@gmod/cram 6.0.0 → 7.0.0

package/esm/cramFile/file.js.map

@@ -1 +1 @@
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package/esm/htscodecs/index.d.ts

@@ -1,5 +1 @@
-export declare function r4x8_uncompress(inputBuffer: Uint8Array): Uint8Array<any>;
-export declare function r4x16_uncompress(inputBuffer: Uint8Array): any;
-export declare function arith_uncompress(inputBuffer: Uint8Array): Uint8Array<any>;
-export declare function fqzcomp_uncompress(inputBuffer: Uint8Array): Uint8Array<ArrayBuffer> | undefined;
-export declare function tok3_uncompress(inputBuffer: Uint8Array): Uint8Array<ArrayBuffer>;
+export { rans_uncompress, rans_uncompress as r4x8_uncompress, r4x16_uncompress, arith_uncompress, fqzcomp_uncompress, tok3_uncompress, bz2_uncompress, } from '../htscodecs-wasm.ts';

package/esm/htscodecs/index.js

@@ -1,5 +1,3 @@
-// @ts-nocheck
-//
 /*
  * Copyright (c) 2020 Genome Research Ltd.
  * Author(s): James Bonfield
@@ -32,33 +30,7 @@
  * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
  * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-// This is an interface to the htscodecs reference implementation of
-// the CRAM 3.1 codecs.
-// This JavaScript file is not part of the reference implementation
-// and is simply and interface to get a consistent interface for cram-js.
-import arith from "./arith_gen.js";
-import * as fqzcomp from "./fqzcomp.js";
-import * as r4x8 from "./rans.js";
-import * as r4x16 from "./rans4x16.js";
-import * as tok3 from "./tok3.js";
-export function r4x8_uncompress(inputBuffer) {
-    return r4x8.decode(inputBuffer);
-}
-export function r4x16_uncompress(inputBuffer) {
-    return r4x16.decode(inputBuffer);
-}
-export function arith_uncompress(inputBuffer) {
-    // fix by @cmdcolin for CRAM 3.1
-    // xref https://github.com/jkbonfield/htscodecs/pull/1/files
-    return new arith().decode(inputBuffer);
-}
-export function fqzcomp_uncompress(inputBuffer) {
-    const q_lens = [];
-    return fqzcomp.decode(inputBuffer, q_lens);
-}
-export function tok3_uncompress(inputBuffer) {
-    // Returns in string form instead of buffer
-    const out = tok3.decode(inputBuffer, 0, '\0');
-    return Uint8Array.from(Array.from(out).map(letter => letter.charCodeAt(0)));
-}
+// This is an interface to the htscodecs library compiled to WASM.
+// The WASM module is built from the official samtools/htscodecs C library.
+export { rans_uncompress, rans_uncompress as r4x8_uncompress, r4x16_uncompress, arith_uncompress, fqzcomp_uncompress, tok3_uncompress, bz2_uncompress, } from "../htscodecs-wasm.js";
 //# sourceMappingURL=index.js.map

package/esm/htscodecs/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/htscodecs/index.ts"],"names":[],"mappings":"AAAA,cAAc;AACd,EAAE;AACF;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+BG;AAEH,oEAAoE;AACpE,uBAAuB;AAEvB,mEAAmE;AACnE,yEAAyE;AAEzE,OAAO,KAAK,MAAM,gBAAgB,CAAA;AAClC,OAAO,KAAK,OAAO,MAAM,cAAc,CAAA;AACvC,OAAO,KAAK,IAAI,MAAM,WAAW,CAAA;AACjC,OAAO,KAAK,KAAK,MAAM,eAAe,CAAA;AACtC,OAAO,KAAK,IAAI,MAAM,WAAW,CAAA;AAEjC,MAAM,UAAU,eAAe,CAAC,WAAuB;IACrD,OAAO,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,CAAA;AACjC,CAAC;AAED,MAAM,UAAU,gBAAgB,CAAC,WAAuB;IACtD,OAAO,KAAK,CAAC,MAAM,CAAC,WAAW,CAAC,CAAA;AAClC,CAAC;AAED,MAAM,UAAU,gBAAgB,CAAC,WAAuB;IACtD,gCAAgC;IAChC,4DAA4D;IAC5D,OAAO,IAAI,KAAK,EAAE,CAAC,MAAM,CAAC,WAAW,CAAC,CAAA;AACxC,CAAC;AAED,MAAM,UAAU,kBAAkB,CAAC,WAAuB;IACxD,MAAM,MAAM,GAAG,EAAE,CAAA;IACjB,OAAO,OAAO,CAAC,MAAM,CAAC,WAAW,EAAE,MAAM,CAAC,CAAA;AAC5C,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,WAAuB;IACrD,2CAA2C;IAC3C,MAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,EAAE,IAAI,CAAC,CAAA;IAC7C,OAAO,UAAU,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,MAAM,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AAC7E,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/htscodecs/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+BG;AAEH,kEAAkE;AAClE,2EAA2E;AAE3E,OAAO,EACL,eAAe,EACf,eAAe,IAAI,eAAe,EAClC,gBAAgB,EAChB,gBAAgB,EAChB,kBAAkB,EAClB,eAAe,EACf,cAAc,GACf,MAAM,sBAAsB,CAAA"}

