@gmod/cram 1.7.4 → 2.0.0

package/esm/cramFile/file.js.map

@@ -1 +1 @@
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package/esm/rans/constants.d.ts

@@ -1,3 +1,4 @@
-export const TF_SHIFT: 12;
-export const TOTFREQ: number;
-export const RANS_BYTE_L: number;
+declare const TF_SHIFT = 12;
+declare const TOTFREQ: number;
+declare const RANS_BYTE_L: number;
+export { TF_SHIFT, TOTFREQ, RANS_BYTE_L };

package/esm/rans/constants.js.map

@@ -1 +1 @@
-{"version":3,"file":"constants.js","sourceRoot":"","sources":["../../src/rans/constants.js"],"names":[],"mappings":"AAAA,MAAM,QAAQ,GAAG,EAAE,CAAA;AACnB,MAAM,OAAO,GAAG,CAAC,IAAI,QAAQ,CAAA;AAC7B,MAAM,WAAW,GAAG,CAAC,IAAI,EAAE,CAAA;AAE3B,OAAO,EAAE,QAAQ,EAAE,OAAO,EAAE,WAAW,EAAE,CAAA"}
+{"version":3,"file":"constants.js","sourceRoot":"","sources":["../../src/rans/constants.ts"],"names":[],"mappings":"AAAA,MAAM,QAAQ,GAAG,EAAE,CAAA;AACnB,MAAM,OAAO,GAAG,CAAC,IAAI,QAAQ,CAAA;AAC7B,MAAM,WAAW,GAAG,CAAC,IAAI,EAAE,CAAA;AAE3B,OAAO,EAAE,QAAQ,EAAE,OAAO,EAAE,WAAW,EAAE,CAAA"}

package/esm/rans/d04.js

@@ -1,3 +1,4 @@
+//@ts-nocheck
 import { CramMalformedError } from '../errors';
 import { TF_SHIFT } from './constants';
 import Decoding from './decoding';

package/esm/rans/d04.js.map

@@ -1 +1 @@
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package/esm/rans/d14.js

@@ -1,3 +1,4 @@
+//@ts-nocheck
 import { TF_SHIFT } from './constants';
 import Decoding from './decoding';
 export default function uncompress(

package/esm/rans/d14.js.map

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package/esm/rans/decoding.d.ts

@@ -1,30 +1,27 @@
-export default Decode;
-declare namespace Decode {
-    export { FC };
-    export { AriDecoder };
-    export { Symbol };
-    export { symbolInit };
-    export { advanceStep };
-    export { advanceSymbolStep };
-    export { get };
-    export { advanceSymbol };
-    export { renormalize };
-}
 declare class FC {
-    F: any;
-    C: any;
+    constructor();
 }
 declare class AriDecoder {
-    fc: any[];
-    R: any;
+    constructor();
 }
 declare class Symbol {
-    start: any;
-    freq: any;
+    constructor();
 }
 declare function symbolInit(sym: any, start: any, freq: any): void;
 declare function advanceStep(r: any, start: any, freq: any, scaleBits: any): number;
 declare function advanceSymbolStep(r: any, sym: any, scaleBits: any): number;
-declare function get(r: any, scaleBits: any): number;
+declare function get(/* final int */ r: any, /* final int */ scaleBits: any): number;
 declare function advanceSymbol(r: any, pptr: any, sym: any, scaleBits: any): any;
 declare function renormalize(r: any, pptr: any): any;
+declare const Decode: {
+    FC: typeof FC;
+    AriDecoder: typeof AriDecoder;
+    Symbol: typeof Symbol;
+    symbolInit: typeof symbolInit;
+    advanceStep: typeof advanceStep;
+    advanceSymbolStep: typeof advanceSymbolStep;
+    get: typeof get;
+    advanceSymbol: typeof advanceSymbol;
+    renormalize: typeof renormalize;
+};
+export default Decode;

package/esm/rans/decoding.js

@@ -1,3 +1,4 @@
+//@ts-nocheck
 import { CramMalformedError } from '../errors';
 import { RANS_BYTE_L } from './constants';
 class FC {

package/esm/rans/decoding.js.map

@@ -1 +1 @@
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package/esm/rans/frequencies.d.ts

