@gmod/cram 5.1.0 → 6.0.0

package/dist/cram-bundle.js.LICENSE.txt

@@ -1,9 +1,3 @@
-/*!
- * Based on xzwasm (c) Steve Sanderson. License: MIT - https://github.com/SteveSanderson/xzwasm
- * Contains xz-embedded by Lasse Collin and Igor Pavlov. License: Public domain - https://tukaani.org/xz/embedded.html
- * and walloc (c) 2020 Igalia, S.L. License: MIT - https://github.com/wingo/walloc
- */
-
 /*!
  * Determine if an object is a Buffer
  *

package/dist/cramFile/codecs/byteArrayLength.js

@@ -13,11 +13,15 @@ class ByteArrayStopCodec extends _base_ts_1.default {
     decode(slice, coreDataBlock, blocksByContentId, cursors) {
         const lengthCodec = this._getLengthCodec();
         const arrayLength = lengthCodec.decode(slice, coreDataBlock, blocksByContentId, cursors) || 0;
-        const dataCodec = this._getDataCodec();
         const data = new Uint8Array(arrayLength);
-        for (let i = 0; i < arrayLength; i += 1) {
-            data[i] =
-                dataCodec.decode(slice, coreDataBlock, blocksByContentId, cursors) || 0;
+        if (arrayLength > 0) {
+            const dataCodec = this._getDataCodec();
+            // Call decode directly on codec to avoid repeated lookups
+            for (let i = 0; i < arrayLength; i += 1) {
+                data[i] =
+                    dataCodec.decode(slice, coreDataBlock, blocksByContentId, cursors) ||
+                        0;
+            }
         }
         return data;
     }

package/dist/cramFile/codecs/byteArrayLength.js.map

@@ -1 +1 @@
-{"version":3,"file":"byteArrayLength.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayLength.ts"],"names":[],"mappings":";;;;;AAAA,0DAA+C;AAK/C,wCAAwC;AAOxC,MAAqB,kBAAmB,SAAQ,kBAG/C;IAGC,YACE,UAAiD,EACjD,QAAqB,EACrB,gBAAkC;QAElC,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,CAAC,gBAAgB,GAAG,gBAAgB,CAAA;IAC1C,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,WAAW,GAAG,IAAI,CAAC,eAAe,EAAE,CAAA;QAC1C,MAAM,WAAW,GACf,WAAW,CAAC,MAAM,CAAC,KAAK,EAAE,aAAa,EAAE,iBAAiB,EAAE,OAAO,CAAC,IAAI,CAAC,CAAA;QAE3E,MAAM,SAAS,GAAG,IAAI,CAAC,aAAa,EAAE,CAAA;QACtC,MAAM,IAAI,GAAG,IAAI,UAAU,CAAC,WAAW,CAAC,CAAA;QACxC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACxC,IAAI,CAAC,CAAC,CAAC;gBACL,SAAS,CAAC,MAAM,CAAC,KAAK,EAAE,aAAa,EAAE,iBAAiB,EAAE,OAAO,CAAC,IAAI,CAAC,CAAA;QAC3E,CAAC;QAED,OAAO,IAAI,CAAA;IACb,CAAC;IAED,UAAU;IACV,eAAe;QACb,MAAM,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,eAAe,CAAA;QACtD,OAAO,IAAI,CAAC,gBAAgB,CAAC,cAAc,EAAE,KAAK,CAAC,CAAA;IACrD,CAAC;IAED,UAAU;IACV,aAAa;QACX,MAAM,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,cAAc,CAAA;QACrD,OAAO,IAAI,CAAC,gBAAgB,CAAC,cAAc,EAAE,MAAM,CAAC,CAAA;IACtD,CAAC;CACF;AA9CD,qCA8CC;AAED,+BAA+B,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE;IAC1D,IAAA,qBAAW,EAAC,kBAAkB,EAAE,MAAM,CAAC,CAAA;AACzC,CAAC,CAAC,CAAA"}
+{"version":3,"file":"byteArrayLength.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayLength.ts"],"names":[],"mappings":";;;;;AAAA,0DAA+C;AAK/C,wCAAwC;AAOxC,MAAqB,kBAAmB,SAAQ,kBAG/C;IAGC,YACE,UAAiD,EACjD,QAAqB,EACrB,gBAAkC;QAElC,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,CAAC,gBAAgB,GAAG,gBAAgB,CAAA;IAC1C,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,WAAW,GAAG,IAAI,CAAC,eAAe,EAAE,CAAA;QAC1C,MAAM,WAAW,GACf,WAAW,CAAC,MAAM,CAAC,KAAK,EAAE,aAAa,EAAE,iBAAiB,EAAE,OAAO,CAAC,IAAI,CAAC,CAAA;QAE3E,MAAM,IAAI,GAAG,IAAI,UAAU,CAAC,WAAW,CAAC,CAAA;QACxC,IAAI,WAAW,GAAG,CAAC,EAAE,CAAC;YACpB,MAAM,SAAS,GAAG,IAAI,CAAC,aAAa,EAAE,CAAA;YACtC,0DAA0D;YAC1D,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;gBACxC,IAAI,CAAC,CAAC,CAAC;oBACL,SAAS,CAAC,MAAM,CAAC,KAAK,EAAE,aAAa,EAAE,iBAAiB,EAAE,OAAO,CAAC;wBAClE,CAAC,CAAA;YACL,CAAC;QACH,CAAC;QAED,OAAO,IAAI,CAAA;IACb,CAAC;IAED,UAAU;IACV,eAAe;QACb,MAAM,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,eAAe,CAAA;QACtD,OAAO,IAAI,CAAC,gBAAgB,CAAC,cAAc,EAAE,KAAK,CAAC,CAAA;IACrD,CAAC;IAED,UAAU;IACV,aAAa;QACX,MAAM,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,cAAc,CAAA;QACrD,OAAO,IAAI,CAAC,gBAAgB,CAAC,cAAc,EAAE,MAAM,CAAC,CAAA;IACtD,CAAC;CACF;AAlDD,qCAkDC;AAED,+BAA+B,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE;IAC1D,IAAA,qBAAW,EAAC,kBAAkB,EAAE,MAAM,CAAC,CAAA;AACzC,CAAC,CAAC,CAAA"}

