Misc

CHANGELOG.md

@@ -18,7 +18,7 @@
 
 ## [1.1.17](https://github.com/GMOD/bam-js/compare/v1.1.16...v1.1.17) (2022-07-18)
 
-- Bump devDeps and generic-filehandle to 3.0.0
+- Bump devDeps and generic-filehandle2 to 3.0.0
 
 ## [1.1.16](https://github.com/GMOD/bam-js/compare/v1.1.15...v1.1.16) (2022-03-30)
 
@@ -289,7 +289,7 @@
 
 ## [1.0.18](https://github.com/GMOD/bam-js/compare/v1.0.17...v1.0.18) (2019-05-01)
 
-- Bump generic-filehandle to 1.0.9 to fix error with using native fetch (global
+- Bump generic-filehandle2 to 1.0.9 to fix error with using native fetch (global
   fetch needed to be bound)
 - Bump abortable-promise-cache to 1.0.1 version to fix error with using native
   fetch and abort signals

README.md

@@ -26,10 +26,10 @@ var records = await t.getRecordsForRange('ctgA', 0, 50000)
 ```
 
 The `bamPath` argument only works on nodejs. In the browser, you should pass
-`bamFilehandle` with a generic-filehandle e.g. `RemoteFile`
+`bamFilehandle` with a generic-filehandle2 e.g. `RemoteFile`
 
 ```typescript
-const { RemoteFile } = require('generic-filehandle')
+const { RemoteFile } = require('generic-filehandle2')
 const bam = new BamFile({
   bamFilehandle: new RemoteFile('yourfile.bam'), // or a full http url
   baiFilehandle: new RemoteFile('yourfile.bam.bai'), // or a full http url
@@ -76,7 +76,7 @@ The BAM class constructor accepts arguments
   yielding
 
 Note: filehandles implement the Filehandle interface from
-https://www.npmjs.com/package/generic-filehandle. This module offers the path
+https://www.npmjs.com/package/generic-filehandle2. This module offers the path
 and url arguments as convenience methods for supplying the LocalFile and
 RemoteFile
 
@@ -112,7 +112,7 @@ for await (const chunk of file.streamRecordsForRange(
 The `getRecordsForRange` simply wraps this process by concatenating chunks into
 an array
 
-### async getHeader(opts: {....anything to pass to generic-filehandle opts})
+### async getHeader(opts: {....anything to pass to generic-filehandle2 opts})
 
 This obtains the header from `HtsgetFile` or `BamFile`. Retrieves BAM file and
 BAI/CSI header if applicable, or API request for refnames from htsget

src/bamFile.ts

@@ -1,7 +1,7 @@
 import { Buffer } from 'buffer'
 import crc32 from 'buffer-crc32'
 import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle'
-import { LocalFile, RemoteFile, GenericFilehandle } from 'generic-filehandle'
+import { LocalFile, RemoteFile, GenericFilehandle } from 'generic-filehandle2'
 import AbortablePromiseCache from 'abortable-promise-cache'
 import QuickLRU from 'quick-lru'
 
@@ -148,23 +148,21 @@ export default class BamFile {
     let buffer
     if (ret) {
       const s = ret + blockLen
-      const res = await this.bam.read(Buffer.alloc(s), 0, s, 0, opts)
-      if (!res.bytesRead) {
-        throw new Error('Error reading header')
-      }
-      buffer = res.buffer.subarray(0, Math.min(res.bytesRead, ret))
+      buffer = await this.bam.read(s, 0, opts)
     } else {
       buffer = (await this.bam.readFile(opts)) as Buffer
     }
 
     const uncba = await unzip(buffer)
+    const dv = new DataView(uncba.buffer, uncba.byteOffset, uncba.byteLength)
 
-    if (uncba.readInt32LE(0) !== BAM_MAGIC) {
+    if (dv.getInt32(0, true) !== BAM_MAGIC) {
       throw new Error('Not a BAM file')
     }
-    const headLen = uncba.readInt32LE(4)
+    const headLen = dv.getInt32(4, true)
+    const decoder = new TextDecoder('utf8')
 
