first commit

index.js

@@ -0,0 +1,161 @@
+"use strict";
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
+    });
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.saveMultifastaFromIds = void 0;
+const https_1 = __importDefault(require("https"));
+const fs_1 = __importDefault(require("fs"));
+///////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+// Donwload and save multifasta from query
+///////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+// save_multifasta_from_ids('Viruses[Organism]+AND+srcdb_refseq[PROP]+AND+vhost_human[Filter]', '/home/thomas/viralHuman.fna')
+// Configs
+const esearch = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi';
+const efetch = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi';
+const regex_sam_restriction = /[>0-9A-Za-z!#$%&+\./:;?@^_|~-]|[\n\t]/g;
+const maxWaiting = 30 * 60 * 1000;
+const invReplace = (regex, string, by = '_') => {
+    return string.split('').map(letter => letter.match(regex) ? letter : by).join('');
+};
+//get_seq_from_id('12175745', (res) => {console.log(res)})
+const get_seq_from_id = (arg, cb) => {
+    const id = arg.id;
+    const NCBI_API = arg.NCBI_API;
+    https_1.default.get(`${efetch}?db=nuccore&id=${id}&rettype=fasta&retmode=text&api_key=${NCBI_API}`, (resp) => {
+        let data = '';
+        resp.on('data', (chunk) => { data += chunk; });
+        resp.on('end', () => {
+            cb(invReplace(regex_sam_restriction, data));
+        });
+    }).on("error", (err) => { console.log("Error: " + err.message); });
+};
+const sleep = (ms) => { return new Promise(resolve => setTimeout(resolve, ms)); };
+const async_get_multiseq_from_ids = (ids, NCBI_API, onProgress, concurrency = 2) => {
+    return new Promise((resolve, reject) => __awaiter(void 0, void 0, void 0, function* () {
+        const q = require('fastq')(get_seq_from_id, concurrency);
+        let data = '';
+        ids.forEach(id => q.push({ id, NCBI_API }, (arg) => { data += arg; }));
+        let currQL = 0;
+        let timePassed = 0;
+        while (!q.idle()) {
+            yield sleep(300);
+            timePassed += 300;
+            if (currQL != q.length()) {
+                currQL = q.length();
+                onProgress(`${ids.length - currQL}/${ids.length}`);
+            }
+            if (timePassed > maxWaiting)
+                reject('timeout');
+        }
+        resolve(data.replace(/(^[ \t]*\n)/gm, ''));
+    }));
+};
+const get_ids_from_query = (arg, cb) => {
+    const { query, from, max, NCBI_API } = arg;
+    const url = `${esearch}?db=nucleotide&term=${query}&usehistory=y&api_key=${NCBI_API}&retstart=${from}&retmax=${max}`;
+    https_1.default.get(url, (resp) => {
+        let data = '';
+        resp.on('data', (chunk) => { data += chunk; });
+        resp.on('end', () => {
+            const keysMatches = data.matchAll(/<Id>(\d+)<\/Id>/g);
+            let keys = [];
+            for (const key of keysMatches)
+                keys.push(key[1]);
+            cb(keys);
+        });
+    });
+};
+// async
+const get_multipage_ids_from_query = (query, onProgress, NCBI_API, retMax = 20) => {
+    return new Promise((resolve, reject) => {
+        https_1.default.get(`${esearch}?db=nucleotide&term=${query}&usehistory=y&api_key=${NCBI_API}`, (resp) => __awaiter(void 0, void 0, void 0, function* () {
+            let data = '';
+            resp.on('data', (chunk) => { data += chunk; });
+            resp.on('end', () => __awaiter(void 0, void 0, void 0, function* () {
+                const tmp = data.match(/<Count>(\d+)<\/Count>/) || [0, 0];
+                const count = parseInt(tmp[1]);
+                const nIter = count % retMax === 0 ? count / retMax : Math.trunc(count / retMax) + 1;
+                const q = require('fastq')(get_ids_from_query, 2);
+                let ids = [];
+                const callback = (arg) => {
+                    const tmp = Array.isArray(arg) ? arg : [arg];
+                    ids = [...ids, ...tmp];
+                };
