@gmod/cram 5.0.6 → 6.0.0

package/dist/xz-decompress/xz-decompress.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"xz-decompress.js","sourceRoot":"","sources":["../../src/xz-decompress/xz-decompress.ts"],"names":[],"mappings":";AAAA;;;;;;;;GAQG;;AAwFH,oCA0DC;AAhJD,uCAA0D;AAE1D,MAAM,KAAK,GAAG,CAAC,CAAA;AACf,MAAM,aAAa,GAAG,CAAC,CAAA;AAUvB,MAAM,SAAS;IAUb,YAAY,cAAoC;QAC9C,IAAI,CAAC,OAAO,GAAG,cAAc,CAAC,OAAiC,CAAA;QAC/D,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,MAAM,CAAA;QACjC,IAAI,CAAC,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,cAAc,EAAE,CAAA;QACxC,IAAI,CAAC,QAAQ,EAAE,CAAA;QACf,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,KAAM,CAAC,CAAC,CAAE,CAAA;QAC9B,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,KAAM,CAAC,CAAC,CAAE,GAAG,IAAI,CAAC,GAAG,CAAA;QACzC,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,KAAM,CAAC,CAAC,CAAE,GAAG,IAAI,CAAC,GAAG,CAAA;IAC5C,CAAC;IAED,WAAW,CAAC,oBAAgC;QAC1C,IAAI,CAAC,QAAQ,EAAE,CAAA;QACf,MAAM,QAAQ,GAAG,IAAI,CAAC,IAAK,CAAC,QAAQ,CAClC,IAAI,CAAC,OAAO,EACZ,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAC5B,CAAA;QACD,QAAQ,CAAC,GAAG,CAAC,oBAAoB,EAAE,CAAC,CAAC,CAAA;QACrC,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,IAAI,CAAC,GAAG,EAAE,oBAAoB,CAAC,UAAU,CAAC,CAAA;IACtE,CAAC;IAED,aAAa;QACX,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QACrD,IAAI,CAAC,QAAQ,EAAE,CAAA;QACf,IAAI,MAAM,KAAK,KAAK,IAAI,MAAM,KAAK,aAAa,EAAE,CAAC;YACjD,MAAM,IAAI,KAAK,CAAC,0CAA0C,MAAM,EAAE,CAAC,CAAA;QACrE,CAAC;QACD,MAAM,QAAQ,GAAG,IAAI,CAAC,IAAK,CAAC,KAAK,CAC/B,IAAI,CAAC,QAAQ,EACb,IAAI,CAAC,QAAQ,GAAG,YAAY,CAAC,IAAI,CAAC,KAAM,CAAC,CAAC,CAAE,CAC7C,CAAA;QACD,OAAO,EAAE,QAAQ,EAAE,QAAQ,EAAE,MAAM,KAAK,aAAa,EAAE,CAAA;IACzD,CAAC;IAED,OAAO;QACL,IAAI,CAAC,OAAO,CAAC,eAAe,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QACtC,IAAI,CAAC,OAAO,GAAG,IAAW,CAAA;IAC5B,CAAC;IAED,QAAQ;QACN,MAAM,aAAa,GAAG,IAAI,CAAC,MAAM,CAAC,MAAM,CAAA;QACxC,IAAI,aAAa,KAAK,IAAI,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC;YACxC,IAAI,CAAC,IAAI,GAAG,IAAI,UAAU,CAAC,aAAa,EAAE,IAAI,CAAC,GAAG,CAAC,CAAA;YACnD,IAAI,CAAC,KAAK,GAAG,IAAI,WAAW,CAAC,aAAa,EAAE,IAAI,CAAC,GAAG,CAAC,CAAA;QACvD,CAAC;IACH,CAAC;CACF;AAED,IAAI,sBAAiD,CAAA;AACrD,IAAI,eAAiD,CAAA;AACrD,MAAM,WAAW,GAAG,IAAI,UAAU,CAAC,CAAC,CAAC,CAAA;AAErC,KAAK,UAAU,kBAAkB;IAC/B,MAAM,UAAU,GAAG,0BAAU,CAAC,OAAO,CAAC,+BAA+B,EAAE,EAAE,CAAC,CAAA;IAC1E,MAAM,YAAY,GAAG,IAAI,CAAC,UAAU,CAAC,CAAA;IACrC,MAAM,GAAG,GAAG,YAAY,CAAC,MAAM,CAAA;IAC/B,MAAM,SAAS,GAAG,IAAI,UAAU,CAAC,GAAG,CAAC,CAAA;IACrC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC;QAC7B,SAAS,CAAC,CAAC,CAAC,GAAG,YAAY,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;IAC3C,CAAC;IACD,MAAM,MAAM,GAAG,MAAM,WAAW,CAAC,WAAW,CAAC,SAAS,CAAC,MAAM,EAAE,EAAE,CAAC,CAAA;IAClE,eAAe,GAAG,MAAM,CAAC,QAAQ,CAAA;AACnC,CAAC;AAEM,KAAK,UAAU,YAAY,CAAC,KAAiB;IAClD,IAAI,CAAC,eAAe,EAAE,CAAC;QACrB,MAAM,CAAC,sBAAsB;YAC3B,CAAC,sBAAsB,GAAG,kBAAkB,EAAE,CAAC,CAAC,CAAA;IACpD,CAAC;IAED,MAAM,OAAO,GAAG,IAAI,SAAS,CAAC,eAAgB,CAAC,CAAA;IAC/C,MAAM,MAAM,GAAiB,EAAE,CAAA;IAC/B,IAAI,MAAM,GAAG,CAAC,CAAA;IACd,IAAI,WAAW,GAAG,KAAK,CAAA;IAEvB,IAAI,CAAC;QACH,uEAAuE;QACvE,OAAO,IAAI,EAAE,CAAC;YACZ,oDAAoD;YACpD,8EAA8E;YAC9E,IAAI,OAAO,CAAC,KAAM,CAAC,CAAC,CAAE,KAAK,OAAO,CAAC,KAAM,CAAC,CAAC,CAAE,EAAE,CAAC;gBAC9C,IAAI,MAAM,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC;oBAC1B,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,OAAO,EAAE,KAAK,CAAC,MAAM,GAAG,MAAM,CAAC,CAAA;oBAClE,OAAO,CAAC,WAAW,CAAC,KAAK,CAAC,QAAQ,CAAC,MAAM,EAAE,MAAM,GAAG,SAAS,CAAC,CAAC,CAAA;oBAC/D,MAAM,IAAI,SAAS,CAAA;gBACrB,CAAC;qBAAM,IAAI,CAAC,WAAW,EAAE,CAAC;oBACxB,2CAA2C;oBAC3C,OAAO,CAAC,WAAW,CAAC,WAAW,CAAC,CAAA;oBAChC,WAAW,GAAG,IAAI,CAAA;gBACpB,CAAC;qBAAM,CAAC;oBACN,2DAA2D;oBAC3D,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;gBACpE,CAAC;YACH,CAAC;YAED,MAAM,MAAM,GAAG,OAAO,CAAC,aAAa,EAAE,CAAA;YACtC,IAAI,MAAM,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBAC/B,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAA;YAC9B,CAAC;YACD,+BAA+B;YAC/B,OAAO,CAAC,KAAM,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;YAErB,IAAI,MAAM,CAAC,QAAQ,EAAE,CAAC;gBACpB,MAAK;YACP,CAAC;QACH,CAAC;QAED,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACxB,OAAO,MAAM,CAAC,CAAC,CAAE,CAAA;QACnB,CAAC;QAED,MAAM,WAAW,GAAG,MAAM,CAAC,MAAM,CAAC,CAAC,GAAG,EAAE,KAAK,EAAE,EAAE,CAAC,GAAG,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,CAAC,CAAA;QACxE,MAAM,MAAM,GAAG,IAAI,UAAU,CAAC,WAAW,CAAC,CAAA;QAC1C,IAAI,QAAQ,GAAG,CAAC,CAAA;QAChB,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;YAC3B,MAAM,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAA;YAC3B,QAAQ,IAAI,KAAK,CAAC,MAAM,CAAA;QAC1B,CAAC;QACD,OAAO,MAAM,CAAA;IACf,CAAC;YAAS,CAAC;QACT,OAAO,CAAC,OAAO,EAAE,CAAA;IACnB,CAAC;AACH,CAAC"}

