@jbrowse/plugin-variants 2.3.1 → 2.3.3

package/esm/VcfFeature/util.js

@@ -0,0 +1,123 @@
+import { parseBreakend } from '@gmod/vcf';
+const altTypeToSO = {
+    DEL: 'deletion',
+    INS: 'insertion',
+    DUP: 'duplication',
+    INV: 'inversion',
+    INVDUP: 'inverted duplication',
+    CNV: 'copy_number_variation',
+    TRA: 'translocation',
+    'DUP:TANDEM': 'tandem_duplication',
+    NON_REF: 'sequence_variant',
+    '*': 'sequence_variant',
+};
+/**
+ * Get a sequence ontology (SO) term that describes the variant type
+ */
+export function getSOTermAndDescription(ref, alt, parser) {
+    // it's just a remark if there are no alternate alleles
+    if (!alt || alt.length === 0) {
+        return ['remark', 'no alternative alleles'];
+    }
+    const soTerms = new Set();
+    let descriptions = new Set();
+    alt.forEach(a => {
+        let [soTerm, description] = getSOAndDescFromAltDefs(ref, a, parser);
+        if (!soTerm) {
+            ;
+            [soTerm, description] = getSOAndDescByExamination(ref, a);
+        }
+        if (soTerm && description) {
+            soTerms.add(soTerm);
+            descriptions.add(description);
+        }
+    });
+    // Combine descriptions like ["SNV G -> A", "SNV G -> T"] to ["SNV G -> A,T"]
+    if (descriptions.size > 1) {
+        const descs = [...descriptions];
+        const prefixes = new Set(descs.map(desc => {
+            const prefix = desc.split('->');
+            return prefix[1] ? prefix[0] : desc;
+        }));
+        descriptions = new Set([...prefixes].map(prefix => {
+            const suffixes = descs
+                .map(desc => {
+                const pref = desc.split('-> ');
+                return pref[1] && pref[0] === prefix ? pref[1] : '';
+            })
+                .filter(f => !!f);
+            return suffixes.length ? prefix + '-> ' + suffixes.join(',') : prefix;
+        }));
+    }
+    if (soTerms.size) {
+        return [[...soTerms].join(','), [...descriptions].join(',')];
+    }
+    return [];
+}
+export function getSOAndDescFromAltDefs(ref, alt, parser) {
+    if (typeof alt === 'string' && !alt.startsWith('<')) {
+        return [];
+    }
+    // look for a definition with an SO type for this
+    let soTerm = altTypeToSO[alt];
+    // if no SO term but ALT is in metadata, assume sequence_variant
+    if (!soTerm && parser.getMetadata('ALT', alt)) {
+        soTerm = 'sequence_variant';
+    }
+    if (soTerm) {
+        return [soTerm, alt];
+    }
+    // try to look for a definition for a parent term if we can
+    const modAlt = alt.split(':');
+    if (modAlt.length > 1) {
+        return getSOAndDescFromAltDefs(ref, `<${modAlt.slice(0, modAlt.length - 1).join(':')}>`, parser);
+    }
+    // no parent
+    return [];
+}
+// note: term SNV is used instead of SNP because SO definition of SNP says
+// abundance must be at least 1% in population, and can't be sure we meet
+// that
+export function getSOAndDescByExamination(ref, alt) {
+    const bnd = parseBreakend(alt);
+    if (bnd) {
+        return ['breakend', alt];
+    }
+    else if (ref.length === 1 && alt.length === 1) {
+        return ['SNV', makeDescriptionString('SNV', ref, alt)];
+    }
+    else if (alt === '<INS>') {
+        return ['insertion', alt];
+    }
+    else if (alt === '<DEL>') {
+        return ['deletion', alt];
+    }
+    else if (alt === '<INV>') {
+        return ['deletion', alt];
+    }
+    else if (alt === '<TRA>') {
+        return ['translocation', alt];
+    }
+    else if (alt.includes('<')) {
+        return ['sv', alt];
+    }
+    else if (ref.length === alt.length) {
+        if (ref.split('').reverse().join('') === alt) {
+            return ['inversion', makeDescriptionString('inversion', ref, alt)];
+        }
+        else {
+            return ['substitution', makeDescriptionString('substitution', ref, alt)];
+        }
+    }
+    else if (ref.length <= alt.length) {
+        return ['insertion', makeDescriptionString('insertion', ref, alt)];
+    }
+    else if (ref.length > alt.length) {
+        return ['deletion', makeDescriptionString('deletion', ref, alt)];
+    }
+    return ['indel', makeDescriptionString('indel', ref, alt)];
+}
+function makeDescriptionString(soTerm, ref, alt) {
+    return `${soTerm} ${ref} -> ${alt}`;
+}
+//# sourceMappingURL=util.js.map

