@jbrowse/text-indexing 3.7.0 → 4.0.1

package/esm/TextIndexing.d.ts

@@ -1,4 +1,4 @@
-import type { Track, indexType } from './util';
+import type { Track, indexType } from './util.ts';
 export declare function indexTracks(args: {
     tracks: Track[];
     outDir?: string;

package/esm/TextIndexing.js

@@ -4,9 +4,9 @@ import { Readable } from 'stream';
 import { isSupportedIndexingAdapter } from '@jbrowse/core/util';
 import { checkStopToken } from '@jbrowse/core/util/stopToken';
 import { ixIxxStream } from 'ixixx';
-import { generateMeta } from './types/common';
-import { indexGff3 } from './types/gff3Adapter';
-import { indexVcf } from './types/vcfAdapter';
+import { generateMeta } from "./types/common.js";
+import { indexGff3 } from "./types/gff3Adapter.js";
+import { indexVcf } from "./types/vcfAdapter.js";
 export async function indexTracks(args) {
     const { tracks, outDir, attributesToIndex, featureTypesToExclude, assemblyNames, indexType, statusCallback, stopToken, } = args;
     const idxType = indexType || 'perTrack';
@@ -41,7 +41,7 @@ async function perTrackIndex({ tracks, statusCallback, outDir: paramOutDir, attr
     if (!fs.existsSync(trixDir)) {
         fs.mkdirSync(trixDir);
     }
-    const supportedTracks = tracks.filter(track => { var _a; return isSupportedIndexingAdapter((_a = track.adapter) === null || _a === void 0 ? void 0 : _a.type); });
+    const supportedTracks = tracks.filter(track => isSupportedIndexingAdapter(track.adapter?.type));
     for (const trackConfig of supportedTracks) {
         const { trackId, assemblyNames } = trackConfig;
         const id = `${trackId}-index`;
@@ -72,7 +72,7 @@ async function aggregateIndex({ tracks, statusCallback, outDir: paramOutDir, att
     for (const asm of assemblyNames) {
         const id = `${asm}-index`;
         const supportedTracks = tracks
-            .filter(track => { var _a; return isSupportedIndexingAdapter((_a = track.adapter) === null || _a === void 0 ? void 0 : _a.type); })
+            .filter(track => isSupportedIndexingAdapter(track.adapter?.type))
             .filter(track => (asm ? track.assemblyNames.includes(asm) : true));
         await indexDriver({
             tracks: supportedTracks,
@@ -176,8 +176,7 @@ async function* indexFiles({ tracks, attributesToIndex: idx1, outDir, featureTyp
     return;
 }
 function getLoc(attr, config) {
-    var _a;
-    const elt = (_a = config.adapter) === null || _a === void 0 ? void 0 : _a[attr];
+    const elt = config.adapter?.[attr];
     if (!elt) {
         throw new Error(`can't get find ${attr} from ${config.adapter} for text indexing`);
     }

package/esm/index.d.ts

@@ -1,5 +1,5 @@
-export * from './util';
-export * from './types/common';
-export { indexTracks } from './TextIndexing';
-export { indexGff3 } from './types/gff3Adapter';
-export { indexVcf } from './types/vcfAdapter';
+export * from './util.ts';
+export * from './types/common.ts';
+export { indexTracks } from './TextIndexing.ts';
+export { indexGff3 } from './types/gff3Adapter.ts';
+export { indexVcf } from './types/vcfAdapter.ts';

package/esm/index.js

@@ -1,5 +1,5 @@
-export * from './util';
-export * from './types/common';
-export { indexTracks } from './TextIndexing';
-export { indexGff3 } from './types/gff3Adapter';
-export { indexVcf } from './types/vcfAdapter';
+export * from "./util.js";
+export * from "./types/common.js";
+export { indexTracks } from "./TextIndexing.js";
+export { indexGff3 } from "./types/gff3Adapter.js";
+export { indexVcf } from "./types/vcfAdapter.js";

package/esm/types/common.d.ts

@@ -1,6 +1,6 @@
 import fs from 'fs';
 import fetch from 'node-fetch';
-import type { LocalPathLocation, Track, UriLocation } from '../util';
+import type { LocalPathLocation, Track, UriLocation } from '../util.ts';
 export declare function createRemoteStream(urlIn: string): Promise<fetch.Response>;
 export declare function isURL(FileName: string): boolean;
 export declare function getLocalOrRemoteStream({ file, out, onBytesReceived, onTotalBytes, }: {