-    this.header = uncba.toString('utf8', 8, 8 + headLen)
+    this.header = decoder.decode(uncba.subarray(8, 8 + headLen))
     const { chrToIndex, indexToChr } = await this._readRefSeqs(
       headLen + 8,
       65535,
@@ -204,30 +202,21 @@ export default class BamFile {
     if (start > refSeqBytes) {
       return this._readRefSeqs(start, refSeqBytes * 2, opts)
     }
-    const size = refSeqBytes + blockLen
-    const { bytesRead, buffer } = await this.bam.read(
-      Buffer.alloc(size),
-      0,
-      refSeqBytes,
-      0,
-      opts,
-    )
-    if (!bytesRead) {
-      throw new Error('Error reading refseqs from header')
-    }
-    const uncba = await unzip(
-      buffer.subarray(0, Math.min(bytesRead, refSeqBytes)),
-    )
-    const nRef = uncba.readInt32LE(start)
+    const buffer = await this.bam.read(refSeqBytes, 0, opts)
+    const uncba = await unzip(buffer)
+    const dv = new DataView(uncba.buffer, uncba.byteOffset, uncba.byteLength)
+    const nRef = dv.getInt32(start, true)
+    const decoder = new TextDecoder('utf8')
     let p = start + 4
     const chrToIndex: { [key: string]: number } = {}
     const indexToChr: { refName: string; length: number }[] = []
     for (let i = 0; i < nRef; i += 1) {
-      const lName = uncba.readInt32LE(p)
+      const lName = dv.getInt32(p, true)
       const refName = this.renameRefSeq(
-        uncba.toString('utf8', p + 4, p + 4 + lName - 1),
+        decoder.decode(uncba.subarray(p + 4, p + 4 + lName - 1)),
       )
-      const lRef = uncba.readInt32LE(p + lName + 4)
+
+      const lRef = dv.getInt32(p + lName + 4, true)
 
       chrToIndex[refName] = i
       indexToChr.push({ refName, length: lRef })
@@ -387,22 +376,10 @@ export default class BamFile {
     return mateFeatPromises.flat()
   }
 
-  async _readRegion(position: number, size: number, opts: BaseOpts = {}) {
-    const { bytesRead, buffer } = await this.bam.read(
-      Buffer.alloc(size),
-      0,
-      size,
-      position,
-      opts,
-    )
-
-    return buffer.subarray(0, Math.min(bytesRead, size))
-  }
-
   async _readChunk({ chunk, opts }: { chunk: Chunk; opts: BaseOpts }) {
-    const buffer = await this._readRegion(
-      chunk.minv.blockPosition,
+    const buffer = await this.bam.read(
       chunk.fetchedSize(),
+      chunk.minv.blockPosition,
       opts,
     )
 
@@ -415,7 +392,7 @@ export default class BamFile {
   }
 
   async readBamFeatures(
-    ba: Buffer,
+    ba: Uint8Array,
     cpositions: number[],
     dpositions: number[],
     chunk: Chunk,
@@ -424,9 +401,10 @@ export default class BamFile {
     const sink = [] as BAMFeature[]
     let pos = 0
     let last = +Date.now()
+    const dv = new DataView(ba.buffer, ba.byteOffset, ba.byteLength)
 
-    while (blockStart + 4 < ba.length) {
-      const blockSize = ba.readInt32LE(blockStart)
+    while (blockStart + 4 < dv.byteLength) {
+      const blockSize = dv.getInt32(blockStart, true)
       const blockEnd = blockStart + 4 + blockSize - 1
 
       // increment position to the current decompressed status
@@ -470,7 +448,8 @@ export default class BamFile {
                 chunk.minv.dataPosition +
                 1
               : // must be slice, not subarray for buffer polyfill on web
-                crc32.signed(ba.slice(blockStart, blockEnd)),
+                // @ts-expect-error
+                crc32.signed(ba.subarray(blockStart, blockEnd)),
         })
 
         sink.push(feature)

src/csi.ts

@@ -37,8 +37,9 @@ export default class CSI extends IndexFile {
     return []
   }
 
