@gmod/cram 4.0.9 → 5.0.0

package/esm/seek-bzip/toHex.js

@@ -0,0 +1,33 @@
+// from https://www.xaymar.com/articles/2020/12/08/fastest-uint8array-to-hex-string-conversion-in-javascript/
+// Pre-Init
+const LUT_HEX_4b = [
+    '0',
+    '1',
+    '2',
+    '3',
+    '4',
+    '5',
+    '6',
+    '7',
+    '8',
+    '9',
+    'A',
+    'B',
+    'C',
+    'D',
+    'E',
+    'F',
+];
+const LUT_HEX_8b = new Array(0x100);
+for (let n = 0; n < 0x100; n++) {
+    LUT_HEX_8b[n] = `${LUT_HEX_4b[(n >>> 4) & 0xf]}${LUT_HEX_4b[n & 0xf]}`;
+}
+// End Pre-Init
+export function toHex(buffer) {
+    let out = '';
+    for (let idx = 0, edx = buffer.length; idx < edx; idx++) {
+        out += LUT_HEX_8b[buffer[idx]];
+    }
+    return out;
+}
+//# sourceMappingURL=toHex.js.map

package/esm/seek-bzip/toHex.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"toHex.js","sourceRoot":"","sources":["../../src/seek-bzip/toHex.ts"],"names":[],"mappings":"AAAA,6GAA6G;AAE7G,WAAW;AACX,MAAM,UAAU,GAAG;IACjB,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;CACJ,CAAA;AACD,MAAM,UAAU,GAAG,IAAI,KAAK,CAAC,KAAK,CAAC,CAAA;AACnC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,EAAE,EAAE,CAAC;IAC/B,UAAU,CAAC,CAAC,CAAC,GAAG,GAAG,UAAU,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,GAAG,GAAG,CAAC,GAAG,UAAU,CAAC,CAAC,GAAG,GAAG,CAAC,EAAE,CAAA;AACxE,CAAC;AACD,eAAe;AACf,MAAM,UAAU,KAAK,CAAC,MAAkB;IACtC,IAAI,GAAG,GAAG,EAAE,CAAA;IACZ,KAAK,IAAI,GAAG,GAAG,CAAC,EAAE,GAAG,GAAG,MAAM,CAAC,MAAM,EAAE,GAAG,GAAG,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC;QACxD,GAAG,IAAI,UAAU,CAAC,MAAM,CAAC,GAAG,CAAE,CAAC,CAAA;IACjC,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC"}

package/package.json

@@ -1,11 +1,19 @@
 {
   "name": "@gmod/cram",
-  "version": "4.0.9",
+  "version": "5.0.0",
   "description": "read CRAM files with pure Javascript",
   "license": "MIT",
   "repository": "GMOD/cram-js",
-  "main": "dist/index.js",
-  "module": "esm/index.js",
+  "type": "module",
+  "types": "./dist/index.d.ts",
+  "exports": {
+    "import": {
+      "import": "./esm/index.js"
+    },
+    "require": {
+      "require": "./dist/index.js"
+    }
+  },
   "author": {
     "name": "Robert Buels",
     "email": "rbuels@gmail.com",
@@ -41,32 +49,29 @@
   ],
   "dependencies": {
     "crc": "^4.3.2",
-    "generic-filehandle2": "^1.0.0",
+    "generic-filehandle2": "^2.0.1",
     "md5": "^2.2.1",
     "pako": "^1.0.4",
     "quick-lru": "^4.0.1",
-    "seek-bzip": "^2.0.0",
     "xz-decompress": "^0.2.1"
   },
   "devDependencies": {
     "@gmod/indexedfasta": "^3.0.0",
     "@types/md5": "^2.3.2",
     "@types/pako": "^1.0.3",
-    "@typescript-eslint/eslint-plugin": "^8.0.0",
-    "@typescript-eslint/parser": "^8.0.0",
     "@vitest/coverage-v8": "^3.0.1",
     "buffer": "^6.0.3",
     "documentation": "^14.0.3",
     "eslint": "^9.9.0",
     "eslint-plugin-import": "^2.31.0",
-    "eslint-plugin-unicorn": "^56.0.1",
+    "eslint-plugin-unicorn": "^59.0.0",
     "mock-fs": "^5.2.0",
     "prettier": "^3.2.5",
     "rimraf": "^6.0.1",
     "typescript": "^5.7.0",
-    "typescript-eslint": "^8.0.1",
+    "typescript-eslint": "^8.31.1",
     "vitest": "^3.0.1",
-    "webpack": "^5.90.3",
+    "webpack": "^5.99.7",
     "webpack-cli": "^6.0.1"
   },
   "publishConfig": {