package/dist/cramFile/codecs/external.d.ts

@@ -1,11 +1,8 @@
-import CramCodec, { Cursor, Cursors } from './_base.ts';
+import CramCodec, { Cursors } from './_base.ts';
 import { CramFileBlock } from '../file.ts';
 import CramSlice from '../slice/index.ts';
 import { ExternalCramEncoding } from '../encoding.ts';
 export default class ExternalCodec extends CramCodec<'int' | 'byte', ExternalCramEncoding['parameters']> {
-    private readonly _decodeData;
     constructor(parameters: ExternalCramEncoding['parameters'], dataType: 'int' | 'byte');
     decode(_slice: CramSlice, _coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): number | undefined;
-    _decodeInt(contentBlock: CramFileBlock, cursor: Cursor): number;
-    _decodeByte(contentBlock: CramFileBlock, cursor: Cursor): number;
 }

package/dist/cramFile/codecs/external.js

@@ -10,33 +10,28 @@ const getBits_ts_1 = require("./getBits.js");
 class ExternalCodec extends _base_ts_1.default {
     constructor(parameters, dataType) {
         super(parameters, dataType);
-        if (this.dataType === 'int') {
-            this._decodeData = this._decodeInt;
-        }
-        else if (this.dataType === 'byte') {
-            this._decodeData = this._decodeByte;
-        }
-        else {
+        if (this.dataType !== 'int' && this.dataType !== 'byte') {
             throw new errors_ts_1.CramUnimplementedError(`${this.dataType} decoding not yet implemented by EXTERNAL codec`);
         }
     }
     decode(_slice, _coreDataBlock, blocksByContentId, cursors) {
         const { blockContentId } = this.parameters;
         const contentBlock = blocksByContentId[blockContentId];
-        return contentBlock
-            ? this._decodeData(contentBlock, cursors.externalBlocks.getCursor(blockContentId))
-            : undefined;
-    }
-    _decodeInt(contentBlock, cursor) {
-        const [result, bytesRead] = (0, util_ts_1.parseItf8)(contentBlock.content, cursor.bytePosition);
-        cursor.bytePosition = cursor.bytePosition + bytesRead;
-        return result;
-    }
-    _decodeByte(contentBlock, cursor) {
-        if (cursor.bytePosition >= contentBlock.content.length) {
-            throw new getBits_ts_1.CramBufferOverrunError('attempted to read beyond end of block. this file seems truncated.');
+        if (!contentBlock) {
+            return undefined;
+        }
+        const cursor = cursors.externalBlocks.getCursor(blockContentId);
+        if (this.dataType === 'int') {
+            const [result, bytesRead] = (0, util_ts_1.parseItf8)(contentBlock.content, cursor.bytePosition);
+            cursor.bytePosition += bytesRead;
+            return result;
+        }
+        else {
+            if (cursor.bytePosition >= contentBlock.content.length) {
+                throw new getBits_ts_1.CramBufferOverrunError('attempted to read beyond end of block. this file seems truncated.');
+            }
+            return contentBlock.content[cursor.bytePosition++];
         }
-        return contentBlock.content[cursor.bytePosition++];
     }
 }
 exports.default = ExternalCodec;