package/esm/types/common.js

@@ -121,8 +121,8 @@ export async function generateMeta({ configs, attributesToIndex, outDir, name, f
             const { trackId, textSearching, adapter } = config;
             return {
                 trackId,
-                attributesIndexed: (textSearching === null || textSearching === void 0 ? void 0 : textSearching.indexingAttributes) || attributesToIndex,
-                excludedTypes: (textSearching === null || textSearching === void 0 ? void 0 : textSearching.indexingFeatureTypesToExclude) ||
+                attributesIndexed: textSearching?.indexingAttributes || attributesToIndex,
+                excludedTypes: textSearching?.indexingFeatureTypesToExclude ||
                     featureTypesToExclude,
                 adapterConf: adapter,
             };

package/esm/types/gff3Adapter.js

@@ -1,7 +1,7 @@
 import readline from 'readline';
 import { createGunzip } from 'zlib';
-import { decodeURIComponentNoThrow } from '../util';
-import { getLocalOrRemoteStream } from './common';
+import { decodeURIComponentNoThrow } from "../util.js";
+import { getLocalOrRemoteStream } from "./common.js";
 export async function* indexGff3({ config, attributesToIndex, inLocation, outDir, featureTypesToExclude, onStart, onUpdate, }) {
     const { trackId } = config;
     const stream = await getLocalOrRemoteStream({

package/esm/types/vcfAdapter.js

@@ -1,7 +1,7 @@
 import readline from 'readline';
 import { createGunzip } from 'zlib';
-import { decodeURIComponentNoThrow } from '../util';
-import { getLocalOrRemoteStream } from './common';
+import { decodeURIComponentNoThrow } from "../util.js";
+import { getLocalOrRemoteStream } from "./common.js";
 export async function* indexVcf({ config, attributesToIndex, inLocation, outDir, onStart, onUpdate, }) {
     const { trackId } = config;
     const stream = await getLocalOrRemoteStream({

package/esm/util.js

@@ -33,7 +33,7 @@ export function findTrackConfigsToIndex(tracks, trackIds, assemblyName) {
         return currentTrack;
     })
         .filter(track => assemblyName ? track.assemblyNames.includes(assemblyName) : true)
-        .filter(track => { var _a; return isSupportedIndexingAdapter((_a = track.adapter) === null || _a === void 0 ? void 0 : _a.type); });
+        .filter(track => isSupportedIndexingAdapter(track.adapter?.type));
 }
 export function decodeURIComponentNoThrow(uri) {
     try {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/text-indexing",
-  "version": "3.7.0",
+  "version": "4.0.1",
   "description": "JBrowse 2 text indexing for desktop",
   "keywords": [
     "jbrowse",
@@ -18,38 +18,15 @@
     "directory": "packages/text-indexing"
   },
   "author": "JBrowse Team",
-  "distMain": "dist/index.js",
-  "distModule": "esm/index.js",
-  "srcMain": "src/index.ts",
-  "srcModule": "src/index.ts",
-  "main": "dist/index.js",
-  "module": "esm/index.js",
+  "main": "esm/index.js",
   "files": [
-    "dist",
     "esm"
   ],
-  "scripts": {
-    "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
-    "build": "npm run build:esm && npm run build:commonjs",
-    "test": "cd ../..; jest --passWithNoTests packages/text-indexing",
-    "clean": "rimraf dist esm *.tsbuildinfo",
-    "prebuild": "yarn clean",
-    "prepack": "yarn build && yarn useDist",
-    "postpack": "yarn useSrc",
-    "useDist": "node ../../scripts/useDist.js",
-    "useSrc": "node ../../scripts/useSrc.js"
-  },
   "dependencies": {
-    "@babel/runtime": "^7.16.3",
-    "@jbrowse/core": "^3.7.0",
-    "ixixx": "^2.0.1",
-    "mobx": "^6.0.0",
-    "mobx-react": "^9.0.0",
-    "mobx-state-tree": "^5.0.0",
-    "node-fetch": "^2.6.0",
-    "rxjs": "^7.0.0",
-    "sanitize-filename": "^1.6.3"
+    "ixixx": "^3.0.2",
+    "node-fetch": "^2.7.0",
+    "sanitize-filename": "^1.6.3",
+    "@jbrowse/core": "^4.0.1"
   },
   "peerDependencies": {
     "react": ">=18.0.0",
@@ -58,5 +35,19 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "85bdd0d58286b7adbfd408146b15847676317635"
-}
+  "sideEffects": false,
+  "scripts": {
+    "build:esm": "tsc -p tsconfig.build.esm.json",
+    "build": "pnpm build:esm",
+    "test": "cd ../..; jest --passWithNoTests packages/text-indexing",
+    "clean": "rimraf esm *.tsbuildinfo",
+    "prebuild": "pnpm clean"
+  },
+  "types": "esm/index.d.ts",
+  "exports": {
+    ".": {
+      "types": "./esm/index.d.ts",
+      "import": "./esm/index.js"
+    }
+  }
+}

