@gmod/cram 3.0.6 → 4.0.0

package/esm/rans/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/rans/index.ts"],"names":[],"mappings":"AAAA,cAAc;AACd,OAAO,EAAE,kBAAkB,EAAE,MAAM,WAAW,CAAA;AAC9C,OAAO,GAAG,MAAM,OAAO,CAAA;AACvB,OAAO,GAAG,MAAM,OAAO,CAAA;AACvB,OAAO,QAAQ,MAAM,YAAY,CAAA;AACjC,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,MAAM,eAAe,CAAA;AAExD,wCAAwC;AACxC,6CAA6C;AAC7C,MAAM,SAAS,CAAC,eAAe,GAAG,CAAC,CAAA;AACnC,uCAAuC;AACvC,iEAAiE;AAEjE,eAAe;AACf,iBAAiB;AAEjB,oDAAoD;AACpD,gBAAgB;AAChB,4CAA4C;AAC5C,6DAA6D;AAC7D,0EAA0E;AAC1E,YAAY;AACZ,QAAQ;AACR,IAAI;AAEJ,gGAAgG;AAChG,kCAAkC;AAClC,+BAA+B;AAE/B,iCAAiC;AACjC,iDAAiD;AAEjD,uBAAuB;AACvB,qBAAqB;AACrB,qDAAqD;AACrD,oBAAoB;AACpB,qDAAqD;AAErD,mBAAmB;AACnB,0EAA0E;AAC1E,QAAQ;AACR,IAAI;AAEJ,oEAAoE;AACpE,+EAA+E;AAC/E,yFAAyF;AACzF,2BAA2B;AAC3B,sDAAsD;AACtD,gDAAgD;AAChD,mEAAmE;AACnE,8CAA8C;AAC9C,sBAAsB;AACtB,IAAI;AAEJ,+DAA+D;AAC/D,qEAAqE;AACrE,mDAAmD;AACnD,oDAAoD;AACpD,2DAA2D;AAC3D,wCAAwC;AAExC,gEAAgE;AAChE,gEAAgE;AAEhE,6CAA6C;AAC7C,oFAAoF;AAEpF,sBAAsB;AACtB,2EAA2E;AAE3E,mEAAmE;AACnE,oCAAoC;AACpC,sBAAsB;AACtB,IAAI;AAEJ,+DAA+D;AAC/D,qEAAqE;AACrE,mDAAmD;AACnD,oDAAoD;AACpD,2DAA2D;AAC3D,wCAAwC;AAExC,kEAAkE;AAClE,kEAAkE;AAElE,6CAA6C;AAC7C,oFAAoF;AAEpF,sBAAsB;AACtB,2EAA2E;AAE3E,mEAAmE;AACnE,oCAAoC;AACpC,sBAAsB;AACtB,IAAI;AAEJ,kFAAkF;AAClF,8IAA8I;AAC9I,6DAA6D;AAC7D,sCAAsC;AACtC,oCAAoC;AACpC,8CAA8C;AAC9C,gEAAgE;AAChE,+DAA+D;AAC/D,sCAAsC;AACtC,kFAAkF;AAClF,8CAA8C;AAC9C,wBAAwB;AACxB,IAAI;AAEJ,SAAiC,oBAAoB;AACnD,uBAAuB,CAAC,KAAK;AAC7B,uBAAuB,CAAC,GAAG;IAE3B,wCAAwC;IACxC,MAAM,CAAC,GAAG,IAAI,QAAQ,CAAC,UAAU,EAAE,CAAA;IACnC,MAAM,IAAI,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;IAC3B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QACxC,IAAI,CAAC,CAAC,CAAC,GAAG,IAAI,QAAQ,CAAC,cAAc,EAAE,CAAA;IACzC,CAAC;IAED,WAAW,CAAC,KAAK,EAAE,CAAC,EAAE,IAAI,CAAC,CAAA;IAE3B,GAAG,CAAC,KAAK,EAAE,CAAC,EAAE,IAAI,EAAE,GAAG,CAAC,CAAA;IAExB,OAAO,GAAG,CAAA;AACZ,CAAC;AAED,SAAiC,oBAAoB;AACnD,sBAAsB,CAAC,KAAK;AAC5B,sBAAsB,CAAC,MAAM;IAE7B,MAAM,CAAC,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;IACxB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QACrC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,QAAQ,CAAC,UAAU,EAAE,CAAA;IAClC,CAAC;IACD,MAAM,iCAAiC,CAAC,IAAI,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;IAC7D,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QACxC,IAAI,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;QACxB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC3C,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,QAAQ,CAAC,cAAc,EAAE,CAAA;QAC5C,CAAC;IACH,CAAC;IACD,WAAW,CAAC,KAAK,EAAE,CAAC,EAAE,IAAI,CAAC,CAAA;IAE3B,GAAG,CAAC,KAAK,EAAE,MAAM,EAAE,