package/esm/htscodecs-wasm.d.ts

@@ -0,0 +1,7 @@
+export declare function rans_uncompress(input: Uint8Array): Promise<Uint8Array<ArrayBuffer>>;
+export declare function r4x16_uncompress(input: Uint8Array): Promise<Uint8Array<ArrayBuffer>>;
+export declare function arith_uncompress(input: Uint8Array): Promise<Uint8Array<ArrayBuffer>>;
+export declare function fqzcomp_uncompress(input: Uint8Array): Promise<Uint8Array<ArrayBuffer>>;
+export declare function zlib_uncompress(input: Uint8Array): Promise<Uint8Array<ArrayBuffer>>;
+export declare function bz2_uncompress(input: Uint8Array, expectedSize: number): Promise<Uint8Array<ArrayBuffer>>;
+export declare function tok3_uncompress(input: Uint8Array): Promise<Uint8Array<ArrayBuffer>>;

package/esm/htscodecs-wasm.js

@@ -0,0 +1,171 @@
+import createHtsCodecsModule from './wasm/htscodecs.js';
+let moduleInstance = null;
+let modulePromise = null;
+async function getModule() {
+    if (moduleInstance) {
+        return moduleInstance;
+    }
+    if (!modulePromise) {
+        modulePromise = createHtsCodecsModule().then(m => {
+            moduleInstance = m;
+            return m;
+        });
+    }
+    return modulePromise;
+}
+function copyToWasm(module, data) {
+    const ptr = module._malloc(data.length);
+    module.HEAPU8.set(data, ptr);
+    return ptr;
+}
+function copyFromWasm(module, ptr, size) {
+    const result = new Uint8Array(size);
+    result.set(module.HEAPU8.subarray(ptr, ptr + size));
+    return result;
+}
+export async function rans_uncompress(input) {
+    // Handle empty input - C implementation returns NULL for in_size < 9
+    if (input.length === 0) {
+        return new Uint8Array(0);
+    }
+    const module = await getModule();
+    const inPtr = copyToWasm(module, input);
+    const outSizePtr = module._malloc(4);
+    try {
+        const outPtr = module._rans_uncompress(inPtr, input.length, outSizePtr);
+        if (outPtr === 0) {
+            throw new Error('rans_uncompress failed');
+        }
+        const outSize = module.getValue(outSizePtr, 'i32');
+        const result = copyFromWasm(module, outPtr, outSize);
+        module._free(outPtr);
+        return result;
+    }
+    finally {
+        module._free(inPtr);
+        module._free(outSizePtr);
+    }
+}
+export async function r4x16_uncompress(input) {
+    const module = await getModule();
+    const inPtr = copyToWasm(module, input);
+    const outSizePtr = module._malloc(4);
+    try {
+        const outPtr = module._rans_uncompress_4x16(inPtr, input.length, outSizePtr);
+        if (outPtr === 0) {
+            throw new Error('rans_uncompress_4x16 failed');
+        }
+        const outSize = module.getValue(outSizePtr, 'i32');
+        const result = copyFromWasm(module, outPtr, outSize);
+        module._free(outPtr);
+        return result;
+    }
+    finally {
+        module._free(inPtr);
+        module._free(outSizePtr);
+    }
+}
+export async function arith_uncompress(input) {
+    const module = await getModule();
+    const inPtr = copyToWasm(module, input);
+    const outSizePtr = module._malloc(4);
+    try {
+        const outPtr = module._arith_uncompress(inPtr, input.length, outSizePtr);
+        if (outPtr === 0) {
+            throw new Error('arith_uncompress failed');
