@jbrowse/plugin-variants 1.7.10 → 2.0.1

package/esm/VcfTabixAdapter/VcfTabixAdapter.d.ts

@@ -0,0 +1,35 @@
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { NoAssemblyRegion, Region } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { TabixIndexedFile } from '@gmod/tabix';
+import VcfParser from '@gmod/vcf';
+import { GenericFilehandle } from 'generic-filehandle';
+export default class extends BaseFeatureDataAdapter {
+    private configured?;
+    private configurePre;
+    protected configure(): Promise<{
+        filehandle: GenericFilehandle;
+        vcf: TabixIndexedFile;
+        parser: VcfParser;
+    }>;
+    getRefNames(opts?: BaseOptions): Promise<any>;
+    getHeader(): Promise<string>;
+    getMetadata(): Promise<any>;
+    getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    /**
+     * Checks if the data source has data for the given reference sequence,
+     * and then gets the features in the region if it does
+     *
+     * Currently this just calls getFeatureInRegion for each region. Adapters that
+     * are frequently called on multiple regions simultaneously may want to
+     * implement a more efficient custom version of this method.
+     *
+     * Also includes a bit of extra logging to warn when fetching a large portion
+     * of a VCF
+     * @param regions - Regions
+     * @param opts - Feature adapter options
+     * @returns Observable of Feature objects in the regions
+     */
+    getFeaturesInMultipleRegions(regions: Region[], opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}

package/esm/VcfTabixAdapter/VcfTabixAdapter.js

@@ -0,0 +1,112 @@
+import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { openLocation } from '@jbrowse/core/util/io';
+import { bytesForRegions } from '@jbrowse/core/util';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import { TabixIndexedFile } from '@gmod/tabix';
+import VcfParser from '@gmod/vcf';
+import { readConfObject } from '@jbrowse/core/configuration';
+import VcfFeature from './VcfFeature';
+export default class extends BaseFeatureDataAdapter {
+    async configurePre() {
+        const vcfGzLocation = readConfObject(this.config, 'vcfGzLocation');
+        const location = readConfObject(this.config, ['index', 'location']);
+        const indexType = readConfObject(this.config, ['index', 'indexType']);
+        const filehandle = openLocation(vcfGzLocation, this.pluginManager);
+        const isCSI = indexType === 'CSI';
+        const vcf = new TabixIndexedFile({
+            filehandle,
+            csiFilehandle: isCSI
+                ? openLocation(location, this.pluginManager)
+                : undefined,
+            tbiFilehandle: !isCSI
+                ? openLocation(location, this.pluginManager)
+                : undefined,
+            chunkCacheSize: 50 * 2 ** 20,
+            chunkSizeLimit: 1000000000,
+        });
+        const header = await vcf.getHeader();
+        return {
+            filehandle,
+            vcf,
+            parser: new VcfParser({ header }),
+        };
+    }
+    async configure() {
+        if (!this.configured) {
+            this.configured = this.configurePre().catch(e => {
+                this.configured = undefined;
+                throw e;
+            });
+        }
+        return this.configured;
+    }
+    async getRefNames(opts = {}) {
+        const { vcf } = await this.configure();
+        return vcf.getReferenceSequenceNames(opts);
+    }
+    async getHeader() {
+        const { vcf } = await this.configure();
+        return vcf.getHeader();
+    }
+    async getMetadata() {
+        const { parser } = await this.configure();
+        return parser.getMetadata();
+    }
+    getFeatures(query, opts = {}) {
+        return ObservableCreate(async (observer) => {
+            const { refName, start, end } = query;
+            const { vcf, parser } = await this.configure();
+            await vcf.getLines(refName, start, end, {
+                lineCallback: (line, fileOffset) => {
+                    observer.next(new VcfFeature({
+                        variant: parser.parseLine(line),
+                        parser,
+                        id: `${this.id}-vcf-${fileOffset}`,
+                    }));
+                },
+                ...opts,
+            });
+            observer.complete();
+        }, opts.signal);
+    }
+    /**
+     * Checks if the data source has data for the given reference sequence,
+     * and then gets the features in the region if it does
+     *
+     * Currently this just calls getFeatureInRegion for each region. Adapters that
+     * are frequently called on multiple regions simultaneously may want to
+     * implement a more efficient custom version of this method.
+     *
+     * Also includes a bit of extra logging to warn when fetching a large portion
+     * of a VCF
+     * @param regions - Regions
+     * @param opts - Feature adapter options
+     * @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
+            const bytes = await bytesForRegions(regions, vcf.index);
+            const { filehandle } = await this.configure();
+            const stat = await filehandle.stat();
+            let pct = Math.round((bytes / stat.size) * 100);
+            if (pct > 100) {
+                // this is just a bad estimate, make 100% if it goes over
+                pct = 100;
+            }
+            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)
+        });
+    }
+    freeResources( /* { region } */) { }
+}
+//# sourceMappingURL=VcfTabixAdapter.js.map

package/esm/VcfTabixAdapter/VcfTabixAdapter.js.map

@@ -0,0 +1 @@
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package/esm/VcfTabixAdapter/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/esm/VcfTabixAdapter/configSchema.js

