npm - @gmod/bam - Versions diffs - 10.0.0 → 10.0.2 - Mend

@gmod/bam 10.0.0 → 10.0.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (18) hide show

package/dist/bamFile.js CHANGED Viewed

@@ -6,7 +6,6 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.DEFAULT_CACHE_IDLE_TIMEOUT_MS = exports.DEFAULT_MAX_CACHE_BYTES = void 0;
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 const shared_read_cache_1 = require("@gmod/shared-read-cache");
-const crc32_1 = __importDefault(require("crc/calculators/crc32"));
 const bai_ts_1 = __importDefault(require("./bai.js"));
 const csi_ts_1 = __importDefault(require("./csi.js"));
 const nullFilehandle_ts_1 = __importDefault(require("./nullFilehandle.js"));
@@ -617,7 +616,7 @@ class BamFile {
                         (blockStart - dpositions[pos]) +
                         chunk.minv.dataPosition +
                         1
-                    : (0, crc32_1.default)(ba.subarray(blockStart, blockEnd)) >>> 0, dataView);
+                    : (0, util_ts_1.contentHash53)(ba, blockStart, blockEnd), dataView);
                 sink.push(feature);
             }
             blockStart = blockEnd + 1;

package/dist/bamFile.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/streamBam.js CHANGED Viewed

@@ -195,12 +195,13 @@ async function* streamBamRecords({ bamFilehandle, bamPath, bamUrl, recordClass,
                 // the window size, so it is as stable as a virtual offset without
                 // pretending to be one.
                 //
-                // NOT the crc32 of the record bytes that readBamFeatures falls back
-                // to when it has no positions. That is a content hash, so the two
-                // byte-identical records in exact_duplicate.bam collide on it, and
-                // hashing every record costs ~40% of the walk (135ms of 340ms over
-                // out.bam) where a counter costs nothing. The fallback only fires on
-                // an unusual path there; here it would fire on every record.
+                // NOT the hash of the record bytes that readBamFeatures falls back
+                // to when it has no positions: the two byte-identical records in
+                // exact_duplicate.bam collide on any content hash, and hashing
+                // every record cost ~40% of the walk (135ms of 340ms over out.bam,
+                // measured with crc32) where a counter costs nothing. The fallback
+                // only fires on an unusual path there; here it would fire on every
+                // record.
                 recordIndex++, dataView));
                 blockStart = blockEnd + 1;
             }

package/dist/streamBam.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/util.d.ts CHANGED Viewed

@@ -11,6 +11,15 @@ export declare const BAM_MAGIC = 21840194;
  * pushing a record per turn until the process runs out of memory.
  */
 export declare function readBlockSize(dataView: DataView, offset: number): number;
+/**
+ * A 53-bit hash of `bytes[start, end)`: cyrb53 (public domain), taken over
+ * bytes. The id of a record read with no file positions, which has to be the
+ * same for the same record in every query, so it hashes content. It is 53 bits
+ * rather than crc32's 32 because ids are deduplicated: at 32 bits a fetch of
+ * 150,000 records expects about 2.6 distinct pairs to collide, each silently
+ * dropping a read, where 53 bits expect about 1e-6.
+ */
+export declare function contentHash53(bytes: Uint8Array, start: number, end: number): number;
 export declare function resolveFilehandle(filehandle?: GenericFilehandle, path?: string, url?: string): GenericFilehandle | undefined;
 export interface BamOpts {
     viewAsPairs?: boolean;

package/dist/util.js CHANGED Viewed

@@ -5,6 +5,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.MAX_CONCURRENT_CHUNK_READS = exports.throwIfAborted = exports.BAM_MAGIC = void 0;
 exports.readBlockSize = readBlockSize;
+exports.contentHash53 = contentHash53;
 exports.resolveFilehandle = resolveFilehandle;
 exports.chunksLikelyRead = chunksLikelyRead;
 exports.optimizeChunks = optimizeChunks;
@@ -34,6 +35,28 @@ function readBlockSize(dataView, offset) {
     }
     return blockSize;
 }
+/**
+ * A 53-bit hash of `bytes[start, end)`: cyrb53 (public domain), taken over
+ * bytes. The id of a record read with no file positions, which has to be the
+ * same for the same record in every query, so it hashes content. It is 53 bits
+ * rather than crc32's 32 because ids are deduplicated: at 32 bits a fetch of
+ * 150,000 records expects about 2.6 distinct pairs to collide, each silently
+ * dropping a read, where 53 bits expect about 1e-6.
+ */
+function contentHash53(bytes, start, end) {
+    let h1 = 0xdeadbeef;
+    let h2 = 0x41c6ce57;
+    for (let i = start; i < end; i++) {
+        const b = bytes[i];
+        h1 = Math.imul(h1 ^ b, 2654435761);
+        h2 = Math.imul(h2 ^ b, 1597334677);
+    }
+    h1 = Math.imul(h1 ^ (h1 >>> 16), 2246822507);
+    h1 ^= Math.imul(h2 ^ (h2 >>> 13), 3266489909);
+    h2 = Math.imul(h2 ^ (h2 >>> 16), 2246822507);
+    h2 ^= Math.imul(h1 ^ (h1 >>> 13), 3266489909);
+    return 4294967296 * (2097151 & h2) + (h1 >>> 0);
+}
 function resolveFilehandle(filehandle, path, url) {
     return (filehandle ??
         (path ? new generic_filehandle2_1.LocalFile(path) : url ? new generic_filehandle2_1.RemoteFile(url) : undefined));

package/dist/util.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/bamFile.js CHANGED Viewed

