@gmod/cram 7.0.3 → 8.0.1

package/dist/cramFile/codecs/beta.js

@@ -4,7 +4,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const _base_ts_1 = __importDefault(require("./_base.js"));
-const getBits_ts_1 = require("./getBits.js");
 const errors_ts_1 = require("../../errors.js");
 class BetaCodec extends _base_ts_1.default {
     constructor(parameters, dataType) {
@@ -14,9 +13,34 @@ class BetaCodec extends _base_ts_1.default {
         }
     }
     decode(_slice, coreDataBlock, _blocksByContentId, cursors) {
-        const fromBits = (0, getBits_ts_1.getBits)(coreDataBlock.content, cursors.coreBlock, this.parameters.length);
-        return fromBits - this.parameters.offset;
+        return decodeBetaInline(coreDataBlock.content, cursors.coreBlock, this.parameters.length, this.parameters.offset);
     }
 }
 exports.default = BetaCodec;
+/**
+ * Optimized beta decoder with inlined bit reading.
+ */
+function decodeBetaInline(data, cursor, numBits, offset) {
+    let { bytePosition, bitPosition } = cursor;
+    // Fast path: reading exactly 8 bits when byte-aligned
+    if (numBits === 8 && bitPosition === 7) {
+        const val = data[bytePosition];
+        cursor.bytePosition = bytePosition + 1;
+        return val - offset;
+    }
+    // General case
+    let val = 0;
+    for (let i = 0; i < numBits; i++) {
+        val <<= 1;
+        val |= (data[bytePosition] >> bitPosition) & 1;
+        bitPosition -= 1;
+        if (bitPosition < 0) {
+            bytePosition += 1;
+            bitPosition = 7;
+        }
+    }
+    cursor.bytePosition = bytePosition;
+    cursor.bitPosition = bitPosition;
+    return val - offset;
+}
 //# sourceMappingURL=beta.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"beta.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/beta.ts"],"names":[],"mappings":";;;;;AAAA,0DAA+C;AAC/C,6CAAsC;AACtC,+CAAwD;AAKxD,MAAqB,SAAU,SAAQ,kBAGtC;IACC,YAAY,UAAsC,EAAE,QAAe;QACjE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,MAAM,IAAI,kCAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,6CAA6C,CAC9D,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,MAAiB,EACjB,aAA4B,EAC5B,kBAAiD,EACjD,OAAgB;QAEhB,MAAM,QAAQ,GAAG,IAAA,oBAAO,EACtB,aAAa,CAAC,OAAO,EACrB,OAAO,CAAC,SAAS,EACjB,IAAI,CAAC,UAAU,CAAC,MAAM,CACvB,CAAA;QACD,OAAO,QAAQ,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IAC1C,CAAC;CACF;AA1BD,4BA0BC"}
+{"version":3,"file":"beta.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/beta.ts"],"names":[],"mappings":";;;;;AAAA,0DAAuD;AACvD,+CAAwD;AAKxD,MAAqB,SAAU,SAAQ,kBAGtC;IACC,YAAY,UAAsC,EAAE,QAAe;QACjE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,MAAM,IAAI,kCAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,6CAA6C,CAC9D,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,MAAiB,EACjB,aAA4B,EAC5B,kBAAiD,EACjD,OAAgB;QAEhB,OAAO,gBAAgB,CACrB,aAAa,CAAC,OAAO,EACrB,OAAO,CAAC,SAAS,EACjB,IAAI,CAAC,UAAU,CAAC,MAAM,EACtB,IAAI,CAAC,UAAU,CAAC,MAAM,CACvB,CAAA;IACH,CAAC;CACF;AA1BD,4BA0BC;AAED;;GAEG;AACH,SAAS,gBAAgB,CACvB,IAAgB,EAChB,MAAc,EACd,OAAe,EACf,MAAc;IAEd,IAAI,EAAE,YAAY,EAAE,WAAW,EAAE,GAAG,MAAM,CAAA;IAE1C,sDAAsD;IACtD,IAAI,OAAO,KAAK,CAAC,IAAI,WAAW,KAAK,CAAC,EAAE,CAAC;QACvC,MAAM,GAAG,GAAG,IAAI,CAAC,YAAY,CAAE,CAAA;QAC/B,MAAM,CAAC,YAAY,GAAG,YAAY,GAAG,CAAC,CAAA;QACtC,OAAO,GAAG,GAAG,MAAM,CAAA;IACrB,CAAC;IAED,eAAe;IACf,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,EAAE,CAAC,EAAE,EAAE,CAAC;QACjC,GAAG,KAAK,CAAC,CAAA;QACT,GAAG,IAAI,CAAC,IAAI,CAAC,YAAY,CAAE,IAAI,WAAW,CAAC,GAAG,CAAC,CAAA;QAC/C,WAAW,IAAI,CAAC,CAAA;QAChB,IAAI,WAAW,GAAG,CAAC,EAAE,CAAC;YACpB,YAAY,IAAI,CAAC,CAAA;YACjB,WAAW,GAAG,CAAC,CAAA;QACjB,CAAC;IACH,CAAC;IAED,MAAM,CAAC,YAAY,GAAG,YAAY,CAAA;IAClC,MAAM,CAAC,WAAW,GAAG,WAAW,CAAA;IAChC,OAAO,GAAG,GAAG,MAAM,CAAA;AACrB,CAAC"}