+        }
+        const outSize = module.getValue(outSizePtr, 'i32');
+        const result = copyFromWasm(module, outPtr, outSize);
+        module._free(outPtr);
+        return result;
+    }
+    finally {
+        module._free(inPtr);
+        module._free(outSizePtr);
+    }
+}
+export async function fqzcomp_uncompress(input) {
+    const module = await getModule();
+    const inPtr = copyToWasm(module, input);
+    const outSizePtr = module._malloc(4);
+    const lenPtr = module._malloc(4);
+    try {
+        const outPtr = module._fqz_decompress(inPtr, input.length, outSizePtr, lenPtr);
+        if (outPtr === 0) {
+            throw new Error('fqz_decompress failed');
+        }
+        const outSize = module.getValue(outSizePtr, 'i32');
+        const result = copyFromWasm(module, outPtr, outSize);
+        module._free(outPtr);
+        return result;
+    }
+    finally {
+        module._free(inPtr);
+        module._free(outSizePtr);
+        module._free(lenPtr);
+    }
+}
+export async function zlib_uncompress(input) {
+    if (input.length === 0) {
+        return new Uint8Array(0);
+    }
+    const module = await getModule();
+    const inPtr = copyToWasm(module, input);
+    const outSizePtr = module._malloc(4);
+    try {
+        const outPtr = module._zlib_uncompress(inPtr, input.length, outSizePtr);
+        if (outPtr === 0) {
+            throw new Error('zlib_uncompress failed');
+        }
+        const outSize = module.getValue(outSizePtr, 'i32');
+        const result = copyFromWasm(module, outPtr, outSize);
+        module._free(outPtr);
+        return result;
+    }
+    finally {
+        module._free(inPtr);
+        module._free(outSizePtr);
+    }
+}
+export async function bz2_uncompress(input, expectedSize) {
+    if (input.length === 0) {
+        return new Uint8Array(0);
+    }
+    const module = await getModule();
+    const inPtr = copyToWasm(module, input);
+    const outSizePtr = module._malloc(4);
+    try {
+        const outPtr = module._bz2_uncompress(inPtr, input.length, expectedSize, outSizePtr);
+        if (outPtr === 0) {
+            throw new Error('bz2_uncompress failed');
+        }
+        const outSize = module.getValue(outSizePtr, 'i32');
+        const result = copyFromWasm(module, outPtr, outSize);
+        module._free(outPtr);
+        return result;
+    }
+    finally {
+        module._free(inPtr);
+        module._free(outSizePtr);
+    }
+}
+export async function tok3_uncompress(input) {
+    const module = await getModule();
+    const inPtr = copyToWasm(module, input);
+    const outSizePtr = module._malloc(4);
+    try {
+        const outPtr = module._tok3_decode_names(inPtr, input.length, outSizePtr);
+        if (outPtr === 0) {
+            throw new Error('tok3_decode_names failed');
+        }
+        const outSize = module.getValue(outSizePtr, 'i32');
+        const result = copyFromWasm(module, outPtr, outSize);
+        module._free(outPtr);
+        return result;
+    }
+    finally {
+        module._free(inPtr);
+        module._free(outSizePtr);
+    }
+}
+//# sourceMappingURL=htscodecs-wasm.js.map

package/esm/htscodecs-wasm.js.map

@@ -0,0 +1 @@
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package/esm/unzip.d.ts