package/dist/cramFile/codecs/external.js.map

@@ -1 +1 @@
-{"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.ts"],"names":[],"mappings":";;;;;AAAA,0DAAuD;AACvD,+CAAwD;AAGxD,wCAAsC;AACtC,6CAAqD;AAGrD,MAAqB,aAAc,SAAQ,kBAG1C;IAMC,YACE,UAA8C,EAC9C,QAAwB;QAExB,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,UAAU,CAAA;QACpC,CAAC;aAAM,IAAI,IAAI,CAAC,QAAQ,KAAK,MAAM,EAAE,CAAC;YACpC,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,WAAW,CAAA;QACrC,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,kCAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,iDAAiD,CAClE,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,MAAiB,EACjB,cAA6B,EAC7B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,EAAE,cAAc,EAAE,GAAG,IAAI,CAAC,UAAU,CAAA;QAC1C,MAAM,YAAY,GAAG,iBAAiB,CAAC,cAAc,CAAC,CAAA;QACtD,OAAO,YAAY;YACjB,CAAC,CAAC,IAAI,CAAC,WAAW,CACd,YAAY,EACZ,OAAO,CAAC,cAAc,CAAC,SAAS,CAAC,cAAc,CAAC,CACjD;YACH,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,UAAU,CAAC,YAA2B,EAAE,MAAc;QACpD,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,IAAA,mBAAS,EACnC,YAAY,CAAC,OAAO,EACpB,MAAM,CAAC,YAAY,CACpB,CAAA;QACD,MAAM,CAAC,YAAY,GAAG,MAAM,CAAC,YAAY,GAAG,SAAS,CAAA;QACrD,OAAO,MAAM,CAAA;IACf,CAAC;IAED,WAAW,CAAC,YAA2B,EAAE,MAAc;QACrD,IAAI,MAAM,CAAC,YAAY,IAAI,YAAY,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC;YACvD,MAAM,IAAI,mCAAsB,CAC9B,mEAAmE,CACpE,CAAA;QACH,CAAC;QACD,OAAO,YAAY,CAAC,OAAO,CAAC,MAAM,CAAC,YAAY,EAAE,CAAE,CAAA;IACrD,CAAC;CACF;AA1DD,gCA0DC"}
+{"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.ts"],"names":[],"mappings":";;;;;AAAA,0DAA+C;AAC/C,+CAAwD;AAGxD,wCAAsC;AACtC,6CAAqD;AAGrD,MAAqB,aAAc,SAAQ,kBAG1C;IACC,YACE,UAA8C,EAC9C,QAAwB;QAExB,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,IAAI,IAAI,CAAC,QAAQ,KAAK,MAAM,EAAE,CAAC;YACxD,MAAM,IAAI,kCAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,iDAAiD,CAClE,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,MAAiB,EACjB,cAA6B,EAC7B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,EAAE,cAAc,EAAE,GAAG,IAAI,CAAC,UAAU,CAAA;QAC1C,MAAM,YAAY,GAAG,iBAAiB,CAAC,cAAc,CAAC,CAAA;QACtD,IAAI,CAAC,YAAY,EAAE,CAAC;YAClB,OAAO,SAAS,CAAA;QAClB,CAAC;QAED,MAAM,MAAM,GAAG,OAAO,CAAC,cAAc,CAAC,SAAS,CAAC,cAAc,CAAC,CAAA;QAE/D,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,IAAA,mBAAS,EACnC,YAAY,CAAC,OAAO,EACpB,MAAM,CAAC,YAAY,CACpB,CAAA;YACD,MAAM,CAAC,YAAY,IAAI,SAAS,CAAA;YAChC,OAAO,MAAM,CAAA;QACf,CAAC;aAAM,CAAC;YACN,IAAI,MAAM,CAAC,YAAY,IAAI,YAAY,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC;gBACvD,MAAM,IAAI,mCAAsB,CAC9B,mEAAmE,CACpE,CAAA;YACH,CAAC;YACD,OAAO,YAAY,CAAC,OAAO,CAAC,MAAM,CAAC,YAAY,EAAE,CAAE,CAAA;QACrD,CAAC;IACH,CAAC;CACF;AA9CD,gCA8CC"}

package/dist/cramFile/file.d.ts

@@ -31,6 +31,7 @@ export default class CramFile {
     };
     featureCache: QuickLRU<string, Promise<CramRecord[]>>;
     private header;
+    private _sectionParsers?;
     constructor(args: CramFileArgs);
     read(length: number, position: number): Promise<Uint8Array<ArrayBuffer>>;
     getDefinition(): Promise<{
@@ -57,13 +58,7 @@ export default class CramFile {
      */
     containerCount(): Promise<number | undefined>;
     getContainerAtPosition(position: number): CramContainer;
-    readBlockHeader(position: number): Promise<{
-        uncompressedSize: number;
-        compressedSize: number;
-        contentId: number;
-        contentType: "FILE_HEADER" | "COMPRESSION_HEADER" | "MAPPED_SLICE_HEADER" | "UNMAPPED_SLICE_HEADER" | "EXTERNAL_DATA" | "CORE_DATA";
-        compressionMethod: CompressionMethod;
-    } & {
+    readBlockHeader(position: number): Promise<BlockHeader & {
         _endPosition: number;
         _size: number;
     }>;