package/src/craiIndex.ts

@@ -1,7 +1,7 @@
-import { CramFileSource } from './cramFile/file'
-import { CramMalformedError } from './errors'
-import { open } from './io'
-import { unzip } from './unzip'
+import { CramFileSource } from './cramFile/file.ts'
+import { CramMalformedError } from './errors.ts'
+import { open } from './io.ts'
+import { unzip } from './unzip.ts'
 
 import type { GenericFilehandle } from 'generic-filehandle2'
 

package/src/cramFile/codecs/_base.ts

@@ -1,6 +1,6 @@
-import { CramFileBlock } from '../file'
-import CramSlice from '../slice'
-import { DataType } from './dataSeriesTypes'
+import { CramFileBlock } from '../file.ts'
+import { DataType } from './dataSeriesTypes.ts'
+import CramSlice from '../slice/index.ts'
 
 export interface DataTypeMapping {
   byte: number

package/src/cramFile/codecs/beta.ts

@@ -1,9 +1,9 @@
-import CramCodec, { Cursors } from './_base'
-import { getBits } from './getBits'
-import { CramUnimplementedError } from '../../errors'
-import { BetaEncoding } from '../encoding'
-import { CramFileBlock } from '../file'
-import CramSlice from '../slice'
+import CramCodec, { Cursors } from './_base.ts'
+import { getBits } from './getBits.ts'
+import { CramUnimplementedError } from '../../errors.ts'
+import { BetaEncoding } from '../encoding.ts'
+import { CramFileBlock } from '../file.ts'
+import CramSlice from '../slice/index.ts'
 
 export default class BetaCodec extends CramCodec<
   'int',
@@ -19,9 +19,9 @@ export default class BetaCodec extends CramCodec<
   }
 
   decode(
-    slice: CramSlice,
+    _slice: CramSlice,
     coreDataBlock: CramFileBlock,
-    blocksByContentId: Record<number, CramFileBlock>,
+    _blocksByContentId: Record<number, CramFileBlock>,
     cursors: Cursors,
   ) {
     const fromBits = getBits(

package/src/cramFile/codecs/byteArrayLength.ts

@@ -1,9 +1,9 @@
-import CramCodec, { Cursors } from './_base'
-import { ByteArrayLengthEncoding, CramEncoding } from '../encoding'
-import { CramFileBlock } from '../file'
-import CramSlice from '../slice'
-import { DataType } from './dataSeriesTypes'
-import { tinyMemoize } from '../util'
+import CramCodec, { Cursors } from './_base.ts'
+import { ByteArrayLengthEncoding, CramEncoding } from '../encoding.ts'
+import { CramFileBlock } from '../file.ts'
+import { DataType } from './dataSeriesTypes.ts'
+import CramSlice from '../slice/index.ts'
+import { tinyMemoize } from '../util.ts'
 
 type CramCodecFactory = <TData extends DataType = DataType>(
   encodingData: CramEncoding,

package/src/cramFile/codecs/byteArrayStop.ts

@@ -1,17 +1,17 @@
-import CramCodec, { Cursor, Cursors } from './_base'
-import { CramMalformedError } from '../../errors'
-import { ByteArrayStopCramEncoding } from '../encoding'
-import { CramFileBlock } from '../file'
-import CramSlice from '../slice'
-import { CramBufferOverrunError } from './getBits'
+import CramCodec, { Cursor, Cursors } from './_base.ts'
+import { CramMalformedError } from '../../errors.ts'
+import { ByteArrayStopCramEncoding } from '../encoding.ts'
+import { CramFileBlock } from '../file.ts'
+import { CramBufferOverrunError } from './getBits.ts'
+import CramSlice from '../slice/index.ts'
 
