@jbrowse/plugin-variants 2.3.1 → 2.3.3

package/dist/VcfAdapter/VcfAdapter.d.ts

@@ -1,6 +1,5 @@
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { Region, Feature } from '@jbrowse/core/util';
 import IntervalTree from '@flatten-js/interval-tree';
 export default class VcfAdapter extends BaseFeatureDataAdapter {
     static capabilities: string[];

package/dist/VcfAdapter/VcfAdapter.js

@@ -10,7 +10,7 @@ const interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 const vcf_1 = __importDefault(require("@gmod/vcf"));
 // local
-const VcfFeature_1 = __importDefault(require("../VcfTabixAdapter/VcfFeature"));
+const VcfFeature_1 = __importDefault(require("../VcfFeature"));
 const readVcf = (f) => {
     const header = [];
     const rest = [];
@@ -88,7 +88,7 @@ class VcfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             try {
                 const { start, end, refName } = region;
                 const { header, intervalTree } = await this.setup();
-                const parser = new vcf_1.default({ header: header });
+                const parser = new vcf_1.default({ header });
                 (_a = intervalTree[refName]) === null || _a === void 0 ? void 0 : _a.search([start, end]).forEach(f => observer.next(new VcfFeature_1.default({
                     variant: parser.parseLine(f.line),
                     parser,

package/dist/VcfAdapter/VcfAdapter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"VcfAdapter.js","sourceRoot":"","sources":["../../src/VcfAdapter/VcfAdapter.ts"],"names":[],"mappings":";;;;;AAAA,yEAGgD;AAEhD,8CAAoD;AACpD,kDAA0D;AAC1D,8EAAoD;AACpD,2DAA6C;AAC7C,oDAA2B;AAE3B,QAAQ;AACR,+DAAsC;AAEtC,MAAM,OAAO,GAAG,CAAC,CAAS,EAAE,EAAE;IAC5B,MAAM,MAAM,GAAa,EAAE,CAAA;IAC3B,MAAM,IAAI,GAAa,EAAE,CAAA;IACzB,CAAC,CAAC,KAAK,CAAC,YAAY,CAAC;SAClB,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,OAAO,CAAC,IAAI,CAAC,EAAE;QACd,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE;YACxB,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAClB;aAAM,IAAI,IAAI,EAAE;YACf,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAChB;IACH,CAAC,CAAC,CAAA;IACJ,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,CAAA;AACnD,CAAC,CAAA;AAED,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,MAAqB,UAAW,SAAQ,oCAAsB;IAQrD,KAAK,CAAC,SAAS;QACpB,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,OAAO,MAAM,CAAA;IACf,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,MAAM,MAAM,GAAG,IAAI,aAAG,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE,CAAC,CAAA;QAC1C,OAAO,MAAM,CAAC,WAAW,EAAE,CAAA;IAC7B,CAAC;IAED,uCAAuC;IAChC,KAAK,CAAC,MAAM;QACjB,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,GAAG,GAAG,MAAM,IAAA,iBAAY,EAAC,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,EAAE,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAA;QAE1E,MAAM,MAAM,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;QAEnD,2CAA2C;QAC3C,IAAI,MAAM,CAAC,MAAM,GAAG,SAAW,EAAE;YAC/B,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;SAC9D;QAED,MAAM,GAAG,GAAG,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QAC5C,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,CAAA;QAEtC,MAAM,YAAY,GAAG,KAAK;aACvB,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,EAAE,EAAE;;YAChB,MAAM,CAAC,OAAO,EAAE,MAAM,EAAE,AAAD,EAAG,GAAG,EAAE,AAAD,EAAG,AAAD,EAAG,AAAD,EAAG,IAAI,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC7D,MAAM,KAAK,GAAG,CAAC,MAAM,GAAG,CAAC,CAAA;YACzB,MAAM,GAAG,GAAG,CAAC,CAAC,CAAA,MAAA,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,0CAAG,CAAC,EAAE,IAAI,EAAE,KAAI,KAAK,GAAG,GAAG,CAAC,MAAM,CAAC,CAAA;YACxE,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,EAAE,EAAE,CAAA;QAC1C,CAAC,CAAC;aACD,MAAM,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,EAAE;YACnB,MAAM,GAAG,GAAG,GAAG,CAAC,OAAO,CAAA;YACvB,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE;gBACb,GAAG,CAAC,GAAG,CAAC,GAAG,IAAI,uBAAY,EAAE,CAAA;aAC9B;YACD,GAAG,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,GAAG,CAAC,EAAE,GAAG,CAAC,CAAA;YAC1C,OAAO,GAAG,CAAA;QACZ,CAAC,EAAE,EAAkC,CAAC,CAAA;QAExC,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,CAAA;IACjC,CAAC;IAEM,KAAK,CAAC,KAAK;QAChB,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE;YACrB,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACzC,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;gBAC5B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,WAAW,CAAA;IACzB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,IAAiB,EAAE;QAC1C,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QAC3C,OAAO,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IAClC,CAAC;IAEM,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QACvD,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;;YAChD,IAAI;gBACF,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;gBACtC,MAAM,EAAE,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;gBACnD,MAAM,MAAM,GAAG,IAAI,aAAG,CAAC,EAAE,MAAM,EAAE,CAAC,CAAA;gBAClC,MAAA,YAAY,CAAC,OAAO,CAAC,0CAAE,MAAM,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,CACtD,QAAQ,CAAC,IAAI,CACX,IAAI,oBAAU,CAAC;oBACb,OAAO,EAAE,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;oBACjC,MAAM;oBACN,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,CAAC,CAAC,EAAE,EAAE;iBACzB,CAAC,CACH,CACF,CAAA;gBACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;aACpB;YAAC,OAAO,CAAC,EAAE;gBACV,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;aAClB;QACH,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,KAAU,CAAC;;AA1FjC,6BA2FC;AA1Fe,uBAAY,GAAG,CAAC,aAAa,EAAE,aAAa,CAAC,CAAA"}

