@jbrowse/plugin-variants 2.16.0 → 2.17.0

package/dist/VariantFeatureWidget/LaunchBreakendPanel.js

@@ -22,12 +22,15 @@ var __importStar = (this && this.__importStar) || function (mod) {
     __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 = BreakendPanel;
 const react_1 = __importStar(require("react"));
 const material_1 = require("@mui/material");
 const util_1 = require("@jbrowse/core/util");
-const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
+const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
 // lazies
 const BreakendMultiLevelOptionDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./BreakendMultiLevelOptionDialog'))));
 const BreakendSingleLevelOptionDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./BreakendSingleLevelOptionDialog'))));
@@ -109,7 +112,7 @@ function BreakendPanel(props) {
     catch (e) {
         // ignore
     }
-    return (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { ...props, title: "Breakends" },
+    return (react_1.default.createElement(BaseCard_1.default, { ...props, title: "Breakends" },
         react_1.default.createElement(LocStringList, { model: model, locStrings: locStrings }),
         viewType ? (react_1.default.createElement(LaunchBreakpointSplitViewPanel, { viewType: viewType, model: model, locStrings: locStrings, feature: feature })) : null));
 }

package/dist/VariantFeatureWidget/VariantAnnotationTable.js

@@ -5,10 +5,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = VariantAnnotationTable;
 const react_1 = __importDefault(require("react"));
-const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
 const AnnotGrid_1 = __importDefault(require("./AnnotGrid"));
+const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
 function VariantAnnotationTable({ data, fields, title, }) {
-    return data.length ? (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { title: title },
+    return data.length ? (react_1.default.createElement(BaseCard_1.default, { title: title },
         react_1.default.createElement(AnnotGrid_1.default, { rows: data.map((elt, id) => ({
                 id,
                 ...Object.fromEntries(elt.split('|').map((e, i) => [fields[i], e])),

package/dist/VariantFeatureWidget/VariantFeatureWidget.js

@@ -29,7 +29,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
 const mobx_react_1 = require("mobx-react");
 const material_1 = require("@mui/material");
-const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
+const FeatureDetails_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails"));
 const vcf_1 = require("@gmod/vcf");
 // locals
 const VariantSampleGrid_1 = __importDefault(require("./VariantSampleGrid"));
@@ -57,7 +57,7 @@ const VariantFeatureWidget = (0, mobx_react_1.observer)(function (props) {
     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(BaseFeatureDetail_1.FeatureDetails, { feature: rest, descriptions: { ...variantFieldDescriptions_1.variantFieldDescriptions, ...descriptions }, ...props }),
+        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 },

package/dist/VariantFeatureWidget/VariantSampleGrid.js

@@ -22,13 +22,16 @@ var __importStar = (this && this.__importStar) || function (mod) {
     __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 material_1 = require("@mui/material");
 const x_data_grid_1 = require("@mui/x-data-grid");
-const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
 const util_1 = require("@jbrowse/core/util");
+const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
 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"),
@@ -69,8 +72,8 @@ function VariantSamples(props) {
     catch (e) {
         error = e;
     }
-    const keys = ['sample', ...Object.keys(((_a = preFilteredRows[0]) === null || _a === void 0 ? void 0 : _a[1]) || {})];
     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) => {
         var _a, _b;
@@ -82,7 +85,7 @@ function VariantSamples(props) {
     });
     // disableRowSelectionOnClick helps avoid
     // https://github.com/mui-org/material-ui-x/issues/1197
-    return !preFilteredRows.length ? null : (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { ...props, title: "Samples" },
+    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);

package/dist/VariantFeatureWidget/stateModelFactory.d.ts

@@ -93,8 +93,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackId: string | undefined;
     trackType: string | undefined;
     maxDepth: number | undefined;
-    formattedFields: any;
     sequenceFeatureDetails: import("mobx-state-tree").ModelSnapshotType<{}>;
+    formattedFields: any;
     finalizedFeatureData: any;
 } & import("mobx-state-tree")._NotCustomized>;
 export type VariantFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;

package/dist/VcfAdapter/VcfAdapter.js

@@ -8,7 +8,6 @@ const util_1 = require("@jbrowse/core/util");
 const io_1 = require("@jbrowse/core/util/io");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
-const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 const vcf_1 = __importDefault(require("@gmod/vcf"));
 // local
 const VcfFeature_1 = __importDefault(require("../VcfFeature"));
@@ -28,20 +27,18 @@ class VcfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     async setupP(opts) {
         const { statusCallback = () => { } } = opts || {};
-        const buf = (await (0, io_1.openLocation)(this.getConf('vcfLocation'), this.pluginManager).readFile(opts));
-        const buffer = (0, util_1.isGzip)(buf)
-            ? await (0, util_1.updateStatus)('Unzipping', statusCallback, () => (0, bgzf_filehandle_1.unzip)(buf))
-            : buf;
+        const loc = (0, io_1.openLocation)(this.getConf('vcfLocation'), this.pluginManager);
+        const buffer = await (0, util_1.fetchAndMaybeUnzip)(loc, opts);
         const headerLines = [];
         const featureMap = {};
         let blockStart = 0;
-        const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
+        const decoder = new TextDecoder('utf8');
         let i = 0;
         while (blockStart < buffer.length) {
             const n = buffer.indexOf('\n', blockStart);
             // could be a non-newline ended file, so slice to end of file if n===-1
             const b = n === -1 ? buffer.subarray(blockStart) : buffer.subarray(blockStart, n);
-            const line = ((decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString()).trim();
+            const line = decoder.decode(b).trim();
             if (line) {
                 if (line.startsWith('#')) {
                     headerLines.push(line);

