Opt

Author: cmdcolin

jest.config.js

@@ -2,4 +2,4 @@
 module.exports = {
   preset: 'ts-jest',
   testEnvironment: 'node',
-};
+}

package.json

@@ -20,24 +20,25 @@
     "preversion": "yarn lint && yarn test --run && yarn build",
     "postbuild:es5": "echo '{\"type\": \"commonjs\"}' > dist/package.json",
     "postversion": "git push --follow-tags",
-    "test": "vitest"
+    "test": "vitest",
+    "format": "prettier --write ."
   },
   "name": "@gmod/trix",
   "author": "Matt Morgan",
   "repository": "GMOD/trix-js",
   "devDependencies": {
-    "@types/node": "^22.15.21",
-    "@typescript-eslint/eslint-plugin": "^8.4.0",
-    "@typescript-eslint/parser": "^8.4.0",
+    "@types/node": "^25.0.9",
+    "@typescript-eslint/eslint-plugin": "^8.53.0",
+    "@typescript-eslint/parser": "^8.53.0",
     "eslint": "^9.0.0",
     "eslint-plugin-import": "^2.31.0",
     "eslint-plugin-unicorn": "^62.0.0",
-    "generic-filehandle2": "^2.0.5",
-    "prettier": "^3.3.3",
+    "generic-filehandle2": "^2.0.18",
+    "prettier": "^3.8.0",
     "rimraf": "^6.0.1",
     "typescript": "^5.7.0",
-    "typescript-eslint": "^8.4.0",
-    "vitest": "^4.0.6"
+    "typescript-eslint": "^8.53.0",
+    "vitest": "^4.0.17"
   },
   "publishConfig": {
     "access": "public"

src/index.ts

@@ -10,6 +10,9 @@ const CHUNK_SIZE = 65536
 const ADDRESS_SIZE = 10
 
 export default class Trix {
+  private decoder = new TextDecoder('utf8')
+  private indexCache?: readonly (readonly [string, number])[]
+
   constructor(
     public ixxFile: GenericFilehandle,
     public ixFile: GenericFilehandle,
@@ -29,11 +32,9 @@ export default class Trix {
 
     let { end, buffer } = res
     let done = false
-    const decoder = new TextDecoder('utf8')
     // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
     while (!done) {
-      let foundSomething = false
-      const str = decoder.decode(buffer)
+      const str = this.decoder.decode(buffer)
 
       // slice to lastIndexOf('\n') to make sure we get complete records
       // since the buffer fetch could get halfway into a record
@@ -46,9 +47,6 @@ export default class Trix {
       for (const line of lines) {
         const word = line.split(' ')[0]
         const match = word.startsWith(searchWord)
-        if (!foundSomething && match) {
-          foundSomething = true
-        }
 
         // we are done scanning if we are lexicographically greater than the
         // search string
@@ -91,11 +89,14 @@ export default class Trix {
   }
 
   private async getIndex(opts?: { signal?: AbortSignal }) {
+    if (this.indexCache) {
+      return this.indexCache
+    }
     const file = await this.ixxFile.readFile({
       encoding: 'utf8',
       ...opts,
     })
-    return file
+    const result = file
       .split('\n')
       .filter(f => !!f)
       .map(line => {
@@ -105,20 +106,22 @@ export default class Trix {
         const pos = Number.parseInt(posStr, 16)
         return [prefix, pos] as const
       })
+    this.indexCache = result
+    return result
   }
 
   private async _getBuffer(
     searchWord: string,
     opts?: { signal?: AbortSignal },
   ) {
     let start = 0
-    let end = 65536
+    let end = CHUNK_SIZE
     const indexes = await this.getIndex(opts)
     for (const [key, value] of indexes) {
       const trimmedKey = key.slice(0, searchWord.length)
       if (trimmedKey < searchWord) {
         start = value
-        end = value + 65536
+        end = value + CHUNK_SIZE
       }
     }
 

test/testData/D39V_annotation_coding_features_sorted.gff_meta.json

@@ -12,10 +12,7 @@
         "NCBI_locus",
         "Alias"
       ],
-      "excludedTypes": [
-        "CDS",
-        "exon"
-      ],
+      "excludedTypes": ["CDS", "exon"],
       "adapterConf": {
         "type": "Gff3TabixAdapter",
         "gffGzLocation": {
@@ -31,7 +28,5 @@
       }
     }
   ],
-  "assemblyNames": [
-    "D39V"
-  ]
-}
+  "assemblyNames": ["D39V"]
+}

test/testData/test4/j.json

@@ -1 +1,16 @@
-{"gmg20150304_scaffold_7313":{"exact":[["GmG20150304_scaffold_7313",1000,"GmG20150304_scaffold_7313",null,0,1000,null]],"prefix":[]}}
+{
+  "gmg20150304_scaffold_7313": {
+    "exact": [
+      [
+        "GmG20150304_scaffold_7313",
+        1000,
+        "GmG20150304_scaffold_7313",
+        null,
+        0,
+        1000,
+        null
+      ]
+    ],
+    "prefix": []
+  }
+}

tsconfig.json

@@ -1,12 +1,7 @@
 {
   "compilerOptions": {
     "moduleResolution": "node",
-    "lib": [
-      "es2017",
-      "es7",
-      "es6",
-      "dom"
-    ],
+    "lib": ["es2017", "es7", "es6", "dom"],
     "declaration": true,
     "outDir": "dist",
     "strict": true,
@@ -15,7 +10,5 @@
     "rewriteRelativeImportExtensions": true,
     "esModuleInterop": true
   },
-  "include": [
-    "src"
-  ]
+  "include": ["src"]
 }