@jbrowse/plugin-variants 3.7.0 → 4.0.0

package/esm/VcfAdapter/VcfAdapter.d.ts

@@ -3,13 +3,14 @@ import VcfParser from '@gmod/vcf';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { Feature, Region } from '@jbrowse/core/util';
-type StatusCallback = (arg: string) => void;
+import type { StatusCallback } from '@jbrowse/core/util/parseLineByLine';
 export default class VcfAdapter extends BaseFeatureDataAdapter {
     calculatedIntervalTreeMap: Record<string, IntervalTree<Feature>>;
     vcfFeatures?: Promise<{
         header: string;
         parser: VcfParser;
         intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree<Feature>>;
+        featureMap: Record<string, string[]>;
     }>;
     static capabilities: string[];
     getHeader(): Promise<string>;
@@ -18,18 +19,20 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
         header: string;
         parser: VcfParser;
         intervalTreeMap: {
-            [k: string]: (sc?: (arg: string) => void) => IntervalTree<Feature>;
+            [k: string]: (sc?: StatusCallback) => IntervalTree<Feature>;
         };
+        featureMap: Record<string, string[]>;
     }>;
     setup(): Promise<{
         header: string;
         parser: VcfParser;
         intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree<Feature>>;
+        featureMap: Record<string, string[]>;
     }>;
     getRefNames(_?: BaseOptions): Promise<string[]>;
     getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    getExportData(regions: Region[], formatType: string, _opts?: BaseOptions): Promise<string | undefined>;
     getSources(): Promise<{
         name: string;
     }[]>;
 }
-export {};

package/esm/VcfAdapter/VcfAdapter.js

@@ -4,13 +4,12 @@ import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
 import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import VcfFeature from '../VcfFeature';
-import { parseVcfBuffer } from './vcfParser';
-class VcfAdapter extends BaseFeatureDataAdapter {
-    constructor() {
-        super(...arguments);
-        this.calculatedIntervalTreeMap = {};
-    }
+import { parseVcfBuffer } from "./vcfParser.js";
+import VcfFeature from "../VcfFeature/index.js";
+export default class VcfAdapter extends BaseFeatureDataAdapter {
+    calculatedIntervalTreeMap = {};
+    vcfFeatures;
+    static capabilities = ['getFeatures', 'getRefNames', 'exportData'];
     async getHeader() {
         const { header } = await this.setup();
         return header;
@@ -29,7 +28,7 @@ class VcfAdapter extends BaseFeatureDataAdapter {
             refName,
             (sc) => {
                 if (!this.calculatedIntervalTreeMap[refName]) {
-                    sc === null || sc === void 0 ? void 0 : sc('Parsing VCF data');
+                    sc?.('Parsing VCF data');
                     let idx = 0;
                     const intervalTree = new IntervalTree();
                     for (const line of lines) {
@@ -49,6 +48,7 @@ class VcfAdapter extends BaseFeatureDataAdapter {
             header,
             parser,
             intervalTreeMap,
+            featureMap,
         };
     }
     async setup() {
@@ -66,23 +66,36 @@ class VcfAdapter extends BaseFeatureDataAdapter {
     }
     getFeatures(region, opts = {}) {
         return ObservableCreate(async (observer) => {
-            var _a;
-            try {
-                const { start, end, refName } = region;
-                const { intervalTreeMap } = await this.setup();
-                for (const f of ((_a = intervalTreeMap[refName]) === null || _a === void 0 ? void 0 : _a.call(intervalTreeMap, opts.statusCallback).search([
-                    start,
-                    end,
-                ])) || []) {
-                    observer.next(f);
-                }
-                observer.complete();
-            }
-            catch (e) {
-                observer.error(e);
+            const { start, end, refName } = region;
+            const { intervalTreeMap } = await this.setup();
+            for (const f of intervalTreeMap[refName]?.(opts.statusCallback).search([
+                start,
+                end,
+            ]) || []) {
+                observer.next(f);
             }
+            observer.complete();
         }, opts.stopToken);
     }
+    async getExportData(regions, formatType, _opts) {
+        if (formatType !== 'vcf') {
+            return undefined;
+        }
+        const { header, featureMap } = await this.setup();
+        const exportLines = [header];
+        for (const region of regions) {
+            const { refName, start, end } = region;
+            const lines = featureMap[refName] || [];
+            for (const line of lines) {
+                const fields = line.split('\t');
+                const pos = parseInt(fields[1], 10);
+                if (pos - 1 >= start && pos - 1 < end) {
+                    exportLines.push(line);
+                }
+            }
+        }
+        return exportLines.join('\n');
+    }
     async getSources() {
         const conf = this.getConf('samplesTsvLocation');
         if (conf.uri === '' || conf.uri === '/path/to/samples.tsv') {
@@ -99,6 +112,7 @@ class VcfAdapter extends BaseFeatureDataAdapter {
             const s = new Set(parser.samples);
             return lines
                 .slice(1)
+                .filter(Boolean)
                 .map(line => {
                 const cols = line.split('\t');
                 return {
@@ -110,5 +124,3 @@ class VcfAdapter extends BaseFeatureDataAdapter {
         }
     }
 }
-VcfAdapter.capabilities = ['getFeatures', 'getRefNames'];
-export default VcfAdapter;

