@gmod/cram 4.0.6 → 4.0.8

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/cram",
-  "version": "4.0.6",
+  "version": "4.0.8",
   "description": "read CRAM files with pure Javascript",
   "license": "MIT",
   "repository": "GMOD/cram-js",
@@ -40,12 +40,16 @@
     "biojs"
   ],
   "dependencies": {
+    "@foxglove/wasm-bz2": "^0.1.1",
+    "bz2": "^1.0.1",
     "bzip2": "^0.1.1",
+    "bzip2-wasm": "^1.0.1",
     "crc": "^4.3.2",
     "generic-filehandle2": "^1.0.0",
     "md5": "^2.2.1",
     "pako": "^1.0.4",
     "quick-lru": "^4.0.1",
+    "seek-bzip": "^2.0.0",
     "xz-decompress": "^0.2.1"
   },
   "devDependencies": {
@@ -54,7 +58,7 @@
     "@types/pako": "^1.0.3",
     "@typescript-eslint/eslint-plugin": "^8.0.0",
     "@typescript-eslint/parser": "^8.0.0",
-    "@vitest/coverage-v8": "^2.0.5",
+    "@vitest/coverage-v8": "^3.0.1",
     "buffer": "^6.0.3",
     "documentation": "^14.0.3",
     "eslint": "^9.9.0",
@@ -65,9 +69,9 @@
     "rimraf": "^6.0.1",
     "typescript": "^5.7.0",
     "typescript-eslint": "^8.0.1",
-    "vitest": "^2.0.5",
+    "vitest": "^3.0.1",
     "webpack": "^5.90.3",
-    "webpack-cli": "^5.0.1"
+    "webpack-cli": "^6.0.1"
   },
   "publishConfig": {
     "access": "public"

package/src/cramFile/declare.d.ts

@@ -1 +1 @@
-declare module 'bzip2'
+declare module 'seek-bzip'

package/src/cramFile/file.ts

@@ -1,6 +1,11 @@
-import bzip2 from 'bzip2'
+// import bzip2 from 'bzip2'
+// import BZip2 from 'bzip2-wasm'
+// import { decompress } from 'bz2'
+
+
 import crc32 from 'crc/calculators/crc32'
 import QuickLRU from 'quick-lru'
+import Bunzip from 'seek-bzip'
 import { XzReadableStream } from 'xz-decompress'
 
 import { CramMalformedError, CramUnimplementedError } from '../errors'
@@ -9,7 +14,6 @@ import { open } from '../io'
 import ransuncompress from '../rans'
 import { parseHeaderText } from '../sam'
 import { unzip } from '../unzip'
-import { concatUint8Array } from '../util'
 import CramContainer from './container'
 import CramRecord from './record'
 import {
@@ -276,26 +280,20 @@ export default class CramFile {
     return data
   }
 
-  async _uncompress(
+  async _uncompressPre(
     compressionMethod: CompressionMethod,
     inputBuffer: Uint8Array,
     uncompressedSize: number,
   ) {
+    // console.log({ compressionMethod })
     if (compressionMethod === 'gzip') {
-      return unzip(inputBuffer)
+      const ret = unzip(inputBuffer)
+      if (ret[0] === 24) {
+        // console.log(ret.slice(0, 500).join(','))
+      }
+      return ret
     } else if (compressionMethod === 'bzip2') {
-      const bits = bzip2.array(inputBuffer)
-      let size = bzip2.header(bits)
-      let chunk: Uint8Array | -1
-      const chunks = []
-      do {
-        chunk = bzip2.decompress(bits, size)
-        if (chunk !== -1) {
-          chunks.push(chunk)
-          size -= chunk.length
-        }
-      } while (chunk !== -1)
-      return concatUint8Array(chunks)
+      return Bunzip.decode(inputBuffer)
     } else if (compressionMethod === 'lzma') {
       const decompressedResponse = new Response(
         new XzReadableStream(bufferToStream(inputBuffer)),
@@ -322,6 +320,24 @@ export default class CramFile {
     }
   }
 
+  async _uncompress(
+    compressionMethod: CompressionMethod,
+    inputBuffer: Uint8Array,
+    uncompressedSize: number,
+  ) {
+    const buf = await this._uncompressPre(
+      compressionMethod,
+      inputBuffer,
+      uncompressedSize,
+    )
+    if (buf.length !== uncompressedSize) {
+      const ret = new Uint8Array(uncompressedSize)
+      ret.set(buf, 0)
+      return ret
+    }
+    return buf
+  }
+
   async readBlock(position: number) {
     const { majorVersion } = await this.getDefinition()
     const sectionParsers = getSectionParsers(majorVersion)

package/src/cramFile/slice/decodeRecord.ts

@@ -371,6 +371,7 @@ export default function decodeRecord(
 
     // mapping quality
     mappingQuality = decodeDataSeries('MQ')!
+
     if (CramFlagsDecoder.isPreservingQualityScores(cramFlags)) {
       qualityScores = new Array(readLength)
       for (let i = 0; i < qualityScores.length; i++) {

package/src/htscodecs/arith_gen.ts

@@ -34,7 +34,7 @@
  * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-import bzip2 from 'bzip2'
+import Bunzip from 'seek-bzip'
 
 import RangeCoder from './arith_sh'
 import ByteModel from './byte_model'
@@ -154,18 +154,7 @@ export default class RangeCoderGen {
   // ----------------------------------------------------------------------
   // External codec
   decodeExt(stream, n_out) {
-    const bits = bzip2.array(stream.buf.slice(stream.pos))
-    let size = bzip2.header(bits)
-    let chunk
-    const chunks = []
-    do {
-      chunk = bzip2.decompress(bits, size)
-      if (chunk !== -1) {
-        chunks.push(chunk)
-        size -= chunk.length
-      }
-    } while (chunk !== -1)
-    return concatUint8Array(chunks)
+    return Bunzip.decode(stream.buf.slice(stream.pos))
   }
 
   // ----------------------------------------------------------------------