@gmod/cram 4.0.6 → 4.0.8

package/dist/cramFile/file.d.ts

@@ -77,6 +77,7 @@ export default class CramFile {
         _endPosition: number;
         _size: number;
     }>;
+    _uncompressPre(compressionMethod: CompressionMethod, inputBuffer: Uint8Array, uncompressedSize: number): Promise<any>;
     _uncompress(compressionMethod: CompressionMethod, inputBuffer: Uint8Array, uncompressedSize: number): Promise<any>;
     readBlock(position: number): Promise<CramFileBlock>;
 }

package/dist/cramFile/file.js

@@ -1,4 +1,7 @@
 "use strict";
+// import bzip2 from 'bzip2'
+// import BZip2 from 'bzip2-wasm'
+// import { decompress } from 'bz2'
 var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
     if (k2 === undefined) k2 = k;
     var desc = Object.getOwnPropertyDescriptor(m, k);
@@ -36,9 +39,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const bzip2_1 = __importDefault(require("bzip2"));
 const crc32_1 = __importDefault(require("crc/calculators/crc32"));
 const quick_lru_1 = __importDefault(require("quick-lru"));
+const seek_bzip_1 = __importDefault(require("seek-bzip"));
 const xz_decompress_1 = require("xz-decompress");
 const errors_1 = require("../errors");
 const htscodecs = __importStar(require("../htscodecs"));
@@ -46,10 +49,9 @@ const io_1 = require("../io");
 const rans_1 = __importDefault(require("../rans"));
 const sam_1 = require("../sam");
 const unzip_1 = require("../unzip");
-const util_1 = require("../util");
 const container_1 = __importDefault(require("./container"));
 const sectionParsers_1 = require("./sectionParsers");
-const util_2 = require("./util");
+const util_1 = require("./util");
 function bufferToStream(buf) {
     return new ReadableStream({
         start(controller) {
@@ -213,33 +215,27 @@ class CramFile {
         const sectionParsers = (0, sectionParsers_1.getSectionParsers)(majorVersion);
         const { cramBlockHeader } = sectionParsers;
         const buffer = await this.file.read(cramBlockHeader.maxLength, position);
-        return (0, util_2.parseItem)(buffer, cramBlockHeader.parser, 0, position);
+        return (0, util_1.parseItem)(buffer, cramBlockHeader.parser, 0, position);
     }
     async _parseSection(section, position, size = section.maxLength, preReadBuffer) {
         const buffer = preReadBuffer ?? (await this.file.read(size, position));
-        const data = (0, util_2.parseItem)(buffer, section.parser, 0, position);
+        const data = (0, util_1.parseItem)(buffer, section.parser, 0, position);
         if (data._size !== size) {
             throw new errors_1.CramMalformedError(`section read error: requested size ${size} does not equal parsed size ${data._size}`);
         }
         return data;
     }
-    async _uncompress(compressionMethod, inputBuffer, uncompressedSize) {
+    async _uncompressPre(compressionMethod, inputBuffer, uncompressedSize) {
+        // console.log({ compressionMethod })
         if (compressionMethod === 'gzip') {
-            return (0, unzip_1.unzip)(inputBuffer);
+            const ret = (0, unzip_1.unzip)(inputBuffer);
+            if (ret[0] === 24) {
+                // console.log(ret.slice(0, 500).join(','))
+            }
+            return ret;
         }
         else if (compressionMethod === 'bzip2') {
-            const bits = bzip2_1.default.array(inputBuffer);
-            let size = bzip2_1.default.header(bits);
-            let chunk;
-            const chunks = [];
-            do {
-                chunk = bzip2_1.default.decompress(bits, size);
-                if (chunk !== -1) {
-                    chunks.push(chunk);
-                    size -= chunk.length;
-                }
-            } while (chunk !== -1);
-            return (0, util_1.concatUint8Array)(chunks);
+            return seek_bzip_1.default.decode(inputBuffer);
         }
         else if (compressionMethod === 'lzma') {
             const decompressedResponse = new Response(new xz_decompress_1.XzReadableStream(bufferToStream(inputBuffer)));
@@ -268,6 +264,15 @@ class CramFile {
             throw new errors_1.CramUnimplementedError(`${compressionMethod} decompression not yet implemented`);
         }
     }
+    async _uncompress(compressionMethod, inputBuffer, uncompressedSize) {
+        const buf = await this._uncompressPre(compressionMethod, inputBuffer, uncompressedSize);
+        if (buf.length !== uncompressedSize) {
+            const ret = new Uint8Array(uncompressedSize);
+            ret.set(buf, 0);
+            return ret;
+        }
+        return buf;
+    }
     async readBlock(position) {
         const { majorVersion } = await this.getDefinition();
         const sectionParsers = (0, sectionParsers_1.getSectionParsers)(majorVersion);
@@ -305,6 +310,6 @@ class CramFile {
 }
 exports.default = CramFile;
 'getDefinition getSectionParsers getSamHeader'.split(' ').forEach(method => {
-    (0, util_2.tinyMemoize)(CramFile, method);
+    (0, util_1.tinyMemoize)(CramFile, method);
 });
 //# sourceMappingURL=file.js.map