package/dist/TextIndexing.d.ts

@@ -1,11 +0,0 @@
-import type { Track, indexType } from './util';
-export declare function indexTracks(args: {
-    tracks: Track[];
-    outDir?: string;
-    stopToken?: string;
-    attributesToIndex?: string[];
-    assemblyNames?: string[];
-    featureTypesToExclude?: string[];
-    indexType?: indexType;
-    statusCallback: (message: string) => void;
-}): Promise<never[]>;

package/dist/TextIndexing.js

@@ -1,196 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.indexTracks = indexTracks;
-const fs_1 = __importDefault(require("fs"));
-const path_1 = __importDefault(require("path"));
-const stream_1 = require("stream");
-const util_1 = require("@jbrowse/core/util");
-const stopToken_1 = require("@jbrowse/core/util/stopToken");
-const ixixx_1 = require("ixixx");
-const common_1 = require("./types/common");
-const gff3Adapter_1 = require("./types/gff3Adapter");
-const vcfAdapter_1 = require("./types/vcfAdapter");
-async function indexTracks(args) {
-    const { tracks, outDir, attributesToIndex, featureTypesToExclude, assemblyNames, indexType, statusCallback, stopToken, } = args;
-    const idxType = indexType || 'perTrack';
-    (0, stopToken_1.checkStopToken)(stopToken);
-    await (idxType === 'perTrack'
-        ? perTrackIndex({
-            tracks,
-            statusCallback,
-            outDir,
-            attributesToIndex,
-            featureTypesToExclude,
-            stopToken,
-        })
-        : aggregateIndex({
-            tracks,
-            statusCallback,
-            outDir,
-            attributesToIndex,
-            assemblyNames,
-            featureTypesToExclude,
-            stopToken,
-        }));
-    (0, stopToken_1.checkStopToken)(stopToken);
-    return [];
-}
-async function perTrackIndex({ tracks, statusCallback, outDir: paramOutDir, attributesToIndex = ['Name', 'ID'], featureTypesToExclude = ['exon', 'CDS'], stopToken, }) {
-    const outFlag = paramOutDir || '.';
-    const isDir = fs_1.default.lstatSync(outFlag).isDirectory();
-    const confFilePath = isDir ? path_1.default.join(outFlag, 'config.json') : outFlag;
-    const outDir = path_1.default.dirname(confFilePath);
-    const trixDir = path_1.default.join(outDir, 'trix');
-    if (!fs_1.default.existsSync(trixDir)) {
-        fs_1.default.mkdirSync(trixDir);
-    }
-    const supportedTracks = tracks.filter(track => { var _a; return (0, util_1.isSupportedIndexingAdapter)((_a = track.adapter) === null || _a === void 0 ? void 0 : _a.type); });
-    for (const trackConfig of supportedTracks) {
-        const { trackId, assemblyNames } = trackConfig;
-        const id = `${trackId}-index`;
-        await indexDriver({
-            tracks: [trackConfig],
-            outDir,
-            attributesToIndex,
-            name: id,
-            featureTypesToExclude,
-            assemblyNames,
-            statusCallback,
-            stopToken,
-        });
-    }
-}
-async function aggregateIndex({ tracks, statusCallback, outDir: paramOutDir, attributesToIndex = ['Name', 'ID'], featureTypesToExclude = ['exon', 'CDS'], stopToken, assemblyNames, }) {
-    const outFlag = paramOutDir || '.';
-    const isDir = fs_1.default.lstatSync(outFlag).isDirectory();
-    const confFilePath = isDir ? path_1.default.join(outFlag, 'config.json') : outFlag;
-    const outDir = path_1.default.dirname(confFilePath);
-    const trixDir = path_1.default.join(outDir, 'trix');
-    if (!fs_1.default.existsSync(trixDir)) {
-        fs_1.default.mkdirSync(trixDir);
-    }
-    if (!assemblyNames) {
-        throw new Error('No assemblies passed. Assmeblies required for aggregate indexes');
-    }
-    for (const asm of assemblyNames) {
-        const id = `${asm}-index`;
-        const supportedTracks = tracks
-            .filter(track => { var _a; return (0, util_1.isSupportedIndexingAdapter)((_a = track.adapter) === null || _a === void 0 ? void 0 : _a.type); })
-            .filter(track => (asm ? track.assemblyNames.includes(asm) : true));
-        await indexDriver({
-            tracks: supportedTracks,
-            outDir: outDir,
-            attributesToIndex,
-            name: id,
-            featureTypesToExclude,
-            assemblyNames: [asm],