CAAC,EAAE,IAAI,CAAC,CAAA;IAE3B,OAAO,MAAM,CAAA;AACf,CAAC;AAED,mEAAmE;AACnE,MAAM,UAAU;IACd,YAAY,UAAU,EAAE,oBAAoB,GAAG,CAAC;QAC9C,IAAI,CAAC,OAAO,GAAG,UAAU,CAAA;QACzB,IAAI,CAAC,SAAS,GAAG,IAAI,QAAQ,CAAC,UAAU,CAAC,MAAM,CAAC,CAAA;QAChD,IAAI,CAAC,SAAS,GAAG,oBAAoB,CAAA;QACrC,IAAI,CAAC,MAAM,GAAG,UAAU,CAAC,MAAM,CAAA;IACjC,CAAC;IAED,GAAG;QACD,MAAM,CAAC,GAAG,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS,CAAC,CAAA;QACtC,IAAI,CAAC,SAAS,IAAI,CAAC,CAAA;QACnB,OAAO,CAAC,CAAA;IACV,CAAC;IAED,OAAO;QACL,OAAO,IAAI,CAAC,GAAG,EAAE,CAAA;IACnB,CAAC;IAED,SAAS,CAAC,QAAQ;QAChB,OAAO,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAA;IAC/B,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,SAAS,CAAA;IACvB,CAAC;IAED,GAAG,CAAC,GAAG;QACL,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS,CAAC,GAAG,GAAG,CAAA;QAClC,IAAI,CAAC,SAAS,IAAI,CAAC,CAAA;QACnB,OAAO,GAAG,CAAA;IACZ,CAAC;IAED,KAAK,CAAC,QAAQ,EAAE,GAAG;QACjB,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,GAAG,GAAG,CAAA;QAC5B,OAAO,GAAG,CAAA;IACZ,CAAC;IAED,WAAW,CAAC,GAAG;QACb,IAAI,CAAC,SAAS,GAAG,GAAG,CAAA;QACpB,OAAO,GAAG,CAAA;IACZ,CAAC;IAED,MAAM;QACJ,MAAM,CAAC,GAAG,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,SAAS,EAAE,IAAI,CAAC,CAAA;QACvD,IAAI,CAAC,SAAS,IAAI,CAAC,CAAA;QACnB,OAAO,CAAC,CAAA;IACV,CAAC;IAED,SAAS;QACP,OAAO,IAAI,CAAC,OAAO,CAAC,MAAM,GAAG,IAAI,CAAC,SAAS,CAAA;IAC7C,CAAC;CACF;AAED,uEAAuE;AACvE,MAAM,CAAC,OAAO,UAAU,UAAU,CAChC,WAAW,EACX,YAAY,EACZ,oBAAoB,GAAG,CAAC;IAExB,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QAC7B,YAAY,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACpB,OAAO,YAAY,CAAA;IACrB,CAAC;IAED,MAAM,KAAK,GAAG,IAAI,UAAU,CAAC,WAAW,EAAE,oBAAoB,CAAC,CAAA;IAC/D,wCAAwC;IAExC,MAAM,KAAK,GAAG,KAAK,CAAC,GAAG,EAAE,CAAA;IACzB,IAAI,KAAK,KAAK,CAAC,IAAI,KAAK,KAAK,CAAC,EAAE,CAAC;QAC/B,MAAM,IAAI,kBAAkB,CAAC,sBAAsB,KAAK,EAAE,CAAC,CAAA;IAC7D,CAAC;IAED,MAAM,SAAS,CAAC,SAAS,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC1C,IAAI,SAAS,KAAK,KAAK,CAAC,SAAS,EAAE,GAAG,eAAe,EAAE,CAAC;QACtD,MAAM,IAAI,kBAAkB,CAAC,yBAAyB,CAAC,CAAA;IACzD,CAAC;IAED,MAAM,SAAS,CAAC,UAAU,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC3C,MAAM,MAAM,GAAG,IAAI,UAAU,CAAC,YAAY,IAAI,IAAI,UAAU,CAAC,UAAU,CAAC,CAAC,CAAA;IACzE,gCAAgC;IAEhC,IAAI,MAAM,CAAC,MAAM,GAAG,UAAU,EAAE,CAAC;QAC/B,MAAM,IAAI,kBAAkB,CAC1B,kCAAkC,UAAU,SAAS,CACtD,CAAA;IACH,CAAC;IAED,QAAQ,KAAK,EAAE,CAAC;QACd,KAAK,CAAC;YACJ,OAAO,oBAAoB,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QAE5C,KAAK,CAAC;YACJ,OAAO,oBAAoB,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QAE5C;YACE,MAAM,IAAI,kBAAkB,CAAC,uBAAuB,KAAK,EAAE,CAAC,CAAA;IAChE,CAAC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package/esm/unzip.d.ts