package/dist/cramFile/file.js

@@ -38,25 +38,17 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const crc32_1 = __importDefault(require("crc/calculators/crc32"));
 const quick_lru_1 = __importDefault(require("quick-lru"));
-const xz_decompress_1 = require("xz-decompress");
 const errors_ts_1 = require("../errors.js");
 const htscodecs = __importStar(require("../htscodecs/index.js"));
 const io_ts_1 = require("../io.js");
 const index_ts_1 = __importDefault(require("../rans/index.js"));
 const sam_ts_1 = require("../sam.js");
+const util_ts_1 = require("./util.js");
 const index_ts_2 = require("../seek-bzip/index.js");
 const unzip_ts_1 = require("../unzip.js");
 const index_ts_3 = __importDefault(require("./container/index.js"));
 const sectionParsers_ts_1 = require("./sectionParsers.js");
-const util_ts_1 = require("./util.js");
-function bufferToStream(buf) {
-    return new ReadableStream({
-        start(controller) {
-            controller.enqueue(buf);
-            controller.close();
-        },
-    });
-}
+const xz_decompress_ts_1 = require("../xz-decompress/xz-decompress.js");
 // source: https://abdulapopoola.com/2019/01/20/check-endianness-with-javascript/
 function getEndianness() {
     const uInt32 = new Uint32Array([0x11223344]);
@@ -129,9 +121,11 @@ class CramFile {
         return this.header;
     }
     async getContainerById(containerNumber) {
-        const { majorVersion } = await this.getDefinition();
-        const sectionParsers = (0, sectionParsers_ts_1.getSectionParsers)(majorVersion);
-        let position = sectionParsers.cramFileDefinition.maxLength;
+        if (!this._sectionParsers) {
+            const { majorVersion } = await this.getDefinition();
+            this._sectionParsers = (0, sectionParsers_ts_1.getSectionParsers)(majorVersion);
+        }
+        let position = this._sectionParsers.cramFileDefinition.maxLength;
         // skip with a series of reads to the proper container
         let currentContainer;
         for (let i = 0; i <= containerNumber; i++) {
@@ -177,10 +171,12 @@ class CramFile {
      * length check, relies on a try catch to read return an error to break
      */
     async containerCount() {
-        const { majorVersion } = await this.getDefinition();
-        const sectionParsers = (0, sectionParsers_ts_1.getSectionParsers)(majorVersion);
+        if (!this._sectionParsers) {
+            const { majorVersion } = await this.getDefinition();
+            this._sectionParsers = (0, sectionParsers_ts_1.getSectionParsers)(majorVersion);
+        }
         let containerCount = 0;
-        let position = sectionParsers.cramFileDefinition.maxLength;
+        let position = this._sectionParsers.cramFileDefinition.maxLength;
         try {
             // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
             while (true) {
@@ -213,9 +209,11 @@ class CramFile {
         return new index_ts_3.default(this, position);
     }
     async readBlockHeader(position) {
-        const { majorVersion } = await this.getDefinition();
-        const sectionParsers = (0, sectionParsers_ts_1.getSectionParsers)(majorVersion);
-        const { cramBlockHeader } = sectionParsers;
+        if (!this._sectionParsers) {
+            const { majorVersion } = await this.getDefinition();
+            this._sectionParsers = (0, sectionParsers_ts_1.getSectionParsers)(majorVersion);
+        }
+        const { cramBlockHeader } = this._sectionParsers;
         const buffer = await this.file.read(cramBlockHeader.maxLength, position);
         return (0, util_ts_1.parseItem)(buffer, cramBlockHeader.parser, 0, position);
     }
@@ -236,8 +234,7 @@ class CramFile {
             return (0, index_ts_2.decode)(inputBuffer);
         }
         else if (compressionMethod === 'lzma') {
-            const decompressedResponse = new Response(new xz_decompress_1.XzReadableStream(bufferToStream(inputBuffer)));
-            return new Uint8Array(await decompressedResponse.arrayBuffer());
+            return (0, xz_decompress_ts_1.xzDecompress)(inputBuffer);
         }
         else if (compressionMethod === 'rans') {
             const outputBuffer = new Uint8Array(uncompressedSize);
@@ -271,7 +268,10 @@ class CramFile {
     }
     async readBlock(position) {
         const { majorVersion } = await this.getDefinition();
-        const sectionParsers = (0, sectionParsers_ts_1.getSectionParsers)(majorVersion);
+        if (!this._sectionParsers) {
+            this._sectionParsers = (0, sectionParsers_ts_1.getSectionParsers)(majorVersion);
+        }
+        const sectionParsers = this._sectionParsers;
         const blockHeader = await this.readBlockHeader(position);
         const blockContentPosition = blockHeader._endPosition;
         const d = await this.file.read(blockHeader.compressedSize, blockContentPosition);