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

@@ -5,4 +5,5 @@ import { ExternalCramEncoding } from '../encoding.ts';
 export default class ExternalCodec extends CramCodec<'int' | 'byte', ExternalCramEncoding['parameters']> {
     constructor(parameters: ExternalCramEncoding['parameters'], dataType: 'int' | 'byte');
     decode(_slice: CramSlice, _coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): number | undefined;
+    getBytesSubarray(blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors, length: number): Uint8Array | undefined;
 }

package/dist/cramFile/codecs/external.js

@@ -33,6 +33,21 @@ class ExternalCodec extends _base_ts_1.default {
             return contentBlock.content[cursor.bytePosition++];
         }
     }
+    getBytesSubarray(blocksByContentId, cursors, length) {
+        const { blockContentId } = this.parameters;
+        const contentBlock = blocksByContentId[blockContentId];
+        if (!contentBlock) {
+            return undefined;
+        }
+        const cursor = cursors.externalBlocks.getCursor(blockContentId);
+        const start = cursor.bytePosition;
+        const end = start + length;
+        if (end > contentBlock.content.length) {
+            throw new getBits_ts_1.CramBufferOverrunError('attempted to read beyond end of block. this file seems truncated.');
+        }
+        cursor.bytePosition = end;
+        return contentBlock.content.subarray(start, end);
+    }
 }
 exports.default = ExternalCodec;
 //# sourceMappingURL=external.js.map

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

@@ -1 +1 @@
-{"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"}
+{"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;IAED,gBAAgB,CACd,iBAAgD,EAChD,OAAgB,EAChB,MAAc;QAEd,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;QAC/D,MAAM,KAAK,GAAG,MAAM,CAAC,YAAY,CAAA;QACjC,MAAM,GAAG,GAAG,KAAK,GAAG,MAAM,CAAA;QAE1B,IAAI,GAAG,GAAG,YAAY,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC;YACtC,MAAM,IAAI,mCAAsB,CAC9B,mEAAmE,CACpE,CAAA;QACH,CAAC;QAED,MAAM,CAAC,YAAY,GAAG,GAAG,CAAA;QACzB,OAAO,YAAY,CAAC,OAAO,CAAC,QAAQ,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;IAClD,CAAC;CACF;AAvED,gCAuEC"}

package/dist/cramFile/codecs/gamma.js

@@ -4,7 +4,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const _base_ts_1 = __importDefault(require("./_base.js"));
-const getBits_ts_1 = require("./getBits.js");
 const errors_ts_1 = require("../../errors.js");
 class GammaCodec extends _base_ts_1.default {
     constructor(parameters, dataType) {
@@ -14,14 +13,51 @@ class GammaCodec extends _base_ts_1.default {
         }
     }
     decode(_slice, coreDataBlock, _blocksByContentId, cursors) {
-        let length = 1;
-        while ((0, getBits_ts_1.getBits)(coreDataBlock.content, cursors.coreBlock, 1) === 0) {
-            length = length + 1;
-        }
-        const readBits = (0, getBits_ts_1.getBits)(coreDataBlock.content, cursors.coreBlock, length - 1);
-        const value = readBits | (1 << (length - 1));
-        return value - this.parameters.offset;
+        return decodeGammaInline(coreDataBlock.content, cursors.coreBlock, this.parameters.offset);
     }
 }
 exports.default = GammaCodec;
+/**
+ * Optimized gamma decoder with inlined bit reading.
+ * Avoids function call overhead by inlining the getBits logic.
+ */
+function decodeGammaInline(data, cursor, offset) {
+    let { bytePosition, bitPosition } = cursor;
+    let length = 1;
+    // Count leading zeros (each 0 bit increases length)
+    // Inline single-bit reads for the while loop
+    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+    while (true) {