@@ -1 +1 @@
-export declare function unzip(input: Uint8Array): Uint8Array;
+export declare function unzip(input: Uint8Array): Promise<Uint8Array>;

package/esm/unzip.js

@@ -1,5 +1,5 @@
-import { inflate } from 'pako-esm2';
-export function unzip(input) {
-    return inflate(input, undefined);
+import { zlib_uncompress } from "./htscodecs-wasm.js";
+export async function unzip(input) {
+    return zlib_uncompress(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,OAAO,EAAE,MAAM,WAAW,CAAA;AAEnC,MAAM,UAAU,KAAK,CAAC,KAAiB;IACrC,OAAO,OAAO,CAAC,KAAK,EAAE,SAAS,CAAC,CAAA;AAClC,CAAC"}
+{"version":3,"file":"unzip.js","sourceRoot":"","sources":["../src/unzip.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,eAAe,EAAE,MAAM,qBAAqB,CAAA;AAErD,MAAM,CAAC,KAAK,UAAU,KAAK,CAAC,KAAiB;IAC3C,OAAO,eAAe,CAAC,KAAK,CAAC,CAAA;AAC/B,CAAC"}

package/esm/wasm/htscodecs.d.ts

@@ -0,0 +1,5 @@
+export = createHtsCodecsModule;
+declare function createHtsCodecsModule(moduleArg?: {}): Promise<{}>;
+declare namespace createHtsCodecsModule {
+    export { createHtsCodecsModule as default };
+}

package/esm/wasm/htscodecs.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/cram",
-  "version": "6.0.0",
+  "version": "7.0.0",
   "description": "read CRAM files with pure Javascript",
   "license": "MIT",
   "repository": "GMOD/cram-js",
@@ -34,9 +34,10 @@
     "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 src/cramFile/file.ts --section=CramFile; documentation readme --shallow src/cramFile/record.ts --section=CramRecord",
     "prebuild": "yarn clean",
     "clean": "rimraf dist esm",
+    "build:wasm": "./htscodecs-wasm/build.sh",
     "build:esm": "tsc --outDir esm",
     "build:es5": "tsc --module commonjs --outDir dist",
-    "build": "yarn build:esm && yarn build:es5",
+    "build": "yarn build:wasm && yarn build:esm && yarn build:es5",
     "postbuild": "webpack",
     "postbuild:es5": "echo '{\"type\": \"commonjs\"}' > dist/package.json",
     "preversion": "yarn test --run && yarn build",
@@ -50,26 +51,25 @@
   ],
   "dependencies": {
     "crc": "^4.3.2",
-    "generic-filehandle2": "^2.0.12",
+    "generic-filehandle2": "^2.0.15",
     "md5": "^2.2.1",
-    "pako-esm2": "^1.0.15",
     "quick-lru": "^4.0.1"
   },
   "devDependencies": {
-    "@gmod/indexedfasta": "^4.0.6",
+    "@gmod/indexedfasta": "^5.0.0",
     "@types/md5": "^2.3.2",
-    "@vitest/coverage-v8": "^4.0.3",
+    "@vitest/coverage-v8": "^4.0.15",
     "buffer": "^6.0.3",
     "documentation": "^14.0.3",
     "eslint": "^9.29.0",
     "eslint-plugin-import": "^2.31.0",
     "eslint-plugin-unicorn": "^62.0.0",
     "mock-fs": "^5.2.0",
-    "prettier": "^3.2.5",
+    "prettier": "^3.7.4",
     "rimraf": "^6.0.1",
     "typescript": "^5.7.0",
-    "typescript-eslint": "^8.34.0",
-    "vitest": "^4.0.3",
+    "typescript-eslint": "^8.49.0",
+    "vitest": "^4.0.15",
     "webpack": "^5.99.9",
     "webpack-cli": "^6.0.1"
   },

package/src/craiIndex.ts

@@ -34,7 +34,7 @@ function addRecordToIndex(index: ParsedIndex, record: number[]) {
   })
 }
 
-function maybeUnzip(data: Uint8Array) {
+async function maybeUnzip(data: Uint8Array) {
   return data[0] === 31 && data[1] === 139 ? unzip(data) : data
 }
 
