diff --git a/.eslintrc.json b/.eslintrc.json index 635ffacd..9b6af237 100644 --- a/.eslintrc.json +++ b/.eslintrc.json @@ -1,9 +1,6 @@ { "parser": "@typescript-eslint/parser", - "plugins": [ - "prettier", - "@typescript-eslint" - ], + "plugins": ["prettier", "@typescript-eslint"], "extends": [ "plugin:@typescript-eslint/recommended", "plugin:prettier/recommended" @@ -12,12 +9,10 @@ "no-underscore-dangle": 0, "curly": "error", "@typescript-eslint/no-explicit-any": 0, + "@typescript-eslint/no-unused-vars": 0, "@typescript-eslint/explicit-module-boundary-types": 0, "@typescript-eslint/ban-ts-comment": 0, - "semi": [ - "error", - "never" - ], + "semi": ["error", "never"], "prettier/prettier": [ "error", { diff --git a/.github/workflows/push.yml b/.github/workflows/push.yml index 5375b10e..639bf2f1 100644 --- a/.github/workflows/push.yml +++ b/.github/workflows/push.yml @@ -4,14 +4,14 @@ on: push jobs: test: - name: Lint, build, and test on node 14.x and ubuntu-latest + name: Lint, build, and test on node 20.x and ubuntu-latest runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 - - name: Use Node.js 14.x - uses: actions/setup-node@v1 + - uses: actions/checkout@v3 + - name: Use Node.js 20.x + uses: actions/setup-node@v3 with: - node-version: 14.x + node-version: 20.x - name: Install deps (with cache) uses: bahmutov/npm-install@v1 - name: Lint codebase diff --git a/.prettierrc b/.prettierrc.json similarity index 80% rename from .prettierrc rename to .prettierrc.json index a9b5b78a..c3e93040 100644 --- a/.prettierrc +++ b/.prettierrc.json @@ -1,7 +1,7 @@ { "semi": false, - "trailingComma": "all", "singleQuote": true, + "trailingComma": "all", "arrowParens": "avoid", - "endOfLine": "auto" + "proseWrap": "always" } diff --git a/CHANGELOG.md b/CHANGELOG.md index 8599183a..f03864d1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -26,7 +26,8 @@ # v1.6.3 -- Optimize CRAM parsing slightly (15% improvement on many short reads). This removes support for big endian machines +- Optimize CRAM parsing slightly (15% improvement on many short reads). This + removes support for big endian machines - Publish src directory for sourceMap # v1.6.2 @@ -93,7 +94,8 @@ # v1.4.3 -- Make sure mate exists for unmated pair, can exist when coordinate slices of cram file are made via samtools view +- Make sure mate exists for unmated pair, can exist when coordinate slices of + cram file are made via samtools view # v1.4.2 diff --git a/README.md b/README.md index 64964ee2..80b831cd 100644 --- a/README.md +++ b/README.md @@ -4,12 +4,16 @@ [![Coverage Status](https://img.shields.io/codecov/c/github/GMOD/cram-js/master.svg?style=flat-square)](https://codecov.io/gh/GMOD/cram-js/branch/master) [![Build Status](https://img.shields.io/github/actions/workflow/status/GMOD/cram-js/push.yml?branch=master)](https://github.com/GMOD/cram-js/actions?query=branch%3Amaster+workflow%3APush+) -Read CRAM files (indexed or unindexed) with pure JS, works in node or in the browser. +Read CRAM files (indexed or unindexed) with pure JS, works in node or in the +browser. - Reads CRAM 3.x and 2.x (3.1 added in v1.6.0) - Does not read CRAM 1.x -- Can use .crai indexes out of the box, for efficient sequence fetching, but also has an [index API](#craiindex) that would allow use with other index types -- Does implement bzip2 but not lzma codecs (yet); if this is important to your use case, please file an issue +- Can use .crai indexes out of the box, for efficient sequence fetching, but + also has an [index API](#craiindex) that would allow use with other index + types +- Does implement bzip2 but not lzma codecs (yet); if this is important to your + use case, please file an issue ## Install @@ -118,7 +122,8 @@ run() // alternatively `cramFilehandle` (for the IndexedCramFile class) and `filehandle` (for the CraiIndex) can be used, see for examples https://github.com/gmod/generic-filehandle ``` -You can use cram-js without NPM also with the cram-bundle.js. See the example directory for usage with script tag +You can use cram-js without NPM also with the cram-bundle.js. See the example +directory for usage with script tag ## API (auto-generated) @@ -136,7 +141,6 @@ You can use cram-js without NPM also with the cram-bundle.js. See the example di ##### Table of Contents - [CramRecord](#cramrecord) - - [Parameters](#parameters) - [isPaired](#ispaired) - [isProperlyPaired](#isproperlypaired) - [isSegmentUnmapped](#issegmentunmapped) @@ -156,137 +160,160 @@ You can use cram-js without NPM also with the cram-bundle.js. See the example di - [getReadBases](#getreadbases) - [getPairOrientation](#getpairorientation) - [addReferenceSequence](#addreferencesequence) - - [Parameters](#parameters-1) + - [Parameters](#parameters) #### CramRecord Class of each CRAM record returned by this API. -##### Parameters - -- `$0` **any** - - - `$0.flags` - - `$0.cramFlags` - - `$0.readLength` - - `$0.mappingQuality` - - `$0.lengthOnRef` - - `$0.qualityScores` - - `$0.mateRecordNumber` - - `$0.readBases` - - `$0.readFeatures` - - `$0.mateToUse` - - `$0.readGroupId` - - `$0.readName` - - `$0.sequenceId` - - `$0.uniqueId` - - `$0.templateSize` - - `$0.alignmentStart` - - `$0.tags` - ##### isPaired -Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the read is paired, regardless of whether both segments are mapped +Returns +**[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** +true if the read is paired, regardless of whether both segments are mapped ##### isProperlyPaired -Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the read