package/esm/VcfAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const VcfAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const VcfAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     vcfLocation: {
         type: string;
         defaultValue: {
@@ -14,5 +14,5 @@ declare const VcfAdapter: import("@jbrowse/core/configuration/configurationSchem
             locationType: string;
         };
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default VcfAdapter;

package/esm/VcfAdapter/index.js

@@ -1,10 +1,11 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
-import configSchema from './configSchema';
+import configSchema from "./configSchema.js";
 export default function VcfAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'VcfAdapter',
         displayName: 'VCF adapter',
         configSchema,
-        getAdapterClass: () => import('./VcfAdapter').then(r => r.default),
+        adapterCapabilities: ['exportData'],
+        getAdapterClass: () => import("./VcfAdapter.js").then(r => r.default),
     }));
 }

package/esm/VcfExtensionPoints/index.d.ts

@@ -0,0 +1,2 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function VcfExtensionPointsF(pluginManager: PluginManager): void;

package/esm/{extensionPoints.js → VcfExtensionPoints/index.js}

@@ -1,6 +1,6 @@
 import { testAdapter } from '@jbrowse/core/util';
 import { getFileName, makeIndex, makeIndexType, } from '@jbrowse/core/util/tracks';
-export default function ExtensionPointsF(pluginManager) {
+export default function VcfExtensionPointsF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
         return (file, index, adapterHint) => {
             const fileName = getFileName(file);

package/esm/VcfFeature/index.js

@@ -1,5 +1,5 @@
 import { max } from '@jbrowse/core/util';
-import { getSOTermAndDescription } from './util';
+import { getSOTermAndDescription } from "./util.js";
 function dataFromVariant(variant, parser) {
     const { REF = '', ALT, POS, CHROM, ID } = variant;
     const start = POS - 1;
@@ -10,15 +10,23 @@ function dataFromVariant(variant, parser) {
         end: getEnd(variant),
         description,
         type,
-        name: ID === null || ID === void 0 ? void 0 : ID.join(','),
+        name: ID?.join(','),
     };
 }
 function getEnd(variant) {
-    var _a;
     const { POS, REF = '', ALT = [] } = variant;
-    const isTRA = ALT.includes('<TRA>');
     const start = POS - 1;
-    const isSymbolic = ALT.some(f => f.includes('<'));
+    let isTRA = false;
+    let isSymbolic = false;
+    for (const a of ALT) {
+        if (a.includes('<')) {
+            isSymbolic = true;
+            if (a === '<TRA>') {
+                isTRA = true;
+                break;
+            }
+        }
+    }
     if (isSymbolic) {
         const info = variant.INFO;
         if (info.END && !isTRA) {
@@ -29,7 +37,7 @@ function getEnd(variant) {
             const svlens = info.SVLEN;
             for (let i = 0; i < svlens.length; i++) {
                 const svlen = svlens[i];
-                if ((_a = ALT[i]) === null || _a === void 0 ? void 0 : _a.startsWith('<INS')) {
+                if (ALT[i]?.startsWith('<INS')) {
                     lens.push(1);
                 }
                 else {
@@ -42,6 +50,10 @@ function getEnd(variant) {
     return start + REF.length;
 }
 export default class VCFFeature {
+    variant;
+    parser;
+    data;
+    _id;
     constructor(args) {
         this.variant = args.variant;
         this.parser = args.parser;
@@ -49,12 +61,12 @@ export default class VCFFeature {
         this._id = args.id;
     }
     get(field) {
-        var _a;
         return field === 'samples'
             ? this.variant.SAMPLES()
             : field === 'genotypes'
                 ? this.variant.GENOTYPES()
-                : ((_a = this.data[field]) !== null && _a !== void 0 ? _a : this.variant[field]);
+                : (this.data[field] ??
+                    this.variant[field]);
     }
     parent() {
         return undefined;

