Vendor the seek-bzip library with modifications to avoid Buffer usage (…

…#153)

eslint.config.mjs

@@ -12,6 +12,7 @@ export default tseslint.config(
       '*.mjs',
       'example/*',
       'src/htscodecs',
+      'src/seek-bzip',
       'coverage',
     ],
   },

package.json

@@ -45,7 +45,6 @@
     "md5": "^2.2.1",
     "pako": "^1.0.4",
     "quick-lru": "^4.0.1",
-    "seek-bzip": "^2.0.0",
     "xz-decompress": "^0.2.1"
   },
   "devDependencies": {

src/cramFile/file.ts

@@ -1,18 +1,13 @@
-// 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'
 import * as htscodecs from '../htscodecs'
 import { open } from '../io'
 import ransuncompress from '../rans'
 import { parseHeaderText } from '../sam'
+import { decode } from '../seek-bzip'
 import { unzip } from '../unzip'
 import CramContainer from './container'
 import CramRecord from './record'
@@ -293,7 +288,7 @@ export default class CramFile {
       }
       return ret
     } else if (compressionMethod === 'bzip2') {
-      return Bunzip.decode(inputBuffer)
+      return decode(inputBuffer)
     } else if (compressionMethod === 'lzma') {
       const decompressedResponse = new Response(
         new XzReadableStream(bufferToStream(inputBuffer)),

src/htscodecs/arith_gen.ts

@@ -34,7 +34,7 @@
  * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-import Bunzip from 'seek-bzip'
+import { decode } from '../seek-bzip'
 
 import RangeCoder from './arith_sh'
 import ByteModel from './byte_model'
@@ -154,7 +154,7 @@ export default class RangeCoderGen {
   // ----------------------------------------------------------------------
   // External codec
   decodeExt(stream, n_out) {
-    return Bunzip.decode(stream.buf.slice(stream.pos))
+    return decode(stream.buf.slice(stream.pos))
   }
 
   // ----------------------------------------------------------------------

src/seek-bzip/README.md

@@ -0,0 +1,6 @@
+## seek-bzip
+
+Vendored copy of seek-bzip, with code modifications to remove Buffer usage by
+Colin Diesh (c) 2025
+
+Original LICENSE MIT https://github.com/cscott/seek-bzip/blob/master/LICENSE

src/seek-bzip/bitreader.ts

@@ -0,0 +1,113 @@
+/*
+node-bzip - a pure-javascript Node.JS module for decoding bzip2 data
+
+Copyright (C) 2012 Eli Skeggs
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+Adapted from bzip2.js, copyright 2011 antimatter15 (antimatter15@gmail.com).
+
+Based on micro-bunzip by Rob Landley (rob@landley.net).
+
+Based on bzip2 decompression code by Julian R Seward (jseward@acm.org),
+which also acknowledges contributions by Mike Burrows, David Wheeler,
+Peter Fenwick, Alistair Moffat, Radford Neal, Ian H. Witten,
+Robert Sedgewick, and Jon L. Bentley.
+*/
+
+import { toHex } from './toHex'
+
+const BITMASK = [0x00, 0x01, 0x03, 0x07, 0x0f, 0x1f, 0x3f, 0x7f, 0xff]
+
+interface Stream {
+  readByte(): number
+  seek(pos: number): void
+}
+
+export default class BitReader {
+  private stream: Stream
+  private bitOffset: number
+  private curByte: number
+  private hasByte: boolean
+
+  constructor(stream: Stream) {
+    this.stream = stream
+    this.bitOffset = 0
+    this.curByte = 0
+    this.hasByte = false
+  }
+
+  private _ensureByte(): void {
+    if (!this.hasByte) {
+      this.curByte = this.stream.readByte()
+      this.hasByte = true
+    }
+  }
+
+  /**
+   * Reads bits from the buffer
+   * @param bits Number of bits to read
+   */
+  read(bits: number): number {
+    let result = 0
+    while (bits > 0) {
+      this._ensureByte()
+      const remaining = 8 - this.bitOffset
+      // if we're in a byte
+      if (bits >= remaining) {
+        result <<= remaining
+        result |= BITMASK[remaining]! & this.curByte
+        this.hasByte = false
+        this.bitOffset = 0
+        bits -= remaining
+      } else {
+        result <<= bits
+        const shift = remaining - bits
+        result |= (this.curByte & (BITMASK[bits]! << shift)) >> shift
+        this.bitOffset += bits
+        bits = 0
+      }
+    }
+    return result
+  }
+
+  /**
+   * Seek to an arbitrary point in the buffer (expressed in bits)
+   * @param pos Position in bits
+   */
+  seek(pos: number): void {
+    const n_bit = pos % 8
+    const n_byte = (pos - n_bit) / 8
+    this.bitOffset = n_bit
+    this.stream.seek(n_byte)
+    this.hasByte = false
+  }
+
+  /**
+   * Reads 6 bytes worth of data using the read method
+   */
+  pi(): string {
+    const buf = new Uint8Array(6)
+    for (let i = 0; i < buf.length; i++) {
+      buf[i] = this.read(8)
+    }
+    return toHex(buf)
+  }
+}

