@jbrowse/plugin-variants 2.0.0 → 2.1.2

package/esm/VariantFeatureWidget/VariantFeatureWidget.js

@@ -1,109 +1,14 @@
 /* eslint-disable @typescript-eslint/no-explicit-any */
-import React, { useState } from 'react';
-import { Divider, Link, Paper, FormControlLabel, Checkbox, TextField, Typography, } from '@mui/material';
-import SimpleFeature from '@jbrowse/core/util/simpleFeature';
-import { DataGrid } from '@mui/x-data-grid';
+import React from 'react';
 import { observer } from 'mobx-react';
-import { getSession } from '@jbrowse/core/util';
-import { getEnv } from 'mobx-state-tree';
-import { FeatureDetails, BaseCard, } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
-import BreakendOptionDialog from './BreakendOptionDialog';
+import { Divider, Paper } from '@mui/material';
+import { FeatureDetails } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
 import { parseBreakend } from '@gmod/vcf';
-function VariantSamples(props) {
-    const [filter, setFilter] = useState({});
-    const [showFilters, setShowFilters] = useState(false);
-    const { feature } = props;
-    const { samples = {} } = feature;
-    const preFilteredRows = Object.entries(samples);
-    if (!preFilteredRows.length) {
-        return null;
-    }
-    const infoFields = ['sample', ...Object.keys(preFilteredRows[0][1])].map(field => ({
-        field,
-    }));
-    let error;
-    let rows = [];
-    const filters = Object.keys(filter);
-    // catch some error thrown from regex
-    // note: maps all values into a string, if this is not done rows are not
-    // sortable by the data-grid
-    try {
-        rows = preFilteredRows
-            .map((row) => ({
-            ...Object.fromEntries(Object.entries(row[1]).map(entry => [entry[0], String(entry[1])])),
-            sample: row[0],
-            id: row[0],
-        }))
-            .filter((row) => {
-            return filters.length
-                ? filters.every(key => {
-                    const val = row[key];
-                    const currFilter = filter[key];
-                    return currFilter ? val.match(new RegExp(currFilter, 'i')) : true;
-                })
-                : true;
-        });
-    }
-    catch (e) {
-        error = e;
-    }
-    // disableSelectionOnClick helps avoid
-    // https://github.com/mui-org/material-ui-x/issues/1197
-    return (React.createElement(BaseCard, { ...props, title: "Samples" },
-        error ? React.createElement(Typography, { color: "error" }, `${error}`) : null,
-        React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: showFilters, onChange: () => setShowFilters(f => !f) }), label: "Show sample filters" }),
-        showFilters ? (React.createElement(React.Fragment, null,
-            React.createElement(Typography, null, "These filters can use a plain text search or regex style query, e.g. in the genotype field, entering 1 will query for all genotypes that include the first alternate allele e.g. 0|1 or 1|1, entering [1-9]\\d* will find any non-zero allele e.g. 0|2 or 2/33"),
-            infoFields.map(({ field }) => {
-                return (React.createElement(TextField, { key: `filter-${field}`, placeholder: `Filter ${field}`, value: filter[field] || '', onChange: event => setFilter({ ...filter, [field]: event.target.value }) }));
-            }))) : null,
-        React.createElement("div", { style: { height: 600, width: '100%', overflow: 'auto' } },
-            React.createElement(DataGrid, { rows: rows, columns: infoFields, disableSelectionOnClick: true, rowHeight: 25, disableColumnMenu: true }))));
-}
-function BreakendPanel(props) {
-    const { model, locStrings, feature } = props;
-    const session = getSession(model);
-    const { pluginManager } = getEnv(session);