+                for (let index = 0; index < nIter; index++) {
+                    q.push({ query, from: (index * retMax), max: retMax, NCBI_API }, callback);
+                }
+                let currQL = 0;
+                let timePassed = 0;
+                while (!q.idle()) {
+                    yield sleep(300);
+                    timePassed += 300;
+                    if (currQL != q.length()) {
+                        currQL = q.length();
+                        onProgress(`${nIter - currQL}/${nIter}`);
+                    }
+                    if (timePassed > maxWaiting)
+                        reject('timeout');
+                }
+                if (ids.length === count) {
+                    resolve(ids);
+                }
+                else {
+                    reject('Error');
+                }
+            }));
+        })).on("error", (err) => {
+            console.log("Error: " + err.message);
+            reject(err);
+        });
+    });
+};
+const saveMultifastaFromIds = (query, path, NCBI_API, onProgress) => {
+    return new Promise((resolve, reject) => __awaiter(void 0, void 0, void 0, function* () {
+        try {
+            console.log('Fetching NCBI IDs from : ', query);
+            const ids = yield get_multipage_ids_from_query(query, onProgress, NCBI_API);
+            if (Array.isArray(ids)) {
+                console.log(`Fetching NCBI Sequences (${ids.length}) of : `, ids);
+                const seq = yield async_get_multiseq_from_ids(ids, NCBI_API, onProgress);
+                if (typeof (seq) === 'string') {
+                    yield fs_1.default.promises.writeFile(path, seq);
+                    resolve(true);
+                }
+                else {
+                    reject('');
+                }
+            }
+            else {
+                reject('');
+            }
+        }
+        catch (error) {
+            reject(error);
+        }
+    }));
+};
+exports.saveMultifastaFromIds = saveMultifastaFromIds;
+// https://www.ncbi.nlm.nih.gov/books/NBK21091/
+// https://www.ncbi.nlm.nih.gov/books/NBK50679/
+// ""Homo sapiens"[Organism] AND biomol_transcribed_rna[PROP] AND refseq[filter]"
+// ""Homo sapiens"[Organism] AND srcdb_refseq[prop] AND biomol_rna[prop] "
+/*
+(async () => {
+    const NCBI_API = '5b283f20e48000e0e9f20874125d4cced808'
+    await saveMultifastaFromIds(
+        '"Homo sapiens"[Organism] AND biomol_transcribed_rna[PROP] AND refseq[filter]',
+        '/home/thomas/Human_Transcriptome_RefSeq.fna',
+        NCBI_API,
+        console.log
+    )
+})()*/ 

index.ts

@@ -0,0 +1,166 @@
+import https from 'https'
+import fs from 'fs'
+
+// Types
+import type { queue, done } from 'fastq'
+type Task = {id: string, NCBI_API: string}
+type TaskBis = {query: string, from: number, max: number, NCBI_API: string}
+///////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+// Donwload and save multifasta from query
+///////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+// save_multifasta_from_ids('Viruses[Organism]+AND+srcdb_refseq[PROP]+AND+vhost_human[Filter]', '/home/thomas/viralHuman.fna')
+
+// Configs
+const esearch: string               = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi'
+const efetch: string                = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi'
+const regex_sam_restriction: RegExp = /[>0-9A-Za-z!#$%&+\./:;?@^_|~-]|[\n\t]/g;
+const maxWaiting                    = 30 * 60 * 1000
+
+const invReplace = (regex: RegExp, string: string, by = '_') => {
+  return string.split('').map(letter => letter.match(regex) ? letter : by).join('')
+}
+
+//get_seq_from_id('12175745', (res) => {console.log(res)})
+const get_seq_from_id = (arg: Task, cb: Function) => {
+  const id = arg.id
+  const NCBI_API = arg.NCBI_API
+  https.get(`${efetch}?db=nuccore&id=${id}&rettype=fasta&retmode=text&api_key=${NCBI_API}`, (resp) => {
+    let data = ''
+    resp.on('data', (chunk) => { data += chunk })
+    resp.on('end', () => {