@@ -68,7 +68,9 @@ export default class CraiIndex {
 
   async parseIndex() {
     const index: ParsedIndex = {}
-    const uncompressedBuffer = maybeUnzip(await this.filehandle.readFile())
+    const uncompressedBuffer = await maybeUnzip(
+      await this.filehandle.readFile(),
+    )
     const dataView = new DataView(uncompressedBuffer.buffer)
     if (
       uncompressedBuffer.length > 4 &&

package/src/cramFile/file.ts

@@ -4,10 +4,8 @@ import QuickLRU from 'quick-lru'
 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 { parseItem, tinyMemoize } from './util.ts'
-import { decode } from '../seek-bzip/index.ts'
 import { unzip } from '../unzip.ts'
 import CramContainer from './container/index.ts'
 import CramRecord from './record.ts'
@@ -285,23 +283,21 @@ export default class CramFile {
   ) {
     // console.log({ compressionMethod })
     if (compressionMethod === 'gzip') {
-      return unzip(inputBuffer)
+      return await unzip(inputBuffer)
     } else if (compressionMethod === 'bzip2') {
-      return decode(inputBuffer)
+      return await htscodecs.bz2_uncompress(inputBuffer, uncompressedSize)
     } else if (compressionMethod === 'lzma') {
       return xzDecompress(inputBuffer)
     } else if (compressionMethod === 'rans') {
-      const outputBuffer = new Uint8Array(uncompressedSize)
-      ransuncompress(inputBuffer, outputBuffer)
-      return outputBuffer
+      return await htscodecs.rans_uncompress(inputBuffer)
     } else if (compressionMethod === 'rans4x16') {
-      return htscodecs.r4x16_uncompress(inputBuffer)
+      return await htscodecs.r4x16_uncompress(inputBuffer)
     } else if (compressionMethod === 'arith') {
-      return htscodecs.arith_uncompress(inputBuffer)
+      return await htscodecs.arith_uncompress(inputBuffer)
     } else if (compressionMethod === 'fqzcomp') {
-      return htscodecs.fqzcomp_uncompress(inputBuffer)
+      return await htscodecs.fqzcomp_uncompress(inputBuffer)
     } else if (compressionMethod === 'tok3') {
-      return htscodecs.tok3_uncompress(inputBuffer)
+      return await htscodecs.tok3_uncompress(inputBuffer)
     } else {
       throw new CramUnimplementedError(
         `${compressionMethod} decompression not yet implemented`,

package/src/htscodecs/index.ts

@@ -1,5 +1,3 @@
-// @ts-nocheck
-//
 /*
  * Copyright (c) 2020 Genome Research Ltd.
  * Author(s): James Bonfield
@@ -33,39 +31,15 @@
  * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-// This is an interface to the htscodecs reference implementation of
-// the CRAM 3.1 codecs.
-
-// This JavaScript file is not part of the reference implementation
-// and is simply and interface to get a consistent interface for cram-js.
-
-import arith from './arith_gen.ts'
-import * as fqzcomp from './fqzcomp.ts'
-import * as r4x8 from './rans.ts'
-import * as r4x16 from './rans4x16.ts'
-import * as tok3 from './tok3.ts'
-
-export function r4x8_uncompress(inputBuffer: Uint8Array) {
-  return r4x8.decode(inputBuffer)
-}
-
-export function r4x16_uncompress(inputBuffer: Uint8Array) {
-  return r4x16.decode(inputBuffer)
-}
-
-export function arith_uncompress(inputBuffer: Uint8Array) {
-  // fix by @cmdcolin for CRAM 3.1
-  // xref https://github.com/jkbonfield/htscodecs/pull/1/files
-  return new arith().decode(inputBuffer)
-}
-
-export function fqzcomp_uncompress(inputBuffer: Uint8Array) {
-  const q_lens = []
-  return fqzcomp.decode(inputBuffer, q_lens)
-}
-
-export function tok3_uncompress(inputBuffer: Uint8Array) {
-  // Returns in string form instead of buffer
-  const out = tok3.decode(inputBuffer, 0, '\0')
-  return Uint8Array.from(Array.from(out).map(letter => letter.charCodeAt(0)))
-}
+// This is an interface to the htscodecs library compiled to WASM.
+// The WASM module is built from the official samtools/htscodecs C library.
+
+export {
+  rans_uncompress,
+  rans_uncompress as r4x8_uncompress,
+  r4x16_uncompress,
+  arith_uncompress,
+  fqzcomp_uncompress,
+  tok3_uncompress,
+  bz2_uncompress,
+} from '../htscodecs-wasm.ts'