package/esm/cramFile/codecs/byteArrayLength.js

@@ -8,11 +8,15 @@ export default class ByteArrayStopCodec extends CramCodec {
     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/esm/cramFile/codecs/byteArrayLength.js.map

@@ -1 +1 @@
-{"version":3,"file":"byteArrayLength.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayLength.ts"],"names":[],"mappings":"AAAA,OAAO,SAAsB,MAAM,YAAY,CAAA;AAK/C,OAAO,EAAE,WAAW,EAAE,MAAM,YAAY,CAAA;AAOxC,MAAM,CAAC,OAAO,OAAO,kBAAmB,SAAQ,SAG/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;AAED,+BAA+B,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE;IAC1D,WAAW,CAAC,kBAAkB,EAAE,MAAM,CAAC,CAAA;AACzC,CAAC,CAAC,CAAA"}
+{"version":3,"file":"byteArrayLength.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayLength.ts"],"names":[],"mappings":"AAAA,OAAO,SAAsB,MAAM,YAAY,CAAA;AAK/C,OAAO,EAAE,WAAW,EAAE,MAAM,YAAY,CAAA;AAOxC,MAAM,CAAC,OAAO,OAAO,kBAAmB,SAAQ,SAG/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;AAED,+BAA+B,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE;IAC1D,WAAW,CAAC,kBAAkB,EAAE,MAAM,CAAC,CAAA;AACzC,CAAC,CAAC,CAAA"}

package/esm/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/esm/cramFile/codecs/external.js