package/dist/{VcfTabixAdapter/VcfFeature.d.ts → VcfFeature/index.d.ts}

@@ -1,7 +1,5 @@
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-/**
- * VCF Feature creation with lazy genotype evaluation.
- */
+import { Feature } from '@jbrowse/core/util';
+import VCF from '@gmod/vcf';
 interface Samples {
     [key: string]: {
         [key: string]: {
@@ -27,7 +25,7 @@ export default class VCFFeature implements Feature {
     private _id;
     constructor(args: {
         variant: any;
-        parser: any;
+        parser: VCF;
         id: string;
     });
     get(field: string): any;
@@ -44,16 +42,6 @@ export default class VCFFeature implements Feature {
         INFO: any;
         ID: string[];
     }): FeatureData;
-    /**
-     * Get a sequence ontology (SO) term that describes the variant type
-     */
-    _getSOTermAndDescription(ref: string, alt: string[]): [string, string] | [undefined, undefined];
-    static _altTypeToSO: {
-        [key: string]: string | undefined;
-    };
-    _getSOAndDescFromAltDefs(ref: string, alt: string): [string, string] | [undefined, undefined];
-    _getSOAndDescByExamination(ref: string, alt: string): [string, string];
-    _makeDescriptionString(soTerm: string, ref: string, alt: string): string;
     toJSON(): any;
 }
 export {};

package/dist/VcfFeature/index.js

@@ -0,0 +1,59 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+// locals
+const util_1 = require("./util");
+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() {
+        return [...Object.keys(this.data), ...Object.keys(this.variant), 'samples'];
+    }
+    id() {
+        return this._id;
+    }
+    dataFromVariant(variant) {
+        const { REF, ALT, POS, CHROM, INFO, ID } = variant;
+        const start = POS - 1;
+        const [type, description] = (0, util_1.getSOTermAndDescription)(REF, ALT, this.parser);
+        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,
+            name: ID === null || ID === void 0 ? void 0 : ID.join(','),
+            aliases: ID && ID.length > 1 ? variant.ID.slice(1) : undefined,
+        };
+    }
+    // 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;
+//# sourceMappingURL=index.js.map

package/dist/VcfFeature/index.js.map

@@ -0,0 +1 @@
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package/dist/VcfFeature/util.d.ts