package/dist/cramFile/file.js.map

@@ -1 +1 @@
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package/dist/cramFile/slice/index.js

@@ -280,10 +280,16 @@ class CramSlice {
                 },
             },
         };
+        // Pre-resolve all codecs to avoid repeated lookups
+        const codecCache = new Map();
         const decodeDataSeries = (dataSeriesName) => {
-            const codec = compressionScheme.getCodecForDataSeries(dataSeriesName);
-            if (!codec) {
-                throw new errors_ts_1.CramMalformedError(`no codec defined for ${dataSeriesName} data series`);
+            let codec = codecCache.get(dataSeriesName);
+            if (codec === undefined) {
+                codec = compressionScheme.getCodecForDataSeries(dataSeriesName);
+                if (!codec) {
+                    throw new errors_ts_1.CramMalformedError(`no codec defined for ${dataSeriesName} data series`);
+                }
+                codecCache.set(dataSeriesName, codec);
             }
             return codec.decode(this, coreDataBlock, blocksByContentId, cursors);
         };
@@ -301,8 +307,11 @@ class CramSlice {
             }
             catch (e) {
                 if (e instanceof getBits_ts_1.CramBufferOverrunError) {
-                    console.warn('read attempted beyond end of buffer, file seems truncated.');
-                    break;
+                    const recordsDecoded = i;
+                    const recordsExpected = sliceHeader.parsedContent.numRecords;
+                    throw new errors_ts_1.CramMalformedError(`Failed to decode all records in slice. Decoded ${recordsDecoded} of ${recordsExpected} expected records. ` +
+                        `Buffer overrun suggests either: (1) file is truncated/corrupted, (2) compression scheme is incorrect, ` +
+                        `or (3) there's a bug in the decoder. Original error: ${e.message}`);
                 }
                 else {
                     throw e;

package/dist/cramFile/slice/index.js.map

@@ -1 +1 @@
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package/dist/cramFile/util.js

@@ -181,14 +181,15 @@ function tinyMemoize(_class, methodName) {
     const method = _class.prototype[methodName];
     const memoAttrName = `_memo_${methodName}`;
     _class.prototype[methodName] = function _tinyMemoized() {
-        if (!(memoAttrName in this)) {
-            const res = method.call(this);
+        let res = this[memoAttrName];
+        if (res === undefined) {
+            res = method.call(this);
             this[memoAttrName] = res;
             Promise.resolve(res).catch(() => {
                 delete this[memoAttrName];
             });
         }
-        return this[memoAttrName];
+        return res;
     };
 }
 function sequenceMD5(seq) {

package/dist/cramFile/util.js.map

@@ -1 +1 @@
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package/dist/indexedCramFile.js

@@ -55,10 +55,21 @@ class IndexedCramFile {
         const seqId = seq;
         const slices = await this.index.getEntriesForRange(seqId, start, end);
         // fetch all the slices and parse the feature data
-        const sliceResults = await Promise.all(slices.map(slice => this.getRecordsInSlice(slice, feature => feature.sequenceId === seq &&
-            feature.alignmentStart <= end &&
-            feature.lengthOnRef !== undefined &&
-            feature.alignmentStart + feature.lengthOnRef - 1 >= start)));
+        const sliceResults = await Promise.all(slices.map(slice => this.getRecordsInSlice(slice, feature => {
+            // Check if feature belongs to this sequence
+            if (feature.sequenceId !== seq) {
+                return false;
+            }
+            // For unmapped reads (lengthOnRef is undefined), they are placed at their
+            // mate's position. Include them if that position is within the range.
+            if (feature.lengthOnRef === undefined) {
+                return (feature.alignmentStart >= start && feature.alignmentStart <= end);
+            }
+            // For mapped reads, check if they overlap the requested range
+            // Use > instead of >= for start boundary to match samtools behavior
+            return (feature.alignmentStart <= end &&
+                feature.alignmentStart + feature.lengthOnRef - 1 > start);
+        })));
         let ret = Array.prototype.concat(...sliceResults);
         if (opts.viewAsPairs) {
             const readNames = {};