-            statusCallback,
-            stopToken,
-        });
-    }
-}
-async function indexDriver({ tracks, outDir, attributesToIndex, name, featureTypesToExclude, assemblyNames, statusCallback, stopToken, }) {
-    const readable = stream_1.Readable.from(indexFiles({
-        tracks,
-        attributesToIndex,
-        outDir,
-        featureTypesToExclude,
-        statusCallback,
-        stopToken,
-    }));
-    statusCallback('Indexing files.');
-    await runIxIxx(readable, outDir, name);
-    (0, stopToken_1.checkStopToken)(stopToken);
-    await (0, common_1.generateMeta)({
-        configs: tracks,
-        attributesToIndex,
-        outDir,
-        name,
-        featureTypesToExclude,
-        assemblyNames,
-    });
-    (0, stopToken_1.checkStopToken)(stopToken);
-}
-async function* indexFiles({ tracks, attributesToIndex: idx1, outDir, featureTypesToExclude: edx1, statusCallback, }) {
-    for (const track of tracks) {
-        const { adapter, textSearching } = track;
-        const { type } = adapter || {};
-        const { indexingFeatureTypesToExclude: featureTypesToExclude = edx1, indexingAttributes: attributesToIndex = idx1, } = textSearching || {};
-        let myTotalBytes;
-        if (type === 'Gff3Adapter') {
-            yield* (0, gff3Adapter_1.indexGff3)({
-                config: track,
-                attributesToIndex,
-                inLocation: getLoc('gffLocation', track),
-                outDir,
-                featureTypesToExclude,
-                onStart: totalBytes => {
-                    myTotalBytes = totalBytes;
-                },
-                onUpdate: progressBytes => {
-                    statusCallback(`${progressBytes}/${myTotalBytes}`);
-                },
-            });
-        }
-        if (type === 'Gff3TabixAdapter') {
-            yield* (0, gff3Adapter_1.indexGff3)({
-                config: track,
-                attributesToIndex,
-                inLocation: getLoc('gffGzLocation', track),
-                outDir,
-                featureTypesToExclude,
-                onStart: totalBytes => {
-                    myTotalBytes = totalBytes;
-                },
-                onUpdate: progressBytes => {
-                    statusCallback(`${progressBytes}/${myTotalBytes}`);
-                },
-            });
-        }
-        else if (type === 'VcfAdapter') {
-            yield* (0, vcfAdapter_1.indexVcf)({
-                config: track,
-                attributesToIndex,
-                inLocation: getLoc('vcfLocation', track),
-                outDir,
-                onStart: totalBytes => {
-                    myTotalBytes = totalBytes;
-                },
-                onUpdate: progressBytes => {
-                    statusCallback(`${progressBytes}/${myTotalBytes}`);
-                },
-            });
-        }
-        else if (type === 'VcfTabixAdapter') {
-            yield* (0, vcfAdapter_1.indexVcf)({
-                config: track,
-                attributesToIndex,
-                inLocation: getLoc('vcfGzLocation', track),
-                outDir,
-                onStart: totalBytes => {
-                    myTotalBytes = totalBytes;
-                },
-                onUpdate: progressBytes => {
-                    statusCallback(`${progressBytes}/${myTotalBytes}`);
-                },
-            });
-        }
-    }
-    return;
-}
-function getLoc(attr, config) {
-    var _a;
-    const elt = (_a = config.adapter) === null || _a === void 0 ? void 0 : _a[attr];
-    if (!elt) {
-        throw new Error(`can't get find ${attr} from ${config.adapter} for text indexing`);
-    }
-    return elt.uri || elt.localPath;
-}
-function runIxIxx(readStream, idxLocation, name) {
-    const ixFilename = path_1.default.join(idxLocation, 'trix', `${name}.ix`);
-    const ixxFilename = path_1.default.join(idxLocation, 'trix', `${name}.ixx`);
-    return (0, ixixx_1.ixIxxStream)(readStream, ixFilename, ixxFilename);
-}

package/dist/index.d.ts

@@ -1,5 +0,0 @@
-export * from './util';
-export * from './types/common';
-export { indexTracks } from './TextIndexing';
-export { indexGff3 } from './types/gff3Adapter';
-export { indexVcf } from './types/vcfAdapter';