@@ -5,33 +5,28 @@ import { CramBufferOverrunError } from "./getBits.js";
 export default class ExternalCodec extends CramCodec {
     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 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] = parseItf8(contentBlock.content, cursor.bytePosition);
-        cursor.bytePosition = cursor.bytePosition + bytesRead;
-        return result;
-    }
-    _decodeByte(contentBlock, cursor) {
-        if (cursor.bytePosition >= contentBlock.content.length) {
-            throw new 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] = parseItf8(contentBlock.content, cursor.bytePosition);
+            cursor.bytePosition += bytesRead;
+            return result;
+        }
+        else {
+            if (cursor.bytePosition >= contentBlock.content.length) {
+                throw new CramBufferOverrunError('attempted to read beyond end of block. this file seems truncated.');
+            }
+            return contentBlock.content[cursor.bytePosition++];
         }
-        return contentBlock.content[cursor.bytePosition++];
     }
 }
 //# sourceMappingURL=external.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.ts"],"names":[],"mappings":"AAAA,OAAO,SAA8B,MAAM,YAAY,CAAA;AACvD,OAAO,EAAE,sBAAsB,EAAE,MAAM,iBAAiB,CAAA;AAGxD,OAAO,EAAE,SAAS,EAAE,MAAM,YAAY,CAAA;AACtC,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AAGrD,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,SAG1C;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,sBAAsB,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,SAAS,CACnC,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,sBAAsB,CAC9B,mEAAmE,CACpE,CAAA;QACH,CAAC;QACD,OAAO,YAAY,CAAC,OAAO,CAAC,MAAM,CAAC,YAAY,EAAE,CAAE,CAAA;IACrD,CAAC;CACF"}
+{"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.ts"],"names":[],"mappings":"AAAA,OAAO,SAAsB,MAAM,YAAY,CAAA;AAC/C,OAAO,EAAE,sBAAsB,EAAE,MAAM,iBAAiB,CAAA;AAGxD,OAAO,EAAE,SAAS,EAAE,MAAM,YAAY,CAAA;AACtC,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AAGrD,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,SAG1C;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,sBAAsB,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,SAAS,CACnC,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,sBAAsB,CAC9B,mEAAmE,CACpE,CAAA;YACH,CAAC;YACD,OAAO,YAAY,CAAC,OAAO,CAAC,MAAM,CAAC,YAAY,EAAE,CAAE,CAAA;QACrD,CAAC;IACH,CAAC;CACF"}

package/esm/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/esm/cramFile/file.js

@@ -1,24 +1,16 @@
 import crc32 from 'crc/calculators/crc32';
 import QuickLRU from 'quick-lru';
-import { XzReadableStream } from 'xz-decompress';
 import { CramMalformedError, CramUnimplementedError } from "../errors.js";
 import * as htscodecs from "../htscodecs/index.js";
 import { open } from "../io.js";
 import ransuncompress from "../rans/index.js";
 import { parseHeaderText } from "../sam.js";
+import { parseItem, tinyMemoize } from "./util.js";
 import { decode } from "../seek-bzip/index.js";
 import { unzip } from "../unzip.js";
 import CramContainer from "./container/index.js";
 import { cramFileDefinition, getSectionParsers, } from "./sectionParsers.js";
-import { parseItem, tinyMemoize } from "./util.js";
-function bufferToStream(buf) {
-    return new ReadableStream({
-        start(controller) {
-            controller.enqueue(buf);
-            controller.close();
-        },
-    });
-}
+import { xzDecompress } from "../xz-decompress/xz-decompress.js";
 // source: https://abdulapopoola.com/2019/01/20/check-endianness-with-javascript/
 function getEndianness() {
     const uInt32 = new Uint32Array([0x11223344]);
@@ -91,9 +83,11 @@ export default class CramFile {
         return this.header;
     }
     async getContainerById(containerNumber) {
-        const { majorVersion } = await this.getDefinition();
-        const sectionParsers = getSectionParsers(majorVersion);
-        let position = sectionParsers.cramFileDefinition.maxLength;
+        if (!this._sectionParsers) {
+            const { majorVersion } = await this.getDefinition();
+            this._sectionParsers = 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++) {
@@ -139,10 +133,12 @@ export default 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 = getSectionParsers(majorVersion);
+        if (!this._sectionParsers) {
+            const { majorVersion } = await this.getDefinition();
+            this._sectionParsers = 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) {
@@ -175,9 +171,11 @@ export default class CramFile {
         return new CramContainer(this, position);
     }
     async readBlockHeader(position) {
-        const { majorVersion } = await this.getDefinition();
-        const sectionParsers = getSectionParsers(majorVersion);
-        const { cramBlockHeader } = sectionParsers;
+        if (!this._sectionParsers) {
+            const { majorVersion } = await this.getDefinition();
+            this._sectionParsers = getSectionParsers(majorVersion);
+        }
+        const { cramBlockHeader } = this._sectionParsers;
         const buffer = await this.file.read(cramBlockHeader.maxLength, position);
         return parseItem(buffer, cramBlockHeader.parser, 0, position);
     }
@@ -198,8 +196,7 @@ export default class CramFile {
             return decode(inputBuffer);
         }
         else if (compressionMethod === 'lzma') {
-            const decompressedResponse = new Response(new XzReadableStream(bufferToStream(inputBuffer)));
-            return new Uint8Array(await decompressedResponse.arrayBuffer());
+            return xzDecompress(inputBuffer);
         }
         else if (compressionMethod === 'rans') {
             const outputBuffer = new Uint8Array(uncompressedSize);
@@ -233,7 +230,10 @@ export default class CramFile {
     }
     async readBlock(position) {
         const { majorVersion } = await this.getDefinition();
-        const sectionParsers = getSectionParsers(majorVersion);
+        if (!this._sectionParsers) {
+            this._sectionParsers = 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/esm/cramFile/file.js.map