package/dist/cramFile/file.js.map

@@ -1 +1 @@
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package/dist/cramFile/slice/decodeRecord.js.map

@@ -1 +1 @@
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package/dist/htscodecs/arith_gen.d.ts

@@ -5,7 +5,7 @@ export default class RangeCoderGen {
     decodeStream(stream: IOStream, n_out?: number): Uint8Array<any>;
     decode0(stream: any, n_out: any): Uint8Array<any>;
     decode1(stream: any, n_out: any): Uint8Array<any>;
-    decodeExt(stream: any, n_out: any): Uint8Array<ArrayBuffer>;
+    decodeExt(stream: any, n_out: any): any;
     decodeRLE0(stream: any, n_out: any): Uint8Array<any>;
     decodeRLE1(stream: any, n_out: any): Uint8Array<any>;
     decodePackMeta(stream: any): any[];

package/dist/htscodecs/arith_gen.js

@@ -37,11 +37,10 @@ Object.defineProperty(exports, "__esModule", { value: true });
  * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
  * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-const bzip2_1 = __importDefault(require("bzip2"));
+const seek_bzip_1 = __importDefault(require("seek-bzip"));
 const arith_sh_1 = __importDefault(require("./arith_sh"));
 const byte_model_1 = __importDefault(require("./byte_model"));
 const iostream_1 = __importDefault(require("./iostream"));
-const util_1 = require("../util");
 const ARITH_ORDER = 1;
 const ARITH_EXT = 4;
 const ARITH_STRIPE = 8;
@@ -134,18 +133,7 @@ class RangeCoderGen {
     // ----------------------------------------------------------------------
     // External codec
     decodeExt(stream, n_out) {
-        const bits = bzip2_1.default.array(stream.buf.slice(stream.pos));
-        let size = bzip2_1.default.header(bits);
-        let chunk;
-        const chunks = [];
-        do {
-            chunk = bzip2_1.default.decompress(bits, size);
-            if (chunk !== -1) {
-                chunks.push(chunk);
-                size -= chunk.length;
-            }
-        } while (chunk !== -1);
-        return (0, util_1.concatUint8Array)(chunks);
+        return seek_bzip_1.default.decode(stream.buf.slice(stream.pos));
     }
     // ----------------------------------------------------------------------
     // Order-0 RLE codec

package/dist/htscodecs/arith_gen.js.map

@@ -1 +1 @@
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package/esm/cramFile/file.d.ts

@@ -77,6 +77,7 @@ export default class CramFile {
         _endPosition: number;
         _size: number;
     }>;
+    _uncompressPre(compressionMethod: CompressionMethod, inputBuffer: Uint8Array, uncompressedSize: number): Promise<any>;
     _uncompress(compressionMethod: CompressionMethod, inputBuffer: Uint8Array, uncompressedSize: number): Promise<any>;
     readBlock(position: number): Promise<CramFileBlock>;
 }