@@ -1 +1 @@
-export { gunzipSync as unzip } from 'zlib';
+export declare function unzip(input: Uint8Array): Uint8Array<ArrayBufferLike>;

package/esm/unzip.js

@@ -1,2 +1,5 @@
-export { gunzipSync as unzip } from 'zlib';
+import { inflate } from 'pako';
+export function unzip(input) {
+    return inflate(input);
+}
 //# sourceMappingURL=unzip.js.map

package/esm/unzip.js.map

@@ -1 +1 @@
-{"version":3,"file":"unzip.js","sourceRoot":"","sources":["../src/unzip.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,IAAI,KAAK,EAAE,MAAM,MAAM,CAAA"}
+{"version":3,"file":"unzip.js","sourceRoot":"","sources":["../src/unzip.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAE9B,MAAM,UAAU,KAAK,CAAC,KAAiB;IACrC,OAAO,OAAO,CAAC,KAAK,CAAC,CAAA;AACvB,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/cram",
-  "version": "3.0.6",
+  "version": "4.0.0",
   "description": "read CRAM files with pure Javascript",
   "license": "MIT",
   "repository": "GMOD/cram-js",
@@ -27,8 +27,8 @@
     "docs": "documentation readme --shallow src/indexedCramFile.ts --section=IndexedCramFile; documentation readme --shallow src/cramFile/file.ts --section=CramFile; documentation readme --shallow src/craiIndex.ts --section=CraiIndex;  documentation readme --shallow errors.ts '--section=Exception Classes'; documentation readme --shallow src/cramFile/file.ts --section=CramFile; documentation readme --shallow src/cramFile/record.ts --section=CramRecord",
     "prebuild": "npm run clean",
     "clean": "rimraf dist esm",
-    "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": "npm run build:esm && npm run build:es5",
     "postbuild": "webpack",
     "prepack": "npm test run && npm run build && cp dist/errors.js errors.js",
@@ -42,9 +42,9 @@
     "biojs"
   ],
   "dependencies": {
-    "@jkbonfield/htscodecs": "^0.5.1",
     "bzip2": "^0.1.1",
     "crc": "^4.3.2",
+    "generic-filehandle2": "^0.0.2",
     "long": "^4.0.0",
     "md5": "^2.2.1",
     "pako": "^1.0.4",
@@ -62,13 +62,12 @@
     "buffer": "^6.0.3",
     "documentation": "^14.0.3",
     "eslint": "^9.9.0",
-    "eslint-config-prettier": "^9.0.0",
-    "eslint-plugin-prettier": "^5.1.3",
+    "eslint-plugin-import": "^2.31.0",
     "eslint-plugin-unicorn": "^55.0.0",
     "mock-fs": "^5.2.0",
     "prettier": "^3.2.5",
     "rimraf": "^6.0.1",
-    "typescript": "^5.0.3",
+    "typescript": "^5.7.0",
     "typescript-eslint": "^8.0.1",
     "vitest": "^2.0.5",
     "webpack": "^5.90.3",
@@ -79,8 +78,6 @@
   },
   "browser": {
     "./dist/io/localFile.js": false,
-    "./esm/io/localFile.js": false,
-    "./esm/unzip.js": "./esm/unzip-pako.js",
-    "./dist/unzip.js": "./dist/unzip-pako.js"
+    "./esm/io/localFile.js": false
   }
 }

