@jbrowse/plugin-variants 2.3.1 → 2.3.2

package/esm/VcfTabixAdapter/VcfTabixAdapter.js

@@ -5,7 +5,7 @@ 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;

package/esm/VcfTabixAdapter/VcfTabixAdapter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"VcfTabixAdapter.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/VcfTabixAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAMhD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,eAAe,EAAE,MAAM,oBAAoB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAE1D,OAAO,EAAE,gBAAgB,EAAE,MAAM,aAAa,CAAA;AAC9C,OAAO,SAAS,MAAM,WAAW,CAAA;AAIjC,QAAQ;AACR,OAAO,UAAU,MAAM,eAAe,CAAA;AAEtC,MAAM,CAAC,OAAO,MAAO,SAAQ,sBAAsB;IAOzC,KAAK,CAAC,YAAY;QACxB,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAC,CAAA;QACnD,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;QACpD,MAAM,SAAS,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;QAEtD,MAAM,UAAU,GAAG,YAAY,CAAC,aAA6B,EAAE,EAAE,CAAC,CAAA;QAClE,MAAM,KAAK,GAAG,SAAS,KAAK,KAAK,CAAA;QACjC,MAAM,GAAG,GAAG,IAAI,gBAAgB,CAAC;YAC/B,UAAU;YACV,aAAa,EAAE,KAAK,CAAC,CAAC,CAAC,YAAY,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YAC7D,aAAa,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,YAAY,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YAC9D,cAAc,EAAE,EAAE,GAAG,CAAC,IAAI,EAAE;YAC5B,cAAc,EAAE,UAAU;SAC3B,CAAC,CAAA;QAEF,MAAM,MAAM,GAAG,MAAM,GAAG,CAAC,SAAS,EAAE,CAAA;QACpC,OAAO;YACL,UAAU;YACV,GAAG;YACH,MAAM,EAAE,IAAI,SAAS,CAAC,EAAE,MAAM,EAAE,CAAC;SAClC,CAAA;IACH,CAAC;IAES,KAAK,CAAC,SAAS;QACvB,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE;YACpB,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC9C,IAAI,CAAC,UAAU,GAAG,SAAS,CAAA;gBAC3B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,UAAU,CAAA;IACxB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,OAAO,GAAG,CAAC,yBAAyB,CAAC,IAAI,CAAC,CAAA;IAC5C,CAAC;IAED,KAAK,CAAC,SAAS;QACb,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,OAAO,GAAG,CAAC,SAAS,EAAE,CAAA;IACxB,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACzC,OAAO,MAAM,CAAC,WAAW,EAAE,CAAA;IAC7B,CAAC;IAEM,WAAW,CAAC,KAAuB,EAAE,OAAoB,EAAE;QAChE,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,KAAK,CAAA;YACrC,MAAM,EAAE,GAAG,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC9C,MAAM,GAAG,CAAC,QAAQ,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE;gBACtC,YAAY,EAAE,CAAC,IAAI,EAAE,UAAU,EAAE,EAAE;oBACjC,QAAQ,CAAC,IAAI,CACX,IAAI,UAAU,CAAC;wBACb,OAAO,EAAE,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC;wBAC/B,MAAM;wBACN,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,QAAQ,UAAU,EAAE;qBACnC,CAAC,CACH,CAAA;gBACH,CAAC;gBACD,GAAG,IAAI;aACR,CAAC,CAAA;YACF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAED;;;;;;;;;;;;;OAaG;IACI,4BAA4B,CACjC,OAAiB,EACjB,OAAoB,EAAE;QAEtB,OAAO,gBAAgB,CAAU,KAAK,EAAE,QAA2B,EAAE,EAAE;YACrE,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAEtC,aAAa;YACb,MAAM,KAAK,GAAG,MAAM,eAAe,CAAC,OAAO,EAAE,GAAG,CAAC,KAAK,CAAC,CAAA;YACvD,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC7C,MAAM,IAAI,GAAG,MAAM,UAAU,CAAC,IAAI,EAAE,CAAA;YACpC,IAAI,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,KAAK,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,GAAG,CAAC,CAAA;YAC/C,IAAI,GAAG,GAAG,GAAG,EAAE;gBACb,yDAAyD;gBACzD,GAAG,GAAG,GAAG,CAAA;aACV;YACD,IAAI,GAAG,GAAG,EAAE,EAAE;gBACZ,OAAO,CAAC,IAAI,CACV,yCAAyC,GAAG,6DAA6D,CAC1G,CAAA;aACF;YACD,KAAK,CAAC,4BAA4B,CAAC,OAAO,EAAE,IAAI,CAAC,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAA;QACvE,CAAC,CAAC,CAAA;IACJ,CAAC;IAEM,aAAa,EAAC,gBAAgB,IAAS,CAAC;CAChD"}