+        const bit = (data[bytePosition] >> bitPosition) & 1;
+        bitPosition -= 1;
+        if (bitPosition < 0) {
+            bytePosition += 1;
+            bitPosition = 7;
+        }
+        if (bit === 1) {
+            break;
+        }
+        length += 1;
+    }
+    // Now read (length - 1) more bits for the value
+    let readBits = 0;
+    const bitsToRead = length - 1;
+    if (bitsToRead > 0) {
+        // Optimized multi-bit read
+        for (let i = 0; i < bitsToRead; i++) {
+            readBits <<= 1;
+            readBits |= (data[bytePosition] >> bitPosition) & 1;
+            bitPosition -= 1;
+            if (bitPosition < 0) {
+                bytePosition += 1;
+                bitPosition = 7;
+            }
+        }
+    }
+    // Update cursor
+    cursor.bytePosition = bytePosition;
+    cursor.bitPosition = bitPosition;
+    const value = readBits | (1 << (length - 1));
+    return value - offset;
+}
 //# sourceMappingURL=gamma.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"gamma.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/gamma.ts"],"names":[],"mappings":";;;;;AAAA,0DAA+C;AAC/C,6CAAsC;AACtC,+CAAwD;AAKxD,MAAqB,UAAW,SAAQ,kBAGvC;IACC,YAAY,UAAuC,EAAE,QAAe;QAClE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,MAAM,IAAI,kCAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,8CAA8C,CAC/D,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,MAAiB,EACjB,aAA4B,EAC5B,kBAAiD,EACjD,OAAgB;QAEhB,IAAI,MAAM,GAAG,CAAC,CAAA;QAEd,OAAO,IAAA,oBAAO,EAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC;YAClE,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;QACrB,CAAC;QAED,MAAM,QAAQ,GAAG,IAAA,oBAAO,EACtB,aAAa,CAAC,OAAO,EACrB,OAAO,CAAC,SAAS,EACjB,MAAM,GAAG,CAAC,CACX,CAAA;QAED,MAAM,KAAK,GAAG,QAAQ,GAAG,CAAC,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAA;QAC5C,OAAO,KAAK,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IACvC,CAAC;CACF;AAlCD,6BAkCC"}
+{"version":3,"file":"gamma.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/gamma.ts"],"names":[],"mappings":";;;;;AAAA,0DAAuD;AACvD,+CAAwD;AAKxD,MAAqB,UAAW,SAAQ,kBAGvC;IACC,YAAY,UAAuC,EAAE,QAAe;QAClE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,MAAM,IAAI,kCAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,8CAA8C,CAC/D,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,MAAiB,EACjB,aAA4B,EAC5B,kBAAiD,EACjD,OAAgB;QAEhB,OAAO,iBAAiB,CACtB,aAAa,CAAC,OAAO,EACrB,OAAO,CAAC,SAAS,EACjB,IAAI,CAAC,UAAU,CAAC,MAAM,CACvB,CAAA;IACH,CAAC;CACF;AAzBD,6BAyBC;AAED;;;GAGG;AACH,SAAS,iBAAiB,CACxB,IAAgB,EAChB,MAAc,EACd,MAAc;IAEd,IAAI,EAAE,YAAY,EAAE,WAAW,EAAE,GAAG,MAAM,CAAA;IAC1C,IAAI,MAAM,GAAG,CAAC,CAAA;IAEd,oDAAoD;IACpD,6CAA6C;IAC7C,uEAAuE;IACvE,OAAO,IAAI,EAAE,CAAC;QACZ,MAAM,GAAG,GAAG,CAAC,IAAI,CAAC,YAAY,CAAE,IAAI,WAAW,CAAC,GAAG,CAAC,CAAA;QACpD,WAAW,IAAI,CAAC,CAAA;QAChB,IAAI,WAAW,GAAG,CAAC,EAAE,CAAC;YACpB,YAAY,IAAI,CAAC,CAAA;YACjB,WAAW,GAAG,CAAC,CAAA;QACjB,CAAC;QACD,IAAI,GAAG,KAAK,CAAC,EAAE,CAAC;YACd,MAAK;QACP,CAAC;QACD,MAAM,IAAI,CAAC,CAAA;IACb,CAAC;IAED,gDAAgD;IAChD,IAAI,QAAQ,GAAG,CAAC,CAAA;IAChB,MAAM,UAAU,GAAG,MAAM,GAAG,CAAC,CAAA;IAC7B,IAAI,UAAU,GAAG,CAAC,EAAE,CAAC;QACnB,2BAA2B;QAC3B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;YACpC,QAAQ,KAAK,CAAC,CAAA;YACd,QAAQ,IAAI,CAAC,IAAI,CAAC,YAAY,CAAE,IAAI,WAAW,CAAC,GAAG,CAAC,CAAA;YACpD,WAAW,IAAI,CAAC,CAAA;YAChB,IAAI,WAAW,GAAG,CAAC,EAAE,CAAC;gBACpB,YAAY,IAAI,CAAC,CAAA;gBACjB,WAAW,GAAG,CAAC,CAAA;YACjB,CAAC;QACH,CAAC;IACH,CAAC;IAED,gBAAgB;IAChB,MAAM,CAAC,YAAY,GAAG,YAAY,CAAA;IAClC,MAAM,CAAC,WAAW,GAAG,WAAoC,CAAA;IAEzD,MAAM,KAAK,GAAG,QAAQ,GAAG,CAAC,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAA;IAC5C,OAAO,KAAK,GAAG,MAAM,CAAA;AACvB,CAAC"}