@@ -0,0 +1,23 @@
+import { types } from 'mobx-state-tree';
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export default ConfigurationSchema('VcfTabixAdapter', {
+    vcfGzLocation: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/my.vcf.gz', locationType: 'UriLocation' },
+    },
+    index: ConfigurationSchema('VcfIndex', {
+        indexType: {
+            model: types.enumeration('IndexType', ['TBI', 'CSI']),
+            type: 'stringEnum',
+            defaultValue: 'TBI',
+        },
+        location: {
+            type: 'fileLocation',
+            defaultValue: {
+                uri: '/path/to/my.vcf.gz.tbi',
+                locationType: 'UriLocation',
+            },
+        },
+    }),
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/esm/VcfTabixAdapter/configSchema.js.map

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

@@ -0,0 +1 @@
+export { default as configSchema } from './configSchema';

package/esm/VcfTabixAdapter/index.js

@@ -0,0 +1,2 @@
+export { default as configSchema } from './configSchema';
+//# sourceMappingURL=index.js.map

package/esm/VcfTabixAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAA"}

package/esm/index.d.ts

@@ -0,0 +1,7 @@
+import Plugin from '@jbrowse/core/Plugin';
+import PluginManager from '@jbrowse/core/PluginManager';
+export default class VariantsPlugin extends Plugin {
+    name: string;
+    install(pluginManager: PluginManager): void;
+}
+export { default as VcfFeature } from './VcfTabixAdapter/VcfFeature';

package/esm/index.js

@@ -0,0 +1,110 @@
+import { lazy } from 'react';
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
+import { createBaseTrackConfig, createBaseTrackModel, } from '@jbrowse/core/pluggableElementTypes/models';
+import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType';
+import WidgetType from '@jbrowse/core/pluggableElementTypes/WidgetType';
+import Plugin from '@jbrowse/core/Plugin';
+import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view';
+import ChordVariantDisplay from './ChordVariantDisplay';
+import { configSchemaFactory as linearVariantDisplayConfigSchemaFactory, modelFactory as linearVariantDisplayModelFactory, } from './LinearVariantDisplay';
+import StructuralVariantChordRendererFactory from './StructuralVariantChordRenderer';
+import { configSchema as variantFeatureWidgetConfigSchema, stateModelFactory as variantFeatureWidgetStateModelFactory, } from './VariantFeatureWidget';
+import { configSchema as vcfTabixAdapterConfigSchema } from './VcfTabixAdapter';
+import { configSchema as vcfAdapterConfigSchema } from './VcfAdapter';
+import { makeIndex, makeIndexType, getFileName, } from '@jbrowse/core/util/tracks';
+export default class VariantsPlugin extends Plugin {
+    constructor() {
+        super(...arguments);
+        this.name = 'VariantsPlugin';
+    }
+    install(pluginManager) {
+        pluginManager.addAdapterType(() => new AdapterType({
+            name: 'VcfTabixAdapter',
+            configSchema: vcfTabixAdapterConfigSchema,
+            getAdapterClass: () => import('./VcfTabixAdapter/VcfTabixAdapter').then(r => r.default),
+        }));
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+            return (file, index, adapterHint) => {
+                const regexGuess = /\.vcf\.b?gz$/i;
+                const adapterName = 'VcfTabixAdapter';
+                const fileName = getFileName(file);
+                const indexName = index && getFileName(index);
+                const obj = {
+                    type: adapterName,
+                    vcfGzLocation: file,
+                    index: {
+                        location: index || makeIndex(file, '.tbi'),
+                        indexType: makeIndexType(indexName, 'CSI', 'TBI'),
+                    },
+                };
+                if (regexGuess.test(fileName) && !adapterHint) {
+                    return obj;
+                }
+                else if (adapterHint === adapterName) {
+                    return obj;
+                }
+                return adapterGuesser(file, index, adapterHint);
+            };
+        });
+        pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
+            return (adapterName) => {
+                if (adapterName === 'VcfTabixAdapter' ||
+                    adapterName === 'VcfAdapter') {
+                    return 'VariantTrack';
+                }
+                return trackTypeGuesser(adapterName);
+            };
+        });
+        pluginManager.addAdapterType(() => new AdapterType({
+            name: 'VcfAdapter',
+            configSchema: vcfAdapterConfigSchema,
+            getAdapterClass: () => import('./VcfAdapter/VcfAdapter').then(r => r.default),
+        }));
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+            return (file, index, adapterHint) => {
+                const regexGuess = /\.vcf$/i;
+                const adapterName = 'VcfAdapter';
+                const fileName = getFileName(file);
+                if (regexGuess.test(fileName) || adapterHint === adapterName) {
+                    return {
+                        type: adapterName,
+                        vcfLocation: file,
+                    };
+                }
+                return adapterGuesser(file, index, adapterHint);
+            };
+        });
+        pluginManager.addRendererType(() => pluginManager.jbrequire(StructuralVariantChordRendererFactory));
+        pluginManager.addTrackType(() => {
+            const configSchema = ConfigurationSchema('VariantTrack', {}, { baseConfiguration: createBaseTrackConfig(pluginManager) });
+            return new TrackType({
+                name: 'VariantTrack',
+                configSchema,
+                stateModel: createBaseTrackModel(pluginManager, 'VariantTrack', configSchema),
+            });
+        });
+        pluginManager.addDisplayType(() => pluginManager.jbrequire(ChordVariantDisplay));
+        pluginManager.addDisplayType(() => {
+            const configSchema = linearVariantDisplayConfigSchemaFactory(pluginManager);
+            return new DisplayType({
+                name: 'LinearVariantDisplay',
+                configSchema,
+                stateModel: linearVariantDisplayModelFactory(configSchema),
+                trackType: 'VariantTrack',
+                viewType: 'LinearGenomeView',
+                ReactComponent: BaseLinearDisplayComponent,
+            });
+        });
+        pluginManager.addWidgetType(() => new WidgetType({
+            name: 'VariantFeatureWidget',
+            heading: 'Feature details',
+            configSchema: variantFeatureWidgetConfigSchema,
+            stateModel: variantFeatureWidgetStateModelFactory(pluginManager),
+            ReactComponent: lazy(() => import('./VariantFeatureWidget/VariantFeatureWidget')),
+        }));
+    }
+}
+export { default as VcfFeature } from './VcfTabixAdapter/VcfFeature';
+//# sourceMappingURL=index.js.map