-    const [breakpointDialog, setBreakpointDialog] = useState(false);
-    let viewType;
-    try {
-        viewType = pluginManager.getViewType('BreakpointSplitView');
-    }
-    catch (e) {
-        // ignore
-    }
-    const simpleFeature = new SimpleFeature(feature);
-    return (React.createElement(BaseCard, { ...props, title: "Breakends" },
-        React.createElement(Typography, null, "Link to linear view of breakend endpoints"),
-        React.createElement("ul", null, locStrings.map(locString => (React.createElement("li", { key: `${JSON.stringify(locString)}` },
-            React.createElement(Link, { href: "#", onClick: event => {
-                    var _a;
-                    event.preventDefault();
-                    const { view } = model;
-                    try {
-                        if (view) {
-                            (_a = view.navToLocString) === null || _a === void 0 ? void 0 : _a.call(view, locString);
-                        }
-                        else {
-                            throw new Error('No view associated with this feature detail panel anymore');
-                        }
-                    }
-                    catch (e) {
-                        console.error(e);
-                        session.notify(`${e}`);
-                    }
-                } }, `LGV - ${locString}`))))),
-        viewType ? (React.createElement("div", null,
-            React.createElement(Typography, null, "Launch split views with breakend source and target"),
-            React.createElement("ul", null, locStrings.map(locString => (React.createElement("li", { key: `${JSON.stringify(locString)}` },
-                React.createElement(Link, { href: "#", onClick: event => {
-                        event.preventDefault();
-                        setBreakpointDialog(true);
-                    } }, `${feature.refName}:${feature.start} // ${locString} (split view)`))))),
-            breakpointDialog ? (React.createElement(BreakendOptionDialog, { model: model, feature: simpleFeature, viewType: viewType, handleClose: () => {
-                    setBreakpointDialog(false);
-                } })) : null)) : null));
-}
+// locals
+import VariantSampleGrid from './VariantSampleGrid';
+import VariantCsqPanel from './VariantCsqPanel';
+import VariantAnnPanel from './VariantAnnPanel';
+import BreakendPanel from './BreakendPanel';
 function VariantFeatureDetails(props) {
     const { model } = props;
     const { featureData, descriptions } = model;
@@ -121,9 +26,13 @@ function VariantFeatureDetails(props) {
     return (React.createElement(Paper, { "data-testid": "variant-side-drawer" },
         React.createElement(FeatureDetails, { feature: rest, descriptions: { ...basicDescriptions, ...descriptions }, ...props }),
         React.createElement(Divider, null),
+        React.createElement(VariantCsqPanel, { feature: rest, descriptions: descriptions }),
+        React.createElement(Divider, null),
+        React.createElement(VariantAnnPanel, { feature: rest, descriptions: descriptions }),
+        React.createElement(Divider, null),
         feat.type === 'breakend' ? (React.createElement(BreakendPanel, { feature: feat, locStrings: feat.ALT.map((alt) => { var _a; return ((_a = parseBreakend(alt)) === null || _a === void 0 ? void 0 : _a.MatePosition) || ''; }), model: model })) : null,
         feat.type === 'translocation' ? (React.createElement(BreakendPanel, { feature: feat, model: model, locStrings: [`${feat.INFO.CHR2[0]}:${feat.INFO.END}`] })) : null,
-        React.createElement(VariantSamples, { feature: feat, ...props })));
+        React.createElement(VariantSampleGrid, { feature: feat, ...props })));
 }
 export default observer(VariantFeatureDetails);
 //# sourceMappingURL=VariantFeatureWidget.js.map