package/dist/cramFile/codecs/getBits.js

@@ -6,13 +6,29 @@ class CramBufferOverrunError extends Error {
 }
 exports.CramBufferOverrunError = CramBufferOverrunError;
 function getBits(data, cursor, numBits) {
-    let val = 0;
     if (cursor.bytePosition + (7 - cursor.bitPosition + numBits) / 8 >
         data.length) {
         throw new CramBufferOverrunError('read error during decoding. the file seems to be truncated.');
     }
+    // Fast path: reading exactly 8 bits when byte-aligned
+    if (numBits === 8 && cursor.bitPosition === 7) {
+        const val = data[cursor.bytePosition];
+        cursor.bytePosition += 1;
+        return val;
+    }
+    // Fast path: reading exactly 1 bit
+    if (numBits === 1) {
+        const val = (data[cursor.bytePosition] >> cursor.bitPosition) & 1;
+        cursor.bitPosition -= 1;
+        if (cursor.bitPosition < 0) {
+            cursor.bytePosition += 1;
+            cursor.bitPosition = 7;
+        }
+        return val;
+    }
+    // General case: bit-by-bit loop
+    let val = 0;
     for (let dlen = numBits; dlen; dlen--) {
-        // get the next `dlen` bits in the input, put them in val
         val <<= 1;
         val |= (data[cursor.bytePosition] >> cursor.bitPosition) & 1;
         cursor.bitPosition -= 1;