is paired, and both segments are mapped +Returns +**[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** +true if the read is paired, and both segments are mapped ##### isSegmentUnmapped -Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the read itself is unmapped; conflictive with isProperlyPaired +Returns +**[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** +true if the read itself is unmapped; conflictive with isProperlyPaired ##### isMateUnmapped -Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the read itself is unmapped; conflictive with isProperlyPaired +Returns +**[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** +true if the read itself is unmapped; conflictive with isProperlyPaired ##### isReverseComplemented -Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the read is mapped to the reverse strand +Returns +**[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** +true if the read is mapped to the reverse strand ##### isMateReverseComplemented -Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the mate is mapped to the reverse strand +Returns +**[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** +true if the mate is mapped to the reverse strand ##### isRead1 -Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if this is read number 1 in a pair +Returns +**[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** +true if this is read number 1 in a pair ##### isRead2 -Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if this is read number 2 in a pair +Returns +**[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** +true if this is read number 2 in a pair ##### isSecondary -Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if this is a secondary alignment +Returns +**[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** +true if this is a secondary alignment ##### isFailedQc -Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if this read has failed QC checks +Returns +**[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** +true if this read has failed QC checks ##### isDuplicate -Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the read is an optical or PCR duplicate +Returns +**[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** +true if the read is an optical or PCR duplicate ##### isSupplementary -Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if this is a supplementary alignment +Returns +**[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** +true if this is a supplementary alignment ##### isDetached -Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the read is detached +Returns +**[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** +true if the read is detached ##### hasMateDownStream -Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the read has a mate in this same CRAM segment +Returns +**[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** +true if the read has a mate in this same CRAM segment ##### isPreservingQualityScores -Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the read contains qual scores +Returns +**[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** +true if the read contains qual scores ##### isUnknownBases -Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the read has no sequence bases +Returns +**[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** +true if the read has no sequence bases ##### getReadBases Get the original sequence of this read. -Returns **[String](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)** sequence basepairs +Returns +**[String](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)** +sequence basepairs ##### getPairOrientation Get the pair orientation of a paired read. Adapted from igv.js -Returns **[String](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)** of paired orientatin +Returns +**[String](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)** +of paired orientatin ##### addReferenceSequence -Annotates this feature with the given reference sequence basepair -information. This will add a `sub` and a `ref` item to base -substitution read features given the actual substituted and reference -base pairs, and will make the `getReadSequence()` method work. +Annotates this feature with the given reference sequence basepair information. +This will add a `sub` and a `ref` item to base subsitution read features given +the actual substituted and reference base pairs, and will make the +`getReadSequence()` method work. ###### Parameters -- `refRegion` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** +- `refRegion` + **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** - - `refRegion.start` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** - - `refRegion.end` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** - - `refRegion.seq` **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)** + - `refRegion.start` + **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** + - `refRegion.end` + **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** + - `refRegion.seq` + **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)** -- `compressionScheme` **CramContainerCompressionScheme** +- `compressionScheme` **CramContainerCompressionScheme** -Returns **[undefined](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/undefined)** nothing +Returns +**[undefined](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/undefined)** +nothing ### ReadFeatures -The feature objects appearing in the `readFeatures` member of CramRecord objects that show