From 4c91a5cb162f1b0b195a336acf0c218821019477 Mon Sep 17 00:00:00 2001
From: Colin <colin.diesh@gmail.com>
Date: Thu, 8 Aug 2024 22:13:55 -0400
Subject: [PATCH] Add polyfill

---
 package.json                    |  3 +--
 src/bigint-polyfill/polyfill.ts | 13 ++++++++++
 src/bigint-polyfill/pure.ts     | 42 +++++++++++++++++++++++++++++++++
 src/declare.d.ts                |  2 --
 src/index.ts                    |  1 +
 src/twoBitFile.ts               |  7 ++++--
 6 files changed, 62 insertions(+), 6 deletions(-)
 create mode 100644 src/bigint-polyfill/polyfill.ts
 create mode 100644 src/bigint-polyfill/pure.ts
 delete mode 100644 src/declare.d.ts

diff --git a/package.json b/package.json
index 970cf30..b22e2ac 100644
--- a/package.json
+++ b/package.json
@@ -38,8 +38,7 @@
     "biojs"
   ],
   "dependencies": {
-    "generic-filehandle": "^3.0.0",
-    "long": "^4.0.0"
+    "generic-filehandle": "^3.0.0"
   },
   "devDependencies": {
     "@types/jest": "^29.2.4",
diff --git a/src/bigint-polyfill/polyfill.ts b/src/bigint-polyfill/polyfill.ts
new file mode 100644
index 0000000..b8e20a2
--- /dev/null
+++ b/src/bigint-polyfill/polyfill.ts
@@ -0,0 +1,13 @@
+import { getBigInt64, getBigUint64 } from './pure'
+
+if (!('getBigInt64' in DataView)) {
+  DataView.prototype.getBigInt64 = function (byteOffset, littleEndian) {
+    return getBigInt64(this, byteOffset, littleEndian)
+  }
+}
+
+if (!('getBigUint64' in DataView)) {
+  DataView.prototype.getBigUint64 = function (byteOffset, littleEndian) {
+    return getBigUint64(this, byteOffset, littleEndian)
+  }
+}
diff --git a/src/bigint-polyfill/pure.ts b/src/bigint-polyfill/pure.ts
new file mode 100644
index 0000000..bdb9500
--- /dev/null
+++ b/src/bigint-polyfill/pure.ts
@@ -0,0 +1,42 @@
+const BigInt32 = BigInt(32)
+
+export function getBigInt64(
+  dataView: DataView,
+  byteOffset: number,
+  littleEndian: boolean | undefined,
+): bigint {
+  const littleEndianMask = Number(!!littleEndian)
+  const bigEndianMask = Number(!littleEndian)
+
+  return (
+    (BigInt(
+      dataView.getInt32(byteOffset, littleEndian) * bigEndianMask +
+        dataView.getInt32(byteOffset + 4, littleEndian) * littleEndianMask,
+    ) <<
+      BigInt32) |
+    BigInt(
+      dataView.getUint32(byteOffset, littleEndian) * littleEndianMask +
+        dataView.getUint32(byteOffset + 4, littleEndian) * bigEndianMask,
+    )
+  )
+}
+
+export function getBigUint64(
+  dataView: DataView,
+  byteOffset: number,
+  littleEndian: boolean | undefined,
+): bigint {
+  const a = dataView.getUint32(byteOffset, littleEndian)
+  const b = dataView.getUint32(byteOffset + 4, littleEndian)
+
+  const littleEndianMask = Number(!!littleEndian)
+  const bigEndianMask = Number(!littleEndian)
+
+  // This branch-less optimization is 77x faster than normal ternary operator.
+  // and only 3% slower than native implementation
+  // https://jsbench.me/p8kyhg1eqv/1
+  return (
+    (BigInt(a * bigEndianMask + b * littleEndianMask) << BigInt32) |
+    BigInt(a * littleEndianMask + b * bigEndianMask)
+  )
+}
diff --git a/src/declare.d.ts b/src/declare.d.ts
deleted file mode 100644
index 963111e..0000000
--- a/src/declare.d.ts
+++ /dev/null
@@ -1,2 +0,0 @@
-declare module '@gmod/binary-parser'
-declare module 'long'
diff --git a/src/index.ts b/src/index.ts
index 9c1abfc..03973f7 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -1 +1,2 @@
+import './bigint-polyfill/polyfill'
 export { default as TwoBitFile } from './twoBitFile'
diff --git a/src/twoBitFile.ts b/src/twoBitFile.ts
index ed36541..bfb17d5 100644
--- a/src/twoBitFile.ts
+++ b/src/twoBitFile.ts
@@ -1,4 +1,3 @@
-import Long from 'long'
 import { LocalFile, GenericFilehandle } from 'generic-filehandle'
 
 const TWOBIT_MAGIC = 0x1a412743
@@ -316,7 +315,11 @@ export default class TwoBitFile {
    * @param {number} [regionEnd] optional 0-based half-open end of the sequence region to fetch. defaults to end of the sequence
    * @returns {Promise} for a string of sequence bases
    */
-  async getSequence(seqName: string, regionStart = 0, regionEnd = Number.POSITIVE_INFINITY) {
+  async getSequence(
+    seqName: string,
+    regionStart = 0,
+    regionEnd = Number.POSITIVE_INFINITY,
+  ) {
     const index = await this.getIndex()
     const offset = index[seqName]
     if (!offset) {