@@ -1,2 +1,2 @@
-export function readStatsO0(cp: any, decoder: any, syms: any): void;
-export function readStatsO1(cp: any, D: any, syms: any): void;
+export declare function readStatsO0(cp: any, decoder: any, syms: any): void;
+export declare function readStatsO1(cp: any, D: any, syms: any): void;

package/esm/rans/frequencies.js

@@ -1,3 +1,4 @@
+//@ts-nocheck
 import { CramMalformedError } from '../errors';
 import { TOTFREQ } from './constants';
 import Decoding from './decoding';

package/esm/rans/frequencies.js.map

@@ -1 +1 @@
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package/esm/rans/index.js

@@ -1,3 +1,4 @@
+//@ts-nocheck
 import { CramMalformedError } from '../errors';
 import Decoding from './decoding';
 import { readStatsO0, readStatsO1 } from './frequencies';

package/esm/rans/index.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/cram",
-  "version": "1.7.4",
+  "version": "2.0.0",
   "description": "read CRAM files with pure Javascript",
   "license": "MIT",
   "repository": "GMOD/cram-js",
@@ -23,7 +23,7 @@
   "scripts": {
     "test": "jest",
     "lint": "eslint src test",
-    "docs": "documentation readme --shallow src/indexedCramFile.js --section=IndexedCramFile; documentation readme --shallow src/cramFile/file.js --section=CramFile; documentation readme --shallow src/craiIndex.js --section=CraiIndex;  documentation readme --shallow errors.js '--section=Exception Classes'; documentation readme --shallow src/cramFile/file.js --section=CramFile; documentation readme --shallow src/cramFile/record.js --section=CramRecord",
+    "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",
@@ -50,34 +50,35 @@
     "long": "^4.0.0",
     "md5": "^2.2.1",
     "pako": "^1.0.4",
-    "quick-lru": "^4.0.1"
+    "quick-lru": "^4.0.1",
+    "xz-decompress": "^0.2.1"
   },
   "devDependencies": {
     "@babel/plugin-transform-modules-commonjs": "^7.18.2",
     "@babel/preset-typescript": "^7.17.12",
-    "@gmod/indexedfasta": "^2.0.2",
+    "@gmod/indexedfasta": "^2.1.0",
     "@types/buffer-crc32": "^0.2.2",
     "@types/jest": "^29.2.4",
     "@types/long": "^4.0.2",
     "@types/md5": "^2.3.2",
     "@types/pako": "^1.0.3",
-    "@typescript-eslint/eslint-plugin": "^5.46.1",
-    "@typescript-eslint/parser": "^5.46.1",
+    "@typescript-eslint/eslint-plugin": "^6.9.1",
+    "@typescript-eslint/parser": "^6.9.1",
     "buffer": "^6.0.3",
     "documentation": "^14.0.1",
     "eslint": "^8.30.0",
-    "eslint-config-prettier": "^8.5.0",
+    "eslint-config-prettier": "^9.0.0",
     "eslint-plugin-import": "^2.25.4",
-    "eslint-plugin-prettier": "^4.0.0",
+    "eslint-plugin-prettier": "^5.0.1",
     "glob": "^10.3.1",
     "jest": "^29.3.1",
     "mock-fs": "^5.2.0",
-    "prettier": "^2.8.1",
+    "prettier": "^3.0.3",
     "rimraf": "^5.0.1",
     "ts-jest": "^29.0.3",
     "typescript": "^5.0.3",
     "url": "^0.11.0",
-    "webpack": "5.88.1",
+    "webpack": "5.89.0",
     "webpack-cli": "^5.0.1"
   },
   "publishConfig": {

package/src/cramFile/container/index.ts

@@ -6,7 +6,10 @@ import CramContainerCompressionScheme from './compressionScheme'
 import CramFile from '../file'
 
 export default class CramContainer {
-  constructor(public file: CramFile, public filePosition: number) {}
+  constructor(
+    public file: CramFile,
+    public filePosition: number,
+  ) {}
 