@@ -0,0 +1,7 @@
+import VCF from '@gmod/vcf';
+/**
+ * Get a sequence ontology (SO) term that describes the variant type
+ */
+export declare function getSOTermAndDescription(ref: string, alt: string[], parser: VCF): string[];
+export declare function getSOAndDescFromAltDefs(ref: string, alt: string, parser: VCF): string[];
+export declare function getSOAndDescByExamination(ref: string, alt: string): string[];

package/dist/VcfFeature/util.js

@@ -0,0 +1,129 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getSOAndDescByExamination = exports.getSOAndDescFromAltDefs = exports.getSOTermAndDescription = void 0;
+const vcf_1 = require("@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
+ */
+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 [];
+}
+exports.getSOTermAndDescription = getSOTermAndDescription;
+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, `<${modAlt.slice(0, modAlt.length - 1).join(':')}>`, parser);
+    }
+    // no parent
+    return [];
+}
+exports.getSOAndDescFromAltDefs = getSOAndDescFromAltDefs;
+// note: term SNV is used instead of SNP because SO definition of SNP says
+// abundance must be at least 1% in population, and can't be sure we meet
+// that
+function getSOAndDescByExamination(ref, alt) {
+    const bnd = (0, vcf_1.parseBreakend)(alt);
+    if (bnd) {
+        return ['breakend', alt];
+    }
+    else if (ref.length === 1 && alt.length === 1) {
+        return ['SNV', makeDescriptionString('SNV', ref, alt)];
+    }
+    else if (alt === '<INS>') {
+        return ['insertion', alt];
+    }
+    else if (alt === '<DEL>') {
+        return ['deletion', alt];
+    }
+    else if (alt === '<INV>') {
+        return ['deletion', alt];
+    }
+    else if (alt === '<TRA>') {
+        return ['translocation', alt];
+    }
+    else if (alt.includes('<')) {
+        return ['sv', alt];
+    }
+    else if (ref.length === alt.length) {
+        if (ref.split('').reverse().join('') === alt) {
+            return ['inversion', makeDescriptionString('inversion', ref, alt)];
+        }
+        else {
+            return ['substitution', makeDescriptionString('substitution', ref, alt)];
+        }
+    }
+    else if (ref.length <= alt.length) {
+        return ['insertion', makeDescriptionString('insertion', ref, alt)];
+    }
+    else if (ref.length > alt.length) {
+        return ['deletion', makeDescriptionString('deletion', ref, alt)];
+    }
+    return ['indel', makeDescriptionString('indel', ref, alt)];
+}
+exports.getSOAndDescByExamination = getSOAndDescByExamination;
+function makeDescriptionString(soTerm, ref, alt) {
+    return `${soTerm} ${ref} -> ${alt}`;
+}
+//# sourceMappingURL=util.js.map

package/dist/VcfFeature/util.js.map

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package/dist/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/dist/VcfTabixAdapter/VcfTabixAdapter.js

@@ -5,12 +5,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const io_1 = require("@jbrowse/core/util/io");
-const util_1 = require("@jbrowse/core/util");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const tabix_1 = require("@gmod/tabix");
 const vcf_1 = __importDefault(require("@gmod/vcf"));
 // local
-const VcfFeature_1 = __importDefault(require("./VcfFeature"));
+const VcfFeature_1 = __importDefault(require("../VcfFeature"));
 class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
     async configurePre() {
         const pm = this.pluginManager;
@@ -28,7 +27,6 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
         });
         const header = await vcf.getHeader();
         return {
-            filehandle,
             vcf,
             parser: new vcf_1.default({ header }),
         };
@@ -71,38 +69,6 @@ class default_1 extends BaseAdapter_1.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 (0, rxjs_1.ObservableCreate)(async (observer) => {
-            const { vcf } = await this.configure();
-            // @ts-ignore
-            const bytes = await (0, util_1.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 } */) { }
 }
 exports.default = default_1;

package/dist/VcfTabixAdapter/VcfTabixAdapter.js.map

@@ -1 +1 @@
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package/dist/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/dist/index.js

@@ -30,6 +30,6 @@ class VariantsPlugin extends Plugin_1.default {
     }
 }
 exports.default = VariantsPlugin;
-var VcfFeature_1 = require("./VcfTabixAdapter/VcfFeature");
+var VcfFeature_1 = require("./VcfFeature");
 Object.defineProperty(exports, "VcfFeature", { enumerable: true, get: function () { return __importDefault(VcfFeature_1).default; } });
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,8DAAsC;AACtC,wEAAgD;AAChD,wEAAgD;AAChD,kEAA0C;AAC1C,kEAAyC;AAEzC,gFAAwD;AACxD,kFAA0D;AAC1D,sGAA8E;AAC9E,kFAA0D;AAE1D,MAAqB,cAAe,SAAQ,gBAAM;IAAlD;;QACE,SAAI,GAAG,gBAAgB,CAAA;IAYzB,CAAC;IAVC,OAAO,CAAC,aAA4B;QAClC,IAAA,oBAAW,EAAC,aAAa,CAAC,CAAA;QAC1B,IAAA,yBAAgB,EAAC,aAAa,CAAC,CAAA;QAC/B,IAAA,8BAAqB,EAAC,aAAa,CAAC,CAAA;QACpC,IAAA,sBAAa,EAAC,aAAa,CAAC,CAAA;QAC5B,IAAA,yBAAgB,EAAC,aAAa,CAAC,CAAA;QAC/B,IAAA,8BAAqB,EAAC,aAAa,CAAC,CAAA;QACpC,IAAA,wCAA+B,EAAC,aAAa,CAAC,CAAA;QAC9C,IAAA,6BAAoB,EAAC,aAAa,CAAC,CAAA;IACrC,CAAC;CACF;AAbD,iCAaC;AAED,2CAAoD;AAA3C,yHAAA,OAAO,OAAc"}

