@jbrowse/plugin-variants 3.6.2 → 3.6.4
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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@@ -10,6 +10,7 @@ const util_1 = require("@jbrowse/core/util");
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const io_1 = require("@jbrowse/core/util/io");
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const rxjs_1 = require("@jbrowse/core/util/rxjs");
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const VcfFeature_1 = __importDefault(require("../VcfFeature"));
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const vcfParser_1 = require("./vcfParser");
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class VcfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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constructor() {
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super(...arguments);
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@@ -27,34 +28,7 @@ class VcfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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const { statusCallback = () => { } } = opts || {};
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const loc = (0, io_1.openLocation)(this.getConf('vcfLocation'), this.pluginManager);
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const buffer = await (0, util_1.fetchAndMaybeUnzip)(loc, opts);
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const
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const featureMap = {};
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let blockStart = 0;
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const decoder = new TextDecoder('utf8');
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let i = 0;
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while (blockStart < buffer.length) {
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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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if (line.startsWith('#')) {
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headerLines.push(line);
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}
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else {
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const ret = line.indexOf('\t');
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const refName = line.slice(0, ret);
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if (!featureMap[refName]) {
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featureMap[refName] = [];
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}
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featureMap[refName].push(line);
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}
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}
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if (i++ % 10000 === 0) {
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statusCallback(`Loading ${(0, util_1.getProgressDisplayStr)(blockStart, buffer.length)}`);
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}
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blockStart = n + 1;
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}
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const header = headerLines.join('\n');
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const { header, featureMap } = (0, vcfParser_1.parseVcfBuffer)(buffer, statusCallback);
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const parser = new vcf_1.default({ header });
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const intervalTreeMap = Object.fromEntries(Object.entries(featureMap).map(([refName, lines]) => [
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refName,
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@@ -0,0 +1,7 @@
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import type { StatusCallback } from '@jbrowse/core/util/parseLineByLine';
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interface VcfParseResult {
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header: string;
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featureMap: Record<string, string[]>;
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}
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export declare function parseVcfBuffer(buffer: Uint8Array, statusCallback?: StatusCallback): VcfParseResult;
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export {};
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@@ -0,0 +1,26 @@
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"use strict";
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.parseVcfBuffer = parseVcfBuffer;
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const parseLineByLine_1 = require("@jbrowse/core/util/parseLineByLine");
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function parseVcfBuffer(buffer, statusCallback = () => { }) {
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const headerLines = [];
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const featureMap = {};
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(0, parseLineByLine_1.parseLineByLine)(buffer, line => {
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if (line.startsWith('#')) {
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headerLines.push(line);
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}
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else {
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const ret = line.indexOf('\t');
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const refName = line.slice(0, ret);
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if (!featureMap[refName]) {
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featureMap[refName] = [];
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}
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featureMap[refName].push(line);
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}
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return true;
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}, statusCallback);
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return {
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header: headerLines.join('\n'),
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featureMap,
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};
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}
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@@ -1,10 +1,11 @@
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import IntervalTree from '@flatten-js/interval-tree';
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import VcfParser from '@gmod/vcf';
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import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
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import { fetchAndMaybeUnzip
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import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
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import { openLocation } from '@jbrowse/core/util/io';
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import { ObservableCreate } from '@jbrowse/core/util/rxjs';
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import VcfFeature from '../VcfFeature';
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import { parseVcfBuffer } from './vcfParser';
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class VcfAdapter extends BaseFeatureDataAdapter {
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constructor() {
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super(...arguments);
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@@ -22,34 +23,7 @@ class VcfAdapter extends BaseFeatureDataAdapter {
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const { statusCallback = () => { } } = opts || {};
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const loc = openLocation(this.getConf('vcfLocation'), this.pluginManager);
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const buffer = await fetchAndMaybeUnzip(loc, opts);
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const
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const featureMap = {};
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let blockStart = 0;
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const decoder = new TextDecoder('utf8');
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let i = 0;
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while (blockStart < buffer.length) {
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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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if (line.startsWith('#')) {
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headerLines.push(line);
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}
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else {
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const ret = line.indexOf('\t');
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const refName = line.slice(0, ret);
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if (!featureMap[refName]) {
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featureMap[refName] = [];
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}
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featureMap[refName].push(line);
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}
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}
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if (i++ % 10000 === 0) {
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statusCallback(`Loading ${getProgressDisplayStr(blockStart, buffer.length)}`);
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}
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blockStart = n + 1;
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}
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const header = headerLines.join('\n');
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const { header, featureMap } = parseVcfBuffer(buffer, statusCallback);
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const parser = new VcfParser({ header });
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const intervalTreeMap = Object.fromEntries(Object.entries(featureMap).map(([refName, lines]) => [
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refName,
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@@ -0,0 +1,7 @@
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import type { StatusCallback } from '@jbrowse/core/util/parseLineByLine';
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interface VcfParseResult {
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header: string;
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featureMap: Record<string, string[]>;
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}
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export declare function parseVcfBuffer(buffer: Uint8Array, statusCallback?: StatusCallback): VcfParseResult;
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export {};
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@@ -0,0 +1,23 @@
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import { parseLineByLine } from '@jbrowse/core/util/parseLineByLine';
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export function parseVcfBuffer(buffer, statusCallback = () => { }) {
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const headerLines = [];
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const featureMap = {};
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parseLineByLine(buffer, line => {
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if (line.startsWith('#')) {
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headerLines.push(line);
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}
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else {
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const ret = line.indexOf('\t');
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const refName = line.slice(0, ret);
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if (!featureMap[refName]) {
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featureMap[refName] = [];
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}
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featureMap[refName].push(line);
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}
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return true;
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}, statusCallback);
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return {
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header: headerLines.join('\n'),
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featureMap,
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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-variants",
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"version": "3.6.
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"version": "3.6.4",
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"description": "JBrowse 2 variant adapters, tracks, etc.",
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"keywords": [
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"jbrowse",
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@@ -40,10 +40,10 @@
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"@gmod/bgzf-filehandle": "^4.0.0",
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"@gmod/tabix": "^3.0.1",
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"@gmod/vcf": "^6.0.8",
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"@jbrowse/core": "^3.6.
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"@jbrowse/plugin-circular-view": "^3.6.
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"@jbrowse/plugin-linear-genome-view": "^3.6.
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"@jbrowse/sv-core": "^3.6.
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"@jbrowse/core": "^3.6.4",
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"@jbrowse/plugin-circular-view": "^3.6.4",
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"@jbrowse/plugin-linear-genome-view": "^3.6.4",
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"@jbrowse/sv-core": "^3.6.4",
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"@mui/icons-material": "^7.0.0",
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"@mui/material": "^7.0.0",
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"@mui/x-data-grid": "^8.0.0",
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@@ -63,5 +63,5 @@
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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": "3db8e50ce2bd9c081efbf6c2e7ae5f342380a25a"
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}
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