Misc

Author: cmdcolin

.prettierrc

@@ -2,5 +2,6 @@
   "semi": false,
   "trailingComma": "all",
   "singleQuote": true,
-  "arrowParens": "avoid"
+  "arrowParens": "avoid",
+  "proseWrap": "always"
 }

CHANGELOG.md

@@ -16,7 +16,8 @@
 
 # 0.1.1
 
-- Adds refName to the feature ID to avoid collisions for code that cares about unique ID
+- Adds refName to the feature ID to avoid collisions for code that cares about
+  unique ID
 
 # 0.1.0
 

README.md

@@ -49,18 +49,26 @@ import NCList from '@gmod/nclist'
 
 ### NCListStore
 
-Sequence feature store using nested containment
-lists held in JSON files that are lazily read.
+Sequence feature store using nested containment lists held in JSON files that
+are lazily read.
 
 #### Parameters
 
-- `args` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** constructor args
-
-  - `args.baseUrl` **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)** base URL for resolving relative URLs
-  - `args.urlTemplate` **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)** Template string for
-    the root file of each reference sequence. The reference sequence
-    name will be interpolated into this string where `{refseq}` appears.
-  - `args.readFile` **[function](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Statements/function)** function to use for reading remote from URLs.
+- `args`
+  **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**
+  constructor args
+
+  - `args.baseUrl`
+    **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)**
+    base URL for resolving relative URLs
+  - `args.urlTemplate`
+    **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)**
+    Template string for the root file of each reference sequence. The reference
+    sequence name will be interpolated into this string where `{refseq}`
+    appears.
+  - `args.readFile`
+    **[function](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Statements/function)**
+    function to use for reading remote from URLs.
   - `args.cacheSize` (optional, default `10`)
 
 #### getRegionFeatureDensities
@@ -69,16 +77,28 @@ fetch binned counts of feature coverage in the given region.
 
 ##### Parameters
 
-- `query` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** 
-
-  - `query.refName` **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)** reference sequence name
-  - `query.start` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** region start
-  - `query.end` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** region end
-  - `query.numBins` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** number of bins desired in the feature counts
-  - `query.basesPerBin` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** number of bp desired in each feature counting bin
-
-Returns **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** as:
-`{ bins: hist, stats: statEntry }`
+- `query`
+  **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** 
+
+  - `query.refName`
+    **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)**
+    reference sequence name
+  - `query.start`
+    **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
+    region start
+  - `query.end`
+    **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
+    region end
+  - `query.numBins`
+    **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
+    number of bins desired in the feature counts
+  - `query.basesPerBin`
+    **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
+    number of bp desired in each feature counting bin
+
+Returns
+**[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**
+as: `{ bins: hist, stats: statEntry }`
 
 #### getFeatures
 
@@ -87,8 +107,15 @@ yielding feature objects.
 
 ##### Parameters
 
-- `args` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** 
-
-  - `args.refName` **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)** reference sequence name
-  - `args.start` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** start of region. 0-based half-open.
-  - `args.end` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** end of region. 0-based half-open.
+- `args`
+  **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** 
+
+  - `args.refName`
+    **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)**
+    reference sequence name
+  - `args.start`
+    **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
+    start of region. 0-based half-open.
+  - `args.end`
+    **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
+    end of region. 0-based half-open.

index.js

@@ -30,15 +30,16 @@
     "docs": "documentation readme --shallow src/feature_store.ts --section API",
     "clean": "rimraf dist esm",
     "prebuild": "yarn docs && yarn clean && yarn lint",
-    "build:esm": "tsc --target es2018 --outDir esm",
-    "build:es5": "tsc --target es2015 --module commonjs --outDir dist",
+    "build:esm": "tsc --outDir esm",
+    "build:es5": "tsc --module commonjs --outDir dist",
     "build": "yarn build:esm && yarn build:es5",
     "prepublishOnly": "yarn test --run && yarn build",
     "postversion": "git push --follow-tags"
   },
   "devDependencies": {
     "@typescript-eslint/eslint-plugin": "^8.18.0",
     "@typescript-eslint/parser": "^8.18.0",
+    "@vitest/coverage-v8": "^2.1.8",
     "cross-fetch": "^3.0.2",
     "documentation": "^14.0.1",
     "eslint": "^9.5.0",

package.json

@@ -90,6 +90,7 @@ export default class NCListStore {
 
     const { histograms } = trackInfo
     if (histograms?.meta) {
+      // eslint-disable-next-line @typescript-eslint/prefer-for-of
       for (let i = 0; i < histograms.meta.length; i += 1) {
         histograms.meta[i].lazyArray = new LazyArray(
           { ...histograms.meta[i].arrayParams, readFile: this.readFile },
@@ -159,16 +160,19 @@ export default class NCListStore {
     const statEntry = stats.find(entry => entry.basesPerBin >= basesPerBin)
 
