@jbrowse/plugin-gff3 2.18.0 → 3.0.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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@@ -25,7 +25,7 @@ class Gff3Adapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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let blockStart = 0;
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let i = 0;
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while (blockStart < buffer.length) {
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const n = buffer.indexOf(
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const n = buffer.indexOf(10, blockStart);
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const b = n === -1 ? buffer.subarray(blockStart) : buffer.subarray(blockStart, n);
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const line = decoder.decode(b).trim();
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if (line) {
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@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
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}) : function(o, v) {
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o["default"] = v;
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});
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var __importStar = (this && this.__importStar) || function (
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};
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var __importStar = (this && this.__importStar) || (function () {
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var ownKeys = function(o) {
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ownKeys = Object.getOwnPropertyNames || function (o) {
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var ar = [];
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for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
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return ar;
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};
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return ownKeys(o);
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};
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return function (mod) {
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if (mod && mod.__esModule) return mod;
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var result = {};
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if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
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__setModuleDefault(result, mod);
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return result;
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};
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})();
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var __importDefault = (this && this.__importDefault) || function (mod) {
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return (mod && mod.__esModule) ? mod : { "default": mod };
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};
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@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
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}) : function(o, v) {
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o["default"] = v;
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});
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var __importStar = (this && this.__importStar) || function (
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};
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var __importStar = (this && this.__importStar) || (function () {
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var ownKeys = function(o) {
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ownKeys = Object.getOwnPropertyNames || function (o) {
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var ar = [];
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for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
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return ar;
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};
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return ownKeys(o);
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};
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return function (mod) {
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if (mod && mod.__esModule) return mod;
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var result = {};
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if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
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__setModuleDefault(result, mod);
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return result;
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};
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})();
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var __importDefault = (this && this.__importDefault) || function (mod) {
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return (mod && mod.__esModule) ? mod : { "default": mod };
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};
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package/dist/GuessGff3/index.js
CHANGED
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@@ -1,17 +1,16 @@
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"use strict";
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.default = GuessGff3F;
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const util_1 = require("@jbrowse/core/util");
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const tracks_1 = require("@jbrowse/core/util/tracks");
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function GuessGff3F(pluginManager) {
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pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
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return (file, index, adapterHint) => {
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const regexGuess = /\.gff3?\.b?gz$/i;
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const adapterName = 'Gff3TabixAdapter';
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const fileName = (0, tracks_1.getFileName)(file);
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const indexName = index && (0, tracks_1.getFileName)(index);
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if (
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if ((0, util_1.testAdapter)(fileName, /\.gff3?\.b?gz$/i, adapterHint, 'Gff3TabixAdapter')) {
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return {
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type:
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type: 'Gff3TabixAdapter',
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bamLocation: file,
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gffGzLocation: file,
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index: {
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@@ -20,25 +19,15 @@ function GuessGff3F(pluginManager) {
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},
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};
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}
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const regexGuess = /\.gff3?$/i;
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const adapterName = 'Gff3Adapter';
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const fileName = (0, tracks_1.getFileName)(file);
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const obj = {
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type: adapterName,
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gffLocation: file,
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};
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if (regexGuess.test(fileName) && !adapterHint) {
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return obj;
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else if ((0, util_1.testAdapter)(fileName, /\.gff3?$/i, adapterHint, 'Gff3Adapter')) {
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return {
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type: 'Gff3Adapter',
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gffLocation: file,
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};
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}
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return
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else {
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return adapterGuesser(file, index, adapterHint);
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}
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return adapterGuesser(file, index, adapterHint);
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};
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});
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}
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@@ -20,7 +20,7 @@ export default class Gff3Adapter extends BaseFeatureDataAdapter {
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let blockStart = 0;
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let i = 0;
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while (blockStart < buffer.length) {
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const n = buffer.indexOf(
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const n = buffer.indexOf(10, blockStart);
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const b = n === -1 ? buffer.subarray(blockStart) : buffer.subarray(blockStart, n);
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const line = decoder.decode(b).trim();
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if (line) {
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package/esm/GuessGff3/index.js
CHANGED
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@@ -1,14 +1,13 @@
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import { testAdapter } from '@jbrowse/core/util';
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import { getFileName, makeIndex, makeIndexType, } from '@jbrowse/core/util/tracks';
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export default function GuessGff3F(pluginManager) {
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pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
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return (file, index, adapterHint) => {
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const regexGuess = /\.gff3?\.b?gz$/i;
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const adapterName = 'Gff3TabixAdapter';
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const fileName = getFileName(file);
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const indexName = index && getFileName(index);
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if (
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if (testAdapter(fileName, /\.gff3?\.b?gz$/i, adapterHint, 'Gff3TabixAdapter')) {
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return {
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type:
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type: 'Gff3TabixAdapter',
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bamLocation: file,
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gffGzLocation: file,
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index: {
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@@ -17,25 +16,15 @@ export default function GuessGff3F(pluginManager) {
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},
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};
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}
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const regexGuess = /\.gff3?$/i;
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const adapterName = 'Gff3Adapter';
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const fileName = getFileName(file);
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const obj = {
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type: adapterName,
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gffLocation: file,
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};
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if (regexGuess.test(fileName) && !adapterHint) {
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return obj;
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else if (testAdapter(fileName, /\.gff3?$/i, adapterHint, 'Gff3Adapter')) {
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return {
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type: 'Gff3Adapter',
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gffLocation: file,
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};
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}
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return
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else {
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return adapterGuesser(file, index, adapterHint);
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return adapterGuesser(file, index, adapterHint);
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};
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});
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}
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package/package.json
CHANGED
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{
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"name": "@jbrowse/plugin-gff3",
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"version": "
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"version": "3.0.1",
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"description": "JBrowse 2 gff3.",
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"keywords": [
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"jbrowse",
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},
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"dependencies": {
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"@flatten-js/interval-tree": "^1.0.15",
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"@gmod/bgzf-filehandle": "^
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"@gmod/tabix": "^
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"
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"peerDependencies": {
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"@jbrowse/core": "^2.0.0",
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"@jbrowse/plugin-linear-genome-view": "^2.0.0",
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"@gmod/bgzf-filehandle": "^2.0.1",
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"@gmod/tabix": "^2.0.0",
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"@jbrowse/core": "^3.0.1",
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"@jbrowse/plugin-linear-genome-view": "^3.0.1",
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"@mui/material": "^6.0.0",
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"gff-nostream": "^1.3.3",
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"mobx": "^6.0.0",
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"mobx-state-tree": "^5.0.0",
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"rxjs": "^7.0.0"
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"distModule": "esm/index.js",
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"srcModule": "src/index.ts",
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"module": "esm/index.js",
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"gitHead": "
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"gitHead": "aa2f1d1a89d2361c7fd1a93fe29506fa4554f5cc"
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}
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