-  parseAuxData(bytes: Buffer, offset: number) {
-    const formatFlags = bytes.readInt32LE(offset)
+  parseAuxData(bytes: Uint8Array, offset: number) {
+    const dv = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength)
+    const formatFlags = dv.getInt32(offset, true)
     const coordinateType =
       formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed'
     const format = (
@@ -50,14 +51,14 @@ export default class CSI extends IndexFile {
       throw new Error(`invalid Tabix preset format flags ${formatFlags}`)
     }
     const columnNumbers = {
-      ref: bytes.readInt32LE(offset + 4),
-      start: bytes.readInt32LE(offset + 8),
-      end: bytes.readInt32LE(offset + 12),
+      ref: dv.getInt32(offset + 4, true),
+      start: dv.getInt32(offset + 8, true),
+      end: dv.getInt32(offset + 12, true),
     }
-    const metaValue = bytes.readInt32LE(offset + 16)
+    const metaValue = dv.getInt32(offset + 16, true)
     const metaChar = metaValue ? String.fromCharCode(metaValue) : ''
-    const skipLines = bytes.readInt32LE(offset + 20)
-    const nameSectionLength = bytes.readInt32LE(offset + 24)
+    const skipLines = dv.getInt32(offset + 20, true)
+    const nameSectionLength = dv.getInt32(offset + 24, true)
 
     return {
       columnNumbers,
@@ -78,24 +79,25 @@ export default class CSI extends IndexFile {
   async _parse(opts: { signal?: AbortSignal }) {
     const buffer = await this.filehandle.readFile(opts)
     const bytes = await unzip(buffer)
+    const dv = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength)
 
     let csiVersion
+    const m = dv.getUint32(0, true)
     // check TBI magic numbers
-    if (bytes.readUInt32LE(0) === CSI1_MAGIC) {
+    if (m === CSI1_MAGIC) {
       csiVersion = 1
-    } else if (bytes.readUInt32LE(0) === CSI2_MAGIC) {
+    } else if (m === CSI2_MAGIC) {
       csiVersion = 2
     } else {
       throw new Error('Not a CSI file')
-      // TODO: do we need to support big-endian CSI files?
     }
 
-    this.minShift = bytes.readInt32LE(4)
-    this.depth = bytes.readInt32LE(8)
+    this.minShift = dv.getInt32(4, true)
+    this.depth = dv.getInt32(8, true)
     this.maxBinNumber = ((1 << ((this.depth + 1) * 3)) - 1) / 7
-    const auxLength = bytes.readInt32LE(12)
+    const auxLength = dv.getInt32(12, true)
     const aux = auxLength >= 30 ? this.parseAuxData(bytes, 16) : undefined
-    const refCount = bytes.readInt32LE(16 + auxLength)
+    const refCount = dv.getInt32(16 + auxLength, true)
 
     type BinIndex = { [key: string]: Chunk[] }
 
@@ -108,20 +110,20 @@ export default class CSI extends IndexFile {
     }>(refCount)
     for (let i = 0; i < refCount; i++) {
       // the binning index
-      const binCount = bytes.readInt32LE(curr)
+      const binCount = dv.getInt32(curr, true)
       curr += 4
       const binIndex: { [key: string]: Chunk[] } = {}
       let stats // < provided by parsing a pseudo-bin, if present
       for (let j = 0; j < binCount; j++) {
-        const bin = bytes.readUInt32LE(curr)
+        const bin = dv.getUint32(curr, true)
         curr += 4
         if (bin > this.maxBinNumber) {
           stats = parsePseudoBin(bytes, curr + 28)
           curr += 28 + 16
         } else {
           firstDataLine = findFirstData(firstDataLine, fromBytes(bytes, curr))
           curr += 8
-          const chunkCount = bytes.readInt32LE(curr)
+          const chunkCount = dv.getInt32(curr, true)
           curr += 4
           const chunks = new Array<Chunk>(chunkCount)
           for (let k = 0; k < chunkCount; k += 1) {

src/indexFile.ts

@@ -1,4 +1,4 @@
-import { GenericFilehandle } from 'generic-filehandle'
+import { GenericFilehandle } from 'generic-filehandle2'
 import Chunk from './chunk'
 import { BaseOpts } from './util'