package/esm/VariantFeatureWidget/VariantFeatureWidget.js.map

@@ -1 +1 @@
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+{"version":3,"file":"VariantFeatureWidget.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/VariantFeatureWidget.tsx"],"names":[],"mappings":"AAAA,uDAAuD;AACvD,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,eAAe,CAAA;AAC9C,OAAO,EAAE,cAAc,EAAE,MAAM,mDAAmD,CAAA;AAClF,OAAO,EAAE,aAAa,EAAE,MAAM,WAAW,CAAA;AAEzC,SAAS;AACT,OAAO,iBAAiB,MAAM,qBAAqB,CAAA;AACnD,OAAO,eAAe,MAAM,mBAAmB,CAAA;AAC/C,OAAO,eAAe,MAAM,mBAAmB,CAAA;AAC/C,OAAO,aAAa,MAAM,iBAAiB,CAAA;AAE3C,SAAS,qBAAqB,CAAC,KAAU;IACvC,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACvB,MAAM,EAAE,WAAW,EAAE,YAAY,EAAE,GAAG,KAAK,CAAA;IAC3C,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,WAAW,CAAC,CAAC,CAAA;IACpD,MAAM,EAAE,OAAO,EAAE,GAAG,IAAI,EAAE,GAAG,IAAI,CAAA;IACjC,MAAM,iBAAiB,GAAG;QACxB,KAAK,EAAE,qDAAqD;QAC5D,GAAG,EAAE,uEAAuE;QAC5E,EAAE,EAAE,6EAA6E;QACjF,GAAG,EAAE,2EAA2E;QAChF,GAAG,EAAE,4EAA4E;QACjF,IAAI,EAAE,mEAAmE;QACzE,MAAM,EACJ,kIAAkI;KACrI,CAAA;IAED,OAAO,CACL,oBAAC,KAAK,mBAAa,qBAAqB;QACtC,oBAAC,cAAc,IACb,OAAO,EAAE,IAAI,EACb,YAAY,EAAE,EAAE,GAAG,iBAAiB,EAAE,GAAG,YAAY,EAAE,KACnD,KAAK,GACT;QACF,oBAAC,OAAO,OAAG;QACX,oBAAC,eAAe,IAAC,OAAO,EAAE,IAAI,EAAE,YAAY,EAAE,YAAY,GAAI;QAC9D,oBAAC,OAAO,OAAG;QACX,oBAAC,eAAe,IAAC,OAAO,EAAE,IAAI,EAAE,YAAY,EAAE,YAAY,GAAI;QAC9D,oBAAC,OAAO,OAAG;QACV,IAAI,CAAC,IAAI,KAAK,UAAU,CAAC,CAAC,CAAC,CAC1B,oBAAC,aAAa,IACZ,OAAO,EAAE,IAAI,EACb,UAAU,EAAE,IAAI,CAAC,GAAG,CAAC,GAAG,CACtB,CAAC,GAAW,EAAE,EAAE,WAAC,OAAA,CAAA,MAAA,aAAa,CAAC,GAAG,CAAC,0CAAE,YAAY,KAAI,EAAE,CAAA,EAAA,CACxD,EACD,KAAK,EAAE,KAAK,GACZ,CACH,CAAC,CAAC,CAAC,IAAI;QACP,IAAI,CAAC,IAAI,KAAK,eAAe,CAAC,CAAC,CAAC,CAC/B,oBAAC,aAAa,IACZ,OAAO,EAAE,IAAI,EACb,KAAK,EAAE,KAAK,EACZ,UAAU,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,CAAC,GACrD,CACH,CAAC,CAAC,CAAC,IAAI;QACR,oBAAC,iBAAiB,IAAC,OAAO,EAAE,IAAI,KAAM,KAAK,GAAI,CACzC,CACT,CAAA;AACH,CAAC;AAED,eAAe,QAAQ,CAAC,qBAAqB,CAAC,CAAA"}

package/esm/VariantFeatureWidget/VariantSampleGrid.d.ts

@@ -0,0 +1,2 @@
+/// <reference types="react" />
+export default function VariantSamples(props: any): JSX.Element | null;

package/esm/VariantFeatureWidget/VariantSampleGrid.js

@@ -0,0 +1,57 @@
+/* eslint-disable @typescript-eslint/no-explicit-any */
+import React, { useState } from 'react';
+import { FormControlLabel, Checkbox, TextField, Typography, } from '@mui/material';
+import { DataGrid } from '@mui/x-data-grid';
+import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
+export default function VariantSamples(props) {
+    const [filter, setFilter] = useState({});
+    const [showFilters, setShowFilters] = useState(false);
+    const { feature } = props;
+    const { samples = {} } = feature;
+    const preFilteredRows = Object.entries(samples);
+    if (!preFilteredRows.length) {
+        return null;
+    }
+    const infoFields = ['sample', ...Object.keys(preFilteredRows[0][1])].map(field => ({
+        field,
+    }));
+    let error;
+    let rows = [];
+    const filters = Object.keys(filter);
+    // catch some error thrown from regex
+    // note: maps all values into a string, if this is not done rows are not
+    // sortable by the data-grid
+    try {
+        rows = preFilteredRows
+            .map((row) => ({
+            ...Object.fromEntries(Object.entries(row[1]).map(entry => [entry[0], String(entry[1])])),
+            sample: row[0],
+            id: row[0],
+        }))
+            .filter((row) => {
+            return filters.length
+                ? filters.every(key => {
+                    const val = row[key];
+                    const currFilter = filter[key];
+                    return currFilter ? val.match(new RegExp(currFilter, 'i')) : true;
+                })
+                : true;
+        });
+    }
+    catch (e) {
+        error = e;
+    }
+    // disableSelectionOnClick helps avoid
+    // https://github.com/mui-org/material-ui-x/issues/1197
+    return (React.createElement(BaseCard, { ...props, title: "Samples" },
+        error ? React.createElement(Typography, { color: "error" }, `${error}`) : null,
+        React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: showFilters, onChange: () => setShowFilters(f => !f) }), label: "Show sample filters" }),
+        showFilters ? (React.createElement(React.Fragment, null,
+            React.createElement(Typography, null, "These filters can use a plain text search or regex style query, e.g. in the genotype field, entering 1 will query for all genotypes that include the first alternate allele e.g. 0|1 or 1|1, entering [1-9]\\d* will find any non-zero allele e.g. 0|2 or 2/33"),
+            infoFields.map(({ field }) => {
+                return (React.createElement(TextField, { key: `filter-${field}`, placeholder: `Filter ${field}`, value: filter[field] || '', onChange: event => setFilter({ ...filter, [field]: event.target.value }) }));
+            }))) : null,
+        React.createElement("div", { style: { height: 600, width: '100%', overflow: 'auto' } },
+            React.createElement(DataGrid, { rows: rows, columns: infoFields, disableSelectionOnClick: true, rowHeight: 25, disableColumnMenu: true }))));
+}
+//# sourceMappingURL=VariantSampleGrid.js.map