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

@@ -1 +1 @@
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+{"version":3,"file":"getBits.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/getBits.ts"],"names":[],"mappings":";;;AAEA,0BA4CC;AA9CD,MAAa,sBAAuB,SAAQ,KAAK;CAAG;AAApD,wDAAoD;AAEpD,SAAgB,OAAO,CACrB,IAAgB,EAChB,MAAqD,EACrD,OAAe;IAEf,IACE,MAAM,CAAC,YAAY,GAAG,CAAC,CAAC,GAAG,MAAM,CAAC,WAAW,GAAG,OAAO,CAAC,GAAG,CAAC;QAC5D,IAAI,CAAC,MAAM,EACX,CAAC;QACD,MAAM,IAAI,sBAAsB,CAC9B,6DAA6D,CAC9D,CAAA;IACH,CAAC;IAED,sDAAsD;IACtD,IAAI,OAAO,KAAK,CAAC,IAAI,MAAM,CAAC,WAAW,KAAK,CAAC,EAAE,CAAC;QAC9C,MAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAC,YAAY,CAAE,CAAA;QACtC,MAAM,CAAC,YAAY,IAAI,CAAC,CAAA;QACxB,OAAO,GAAG,CAAA;IACZ,CAAC;IAED,mCAAmC;IACnC,IAAI,OAAO,KAAK,CAAC,EAAE,CAAC;QAClB,MAAM,GAAG,GAAG,CAAC,IAAI,CAAC,MAAM,CAAC,YAAY,CAAE,IAAI,MAAM,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QAClE,MAAM,CAAC,WAAW,IAAI,CAAC,CAAA;QACvB,IAAI,MAAM,CAAC,WAAW,GAAG,CAAC,EAAE,CAAC;YAC3B,MAAM,CAAC,YAAY,IAAI,CAAC,CAAA;YACxB,MAAM,CAAC,WAAW,GAAG,CAAC,CAAA;QACxB,CAAC;QACD,OAAO,GAAG,CAAA;IACZ,CAAC;IAED,gCAAgC;IAChC,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,KAAK,IAAI,IAAI,GAAG,OAAO,EAAE,IAAI,EAAE,IAAI,EAAE,EAAE,CAAC;QACtC,GAAG,KAAK,CAAC,CAAA;QACT,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,YAAY,CAAE,IAAI,MAAM,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QAC7D,MAAM,CAAC,WAAW,IAAI,CAAC,CAAA;QACvB,IAAI,MAAM,CAAC,WAAW,GAAG,CAAC,EAAE,CAAC;YAC3B,MAAM,CAAC,YAAY,IAAI,CAAC,CAAA;QAC1B,CAAC;QACD,MAAM,CAAC,WAAW,IAAI,CAAC,CAAA;IACzB,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC"}

package/dist/cramFile/codecs/huffman.js

@@ -4,8 +4,39 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const _base_ts_1 = __importDefault(require("./_base.js"));
-const getBits_ts_1 = require("./getBits.js");
 const errors_ts_1 = require("../../errors.js");
+/**
+ * Inlined getBits for huffman decoding - avoids function call overhead
+ */
+function getBitsInline(data, cursor, numBits) {
+    let { bytePosition, bitPosition } = cursor;
+    // Fast path for single bit (common in huffman)
+    if (numBits === 1) {
+        const val = (data[bytePosition] >> bitPosition) & 1;
+        bitPosition -= 1;
+        if (bitPosition < 0) {
+            bytePosition += 1;
+            bitPosition = 7;
+        }
+        cursor.bytePosition = bytePosition;
+        cursor.bitPosition = bitPosition;
+        return val;
+    }
+    // General case
+    let val = 0;
+    for (let i = 0; i < numBits; i++) {
+        val <<= 1;
+        val |= (data[bytePosition] >> bitPosition) & 1;
+        bitPosition -= 1;
+        if (bitPosition < 0) {
+            bytePosition += 1;
+            bitPosition = 7;
+        }
+    }
+    cursor.bytePosition = bytePosition;
+    cursor.bitPosition = bitPosition;
+    return val;
+}
 function numberOfSetBits(ii) {
     let i = (ii - (ii >> 1)) & 0x55555555;
     i = (i & 0x33333333) + ((i >> 2) & 0x33333333);
@@ -103,8 +134,11 @@ class HuffmanIntCodec extends _base_ts_1.default {
         let bits = 0;
         for (let i = 0; i < this.sortedCodes.length; i += 1) {
             const length = this.sortedCodes[i].bitLength;
-            bits <<= length - prevLen;
-            bits |= (0, getBits_ts_1.getBits)(input, coreCursor, length - prevLen);
+            const bitsToRead = length - prevLen;
+            if (bitsToRead > 0) {
+                bits <<= bitsToRead;
+                bits |= getBitsInline(input, coreCursor, bitsToRead);
+            }
             prevLen = length;
             {
                 const index = this.bitCodeToValue[bits];