package/esm/VcfFeature/util.js.map

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

@@ -1,14 +1,12 @@
 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 { NoAssemblyRegion } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util';
 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;
     }>;
@@ -16,20 +14,5 @@ export default class extends BaseFeatureDataAdapter {
     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

@@ -1,11 +1,10 @@
 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';
 // local
-import VcfFeature from './VcfFeature';
+import VcfFeature from '../VcfFeature';
 export default class extends BaseFeatureDataAdapter {
     async configurePre() {
         const pm = this.pluginManager;
@@ -23,7 +22,6 @@ export default class extends BaseFeatureDataAdapter {
         });
         const header = await vcf.getHeader();
         return {
-            filehandle,
             vcf,
             parser: new VcfParser({ header }),
         };
@@ -66,38 +64,6 @@ export default class extends BaseFeatureDataAdapter {
             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 = {}) {
-        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`);
-            }
-            super.getFeaturesInMultipleRegions(regions, opts).subscribe(observer);
-        });
-    }
     freeResources( /* { region } */) { }
 }
 //# sourceMappingURL=VcfTabixAdapter.js.map

package/esm/VcfTabixAdapter/VcfTabixAdapter.js.map

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

@@ -4,4 +4,4 @@ export default class VariantsPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;
 }
-export { default as VcfFeature } from './VcfTabixAdapter/VcfFeature';
+export { default as VcfFeature } from './VcfFeature';

package/esm/index.js

@@ -23,5 +23,5 @@ export default class VariantsPlugin extends Plugin {
         ChordVariantDisplayF(pluginManager);
     }
 }
-export { default as VcfFeature } from './VcfTabixAdapter/VcfFeature';
+export { default as VcfFeature } from './VcfFeature';
 //# sourceMappingURL=index.js.map

package/esm/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,WAAW,MAAM,cAAc,CAAA;AACtC,OAAO,gBAAgB,MAAM,mBAAmB,CAAA;AAChD,OAAO,gBAAgB,MAAM,mBAAmB,CAAA;AAChD,OAAO,aAAa,MAAM,gBAAgB,CAAA;AAC1C,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAEzC,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AACxD,OAAO,qBAAqB,MAAM,wBAAwB,CAAA;AAC1D,OAAO,+BAA+B,MAAM,kCAAkC,CAAA;AAC9E,OAAO,qBAAqB,MAAM,wBAAwB,CAAA;AAE1D,MAAM,CAAC,OAAO,OAAO,cAAe,SAAQ,MAAM;IAAlD;;QACE,SAAI,GAAG,gBAAgB,CAAA;IAYzB,CAAC;IAVC,OAAO,CAAC,aAA4B;QAClC,WAAW,CAAC,aAAa,CAAC,CAAA;QAC1B,gBAAgB,CAAC,aAAa,CAAC,CAAA;QAC/B,qBAAqB,CAAC,aAAa,CAAC,CAAA;QACpC,aAAa,CAAC,aAAa,CAAC,CAAA;QAC5B,gBAAgB,CAAC,aAAa,CAAC,CAAA;QAC/B,qBAAqB,CAAC,aAAa,CAAC,CAAA;QACpC,+BAA+B,CAAC,aAAa,CAAC,CAAA;QAC9C,oBAAoB,CAAC,aAAa,CAAC,CAAA;IACrC,CAAC;CACF;AAED,OAAO,EAAE,OAAO,IAAI,UAAU,EAAE,MAAM,cAAc,CAAA"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "2.3.1",
+  "version": "2.3.3",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -55,7 +55,7 @@
     "mobx-react": "^7.0.0",
     "mobx-state-tree": "^5.0.0",
     "react": ">=16.8.0",
-    "rxjs": "^6.0.0",
+    "rxjs": "^7.0.0",
     "tss-react": "^4.0.0"
   },
   "publishConfig": {
@@ -64,5 +64,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "75c4cba2f50c626c62881abd5851dbf2435c2401"
+  "gitHead": "283e0387ccd5acc9f092cf00804d1fcac212e68d"
 }