+      cb(invReplace(regex_sam_restriction, data))
+    })
+  }).on("error", (err) => { console.log("Error: " + err.message) })
+}
+
+const sleep = (ms: number) => {return new Promise(resolve => setTimeout(resolve, ms))}
+
+const async_get_multiseq_from_ids = (
+    ids: any[], 
+    NCBI_API: string,
+    onProgress: Function, 
+    concurrency = 2
+) => {
+  return new Promise(async (resolve, reject) => {
+    const q: queue<Task> = require('fastq')(get_seq_from_id, concurrency)
+    let data = ''
+    ids.forEach(id => q.push({id, NCBI_API}, (arg) => {data += arg}))
+    let currQL = 0
+    let timePassed = 0
+    while(!q.idle()) {
+      await sleep(300);
+      timePassed += 300
+      if (currQL != q.length()) {
+        currQL = q.length();
+        onProgress(`${ids.length-currQL}/${ids.length}`)
+      }
+      if(timePassed > maxWaiting) reject('timeout')
+    }
+    resolve(data.replace(/(^[ \t]*\n)/gm, ''));
+  })
+}
+
+const get_ids_from_query = (arg: TaskBis, cb: Function) => {
+  const {query, from, max, NCBI_API} = arg
+  const url = `${esearch}?db=nucleotide&term=${query}&usehistory=y&api_key=${NCBI_API}&retstart=${from}&retmax=${max}`
+  https.get(url, (resp) => {
+    let data = ''
+    resp.on('data', (chunk) => { data += chunk })
+    resp.on('end', () => {
+      const keysMatches = data.matchAll(/<Id>(\d+)<\/Id>/g)
+      let keys: any[] = []
+      for (const key of keysMatches) keys.push(key[1])
+      cb(keys)
+    })
+  })
+}
+
+// async
+const get_multipage_ids_from_query = (
+    query: string,
+    onProgress: Function,
+    NCBI_API: string,
+    retMax = 20
+) => {
+  return new Promise((resolve, reject) => {
+    https.get(`${esearch}?db=nucleotide&term=${query}&usehistory=y&api_key=${NCBI_API}`, async (resp) => {
+      let data: string = ''
+      resp.on('data', (chunk) => { data += chunk })
+      resp.on('end', async () => {
+        const tmp: any[] = data.match(/<Count>(\d+)<\/Count>/) || [0,0]
+        const count = parseInt(tmp[1]) 
+
+        const nIter = count%retMax === 0 ? count/retMax : Math.trunc(count/retMax) + 1
+
+        const q: queue<TaskBis> = require('fastq')(get_ids_from_query, 2)
+        let ids: any[] = []
+        const callback: done = (arg) => {
+            const tmp = Array.isArray(arg) ? arg : [arg]
+            ids = [...ids, ...tmp]
+        }
+
+        for (let index = 0; index < nIter; index++) {
+          q.push({query, from: (index*retMax), max: retMax, NCBI_API}, callback)
+        }
+        let currQL = 0
+        let timePassed = 0
+        while(!q.idle()) {
+          await sleep(300)
+          timePassed += 300
+          if (currQL != q.length()) {
+            currQL = q.length();
+            onProgress(`${nIter-currQL}/${nIter}`)
+          }
+          if(timePassed > maxWaiting) reject('timeout')
+        }
+        if(ids.length === count) {
+            resolve(ids)
+        } else {
+            reject('Error')
+        }
+      })
+    }).on("error", (err) => {
+      console.log("Error: " + err.message);
+      reject(err);
+    })
+  });
+}
+
+const saveMultifastaFromIds = (
+    query: string,
+    path: string,
+    NCBI_API: string,
+    onProgress: Function
+) => {
+  return new Promise(async (resolve, reject) => {
+    try {
+        console.log('Fetching NCBI IDs from : ', query)
+        const ids = await get_multipage_ids_from_query(query, onProgress, NCBI_API)
+        if (Array.isArray(ids)) {
+            console.log(`Fetching NCBI Sequences (${ids.length}) of : `, ids)
+            const seq = await async_get_multiseq_from_ids(ids, NCBI_API, onProgress)
+            if (typeof(seq) === 'string') {
+                await fs.promises.writeFile(path, seq)
+                resolve(true)
+            } else { reject('') }
+        } else { reject('') }
+    } catch (error) { reject(error) }
+  })
+}
+
+export { saveMultifastaFromIds }
+
+// https://www.ncbi.nlm.nih.gov/books/NBK21091/
+// https://www.ncbi.nlm.nih.gov/books/NBK50679/