package/src/craiIndex.ts

@@ -1,8 +1,9 @@
-import { unzip } from './unzip'
-import { open } from './io'
-import { CramMalformedError } from './errors'
 import { CramFileSource } from './cramFile/file'
-import { Filehandle } from './cramFile/filehandle'
+import { CramMalformedError } from './errors'
+import { open } from './io'
+import { unzip } from './unzip'
+
+import type { GenericFilehandle } from 'generic-filehandle2'
 
 const BAI_MAGIC = 21_578_050 // BAI\1
 
@@ -33,11 +34,8 @@ function addRecordToIndex(index: ParsedIndex, record: number[]) {
   })
 }
 
-function maybeUnzip(data: Buffer) {
-  if (data[0] === 31 && data[1] === 139) {
-    return unzip(data)
-  }
-  return data
+function maybeUnzip(data: Uint8Array) {
+  return data[0] === 31 && data[1] === 139 ? unzip(data) : data
 }
 
 export default class CraiIndex {
@@ -50,10 +48,12 @@ export default class CraiIndex {
   // 4. Container start byte position in the file
   // 5. Slice start byte position in the container data (‘blocks’)
   // 6. Slice size in bytes
-  // Each line represents a slice in the CRAM file. Please note that all slices must be listed in index file.
+  //
+  // Each line represents a slice in the CRAM file. Please note that all slices
+  // must be listed in index file.
   private parseIndexP?: Promise<ParsedIndex>
 
-  private filehandle: Filehandle
+  private filehandle: GenericFilehandle
 
   /**
    *
@@ -69,18 +69,19 @@ export default class CraiIndex {
   async parseIndex() {
     const index: ParsedIndex = {}
     const uncompressedBuffer = maybeUnzip(await this.filehandle.readFile())
+    const dataView = new DataView(uncompressedBuffer.buffer)
     if (
       uncompressedBuffer.length > 4 &&
-      uncompressedBuffer.readUInt32LE(0) === BAI_MAGIC
+      dataView.getUint32(0, true) === BAI_MAGIC
     ) {
       throw new CramMalformedError(
         'invalid .crai index file. note: file appears to be a .bai index. this is technically legal but please open a github issue if you need support',
       )
     }
-    // interpret the text as regular ascii, since it is
-    // supposed to be only digits and whitespace characters
-    // this is written in a deliberately low-level fashion for performance,
-    // because some .crai files can be pretty large.
+    // interpret the text as regular ascii, since it is supposed to be only
+    // digits and whitespace characters this is written in a deliberately
+    // low-level fashion for performance, because some .crai files can be
+    // pretty large.
     let currentRecord: number[] = []
     let currentString = ''
     for (const charCode of uncompressedBuffer) {