package/esm/VcfFeature/util.d.ts

@@ -1,6 +1,5 @@
 import type VCF from '@gmod/vcf';
 export declare function getSOTermAndDescription(ref: string, alt: string[] | undefined, parser: VCF): string[];
 export declare function getSOAndDescFromAltDefs(alt: string, parser: VCF): string[];
-export declare function getSOAndDescByExamination(ref: string, alt: string): string[];
 export declare function getMinimalDesc(ref: string, alt: string): string;
 export declare function makeSimpleAltString(genotype: string, ref: string, alt: string[]): string;

package/esm/VcfFeature/util.js

@@ -1,216 +1,98 @@
 import { parseBreakend } from '@gmod/vcf';
 import { getBpDisplayStr } from '@jbrowse/core/util';
+const genotypeDelimRegex = /[/|]/;
+function isBreakend(alt) {
+    return (alt.includes('[') ||
+        alt.includes(']') ||
+        alt.startsWith('.') ||
+        alt.endsWith('.'));
+}
+function isSymbolic(alt) {
+    return alt.startsWith('<') || isBreakend(alt);
+}
+function isInversion(ref, alt) {
+    return ref.split('').reverse().join('') === alt;
+}
 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',
+    '<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',
 };
 export function getSOTermAndDescription(ref, alt, parser) {
     if (!alt || alt.length === 0) {
         return ['remark', 'no alternative alleles'];
     }
-    const soTerms = new Set();
-    let descriptions = new Set();
-    for (const a of alt) {
-        let [soTerm, description] = getSOAndDescFromAltDefs(a, parser);
-        if (!soTerm) {
-            ;
-            [soTerm, description] = getSOAndDescByExamination(ref, a);
-        }
-        if (soTerm && description) {
-            soTerms.add(soTerm);
-            descriptions.add(description);
-        }
-    }
-    if (descriptions.size > 1) {
-        const descs = [...descriptions];
-        const prefixes = new Set(descs
-            .map(desc => {
-            const prefix = desc.split('->');
-            return prefix[1] ? prefix[0] : desc;
-        })
-            .filter((f) => !!f));
-        descriptions = new Set([...prefixes]
-            .map(r => r.trim())
-            .map(prefix => {
-            const suffixes = descs
-                .map(desc => desc.split('->').map(r => r.trim()))
-                .map(pref => (pref[1] && pref[0] === prefix ? pref[1] : ''))
-                .filter(f => !!f);
-            return suffixes.length ? `${prefix} -> ${suffixes.join(',')}` : prefix;
-        }));
-    }
-    return soTerms.size
-        ? [[...soTerms].join(','), [...descriptions].join(',')]
-        : [];
-}
-export function getSOAndDescFromAltDefs(alt, parser) {
-    if (typeof alt === 'string' && !alt.startsWith('<')) {
-        return [];
-    }
-    let soTerm = altTypeToSO[alt];
-    if (!soTerm && parser.getMetadata('ALT', alt)) {
-        soTerm = 'sequence_variant';
-    }
-    if (soTerm) {
-        return [soTerm, alt];
-    }
-    const modAlt = alt.split(':');
-    return modAlt.length > 1
-        ? getSOAndDescFromAltDefs(`<${modAlt.slice(0, -1).join(':')}>`, parser)
-        : [];
+    const soTerms = alt.map(a => getSOTerm(a, ref, parser));
+    const uniqueSoTerms = [...new Set(soTerms)];
+    const description = formatGroupDescription(ref, alt);
