@gmod/cram 7.0.2 → 8.0.0

package/dist/wasm/noodles-cram/noodles_cram_wasm_bg.js.map

@@ -0,0 +1 @@
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package/esm/cramFile/codecs/beta.js

@@ -1,5 +1,4 @@
 import CramCodec from "./_base.js";
-import { getBits } from "./getBits.js";
 import { CramUnimplementedError } from "../../errors.js";
 export default class BetaCodec extends CramCodec {
     constructor(parameters, dataType) {
@@ -9,8 +8,33 @@ export default class BetaCodec extends CramCodec {
         }
     }
     decode(_slice, coreDataBlock, _blocksByContentId, cursors) {
-        const fromBits = 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);
     }
 }
+/**
+ * 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/esm/cramFile/codecs/beta.js.map

@@ -1 +1 @@
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+{"version":3,"file":"beta.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/beta.ts"],"names":[],"mappings":"AAAA,OAAO,SAA8B,MAAM,YAAY,CAAA;AACvD,OAAO,EAAE,sBAAsB,EAAE,MAAM,iBAAiB,CAAA;AAKxD,MAAM,CAAC,OAAO,OAAO,SAAU,SAAQ,SAGtC;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,sBAAsB,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;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/esm/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/esm/cramFile/codecs/external.js

@@ -28,5 +28,20 @@ export default class ExternalCodec extends CramCodec {
             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 CramBufferOverrunError('attempted to read beyond end of block. this file seems truncated.');
+        }
+        cursor.bytePosition = end;
+        return contentBlock.content.subarray(start, end);
+    }
 }
 //# 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,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"}
+{"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;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,sBAAsB,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"}

package/esm/cramFile/codecs/gamma.js

@@ -1,5 +1,4 @@
 import CramCodec from "./_base.js";
-import { getBits } from "./getBits.js";
 import { CramUnimplementedError } from "../../errors.js";
 export default class GammaCodec extends CramCodec {
     constructor(parameters, dataType) {
@@ -9,13 +8,50 @@ export default class GammaCodec extends CramCodec {
         }
     }
     decode(_slice, coreDataBlock, _blocksByContentId, cursors) {
-        let length = 1;
-        while (getBits(coreDataBlock.content, cursors.coreBlock, 1) === 0) {
-            length = length + 1;
+        return decodeGammaInline(coreDataBlock.content, cursors.coreBlock, this.parameters.offset);
+    }
+}
+/**
+ * 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;
+            }
         }
-        const readBits = getBits(coreDataBlock.content, cursors.coreBlock, length - 1);
-        const value = readBits | (1 << (length - 1));
-        return value - this.parameters.offset;
     }
+    // Update cursor
+    cursor.bytePosition = bytePosition;
+    cursor.bitPosition = bitPosition;
+    const value = readBits | (1 << (length - 1));
+    return value - offset;
 }
 //# sourceMappingURL=gamma.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"gamma.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/gamma.ts"],"names":[],"mappings":"AAAA,OAAO,SAA8B,MAAM,YAAY,CAAA;AACvD,OAAO,EAAE,sBAAsB,EAAE,MAAM,iBAAiB,CAAA;AAKxD,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,SAGvC;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,sBAAsB,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;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/esm/cramFile/codecs/getBits.js

@@ -1,13 +1,29 @@
 export class CramBufferOverrunError extends Error {
 }
 export 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/esm/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":"AAAA,MAAM,OAAO,sBAAuB,SAAQ,KAAK;CAAG;AAEpD,MAAM,UAAU,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/esm/cramFile/codecs/huffman.js

@@ -1,6 +1,37 @@
 import CramCodec from "./_base.js";
-import { getBits } from "./getBits.js";
 import { CramMalformedError } from "../../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);
@@ -98,8 +129,11 @@ export default class HuffmanIntCodec extends CramCodec {
         let bits = 0;
         for (let i = 0; i < this.sortedCodes.length; i += 1) {
             const length = this.sortedCodes[i].bitLength;
-            bits <<= length - prevLen;
-            bits |= 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/esm/cramFile/codecs/huffman.js.map

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package/esm/cramFile/codecs/subexp.js

@@ -1,5 +1,4 @@
 import CramCodec from "./_base.js";
-import { getBits } from "./getBits.js";
 import { CramUnimplementedError } from "../../errors.js";
 export default class SubexpCodec extends CramCodec {
     constructor(parameters, dataType) {
@@ -9,22 +8,45 @@ export default class SubexpCodec extends CramCodec {
         }
     }
     decode(_slice, coreDataBlock, _blocksByContentId, cursors) {
-        let numLeadingOnes = 0;
-        while (getBits(coreDataBlock.content, cursors.coreBlock, 1)) {
-            numLeadingOnes = numLeadingOnes + 1;
+        return decodeSubexpInline(coreDataBlock.content, cursors.coreBlock, this.parameters.K, this.parameters.offset);
+    }
+}
+/**
+ * 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 = getBits(coreDataBlock.content, cursors.coreBlock, b);
+        if (bit === 0) {
+            break;
         }
-        else {
-            b = numLeadingOnes + this.parameters.K - 1;
-            const bits = 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;
 }
 //# sourceMappingURL=subexp.js.map

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

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

@@ -1,4 +1,4 @@
-import QuickLRU from 'quick-lru';
+import QuickLRU from '@jbrowse/quick-lru';
 import CramContainer from './container/index.ts';
 import CramRecord from './record.ts';
 import { BlockHeader, CompressionMethod } from './sectionParsers.ts';

package/esm/cramFile/file.js

@@ -1,5 +1,5 @@
+import QuickLRU from '@jbrowse/quick-lru';
 import crc32 from 'crc/calculators/crc32';
-import QuickLRU from 'quick-lru';
 import { CramMalformedError, CramUnimplementedError } from "../errors.js";
 import * as htscodecs from "../htscodecs/index.js";
 import { open } from "../io.js";

package/esm/cramFile/file.js.map

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package/esm/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/esm/cramFile/record.js

@@ -1,4 +1,7 @@
 import Constants from "./constants.js";
+export const defaultDecodeOptions = {
+    decodeTags: true,
+};
 function decodeReadSequence(cramRecord, refRegion) {
     // if it has no length, it has no sequence
     if (!cramRecord.lengthOnRef && !cramRecord.readLength) {
@@ -197,6 +200,14 @@ export default 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
      */
@@ -286,8 +297,7 @@ export default 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 = ' ';
@@ -341,11 +351,11 @@ export default 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
@@ -365,6 +375,9 @@ export default class CramRecord {
             data[k] = this[k];
         });
         data.readBases = this.getReadBases();
+        data.qualityScores = this.qualityScores
+            ? Array.from(this.qualityScores)
+            : this.qualityScores;
         return data;
     }
 }

package/esm/cramFile/record.js.map

@@ -1 +1 @@
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