   // memoize
   getHeader() {

package/src/cramFile/file.ts

@@ -1,9 +1,11 @@
 import { unzip } from '../unzip'
 import crc32 from 'buffer-crc32'
 import QuickLRU from 'quick-lru'
+import htscodecs from '@jkbonfield/htscodecs'
+import { Parser } from '@gmod/binary-parser'
 // @ts-expect-error
 import bzip2 from 'bzip2'
-
+import { XzReadableStream } from 'xz-decompress'
 import { CramMalformedError, CramUnimplementedError } from '../errors'
 import ransuncompress from '../rans'
 import {
@@ -12,16 +14,24 @@ import {
   cramFileDefinition as cramFileDefinitionParser,
   getSectionParsers,
 } from './sectionParsers'
-import htscodecs from '@jkbonfield/htscodecs'
+
 import CramContainer from './container'
 
 import { open } from '../io'
 import { parseItem, tinyMemoize } from './util'
 import { parseHeaderText } from '../sam'
-import { Parser } from '@gmod/binary-parser'
 import CramRecord from './record'
 import { Filehandle } from './filehandle'
 
+function bufferToStream(buf: Buffer) {
+  return new ReadableStream({
+    start(controller) {
+      controller.enqueue(buf)
+      controller.close()
+    },
+  })
+}
+
 //source:https://abdulapopoola.com/2019/01/20/check-endianness-with-javascript/
 function getEndianness() {
   const uInt32 = new Uint32Array([0x11223344])
@@ -99,17 +109,6 @@ export default class CramFile {
     }
   }
 
-  // toString() {
-  //   if (this.file.filename) {
-  //     return this.file.filename
-  //   }
-  //   if (this.file.url) {
-  //     return this.file.url
-  //   }
-  //
-  //   return '(cram file)'
-  // }
-
   // can just read this object like a filehandle
   read(
     buffer: Buffer,
@@ -247,9 +246,8 @@ export default class CramFile {
     let containerCount = 0
     let position = sectionParsers.cramFileDefinition.maxLength
     while (position + cramContainerHeader1.maxLength + 8 < fileSize) {
-      const currentHeader = await this.getContainerAtPosition(
-        position,
-      ).getHeader()
+      const currentHeader =
+        await this.getContainerAtPosition(position).getHeader()
       if (!currentHeader) {
         break
       }
@@ -319,7 +317,7 @@ export default class CramFile {
     return data
   }
 
-  _uncompress(
+  async _uncompress(
     compressionMethod: CompressionMethod,
     inputBuffer: Buffer,
     outputBuffer: Buffer,
@@ -340,6 +338,12 @@ export default class CramFile {
           size -= chunk.length
         }
       } while (chunk != -1)
+    } else if (compressionMethod === 'lzma') {
+      const decompressedResponse = new Response(
+        new XzReadableStream(bufferToStream(inputBuffer)),
+      )
+      const ret = Buffer.from(await decompressedResponse.arrayBuffer())
+      ret.copy(outputBuffer)
     } else if (compressionMethod === 'rans') {
       ransuncompress(inputBuffer, outputBuffer)
       //htscodecs r4x8 is slower, but compatible.
@@ -386,7 +390,7 @@ export default class CramFile {
         blockContentPosition,
       )
 
-      this._uncompress(
+      await this._uncompress(
         blockHeader.compressionMethod,
         compressedData,
         uncompressedData,

package/src/rans/{d04.js → d04.ts}

@@ -1,3 +1,4 @@
+//@ts-nocheck
 import { CramMalformedError } from '../errors'
 
 import { TF_SHIFT } from './constants'

package/src/rans/{d14.js → d14.ts}

@@ -1,3 +1,4 @@
+//@ts-nocheck
 import { TF_SHIFT } from './constants'
 import Decoding from './decoding'
 

package/src/rans/{decoding.js → decoding.ts}

@@ -1,3 +1,4 @@
+//@ts-nocheck
 import { CramMalformedError } from '../errors'
 
 import { RANS_BYTE_L } from './constants'

package/src/rans/{frequencies.js → frequencies.ts}

@@ -1,3 +1,4 @@
+//@ts-nocheck
 import { CramMalformedError } from '../errors'
 
 import { TOTFREQ } from './constants'

package/src/rans/{index.js → index.ts}

@@ -1,3 +1,4 @@
+//@ts-nocheck
 import { CramMalformedError } from '../errors'
 
 import Decoding from './decoding'