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 @@
-{"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,8BAA8B,CAAA"}
+{"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": "2.3.2",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -64,5 +64,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "75c4cba2f50c626c62881abd5851dbf2435c2401"
+  "gitHead": "467d973535bb7b2664e9f66311fb0dc21c1ce5ba"
 }

package/src/VcfAdapter/VcfAdapter.test.ts

@@ -1,8 +1,6 @@
 import { toArray } from 'rxjs/operators'
 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(

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,
+    }
+  }
+}

package/src/VcfFeature/util.ts

@@ -0,0 +1,140 @@
+import VCF, { parseBreakend } from '@gmod/vcf'
+
+const altTypeToSO: { [key: string]: string | undefined } = {
+  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: string,
+  alt: string[],
+  parser: VCF,
+): string[] {
+  // 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<string>()
+  let descriptions = new Set<string>()
+  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: string,
+  alt: string,
+  parser: VCF,
+): string[] {
+  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,
+      `<${modAlt.slice(0, modAlt.length - 1).join(':')}>`,
+      parser,
+    )
+  }
+
+  // no parent
+  return []
+}
+
+// note: term SNV is used instead of SNP because SO definition of SNP says
+// abundance must be at least 1% in population, and can't be sure we meet
+// that
+export function getSOAndDescByExamination(ref: string, alt: string) {
+  const bnd = parseBreakend(alt)
+  if (bnd) {
+    return ['breakend', alt]
+  } else if (ref.length === 1 && alt.length === 1) {
+    return ['SNV', makeDescriptionString('SNV', ref, alt)]
+  } else if (alt === '<INS>') {
+    return ['insertion', alt]
+  } else if (alt === '<DEL>') {
+    return ['deletion', alt]
+  } else if (alt === '<INV>') {
+    return ['deletion', alt]
+  } else if (alt === '<TRA>') {
+    return ['translocation', alt]
+  } else if (alt.includes('<')) {
+    return ['sv', alt]
+  } else if (ref.length === alt.length) {
+    if (ref.split('').reverse().join('') === alt) {
+      return ['inversion', makeDescriptionString('inversion', ref, alt)]
+    } else {
+      return ['substitution', makeDescriptionString('substitution', ref, alt)]
+    }
+  } else if (ref.length <= alt.length) {
+    return ['insertion', makeDescriptionString('insertion', ref, alt)]
+  } else if (ref.length > alt.length) {
+    return ['deletion', makeDescriptionString('deletion', ref, alt)]
+  }
+
+  return ['indel', makeDescriptionString('indel', ref, alt)]
+}
+
+function makeDescriptionString(soTerm: string, ref: string, alt: string) {
+  return `${soTerm} ${ref} -> ${alt}`
+}

package/src/VcfTabixAdapter/VcfTabixAdapter.ts

@@ -17,7 +17,7 @@ import { Observer } from 'rxjs'
 import { GenericFilehandle } from 'generic-filehandle'
 
 // local
-import VcfFeature from './VcfFeature'
+import VcfFeature from '../VcfFeature'
 
 export default class extends BaseFeatureDataAdapter {
   private configured?: Promise<{

package/src/index.ts

@@ -24,4 +24,4 @@ export default class VariantsPlugin extends Plugin {
   }
 }
 
-export { default as VcfFeature } from './VcfTabixAdapter/VcfFeature'
+export { default as VcfFeature } from './VcfFeature'