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

@@ -1 +1 @@
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+{"version":3,"file":"huffman.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/huffman.ts"],"names":[],"mappings":";;;;;AAAA,0DAAuD;AACvD,+CAAoD;AAKpD;;GAEG;AACH,SAAS,aAAa,CACpB,IAAgB,EAChB,MAAc,EACd,OAAe;IAEf,IAAI,EAAE,YAAY,EAAE,WAAW,EAAE,GAAG,MAAM,CAAA;IAE1C,+CAA+C;IAC/C,IAAI,OAAO,KAAK,CAAC,EAAE,CAAC;QAClB,MAAM,GAAG,GAAG,CAAC,IAAI,CAAC,YAAY,CAAE,IAAI,WAAW,CAAC,GAAG,CAAC,CAAA;QACpD,WAAW,IAAI,CAAC,CAAA;QAChB,IAAI,WAAW,GAAG,CAAC,EAAE,CAAC;YACpB,YAAY,IAAI,CAAC,CAAA;YACjB,WAAW,GAAG,CAAC,CAAA;QACjB,CAAC;QACD,MAAM,CAAC,YAAY,GAAG,YAAY,CAAA;QAClC,MAAM,CAAC,WAAW,GAAG,WAAoC,CAAA;QACzD,OAAO,GAAG,CAAA;IACZ,CAAC;IAED,eAAe;IACf,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,EAAE,CAAC,EAAE,EAAE,CAAC;QACjC,GAAG,KAAK,CAAC,CAAA;QACT,GAAG,IAAI,CAAC,IAAI,CAAC,YAAY,CAAE,IAAI,WAAW,CAAC,GAAG,CAAC,CAAA;QAC/C,WAAW,IAAI,CAAC,CAAA;QAChB,IAAI,WAAW,GAAG,CAAC,EAAE,CAAC;YACpB,YAAY,IAAI,CAAC,CAAA;YACjB,WAAW,GAAG,CAAC,CAAA;QACjB,CAAC;IACH,CAAC;IAED,MAAM,CAAC,YAAY,GAAG,YAAY,CAAA;IAClC,MAAM,CAAC,WAAW,GAAG,WAAW,CAAA;IAChC,OAAO,GAAG,CAAA;AACZ,CAAC;AAED,SAAS,eAAe,CAAC,EAAU;IACjC,IAAI,CAAC,GAAG,CAAC,EAAE,GAAG,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,GAAG,UAAU,CAAA;IACrC,CAAC,GAAG,CAAC,CAAC,GAAG,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,UAAU,CAAC,CAAA;IAC9C,OAAO,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,GAAG,UAAU,CAAC,GAAG,UAAU,CAAC,IAAI,EAAE,CAAA;AAC3D,CAAC;AAQD,MAAqB,eAAgB,SAAQ,kBAG5C;IASC,YACE,UAAyC,EACzC,QAAwB;QAExB,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAZrB,UAAK,GAAyB,EAAE,CAAA;QAChC,aAAQ,GAA6B,EAAE,CAAA;QACvC,gBAAW,GAAW,EAAE,CAAA;QACxB,0BAAqB,GAAa,EAAE,CAAA;QACpC,mBAAc,GAAa,EAAE,CAAA;QAC7B,8BAAyB,GAAa,EAAE,CAAA;QACxC,mBAAc,GAAa,EAAE,CAAA;QAOnC,IAAI,CAAC,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,QAAQ,CAAC,EAAE,CAAC;YAC7C,MAAM,IAAI,SAAS,CACjB,GAAG,IAAI,CAAC,QAAQ,oDAAoD,CACrE,CAAA;QACH,CAAC;QAED,IAAI,CAAC,aAAa,EAAE,CAAA;QACpB,IAAI,CAAC,UAAU,EAAE,CAAA;QACjB,IAAI,CAAC,WAAW,EAAE,CAAA;QAElB,qEAAqE;QACrE,WAAW;QACX,IAAI,IAAI,CAAC,WAAW,CAAC,CAAC,CAAE,CAAC,SAAS,KAAK,CAAC,EAAE,CAAC;YACzC,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,qBAAqB,CAAA;QAC3C,CAAC;IACH,CAAC;IAED,aAAa;QACX,8DAA8D;QAC9D,IAAI,KAAK,GAAG,IAAI,KAAK,CACnB,IAAI,CAAC,UAAU,CAAC,QAAQ,CACzB,CAAA;QACD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;YAClD,KAAK,CAAC,CAAC,CAAC,GAAG;gBACT,MAAM,EAAE,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC,CAAC,CAAE;gBACnC,SAAS,EAAE,IAAI,CAAC,UAAU,CAAC,UAAU,CAAC,CAAC,CAAE;aAC1C,CAAA;QACH,CAAC;QACD,gDAAgD;QAChD,KAAK,GAAG,KAAK,CAAC,IAAI,CAChB,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,MAAM,CAC3D,CAAA;QAED,IAAI,CAAC,QAAQ,GAAG,EAAE,CAAA;QAClB,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;YACnB,IAAI,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,SAAS,CAAC,EAAE,CAAC;gBACnC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,SAAS,CAAC,GAAG,EAAE,CAAA;YACpC,CAAC;YACD,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,SAAS,CAAE,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QAClD,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,UAAU;QACR,IAAI,CAAC,KAAK,GAAG,EAAE,CAAA,CAAC,8CAA8C;QAC9D,IAAI,UAAU,GAAG,CAAC,CAAA;QAClB,IAAI,SAAS,GAAG,CAAC,CAAC,CAAA;QAClB,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,SAAS,EAAE,OAAO,CAAC,EAAE,EAAE;YAC7D,MAAM,YAAY,GAAG,MAAM,CAAC,QAAQ,CAAC,SAAS,EAAE,EAAE,CAAC,CAAA;YACnD,OAAO,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE;gBACvB,MAAM,IAAI,GAAG;oBACX,SAAS,EAAE,YAAY;oBACvB,KAAK,EAAE,MAAM;oBACb,OAAO,EAAE,CAAC;iBACX,CAAA;gBACD,SAAS,GAAG,SAAS,GAAG,CAAC,CAAA;gBACzB,MAAM,KAAK,GAAG,YAAY,GAAG,UAAU,CAAA,CAAC,cAAc;gBACtD,SAAS,GAAG,SAAS,IAAI,KAAK,CAAA,CAAC,eAAe;gBAC9C,IAAI,CAAC,OAAO,GAAG,SAAS,CAAA,CAAC,2BAA2B;gBACpD,UAAU,GAAG,UAAU,GAAG,KAAK,CAAA,CAAC,6BAA6B;gBAE7D,IAAI,eAAe,CAAC,SAAS,CAAC,GAAG,YAAY,EAAE,CAAC;oBAC9C,MAAM,IAAI,8BAAkB,CAAC,qBAAqB,CAAC,CAAA;gBACrD,CAAC;gBAED,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,GAAG,IAAI,CAAA;YAC3B,CAAC,CAAC,CAAA;QACJ,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,WAAW;QACT,IAAI,CAAC,WAAW,GAAG,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,IAAI,CAC/C,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC,OAAO,CAC7D,CAAA;QAED,IAAI,CAAC,qBAAqB,GAAG,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;QAC/D,IAAI,CAAC,cAAc,GAAG,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAA;QAC1D,IAAI,CAAC,yBAAyB,GAAG,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,SAAS,CAAC,CAAA;QACvE,MAAM,UAAU,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,cAAc,CAAC,CAAA;QAEnD,IAAI,CAAC,cAAc,GAAG,IAAI,KAAK,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAA;QACxD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,cAAc,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACvD,IAAI,CAAC,cAAc,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,CAAE,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;QACvD,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,kBAAiD,EACjD,OAAgB;QAEhB,OAAO,IAAI,CAAC,OAAO,CAAC,KAAK,EAAE,aAAa,EAAE,OAAO,CAAC,SAAS,CAAC,CAAA;IAC9D,CAAC;IAED,kBAAkB;IAClB,cAAc;IACd,IAAI;IAEJ,yCAAyC;IACzC,qBAAqB;QACnB,OAAO,IAAI,CAAC,WAAW,CAAC,CAAC,CAAE,CAAC,KAAK,CAAA;IACnC,CAAC;IAED,OAAO,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package/dist/cramFile/codecs/subexp.js