src/seek-bzip/crc32.ts

@@ -0,0 +1,116 @@
+// @ts-nocheck
+
+/* CRC32, used in Bzip2 implementation.
+ * This is a port of CRC32.java from the jbzip2 implementation at
+ *   https://code.google.com/p/jbzip2
+ * which is:
+ *   Copyright (c) 2011 Matthew Francis
+ *
+ *   Permission is hereby granted, free of charge, to any person
+ *   obtaining a copy of this software and associated documentation
+ *   files (the "Software"), to deal in the Software without
+ *   restriction, including without limitation the rights to use,
+ *   copy, modify, merge, publish, distribute, sublicense, and/or sell
+ *   copies of the Software, and to permit persons to whom the
+ *   Software is furnished to do so, subject to the following
+ *   conditions:
+ *
+ *   The above copyright notice and this permission notice shall be
+ *   included in all copies or substantial portions of the Software.
+ *
+ *   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ *   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ *   OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ *   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ *   HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ *   WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ *   FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ *   OTHER DEALINGS IN THE SOFTWARE.
+ * This JavaScript implementation is:
+ *   Copyright (c) 2013 C. Scott Ananian
+ * with the same licensing terms as Matthew Francis' original implementation.
+ */
+module.exports = (function () {
+  /**
+   * A static CRC lookup table
+   */
+  const crc32Lookup = new Uint32Array([
+    0x00000000, 0x04c11db7, 0x09823b6e, 0x0d4326d9, 0x130476dc, 0x17c56b6b,
+    0x1a864db2, 0x1e475005, 0x2608edb8, 0x22c9f00f, 0x2f8ad6d6, 0x2b4bcb61,
+    0x350c9b64, 0x31cd86d3, 0x3c8ea00a, 0x384fbdbd, 0x4c11db70, 0x48d0c6c7,
+    0x4593e01e, 0x4152fda9, 0x5f15adac, 0x5bd4b01b, 0x569796c2, 0x52568b75,
+    0x6a1936c8, 0x6ed82b7f, 0x639b0da6, 0x675a1011, 0x791d4014, 0x7ddc5da3,
+    0x709f7b7a, 0x745e66cd, 0x9823b6e0, 0x9ce2ab57, 0x91a18d8e, 0x95609039,
+    0x8b27c03c, 0x8fe6dd8b, 0x82a5fb52, 0x8664e6e5, 0xbe2b5b58, 0xbaea46ef,
+    0xb7a96036, 0xb3687d81, 0xad2f2d84, 0xa9ee3033, 0xa4ad16ea, 0xa06c0b5d,
+    0xd4326d90, 0xd0f37027, 0xddb056fe, 0xd9714b49, 0xc7361b4c, 0xc3f706fb,
+    0xceb42022, 0xca753d95, 0xf23a8028, 0xf6fb9d9f, 0xfbb8bb46, 0xff79a6f1,
+    0xe13ef6f4, 0xe5ffeb43, 0xe8bccd9a, 0xec7dd02d, 0x34867077, 0x30476dc0,
+    0x3d044b19, 0x39c556ae, 0x278206ab, 0x23431b1c, 0x2e003dc5, 0x2ac12072,
+    0x128e9dcf, 0x164f8078, 0x1b0ca6a1, 0x1fcdbb16, 0x018aeb13, 0x054bf6a4,
+    0x0808d07d, 0x0cc9cdca, 0x7897ab07, 0x7c56b6b0, 0x71159069, 0x75d48dde,
+    0x6b93dddb, 0x6f52c06c, 0x6211e6b5, 0x66d0fb02, 0x5e9f46bf, 0x5a5e5b08,
+    0x571d7dd1, 0x53dc6066, 0x4d9b3063, 0x495a2dd4, 0x44190b0d, 0x40d816ba,