@@ -1,13 +1,12 @@
 import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle';
 import { SharedReadCache } from '@gmod/shared-read-cache';
-import crc32 from 'crc/calculators/crc32';
 import BAI from "./bai.js";
 import CSI from "./csi.js";
 import NullFilehandle from "./nullFilehandle.js";
 import BAMFeature from "./record.js";
 import { packReference, referenceCovers } from "./reference.js";
 import { parseHeaderText } from "./sam.js";
-import { BAM_MAGIC, MAX_CONCURRENT_CHUNK_READS, appendInRange, decodeHeaderText, optimizeChunks, parseRefSeqs, readBlockSize, resolveFilehandle, throwIfAborted, } from "./util.js";
+import { BAM_MAGIC, MAX_CONCURRENT_CHUNK_READS, appendInRange, contentHash53, decodeHeaderText, optimizeChunks, parseRefSeqs, readBlockSize, resolveFilehandle, throwIfAborted, } from "./util.js";
 const blockLen = 1 << 16;
 // Ceiling on GROWING the header read. A million contigs is roughly 10MB of
 // compressed @SQ lines and ref-seq table, so a read that has doubled past this
@@ -611,7 +610,7 @@ export default class BamFile {
                         (blockStart - dpositions[pos]) +
                         chunk.minv.dataPosition +
                         1
-                    : crc32(ba.subarray(blockStart, blockEnd)) >>> 0, dataView);
+                    : contentHash53(ba, blockStart, blockEnd), dataView);
                 sink.push(feature);
             }
             blockStart = blockEnd + 1;

package/esm/bamFile.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/streamBam.js CHANGED Viewed

@@ -189,12 +189,13 @@ export async function* streamBamRecords({ bamFilehandle, bamPath, bamUrl, record
                 // the window size, so it is as stable as a virtual offset without
                 // pretending to be one.
                 //
-                // NOT the crc32 of the record bytes that readBamFeatures falls back
-                // to when it has no positions. That is a content hash, so the two
-                // byte-identical records in exact_duplicate.bam collide on it, and
-                // hashing every record costs ~40% of the walk (135ms of 340ms over
-                // out.bam) where a counter costs nothing. The fallback only fires on
-                // an unusual path there; here it would fire on every record.
+                // NOT the hash of the record bytes that readBamFeatures falls back
+                // to when it has no positions: the two byte-identical records in
+                // exact_duplicate.bam collide on any content hash, and hashing
+                // every record cost ~40% of the walk (135ms of 340ms over out.bam,
+                // measured with crc32) where a counter costs nothing. The fallback
+                // only fires on an unusual path there; here it would fire on every
+                // record.
                 recordIndex++, dataView));
                 blockStart = blockEnd + 1;
             }

package/esm/streamBam.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/esm/util.d.ts CHANGED Viewed

@@ -11,6 +11,15 @@ export declare const BAM_MAGIC = 21840194;
  * pushing a record per turn until the process runs out of memory.
  */
 export declare function readBlockSize(dataView: DataView, offset: number): number;
+/**
+ * A 53-bit hash of `bytes[start, end)`: cyrb53 (public domain), taken over
+ * bytes. The id of a record read with no file positions, which has to be the
+ * same for the same record in every query, so it hashes content. It is 53 bits
+ * rather than crc32's 32 because ids are deduplicated: at 32 bits a fetch of
+ * 150,000 records expects about 2.6 distinct pairs to collide, each silently
+ * dropping a read, where 53 bits expect about 1e-6.
+ */
+export declare function contentHash53(bytes: Uint8Array, start: number, end: number): number;
 export declare function resolveFilehandle(filehandle?: GenericFilehandle, path?: string, url?: string): GenericFilehandle | undefined;
 export interface BamOpts {
     viewAsPairs?: boolean;

package/esm/util.js CHANGED Viewed

@@ -16,6 +16,28 @@ export function readBlockSize(dataView, offset) {
     }
     return blockSize;
 }
+/**
+ * A 53-bit hash of `bytes[start, end)`: cyrb53 (public domain), taken over
+ * bytes. The id of a record read with no file positions, which has to be the
+ * same for the same record in every query, so it hashes content. It is 53 bits
+ * rather than crc32's 32 because ids are deduplicated: at 32 bits a fetch of
+ * 150,000 records expects about 2.6 distinct pairs to collide, each silently
+ * dropping a read, where 53 bits expect about 1e-6.
+ */
+export function contentHash53(bytes, start, end) {
+    let h1 = 0xdeadbeef;
+    let h2 = 0x41c6ce57;
+    for (let i = start; i < end; i++) {
+        const b = bytes[i];
+        h1 = Math.imul(h1 ^ b, 2654435761);
+        h2 = Math.imul(h2 ^ b, 1597334677);
+    }
+    h1 = Math.imul(h1 ^ (h1 >>> 16), 2246822507);
+    h1 ^= Math.imul(h2 ^ (h2 >>> 13), 3266489909);
+    h2 = Math.imul(h2 ^ (h2 >>> 16), 2246822507);
+    h2 ^= Math.imul(h1 ^ (h1 >>> 13), 3266489909);
+    return 4294967296 * (2097151 & h2) + (h1 >>> 0);
+}
 export function resolveFilehandle(filehandle, path, url) {
     return (filehandle ??
         (path ? new LocalFile(path) : url ? new RemoteFile(url) : undefined));