 export default class ByteArrayStopCodec extends CramCodec<
   'byteArray',
   ByteArrayStopCramEncoding['parameters']
 > {
   decode(
-    slice: CramSlice,
-    coreDataBlock: CramFileBlock,
+    _slice: CramSlice,
+    _coreDataBlock: CramFileBlock,
     blocksByContentId: Record<number, CramFileBlock>,
     cursors: Cursors,
   ) {

package/src/cramFile/codecs/dataSeriesTypes.ts

@@ -1,4 +1,4 @@
-import { CramEncoding } from '../encoding'
+import { CramEncoding } from '../encoding.ts'
 
 export type DataType = 'int' | 'byte' | 'long' | 'byteArray'
 

package/src/cramFile/codecs/external.ts

@@ -1,10 +1,10 @@
-import CramCodec, { Cursor, Cursors } from './_base'
-import { CramUnimplementedError } from '../../errors'
-import { CramFileBlock } from '../file'
-import CramSlice from '../slice'
-import { parseItf8 } from '../util'
-import { CramBufferOverrunError } from './getBits'
-import { ExternalCramEncoding } from '../encoding'
+import CramCodec, { Cursor, Cursors } from './_base.ts'
+import { CramUnimplementedError } from '../../errors.ts'
+import { CramFileBlock } from '../file.ts'
+import CramSlice from '../slice/index.ts'
+import { parseItf8 } from '../util.ts'
+import { CramBufferOverrunError } from './getBits.ts'
+import { ExternalCramEncoding } from '../encoding.ts'
 
 export default class ExternalCodec extends CramCodec<
   'int' | 'byte',
@@ -32,16 +32,19 @@ export default class ExternalCodec extends CramCodec<
   }
 
   decode(
-    slice: CramSlice,
-    coreDataBlock: CramFileBlock,
+    _slice: CramSlice,
+    _coreDataBlock: CramFileBlock,
     blocksByContentId: Record<number, CramFileBlock>,
     cursors: Cursors,
   ) {
     const { blockContentId } = this.parameters
     const contentBlock = blocksByContentId[blockContentId]
-
-    const cursor = cursors.externalBlocks.getCursor(blockContentId)
-    return contentBlock ? this._decodeData(contentBlock, cursor) : undefined
+    return contentBlock
+      ? this._decodeData(
+          contentBlock,
+          cursors.externalBlocks.getCursor(blockContentId),
+        )
+      : undefined
   }
 
   _decodeInt(contentBlock: CramFileBlock, cursor: Cursor) {

package/src/cramFile/codecs/gamma.ts

@@ -1,9 +1,9 @@
-import CramCodec, { Cursors } from './_base'
-import { getBits } from './getBits'
-import { CramUnimplementedError } from '../../errors'
-import { GammaEncoding } from '../encoding'
-import { CramFileBlock } from '../file'
-import CramSlice from '../slice'
+import CramCodec, { Cursors } from './_base.ts'
+import { getBits } from './getBits.ts'
+import { CramUnimplementedError } from '../../errors.ts'
+import { GammaEncoding } from '../encoding.ts'
+import { CramFileBlock } from '../file.ts'
+import CramSlice from '../slice/index.ts'
 
 export default class GammaCodec extends CramCodec<
   'int',
@@ -19,9 +19,9 @@ export default class GammaCodec extends CramCodec<
   }
 
   decode(
-    slice: CramSlice,
+    _slice: CramSlice,
     coreDataBlock: CramFileBlock,
-    blocksByContentId: Record<number, CramFileBlock>,
+    _blocksByContentId: Record<number, CramFileBlock>,
     cursors: Cursors,
   ) {
     let length = 1

package/src/cramFile/codecs/huffman.ts

@@ -1,9 +1,9 @@
-import CramCodec, { Cursor, Cursors } from './_base'
-import { getBits } from './getBits'
-import { CramMalformedError } from '../../errors'
-import { HuffmanEncoding } from '../encoding'
-import { CramFileBlock } from '../file'
-import CramSlice from '../slice'
+import CramCodec, { Cursor, Cursors } from './_base.ts'
+import { getBits } from './getBits.ts'
+import { CramMalformedError } from '../../errors.ts'
+import { HuffmanEncoding } from '../encoding.ts'
+import { CramFileBlock } from '../file.ts'
+import CramSlice from '../slice/index.ts'
 