package/src/VariantFeatureWidget/VariantFeatureWidget.test.tsx

@@ -0,0 +1,42 @@
+import React from 'react'
+import { render } from '@testing-library/react'
+import { types } from 'mobx-state-tree'
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+import PluginManager from '@jbrowse/core/PluginManager'
+
+// locals
+import { stateModelFactory } from '.'
+import VariantFeatureDetails from './VariantFeatureWidget'
+
+test('renders with just the required model elements', () => {
+  const pluginManager = new PluginManager([])
+  const Session = types.model({
+    rpcManager: types.optional(types.frozen(), {}),
+    configuration: ConfigurationSchema('test', {}),
+    widget: stateModelFactory(pluginManager),
+  })
+  const model = Session.create(
+    {
+      widget: {
+        // @ts-ignore
+        type: 'VariantFeatureWidget',
+      },
+    },
+    { pluginManager },
+  )
+  model.widget.setFeatureData({
+    refName: 'ctgA',
+    start: 176,
+    end: 177,
+    name: 'rs123',
+    REF: 'A',
+    ALT: ['<TRA>'],
+    QUAL: 10.4,
+    INFO: {
+      MQ: 5,
+    },
+  })
+
+  const { container } = render(<VariantFeatureDetails model={model.widget} />)
+  expect(container.firstChild).toMatchSnapshot()
+})

package/src/VariantFeatureWidget/__snapshots__/{VariantFeatureWidget.test.js.snap → VariantFeatureWidget.test.tsx.snap}

@@ -1,6 +1,6 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
-exports[`VariantTrack widget renders with just the required model elements 1`] = `
+exports[`renders with just the required model elements 1`] = `
 <div
   class="MuiPaper-root MuiPaper-elevation MuiPaper-rounded MuiPaper-elevation1 css-1ps6pg7-MuiPaper-root"
   data-testid="variant-side-drawer"

package/src/VcfAdapter/VcfAdapter.test.ts

@@ -1,8 +1,7 @@
 import { toArray } from 'rxjs/operators'
+import { firstValueFrom } from 'rxjs'
 import Adapter from './VcfAdapter'
 import configSchema from './configSchema'
-import { TextDecoder } from 'web-encoding'
-window.TextDecoder = TextDecoder
 
 test('adapter can fetch variants from volvox.vcf', async () => {
   const adapter = new Adapter(
@@ -14,7 +13,7 @@ test('adapter can fetch variants from volvox.vcf', async () => {
     }),
   )
 
-  const features = adapter.getFeatures({
+  const feat = adapter.getFeatures({
     assemblyName: 'volvox',
     refName: 'ctgA',
     start: 0,
@@ -24,6 +23,6 @@ test('adapter can fetch variants from volvox.vcf', async () => {
   const names = await adapter.getRefNames()
   expect(names).toMatchSnapshot()
 