+    return [uniqueSoTerms.join(','), description];
 }
-export function getSOAndDescByExamination(ref, alt) {
-    const bnd = parseBreakend(alt);
-    if (bnd) {
-        return ['breakend', alt];
+function getSOTerm(alt, ref, parser) {
+    if (alt.startsWith('<')) {
+        return findSOTerm(alt, parser) ?? 'variant';
     }
-    else if (ref.length === 1 && alt.length === 1) {
-        return ['SNV', makeDescriptionString('SNV', ref, alt)];
+    if (isBreakend(alt) && parseBreakend(alt)) {
+        return 'breakend';
     }
-    else if (alt === '<INS>') {
-        return ['insertion', alt];
+    const lenRef = ref.length;
+    const lenAlt = alt.length;
+    if (lenRef === 1 && lenAlt === 1) {
+        return 'SNV';
     }
-    else if (alt === '<DEL>') {
-        return ['deletion', alt];
-    }
-    else if (alt === '<DUP>') {
-        return ['duplication', alt];
-    }
-    else if (alt === '<CNV>') {
-        return ['cnv', alt];
-    }
-    else if (alt === '<INV>') {
-        return ['inversion', alt];
-    }
-    else if (alt === '<TRA>') {
-        return ['translocation', alt];
-    }
-    else if (alt.includes('<')) {
-        return ['sv', alt];
-    }
-    else if (ref.length === alt.length) {
-        const lenRef = ref.length;
-        const lenAlt = alt.length;
-        if (lenRef > 5 || lenAlt > 5) {
-            const lena = getBpDisplayStr(lenRef);
-            const lenb = getBpDisplayStr(lenAlt);
-            return ref.split('').reverse().join('') === alt
-                ? ['inverson', makeDescriptionString('inv', lena, lenb)]
-                : ['substitution', makeDescriptionString('substitution', lena, lenb)];
-        }
-        else {
-            return ref.split('').reverse().join('') === alt
-                ? ['inversion', makeDescriptionString('inv', ref, alt)]
-                : ['substitution', makeDescriptionString('substitution', ref, alt)];
-        }
-    }
-    else if (ref.length <= alt.length) {
-        const len = alt.length - ref.length;
-        const lenAlt = alt.length;
-        const lenRef = ref.length;
-        const lena = getBpDisplayStr(len);
-        return [
-            'insertion',
-            lenRef > 5 || lenAlt > 5
-                ? `${lena} INS`
-                : makeDescriptionString('insertion', len > 5 ? lena : ref, alt),
-        ];
-    }
-    else if (ref.length > alt.length) {
-        const lenRef = ref.length;
-        const lenAlt = alt.length;
-        const lena = getBpDisplayStr(lenRef - lenAlt);
-        return [
-            'deletion',
-            lenRef > 5 || lenAlt > 5
-                ? `${lena} DEL`
-                : makeDescriptionString('deletion', ref, alt),
-        ];
+    else if (lenRef === lenAlt) {
+        return isInversion(ref, alt) ? 'inversion' : 'substitution';
     }
     else {
-        return ['indel', makeDescriptionString('indel', ref, alt)];
+        return lenRef < lenAlt ? 'insertion' : 'deletion';
     }
 }
-export function getMinimalDesc(ref, alt) {
-    const bnd = parseBreakend(alt);
-    if (bnd) {
-        return alt;
-    }
-    else if (ref.length === 1 && alt.length === 1) {
-        return alt;
-    }
-    else if (alt === '<INS>') {
-        return alt;
+function formatGroupDescription(ref, alts) {