 function numberOfSetBits(ii: number) {
   let i = (ii - (ii >> 1)) & 0x55555555
@@ -122,7 +122,7 @@ export default class HuffmanIntCodec extends CramCodec<
   decode(
     slice: CramSlice,
     coreDataBlock: CramFileBlock,
-    blocksByContentId: Record<number, CramFileBlock>,
+    _blocksByContentId: Record<number, CramFileBlock>,
     cursors: Cursors,
   ) {
     return this._decode(slice, coreDataBlock, cursors.coreBlock)
@@ -137,7 +137,7 @@ export default class HuffmanIntCodec extends CramCodec<
     return this.sortedCodes[0]!.value
   }
 
-  _decode(slice: CramSlice, coreDataBlock: CramFileBlock, coreCursor: Cursor) {
+  _decode(_slice: CramSlice, coreDataBlock: CramFileBlock, coreCursor: Cursor) {
     const input = coreDataBlock.content
 
     let prevLen = 0

package/src/cramFile/codecs/index.ts

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

package/src/cramFile/codecs/subexp.ts

@@ -1,9 +1,9 @@
-import CramCodec, { Cursors } from './_base'
-import { getBits } from './getBits'
-import { CramUnimplementedError } from '../../errors'
-import { SubexpEncoding } from '../encoding'
-import { CramFileBlock } from '../file'
-import CramSlice from '../slice'
+import CramCodec, { Cursors } from './_base.ts'
+import { getBits } from './getBits.ts'
+import { CramUnimplementedError } from '../../errors.ts'
+import { SubexpEncoding } from '../encoding.ts'
+import { CramFileBlock } from '../file.ts'
+import CramSlice from '../slice/index.ts'
 
 export default class SubexpCodec extends CramCodec<
   'int',
@@ -19,9 +19,9 @@ export default class SubexpCodec extends CramCodec<
   }
 
   decode(
-    slice: CramSlice,
+    _slice: CramSlice,
     coreDataBlock: CramFileBlock,
-    blocksByContentId: Record<number, CramFileBlock>,
+    _blocksByContentId: Record<number, CramFileBlock>,
     cursors: Cursors,
   ) {
     let numLeadingOnes = 0

package/src/cramFile/container/compressionScheme.ts

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

package/src/cramFile/container/index.ts

@@ -1,10 +1,9 @@
-import { CramMalformedError } from '../../errors'
-// locals
-import CramSlice from '../slice'
-import { itf8Size, parseItem, tinyMemoize } from '../util'
-import CramContainerCompressionScheme from './compressionScheme'
-import CramFile from '../file'
-import { getSectionParsers } from '../sectionParsers'
+import { CramMalformedError } from '../../errors.ts'
+import CramSlice from '../slice/index.ts'
+import { itf8Size, parseItem, tinyMemoize } from '../util.ts'
+import CramContainerCompressionScheme from './compressionScheme.ts'
+import CramFile from '../file.ts'
+import { getSectionParsers } from '../sectionParsers.ts'
 
 export default class CramContainer {
   constructor(

package/src/cramFile/file.ts

@@ -1,28 +1,23 @@
-// 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 { unzip } from '../unzip'
-import CramContainer from './container'
-import CramRecord from './record'
+import { CramMalformedError, CramUnimplementedError } from '../errors.ts'
+import * as htscodecs from '../htscodecs/index.ts'
+import { open } from '../io.ts'
+import ransuncompress from '../rans/index.ts'
+import { parseHeaderText } from '../sam.ts'
+import { decode } from '../seek-bzip/index.ts'
+import { unzip } from '../unzip.ts'
+import CramContainer from './container/index.ts'
+import CramRecord from './record.ts'
 import {
   BlockHeader,
   CompressionMethod,
   cramFileDefinition,
   getSectionParsers,
-} from './sectionParsers'
-import { parseItem, tinyMemoize } from './util'
+} from './sectionParsers.ts'
+import { parseItem, tinyMemoize } from './util.ts'
 
 import type { GenericFilehandle } from 'generic-filehandle2'
 