package/dist/indexedCramFile.js.map

@@ -1 +1 @@
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+{"version":3,"file":"indexedCramFile.js","sourceRoot":"","sources":["../src/indexedCramFile.ts"],"names":[],"mappings":";;;;;AAEA,mEAA0C;AAE1C,2CAAoD;AAmBpD,MAAqB,eAAe;IAIlC;;;;;;;;;;;;;;;OAeG;IACH,YACE,IAUC;QAED,IAAI,CAAC,IAAI;YACP,IAAI,CAAC,IAAI;gBACT,IAAI,kBAAQ,CAAC;oBACX,GAAG,EAAE,IAAI,CAAC,OAAO;oBACjB,IAAI,EAAE,IAAI,CAAC,QAAQ;oBACnB,UAAU,EAAE,IAAI,CAAC,cAAc;oBAC/B,QAAQ,EAAE,IAAI,CAAC,QAAQ;oBACvB,gBAAgB,EAAE,IAAI,CAAC,gBAAgB;oBACvC,SAAS,EAAE,IAAI,CAAC,SAAS;iBAC1B,CAAC,CAAA;QAEJ,IAAI,CAAC,CAAC,IAAI,CAAC,IAAI,YAAY,kBAAQ,CAAC,EAAE,CAAC;YACrC,MAAM,IAAI,KAAK,CAAC,gCAAgC,CAAC,CAAA;QACnD,CAAC;QAED,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,CAAA;IACzB,CAAC;IAED;;;;;OAKG;IACH,KAAK,CAAC,kBAAkB,CACtB,GAAW,EACX,KAAa,EACb,GAAW,EACX,OAII,EAAE;QAEN,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,WAAW,IAAI,KAAK,CAAA;QAC5C,IAAI,CAAC,aAAa,GAAG,IAAI,CAAC,aAAa,IAAI,KAAK,CAAA;QAChD,IAAI,CAAC,aAAa,GAAG,IAAI,CAAC,aAAa,IAAI,MAAM,CAAA;QAEjD,IAAI,OAAO,GAAG,KAAK,QAAQ,EAAE,CAAC;YAC5B,wDAAwD;YACxD,MAAM,IAAI,kCAAsB,CAC9B,yCAAyC,CAC1C,CAAA;QACH,CAAC;QACD,MAAM,KAAK,GAAG,GAAG,CAAA;QACjB,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,kBAAkB,CAAC,KAAK,EAAE,KAAK,EAAE,GAAG,CAAC,CAAA;QAErE,kDAAkD;QAClD,MAAM,YAAY,GAAG,MAAM,OAAO,CAAC,GAAG,CACpC,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CACjB,IAAI,CAAC,iBAAiB,CAAC,KAAK,EAAE,OAAO,CAAC,EAAE;YACtC,4CAA4C;YAC5C,IAAI,OAAO,CAAC,UAAU,KAAK,GAAG,EAAE,CAAC;gBAC/B,OAAO,KAAK,CAAA;YACd,CAAC;YAED,0EAA0E;YAC1E,sEAAsE;YACtE,IAAI,OAAO,CAAC,WAAW,KAAK,SAAS,EAAE,CAAC;gBACtC,OAAO,CACL,OAAO,CAAC,cAAc,IAAI,KAAK,IAAI,OAAO,CAAC,cAAc,IAAI,GAAG,CACjE,CAAA;YACH,CAAC;YAED,8DAA8D;YAC9D,oEAAoE;YACpE,OAAO,CACL,OAAO,CAAC,cAAc,IAAI,GAAG;gBAC7B,OAAO,CAAC,cAAc,GAAG,OAAO,CAAC,WAAW,GAAG,CAAC,GAAG,KAAK,CACzD,CAAA;QACH,CAAC,CAAC,CACH,CACF,CAAA;QAED,IAAI,GAAG,GAAiB,KAAK,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,YAAY,CAAC,CAAA;QAC/D,IAAI,IAAI,CAAC,WAAW,EAAE,CAAC;YACrB,MAAM,SAAS,GAA2B,EAAE,CAAA;YAC5C,MAAM,OAAO,GAA2B,EAAE,CAAA;YAC1C,KAAK,MAAM,IAAI,IAAI,GAAG,EAAE,CAAC;gBACvB,MAAM,IAAI,GAAG,IAAI,CAAC,QAAQ,CAAA;gBAC1B,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;oBACvB,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAA;gBACvC,CAAC;gBACD,MAAM,EAAE,GAAG,IAAI,CAAC,QAAQ,CAAA;gBACxB,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,EAAE,CAAC;oBACrB,SAAS,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;gBACrB,CAAC;gBACD,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBACpB,OAAO,CAAC,EAAE,CAAC,GAAG,CAAC,CAAA;YACjB,CAAC;YACD,MAAM,YAAY,GAA4B,EAAE,CAAA;YAChD,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE;gBAC3C,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;oBACZ,YAAY,CAAC,CAAC,CAAC,GAAG,IAAI,CAAA;gBACxB,CAAC;YACH,CAAC,CAAC,CAAA;YACF,MAAM,YAAY,GAAG,EAAE,CAAA;YACvB,KAAK,MAAM,UAAU,IAAI,GAAG,EAAE,CAAC;gBAC7B,MAAM,IAAI,GAAG,UAAU,CAAC,QAAQ,CAAA;gBAChC,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;oBACvB,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAA;gBACvC,CAAC;gBACD,IACE,YAAY,CAAC,IAAI,CAAC;oBAClB,UAAU,CAAC,IAAI;oBACf,CAAC,UAAU,CAAC,IAAI,CAAC,UAAU,KAAK,KAAK,IAAI,IAAI,CAAC,aAAa,CAAC;oBAC5D,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,cAAc,GAAG,UAAU,CAAC,IAAI,CAAC,cAAc,CAAC;wBAClE,IAAI,CAAC,aAAa,EACpB,CAAC;oBACD,MAAM,UAAU,GAAG,IAAI,CAAC,KAAK,CAAC,kBAAkB,CAC9C,UAAU,CAAC,IAAI,CAAC,UAAU,EAC1B,UAAU,CAAC,IAAI,CAAC,cAAc,EAC9B,UAAU,CAAC,IAAI,CAAC,cAAc,GAAG,CAAC,CACnC,CAAA;oBACD,YAAY,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;gBAC/B,CAAC;YACH,CAAC;YACD,MAAM,UAAU,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;YAClD,IAAI,UAAU,GAAG,EAAa,CAAA;YAC9B,KAAK,MAAM,KAAK,IAAI,UAAU,EAAE,CAAC;gBAC/B,UAAU,CAAC,IAAI,CAAC,GAAG,KAAK,CAAC,CAAA;YAC3B,CAAC;YACD,wBAAwB;YACxB,UAAU,GAAG,UAAU;iBACpB,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,aAAa,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC;iBACxD,MAAM,CACL,CAAC,IAAI,EAAE,GAAG,EAAE,GAAG,EAAE,EAAE,CACjB,CAAC,GAAG,IAAI,IAAI,CAAC,QAAQ,EAAE,KAAK,GAAG,CAAC,GAAG,GAAG,CAAC,CAAE,CAAC,QAAQ,EAAE,CACvD,CAAA;YAEH,MAAM,kBAAkB,GAAG,EAAE,CAAA;YAC7B,MAAM,gBAAgB,GAA4B,EAAE,CAAA;YACpD,KAAK,MAAM,CAAC,IAAI,UAAU,EAAE,CAAC;gBAC3B,IAAI,aAAa,GAAG,IAAI,CAAC,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAA;gBAC5D,IAAI,CAAC,aAAa,EAAE,CAAC;oBACnB,aAAa,GAAG,IAAI,CAAC,iBAAiB,CAAC,CAAC,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,CAAA;oBACrD,IAAI,CAAC,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,EAAE,aAAa,CAAC,CAAA;gBACzD,CAAC;gBACD,kBAAkB,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;gBACtC,MAAM,WAAW,GAAG,aAAa,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE;oBAC7C,MAAM,QAAQ,GAAG,EAAE,CAAA;oBACnB,KAAK,MAAM,OAAO,IAAI,KAAK,EAAE,CAAC;wBAC5B,IAAI,OAAO,CAAC,QAAQ,KAAK,SAAS,EAAE,CAAC;4BACnC,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAA;wBACvC,CAAC;wBACD,IAAI,YAAY,CAAC,OAAO,CAAC,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,OAAO,CAAC,QAAQ,CAAC,EAAE,CAAC;4BACjE,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;wBACxB,CAAC;oBACH,CAAC;oBACD,OAAO,QAAQ,CAAA;gBACjB,CAAC,CAAC,CAAA;gBACF,gBAAgB,CAAC,IAAI,CAAC,WAAW,CAAC,CAAA;YACpC,CAAC;YACD,MAAM,YAAY,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC,gBAAgB,CAAC,CAAA;YACxD,IAAI,YAAY,CAAC,MAAM,EAAE,CAAC;gBACxB,MAAM,QAAQ,GAAG,YAAY,CAAC,MAAM,CAAC,CAAC,MAAM,EAAE,OAAO,EAAE,EAAE,CACvD,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,CACvB,CAAA;gBACD,GAAG,GAAG,GAAG,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAA;YAC5B,CAAC;QACH,CAAC;QACD,OAAO,GAAG,CAAA;IACZ,CAAC;IAED,iBAAiB,CACf,EACE,cAAc,EACd,UAAU,EACV,UAAU,GACyD,E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package/dist/rans/d04.js