+    if (alts.every(isSymbolic)) {
+        return alts.join(',');
     }
-    else if (alt === '<DEL>') {
-        return alt;
-    }
-    else if (alt === '<DUP>') {
-        return alt;
+    const lenRef = ref.length;
+    return `${ref.length > 10 ? getBpDisplayStr(lenRef) : ref} -> ${alts.map(a => (a.length > 10 ? getBpDisplayStr(a.length) : a)).join(',')}`;
+}
+function findSOTerm(alt, parser) {
+    if (altTypeToSO[alt]) {
+        return altTypeToSO[alt];
     }
-    else if (alt === '<CNV>') {
-        return alt;
+    if (parser.getMetadata('ALT', alt)) {
+        return 'sequence_variant';
     }
-    else if (alt === '<INV>') {
-        return alt;
-    }
-    else if (alt === '<TRA>') {
-        return alt;
+    const parts = alt.slice(1, -1).split(':');
+    return parts.length > 1
+        ? findSOTerm(`<${parts.slice(0, -1).join(':')}>`, parser)
+        : undefined;
+}
+export function getSOAndDescFromAltDefs(alt, parser) {
+    if (!alt.startsWith('<')) {
+        return [];
     }
-    else if (alt.includes('<')) {
+    const soTerm = findSOTerm(alt, parser);
+    return [soTerm ?? 'variant', alt];
+}
+export function getMinimalDesc(ref, alt) {
+    if (isSymbolic(alt) || (ref.length === 1 && alt.length === 1)) {
         return alt;
     }
-    else if (ref.length === alt.length) {
-        const lenRef = ref.length;
-        const lenAlt = alt.length;
-        if (lenRef > 5 || lenAlt > 5) {
-            const lena = getBpDisplayStr(lenRef);
-            const lenb = getBpDisplayStr(lenAlt);
-            return ref.split('').reverse().join('') === alt
-                ? makeDescriptionString('inv', lena, lenb)
-                : makeDescriptionString('substitution', lena, lenb);
-        }
-        else {
-            return ref.split('').reverse().join('') === alt
-                ? makeDescriptionString('inv', ref, alt)
-                : makeDescriptionString('substitution', ref, alt);
-        }
-    }
-    else if (ref.length <= alt.length) {
-        const len = alt.length - ref.length;
-        const lenAlt = alt.length;
-        const lenRef = ref.length;
-        const lena = getBpDisplayStr(len);
-        return lenRef > 5 || lenAlt > 5
-            ? `${lena} INS`
-            : makeDescriptionString('insertion', len > 5 ? lena : ref, alt);
-    }
-    else if (ref.length > alt.length) {
-        const lenRef = ref.length;
-        const lenAlt = alt.length;
-        const lena = getBpDisplayStr(lenRef - lenAlt);
-        return lenRef > 5 || lenAlt > 5
-            ? `${lena} DEL`
-            : makeDescriptionString('deletion', ref, alt);
-    }
-    else {
-        return makeDescriptionString('indel', ref, alt);
-    }
-}
-function makeDescriptionString(soTerm, ref, alt) {
-    return `${soTerm} ${[ref, alt].join(' -> ')}`;
+    const lenRef = ref.length;
+    const lenAlt = alt.length;
+    const isLong = lenRef > 5 || lenAlt > 5;
+    return isLong
+        ? `${getBpDisplayStr(lenRef)} -> ${getBpDisplayStr(lenAlt)}`
+        : `${ref} -> ${alt}`;
 }
 export function makeSimpleAltString(genotype, ref, alt) {
     return genotype
-        .split(/[/|]/)
+        .split(genotypeDelimRegex)
         .map(r => r === '.'
         ? '.'
         : +r === 0