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

@@ -275,10 +275,16 @@ export default 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 CramMalformedError(`no codec defined for ${dataSeriesName} data series`);
+            let codec = codecCache.get(dataSeriesName);
+            if (codec === undefined) {
+                codec = compressionScheme.getCodecForDataSeries(dataSeriesName);
+                if (!codec) {
+                    throw new CramMalformedError(`no codec defined for ${dataSeriesName} data series`);
+                }
+                codecCache.set(dataSeriesName, codec);
             }
             return codec.decode(this, coreDataBlock, blocksByContentId, cursors);
         };
@@ -296,8 +302,11 @@ export default class CramSlice {
             }
             catch (e) {
                 if (e instanceof CramBufferOverrunError) {
-                    console.warn('read attempted beyond end of buffer, file seems truncated.');
-                    break;
+                    const recordsDecoded = i;
+                    const recordsExpected = sliceHeader.parsedContent.numRecords;
+                    throw new 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/esm/cramFile/slice/index.js.map

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

@@ -169,14 +169,15 @@ export 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;
     };
 }
 export function sequenceMD5(seq) {

package/esm/cramFile/util.js.map

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

@@ -50,10 +50,21 @@ export default 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/esm/indexedCramFile.js.map

@@ -1 +1 @@
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package/esm/rans/d04.js

@@ -2,6 +2,9 @@
 import { CramMalformedError } from "../errors.js";
 import { TF_SHIFT } from "./constants.js";
 import Decoding from "./decoding.js";
+// Inline constants for performance
+const RANS_BYTE_L = 8388608; // 1 << 23
+const MASK = 4095; // (1 << 12) - 1
 export default function uncompress(
 /* ByteBuffer */ input, 
 /* Decoding.AriDecoder */ D, 
@@ -13,23 +16,46 @@ export default 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.get(rans0, TF_SHIFT)];
-        const /* byte */ c1 = D.R[Decoding.get(rans1, TF_SHIFT)];
-        const /* byte */ c2 = D.R[Decoding.get(rans2, TF_SHIFT)];
-        const /* byte */ c3 = D.R[Decoding.get(rans3, TF_SHIFT)];
-        out.putAt(i, c0);
-        out.putAt(i + 1, c1);
-        out.putAt(i + 2, c2);
-        out.putAt(i + 3, c3);
-        rans0 = Decoding.advanceSymbolStep(rans0, syms[0xff & c0], TF_SHIFT);
-        rans1 = Decoding.advanceSymbolStep(rans1, syms[0xff & c1], TF_SHIFT);
-        rans2 = Decoding.advanceSymbolStep(rans2, syms[0xff & c2], TF_SHIFT);
-        rans3 = Decoding.advanceSymbolStep(rans3, syms[0xff & c3], TF_SHIFT);
-        rans0 = Decoding.renormalize(rans0, input);
-        rans1 = Decoding.renormalize(rans1, input);
-        rans2 = Decoding.renormalize(rans2, input);
-        rans3 = Decoding.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 >> TF_SHIFT) + (rans0 & MASK) - sym0.start;
+        rans1 = sym1.freq * (rans1 >> TF_SHIFT) + (rans1 & MASK) - sym1.start;
+        rans2 = sym2.freq * (rans2 >> TF_SHIFT) + (rans2 & MASK) - sym2.start;
+        rans3 = sym3.freq * (rans3 >> 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/esm/rans/d04.js.map

@@ -1 +1 @@
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