package/dist/index.js

@@ -1,25 +0,0 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __exportStar = (this && this.__exportStar) || function(m, exports) {
-    for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.indexVcf = exports.indexGff3 = exports.indexTracks = void 0;
-__exportStar(require("./util"), exports);
-__exportStar(require("./types/common"), exports);
-var TextIndexing_1 = require("./TextIndexing");
-Object.defineProperty(exports, "indexTracks", { enumerable: true, get: function () { return TextIndexing_1.indexTracks; } });
-var gff3Adapter_1 = require("./types/gff3Adapter");
-Object.defineProperty(exports, "indexGff3", { enumerable: true, get: function () { return gff3Adapter_1.indexGff3; } });
-var vcfAdapter_1 = require("./types/vcfAdapter");
-Object.defineProperty(exports, "indexVcf", { enumerable: true, get: function () { return vcfAdapter_1.indexVcf; } });

package/dist/types/common.d.ts

@@ -1,21 +0,0 @@
-import fs from 'fs';
-import fetch from 'node-fetch';
-import type { LocalPathLocation, Track, UriLocation } from '../util';
-export declare function createRemoteStream(urlIn: string): Promise<fetch.Response>;
-export declare function isURL(FileName: string): boolean;
-export declare function getLocalOrRemoteStream({ file, out, onBytesReceived, onTotalBytes, }: {
-    file: string;
-    out: string;
-    onBytesReceived: (totalBytesReceived: number) => void;
-    onTotalBytes: (totalBytes: number) => void;
-}): Promise<NodeJS.ReadableStream | fs.ReadStream>;
-export declare function makeLocation(location: string, protocol: string): UriLocation | LocalPathLocation;
-export declare function guessAdapterFromFileName(filePath: string): Track;
-export declare function generateMeta({ configs, attributesToIndex, outDir, name, featureTypesToExclude, assemblyNames, }: {
-    configs: Track[];
-    attributesToIndex: string[];
-    outDir: string;
-    name: string;
-    featureTypesToExclude: string[];
-    assemblyNames: string[];
-}): Promise<void>;

package/dist/types/common.js

@@ -1,143 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.createRemoteStream = createRemoteStream;
-exports.isURL = isURL;
-exports.getLocalOrRemoteStream = getLocalOrRemoteStream;
-exports.makeLocation = makeLocation;
-exports.guessAdapterFromFileName = guessAdapterFromFileName;
-exports.generateMeta = generateMeta;
-const fs_1 = __importDefault(require("fs"));
-const path_1 = __importDefault(require("path"));
-const node_fetch_1 = __importDefault(require("node-fetch"));
-async function createRemoteStream(urlIn) {
-    const res = await (0, node_fetch_1.default)(urlIn);
-    if (!res.ok) {
-        throw new Error(`Failed to fetch ${urlIn} status ${res.status} ${await res.text()}`);
-    }
-    return res;
-}
-function isURL(FileName) {
-    let url;
-    try {
-        url = new URL(FileName);
-    }
-    catch (_) {
-        return false;
-    }
-    return url.protocol === 'http:' || url.protocol === 'https:';
-}
-async function getLocalOrRemoteStream({ file, out, onBytesReceived, onTotalBytes, }) {
-    let receivedBytes = 0;
-    if (isURL(file)) {
-        const result = await createRemoteStream(file);
-        result.body.on('data', chunk => {
-            receivedBytes += chunk.length;
-            onBytesReceived(receivedBytes);
-        });
-        onTotalBytes(+(result.headers.get('Content-Length') || 0));
-        return result.body;
-    }
-    else {
-        const filename = path_1.default.isAbsolute(file) ? file : path_1.default.join(out, file);
-        const stream = fs_1.default.createReadStream(filename);
-        stream.on('data', chunk => {
-            receivedBytes += chunk.length;
-            onBytesReceived(receivedBytes);
-        });
-        onTotalBytes(fs_1.default.statSync(filename).size);
-        return stream;
-    }
-}
-function makeLocation(location, protocol) {
-    if (protocol === 'uri') {
-        return { uri: location, locationType: 'UriLocation' };
-    }
-    if (protocol === 'localPath') {
-        return {
-            localPath: path_1.default.resolve(location),
-            locationType: 'LocalPathLocation',
-        };
-    }
-    throw new Error(`invalid protocol ${protocol}`);
-}
-function guessAdapterFromFileName(filePath) {
-    const protocol = isURL(filePath) ? 'uri' : 'localPath';
-    const name = path_1.default.basename(filePath);
-    if (/\.vcf\.b?gz$/i.test(filePath)) {
-        return {
-            trackId: name,
-            name: name,
-            assemblyNames: [],
-            adapter: {
-                type: 'VcfTabixAdapter',
-                vcfGzLocation: makeLocation(filePath, protocol),
-            },
-        };
-    }
-    else if (/\.gff3?\.b?gz$/i.test(filePath)) {
-        return {
-            trackId: name,
-            name,
-            assemblyNames: [],
-            adapter: {
-                type: 'Gff3TabixAdapter',
-                gffGzLocation: makeLocation(filePath, protocol),
-            },
-        };
-    }
-    else if (/\.gtf?$/i.test(filePath)) {
-        return {
-            trackId: name,
-            name,
-            assemblyNames: [],
-            adapter: {
-                type: 'GtfAdapter',
-                gtfLocation: makeLocation(filePath, protocol),
-            },
-        };
-    }
-    else if (/\.vcf$/i.test(filePath)) {
-        return {
-            trackId: name,
-            name,
-            assemblyNames: [],
-            adapter: {
-                type: 'VcfAdapter',
-                vcfLocation: makeLocation(filePath, protocol),
-            },
-        };
-    }
-    else if (/\.gff3?$/i.test(filePath)) {
-        return {
-            trackId: name,
-            name,
-            assemblyNames: [],
-            adapter: {
-                type: 'Gff3Adapter',
-                gffLocation: makeLocation(filePath, protocol),
-            },
-        };
-    }
-    else {
-        throw new Error(`Unsupported file type ${filePath}`);
-    }
-}
-async function generateMeta({ configs, attributesToIndex, outDir, name, featureTypesToExclude, assemblyNames, }) {
-    fs_1.default.writeFileSync(path_1.default.join(outDir, 'trix', `${name}_meta.json`), JSON.stringify({
-        dateCreated: new Date().toISOString(),
-        tracks: configs.map(config => {
-            const { trackId, textSearching, adapter } = config;
-            return {
-                trackId,
-                attributesIndexed: (textSearching === null || textSearching === void 0 ? void 0 : textSearching.indexingAttributes) || attributesToIndex,
-                excludedTypes: (textSearching === null || textSearching === void 0 ? void 0 : textSearching.indexingFeatureTypesToExclude) ||
-                    featureTypesToExclude,
-                adapterConf: adapter,
-            };
-        }),
-        assemblyNames,
-    }, null, 2));
-}