package/esm/cramFile/file.js

@@ -1,6 +1,9 @@
-import bzip2 from 'bzip2';
+// 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';
@@ -8,7 +11,6 @@ import { open } from '../io';
 import ransuncompress from '../rans';
 import { parseHeaderText } from '../sam';
 import { unzip } from '../unzip';
-import { concatUint8Array } from '../util';
 import CramContainer from './container';
 import { cramFileDefinition, getSectionParsers, } from './sectionParsers';
 import { parseItem, tinyMemoize } from './util';
@@ -185,23 +187,17 @@ export default class CramFile {
         }
         return data;
     }
-    async _uncompress(compressionMethod, inputBuffer, uncompressedSize) {
+    async _uncompressPre(compressionMethod, inputBuffer, uncompressedSize) {
+        // console.log({ compressionMethod })
         if (compressionMethod === 'gzip') {
-            return unzip(inputBuffer);
+            const ret = unzip(inputBuffer);
+            if (ret[0] === 24) {
+                // console.log(ret.slice(0, 500).join(','))
+            }
+            return ret;
         }
         else if (compressionMethod === 'bzip2') {
-            const bits = bzip2.array(inputBuffer);
-            let size = bzip2.header(bits);
-            let chunk;
-            const chunks = [];
-            do {
-                chunk = bzip2.decompress(bits, size);
-                if (chunk !== -1) {
-                    chunks.push(chunk);
-                    size -= chunk.length;
-                }
-            } while (chunk !== -1);
-            return concatUint8Array(chunks);
+            return Bunzip.decode(inputBuffer);
         }
         else if (compressionMethod === 'lzma') {
             const decompressedResponse = new Response(new XzReadableStream(bufferToStream(inputBuffer)));
@@ -230,6 +226,15 @@ export default class CramFile {
             throw new CramUnimplementedError(`${compressionMethod} decompression not yet implemented`);
         }
     }
+    async _uncompress(compressionMethod, inputBuffer, uncompressedSize) {
+        const buf = await this._uncompressPre(compressionMethod, inputBuffer, uncompressedSize);
+        if (buf.length !== uncompressedSize) {
+            const ret = new Uint8Array(uncompressedSize);
+            ret.set(buf, 0);
+            return ret;
+        }
+        return buf;
+    }
     async readBlock(position) {
         const { majorVersion } = await this.getDefinition();
         const sectionParsers = getSectionParsers(majorVersion);

package/esm/cramFile/file.js.map

@@ -1 +1 @@
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package/esm/cramFile/slice/decodeRecord.js.map

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

@@ -5,7 +5,7 @@ export default class RangeCoderGen {
     decodeStream(stream: IOStream, n_out?: number): Uint8Array<any>;
     decode0(stream: any, n_out: any): Uint8Array<any>;
     decode1(stream: any, n_out: any): Uint8Array<any>;
-    decodeExt(stream: any, n_out: any): Uint8Array<ArrayBuffer>;
+    decodeExt(stream: any, n_out: any): any;
     decodeRLE0(stream: any, n_out: any): Uint8Array<any>;
     decodeRLE1(stream: any, n_out: any): Uint8Array<any>;
     decodePackMeta(stream: any): any[];

package/esm/htscodecs/arith_gen.js

@@ -32,11 +32,10 @@
  * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
  * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-import bzip2 from 'bzip2';
+import Bunzip from 'seek-bzip';
 import RangeCoder from './arith_sh';
 import ByteModel from './byte_model';
 import IOStream from './iostream';
-import { concatUint8Array } from '../util';
 const ARITH_ORDER = 1;
 const ARITH_EXT = 4;
 const ARITH_STRIPE = 8;
@@ -129,18 +128,7 @@ export default class RangeCoderGen {
     // ----------------------------------------------------------------------
     // External codec
     decodeExt(stream, n_out) {
-        const bits = bzip2.array(stream.buf.slice(stream.pos));
-        let size = bzip2.header(bits);
-        let chunk;
-        const chunks = [];
-        do {
-            chunk = bzip2.decompress(bits, size);
-            if (chunk !== -1) {
-                chunks.push(chunk);
-                size -= chunk.length;
-            }
-        } while (chunk !== -1);
-        return concatUint8Array(chunks);
+        return Bunzip.decode(stream.buf.slice(stream.pos));
     }
     // ----------------------------------------------------------------------
     // Order-0 RLE codec

package/esm/htscodecs/arith_gen.js.map

@@ -1 +1 @@
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