+// ""Homo sapiens"[Organism] AND biomol_transcribed_rna[PROP] AND refseq[filter]"
+// ""Homo sapiens"[Organism] AND srcdb_refseq[prop] AND biomol_rna[prop] "
+/*
+(async () => {
+    const NCBI_API = '5b283f20e48000e0e9f20874125d4cced808'
+    await saveMultifastaFromIds(
+        '"Homo sapiens"[Organism] AND biomol_transcribed_rna[PROP] AND refseq[filter]', 
+        '/home/thomas/Human_Transcriptome_RefSeq.fna',
+        NCBI_API,
+        console.log
+    )
+})()*/

package-lock.json

@@ -0,0 +1,86 @@
+{
+  "name": "ncbiref",
+  "version": "1.0.0",
+  "lockfileVersion": 2,
+  "requires": true,
+  "packages": {
+    "": {
+      "name": "ncbiref",
+      "version": "1.0.0",
+      "license": "ISC",
+      "dependencies": {
+        "fastq": "^1.13.0"
+      },
+      "devDependencies": {
+        "@types/node": "^17.0.18",
+        "typescript": "^4.5.5"
+      }
+    },
+    "node_modules/@types/node": {
+      "version": "17.0.18",
+      "resolved": "https://registry.npmjs.org/@types/node/-/node-17.0.18.tgz",
+      "integrity": "sha512-eKj4f/BsN/qcculZiRSujogjvp5O/k4lOW5m35NopjZM/QwLOR075a8pJW5hD+Rtdm2DaCVPENS6KtSQnUD6BA==",
+      "dev": true
+    },
+    "node_modules/fastq": {
+      "version": "1.13.0",
+      "resolved": "https://registry.npmjs.org/fastq/-/fastq-1.13.0.tgz",
+      "integrity": "sha512-YpkpUnK8od0o1hmeSc7UUs/eB/vIPWJYjKck2QKIzAf71Vm1AAQ3EbuZB3g2JIy+pg+ERD0vqI79KyZiB2e2Nw==",
+      "license": "ISC",
+      "dependencies": {
+        "reusify": "^1.0.4"
+      }
+    },
+    "node_modules/reusify": {
+      "version": "1.0.4",
+      "resolved": "https://registry.npmjs.org/reusify/-/reusify-1.0.4.tgz",
+      "integrity": "sha512-U9nH88a3fc/ekCF1l0/UP1IosiuIjyTh7hBvXVMHYgVcfGvt897Xguj2UOLDeI5BG2m7/uwyaLVT6fbtCwTyzw==",
+      "license": "MIT",
+      "engines": {
+        "iojs": ">=1.0.0",
+        "node": ">=0.10.0"
+      }
+    },
+    "node_modules/typescript": {
+      "version": "4.5.5",
+      "resolved": "https://registry.npmjs.org/typescript/-/typescript-4.5.5.tgz",
+      "integrity": "sha512-TCTIul70LyWe6IJWT8QSYeA54WQe8EjQFU4wY52Fasj5UKx88LNYKCgBEHcOMOrFF1rKGbD8v/xcNWVUq9SymA==",
+      "dev": true,
+      "license": "Apache-2.0",
+      "bin": {
+        "tsc": "bin/tsc",
+        "tsserver": "bin/tsserver"
+      },
+      "engines": {
+        "node": ">=4.2.0"
+      }
+    }
+  },
+  "dependencies": {
+    "@types/node": {
+      "version": "17.0.18",
+      "resolved": "https://registry.npmjs.org/@types/node/-/node-17.0.18.tgz",
+      "integrity": "sha512-eKj4f/BsN/qcculZiRSujogjvp5O/k4lOW5m35NopjZM/QwLOR075a8pJW5hD+Rtdm2DaCVPENS6KtSQnUD6BA==",
+      "dev": true
+    },
+    "fastq": {
+      "version": "1.13.0",
+      "resolved": "https://registry.npmjs.org/fastq/-/fastq-1.13.0.tgz",
+      "integrity": "sha512-YpkpUnK8od0o1hmeSc7UUs/eB/vIPWJYjKck2QKIzAf71Vm1AAQ3EbuZB3g2JIy+pg+ERD0vqI79KyZiB2e2Nw==",
+      "requires": {
+        "reusify": "^1.0.4"
+      }
+    },
+    "reusify": {
+      "version": "1.0.4",
+      "resolved": "https://registry.npmjs.org/reusify/-/reusify-1.0.4.tgz",
+      "integrity": "sha512-U9nH88a3fc/ekCF1l0/UP1IosiuIjyTh7hBvXVMHYgVcfGvt897Xguj2UOLDeI5BG2m7/uwyaLVT6fbtCwTyzw=="
+    },
+    "typescript": {
+      "version": "4.5.5",
+      "resolved": "https://registry.npmjs.org/typescript/-/typescript-4.5.5.tgz",
+      "integrity": "sha512-TCTIul70LyWe6IJWT8QSYeA54WQe8EjQFU4wY52Fasj5UKx88LNYKCgBEHcOMOrFF1rKGbD8v/xcNWVUq9SymA==",
+      "dev": true
+    }
+  }
+}

package.json

@@ -0,0 +1,21 @@
+{
+  "name": "ncbiref",
+  "version": "1.0.0",
+  "description": "",
+  "main": "index.js",
+  "scripts": {
+    "prepublish": "npm run build",
+    "build": "tsc",
+    "test": "echo \"Error: no test specified\" && exit 1"
+  },
+  "keywords": [],
+  "author": "",
+  "license": "ISC",
+  "devDependencies": {
+    "@types/node": "^17.0.18",
+    "typescript": "^4.5.5"
+  },
+  "dependencies": {
+    "fastq": "^1.13.0"
+  }
+}

tsconfig.json

@@ -0,0 +1,101 @@
+{
+  "compilerOptions": {
