@gmod/bam 7.1.19 → 7.1.21

package/package.json

@@ -1,27 +1,23 @@
 {
   "name": "@gmod/bam",
-  "version": "7.1.19",
+  "version": "7.1.21",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
-  "repository": "GMOD/bam-js",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/GMOD/bam-js.git"
+  },
   "type": "module",
-  "types": "./dist/index.d.ts",
+  "main": "dist/index.js",
   "exports": {
-    "import": {
-      "import": "./esm/index.js"
-    },
-    "require": {
-      "require": "./dist/index.js"
-    }
+    "import": "./esm/index.js",
+    "require": "./dist/index.js"
   },
   "author": {
     "name": "Colin Diesh",
     "email": "colin.diesh@gmail.com",
     "url": "https://github.com/cmdcolin"
   },
-  "engines": {
-    "node": ">=6"
-  },
   "files": [
     "dist",
     "esm",
@@ -29,19 +25,19 @@
   ],
   "scripts": {
     "test": "vitest",
-    "benchonly": "vitest bench",
-    "bench": "./scripts/build-both-branches.sh \"$BRANCH1\" \"$BRANCH2\" && vitest bench",
-    "lint": "eslint --report-unused-disable-directives --max-warnings 0",
     "clean": "rimraf dist esm",
     "format": "prettier --write .",
+    "lint": "eslint --report-unused-disable-directives --max-warnings 0",
+    "prebuild": "pnpm clean",
     "build:esm": "tsc --outDir esm",
-    "build:es5": "tsc --module commonjs --outDir dist",
-    "build": "yarn build:esm && yarn build:es5",
-    "prebuild": "yarn clean",
+    "build:es5": "tsc --module commonjs --moduleResolution bundler --outDir dist",
     "postbuild:es5": "echo '{\"type\": \"commonjs\"}' > dist/package.json",
-    "preversion": "yarn lint && yarn test --run && yarn build",
-    "version": "standard-changelog && git add CHANGELOG.md",
-    "postversion": "git push --follow-tags"
+    "preversion": "pnpm lint && pnpm test --run && pnpm build",
+    "postversion": "git push --follow-tags",
+    "build": "pnpm build:esm && pnpm build:es5",
+    "benchonly": "vitest bench",
+    "bench": "./scripts/build-both-branches.sh \"$BRANCH1\" \"$BRANCH2\" && vitest bench",
+    "version": "standard-changelog && git add CHANGELOG.md"
   },
   "keywords": [
     "bionode",
@@ -50,24 +46,24 @@
     "genomics"
   ],
   "dependencies": {
-    "@gmod/bgzf-filehandle": "^6.0.12",
+    "@gmod/bgzf-filehandle": "^6.0.18",
     "@jbrowse/quick-lru": "^7.3.5",
     "crc": "^4.3.2",
-    "generic-filehandle2": "^2.0.18"
+    "generic-filehandle2": "^2.1.4"
   },
   "devDependencies": {
     "@eslint/js": "^10.0.1",
-    "@types/node": "^25.3.3",
-    "@vitest/coverage-v8": "^4.0.18",
-    "eslint": "^10.0.2",
-    "eslint-plugin-import": "^2.31.0",
-    "eslint-plugin-unicorn": "^63.0.0",
-    "prettier": "^3.8.1",
+    "@types/node": "^25.6.0",
+    "@vitest/coverage-v8": "^4.1.5",
+    "eslint": "^10.2.1",
+    "eslint-plugin-import-x": "^4.16.2",
+    "eslint-plugin-unicorn": "^64.0.0",
+    "prettier": "^3.8.3",
     "rimraf": "^6.1.3",
     "standard-changelog": "^7.0.1",
-    "typescript": "^5.0.4",
-    "typescript-eslint": "^8.56.1",
-    "vitest": "^4.0.18"
+    "typescript": "^6.0.3",
+    "typescript-eslint": "^8.59.0",
+    "vitest": "^4.1.5"
   },
   "publishConfig": {
     "access": "public"

package/src/bai.ts

@@ -2,13 +2,11 @@ import QuickLRU from '@jbrowse/quick-lru'
 
 import Chunk from './chunk.ts'
 import IndexFile from './indexFile.ts'
-import {
-  BaseOpts,
-  findFirstData,
-  optimizeChunks,
-  parsePseudoBin,
-} from './util.ts'
-import { VirtualOffset, fromBytes } from './virtualOffset.ts'
+import { findFirstData, optimizeChunks, parsePseudoBin } from './util.ts'
+import { fromBytes } from './virtualOffset.ts'
+
+import type { BaseOpts } from './util.ts'
+import type { VirtualOffset } from './virtualOffset.ts'
 
 const BAI_MAGIC = 21578050 // BAI\1
 

package/src/bamFile.ts

@@ -4,7 +4,6 @@ import crc32 from 'crc/calculators/crc32'
 import { LocalFile, RemoteFile } from 'generic-filehandle2'
 
 import BAI from './bai.ts'
-import Chunk from './chunk.ts'
 import CSI from './csi.ts'
 import NullFilehandle from './nullFilehandle.ts'
 import BAMFeature from './record.ts'
@@ -16,6 +15,7 @@ import {
   makeOpts,
 } from './util.ts'
 
