@jbrowse/plugin-variants 2.3.1 → 2.3.3

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.test.ts

@@ -1,4 +1,5 @@
 import { toArray } from 'rxjs/operators'
+import { firstValueFrom } from 'rxjs'
 import Adapter from './VcfTabixAdapter'
 import configSchema from './configSchema'
 
@@ -46,25 +47,23 @@ test('adapter can fetch variants from volvox.vcf.gz', async () => {
   expect(names).toEqual(csiNames)
   expect(names).toMatchSnapshot()
 
-  const features = adapter.getFeatures({
+  const feat = adapter.getFeatures({
     refName: 'ctgA',
     start: 0,
     end: 20000,
   })
 
-  const featuresArray = await features.pipe(toArray()).toPromise()
-  const csiFeaturesArray = await csiFeatures.pipe(toArray()).toPromise()
-  expect(featuresArray.slice(0, 5)).toMatchSnapshot()
-  expect(csiFeaturesArray.slice(0, 5)).toEqual(featuresArray.slice(0, 5))
+  const featArray = await firstValueFrom(feat.pipe(toArray()))
+  const csiFeaturesArray = await firstValueFrom(csiFeatures.pipe(toArray()))
+  expect(featArray.slice(0, 5)).toMatchSnapshot()
+  expect(csiFeaturesArray.slice(0, 5)).toEqual(featArray.slice(0, 5))
 
-  const featuresNonExist = adapter.getFeatures({
+  const featNonExist = adapter.getFeatures({
     refName: 'ctgC',
     start: 0,
     end: 20000,
   })
 
-  const featuresArrayNonExist = await featuresNonExist
-    .pipe(toArray())
-    .toPromise()
-  expect(featuresArrayNonExist).toEqual([])
+  const featArrayNonExist = await firstValueFrom(featNonExist.pipe(toArray()))
+  expect(featArrayNonExist).toEqual([])
 })

package/src/VcfTabixAdapter/VcfTabixAdapter.ts

@@ -2,26 +2,18 @@ import {
   BaseFeatureDataAdapter,
   BaseOptions,
 } from '@jbrowse/core/data_adapters/BaseAdapter'
-import {
-  FileLocation,
-  NoAssemblyRegion,
-  Region,
-} from '@jbrowse/core/util/types'
+import { FileLocation, NoAssemblyRegion } from '@jbrowse/core/util/types'
 import { openLocation } from '@jbrowse/core/util/io'
-import { bytesForRegions } from '@jbrowse/core/util'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import { Feature } from '@jbrowse/core/util/simpleFeature'
+import { Feature } from '@jbrowse/core/util'
 import { TabixIndexedFile } from '@gmod/tabix'
 import VcfParser from '@gmod/vcf'
-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<{
-    filehandle: GenericFilehandle
     vcf: TabixIndexedFile
     parser: VcfParser
   }>
@@ -44,7 +36,6 @@ export default class extends BaseFeatureDataAdapter {
 
     const header = await vcf.getHeader()
     return {
-      filehandle,
       vcf,
       parser: new VcfParser({ header }),
     }
@@ -95,44 +86,5 @@ export default class extends BaseFeatureDataAdapter {
     }, 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
-   */
-  public getFeaturesInMultipleRegions(
-    regions: Region[],
-    opts: BaseOptions = {},
-  ) {
-    return ObservableCreate<Feature>(async (observer: Observer<Feature>) => {
-      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)
-    })
-  }
-
   public freeResources(/* { region } */): void {}
 }

package/src/{index.test.js → index.test.ts}

@@ -5,7 +5,6 @@ import { getSnapshot } from 'mobx-state-tree'
 import ThisPlugin from '.'
 
 test('plugin in a stock JBrowse', () => {
-  console.warn = jest.fn()
   const pluginManager = new PluginManager([
     new ThisPlugin(),
     new Alignments(),

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

package/dist/VcfTabixAdapter/VcfFeature.js.map

@@ -1 +0,0 @@
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package/esm/VcfTabixAdapter/VcfFeature.js

@@ -1,184 +0,0 @@
-import { parseBreakend } from '@gmod/vcf';
-export default 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, `<${modAlt.slice(0, modAlt.length - 1).join(':')}>`);
-        }
-        // no parent
-        return [undefined, undefined];
-    }
-    // note: term SNV is used instead of SNP because SO definition of SNP says
-    // abundance must be at least 1% in population, and can't be sure we meet
-    // that
-    _getSOAndDescByExamination(ref, alt) {
-        const bnd = parseBreakend(alt);
-        if (bnd) {
-            return ['breakend', alt];
-        }
-        else if (ref.length === 1 && alt.length === 1) {
-            return ['SNV', this._makeDescriptionString('SNV', ref, alt)];
-        }
-        else if (alt === '<INS>') {
-            return ['insertion', alt];
-        }
-        else if (alt === '<DEL>') {
-            return ['deletion', alt];
-        }
-        else if (alt === '<INV>') {
-            return ['deletion', alt];
-        }
-        else if (alt === '<TRA>') {
-            return ['translocation', alt];
-        }
-        else if (alt.includes('<')) {
-            return ['sv', alt];
-        }
-        else if (ref.length === alt.length) {
-            if (ref.split('').reverse().join('') === alt) {
-                return ['inversion', this._makeDescriptionString('inversion', ref, alt)];
-            }
-            return [
-                'substitution',
-                this._makeDescriptionString('substitution', ref, alt),
-            ];
-        }
-        else if (ref.length <= alt.length) {
-            return ['insertion', this._makeDescriptionString('insertion', ref, alt)];
-        }
-        else if (ref.length > alt.length) {
-            return ['deletion', this._makeDescriptionString('deletion', ref, alt)];
-        }
-        return ['indel', this._makeDescriptionString('indel', ref, alt)];
-    }
-    _makeDescriptionString(soTerm, ref, alt) {
-        return `${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,
-        };
-    }
-}
-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

package/esm/VcfTabixAdapter/VcfFeature.js.map

@@ -1 +0,0 @@
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