@@ -8,6 +8,9 @@ exports.default = uncompress;
 const errors_ts_1 = require("../errors.js");
 const constants_ts_1 = require("./constants.js");
 const decoding_ts_1 = __importDefault(require("./decoding.js"));
+// Inline constants for performance
+const RANS_BYTE_L = 8388608; // 1 << 23
+const MASK = 4095; // (1 << 12) - 1
 function uncompress(
 /* ByteBuffer */ input, 
 /* Decoding.AriDecoder */ D, 
@@ -19,23 +22,46 @@ function uncompress(
     let rans3 = input.getInt();
     const /* int */ outputSize = out.remaining();
     const /* int */ outputEnd = outputSize & ~3;
+    const D_R = D.R;
     for (let i = 0; i < outputEnd; i += 4) {
-        const /* byte */ c0 = D.R[decoding_ts_1.default.get(rans0, constants_ts_1.TF_SHIFT)];
-        const /* byte */ c1 = D.R[decoding_ts_1.default.get(rans1, constants_ts_1.TF_SHIFT)];
-        const /* byte */ c2 = D.R[decoding_ts_1.default.get(rans2, constants_ts_1.TF_SHIFT)];
-        const /* byte */ c3 = D.R[decoding_ts_1.default.get(rans3, constants_ts_1.TF_SHIFT)];
-        out.putAt(i, c0);
-        out.putAt(i + 1, c1);
-        out.putAt(i + 2, c2);
-        out.putAt(i + 3, c3);
-        rans0 = decoding_ts_1.default.advanceSymbolStep(rans0, syms[0xff & c0], constants_ts_1.TF_SHIFT);
-        rans1 = decoding_ts_1.default.advanceSymbolStep(rans1, syms[0xff & c1], constants_ts_1.TF_SHIFT);
-        rans2 = decoding_ts_1.default.advanceSymbolStep(rans2, syms[0xff & c2], constants_ts_1.TF_SHIFT);
-        rans3 = decoding_ts_1.default.advanceSymbolStep(rans3, syms[0xff & c3], constants_ts_1.TF_SHIFT);
-        rans0 = decoding_ts_1.default.renormalize(rans0, input);
-        rans1 = decoding_ts_1.default.renormalize(rans1, input);
-        rans2 = decoding_ts_1.default.renormalize(rans2, input);
-        rans3 = decoding_ts_1.default.renormalize(rans3, input);
+        const /* byte */ c0 = D_R[rans0 & MASK];
+        const /* byte */ c1 = D_R[rans1 & MASK];
+        const /* byte */ c2 = D_R[rans2 & MASK];
+        const /* byte */ c3 = D_R[rans3 & MASK];
+        // Inline putAt to avoid function call overhead
+        out._buffer[i] = c0;
+        out._buffer[i + 1] = c1;
+        out._buffer[i + 2] = c2;
+        out._buffer[i + 3] = c3;
+        const sym0 = syms[0xff & c0];
+        const sym1 = syms[0xff & c1];
+        const sym2 = syms[0xff & c2];
+        const sym3 = syms[0xff & c3];
+        rans0 = sym0.freq * (rans0 >> constants_ts_1.TF_SHIFT) + (rans0 & MASK) - sym0.start;
+        rans1 = sym1.freq * (rans1 >> constants_ts_1.TF_SHIFT) + (rans1 & MASK) - sym1.start;
+        rans2 = sym2.freq * (rans2 >> constants_ts_1.TF_SHIFT) + (rans2 & MASK) - sym2.start;
+        rans3 = sym3.freq * (rans3 >> constants_ts_1.TF_SHIFT) + (rans3 & MASK) - sym3.start;
+        // Inline renormalize to avoid function call overhead
+        if (rans0 < RANS_BYTE_L) {
+            do {
+                rans0 = (rans0 << 8) | (0xff & input.get());
+            } while (rans0 < RANS_BYTE_L);
+        }
+        if (rans1 < RANS_BYTE_L) {
+            do {
+                rans1 = (rans1 << 8) | (0xff & input.get());
+            } while (rans1 < RANS_BYTE_L);
+        }
+        if (rans2 < RANS_BYTE_L) {
+            do {
+                rans2 = (rans2 << 8) | (0xff & input.get());
+            } while (rans2 < RANS_BYTE_L);
+        }
+        if (rans3 < RANS_BYTE_L) {
+            do {
+                rans3 = (rans3 << 8) | (0xff & input.get());
+            } while (rans3 < RANS_BYTE_L);
+        }
     }
     out.setPosition(outputEnd);
     let /* byte */ c;

package/dist/rans/d04.js.map

@@ -1 +1 @@
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