+import type Chunk from './chunk.ts'
 import type { Bytes } from './record.ts'
 import type { BamOpts, BaseOpts, FilterBy } from './util.ts'
 import type { GenericFilehandle } from 'generic-filehandle2'
@@ -35,6 +35,7 @@ export interface BamRecordLike {
 export type BamRecordClass<T extends BamRecordLike = BAMFeature> = new (args: {
   bytes: Bytes
   fileOffset: number
+  dataView: DataView
 }) => T
 
 export const BAM_MAGIC = 21840194
@@ -501,6 +502,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
               chunk.minv.dataPosition +
               1
             : crc32(ba.subarray(blockStart, blockEnd)) >>> 0,
+          dataView,
         })
 
         sink.push(feature)

package/src/chunk.ts

@@ -1,4 +1,4 @@
-import { Offset } from './virtualOffset.ts'
+import type { Offset } from './virtualOffset.ts'
 
 // little class representing a chunk in the index
 export default class Chunk {

package/src/htsget.ts

@@ -2,11 +2,12 @@ import { unzip } from '@gmod/bgzf-filehandle'
 
 import BamFile, { BAM_MAGIC } from './bamFile.ts'
 import Chunk from './chunk.ts'
-import BamRecord from './record.ts'
 import { parseHeaderText } from './sam.ts'
 import { concatUint8Array } from './util.ts'
+import { VirtualOffset } from './virtualOffset.ts'
 
 import type { BamRecordClass, BamRecordLike } from './bamFile.ts'
+import type BamRecord from './record.ts'
 import type { BamOpts, BaseOpts } from './util.ts'
 
 interface HtsgetChunk {
@@ -14,7 +15,7 @@ interface HtsgetChunk {
   headers?: Record<string, string>
 }
 
-async function concat(arr: HtsgetChunk[], opts?: Record<string, any>) {
+async function concat(arr: HtsgetChunk[], opts?: RequestInit) {
   const res = await Promise.all(
     arr.map(async chunk => {
       const { url, headers } = chunk
@@ -29,12 +30,10 @@ async function concat(arr: HtsgetChunk[], opts?: Record<string, any>) {
         return new Uint8Array(ret)
       } else {
         // remove referer header, it is not even allowed to be specified
-        // @ts-expect-error
-
-        const { referer, ...rest } = headers
+        const { referer: _referer, ...rest } = headers ?? {}
         const res = await fetch(url, {
           ...opts,
-          headers: { ...opts?.headers, ...rest },
+          headers: rest,
         })
         if (!res.ok) {
           throw new Error(
@@ -85,12 +84,17 @@ export default class HtsgetFile<
       )
     }
     const data = await result.json()
-    const uncba = await concat(data.htsget.urls.slice(1), opts)
-
-    const allRecords = await this.readBamFeatures(uncba, [], [], {
-      minv: { dataPosition: 0, blockPosition: 0 },
-      maxv: { dataPosition: 0, blockPosition: 0 },
-    } as Chunk)
+    const uncba = await concat(data.htsget.urls.slice(1), {
+      signal: opts?.signal,
+    })
+
+    const zero = new VirtualOffset(0, 0)
+    const allRecords = await this.readBamFeatures(
+      uncba,
+      [],
+      [],
+      new Chunk(zero, zero, 0),
+    )
 
     const records: T[] = []
     for (let i = 0, l = allRecords.length; i < l; i++) {
@@ -115,7 +119,7 @@ export default class HtsgetFile<
       )
     }
     const data = await result.json()
-    const uncba = await concat(data.htsget.urls, opts)
+    const uncba = await concat(data.htsget.urls, { signal: opts.signal })
     const dataView = new DataView(uncba.buffer)
 
     if (dataView.getInt32(0, true) !== BAM_MAGIC) {
@@ -123,7 +127,7 @@ export default class HtsgetFile<
     }
     const headLen = dataView.getInt32(4, true)
 
-    const decoder = new TextDecoder('utf8')
+    const decoder = new TextDecoder()
     const headerText = decoder.decode(uncba.subarray(8, 8 + headLen))
     const samHeader = parseHeaderText(headerText)
 

package/src/indexFile.ts

@@ -1,6 +1,7 @@
-import Chunk from './chunk.ts'
-import { BaseOpts, optimizeChunks } from './util.ts'
+import { optimizeChunks } from './util.ts'
 
+import type Chunk from './chunk.ts'
+import type { BaseOpts } from './util.ts'
 import type { GenericFilehandle } from 'generic-filehandle2'
 
 export interface Region {

package/src/nullFilehandle.ts

@@ -1,16 +1,16 @@
 export default class NullFilehandle {
-  public read(): Promise<any> {
+  public read(): Promise<never> {
     throw new Error('never called')
   }
-  public stat(): Promise<any> {
+  public stat(): Promise<never> {
     throw new Error('never called')
   }
 
-  public readFile(): Promise<any> {
+  public readFile(): Promise<never> {
     throw new Error('never called')
   }
 
-  public close(): Promise<any> {
+  public close(): Promise<never> {
     throw new Error('never called')
   }
 }

package/src/nullIndex.ts

@@ -1,18 +1,18 @@
 import IndexFile from './indexFile.ts'
 
 export default class NullIndex extends IndexFile {
-  public lineCount(): Promise<any> {
+  public lineCount(): Promise<never> {
     throw new Error('never called')
   }
-  protected _parse(): Promise<any> {
+  protected _parse(): Promise<never> {
     throw new Error('never called')
   }
 
-  public async indexCov(): Promise<any> {
+  public async indexCov(): Promise<never> {
     throw new Error('never called')
   }
 
-  public blocksForRange(): Promise<any> {
+  public blocksForRange(): Promise<never> {
     throw new Error('never called')
   }
 }