package/dist/types/gff3Adapter.d.ts

@@ -1,11 +0,0 @@
-export declare function indexGff3({ config, attributesToIndex, inLocation, outDir, featureTypesToExclude, onStart, onUpdate, }: {
-    config: {
-        trackId: string;
-    };
-    attributesToIndex: string[];
-    inLocation: string;
-    outDir: string;
-    featureTypesToExclude: string[];
-    onStart: (totalBytes: number) => void;
-    onUpdate: (progressBytes: number) => void;
-}): AsyncGenerator<string, void, unknown>;

package/dist/types/gff3Adapter.js

@@ -1,59 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.indexGff3 = indexGff3;
-const readline_1 = __importDefault(require("readline"));
-const zlib_1 = require("zlib");
-const util_1 = require("../util");
-const common_1 = require("./common");
-async function* indexGff3({ config, attributesToIndex, inLocation, outDir, featureTypesToExclude, onStart, onUpdate, }) {
-    const { trackId } = config;
-    const stream = await (0, common_1.getLocalOrRemoteStream)({
-        file: inLocation,
-        out: outDir,
-        onTotalBytes: onStart,
-        onBytesReceived: onUpdate,
-    });
-    const rl = readline_1.default.createInterface({
-        input: /.b?gz$/.exec(inLocation) ? stream.pipe((0, zlib_1.createGunzip)()) : stream,
-    });
-    for await (const line of rl) {
-        if (!line.trim()) {
-            continue;
-        }
-        else if (line.startsWith('#')) {
-            continue;
-        }
-        else if (line.startsWith('>')) {
-            break;
-        }
-        const [seq_id, , type, start, end, , , , col9] = line.split('\t');
-        const locStr = `${seq_id}:${start}..${end}`;
-        if (!featureTypesToExclude.includes(type)) {
-            const col9attrs = Object.fromEntries(col9
-                .split(';')
-                .map(f => f.trim())
-                .filter(f => !!f)
-                .map(f => f.split('='))
-                .map(([key, val]) => [
-                key.trim(),
-                val
-                    ? (0, util_1.decodeURIComponentNoThrow)(val).trim().split(',').join(' ')
-                    : undefined,
-            ]));
-            const attrs = attributesToIndex
-                .map(attr => col9attrs[attr])
-                .filter((f) => !!f);
-            if (attrs.length) {
-                const record = JSON.stringify([
-                    encodeURIComponent(locStr),
-                    encodeURIComponent(trackId),
-                    ...attrs.map(a => encodeURIComponent(a)),
-                ]).replaceAll(',', '|');
-                yield `${record} ${[...new Set(attrs)].join(' ')}\n`;
-            }
-        }
-    }
-}