package/esm/index.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "1.7.10",
+  "version": "2.0.1",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -20,17 +20,21 @@
   "main": "dist/index.js",
   "files": [
     "dist",
-    "src"
+    "src",
+    "esm"
   ],
   "scripts": {
-    "build": "babel src --root-mode upward --out-dir dist --extensions .ts,.js,.tsx,.jsx",
+    "build": "npm-run-all build:*",
     "test": "cd ../..; jest plugins/variants",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build; yarn useDist",
     "postpack": "yarn useSrc",
     "useDist": "node ../../scripts/useDist.js",
     "useSrc": "node ../../scripts/useSrc.js",
-    "postbuild": "tsc --build tsconfig.build.json"
+    "prebuild": "npm run clean",
+    "build:esm": "tsc --build tsconfig.build.esm.json",
+    "build:es5": "tsc --build tsconfig.build.es5.json",
+    "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
     "@babel/runtime": "^7.17.9",
@@ -38,24 +42,29 @@
     "@gmod/bgzf-filehandle": "^1.4.3",
     "@gmod/tabix": "^1.5.2",
     "@gmod/vcf": "^5.0.5",
-    "@material-ui/icons": "^4.11.2",
-    "@mui/x-data-grid": "^4.0.1",
+    "@mui/icons-material": "^5.0.2",
+    "@mui/x-data-grid": "^5.0.1",
     "generic-filehandle": "^2.2.2"
   },
   "peerDependencies": {
-    "@jbrowse/core": "^1.0.0",
-    "@jbrowse/plugin-alignments": "^1.0.0",
-    "@jbrowse/plugin-circular-view": "^1.0.0",
-    "@jbrowse/plugin-linear-genome-view": "^1.0.0",
-    "@material-ui/core": "^4.12.2",
-    "mobx-react": "^6.0.0",
-    "mobx-state-tree": "3.14.1",
+    "@jbrowse/core": "^2.0.0",
+    "@jbrowse/plugin-alignments": "^2.0.0",
+    "@jbrowse/plugin-circular-view": "^2.0.0",
+    "@jbrowse/plugin-linear-genome-view": "^2.0.0",
+    "@mui/material": "^5.0.0",
+    "mobx": "^6.0.0",
+    "mobx-react": "^7.0.0",
+    "mobx-state-tree": "^5.0.0",
     "prop-types": "^15.0.0",
     "react": ">=16.8.0",
-    "rxjs": "^6.0.0"
+    "rxjs": "^6.0.0",
+    "tss-react": "^3.0.0"
   },
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "02d8c1e88e5603ea5855faed4ccb814e28071b32"
+  "distModule": "esm/index.js",
+  "srcModule": "src/index.ts",
+  "module": "esm/index.js",
+  "gitHead": "ed935bf5612af3818abdc8ef52d100d5d81d33a2"
 }