package/esm/VcfTabixAdapter/VcfTabixAdapter.d.ts

@@ -5,6 +5,7 @@ import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { Feature } from '@jbrowse/core/util';
 import type { NoAssemblyRegion } from '@jbrowse/core/util/types';
 export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
+    static capabilities: string[];
     private configured?;
     private configurePre;
     protected configurePre2(): Promise<{
@@ -18,6 +19,7 @@ export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getHeader(opts?: BaseOptions): Promise<string>;
     getMetadata(opts?: BaseOptions): Promise<any>;
+    getExportData(regions: NoAssemblyRegion[], formatType: string, opts?: BaseOptions): Promise<string | undefined>;
     getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     getSources(): Promise<{
         name: string;

package/esm/VcfTabixAdapter/VcfTabixAdapter.js

@@ -4,8 +4,10 @@ import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
 import { fetchAndMaybeUnzipText, shorten2, updateStatus, } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import VcfFeature from '../VcfFeature';
+import VcfFeature from "../VcfFeature/index.js";
 export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
+    static capabilities = ['getFeatures', 'getRefNames', 'exportData'];
+    configured;
     async configurePre(_opts) {
         const vcfGzLocation = this.getConf('vcfGzLocation');
         const location = this.getConf(['index', 'location']);
@@ -54,6 +56,29 @@ export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
         const { parser } = await this.configure(opts);
         return parser.getMetadata();
     }
+    async getExportData(regions, formatType, opts) {
+        if (formatType !== 'vcf') {
+            return undefined;
+        }
+        const { statusCallback = () => { } } = opts || {};
+        const { vcf } = await this.configure(opts);
+        const headerText = await vcf.getHeader();
+        const exportLines = headerText.split('\n').filter(Boolean);
+        for (const region of regions) {
+            const { refName, start, end } = region;
+            const regionLines = [];
+            await updateStatus('Exporting variants', statusCallback, () => vcf.getLines(refName, start, end, {
+                lineCallback: (line) => {
+                    regionLines.push(line);
+                },
+                ...opts,
+            }));
+            for (const line of regionLines) {
+                exportLines.push(line);
+            }
+        }
+        return exportLines.join('\n');
+    }
     getFeatures(query, opts = {}) {
         return ObservableCreate(async (observer) => {
             const { refName, start, end } = query;
@@ -87,7 +112,7 @@ export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
             const { parser } = await this.configure();
             const metadataLines = lines
                 .slice(1)
-                .filter(f => !!f)
+                .filter(Boolean)
                 .map(line => {
                 const [name, ...rest] = line.split('\t');
                 return {
@@ -103,7 +128,7 @@ export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
                 console.warn(`There are ${metadataNotInVcfSamples.length} samples in metadata file (${metadataLines.length} lines) not in VCF (${parser.samples.length} samples):`, shorten2(metadataNotInVcfSamples.join(',')));
             }
             if (vcfSamplesNotInMetadata.length) {
-                console.warn(`There are ${vcfSamplesNotInMetadata.length} samples in VCF file (${parser.samples.length} samples) not in metadata file (${metadataLines.length} lines):`, shorten2(vcfSamplesNotInMetadata.map(m => m).join(',')));
+                console.warn(`There are ${vcfSamplesNotInMetadata.length} samples in VCF file (${parser.samples.length} samples) not in metadata file (${metadataLines.length} lines):`, shorten2(vcfSamplesNotInMetadata.join(',')));
             }
             return metadataLines.filter(f => vcfSampleSet.has(f.name));
         }

package/esm/VcfTabixAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const VcfTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const VcfTabixAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     vcfGzLocation: {
         type: string;
         defaultValue: {
@@ -6,9 +6,9 @@ declare const VcfTabixAdapter: import("@jbrowse/core/configuration/configuration
             locationType: string;
         };
     };
-    index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    index: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
         indexType: {
-            model: import("mobx-state-tree").ISimpleType<string>;
+            model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
             type: string;
             defaultValue: string;
         };
@@ -19,7 +19,7 @@ declare const VcfTabixAdapter: import("@jbrowse/core/configuration/configuration
                 locationType: string;
             };
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
     samplesTsvLocation: {
         type: string;
         defaultValue: {
@@ -28,5 +28,5 @@ declare const VcfTabixAdapter: import("@jbrowse/core/configuration/configuration
             locationType: string;
         };
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default VcfTabixAdapter;

package/esm/VcfTabixAdapter/configSchema.js

@@ -1,5 +1,5 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import { types } from 'mobx-state-tree';
+import { types } from '@jbrowse/mobx-state-tree';
 function x() { }
 const VcfTabixAdapter = ConfigurationSchema('VcfTabixAdapter', {
     vcfGzLocation: {