package/esm/VariantFeatureWidget/LaunchBreakendPanel.js

@@ -1,7 +1,7 @@
 import React, { lazy } from 'react';
 import { Link, Typography } from '@mui/material';
 import { getEnv, getSession, SimpleFeature, } from '@jbrowse/core/util';
-import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
+import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
 // lazies
 const BreakendMultiLevelOptionDialog = lazy(() => import('./BreakendMultiLevelOptionDialog'));
 const BreakendSingleLevelOptionDialog = lazy(() => import('./BreakendSingleLevelOptionDialog'));

package/esm/VariantFeatureWidget/VariantAnnotationTable.js

@@ -1,6 +1,6 @@
 import React from 'react';
-import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
 import AnnotGrid from './AnnotGrid';
+import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
 export default function VariantAnnotationTable({ data, fields, title, }) {
     return data.length ? (React.createElement(BaseCard, { title: title },
         React.createElement(AnnotGrid, { rows: data.map((elt, id) => ({

package/esm/VariantFeatureWidget/VariantFeatureWidget.js

@@ -1,7 +1,7 @@
 import React, { lazy, Suspense } from 'react';
 import { observer } from 'mobx-react';
 import { Paper } from '@mui/material';
-import { FeatureDetails } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
+import FeatureDetails from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails';
 import { parseBreakend } from '@gmod/vcf';
 // locals
 import VariantSampleGrid from './VariantSampleGrid';

package/esm/VariantFeatureWidget/VariantSampleGrid.js

@@ -1,8 +1,8 @@
 import React, { useState } from 'react';
 import { FormControlLabel, Checkbox, TextField, Typography, } from '@mui/material';
 import { DataGrid, GridToolbar } from '@mui/x-data-grid';
-import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
 import { measureGridWidth } from '@jbrowse/core/util';
+import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
 function SampleFilters({ columns, filter, setFilter, }) {
     return (React.createElement(React.Fragment, null,
         React.createElement(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"),
@@ -43,8 +43,8 @@ export default function VariantSamples(props) {
     catch (e) {
         error = e;
     }
-    const keys = ['sample', ...Object.keys(((_a = preFilteredRows[0]) === null || _a === void 0 ? void 0 : _a[1]) || {})];
     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) => {
         var _a, _b;

package/esm/VariantFeatureWidget/stateModelFactory.d.ts

@@ -93,8 +93,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackId: string | undefined;
     trackType: string | undefined;
     maxDepth: number | undefined;
-    formattedFields: any;
     sequenceFeatureDetails: import("mobx-state-tree").ModelSnapshotType<{}>;
+    formattedFields: any;
     finalizedFeatureData: any;
 } & import("mobx-state-tree")._NotCustomized>;
 export type VariantFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;

package/esm/VcfAdapter/VcfAdapter.js

@@ -1,9 +1,8 @@
 import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { updateStatus, isGzip } from '@jbrowse/core/util';
+import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import IntervalTree from '@flatten-js/interval-tree';
-import { unzip } from '@gmod/bgzf-filehandle';
 import VCF from '@gmod/vcf';
 // local
 import VcfFeature from '../VcfFeature';
@@ -23,20 +22,18 @@ class VcfAdapter extends BaseFeatureDataAdapter {
     }
     async setupP(opts) {
         const { statusCallback = () => { } } = opts || {};
-        const buf = (await openLocation(this.getConf('vcfLocation'), this.pluginManager).readFile(opts));
-        const buffer = isGzip(buf)
-            ? await updateStatus('Unzipping', statusCallback, () => unzip(buf))
-            : buf;
+        const loc = openLocation(this.getConf('vcfLocation'), this.pluginManager);
+        const buffer = await fetchAndMaybeUnzip(loc, opts);
         const headerLines = [];
         const featureMap = {};
         let blockStart = 0;
-        const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
+        const decoder = new TextDecoder('utf8');
         let i = 0;
         while (blockStart < buffer.length) {
             const n = buffer.indexOf('\n', blockStart);
             // could be a non-newline ended file, so slice to end of file if n===-1
             const b = n === -1 ? buffer.subarray(blockStart) : buffer.subarray(blockStart, n);
-            const line = ((decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString()).trim();
+            const line = decoder.decode(b).trim();
             if (line) {
                 if (line.startsWith('#')) {
                     headerLines.push(line);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "2.16.0",
+  "version": "2.17.0",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -40,7 +40,7 @@
     "@gmod/bgzf-filehandle": "^1.4.3",
     "@gmod/tabix": "^1.5.6",
     "@gmod/vcf": "^5.0.9",
-    "@jbrowse/sv-core": "^2.16.0",
+    "@jbrowse/sv-core": "^2.17.0",
     "@mui/icons-material": "^6.0.0",
     "@mui/x-data-grid": "^7.0.0",
     "generic-filehandle": "^3.0.0"
@@ -63,5 +63,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "1e6d4fbc27ce684eed19e3c217f34bd2da24ab75"
+  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
 }