package/esm/VariantFeatureWidget/VariantSampleGrid.js.map

@@ -0,0 +1 @@
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package/esm/VariantFeatureWidget/index.d.ts

@@ -35,3 +35,5 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     formattedFields: any;
     finalizedFeatureData: any;
 } & import("mobx-state-tree")._NotCustomized>;
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/esm/VariantFeatureWidget/index.js

@@ -1,4 +1,6 @@
+import { lazy } from 'react';
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import WidgetType from '@jbrowse/core/pluggableElementTypes/WidgetType';
 import { types } from 'mobx-state-tree';
 import { stateModelFactory as baseModelFactory } from '@jbrowse/core/BaseFeatureWidget';
 export const configSchema = ConfigurationSchema('VariantFeatureWidget', {});
@@ -9,4 +11,13 @@ export function stateModelFactory(pluginManager) {
         descriptions: types.frozen(),
     }));
 }
+export default (pluginManager) => {
+    pluginManager.addWidgetType(() => new WidgetType({
+        name: 'VariantFeatureWidget',
+        heading: 'Feature details',
+        configSchema,
+        stateModel: stateModelFactory(pluginManager),
+        ReactComponent: lazy(() => import('./VariantFeatureWidget')),
+    }));
+};
 //# sourceMappingURL=index.js.map

package/esm/VariantFeatureWidget/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AACvC,OAAO,EAAE,iBAAiB,IAAI,gBAAgB,EAAE,MAAM,iCAAiC,CAAA;AAEvF,MAAM,CAAC,MAAM,YAAY,GAAG,mBAAmB,CAAC,sBAAsB,EAAE,EAAE,CAAC,CAAA;AAE3E,MAAM,UAAU,iBAAiB,CAAC,aAA4B;IAC5D,MAAM,SAAS,GAAG,gBAAgB,CAAC,aAAa,CAAC,CAAA;IACjD,OAAO,KAAK,CAAC,OAAO,CAClB,SAAS,EACT,KAAK,CAAC,KAAK,CAAC,sBAAsB,EAAE;QAClC,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,sBAAsB,CAAC;QAC3C,YAAY,EAAE,KAAK,CAAC,MAAM,EAAE;KAC7B,CAAC,CACH,CAAA;AACH,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAC5B,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,UAAU,MAAM,gDAAgD,CAAA;AAEvE,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AACvC,OAAO,EAAE,iBAAiB,IAAI,gBAAgB,EAAE,MAAM,iCAAiC,CAAA;AAEvF,MAAM,CAAC,MAAM,YAAY,GAAG,mBAAmB,CAAC,sBAAsB,EAAE,EAAE,CAAC,CAAA;AAE3E,MAAM,UAAU,iBAAiB,CAAC,aAA4B;IAC5D,MAAM,SAAS,GAAG,gBAAgB,CAAC,aAAa,CAAC,CAAA;IACjD,OAAO,KAAK,CAAC,OAAO,CAClB,SAAS,EACT,KAAK,CAAC,KAAK,CAAC,sBAAsB,EAAE;QAClC,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,sBAAsB,CAAC;QAC3C,YAAY,EAAE,KAAK,CAAC,MAAM,EAAE;KAC7B,CAAC,CACH,CAAA;AACH,CAAC;AAED,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,aAAa,CACzB,GAAG,EAAE,CACH,IAAI,UAAU,CAAC;QACb,IAAI,EAAE,sBAAsB;QAC5B,OAAO,EAAE,iBAAiB;QAC1B,YAAY;QACZ,UAAU,EAAE,iBAAiB,CAAC,aAAa,CAAC;QAC5C,cAAc,EAAE,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,wBAAwB,CAAC,CAAC;KAC7D,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/esm/VariantTrack/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/esm/VariantTrack/index.js