insertions, deletions, substitutions, etc. +The feature objects appearing in the `readFeatures` member of CramRecord objects +that show insertions, deletions, substitutions, etc. #### Static fields -- **code** (`character`): One of "bqBXIDiQNSPH". See page 15 of the CRAM v3 spec for their meanings. -- **data** (`any`): the data associated with the feature. The format of this varies depending on the feature code. +- **code** (`character`): One of "bqBXIDiQNSPH". See page 15 of the CRAM v3 spec + for their meanings. +- **data** (`any`): the data associated with the feature. The format of this + varies depending on the feature code. - **pos** (`number`): location relative to the read (1-based) - **refPos** (`number`): location relative to the reference (1-based) @@ -307,32 +334,51 @@ The feature objects appearing in the `readFeatures` member of CramRecord objects ##### Parameters -- `args` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** - - - `args.cram` **CramFile** - - `args.index` **Index-like** object that supports getEntriesForRange(seqId,start,end) -> Promise\[Array\[index entries]] - - `args.cacheSize` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)?** optional maximum number of CRAM records to cache. default 20,000 - - `args.fetchSizeLimit` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)?** optional maximum number of bytes to fetch in a single getRecordsForRange call. Default 3 MiB. - - `args.checkSequenceMD5` **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)?** default true. if false, disables verifying the MD5 - checksum of the reference sequence underlying a slice. In some applications, this check can cause an inconvenient amount (many megabases) of sequences to be fetched. +- `args` + **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** + + - `args.cram` **CramFile** + - `args.index` **Index-like** object that supports + getEntriesForRange(seqId,start,end) -> Promise\[Array\[index entries]] + - `args.cacheSize` + **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)?** + optional maximum number of CRAM records to cache. default 20,000 + - `args.fetchSizeLimit` + **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)?** + optional maximum number of bytes to fetch in a single getRecordsForRange + call. Default 3 MiB. + - `args.checkSequenceMD5` + **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)?** + default true. if false, disables verifying the MD5 checksum of the reference + sequence underlying a slice. In some applications, this check can cause an + inconvenient amount (many megabases) of sequences to be fetched. #### getRecordsForRange ##### Parameters -- `seq` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** numeric ID of the reference sequence -- `start` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** start of the range of interest. 1-based closed coordinates. -- `end` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** end of the range of interest. 1-based closed coordinates. -- `opts` **{viewAsPairs: [boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)?, pairAcrossChr: [boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)?, maxInsertSize: [number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)?}** (optional, default `{}`) +- `seq` + **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** + numeric ID of the reference sequence +- `start` + **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** + start of the range of interest. 1-based closed coordinates. +- `end` + **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** + end of the range of interest. 1-based closed coordinates. +- `opts` (optional, default `{}`) #### hasDataForReferenceSequence ##### Parameters -- `seqId` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** +- `seqId` + **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** -Returns **[Promise](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Promise)** true if the CRAM file contains data for the given -reference sequence numerical ID +Returns +**[Promise](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Promise)** +true if the CRAM file contains data for the given reference sequence numerical +ID ### CramFile @@ -340,11 +386,41 @@ reference sequence numerical ID ##### Table of Contents +- [constructor](#constructor) + - [Parameters](#parameters) - [containerCount](#containercount) -#### containerCount +#### constructor -Returns **[Promise](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Promise)<([number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number) | [undefined](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/undefined))>** +##### Parameters + +- `args` + **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** + + - `args.filehandle` + **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)?** + a filehandle that implements the stat() and read() methods of the Node + filehandle API + - `args.path` + **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)?** + path to the cram file + - `args.url` + **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)?** + url for the cram file. also supports file:// urls for local files + - `args.seqFetch` + **[function](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Statements/function)?** + a function with signature `(seqId, startCoordinate, endCoordinate)` that + returns a promise for a string of sequence bases + - `args.cacheSize` + **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)?