+    /* Visit https://aka.ms/tsconfig.json to read more about this file */
+
+    /* Projects */
+    // "incremental": true,                              /* Enable incremental compilation */
+    // "composite": true,                                /* Enable constraints that allow a TypeScript project to be used with project references. */
+    // "tsBuildInfoFile": "./",                          /* Specify the folder for .tsbuildinfo incremental compilation files. */
+    // "disableSourceOfProjectReferenceRedirect": true,  /* Disable preferring source files instead of declaration files when referencing composite projects */
+    // "disableSolutionSearching": true,                 /* Opt a project out of multi-project reference checking when editing. */
+    // "disableReferencedProjectLoad": true,             /* Reduce the number of projects loaded automatically by TypeScript. */
+
+    /* Language and Environment */
+    "target": "es2016",                                  /* Set the JavaScript language version for emitted JavaScript and include compatible library declarations. */
+    // "lib": [],                                        /* Specify a set of bundled library declaration files that describe the target runtime environment. */
+    // "jsx": "preserve",                                /* Specify what JSX code is generated. */
+    // "experimentalDecorators": true,                   /* Enable experimental support for TC39 stage 2 draft decorators. */
+    // "emitDecoratorMetadata": true,                    /* Emit design-type metadata for decorated declarations in source files. */
+    // "jsxFactory": "",                                 /* Specify the JSX factory function used when targeting React JSX emit, e.g. 'React.createElement' or 'h' */
+    // "jsxFragmentFactory": "",                         /* Specify the JSX Fragment reference used for fragments when targeting React JSX emit e.g. 'React.Fragment' or 'Fragment'. */
+    // "jsxImportSource": "",                            /* Specify module specifier used to import the JSX factory functions when using `jsx: react-jsx*`.` */
+    // "reactNamespace": "",                             /* Specify the object invoked for `createElement`. This only applies when targeting `react` JSX emit. */
+    // "noLib": true,                                    /* Disable including any library files, including the default lib.d.ts. */
+    // "useDefineForClassFields": true,                  /* Emit ECMAScript-standard-compliant class fields. */
+
+    /* Modules */
+    "module": "commonjs",                                /* Specify what module code is generated. */
+    // "rootDir": "./",                                  /* Specify the root folder within your source files. */
+    // "moduleResolution": "node",                       /* Specify how TypeScript looks up a file from a given module specifier. */
+    // "baseUrl": "./",                                  /* Specify the base directory to resolve non-relative module names. */
+    // "paths": {},                                      /* Specify a set of entries that re-map imports to additional lookup locations. */
+    // "rootDirs": [],                                   /* Allow multiple folders to be treated as one when resolving modules. */
+    // "typeRoots": [],                                  /* Specify multiple folders that act like `./node_modules/@types`. */
+    // "types": [],                                      /* Specify type package names to be included without being referenced in a source file. */
+    // "allowUmdGlobalAccess": true,                     /* Allow accessing UMD globals from modules. */
+    // "resolveJsonModule": true,                        /* Enable importing .json files */
+    // "noResolve": true,                                /* Disallow `import`s, `require`s or `<reference>`s from expanding the number of files TypeScript should add to a project. */
+
+    /* JavaScript Support */
