.textAreaFont,
+                                },
+                            },
+                        } })] }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
+                            const lines = val
+                                .split('\n')
+                                .map(f => f.trim())
+                                .filter(f => !!f);
+                            const fields = lines[0].split(/[,\t]/gm);
+                            if (fields.includes('name')) {
+                                setError('');
+                                const oldLayout = Object.fromEntries(currLayout.map(record => [record.name, record]));
+                                const newData = Object.fromEntries(lines.slice(1).map(line => {
+                                    const cols = line.split(/[,\t]/gm);
+                                    const newRecord = Object.fromEntries(cols.map((col, idx) => [fields[idx], col]));
+                                    return [
+                                        newRecord.name,
+                                        {
+                                            ...newRecord,
+                                            ...oldLayout[newRecord.name],
+                                        },
+                                    ];
+                                }));
+                                onClose(currLayout.map(record => ({
+                                    ...record,
+                                    ...newData[record.name],
+                                })));
+                            }
+                            else {
+                                setError(new Error('No "name" column found on line 1'));
+                            }
+                        }, children: "Update rows" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "primary", onClick: () => {
+                            const lines = val
+                                .split('\n')
+                                .map(f => f.trim())
+                                .filter(f => !!f);
+                            const fields = lines[0].split(/[,\t]/gm);
+                            if (fields.includes('name')) {
+                                setError('');
+                                const oldLayout = Object.fromEntries(currLayout.map(record => [record.name, record]));
+                                const newData = Object.fromEntries(lines.slice(1).map(line => {
+                                    const cols = line.split(/[,\t]/gm);
+                                    const newRecord = Object.fromEntries(cols.map((col, idx) => [fields[idx], col]));
+                                    return [
+                                        newRecord.name,
+                                        {
+                                            ...newRecord,
+                                            ...oldLayout[newRecord.name],
+                                        },
+                                    ];
+                                }));
+                                onClose(currLayout.map(record => ({
+                                    ...newData[record.name],
+                                })));
+                            }
+                            else {
+                                setError(new Error('No "name" column found on line 1'));
+                            }
+                        }, children: "Replace rows" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "inherit", onClick: () => {
+                            onClose();
+                        }, children: "Cancel" })] })] }));
 }

package/dist/shared/ClusterDialog.d.ts

@@ -1,12 +1,11 @@
-import React from 'react';
-import type { Source } from '../util';
+import type { Source } from '../types';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-export default function HierarchicalCluster({ model, handleClose, }: {
+export default function ClusterDialog({ model, handleClose, }: {
     model: {
         sources?: Source[];
-        mafFilter?: number;
+        minorAlleleFrequencyFilter?: number;
         adapterConfig: AnyConfigurationModel;
         setLayout: (arg: Source[]) => void;
     };
     handleClose: () => void;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;