** + optional maximum number of CRAM records to cache. default 20,000 + - `args.checkSequenceMD5` + **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)?** + default true. if false, disables verifying the MD5 checksum of the reference + sequence underlying a slice. In some applications, this check can cause an + inconvenient amount (many megabases) of sequences to be fetched. + +#### containerCount ### CraiIndex @@ -363,20 +439,26 @@ Returns **[Promise](https://developer.mozilla.org/docs/Web/JavaScript/Reference/ ##### Parameters -- `args` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** +- `args` + **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** - - `args.path` **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)?** - - `args.url` **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)?** - - `args.filehandle` **FileHandle?** + - `args.path` + **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)?** + - `args.url` + **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)?** + - `args.filehandle` **FileHandle?** #### hasDataForReferenceSequence ##### Parameters -- `seqId` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** +- `seqId` + **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** -Returns **[Promise](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Promise)** true if the index contains entries for -the given reference sequence ID, false otherwise +Returns +**[Promise](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Promise)** +true if the index contains entries for the given reference sequence ID, false +otherwise #### getEntriesForRange @@ -384,19 +466,24 @@ fetch index entries for the given range ##### Parameters -- `seqId` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** -- `queryStart` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** -- `queryEnd` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** +- `seqId` + **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** +- `queryStart` + **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** +- `queryEnd` + **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** -Returns **[Promise](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Promise)** promise for -an array of objects of the form +Returns +**[Promise](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Promise)** +promise for an array of objects of the form `{start, span, containerStart, sliceStart, sliceBytes }` ### CramUnimplementedError **Extends Error** -Error caused by encountering a part of the CRAM spec that has not yet been implemented +Error caused by encountering a part of the CRAM spec that has not yet been +implemented ### CramMalformedError @@ -410,15 +497,12 @@ An error caused by malformed data. An error caused by attempting to read beyond the end of the defined data. -## Exception Classes - - - -### Table of Contents - ## Academic Use -This package was written with funding from the [NHGRI](http://genome.gov) as part of the [JBrowse](http://jbrowse.org) project. If you use it in an academic project that you publish, please cite the most recent JBrowse paper, which will be linked from [jbrowse.org](http://jbrowse.org). +This package was written with funding from the [NHGRI](http://genome.gov) as +part of the [JBrowse](http://jbrowse.org) project. If you use it in an academic +project that you publish, please cite the most recent JBrowse paper, which will +be linked from [jbrowse.org](http://jbrowse.org). ## License diff --git a/jest.config.js b/jest.config.js index 8e19dbb4..9f383d5e 100644 --- a/jest.config.js +++ b/jest.config.js @@ -1,9 +1,6 @@ -/** @type {import("ts-jest/dist/types").InitialOptionsTsJest} */ +/** @type {import('ts-jest').JestConfigWithTsJest} */ module.exports = { preset: 'ts-jest', - transform: { - '^.+\\.(ts|js)x?$': 'ts-jest', - }, + testEnvironment: 'node', transformIgnorePatterns: ['[/\\\\]node_modules[/\\\\](?!quick-lru/).+\\.js$'], - testTimeout: 1000, } diff --git a/package.json b/package.json index 2a2b50df..b2e45345 100644 --- a/package.json +++ b/package.json @@ -50,34 +50,35 @@ "long": "^4.0.0", "md5": "^2.2.1", "pako": "^1.0.4", - "quick-lru": "^4.0.1" + "quick-lru": "^4.0.1", + "xz-decompress": "^0.2.1" }, "devDependencies": { "@babel/plugin-transform-modules-commonjs": "^7.18.2", "@babel/preset-typescript": "^7.17.12", - "@gmod/indexedfasta": "^2.0.2", + "@gmod/indexedfasta": "^2.1.0", "@types/buffer-crc32": "^0.2.2", "@types/jest": "^29.2.4", "@types/long": "^4.0.2", "@types/md5": "^2.3.2", "@types/pako": "^1.0.3", - "@typescript-eslint/eslint-plugin": "^5.46.1", - "@typescript-eslint/parser": "^5.46.1", + "@typescript-eslint/eslint-plugin": "^6.9.1", + "@typescript-eslint/parser": "^6.9.1", "buffer": "^6.0.3", "documentation": "^14.0.1", "eslint": "^8.30.0", - "eslint-config-prettier": "^8.5.0", + "eslint-config-prettier": "^9.0.0", "eslint-plugin-import": "^2.25.4", - "eslint-plugin-prettier": "^4.0.0", + "eslint-plugin-prettier": "^5.0.1", "glob": "^10.3.1", "jest": "^29.3.1", "mock-fs": "^5.2.0", - "prettier": "^2.8.1", + "prettier": "^3.0.3", "rimraf": "^5.0.1", "ts-jest": "^29.0.3", "typescript": "^5.0.3", "url": "^0.11.0", - "webpack": "5.88.1", + "webpack": "5.89.0", "webpack-cli": "^5.0.1" }, "publishConfig": { diff --git a/src/cramFile/container/index.ts b/src/cramFile/container/index.ts index b7727048..92fcd88e 100644 --- a/src/cramFile/container/index.ts +++ b/src/cramFile/container/index.ts @@ -6,7 +6,10 @@ import CramContainerCompressionScheme from './compressionScheme' import CramFile from '../file' export default class CramContainer { - constructor(public file: CramFile, public filePosition: number) {} + constructor( + public file: CramFile, + public filePosition: number, + ) {} // memoize getHeader() { diff --git a/src/cramFile/file.ts b/src/cramFile/file.ts index 405953a6..f6c386ec 100644 --- a/src/cramFile/file.ts +++ b/src/cramFile/file.ts @@ -1,9 +1,11 @@ import { unzip } from '../unzip' import crc32 from 'buffer-crc32' import QuickLRU from 'quick-lru' +import htscodecs from '@jkbonfield/htscodecs' +import { Parser } from '@gmod/binary-parser' // @ts-expect-error import bzip2 from 'bzip2' - +import { XzReadableStream } from 'xz-decompress' import { CramMalformedError, CramUnimplementedError } from '../errors' import ransuncompress from '../rans' import { @@ -12,16 +14,24 @@ import { cramFileDefinition as cramFileDefinitionParser, getSectionParsers, } from './sectionParsers' -import htscodecs from '@jkbonfield/htscodecs' + import CramContainer from './container' import { open } from '../io' import { parseItem, tinyMemoize } from './util' import { parseHeaderText } from '../sam' -import { Parser } from '@gmod/binary-parser' import CramRecord from './record' import { Filehandle } from './filehandle' +function bufferToStream(buf: Buffer) { + return new ReadableStream({ + start(controller) { + controller.enqueue(buf) + controller.close() + }, + }) +} + //source:https://abdulapopoola.com/2019/01/20/check-endianness-with-javascript/ function getEndianness() { const uInt32 = new Uint32Array([0x11223344]) @@ -99,17 +109,6 @@ export default class CramFile { } } - // toString() { - // if (this.file.filename) { - // return this.file.filename - // } - // if (this.file.url) { - // return this.file.url - // } - // - // return '(cram file)' - // } - // can just read this object like a filehandle read( buffer: Buffer, @@ -247,9 +246,8 @@ export default class CramFile { let containerCount = 0 let position = sectionParsers.cramFileDefinition.maxLength while (position + cramContainerHeader1.maxLength + 8 < fileSize) { - const currentHeader = await this.getContainerAtPosition( - position, - ).getHeader() + const currentHeader = + await this.getContainerAtPosition(position).getHeader() if (!currentHeader) { break } @@ -319,7 +317,7 @@ export default class CramFile { return data } - _uncompress( + async _uncompress( compressionMethod: CompressionMethod, inputBuffer: Buffer, outputBuffer: Buffer, @@ -340,6 +338,12 @@ export default class CramFile { size -= chunk.length } } while (chunk != -1) + } else if (compressionMethod === 'lzma') { + const decompressedResponse = new Response( + new XzReadableStream(bufferToStream(inputBuffer)), + ) + const ret = Buffer.from(await decompressedResponse.arrayBuffer()) + ret.copy(outputBuffer) } else if (compressionMethod === 'rans') { ransuncompress(inputBuffer, outputBuffer) //htscodecs r4x8 is slower, but compatible. @@ -386,7 +390,7 @@ export default class CramFile { blockContentPosition, ) - this._uncompress( + await this._uncompress( blockHeader.compressionMethod, compressedData, uncompressedData, diff --git a/src/rans/constants.js b/src/rans/constants.ts similarity index 100% rename from src/rans/constants.js rename to src/rans/constants.ts diff --git a/src/rans/d04.js b/src/rans/d04.ts similarity index 99% rename from src/rans/d04.js rename to src/rans/d04.ts index 837d340d..ef22d60a 100644 --- a/src/rans/d04.js +++ b/src/rans/d04.ts @@ -1,3 +1,4 @@ +//@ts-nocheck import { CramMalformedError } from '../errors' import { TF_SHIFT } from './constants' diff --git a/src/rans/d14.js b/src/rans/d14.ts similarity index 99% rename from src/rans/d14.js rename to src/rans/d14.ts index 1f4badf7..5e49ed16 100644 --- a/src/rans/d14.js +++ b/src/rans/d14.ts @@ -1,3 +1,4 @@ +//@ts-nocheck import { TF_SHIFT } from './constants' import Decoding from './decoding' diff --git a/src/rans/decoding.js b/src/rans/decoding.ts similarity index 99% rename from src/rans/decoding.js rename to src/rans/decoding.ts index f2f7855f..eb98b74f 100644 --- a/src/rans/decoding.js +++ b/src/rans/decoding.ts @@ -1,3 +1,4 @@ +//@ts-nocheck import { CramMalformedError } from '../errors' import { RANS_BYTE_L } from './constants' diff --git a/src/rans/frequencies.js b/src/rans/frequencies.ts similarity index 99% rename from src/rans/frequencies.js rename to src/rans/frequencies.ts index b9299b4d..68c3573f 100644 --- a/src/rans/frequencies.js +++ b/src/rans/frequencies.ts @@ -1,3 +1,4 @@ +//@ts-nocheck import { CramMalformedError } from '../errors' import { TOTFREQ } from './constants' diff --git a/src/rans/index.js b/src/rans/index.ts similarity index 99% rename from src/rans/index.js rename to src/rans/index.ts index 64644334..a9e69198 100644 --- a/src/rans/index.js +++ b/src/rans/index.ts @@ -1,3 +1,4 @@ +//@ts-nocheck import { CramMalformedError } from '../errors' import Decoding from './decoding' diff --git a/test/__snapshots__/compressions.test.ts.snap b/test/__snapshots__/compressions.test.ts.snap new file mode 100644 index 00000000..daf7dd87 --- /dev/null +++ b/test/__snapshots__/compressions.test.ts.snap @@ -0,0 +1,23 @@ +// Jest Snapshot v1, https://goo.gl/fbAQLP + +exports[`bzip2 1`] = ` +{ + "code": "X", + "data": 1, + "pos": 51, + "ref": "A", + "refPos": 1050, + "sub": "G", +} +`; + +exports[`lzma 1`] = ` +{ + "code": "X", + "data": 1, + "pos": 51, + "ref": "A", + "refPos": 1050, + "sub": "G", +} +`; diff --git a/test/compressions.test.ts b/test/compressions.test.ts new file mode 100644 index 00000000..e3b04e14 --- /dev/null +++ b/test/compressions.test.ts @@ -0,0 +1,31 @@ +//@ts-nocheck +import { testDataFile } from './lib/util' +import { dumpWholeFile } from './lib/dumpFile' +import { CramFile } from '../src/index' +import { FetchableSmallFasta } from './lib/fasta' + +test('lzma', async () => { + const fasta = new FetchableSmallFasta(testDataFile('ce.fa')) + const seqFetch = fasta.fetch.bind(fasta) + const file = new CramFile({ + filehandle: testDataFile('hts-specs/0903_comp_lzma.cram'), + seqFetch, + }) + const fileData = await dumpWholeFile(file) + const feat = fileData[2].data[1].features[0] + const hardClip = feat.readFeatures[0] + expect(hardClip).toMatchSnapshot() +}) + +test('bzip2', async () => { + const fasta = new FetchableSmallFasta(testDataFile('ce.fa')) + const seqFetch = fasta.fetch.bind(fasta) + const file = new CramFile({ + filehandle: testDataFile('hts-specs/0902_comp_bz2.cram'), + seqFetch, + }) + const fileData = await dumpWholeFile(file) + const feat = fileData[2].data[1].features[0] + const hardClip = feat.readFeatures[0] + expect(hardClip).toMatchSnapshot() +}) diff --git a/test/data/hts-specs/0902_comp_bz2.cram b/test/data/hts-specs/0902_comp_bz2.cram new file mode 100644 index 00000000..61d1c9fc Binary files /dev/null and b/test/data/hts-specs/0902_comp_bz2.cram differ diff --git a/test/data/hts-specs/0902_comp_bz2.sam b/test/data/hts-specs/0902_comp_bz2.sam new file mode 100644 index 00000000..c91aac0e --- /dev/null +++ b/test/data/hts-specs/0902_comp_bz2.sam @@ -0,0 +1,7 @@ +@SQ SN:CHROMOSOME_I LN:1009800 M5:8ede36131e0dbf3417807e48f77f3ebd UR:/nfs/users/nfs_j/jkb/work/samtools_master/hts-specs/test/CRAM/passed/ce.fa +@RG ID:rg SM:test +@RG ID:rg2 SM:test +r1 99 CHROMOSOME_I 1000 40 100M = 1200 300 ATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTTGTGCGNGCATCTGAAAGTTTGTTTTTCTTGTTTTCTTGCACTTTGTGCAGAATT #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:rg +r1 147 CHROMOSOME_I 1200 40 100M = 1000 -300 TTTTTTTAGAAAAATTATTTTTAAGAATTTTTCATTTTAGGAATATTGTTCNCTCAGAAAATAGCTAAATGTGATTTCTGTAATTTTGCCTGCCAAATTC #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:rg +r2 99 CHROMOSOME_I 1000 40 100M = 1200 300 ATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTTGTGCGNGCATCTGAAAGTTTGTTTTTCTTGTTTTCTTGCACTTTGTGCAGAATT #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:rg2 +r2 147 CHROMOSOME_I 1200 40 100M = 1000 -300 TTTTTTTAGAAAAATTATTTTTAAGAATTTTTCATTTTAGGAATATTGTTCNCTCAGAAAATAGCTAAATGTGATTTCTGTAATTTTGCCTGCCAAATTC #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:rg2 diff --git a/test/data/hts-specs/0903_comp_lzma.cram b/test/data/hts-specs/0903_comp_lzma.cram new file mode 100644 index 00000000..8e5fe766 Binary files /dev/null and b/test/data/hts-specs/0903_comp_lzma.cram differ diff --git a/test/data/hts-specs/0903_comp_lzma.sam b/test/data/hts-specs/0903_comp_lzma.sam new file mode 100644 index 00000000..c91aac0e --- /dev/null +++ b/test/data/hts-specs/0903_comp_lzma.sam @@ -0,0 +1,7 @@ +@SQ SN:CHROMOSOME_I LN:1009800 M5:8ede36131e0dbf3417807e48f77f3ebd UR:/nfs/users/nfs_j/jkb/work/samtools_master/hts-specs/test/CRAM/passed/ce.fa +@RG ID:rg SM:test +@RG ID:rg2 SM:test +r1 99 CHROMOSOME_I 1000 40 100M = 1200 300 ATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTTGTGCGNGCATCTGAAAGTTTGTTTTTCTTGTTTTCTTGCACTTTGTGCAGAATT #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:rg +r1 147 CHROMOSOME_I 1200 40 100M = 1000 -300 TTTTTTTAGAAAAATTATTTTTAAGAATTTTTCATTTTAGGAATATTGTTCNCTCAGAAAATAGCTAAATGTGATTTCTGTAATTTTGCCTGCCAAATTC #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:rg +r2 99 CHROMOSOME_I 1000 40 100M = 1200 300 ATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTTGTGCGNGCATCTGAAAGTTTGTTTTTCTTGTTTTCTTGCACTTTGTGCAGAATT #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:rg2 +r2 147 CHROMOSOME_I 1200 40 100M = 1000 -300 TTTTTTTAGAAAAATTATTTTTAAGAATTTTTCATTTTAGGAATATTGTTCNCTCAGAAAATAGCTAAATGTGATTTCTGTAATTTTGCCTGCCAAATTC #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:rg2 diff --git a/test/dump.test.ts b/test/dump.test.ts index 2b6d11af..56277ef5 100644 --- a/test/dump.test.ts +++ b/test/dump.test.ts @@ -61,25 +61,22 @@ describe('dumping cram files', () => { }, 10000) }) }) - -describe('works with hard clipping', () => { - it('hard clipped volvox data file', async () => { - const fasta = new FetchableSmallFasta(testDataFile('volvox.fa')) - const seqFetch = fasta.fetch.bind(fasta) - const file = new CramFile({ - filehandle: testDataFile('hard_clipping.cram'), - seqFetch, - }) - const fileData = await dumpWholeFile(file) - const feat = fileData[2].data[1].features[0] - const hardClip = feat.readFeatures[0] - const nextReadFeature = feat.readFeatures[0] - expect(hardClip.refPos).toEqual(737) - expect(nextReadFeature.refPos).toEqual(737) - expect(hardClip.refPos).toEqual(feat.alignmentStart) - expect(hardClip.pos).toEqual(1) - expect(hardClip.data).toEqual(803) +test('works with hard clipping', async () => { + const fasta = new FetchableSmallFasta(testDataFile('volvox.fa')) + const seqFetch = fasta.fetch.bind(fasta) + const file = new CramFile({ + filehandle: testDataFile('hard_clipping.cram'), + seqFetch, }) + const fileData = await dumpWholeFile(file) + const feat = fileData[2].data[1].features[0] + const hardClip = feat.readFeatures[0] + const nextReadFeature = feat.readFeatures[0] + expect(hardClip.refPos).toEqual(737) + expect(nextReadFeature.refPos).toEqual(737) + expect(hardClip.refPos).toEqual(feat.alignmentStart) + expect(hardClip.pos).toEqual(1) + expect(hardClip.data).toEqual(803) }) function isIterable(input) { diff --git a/test/lib/dumpFile.js b/test/lib/dumpFile.ts similarity index 99% rename from