@@ -4,7 +4,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const _base_ts_1 = __importDefault(require("./_base.js"));
-const getBits_ts_1 = require("./getBits.js");
 const errors_ts_1 = require("../../errors.js");
 class SubexpCodec extends _base_ts_1.default {
     constructor(parameters, dataType) {
@@ -14,23 +13,46 @@ class SubexpCodec extends _base_ts_1.default {
         }
     }
     decode(_slice, coreDataBlock, _blocksByContentId, cursors) {
-        let numLeadingOnes = 0;
-        while ((0, getBits_ts_1.getBits)(coreDataBlock.content, cursors.coreBlock, 1)) {
-            numLeadingOnes = numLeadingOnes + 1;
+        return decodeSubexpInline(coreDataBlock.content, cursors.coreBlock, this.parameters.K, this.parameters.offset);
+    }
+}
+exports.default = SubexpCodec;
+/**
+ * Optimized subexp decoder with inlined bit reading.
+ */
+function decodeSubexpInline(data, cursor, K, offset) {
+    let { bytePosition, bitPosition } = cursor;
+    // Count leading ones (inline single-bit reads)
+    let numLeadingOnes = 0;
+    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+    while (true) {
+        const bit = (data[bytePosition] >> bitPosition) & 1;
+        bitPosition -= 1;
+        if (bitPosition < 0) {
+            bytePosition += 1;
+            bitPosition = 7;
         }
-        let b;
-        let n;
-        if (numLeadingOnes === 0) {
-            b = this.parameters.K;
-            n = (0, getBits_ts_1.getBits)(coreDataBlock.content, cursors.coreBlock, b);
+        if (bit === 0) {
+            break;
         }
-        else {
-            b = numLeadingOnes + this.parameters.K - 1;
-            const bits = (0, getBits_ts_1.getBits)(coreDataBlock.content, cursors.coreBlock, b);
-            n = (1 << b) | bits;
+        numLeadingOnes += 1;
+    }
+    // Determine how many bits to read for the value
+    const b = numLeadingOnes === 0 ? K : numLeadingOnes + K - 1;
+    // Read b bits
+    let bits = 0;
+    for (let i = 0; i < b; i++) {
+        bits <<= 1;
+        bits |= (data[bytePosition] >> bitPosition) & 1;
+        bitPosition -= 1;
+        if (bitPosition < 0) {
+            bytePosition += 1;
+            bitPosition = 7;
         }
-        return n - this.parameters.offset;
     }
+    cursor.bytePosition = bytePosition;
+    cursor.bitPosition = bitPosition;
+    const n = numLeadingOnes === 0 ? bits : (1 << b) | bits;
+    return n - offset;
 }
-exports.default = SubexpCodec;
 //# sourceMappingURL=subexp.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"subexp.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/subexp.ts"],"names":[],"mappings":";;;;;AAAA,0DAA+C;AAC/C,6CAAsC;AACtC,+CAAwD;AAKxD,MAAqB,WAAY,SAAQ,kBAGxC;IACC,YAAY,UAAwC,EAAE,QAAe;QACnE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,MAAM,IAAI,kCAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,+CAA+C,CAChE,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,MAAiB,EACjB,aAA4B,EAC5B,kBAAiD,EACjD,OAAgB;QAEhB,IAAI,cAAc,GAAG,CAAC,CAAA;QACtB,OAAO,IAAA,oBAAO,EAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,EAAE,CAAC;YAC5D,cAAc,GAAG,cAAc,GAAG,CAAC,CAAA;QACrC,CAAC;QAED,IAAI,CAAS,CAAA;QACb,IAAI,CAAS,CAAA;QACb,IAAI,cAAc,KAAK,CAAC,EAAE,CAAC;YACzB,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,CAAA;YACrB,CAAC,GAAG,IAAA,oBAAO,EAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;QAC1D,CAAC;aAAM,CAAC;YACN,CAAC,GAAG,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,GAAG,CAAC,CAAA;YAC1C,MAAM,IAAI,GAAG,IAAA,oBAAO,EAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;YACjE,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,IAAI,CAAA;QACrB,CAAC;QAED,OAAO,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IACnC,CAAC;CACF;AArCD,8BAqCC"}
+{"version":3,"file":"subexp.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/subexp.ts"],"names":[],"mappings":";;;;;AAAA,0DAAuD;AACvD,+CAAwD;AAKxD,MAAqB,WAAY,SAAQ,kBAGxC;IACC,YAAY,UAAwC,EAAE,QAAe;QACnE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,MAAM,IAAI,kCAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,+CAA+C,CAChE,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,MAAiB,EACjB,aAA4B,EAC5B,kBAAiD,EACjD,OAAgB;QAEhB,OAAO,kBAAkB,CACvB,aAAa,CAAC,OAAO,EACrB,OAAO,CAAC,SAAS,EACjB,IAAI,CAAC,UAAU,CAAC,CAAC,EACjB,IAAI,CAAC,UAAU,CAAC,MAAM,CACvB,CAAA;IACH,CAAC;CACF;AA1BD,8BA0BC;AAED;;GAEG;AACH,SAAS,kBAAkB,CACzB,IAAgB,EAChB,MAAc,EACd,CAAS,EACT,MAAc;IAEd,IAAI,EAAE,YAAY,EAAE,WAAW,EAAE,GAAG,MAAM,CAAA;IAE1C,+CAA+C;IAC/C,IAAI,cAAc,GAAG,CAAC,CAAA;IACtB,uEAAuE;IACvE,OAAO,IAAI,EAAE,CAAC;QACZ,MAAM,GAAG,GAAG,CAAC,IAAI,CAAC,YAAY,CAAE,IAAI,WAAW,CAAC,GAAG,CAAC,CAAA;QACpD,WAAW,IAAI,CAAC,CAAA;QAChB,IAAI,WAAW,GAAG,CAAC,EAAE,CAAC;YACpB,YAAY,IAAI,CAAC,CAAA;YACjB,WAAW,GAAG,CAAC,CAAA;QACjB,CAAC;QACD,IAAI,GAAG,KAAK,CAAC,EAAE,CAAC;YACd,MAAK;QACP,CAAC;QACD,cAAc,IAAI,CAAC,CAAA;IACrB,CAAC;IAED,gDAAgD;IAChD,MAAM,CAAC,GAAG,cAAc,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,cAAc,GAAG,CAAC,GAAG,CAAC,CAAA;IAE3D,cAAc;IACd,IAAI,IAAI,GAAG,CAAC,CAAA;IACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3B,IAAI,KAAK,CAAC,CAAA;QACV,IAAI,IAAI,CAAC,IAAI,CAAC,YAAY,CAAE,IAAI,WAAW,CAAC,GAAG,CAAC,CAAA;QAChD,WAAW,IAAI,CAAC,CAAA;QAChB,IAAI,WAAW,GAAG,CAAC,EAAE,CAAC;YACpB,YAAY,IAAI,CAAC,CAAA;YACjB,WAAW,GAAG,CAAC,CAAA;QACjB,CAAC;IACH,CAAC;IAED,MAAM,CAAC,YAAY,GAAG,YAAY,CAAA;IAClC,MAAM,CAAC,WAAW,GAAG,WAAoC,CAAA;IAEzD,MAAM,CAAC,GAAG,cAAc,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,IAAI,CAAA;IACvD,OAAO,CAAC,GAAG,MAAM,CAAA;AACnB,CAAC"}