package/src/cramFile/codecs/_base.ts

@@ -1,5 +1,5 @@
-import CramSlice from '../slice'
 import { CramFileBlock } from '../file'
+import CramSlice from '../slice'
 import { DataType } from './dataSeriesTypes'
 
 export interface DataTypeMapping {

package/src/cramFile/codecs/beta.ts

@@ -1,9 +1,9 @@
-import { CramUnimplementedError } from '../../errors'
 import CramCodec, { Cursors } from './_base'
 import { getBits } from './getBits'
-import CramSlice from '../slice'
-import { CramFileBlock } from '../file'
+import { CramUnimplementedError } from '../../errors'
 import { BetaEncoding } from '../encoding'
+import { CramFileBlock } from '../file'
+import CramSlice from '../slice'
 
 export default class BetaCodec extends CramCodec<
   'int',

package/src/cramFile/codecs/byteArrayLength.ts

@@ -1,7 +1,7 @@
 import CramCodec, { Cursors } from './_base'
 import { ByteArrayLengthEncoding, CramEncoding } from '../encoding'
-import CramSlice from '../slice'
 import { CramFileBlock } from '../file'
+import CramSlice from '../slice'
 import { DataType } from './dataSeriesTypes'
 import { tinyMemoize } from '../util'
 

package/src/cramFile/codecs/byteArrayStop.ts

@@ -1,9 +1,8 @@
-import { CramMalformedError } from '../../errors'
-
 import CramCodec, { Cursor, Cursors } from './_base'
-import CramSlice from '../slice'
-import { CramFileBlock } from '../file'
+import { CramMalformedError } from '../../errors'
 import { ByteArrayStopCramEncoding } from '../encoding'
+import { CramFileBlock } from '../file'
+import CramSlice from '../slice'
 import { CramBufferOverrunError } from './getBits'
 
 export default class ByteArrayStopCodec extends CramCodec<

package/src/cramFile/codecs/external.ts

@@ -1,8 +1,8 @@
-import { CramMalformedError, CramUnimplementedError } from '../../errors'
 import CramCodec, { Cursor, Cursors } from './_base'
-import { parseItf8 } from '../util'
-import CramSlice from '../slice'
+import { CramMalformedError, CramUnimplementedError } from '../../errors'
 import { CramFileBlock } from '../file'
+import CramSlice from '../slice'
+import { parseItf8 } from '../util'
 import { CramBufferOverrunError } from './getBits'
 import { ExternalCramEncoding } from '../encoding'
 

package/src/cramFile/codecs/gamma.ts

@@ -1,9 +1,9 @@
-import { CramUnimplementedError } from '../../errors'
 import CramCodec, { Cursors } from './_base'
 import { getBits } from './getBits'
+import { CramUnimplementedError } from '../../errors'
 import { GammaEncoding } from '../encoding'
-import CramSlice from '../slice'
 import { CramFileBlock } from '../file'
+import CramSlice from '../slice'
 
 export default class GammaCodec extends CramCodec<
   'int',

package/src/cramFile/codecs/getBits.ts

@@ -1,7 +1,7 @@
 export class CramBufferOverrunError extends Error {}
 
 export function getBits(
-  data: Buffer,
+  data: Uint8Array,
   cursor: { bytePosition: number; bitPosition: number },
   numBits: number,
 ) {

package/src/cramFile/codecs/huffman.ts

@@ -1,10 +1,9 @@
-import { CramMalformedError } from '../../errors'
 import CramCodec, { Cursor, Cursors } from './_base'
 import { getBits } from './getBits'
+import { CramMalformedError } from '../../errors'
 import { HuffmanEncoding } from '../encoding'
-
-import CramSlice from '../slice'
 import { CramFileBlock } from '../file'
+import CramSlice from '../slice'
 