test/lib/dumpFile.js rename to test/lib/dumpFile.ts index 1b448252..74349feb 100644 --- a/test/lib/dumpFile.js +++ b/test/lib/dumpFile.ts @@ -1,3 +1,4 @@ +//@ts-nocheck async function dumpSlice(container, sliceOffset) { const slice = container.getSlice(sliceOffset) const header = await slice.getHeader() diff --git a/test/lib/fasta/index.js b/test/lib/fasta/index.ts similarity index 65% rename from test/lib/fasta/index.js rename to test/lib/fasta/index.ts index fc6ee43c..ff081a2c 100644 --- a/test/lib/fasta/index.js +++ b/test/lib/fasta/index.ts @@ -1,15 +1,13 @@ -import IndexedFasta from './indexedFasta' - -function parseSmallFasta(text) { +//@ts-nocheck +function parseSmallFasta(text: string) { return text .split('>') .filter(t => /\S/.test(t)) .map(entryText => { - let [defLine, ...seqLines] = entryText.split('\n') - let [id, ...description] = defLine.split(' ') - description = description.join(' ') - seqLines = seqLines.join('') - const sequence = seqLines.replace(/\s/g, '') + const [defLine, ...seq] = entryText.split('\n') + const [id, ...des] = defLine.split(' ') + const description = des.join(' ') + const sequence = seq.join('').replace(/\s/g, '') return { id, description, sequence } }) } @@ -38,4 +36,4 @@ class FetchableSmallFasta { } } -export { parseSmallFasta, FetchableSmallFasta, IndexedFasta } +export { parseSmallFasta, FetchableSmallFasta } diff --git a/test/lib/fasta/indexedFasta.js b/test/lib/fasta/indexedFasta.js deleted file mode 100644 index db2270cc..00000000 --- a/test/lib/fasta/indexedFasta.js +++ /dev/null @@ -1,120 +0,0 @@ -export default class IndexedFasta { - constructor({ fasta, fai, chunkSizeLimit = 50000 }) { - this.fasta = fasta - this.fai = fai - - this.chunkSizeLimit = chunkSizeLimit - } - - async _getIndexes() { - if (!this.indexes) { - this.indexes = await this._readFAI() - } - return this.indexes - } - - async _readFAI() { - const indexByName = {} - const indexById = {} - const text = await this.fai.readFile() - if (!(text && text.length)) { - throw new Error('No data read from FASTA index (FAI) file') - } - - let idCounter = 0 - let currSeq - text - .toString('utf8') - .split(/\r?\n/) - .filter(line => /\S/.test(line)) - .forEach(line => { - const row = line.split('\t') - if (row[0] === '') { - return - } - - if (!currSeq || currSeq.name !== row[0]) { - currSeq = { name: row[0], id: idCounter } - idCounter += 1 - } - - const entry = { - id: currSeq.id, - name: row[0], - length: +row[1], - start: 0, - end: +row[1], - offset: +row[2], - lineLength: +row[3], - lineBytes: +row[4], - } - indexByName[entry.name] = entry - indexById[entry.id] = entry - }) - return { name: indexByName, id: indexById } - } - - /** - * @returns {array[string]} array of string sequence - * names that are present in the index, in which the - * array index indicates the sequence ID, and the value - * is the sequence name - */ - async getSequenceList() { - return (await this._getIndexes()).id.map(entry => entry.name) - } - - /** - * - * @param {string} name - * @returns {Promise[boolean]} true if the file contains the given reference sequence name - */ - async hasReferenceSequence(name) { - return !!(await this._getIndexes()).name[name] - } - - /** - * - * @param {number} seqId - * @param {number} min - * @param {number} max - */ - async getResiduesById(seqId, min, max) { - const indexEntry = (await this._getIndexes()).id[seqId] - return this._fetchFromIndexEntry(indexEntry, min, max) - } - - /** - * @param {string} seqName - * @param {number} min - * @param {number} max - */ - async getResiduesByName(seqName, min, max) { - const indexEntry = (await this._getIndexes()).name[seqName] - return this._fetchFromIndexEntry(indexEntry, min, max) - } - - async _fetchFromIndexEntry(indexEntry, min, max) { - const start = Math.max(0, min) - const position = this._faiOffset(indexEntry, start) - const readlen = this._faiOffset(indexEntry, max) - position - - if (readlen > this.chunkSizeLimit) { - throw new Error('chunkSizeLimit exceeded') - } - - let residues = Buffer.allocUnsafe(readlen) - await this.data.read(residues, 0, readlen, position) - residues = residues.toString('utf8').replace(/\s+/g, '') - - return residues - } - - _faiOffset(idx, pos) { - return ( - idx.offset + - idx.linebytelen * Math.floor(pos / idx.linelen) + - (pos % idx.linelen) - ) - } -} diff --git a/test/lib/md5.js b/test/lib/md5.ts similarity index 100% rename from test/lib/md5.js rename to test/lib/md5.ts diff --git a/test/lib/syncLocalFile.js b/test/lib/syncLocalFile.ts similarity index 98% rename from test/lib/syncLocalFile.js rename to test/lib/syncLocalFile.ts index b770e8f2..316a9d96 100644 --- a/test/lib/syncLocalFile.js +++ b/test/lib/syncLocalFile.ts @@ -1,3 +1,4 @@ +//@ts-nocheck // don't load fs native module if running in webpacked code const fs = typeof __webpack_require__ !== 'function' ? require('fs') : null // eslint-disable-line camelcase diff --git a/test/lib/testFileList.js b/test/lib/testFileList.ts similarity index 100% rename from test/lib/testFileList.js rename to test/lib/testFileList.ts diff --git a/test/lib/util.js b/test/lib/util.ts similarity index 98% rename from test/lib/util.js rename to test/lib/util.ts index 4501289c..a85d49cb 100644 --- a/test/lib/util.js +++ b/test/lib/util.ts @@ -1,3 +1,4 @@ +//@ts-nocheck const path = typeof __webpack_require__ !== 'function' ? require('path') : null // eslint-disable-line camelcase const fs = typeof __webpack_require__ !