@@ -0,0 +1,14 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType';
+import { createBaseTrackConfig, createBaseTrackModel, } from '@jbrowse/core/pluggableElementTypes/models';
+export default (pluginManager) => {
+    pluginManager.addTrackType(() => {
+        const configSchema = ConfigurationSchema('VariantTrack', {}, { baseConfiguration: createBaseTrackConfig(pluginManager) });
+        return new TrackType({
+            name: 'VariantTrack',
+            configSchema,
+            stateModel: createBaseTrackModel(pluginManager, 'VariantTrack', configSchema),
+        });
+    });
+};
+//# sourceMappingURL=index.js.map

package/esm/VariantTrack/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VariantTrack/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,SAAS,MAAM,+CAA+C,CAAA;AACrE,OAAO,EACL,qBAAqB,EACrB,oBAAoB,GACrB,MAAM,4CAA4C,CAAA;AAEnD,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,YAAY,CAAC,GAAG,EAAE;QAC9B,MAAM,YAAY,GAAG,mBAAmB,CACtC,cAAc,EACd,EAAE,EACF,EAAE,iBAAiB,EAAE,qBAAqB,CAAC,aAAa,CAAC,EAAE,CAC5D,CAAA;QACD,OAAO,IAAI,SAAS,CAAC;YACnB,IAAI,EAAE,cAAc;YACpB,YAAY;YACZ,UAAU,EAAE,oBAAoB,CAC9B,aAAa,EACb,cAAc,EACd,YAAY,CACb;SACF,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/esm/VcfAdapter/VcfAdapter.js

@@ -1,16 +1,17 @@
 import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { readConfObject } from '@jbrowse/core/configuration';
 import IntervalTree from '@flatten-js/interval-tree';
 import { unzip } from '@gmod/bgzf-filehandle';
 import VCF from '@gmod/vcf';
 import VcfFeature from '../VcfTabixAdapter/VcfFeature';
 const readVcf = (f) => {
-    const lines = f.split('\n');
     const header = [];
     const rest = [];
-    lines.forEach(line => {
+    f.split('\n')
+        .map(f => f.trim())
+        .filter(f => !!f)
+        .forEach(line => {
         if (line.startsWith('#')) {
             header.push(line);
         }
@@ -35,13 +36,14 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
     }
     // converts lines into an interval tree
     async setupP() {
-        const buffer = await openLocation(readConfObject(this.config, 'vcfLocation'), this.pluginManager).readFile();
-        const buf = isGzip(buffer) ? await unzip(buffer) : buffer;
+        const pm = this.pluginManager;
+        const buf = await openLocation(this.getConf('vcfLocation'), pm).readFile();
+        const buffer = isGzip(buf) ? await unzip(buf) : buf;
         // 512MB  max chrome string length is 512MB
-        if (buf.length > 536870888) {
+        if (buffer.length > 536870888) {
             throw new Error('Data exceeds maximum string length (512MB)');
         }
-        const str = new TextDecoder().decode(buf);
+        const str = new TextDecoder().decode(buffer);
         const { header, lines } = readVcf(str);
         const intervalTree = lines
             .map((line, id) => {

package/esm/VcfAdapter/VcfAdapter.js.map

@@ -1 +1 @@
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package/esm/VcfAdapter/index.d.ts

@@ -1 +1,3 @@
-export { default as configSchema } from './configSchema';
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/esm/VcfAdapter/index.js

@@ -1,2 +1,10 @@
-export { default as configSchema } from './configSchema';
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import configSchema from './configSchema';
+export default (pluginManager) => {
+    pluginManager.addAdapterType(() => new AdapterType({
+        name: 'VcfAdapter',
+        configSchema,
+        getAdapterClass: () => import('./VcfAdapter').then(r => r.default),
+    }));
+};
 //# sourceMappingURL=index.js.map

package/esm/VcfAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VcfAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VcfAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AACzE,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;QACd,IAAI,EAAE,YAAY;QAClB,YAAY;QACZ,eAAe,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,cAAc,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACnE,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/esm/VcfTabixAdapter/VcfFeature.js