-  const featuresArray = await features.pipe(toArray()).toPromise()
-  expect(featuresArray.slice(0, 5)).toMatchSnapshot()
+  const featArray = await firstValueFrom(feat.pipe(toArray()))
+  expect(featArray.slice(0, 5)).toMatchSnapshot()
 })

package/src/VcfAdapter/VcfAdapter.ts

@@ -2,16 +2,15 @@ import {
   BaseFeatureDataAdapter,
   BaseOptions,
 } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { Region } from '@jbrowse/core/util/types'
+import { Region, Feature } from '@jbrowse/core/util'
 import { openLocation } from '@jbrowse/core/util/io'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import { Feature } from '@jbrowse/core/util/simpleFeature'
 import IntervalTree from '@flatten-js/interval-tree'
 import { unzip } from '@gmod/bgzf-filehandle'
 import VCF from '@gmod/vcf'
 
 // local
-import VcfFeature from '../VcfTabixAdapter/VcfFeature'
+import VcfFeature from '../VcfFeature'
 
 const readVcf = (f: string) => {
   const header: string[] = []
@@ -106,7 +105,7 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
       try {
         const { start, end, refName } = region
         const { header, intervalTree } = await this.setup()
-        const parser = new VCF({ header: header })
+        const parser = new VCF({ header })
         intervalTree[refName]?.search([start, end]).forEach(f =>
           observer.next(
             new VcfFeature({

package/src/VcfFeature/index.test.ts

@@ -0,0 +1,132 @@
+import VcfParser from '@gmod/vcf'
+import VcfFeature from './index'
+
+test('test usage of the VcfFeature', () => {
+  const parser = new VcfParser({
+    header: `#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam`,
+  })
+  const line = `lcl|Scaffald_1\t80465\trs118266897\tR\tA\t29\tPASS\tNS=3;0,14;AF=0.5;DB;112;PG2.1`
+
+  const variant = parser.parseLine(line)
+
+  const f = new VcfFeature({
+    parser,
+    variant,
+    id: 'myuniqueid',
+  })
+  expect(f.id()).toEqual('myuniqueid')
+  expect(f.get('name')).toEqual('rs118266897')
+})
+
+test('try INS feature with END less than start', () => {
+  const parser = new VcfParser({
+    header: `#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam`,
+  })
+  const line = `chr1\t100\trs123\tR\tA\t29\tPASS\tEND=1;SVTYPE=INS`
+
+  const variant = parser.parseLine(line)
+
+  const f = new VcfFeature({
+    parser,
+    variant,
+    id: 'myuniqueid',
+  })
+  expect(f.id()).toEqual('myuniqueid')
+  expect(f.get('start')).toEqual(99)
+  expect(f.get('end')).toEqual(100)
+})
+
+test('try DEL feature with END info field valid', () => {
+  const parser = new VcfParser({
+    header: `#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam`,
+  })
+  const line = `chr1\t100\trs123\tR\t<DEL>\t29\tPASS\tEND=1000;SVTYPE=DEL`
+
+  const variant = parser.parseLine(line)
+
+  const f = new VcfFeature({
+    parser,
+    variant,
+    id: 'myuniqueid',
+  })
+  expect(f.id()).toEqual('myuniqueid')
+  expect(f.get('start')).toEqual(99)
+  expect(f.get('end')).toEqual(1000)
+})
+
+test('multiple SVs', () => {
+  const parser = new VcfParser({
+    header: `#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam`,
+  })
+  const line = `chr1\t100\trs123\tR\t<INVDUP>,<INV>\t29\tPASS\tEND=1000;SVTYPE=DEL`
+
+  const variant = parser.parseLine(line)
+
+  const f = new VcfFeature({
+    parser,
+    variant,
+    id: 'myuniqueid',
+  })
+  expect(f.get('description')).toEqual('<INVDUP>,<INV>')
+})
+test('BND', () => {
+  const parser = new VcfParser({
+    header: `#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam`,
+  })
+  const line = `chr1\t100\trs123\tR\tG[ctgA:34200[\t29\tPASS\tEND=1000;SVTYPE=BND`
+
+  const variant = parser.parseLine(line)
+
+  const f = new VcfFeature({
+    parser,
+    variant,
+    id: 'myuniqueid',
+  })
+  expect(f.get('description')).toEqual('G[ctgA:34200[')
+})
+test('multiple BND', () => {
+  const parser = new VcfParser({
+    header: `#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam`,
+  })
+  const line = `chr1\t100\trs123\tR\tG[ctgA:34200[,G[ctgA:44200[\t29\tPASS\tEND=1000;SVTYPE=BND`
+
+  const variant = parser.parseLine(line)
+
+  const f = new VcfFeature({
+    parser,
+    variant,
+    id: 'myuniqueid',
+  })
+  expect(f.get('description')).toEqual('G[ctgA:34200[,G[ctgA:44200[')
+})
+test('multiple SNV', () => {
+  const parser = new VcfParser({
+    header: `#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam`,
+  })
+  const line = `chr1\t100\trs123\tG\tA,C\t29\tPASS\tHELLO=world`
+
+  const variant = parser.parseLine(line)
+
+  const f = new VcfFeature({
+    parser,
+    variant,
+    id: 'myuniqueid',
+  })
+  expect(f.get('description')).toEqual('SNV G -> A,C')
+})
+
+test('multiple SNV2', () => {
+  const parser = new VcfParser({
+    header: `#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam`,
+  })
+  const line = `chr1\t100\trs123\tG\tAT,<*>\t29\tPASS\tHELLO=world`
+
+  const variant = parser.parseLine(line)
+
+  const f = new VcfFeature({
+    parser,
+    variant,
+    id: 'myuniqueid',
+  })
+  expect(f.get('description')).toEqual('insertion G -> AT,<*>')
+})