== 'function' ? require('fs') : null // eslint-disable-line camelcase import { fromUrl } from '../../src/io' diff --git a/yarn.lock b/yarn.lock index e877d252..5e22099b 100644 --- a/yarn.lock +++ b/yarn.lock @@ -15,45 +15,46 @@ "@jridgewell/gen-mapping" "^0.3.0" "@jridgewell/trace-mapping" "^0.3.9" -"@babel/code-frame@^7.0.0", "@babel/code-frame@^7.12.13", "@babel/code-frame@^7.22.5": - version "7.22.5" - resolved "https://registry.yarnpkg.com/@babel/code-frame/-/code-frame-7.22.5.tgz#234d98e1551960604f1246e6475891a570ad5658" - integrity 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estraverse "^4.1.1" -eslint-scope@^7.2.0: - version "7.2.0" - resolved "https://registry.yarnpkg.com/eslint-scope/-/eslint-scope-7.2.0.tgz#f21ebdafda02352f103634b96dd47d9f81ca117b" - integrity sha512-DYj5deGlHBfMt15J7rdtyKNq/Nqlv5KfU4iodrQ019XESsRnwXH9KAE0y3cwtUHDo2ob7CypAnCqefh6vioWRw== +eslint-scope@^7.2.2: + version "7.2.2" + resolved "https://registry.yarnpkg.com/eslint-scope/-/eslint-scope-7.2.2.tgz#deb4f92563390f32006894af62a22dba1c46423f" + integrity sha512-dOt21O7lTMhDM+X9mB4GX+DZrZtCUJPL/wlcTqxyrx5IvO0IYtILdtrQGQp+8n5S0gwSVmOf9NQrjMOgfQZlIg== dependencies: esrecurse "^4.3.0" estraverse "^5.2.0" -eslint-visitor-keys@^3.3.0, eslint-visitor-keys@^3.4.1: - version "3.4.1" - resolved "https://registry.yarnpkg.com/eslint-visitor-keys/-/eslint-visitor-keys-3.4.1.tgz#c22c48f48942d08ca824cc526211ae400478a994" - integrity sha512-pZnmmLwYzf+kWaM/Qgrvpen51upAktaaiI01nsJD/Yr3lMOdNtq0cxkrrg16w64VtisN6okbs7Q8AfGqj4c9fA== +eslint-visitor-keys@^3.3.0, eslint-visitor-keys@^3.4.1, eslint-visitor-keys@^3.4.3: + version "3.4.3" + resolved "https://registry.yarnpkg.com/eslint-visitor-keys/-/eslint-visitor-keys-3.4.3.tgz#0cd72fe8550e3c2eae156a96a4dddcd1c8ac5800" + integrity sha512-wpc+LXeiyiisxPlEkUzU6svyS1frIO3Mgxj1fdy7Pm8Ygzguax2N3Fa/D/ag1WqbOprdI+uY6wMUl8/a2G+iag== eslint@^8.30.0: - version "8.44.0" - resolved "https://registry.yarnpkg.com/eslint/-/eslint-8.44.0.tgz#51246e3889b259bbcd1d7d736a0c10add4f0e500" - integrity sha512-0wpHoUbDUHgNCyvFB5aXLiQVfK9B0at6gUvzy83k4kAsQ/u769TQDX6iKC+aO4upIHO9WSaA3QoXYQDHbNwf1A== + version "8.53.0" + resolved "https://registry.yarnpkg.com/eslint/-/eslint-8.53.0.tgz#14f2c8244298fcae1f46945459577413ba2697ce" + integrity sha512-N4VuiPjXDUa4xVeV/GC/RV3hQW9Nw+Y463lkWaKKXKYMvmRiRDAtfpuPFLN+E1/6ZhyR8J2ig+eVREnYgUsiag== dependencies: "@eslint-community/eslint-utils" "^4.2.0" - "@eslint-community/regexpp" "^4.4.0" - "@eslint/eslintrc" "^2.1.0" - "@eslint/js" "8.44.0" - "@humanwhocodes/config-array" "^0.11.10" + "@eslint-community/regexpp" 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sha512-RD97prjEt9EL8YgAgpOkf3O4IF9lhJFr9g0htQkm0rchFp/Vx7LW5Q8fSXXub7BXAODyUQohRMyOc3faCPd0hg== + dependencies: + available-typed-arrays "^1.0.5" + call-bind "^1.0.2" + for-each "^0.3.3" + has-proto "^1.0.1" + is-typed-array "^1.1.10" + typed-array-length@^1.0.4: version "1.0.4" resolved "https://registry.yarnpkg.com/typed-array-length/-/typed-array-length-1.0.4.tgz#89d83785e5c4098bec72e08b319651f0eac9c1bb" @@ -5198,9 +5496,9 @@ typed-array-length@^1.0.4: is-typed-array "^1.1.9" typescript@^5.0.3: - version "5.1.6" - resolved "https://registry.yarnpkg.com/typescript/-/typescript-5.1.6.tgz#02f8ac202b6dad2c0dd5e0913745b47a37998274" - integrity sha512-zaWCozRZ6DLEWAWFrVDz1H6FVXzUSfTy5FUMWsQlU8Ym5JP9eO4xkTIROFCQvhQf61z6O/G6ugw3SgAnvvm+HA== + version "5.2.2" + resolved "https://registry.yarnpkg.com/typescript/-/typescript-5.2.2.tgz#5ebb5e5a5b75f085f22bc3f8460fba308310fa78" + integrity sha512-mI4WrpHsbCIcwT9cF4FZvr80QUeKvsUsUvKDoR+X/7XHQH98xYD8YHZg7ANtz2GtZt/CBq2QJ0thkGJMHfqc1w== unbox-primitive@^1.0.2: version "1.0.2" @@ -5217,6 +5515,11 @@ unc-path-regex@^0.1.2: resolved "https://registry.yarnpkg.com/unc-path-regex/-/unc-path-regex-0.1.2.tgz#e73dd3d7b0d7c5ed86fbac6b0ae7d8c6a69d50fa" integrity sha512-eXL4nmJT7oCpkZsHZUOJo8hcX3GbsiDOa0Qu9F646fi8dT3XuSVopVqAcEiVzSKKH7UoDti23wNX3qGFxcW5Qg== +undici-types@~5.26.4: + version "5.26.5" + resolved "https://registry.yarnpkg.com/undici-types/-/undici-types-5.26.5.tgz#bcd539893d00b56e964fd2657a4866b221a65617" + integrity sha512-JlCMO+ehdEIKqlFxk6IfVoAUVmgz7cU7zD/h9XZ0qzeosSHmUJVOzSQvvYSYWXkFXC+IfLKSIffhv0sVZup6pA== + unified@^10.0.0: version "10.1.2" resolved "https://registry.yarnpkg.com/unified/-/unified-10.1.2.tgz#b1d64e55dafe1f0b98bb6c719881103ecf6c86df" @@ -5280,10 +5583,15 @@ unist-util-visit@^4.0.0, unist-util-visit@^4.1.0: unist-util-is "^5.0.0" unist-util-visit-parents "^5.1.1" -update-browserslist-db@^1.0.11: - version "1.0.11" - resolved 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+5742,12 @@ webpack-cli@^5.0.1: webpack-merge "^5.7.3" webpack-merge@^5.7.3: - version "5.9.0" - resolved "https://registry.yarnpkg.com/webpack-merge/-/webpack-merge-5.9.0.tgz#dc160a1c4cf512ceca515cc231669e9ddb133826" - integrity sha512-6NbRQw4+Sy50vYNTw7EyOn41OZItPiXB8GNv3INSoe3PSFaHJEz3SHTrYVaRm2LilNGnFUzh0FAwqPEmU/CwDg== + version "5.10.0" + resolved "https://registry.yarnpkg.com/webpack-merge/-/webpack-merge-5.10.0.tgz#a3ad5d773241e9c682803abf628d4cd62b8a4177" + integrity sha512-+4zXKdx7UnO+1jaN4l2lHVD+mFvnlZQP/6ljaJVb4SZiwIKeUnrT5l0gkT8z+n4hKpC+jpOv6O9R+gLtag7pSA== dependencies: clone-deep "^4.0.1" + flat "^5.0.2" wildcard "^2.0.0" webpack-sources@^3.2.3: @@ -5446,10 +5755,10 @@ webpack-sources@^3.2.3: resolved "https://registry.yarnpkg.com/webpack-sources/-/webpack-sources-3.2.3.tgz#2d4daab8451fd4b240cc27055ff6a0c2ccea0cde" integrity sha512-/DyMEOrDgLKKIG0fmvtz+4dUX/3Ghozwgm6iPp8KRhvn+eQf9+Q7GWxVNMk3+uCPWfdXYC4ExGBckIXdFEfH1w== -webpack@5.88.1: - version "5.88.1" - resolved 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