package/dist/VcfTabixAdapter/VcfFeature.js

@@ -1,187 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const vcf_1 = require("@gmod/vcf");
-class VCFFeature {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    constructor(args) {
-        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) {
-        return field === 'samples'
-            ? this.variant.SAMPLES
-            : this.data[field] || this.variant[field];
-    }
-    set() { }
-    parent() {
-        return undefined;
-    }
-    children() {
-        return undefined;
-    }
-    tags() {
-        const t = [
-            ...Object.keys(this.data),
-            ...Object.keys(this.variant),
-            'samples',
-        ];
-        return t;
-    }
-    id() {
-        return this._id;
-    }
-    dataFromVariant(variant) {
-        const { REF, ALT, POS, CHROM, INFO, ID } = variant;
-        const start = POS - 1;
-        const [SO_term, description] = this._getSOTermAndDescription(REF, ALT);
-        const isTRA = ALT === null || ALT === void 0 ? void 0 : ALT.some(f => f === '<TRA>');
-        const isSymbolic = ALT === null || ALT === void 0 ? void 0 : ALT.some(f => f.indexOf('<') !== -1);
-        return {
-            refName: CHROM,
-            start,
-            end: isSymbolic && INFO.END && !isTRA ? +INFO.END[0] : start + REF.length,
-            description,
-            type: SO_term,
-            name: ID === null || ID === void 0 ? void 0 : ID.join(','),
-            aliases: ID && ID.length > 1 ? variant.ID.slice(1) : undefined,
-        };
-    }
-    /**
-     * Get a sequence ontology (SO) term that describes the variant type
-     */
-    _getSOTermAndDescription(ref, alt) {
-        // 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] = this._getSOAndDescFromAltDefs(ref, a);
-            if (!soTerm) {
-                ;
-                [soTerm, description] = this._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 prefixes = new Set([...descriptions].map(desc => {
-                const prefix = desc.split('->');
-                return prefix[1] ? prefix[0] : desc;
-            }));
-            const new_descs = [...prefixes].map(prefix => {
-                const suffixes = [...descriptions]
-                    .map(desc => {
-                    const pref = desc.split('-> ');
-                    return pref[1] && pref[0] === prefix ? pref[1] : '';
-                })
-                    .filter(f => !!f);
-                return suffixes.length
-                    ? prefix + '-> ' + suffixes.join(',')
-                    : [...descriptions].join(',');
-            });
-            descriptions = new Set(new_descs);
-        }
-        if (soTerms.size) {
-            return [[...soTerms].join(','), [...descriptions].join(',')];
-        }
-        return [undefined, undefined];
-    }
-    _getSOAndDescFromAltDefs(ref, alt) {
-        if (typeof alt === 'string' && !alt.startsWith('<')) {
-            return [undefined, undefined];
-        }
-        // look for a definition with an SO type for this
-        let soTerm = VCFFeature._altTypeToSO[alt];
-        // if no SO term but ALT is in metadata, assume sequence_variant
-        if (!soTerm && this.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 this._getSOAndDescFromAltDefs(ref, `<${modAlt.slice(0, modAlt.length - 1).join(':')}>`);
-        }
-        // no parent
-        return [undefined, undefined];
-    }
-    // note: term SNV is used instead of SNP because SO definition of SNP says
-    // abundance must be at least 1% in population, and can't be sure we meet
-    // that
-    _getSOAndDescByExamination(ref, alt) {
-        const bnd = (0, vcf_1.parseBreakend)(alt);
-        if (bnd) {
-            return ['breakend', alt];
-        }
-        else if (ref.length === 1 && alt.length === 1) {
-            return ['SNV', this._makeDescriptionString('SNV', ref, alt)];
-        }
-        else if (alt === '<INS>') {
-            return ['insertion', alt];
-        }
-        else if (alt === '<DEL>') {
-            return ['deletion', alt];
-        }
-        else if (alt === '<INV>') {
-            return ['deletion', alt];
-        }
-        else if (alt === '<TRA>') {
-            return ['translocation', alt];
-        }
-        else if (alt.includes('<')) {
-            return ['sv', alt];
-        }
-        else if (ref.length === alt.length) {
-            if (ref.split('').reverse().join('') === alt) {
-                return ['inversion', this._makeDescriptionString('inversion', ref, alt)];
-            }
-            return [
-                'substitution',
-                this._makeDescriptionString('substitution', ref, alt),
-            ];
-        }
-        else if (ref.length <= alt.length) {
-            return ['insertion', this._makeDescriptionString('insertion', ref, alt)];
-        }
-        else if (ref.length > alt.length) {
-            return ['deletion', this._makeDescriptionString('deletion', ref, alt)];
-        }
-        return ['indel', this._makeDescriptionString('indel', ref, alt)];
-    }
-    _makeDescriptionString(soTerm, ref, alt) {
-        return `${soTerm} ${ref} -> ${alt}`;
-    }
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    toJSON() {
-        return {
-            uniqueId: this._id,
-            ...this.variant,
-            ...this.data,
-            samples: this.variant.SAMPLES,
-        };
-    }
-}
-exports.default = VCFFeature;
-VCFFeature._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',
-};
-//# sourceMappingURL=VcfFeature.js.map