From 0fd594e47b5c336e588cb9205ca5f8c6ad6bae4b Mon Sep 17 00:00:00 2001
From: Colin <colin.diesh@gmail.com>
Date: Wed, 11 Dec 2024 23:12:19 -0500
Subject: [PATCH] Make gf2

---
 package.json        |  3 +--
 src/indexedFasta.ts | 20 ++++++++++----------
 yarn.lock           | 23 +++++------------------
 3 files changed, 16 insertions(+), 30 deletions(-)

diff --git a/package.json b/package.json
index 758c40e..0560ff1 100644
--- a/package.json
+++ b/package.json
@@ -41,8 +41,7 @@
   ],
   "dependencies": {
     "@gmod/bgzf-filehandle": "^1.4.0",
-    "buffer": "^6.0.3",
-    "generic-filehandle": "^3.0.0"
+    "generic-filehandle2": "^0.0.1"
   },
   "devDependencies": {
     "@typescript-eslint/eslint-plugin": "^8.17.0",
diff --git a/src/indexedFasta.ts b/src/indexedFasta.ts
index e051dd5..6eacb9c 100644
--- a/src/indexedFasta.ts
+++ b/src/indexedFasta.ts
@@ -1,5 +1,4 @@
-import { LocalFile, GenericFilehandle } from 'generic-filehandle'
-import { Buffer } from 'buffer'
+import { LocalFile, GenericFilehandle } from 'generic-filehandle2'
 
 interface BaseOpts {
   signal?: AbortSignal
@@ -134,18 +133,18 @@ export default class IndexedFasta {
   }
 
   /**
+   * @param name
    *
-   * @param {string} name
-   * @returns {Promise[boolean]} true if the file contains the given reference sequence name
+   * @returns true if the file contains the given reference sequence name
    */
   async hasReferenceSequence(name: string, opts?: BaseOpts) {
     return !!(await this._getIndexes(opts))[name]
   }
 
   /**
-   * @param {string} seqName
-   * @param {number} min
-   * @param {number} max
+   * @param seqName
+   * @param min
+   * @param max
    */
   async getResiduesByName(
     seqName: string,
@@ -189,8 +188,9 @@ export default class IndexedFasta {
     const position = _faiOffset(indexEntry, min)
     const readlen = _faiOffset(indexEntry, end) - position
 
-    const residues = Buffer.allocUnsafe(readlen)
-    await this.fasta.read(residues, 0, readlen, position, opts)
-    return residues.toString('utf8').replace(/\s+/g, '')
+    const decoder = new TextDecoder('utf8')
+    return decoder
+      .decode(await this.fasta.read(readlen, position, opts))
+      .replace(/\s+/g, '')
   }
 }
diff --git a/yarn.lock b/yarn.lock
index 2e8e717..7582a65 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -891,11 +891,6 @@ balanced-match@^1.0.0:
   resolved "https://registry.yarnpkg.com/balanced-match/-/balanced-match-1.0.2.tgz#e83e3a7e3f300b34cb9d87f615fa0cbf357690ee"
   integrity sha512-3oSeUO0TMV67hN1AmbXsK4yaqU7tjiHlbxRDZOpH0KW9+CeX4bRAaX0Anxt0tx2MrpRpWwQaPwIlISEJhYU5Pw==
 
-base64-js@^1.3.1:
-  version "1.5.1"
-  resolved "https://registry.yarnpkg.com/base64-js/-/base64-js-1.5.1.tgz#1b1b440160a5bf7ad40b650f095963481903930a"
-  integrity sha512-AKpaYlHn8t4SVbOHCy+b5+KKgvR4vrsD8vbvrbiQJps7fKDTkjkDry6ji0rUJjC0kzbNePLwzxq8iypo41qeWA==
-
 binary-extensions@^2.0.0:
   version "2.3.0"
   resolved "https://registry.yarnpkg.com/binary-extensions/-/binary-extensions-2.3.0.tgz#f6e14a97858d327252200242d4ccfe522c445522"
@@ -933,14 +928,6 @@ browserslist@^4.24.0, browserslist@^4.24.2:
     node-releases "^2.0.18"
     update-browserslist-db "^1.1.1"
 
-buffer@^6.0.3:
-  version "6.0.3"
-  resolved "https://registry.yarnpkg.com/buffer/-/buffer-6.0.3.tgz#2ace578459cc8fbe2a70aaa8f52ee63b6a74c6c6"
-  integrity sha512-FTiCpNxtwiZZHEZbcbTIcZjERVICn9yq/pDFkTl95/AxzD1naBctN7YO68riM/gLSDY7sdrMby8hofADYuuqOA==
-  dependencies:
-    base64-js "^1.3.1"
-    ieee754 "^1.2.1"
-
 builtin-modules@^3.3.0:
   version "3.3.0"
   resolved "https://registry.yarnpkg.com/builtin-modules/-/builtin-modules-3.3.0.tgz#cae62812b89801e9656336e46223e030386be7b6"
@@ -1592,6 +1579,11 @@ function-bind@^1.1.2:
   resolved "https://registry.yarnpkg.com/function-bind/-/function-bind-1.1.2.tgz#2c02d864d97f3ea6c8830c464cbd11ab6eab7a1c"
   integrity sha512-7XHNxH7qX9xG5mIwxkhumTox/MIRNcOgDrxWsMt2pAr23WHp6MrRlN7FBSFpCpr+oVO0F744iUgR82nJMfG2SA==
 
+generic-filehandle2@^0.0.1:
+  version "0.0.1"
+  resolved "https://registry.yarnpkg.com/generic-filehandle2/-/generic-filehandle2-0.0.1.tgz#7f26ee54a939ed588d6bdb3a453bb2255ccd2be9"
+  integrity sha512-cySnWoVmNUSkRztAwlghNVAYXUh+VVy/fxn8tT3jZIo8UQEHkYL7ueSUseBZrwqBCq9n06Wp/F4xv2q2/SwYCQ==
+
 generic-filehandle@^3.0.0:
   version "3.2.0"
   resolved "https://registry.yarnpkg.com/generic-filehandle/-/generic-filehandle-3.2.0.tgz#f65401ce71bccadb796335495c3d9250185876d4"
@@ -1876,11 +1868,6 @@ html-void-elements@^2.0.0:
   resolved "https://registry.yarnpkg.com/html-void-elements/-/html-void-elements-2.0.1.tgz#29459b8b05c200b6c5ee98743c41b979d577549f"
   integrity sha512-0quDb7s97CfemeJAnW9wC0hw78MtW7NU3hqtCD75g2vFlDLt36llsYD7uB7SUzojLMP24N5IatXf7ylGXiGG9A==
 
-ieee754@^1.2.1:
-  version "1.2.1"
-  resolved "https://registry.yarnpkg.com/ieee754/-/ieee754-1.2.1.tgz#8eb7a10a63fff25d15a57b001586d177d1b0d352"
-  integrity sha512-dcyqhDvX1C46lXZcVqCpK+FtMRQVdIMN6/Df5js2zouUsqG7I6sFxitIC+7KYK29KdXOLHdu9zL4sFnoVQnqaA==
-
 ignore@^5.2.0, ignore@^5.3.1:
   version "5.3.2"
   resolved "https://registry.yarnpkg.com/ignore/-/ignore-5.3.2.tgz#3cd40e729f3643fd87cb04e50bf0eb722bc596f5"