 function numberOfSetBits(ii: number) {
   let i = (ii - (ii >> 1)) & 0x55555555

package/src/cramFile/codecs/index.ts

@@ -1,15 +1,14 @@
-import { CramUnimplementedError } from '../../errors'
-
-import HuffmanIntCodec from './huffman'
-import ExternalCodec from './external'
-import ByteArrayStopCodec from './byteArrayStop'
-import ByteArrayLengthCodec from './byteArrayLength'
+import CramCodec from './_base'
 import BetaCodec from './beta'
+import ByteArrayLengthCodec from './byteArrayLength'
+import ByteArrayStopCodec from './byteArrayStop'
+import { DataType } from './dataSeriesTypes'
+import ExternalCodec from './external'
 import GammaCodec from './gamma'
+import HuffmanIntCodec from './huffman'
 import SubexpCodec from './subexp'
-import CramCodec from './_base'
+import { CramUnimplementedError } from '../../errors'
 import { CramEncoding } from '../encoding'
-import { DataType } from './dataSeriesTypes'
 
 const codecClasses = {
   1: ExternalCodec,

package/src/cramFile/codecs/subexp.ts

@@ -1,9 +1,9 @@
-import { CramUnimplementedError } from '../../errors'
 import CramCodec, { Cursors } from './_base'
 import { getBits } from './getBits'
-import CramSlice from '../slice'
-import { CramFileBlock } from '../file'
+import { CramUnimplementedError } from '../../errors'
 import { SubexpEncoding } from '../encoding'
+import { CramFileBlock } from '../file'
+import CramSlice from '../slice'
 
 export default class SubexpCodec extends CramCodec<
   'int',

package/src/cramFile/container/compressionScheme.ts

@@ -1,12 +1,12 @@
+import { CramMalformedError } from '../../errors'
 import { instantiateCodec } from '../codecs'
 import CramCodec from '../codecs/_base'
-import { CramCompressionHeader } from '../sectionParsers'
-import { CramEncoding } from '../encoding'
-import { CramMalformedError } from '../../errors'
 import {
   DataSeriesEncodingKey,
   DataSeriesEncodingMap,
 } from '../codecs/dataSeriesTypes'
+import { CramEncoding } from '../encoding'
+import { CramCompressionHeader } from '../sectionParsers'
 
 // the hardcoded data type to be decoded for each core
 // data field

package/src/cramFile/container/index.ts

@@ -1,8 +1,7 @@
-import { Buffer } from 'buffer'
 import { CramMalformedError } from '../../errors'
 // locals
-import { itf8Size, parseItem, tinyMemoize } from '../util'
 import CramSlice from '../slice'
+import { itf8Size, parseItem, tinyMemoize } from '../util'
 import CramContainerCompressionScheme from './compressionScheme'
 import CramFile from '../file'
 import { getSectionParsers } from '../sectionParsers'
@@ -88,8 +87,10 @@ export default class CramContainer {
 
     // parse the container header. do it in 2 pieces because you cannot tell
     // how much to buffer until you read numLandmarks
-    const bytes1 = Buffer.allocUnsafe(cramContainerHeader1.maxLength)
-    await this.file.read(bytes1, 0, cramContainerHeader1.maxLength, position)
+    const bytes1 = await this.file.read(
+      cramContainerHeader1.maxLength,
+      position,
+    )
     const header1 = parseItem(bytes1, cramContainerHeader1.parser)
     const numLandmarksSize = itf8Size(header1.numLandmarks)
     if (position + header1.length >= fileSize) {
@@ -99,12 +100,8 @@ export default class CramContainer {
       )
       return undefined
     }
-    const bytes2 = Buffer.allocUnsafe(
-      cramContainerHeader2.maxLength(header1.numLandmarks),
-    )
-    await this.file.read(
-      bytes2,
-      0,
+
+    const bytes2 = await this.file.read(
       cramContainerHeader2.maxLength(header1.numLandmarks),
       position + header1._size - numLandmarksSize,
     )