package/src/ChordVariantDisplay/index.ts

@@ -1,10 +1,10 @@
 import PluginManager from '@jbrowse/core/PluginManager'
-import { BaseChordDisplayComponentFactory } from '@jbrowse/plugin-circular-view'
+import { BaseChordDisplayComponent } from '@jbrowse/plugin-circular-view'
 import ChordVariantDisplay from './models/ChordVariantDisplay'
+import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
 
 export default (pluginManager: PluginManager) => {
-  const { lib, load } = pluginManager
-  const DisplayType = lib['@jbrowse/core/pluggableElementTypes/DisplayType']
+  const { load } = pluginManager
 
   const { stateModel, configSchema } = load(ChordVariantDisplay)
 
@@ -14,6 +14,6 @@ export default (pluginManager: PluginManager) => {
     stateModel,
     trackType: 'VariantTrack',
     viewType: 'CircularView',
-    ReactComponent: BaseChordDisplayComponentFactory(pluginManager),
+    ReactComponent: BaseChordDisplayComponent,
   })
 }

package/src/ChordVariantDisplay/models/ChordVariantDisplay.js

@@ -2,16 +2,15 @@ import {
   baseChordDisplayConfig,
   BaseChordDisplayModel,
 } from '@jbrowse/plugin-circular-view'
+import {
+  ConfigurationSchema,
+  ConfigurationReference,
+} from '@jbrowse/core/configuration'
+import { types } from 'mobx-state-tree'
+import { getContainingView } from '@jbrowse/core/util'
+import { getParentRenderProps } from '@jbrowse/core/util/tracks'
 
 const ChordVariantDisplayF = pluginManager => {
-  const { jbrequire } = pluginManager
-
-  const { types } = jbrequire('mobx-state-tree')
-  const { ConfigurationSchema, ConfigurationReference } = jbrequire(
-    '@jbrowse/core/configuration',
-  )
-  const { getContainingView } = jbrequire('@jbrowse/core/util')
-  const { getParentRenderProps } = jbrequire('@jbrowse/core/util/tracks')
   const configSchema = ConfigurationSchema(
     'ChordVariantDisplay',
     {

package/src/VariantFeatureWidget/BreakendOptionDialog.tsx

@@ -3,22 +3,21 @@ import React, { useState } from 'react'
 import { observer } from 'mobx-react'
 import {
   Button,
+  Checkbox,
   Dialog,
   DialogActions,
   DialogContent,
   DialogTitle,
   Divider,
-  IconButton,
   FormControlLabel,
-  Checkbox,
-  makeStyles,
-} from '@material-ui/core'
-import CloseIcon from '@material-ui/icons/Close'
+  IconButton,
+} from '@mui/material'
+import { makeStyles } from 'tss-react/mui'
+import CloseIcon from '@mui/icons-material/Close'
 import { getSnapshot } from 'mobx-state-tree'
-import { getSession } from '@jbrowse/core/util'
-import { Feature } from '@jbrowse/core/util/simpleFeature'
+import { getSession, Feature } from '@jbrowse/core/util'
 
-const useStyles = makeStyles(theme => ({
+const useStyles = makeStyles()(theme => ({
   closeButton: {
     position: 'absolute',
     right: theme.spacing(1),
@@ -41,7 +40,7 @@ function BreakendOptionDialog({
   feature: Feature
   viewType: any
 }) {
-  const classes = useStyles()
+  const { classes } = useStyles()
   const [copyTracks, setCopyTracks] = useState(true)
   const [mirrorTracks, setMirrorTracks] = useState(true)
 

package/src/VariantFeatureWidget/VariantFeatureWidget.tsx

@@ -8,7 +8,7 @@ import {
   Checkbox,
   TextField,
   Typography,
-} from '@material-ui/core'
+} from '@mui/material'
 import SimpleFeature, {
   SimpleFeatureSerialized,
 } from '@jbrowse/core/util/simpleFeature'
@@ -107,9 +107,8 @@ function VariantSamples(props: any) {
         <DataGrid
           rows={rows}
           columns={infoFields}
-          rowHeight={20}
-          headerHeight={25}
           disableSelectionOnClick
+          rowHeight={25}
           disableColumnMenu
         />
       </div>