package/dist/types/vcfAdapter.d.ts

@@ -1,8 +0,0 @@
-export declare function indexVcf({ config, attributesToIndex, inLocation, outDir, onStart, onUpdate, }: {
-    config: any;
-    attributesToIndex: string[];
-    inLocation: string;
-    outDir: string;
-    onStart: (totalBytes: number) => void;
-    onUpdate: (progressBytes: number) => void;
-}): AsyncGenerator<string, void, unknown>;

package/dist/types/vcfAdapter.js

@@ -1,61 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.indexVcf = indexVcf;
-const readline_1 = __importDefault(require("readline"));
-const zlib_1 = require("zlib");
-const util_1 = require("../util");
-const common_1 = require("./common");
-async function* indexVcf({ config, attributesToIndex, inLocation, outDir, onStart, onUpdate, }) {
-    const { trackId } = config;
-    const stream = await (0, common_1.getLocalOrRemoteStream)({
-        file: inLocation,
-        out: outDir,
-        onTotalBytes: onStart,
-        onBytesReceived: onUpdate,
-    });
-    const gzStream = /.b?gz$/.exec(inLocation)
-        ? stream.pipe((0, zlib_1.createGunzip)())
-        : stream;
-    const rl = readline_1.default.createInterface({
-        input: gzStream,
-    });
-    for await (const line of rl) {
-        if (line.startsWith('#')) {
-            continue;
-        }
-        const [ref, pos, id, _ref, _alt, _qual, _filter, info] = line.split('\t');
-        const fields = Object.fromEntries(info
-            .split(';')
-            .map(f => f.trim())
-            .filter(f => !!f)
-            .map(f => f.split('='))
-            .map(([key, val]) => [
-            key.trim(),
-            val
-                ? (0, util_1.decodeURIComponentNoThrow)(val).trim().split(',').join(' ')
-                : undefined,
-        ]));
-        const end = fields.END;
-        const locStr = `${ref}:${pos}..${end || +pos + 1}`;
-        if (id === '.') {
-            continue;
-        }
-        const infoAttrs = attributesToIndex
-            .map(attr => fields[attr])
-            .filter((f) => !!f);
-        const ids = id.split(',');
-        for (const id of ids) {
-            const attrs = [id];
-            const record = JSON.stringify([
-                encodeURIComponent(locStr),
-                encodeURIComponent(trackId),
-                encodeURIComponent(id || ''),
-                ...infoAttrs.map(a => encodeURIComponent(a || '')),
-            ]).replaceAll(',', '|');
-            yield `${record} ${[...new Set(attrs)].join(' ')}\n`;
-        }
-    }
-}