package/src/VcfFeature/index.ts

@@ -0,0 +1,104 @@
+import { Feature } from '@jbrowse/core/util'
+import VCF from '@gmod/vcf'
+
+// locals
+import { getSOTermAndDescription } from './util'
+
+/* eslint-disable no-underscore-dangle */
+
+interface Samples {
+  [key: string]: {
+    [key: string]: { values: string[] | number[] | null }
+  }
+}
+
+interface FeatureData {
+  [key: string]: unknown
+  refName: string
+  start: number
+  end: number
+  description?: string
+  type?: string
+  name?: string
+  aliases?: string[]
+  samples?: Samples
+}
+
+export default class VCFFeature implements Feature {
+  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  private variant: any
+
+  private parser: VCF
+
+  private data: FeatureData
+
+  private _id: string
+
+  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  constructor(args: { variant: any; parser: VCF; id: string }) {
+    this.variant = args.variant
+    this.parser = args.parser
+    this.data = this.dataFromVariant(this.variant)
+    this._id = args.id
+  }
+
+  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  get(field: string): any {
+    return field === 'samples'
+      ? this.variant.SAMPLES
+      : this.data[field] || this.variant[field]
+  }
+
+  set() {}
+
+  parent() {
+    return undefined
+  }
+
+  children() {
+    return undefined
+  }
+
+  tags() {
+    return [...Object.keys(this.data), ...Object.keys(this.variant), 'samples']
+  }
+
+  id() {
+    return this._id
+  }
+
+  dataFromVariant(variant: {
+    REF: string
+    POS: number
+    ALT: string[]
+    CHROM: string
+    INFO: any // eslint-disable-line @typescript-eslint/no-explicit-any
+    ID: string[]
+  }): FeatureData {
+    const { REF, ALT, POS, CHROM, INFO, ID } = variant
+    const start = POS - 1
+    const [type, description] = getSOTermAndDescription(REF, ALT, this.parser)
+    const isTRA = ALT?.some(f => f === '<TRA>')
+    const isSymbolic = ALT?.some(f => f.indexOf('<') !== -1)
+
+    return {
+      refName: CHROM,
+      start,
+      end: isSymbolic && INFO.END && !isTRA ? +INFO.END[0] : start + REF.length,
+      description,
+      type,
+      name: ID?.join(','),
+      aliases: ID && ID.length > 1 ? variant.ID.slice(1) : undefined,
+    }
+  }
+
+  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  toJSON(): any {
+    return {
+      uniqueId: this._id,
+      ...this.variant,
+      ...this.data,
+      samples: this.variant.SAMPLES,
+    }
+  }
+}