+    // "allowJs": true,                                  /* Allow JavaScript files to be a part of your program. Use the `checkJS` option to get errors from these files. */
+    // "checkJs": true,                                  /* Enable error reporting in type-checked JavaScript files. */
+    // "maxNodeModuleJsDepth": 1,                        /* Specify the maximum folder depth used for checking JavaScript files from `node_modules`. Only applicable with `allowJs`. */
+
+    /* Emit */
+    // "declaration": true,                              /* Generate .d.ts files from TypeScript and JavaScript files in your project. */
+    // "declarationMap": true,                           /* Create sourcemaps for d.ts files. */
+    // "emitDeclarationOnly": true,                      /* Only output d.ts files and not JavaScript files. */
+    // "sourceMap": true,                                /* Create source map files for emitted JavaScript files. */
+    // "outFile": "./",                                  /* Specify a file that bundles all outputs into one JavaScript file. If `declaration` is true, also designates a file that bundles all .d.ts output. */
+    // "outDir": "./",                                   /* Specify an output folder for all emitted files. */
+    // "removeComments": true,                           /* Disable emitting comments. */
+    // "noEmit": true,                                   /* Disable emitting files from a compilation. */
+    // "importHelpers": true,                            /* Allow importing helper functions from tslib once per project, instead of including them per-file. */
+    // "importsNotUsedAsValues": "remove",               /* Specify emit/checking behavior for imports that are only used for types */
+    // "downlevelIteration": true,                       /* Emit more compliant, but verbose and less performant JavaScript for iteration. */
+    // "sourceRoot": "",                                 /* Specify the root path for debuggers to find the reference source code. */
+    // "mapRoot": "",                                    /* Specify the location where debugger should locate map files instead of generated locations. */
+    // "inlineSourceMap": true,                          /* Include sourcemap files inside the emitted JavaScript. */
+    // "inlineSources": true,                            /* Include source code in the sourcemaps inside the emitted JavaScript. */
+    // "emitBOM": true,                                  /* Emit a UTF-8 Byte Order Mark (BOM) in the beginning of output files. */
+    // "newLine": "crlf",                                /* Set the newline character for emitting files. */
+    // "stripInternal": true,                            /* Disable emitting declarations that have `@internal` in their JSDoc comments. */
+    // "noEmitHelpers": true,                            /* Disable generating custom helper functions like `__extends` in compiled output. */
+    // "noEmitOnError": true,                            /* Disable emitting files if any type checking errors are reported. */
+    // "preserveConstEnums": true,                       /* Disable erasing `const enum` declarations in generated code. */
+    // "declarationDir": "./",                           /* Specify the output directory for generated declaration files. */
+    // "preserveValueImports": true,                     /* Preserve unused imported values in the JavaScript output that would otherwise be removed. */
+
+    /* Interop Constraints */
+    // "isolatedModules": true,                          /* Ensure that each file can be safely transpiled without relying on other imports. */
+    // "allowSyntheticDefaultImports": true,             /* Allow 'import x from y' when a module doesn't have a default export. */
+    "esModuleInterop": true,                             /* Emit additional JavaScript to ease support for importing CommonJS modules. This enables `allowSyntheticDefaultImports` for type compatibility. */