package/esm/VcfAdapter/VcfAdapter.d.ts

@@ -1,6 +1,5 @@
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { Region, Feature } from '@jbrowse/core/util';
 import IntervalTree from '@flatten-js/interval-tree';
 export default class VcfAdapter extends BaseFeatureDataAdapter {
     static capabilities: string[];

package/esm/VcfAdapter/VcfAdapter.js

@@ -5,7 +5,7 @@ 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) => {
     const header = [];
     const rest = [];
@@ -83,7 +83,7 @@ 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 });
                 (_a = intervalTree[refName]) === null || _a === void 0 ? void 0 : _a.search([start, end]).forEach(f => observer.next(new VcfFeature({
                     variant: parser.parseLine(f.line),
                     parser,

package/esm/VcfAdapter/VcfAdapter.js.map

@@ -1 +1 @@
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package/esm/{VcfTabixAdapter/VcfFeature.d.ts → VcfFeature/index.d.ts}

@@ -1,7 +1,5 @@
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-/**
- * VCF Feature creation with lazy genotype evaluation.
- */
+import { Feature } from '@jbrowse/core/util';
+import VCF from '@gmod/vcf';
 interface Samples {
     [key: string]: {
         [key: string]: {
@@ -27,7 +25,7 @@ export default class VCFFeature implements Feature {
     private _id;
     constructor(args: {
         variant: any;
-        parser: any;
+        parser: VCF;
         id: string;
     });
     get(field: string): any;
@@ -44,16 +42,6 @@ export default class VCFFeature implements Feature {
         INFO: any;
         ID: string[];
     }): FeatureData;
-    /**
-     * Get a sequence ontology (SO) term that describes the variant type
-     */
-    _getSOTermAndDescription(ref: string, alt: string[]): [string, string] | [undefined, undefined];
-    static _altTypeToSO: {
-        [key: string]: string | undefined;
-    };
-    _getSOAndDescFromAltDefs(ref: string, alt: string): [string, string] | [undefined, undefined];
-    _getSOAndDescByExamination(ref: string, alt: string): [string, string];
-    _makeDescriptionString(soTerm: string, ref: string, alt: string): string;
     toJSON(): any;
 }
 export {};

package/esm/VcfFeature/index.js

@@ -0,0 +1,56 @@
+// locals
+import { getSOTermAndDescription } from './util';
+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() {
+        return [...Object.keys(this.data), ...Object.keys(this.variant), 'samples'];
+    }
+    id() {
+        return this._id;
+    }
+    dataFromVariant(variant) {
+        const { REF, ALT, POS, CHROM, INFO, ID } = variant;
+        const start = POS - 1;
+        const [type, description] = getSOTermAndDescription(REF, ALT, this.parser);
+        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,
+            name: ID === null || ID === void 0 ? void 0 : ID.join(','),
+            aliases: ID && ID.length > 1 ? variant.ID.slice(1) : undefined,
+        };
+    }
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    toJSON() {
+        return {
+            uniqueId: this._id,
+            ...this.variant,
+            ...this.data,
+            samples: this.variant.SAMPLES,
+        };
+    }
+}
+//# sourceMappingURL=index.js.map

package/esm/VcfFeature/index.js.map

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

@@ -0,0 +1,7 @@
+import VCF from '@gmod/vcf';
+/**
+ * Get a sequence ontology (SO) term that describes the variant type
+ */
+export declare function getSOTermAndDescription(ref: string, alt: string[], parser: VCF): string[];
+export declare function getSOAndDescFromAltDefs(ref: string, alt: string, parser: VCF): string[];
+export declare function getSOAndDescByExamination(ref: string, alt: string): string[];