@@ -287,13 +282,9 @@ export default class CramFile {
   ) {
     // console.log({ compressionMethod })
     if (compressionMethod === 'gzip') {
-      const ret = unzip(inputBuffer)
-      if (ret[0] === 24) {
-        // console.log(ret.slice(0, 500).join(','))
-      }
-      return ret
+      return unzip(inputBuffer)
     } else if (compressionMethod === 'bzip2') {
-      return Bunzip.decode(inputBuffer)
+      return decode(inputBuffer)
     } else if (compressionMethod === 'lzma') {
       const decompressedResponse = new Response(
         new XzReadableStream(bufferToStream(inputBuffer)),
@@ -303,8 +294,6 @@ export default class CramFile {
       const outputBuffer = new Uint8Array(uncompressedSize)
       ransuncompress(inputBuffer, outputBuffer)
       return outputBuffer
-      // htscodecs r4x8 is slower, but compatible.
-      // htscodecs.r4x8_uncompress(inputBuffer, outputBuffer);
     } else if (compressionMethod === 'rans4x16') {
       return htscodecs.r4x16_uncompress(inputBuffer)
     } else if (compressionMethod === 'arith') {

package/src/cramFile/index.ts

@@ -1,3 +1,3 @@
-export { default as CramRecord } from './record'
+export { default as CramRecord } from './record.ts'
 
-export { default } from './file'
+export { default } from './file.ts'

package/src/cramFile/record.ts

@@ -1,7 +1,7 @@
-import Constants from './constants'
-import CramContainerCompressionScheme from './container/compressionScheme'
+import Constants from './constants.ts'
+import CramContainerCompressionScheme from './container/compressionScheme.ts'
 
-import type decodeRecord from './slice/decodeRecord'
+import type decodeRecord from './slice/decodeRecord.ts'
 
 export interface RefRegion {
   start: number

package/src/cramFile/sectionParsers.ts

@@ -1,7 +1,7 @@
-import { TupleOf } from '../typescript'
-import { DataSeriesEncodingMap } from './codecs/dataSeriesTypes'
-import { CramEncoding } from './encoding'
-import { parseItf8, parseLtf8 } from './util'
+import { TupleOf } from '../typescript.ts'
+import { DataSeriesEncodingMap } from './codecs/dataSeriesTypes.ts'
+import { CramEncoding } from './encoding.ts'
+import { parseItf8, parseLtf8 } from './util.ts'
 
 export function cramFileDefinition() {
   return {

package/src/cramFile/slice/decodeRecord.ts

@@ -1,18 +1,18 @@
-import { CramMalformedError } from '../../errors'
-import { Cursors, DataTypeMapping } from '../codecs/_base'
-import { DataSeriesEncodingKey } from '../codecs/dataSeriesTypes'
+import { CramMalformedError } from '../../errors.ts'
+import { Cursors, DataTypeMapping } from '../codecs/_base.ts'
+import { DataSeriesEncodingKey } from '../codecs/dataSeriesTypes.ts'
 import CramContainerCompressionScheme, {
   DataSeriesTypes,
-} from '../container/compressionScheme'
+} from '../container/compressionScheme.ts'
 import {
   BamFlagsDecoder,
   CramFlagsDecoder,
   MateFlagsDecoder,
   ReadFeature,
-} from '../record'
-import CramSlice, { SliceHeader } from './index'
-import { CramFileBlock } from '../file'
-import { isMappedSliceHeader } from '../sectionParsers'
+} from '../record.ts'
+import CramSlice, { SliceHeader } from './index.ts'
+import { CramFileBlock } from '../file.ts'
+import { isMappedSliceHeader } from '../sectionParsers.ts'
 