package/dist/cramFile/file.d.ts

@@ -75,4 +75,5 @@ export default class CramFile {
     _uncompressPre(compressionMethod: CompressionMethod, inputBuffer: Uint8Array, uncompressedSize: number): Promise<Uint8Array<ArrayBufferLike>>;
     _uncompress(compressionMethod: CompressionMethod, inputBuffer: Uint8Array, uncompressedSize: number): Promise<Uint8Array<ArrayBufferLike>>;
     readBlock(position: number): Promise<CramFileBlock>;
+    readBlockFromBuffer(buffer: Uint8Array, bufferOffset: number, filePosition: number): Promise<CramFileBlock>;
 }

package/dist/cramFile/file.js

@@ -36,8 +36,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const crc32_1 = __importDefault(require("crc/calculators/crc32"));
 const quick_lru_1 = __importDefault(require("@jbrowse/quick-lru"));
+const crc32_1 = __importDefault(require("crc/calculators/crc32"));
 const errors_ts_1 = require("../errors.js");
 const htscodecs = __importStar(require("../htscodecs/index.js"));
 const io_ts_1 = require("../io.js");
@@ -299,6 +299,49 @@ class CramFile {
         }
         return block;
     }
+    async readBlockFromBuffer(buffer, bufferOffset, filePosition) {
+        const { majorVersion } = await this.getDefinition();
+        if (!this._sectionParsers) {
+            this._sectionParsers = (0, sectionParsers_ts_1.getSectionParsers)(majorVersion);
+        }
+        const sectionParsers = this._sectionParsers;
+        const { cramBlockHeader } = sectionParsers;
+        const headerBytes = buffer.subarray(bufferOffset, bufferOffset + cramBlockHeader.maxLength);
+        const blockHeader = (0, util_ts_1.parseItem)(headerBytes, cramBlockHeader.parser, 0, filePosition);
+        const blockContentPosition = blockHeader._endPosition;
+        const contentOffset = bufferOffset + blockHeader._size;
+        const d = buffer.subarray(contentOffset, contentOffset + blockHeader.compressedSize);
+        const uncompressedData = blockHeader.compressionMethod !== 'raw'
+            ? await this._uncompress(blockHeader.compressionMethod, d, blockHeader.uncompressedSize)
+            : d;
+        const block = {
+            ...blockHeader,
+            _endPosition: blockContentPosition,
+            contentPosition: blockContentPosition,
+            content: uncompressedData,
+        };
+        if (majorVersion >= 3) {
+            const crcOffset = contentOffset + blockHeader.compressedSize;
+            const crcBytes = buffer.subarray(crcOffset, crcOffset + sectionParsers.cramBlockCrc32.maxLength);
+            const crc = (0, util_ts_1.parseItem)(crcBytes, sectionParsers.cramBlockCrc32.parser, 0, blockContentPosition + blockHeader.compressedSize);
+            block.crc32 = crc.crc32;
+            if (this.validateChecksums) {
+                const blockData = buffer.subarray(bufferOffset, bufferOffset + blockHeader._size + blockHeader.compressedSize);
+                const calculatedCrc32 = (0, crc32_1.default)(blockData) >>> 0;
+                if (calculatedCrc32 !== crc.crc32) {
+                    throw new errors_ts_1.CramMalformedError(`crc mismatch in block data: recorded CRC32 = ${crc.crc32}, but calculated CRC32 = ${calculatedCrc32}`);
+                }
+            }
+            block._endPosition = crc._endPosition;
+            block._size =
+                block.compressedSize + sectionParsers.cramBlockCrc32.maxLength;
+        }
+        else {
+            block._endPosition = blockContentPosition + block.compressedSize;
+            block._size = block.compressedSize;
+        }
+        return block;
+    }
 }
 exports.default = CramFile;
 'getDefinition getSectionParsers getSamHeader'.split(' ').forEach(method => {

package/dist/cramFile/file.js.map

@@ -1 +1 @@
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package/dist/cramFile/record.d.ts

@@ -13,6 +13,11 @@ export interface ReadFeature {
     ref?: string;
     sub?: string;
 }
+export interface DecodeOptions {
+    /** Whether to parse tags. If false, raw tag data is stored for lazy parsing. Default true. */
+    decodeTags?: boolean;
+}
+export declare const defaultDecodeOptions: Required<DecodeOptions>;
 export interface MateRecord {
     readName?: string;
     sequenceId: number;
@@ -54,10 +59,16 @@ export default class CramRecord {
     sequenceId: number;
     readGroupId: number;
     mappingQuality: number | undefined;
-    qualityScores: number[] | null | undefined;
+    qualityScores: Uint8Array | null | undefined;
     constructor({ flags, cramFlags, readLength, mappingQuality, lengthOnRef, qualityScores, mateRecordNumber, readBases, readFeatures, mateToUse, readGroupId, readName, sequenceId, uniqueId, templateSize, alignmentStart, tags, }: ReturnType<typeof decodeRecord> & {
         uniqueId: number;
     });
+    /**
+     * Get a single quality score at the given index.
+     * @param index 0-based index into the quality scores
+     * @returns the quality score at that index, or undefined if not available
+     */
+    qualityScoreAt(index: number): number | undefined;
     /**
      * @returns {boolean} true if the read is paired, regardless of whether both segments are mapped
      */

package/dist/cramFile/record.js

@@ -3,8 +3,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.MateFlagsDecoder = exports.CramFlagsDecoder = exports.BamFlagsDecoder = exports.MateFlags = exports.CramFlags = exports.BamFlags = void 0;
+exports.MateFlagsDecoder = exports.CramFlagsDecoder = exports.BamFlagsDecoder = exports.MateFlags = exports.CramFlags = exports.BamFlags = exports.defaultDecodeOptions = void 0;
 const constants_ts_1 = __importDefault(require("./constants.js"));
+exports.defaultDecodeOptions = {
+    decodeTags: true,
+};
 function decodeReadSequence(cramRecord, refRegion) {
     // if it has no length, it has no sequence
     if (!cramRecord.lengthOnRef && !cramRecord.readLength) {
@@ -203,6 +206,14 @@ class CramRecord {
             this.mateRecordNumber = mateRecordNumber;
         }
     }
+    /**
+     * Get a single quality score at the given index.
+     * @param index 0-based index into the quality scores
+     * @returns the quality score at that index, or undefined if not available
+     */
+    qualityScoreAt(index) {
+        return this.qualityScores?.[index];
+    }
     /**
      * @returns {boolean} true if the read is paired, regardless of whether both segments are mapped
      */
@@ -292,8 +303,7 @@ class CramRecord {
         if (!this.isSegmentUnmapped() &&
             this.isPaired() &&
             !this.isMateUnmapped() &&
-            this.mate &&
-            this.sequenceId === this.mate.sequenceId) {
+            this.sequenceId === this.mate?.sequenceId) {
             const s1 = this.isReverseComplemented() ? 'R' : 'F';
             const s2 = this.isMateReverseComplemented() ? 'R' : 'F';
             let o1 = ' ';
@@ -347,11 +357,11 @@ class CramRecord {
         if (this.readFeatures) {
             // use the reference bases to decode the bases substituted in each base
             // substitution
-            this.readFeatures.forEach(readFeature => {
+            for (const readFeature of this.readFeatures) {
                 if (readFeature.code === 'X') {
                     decodeBaseSubstitution(this, refRegion, compressionScheme, readFeature);
                 }
-            });
+            }
         }
         // if this region completely covers this read,
         // keep a reference to it
@@ -371,6 +381,9 @@ class CramRecord {
             data[k] = this[k];
         });
         data.readBases = this.getReadBases();
+        data.qualityScores = this.qualityScores
+            ? Array.from(this.qualityScores)
+            : this.qualityScores;
         return data;
     }
 }