@@ -52,7 +52,7 @@ export default class VCFFeature {
      */
     _getSOTermAndDescription(ref, alt) {
         // it's just a remark if there are no alternate alleles
-        if (!alt || alt === []) {
+        if (!alt || alt.length === 0) {
             return ['remark', 'no alternative alleles'];
         }
         const soTerms = new Set();

package/esm/VcfTabixAdapter/VcfFeature.js.map

@@ -1 +1 @@
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package/esm/VcfTabixAdapter/VcfTabixAdapter.js

@@ -84,9 +84,6 @@ export default class extends BaseFeatureDataAdapter {
      * @returns Observable of Feature objects in the regions
      */
     getFeaturesInMultipleRegions(regions, opts = {}) {
-        // TODO: restore commented version below once TSDX supports Rollup v2
-        // xref: https://github.com/rollup/rollup/blob/master/CHANGELOG.md#bug-fixes-45
-        const superGetFeaturesInMultipleRegions = super.getFeaturesInMultipleRegions;
         return ObservableCreate(async (observer) => {
             const { vcf } = await this.configure();
             // @ts-ignore
@@ -101,10 +98,7 @@ export default class extends BaseFeatureDataAdapter {
             if (pct > 60) {
                 console.warn(`getFeaturesInMultipleRegions fetching ${pct}% of VCF file, but whole-file streaming not yet implemented`);
             }
-            superGetFeaturesInMultipleRegions
-                .call(this, regions, opts)
-                .subscribe(observer);
-            // super.getFeaturesInMultipleRegions(regions, opts).subscribe(observer)
+            super.getFeaturesInMultipleRegions(regions, opts).subscribe(observer);
         });
     }
     freeResources( /* { region } */) { }

package/esm/VcfTabixAdapter/VcfTabixAdapter.js.map

@@ -1 +1 @@
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package/esm/VcfTabixAdapter/index.d.ts

@@ -1 +1,4 @@
+import PluginManager from '@jbrowse/core/PluginManager';
 export { default as configSchema } from './configSchema';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/esm/VcfTabixAdapter/index.js

@@ -1,2 +1,11 @@
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import configSchema from './configSchema';
 export { default as configSchema } from './configSchema';
+export default (pluginManager) => {
+    pluginManager.addAdapterType(() => new AdapterType({
+        name: 'VcfTabixAdapter',
+        configSchema,
+        getAdapterClass: () => import('./VcfTabixAdapter').then(r => r.default),
+    }));
+};
 //# sourceMappingURL=index.js.map

package/esm/VcfTabixAdapter/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AACzE,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAA;AAExD,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;QACd,IAAI,EAAE,iBAAiB;QACvB,YAAY;QACZ,eAAe,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,mBAAmB,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACxE,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/esm/extensionPoints.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/esm/extensionPoints.js

@@ -0,0 +1,49 @@
+import { makeIndex, makeIndexType, getFileName, } from '@jbrowse/core/util/tracks';
+export default (pluginManager) => {
+    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+        return (file, index, adapterHint) => {
+            const regexGuess = /\.vcf\.b?gz$/i;
+            const adapterName = 'VcfTabixAdapter';
+            const fileName = getFileName(file);
+            const indexName = index && getFileName(index);
+            const obj = {
+                type: adapterName,
+                vcfGzLocation: file,
+                index: {
+                    location: index || makeIndex(file, '.tbi'),
+                    indexType: makeIndexType(indexName, 'CSI', 'TBI'),
+                },
+            };
+            if (regexGuess.test(fileName) && !adapterHint) {
+                return obj;
+            }
+            else if (adapterHint === adapterName) {
+                return obj;
+            }
+            return adapterGuesser(file, index, adapterHint);
+        };
+    });
+    pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
+        return (adapterName) => {
+            if (adapterName === 'VcfTabixAdapter' || adapterName === 'VcfAdapter') {
+                return 'VariantTrack';
+            }
+            return trackTypeGuesser(adapterName);
+        };
+    });
+    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+        return (file, index, adapterHint) => {
+            const regexGuess = /\.vcf$/i;
+            const adapterName = 'VcfAdapter';
+            const fileName = getFileName(file);
+            if (regexGuess.test(fileName) || adapterHint === adapterName) {
+                return {
+                    type: adapterName,
+                    vcfLocation: file,
+                };
+            }
+            return adapterGuesser(file, index, adapterHint);
+        };
+    });
+};
+//# sourceMappingURL=extensionPoints.js.map

package/esm/extensionPoints.js.map

@@ -0,0 +1 @@
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