 /**
  * given a Buffer, read a string up to the first null character

package/src/cramFile/slice/index.ts

@@ -1,20 +1,20 @@
-import { CramArgumentError, CramMalformedError } from '../../errors'
-import { Cursors, DataTypeMapping } from '../codecs/_base'
-import { CramBufferOverrunError } from '../codecs/getBits'
-import Constants from '../constants'
-import decodeRecord, { DataSeriesDecoder } from './decodeRecord'
-import { DataSeriesEncodingKey } from '../codecs/dataSeriesTypes'
-import CramContainer from '../container'
-import { DataSeriesTypes } from '../container/compressionScheme'
-import CramFile, { CramFileBlock } from '../file'
-import CramRecord from '../record'
+import { CramArgumentError, CramMalformedError } from '../../errors.ts'
+import { Cursors, DataTypeMapping } from '../codecs/_base.ts'
+import { CramBufferOverrunError } from '../codecs/getBits.ts'
+import Constants from '../constants.ts'
+import decodeRecord, { DataSeriesDecoder } from './decodeRecord.ts'
+import { DataSeriesEncodingKey } from '../codecs/dataSeriesTypes.ts'
+import { DataSeriesTypes } from '../container/compressionScheme.ts'
+import CramContainer from '../container/index.ts'
+import CramFile, { CramFileBlock } from '../file.ts'
+import CramRecord from '../record.ts'
 import {
   MappedSliceHeader,
   UnmappedSliceHeader,
   getSectionParsers,
   isMappedSliceHeader,
-} from '../sectionParsers'
-import { parseItem, sequenceMD5, tinyMemoize } from '../util'
+} from '../sectionParsers.ts'
+import { parseItem, sequenceMD5, tinyMemoize } from '../util.ts'
 
 export type SliceHeader = CramFileBlock & {
   parsedContent: MappedSliceHeader | UnmappedSliceHeader
@@ -28,15 +28,12 @@ interface RefRegion {
 }
 
 /**
- * @private
- * Try to estimate the template length from a bunch of interrelated multi-segment reads.
- * @param {Array[CramRecord]} allRecords
- * @param {number} currentRecordNumber
- * @param {CramRecord} thisRecord
+ * Try to estimate the template length from a bunch of interrelated
+ * multi-segment reads.
  */
 function calculateMultiSegmentMatedTemplateLength(
   allRecords: CramRecord[],
-  currentRecordNumber: number,
+  _currentRecordNumber: number,
   thisRecord: CramRecord,
 ) {
   function getAllMatedRecords(startRecord: CramRecord) {
@@ -73,18 +70,16 @@ function calculateMultiSegmentMatedTemplateLength(
 }
 
 /**
- * @private
- * Attempt to calculate the `templateLength` for a pair of intra-slice paired reads.
- * Ported from htslib. Algorithm is imperfect.
- * @param {CramRecord} thisRecord
- * @param {CramRecord} mateRecord
+ * Attempt to calculate the `templateLength` for a pair of intra-slice paired
+ * reads. Ported from htslib. Algorithm is imperfect.
  */
 function calculateIntraSliceMatePairTemplateLength(
   thisRecord: CramRecord,
   mateRecord: CramRecord,
 ) {
-  // this just estimates the template length by using the simple (non-gapped) end coordinate of each
-  // read, because gapping in the alignment doesn't mean the template is longer or shorter
+  // this just estimates the template length by using the simple (non-gapped)
+  // end coordinate of each read, because gapping in the alignment doesn't mean
+  // the template is longer or shorter
   const start = Math.min(thisRecord.alignmentStart, mateRecord.alignmentStart)
   const end = Math.max(
     thisRecord.alignmentStart + thisRecord.readLength - 1,
@@ -96,10 +91,9 @@ function calculateIntraSliceMatePairTemplateLength(
 }
 
 /**
- * @private establishes a mate-pair relationship between two records in the
- * same slice. CRAM compresses mate-pair relationships between records in the
- * same slice down into just one record having the index in the slice of its
- * mate
+ * establishes a mate-pair relationship between two records in the same slice.
+ * CRAM compresses mate-pair relationships between records in the same slice
+ * down into just one record having the index in the slice of its mate
  */
 function associateIntraSliceMate(
   allRecords: CramRecord[],

package/src/htscodecs/arith_gen.ts

@@ -34,12 +34,12 @@
  * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-import Bunzip from 'seek-bzip'
+import { decode } from '../seek-bzip/index.ts'
 
-import RangeCoder from './arith_sh'
-import ByteModel from './byte_model'
-import IOStream from './iostream'
-import { concatUint8Array } from '../util'
+import RangeCoder from './arith_sh.ts'
+import ByteModel from './byte_model.ts'
+import IOStream from './iostream.ts'
+import { concatUint8Array } from '../util.ts'
 
 const ARITH_ORDER = 1
 const ARITH_EXT = 4
@@ -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))
   }
 
   // ----------------------------------------------------------------------