+    0xaca5c697, 0xa864db20, 0xa527fdf9, 0xa1e6e04e, 0xbfa1b04b, 0xbb60adfc,
+    0xb6238b25, 0xb2e29692, 0x8aad2b2f, 0x8e6c3698, 0x832f1041, 0x87ee0df6,
+    0x99a95df3, 0x9d684044, 0x902b669d, 0x94ea7b2a, 0xe0b41de7, 0xe4750050,
+    0xe9362689, 0xedf73b3e, 0xf3b06b3b, 0xf771768c, 0xfa325055, 0xfef34de2,
+    0xc6bcf05f, 0xc27dede8, 0xcf3ecb31, 0xcbffd686, 0xd5b88683, 0xd1799b34,
+    0xdc3abded, 0xd8fba05a, 0x690ce0ee, 0x6dcdfd59, 0x608edb80, 0x644fc637,
+    0x7a089632, 0x7ec98b85, 0x738aad5c, 0x774bb0eb, 0x4f040d56, 0x4bc510e1,
+    0x46863638, 0x42472b8f, 0x5c007b8a, 0x58c1663d, 0x558240e4, 0x51435d53,
+    0x251d3b9e, 0x21dc2629, 0x2c9f00f0, 0x285e1d47, 0x36194d42, 0x32d850f5,
+    0x3f9b762c, 0x3b5a6b9b, 0x0315d626, 0x07d4cb91, 0x0a97ed48, 0x0e56f0ff,
+    0x1011a0fa, 0x14d0bd4d, 0x19939b94, 0x1d528623, 0xf12f560e, 0xf5ee4bb9,
+    0xf8ad6d60, 0xfc6c70d7, 0xe22b20d2, 0xe6ea3d65, 0xeba91bbc, 0xef68060b,
+    0xd727bbb6, 0xd3e6a601, 0xdea580d8, 0xda649d6f, 0xc423cd6a, 0xc0e2d0dd,
+    0xcda1f604, 0xc960ebb3, 0xbd3e8d7e, 0xb9ff90c9, 0xb4bcb610, 0xb07daba7,
+    0xae3afba2, 0xaafbe615, 0xa7b8c0cc, 0xa379dd7b, 0x9b3660c6, 0x9ff77d71,
+    0x92b45ba8, 0x9675461f, 0x8832161a, 0x8cf30bad, 0x81b02d74, 0x857130c3,
+    0x5d8a9099, 0x594b8d2e, 0x5408abf7, 0x50c9b640, 0x4e8ee645, 0x4a4ffbf2,
+    0x470cdd2b, 0x43cdc09c, 0x7b827d21, 0x7f436096, 0x7200464f, 0x76c15bf8,
+    0x68860bfd, 0x6c47164a, 0x61043093, 0x65c52d24, 0x119b4be9, 0x155a565e,
+    0x18197087, 0x1cd86d30, 0x029f3d35, 0x065e2082, 0x0b1d065b, 0x0fdc1bec,
+    0x3793a651, 0x3352bbe6, 0x3e119d3f, 0x3ad08088, 0x2497d08d, 0x2056cd3a,
+    0x2d15ebe3, 0x29d4f654, 0xc5a92679, 0xc1683bce, 0xcc2b1d17, 0xc8ea00a0,
+    0xd6ad50a5, 0xd26c4d12, 0xdf2f6bcb, 0xdbee767c, 0xe3a1cbc1, 0xe760d676,
+    0xea23f0af, 0xeee2ed18, 0xf0a5bd1d, 0xf464a0aa, 0xf9278673, 0xfde69bc4,
+    0x89b8fd09, 0x8d79e0be, 0x803ac667, 0x84fbdbd0, 0x9abc8bd5, 0x9e7d9662,
+    0x933eb0bb, 0x97ffad0c, 0xafb010b1, 0xab710d06, 0xa6322bdf, 0xa2f33668,
+    0xbcb4666d, 0xb8757bda, 0xb5365d03, 0xb1f740b4,
+  ])
+
+  const CRC32 = function () {
+    /**
+     * The current CRC
+     */
+    let crc = 0xffffffff
+
+    /**
+     * @return The current CRC
+     */
+    this.getCRC = function () {
+      return ~crc >>> 0 // return an unsigned value
+    }
+
+    /**
+     * Update the CRC with a single byte
+     * @param value The value to update the CRC with
+     */
+    this.updateCRC = function (value) {
+      crc = (crc << 8) ^ crc32Lookup[((crc >>> 24) ^ value) & 0xff]
+    }
+
+    /**
+     * Update the CRC with a sequence of identical bytes
+     * @param value The value to update the CRC with
+     * @param count The number of bytes
+     */
+    this.updateCRCRun = function (value, count) {
+      while (count-- > 0) {
+        crc = (crc << 8) ^ crc32Lookup[((crc >>> 24) ^ value) & 0xff]
+      }
+    }
+  }
+  return CRC32
+})()