package/dist/util.d.ts

@@ -1,127 +0,0 @@
-export interface UriLocation {
-    uri: string;
-    locationType: 'UriLocation';
-}
-export interface LocalPathLocation {
-    localPath: string;
-    locationType: 'LocalPathLocation';
-}
-export interface IndexedFastaAdapter {
-    type: 'IndexedFastaAdapter';
-    fastaLocation: UriLocation;
-    faiLocation: UriLocation;
-}
-export interface BgzipFastaAdapter {
-    type: 'BgzipFastaAdapter';
-    fastaLocation: UriLocation;
-    faiLocation: UriLocation;
-    gziLocation: UriLocation;
-}
-export interface TwoBitAdapter {
-    type: 'TwoBitAdapter';
-    twoBitLocation: UriLocation;
-}
-export interface ChromeSizesAdapter {
-    type: 'ChromSizesAdapter';
-    chromSizesLocation: UriLocation;
-}
-export interface CustomSequenceAdapter {
-    type: string;
-}
-export interface RefNameAliasAdapter {
-    type: 'RefNameAliasAdapter';
-    location: UriLocation;
-}
-export interface CustomRefNameAliasAdapter {
-    type: string;
-}
-export interface Assembly {
-    displayName?: string;
-    name: string;
-    aliases?: string[];
-    sequence: Sequence;
-    refNameAliases?: {
-        adapter: RefNameAliasAdapter | CustomRefNameAliasAdapter;
-    };
-    refNameColors?: string[];
-}
-export interface Sequence {
-    type: 'ReferenceSequenceTrack';
-    trackId: string;
-    adapter: IndexedFastaAdapter | BgzipFastaAdapter | TwoBitAdapter | ChromeSizesAdapter | CustomSequenceAdapter;
-}
-type Loc = UriLocation | LocalPathLocation;
-export interface Gff3TabixAdapter {
-    type: 'Gff3TabixAdapter';
-    gffGzLocation: Loc;
-}
-export interface Gff3Adapter {
-    type: 'Gff3Adapter';
-    gffLocation: Loc;
-}
-export interface GtfAdapter {
-    type: 'GtfAdapter';
-    gtfLocation: Loc;
-}
-export interface VcfTabixAdapter {
-    type: 'VcfTabixAdapter';
-    vcfGzLocation: Loc;
-}
-export interface VcfAdapter {
-    type: 'VcfAdapter';
-    vcfLocation: Loc;
-}
-export interface Track {
-    adapter?: {
-        type: string;
-        [key: string]: unknown;
-    };
-    textSearching?: TextSearching;
-    name: string;
-    assemblyNames: string[];
-    trackId: string;
-}
-export interface TextSearching {
-    indexingFeatureTypesToExclude?: string[];
-    indexingAttributes?: string[];
-    textSearchAdapter: TrixTextSearchAdapter;
-}
-export interface TrixTextSearchAdapter {
-    type: string;
-    textSearchAdapterId: string;
-    ixFilePath: UriLocation;
-    ixxFilePath: UriLocation;
-    metaFilePath: UriLocation;
-    assemblyNames: string[];
-}
-export interface Config {
-    assemblies?: Assembly[];
-    assembly?: Assembly;
-    configuration?: Record<string, unknown>;
-    aggregateTextSearchAdapters?: TrixTextSearchAdapter[];
-    connections?: unknown[];
-    defaultSession?: Record<string, unknown>;
-    tracks?: Track[];
-}
-export type indexType = 'aggregate' | 'perTrack';
-export declare function createTextSearchConf(name: string, trackIds: string[], assemblyNames: string[], locationPath: string): {
-    type: string;
-    textSearchAdapterId: string;
-    ixFilePath: {
-        localPath: string;
-        locationType: string;
-    };
-    ixxFilePath: {
-        localPath: string;
-        locationType: string;
-    };
-    metaFilePath: {
-        localPath: string;
-        locationType: string;
-    };
-    tracks: string[];
-    assemblyNames: string[];
-};
-export declare function findTrackConfigsToIndex(tracks: Track[], trackIds: string[], assemblyName?: string): Track[];
-export declare function decodeURIComponentNoThrow(uri: string): string;
-export {};

package/dist/util.js

@@ -1,53 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.createTextSearchConf = createTextSearchConf;
-exports.findTrackConfigsToIndex = findTrackConfigsToIndex;
-exports.decodeURIComponentNoThrow = decodeURIComponentNoThrow;
-const path_1 = __importDefault(require("path"));
-const util_1 = require("@jbrowse/core/util");
-const sanitize_filename_1 = __importDefault(require("sanitize-filename"));
-function createTextSearchConf(name, trackIds, assemblyNames, locationPath) {
-    const base = path_1.default.join(locationPath, 'trix');
-    const n = (0, sanitize_filename_1.default)(name);
-    return {
-        type: 'TrixTextSearchAdapter',
-        textSearchAdapterId: name,
-        ixFilePath: {
-            localPath: path_1.default.join(base, `${n}.ix`),
-            locationType: 'LocalPathLocation',
-        },
-        ixxFilePath: {
-            localPath: path_1.default.join(base, `${n}.ixx`),
-            locationType: 'LocalPathLocation',
-        },
-        metaFilePath: {
-            localPath: path_1.default.join(base, `${n}.json`),
-            locationType: 'LocalPathLocation',
-        },
-        tracks: trackIds,
-        assemblyNames,
-    };
-}
-function findTrackConfigsToIndex(tracks, trackIds, assemblyName) {
-    return trackIds
-        .map(trackId => {
-        const currentTrack = tracks.find(t => trackId === t.trackId);
-        if (!currentTrack) {
-            throw new Error(`Track not found in session for trackId ${trackId}`);
-        }
-        return currentTrack;
-    })
-        .filter(track => assemblyName ? track.assemblyNames.includes(assemblyName) : true)
-        .filter(track => { var _a; return (0, util_1.isSupportedIndexingAdapter)((_a = track.adapter) === null || _a === void 0 ? void 0 : _a.type); });
-}
-function decodeURIComponentNoThrow(uri) {
-    try {
-        return decodeURIComponent(uri);
-    }
-    catch (e) {
-        return uri;
-    }
-}