package/esm/util.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bam",
-  "version": "10.0.0",
+  "version": "10.0.2",
   "packageManager": "pnpm@11.15.1",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
@@ -53,14 +53,14 @@
   "dependencies": {
     "@gmod/bgzf-filehandle": "^6.6.0",
     "@gmod/shared-read-cache": "^1.7.2",
-    "@jbrowse/quick-lru": "^7.3.5",
-    "crc": "^4.3.2",
+    "@jbrowse/quick-lru": "^8.0.0",
     "generic-filehandle2": "^2.4.0"
   },
   "devDependencies": {
     "@eslint/js": "^10.0.1",
     "@types/node": "^26.2.0",
     "@vitest/coverage-v8": "^4.1.11",
+    "crc": "^4.3.2",
     "eslint": "^10.9.0",
     "eslint-plugin-import-x": "^4.17.1",
     "git-cliff": "^2.13.1",

package/src/bamFile.ts CHANGED Viewed

@@ -1,6 +1,5 @@
 import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle'
 import { SharedReadCache } from '@gmod/shared-read-cache'
-import crc32 from 'crc/calculators/crc32'
 import BAI from './bai.ts'
 import CSI from './csi.ts'
@@ -12,6 +11,7 @@ import {
   BAM_MAGIC,
   MAX_CONCURRENT_CHUNK_READS,
   appendInRange,
+  contentHash53,
   decodeHeaderText,
   optimizeChunks,
   parseRefSeqs,
@@ -974,7 +974,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
                 (blockStart - dpositions[pos]!) +
                 chunk.minv.dataPosition +
                 1
-            : crc32(ba.subarray(blockStart, blockEnd)) >>> 0,
+            : contentHash53(ba, blockStart, blockEnd),
           dataView,
         )

package/src/streamBam.ts CHANGED Viewed

@@ -305,12 +305,13 @@ export async function* streamBamRecords<T extends BamRecordLike = BAMFeature>({
             // the window size, so it is as stable as a virtual offset without
             // pretending to be one.
             //
-            // NOT the crc32 of the record bytes that readBamFeatures falls back
-            // to when it has no positions. That is a content hash, so the two
-            // byte-identical records in exact_duplicate.bam collide on it, and
-            // hashing every record costs ~40% of the walk (135ms of 340ms over
-            // out.bam) where a counter costs nothing. The fallback only fires on
-            // an unusual path there; here it would fire on every record.
+            // NOT the hash of the record bytes that readBamFeatures falls back
+            // to when it has no positions: the two byte-identical records in
+            // exact_duplicate.bam collide on any content hash, and hashing
+            // every record cost ~40% of the walk (135ms of 340ms over out.bam,
+            // measured with crc32) where a counter costs nothing. The fallback
+            // only fires on an unusual path there; here it would fire on every
+            // record.
             recordIndex++,
             dataView,
           ),

package/src/util.ts CHANGED Viewed

@@ -25,6 +25,29 @@ export function readBlockSize(dataView: DataView, offset: number) {
   return blockSize
 }
+/**
+ * A 53-bit hash of `bytes[start, end)`: cyrb53 (public domain), taken over
+ * bytes. The id of a record read with no file positions, which has to be the
+ * same for the same record in every query, so it hashes content. It is 53 bits
+ * rather than crc32's 32 because ids are deduplicated: at 32 bits a fetch of
+ * 150,000 records expects about 2.6 distinct pairs to collide, each silently
+ * dropping a read, where 53 bits expect about 1e-6.
+ */
+export function contentHash53(bytes: Uint8Array, start: number, end: number) {
+  let h1 = 0xdeadbeef
+  let h2 = 0x41c6ce57
+  for (let i = start; i < end; i++) {
+    const b = bytes[i]!
+    h1 = Math.imul(h1 ^ b, 2654435761)
+    h2 = Math.imul(h2 ^ b, 1597334677)
+  }
+  h1 = Math.imul(h1 ^ (h1 >>> 16), 2246822507)
+  h1 ^= Math.imul(h2 ^ (h2 >>> 13), 3266489909)
+  h2 = Math.imul(h2 ^ (h2 >>> 16), 2246822507)
+  h2 ^= Math.imul(h1 ^ (h1 >>> 13), 3266489909)
+  return 4294967296 * (2097151 & h2) + (h1 >>> 0)
+}
 export function resolveFilehandle(
   filehandle?: GenericFilehandle,
   path?: string,