     // The histogramMeta array describes multiple levels of histogram detail,
-    // going from the finest (smallest number of bases per bin) to the
-    // coarsest (largest number of bases per bin).
-    // We want to use coarsest histogramMeta that's at least as fine as the
-    // one we're currently rendering.
-    // TODO: take into account that the histogramMeta chosen here might not
-    // fit neatly into the current histogram (e.g., if the current histogram
-    // is at 50,000 bases/bin, and we have server histograms at 20,000
-    // and 2,000 bases/bin, then we should choose the 2,000 histogramMeta
-    // rather than the 20,000)
+    // going from the finest (smallest number of bases per bin) to the coarsest
+    // (largest number of bases per bin).
+    //
+    // We want to use coarsest histogramMeta that's at least as fine as the one
+    // we're currently rendering.
+    //
+    // TODO: take into account that the histogramMeta chosen here might not fit
+    // neatly into the current histogram (e.g., if the current histogram is at
+    // 50,000 bases/bin, and we have server histograms at 20,000 and 2,000
+    // bases/bin, then we should choose the 2,000 histogramMeta rather than the
+    // 20,000)
     let histogramMeta = data._histograms.meta[0]
+    // eslint-disable-next-line @typescript-eslint/prefer-for-of
     for (let i = 0; i < data._histograms.meta.length; i += 1) {
       if (basesPerBin >= data._histograms.meta[i].basesPerBin) {
         histogramMeta = data._histograms.meta[i]

src/feature_store.ts

@@ -54,8 +54,8 @@ export default class LazyArray {
     for (let chunk = firstChunk; chunk <= lastChunk; chunk += 1) {
       chunkreadFiles.push(this.chunkCache.get(chunk, chunk))
     }
-    for (let i = 0; i < chunkreadFiles.length; i += 1) {
-      const [chunkNumber, chunkData] = await chunkreadFiles[i]
+    for (const elt of chunkreadFiles) {
+      const [chunkNumber, chunkData] = await elt
       yield* this.filterChunkData(start, end, chunkNumber, chunkData)
     }
   }

src/lazy_array.ts

@@ -93,8 +93,8 @@ export default class NCList {
       }
     }
 
-    for (let i = 0; i < pendingPromises.length; i += 1) {
-      const [item, chunkNum] = await pendingPromises[i]
+    for (const p of pendingPromises) {
+      const [item, chunkNum] = await p
       if (item) {
         yield* this.iterateSublist(item, from, to, inc, searchGet, testGet, [
           ...path,

src/nclist.ts

@@ -3,10 +3,10 @@ import resolve from '@jridgewell/resolve-uri'
 
 export async function readJSON(url, readFile, options = {}) {
   const { defaultContent = {} } = options
-  let str
   try {
-    str = await readFile(url, { encoding: 'utf8' })
-    return JSON.parse(str)
+    const str = await readFile(url, { encoding: 'utf8' })
+    const decoder = new TextDecoder('utf8')
+    return JSON.parse(decoder.decode(str))
   } catch (error) {
     if (
       error.code === 'ENOENT' ||
@@ -20,8 +20,6 @@ export async function readJSON(url, readFile, options = {}) {
   }
 }
 
-export function foo() {}
-
 export function newURL(arg: string, base = '.') {
   return resolve(arg, base)
 }

src/util.ts

@@ -1,6 +1,6 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
+// Vitest Snapshot v1, https://vitest.dev/guide/snapshot.html
 
-exports[`ensembl genes read with generic-filehandle RemoteFile with http urls small feature queries 1`] = `
+exports[`ensembl genes > read with generic-filehandle2 RemoteFile with http urls small feature queries 1`] = `
 {
   "bins": [
     1,
@@ -22,7 +22,7 @@ exports[`ensembl genes read with generic-filehandle RemoteFile with http urls sm
 }
 `;
 
-exports[`ensembl genes read with generic-filehandle RemoteFile with http urls small feature queries 2`] = `
+exports[`ensembl genes > read with generic-filehandle2 RemoteFile with http urls small feature queries 2`] = `
 {
   "bins": [
     86,
@@ -1034,7 +1034,7 @@ exports[`ensembl genes read with generic-filehandle RemoteFile with http urls sm
 }
 `;
 
-exports[`ensembl genes read with generic-filehandle RemoteFile with http urls whole dataset 1`] = `
+exports[`ensembl genes > read with generic-filehandle2 RemoteFile with http urls whole dataset 1`] = `
 [
   [
     1,