+    // "preserveSymlinks": true,                         /* Disable resolving symlinks to their realpath. This correlates to the same flag in node. */
+    "forceConsistentCasingInFileNames": true,            /* Ensure that casing is correct in imports. */
+
+    /* Type Checking */
+    "strict": true,                                      /* Enable all strict type-checking options. */
+    // "noImplicitAny": true,                            /* Enable error reporting for expressions and declarations with an implied `any` type.. */
+    // "strictNullChecks": true,                         /* When type checking, take into account `null` and `undefined`. */
+    // "strictFunctionTypes": true,                      /* When assigning functions, check to ensure parameters and the return values are subtype-compatible. */
+    // "strictBindCallApply": true,                      /* Check that the arguments for `bind`, `call`, and `apply` methods match the original function. */
+    // "strictPropertyInitialization": true,             /* Check for class properties that are declared but not set in the constructor. */
+    // "noImplicitThis": true,                           /* Enable error reporting when `this` is given the type `any`. */
+    // "useUnknownInCatchVariables": true,               /* Type catch clause variables as 'unknown' instead of 'any'. */
+    // "alwaysStrict": true,                             /* Ensure 'use strict' is always emitted. */
+    // "noUnusedLocals": true,                           /* Enable error reporting when a local variables aren't read. */
+    // "noUnusedParameters": true,                       /* Raise an error when a function parameter isn't read */
+    // "exactOptionalPropertyTypes": true,               /* Interpret optional property types as written, rather than adding 'undefined'. */
+    // "noImplicitReturns": true,                        /* Enable error reporting for codepaths that do not explicitly return in a function. */
+    // "noFallthroughCasesInSwitch": true,               /* Enable error reporting for fallthrough cases in switch statements. */
+    // "noUncheckedIndexedAccess": true,                 /* Include 'undefined' in index signature results */
+    // "noImplicitOverride": true,                       /* Ensure overriding members in derived classes are marked with an override modifier. */
+    // "noPropertyAccessFromIndexSignature": true,       /* Enforces using indexed accessors for keys declared using an indexed type */
+    // "allowUnusedLabels": true,                        /* Disable error reporting for unused labels. */
+    // "allowUnreachableCode": true,                     /* Disable error reporting for unreachable code. */
+
+    /* Completeness */
+    // "skipDefaultLibCheck": true,                      /* Skip type checking .d.ts files that are included with TypeScript. */
+    "skipLibCheck": true                                 /* Skip type checking all .d.ts files. */
+  }
+}

yarn.lock

@@ -0,0 +1,25 @@
+# THIS IS AN AUTOGENERATED FILE. DO NOT EDIT THIS FILE DIRECTLY.
+# yarn lockfile v1
+
+
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+  "resolved" "https://registry.npmjs.org/@types/node/-/node-17.0.18.tgz"
+  "version" "17.0.18"
+
+"fastq@^1.13.0":
+  "integrity" "sha512-YpkpUnK8od0o1hmeSc7UUs/eB/vIPWJYjKck2QKIzAf71Vm1AAQ3EbuZB3g2JIy+pg+ERD0vqI79KyZiB2e2Nw=="
+  "resolved" "https://registry.npmjs.org/fastq/-/fastq-1.13.0.tgz"
+  "version" "1.13.0"
+  dependencies:
+    "reusify" "^1.0.4"
+
+"reusify@^1.0.4":
+  "integrity" "sha512-U9nH88a3fc/ekCF1l0/UP1IosiuIjyTh7hBvXVMHYgVcfGvt897Xguj2UOLDeI5BG2m7/uwyaLVT6fbtCwTyzw=="
+  "resolved" "https://registry.npmjs.org/reusify/-/reusify-1.0.4.tgz"
+  "version" "1.0.4"
+
+"typescript@^4.5.5":
+  "integrity" "sha512-TCTIul70LyWe6IJWT8QSYeA54WQe8EjQFU4wY52Fasj5UKx88LNYKCgBEHcOMOrFF1rKGbD8v/xcNWVUq9SymA=="
+  "resolved" "https://registry.npmjs.org/typescript/-/typescript-4.5.5.tgz"
+  "version" "4.5.5"