@gmod/hic 1.0.0 → 1.2.0

package/esm/hicFile.js

@@ -1,5 +1,5 @@
+import { inflateRawUnknownSize } from '@gmod/inflate';
 import { LocalFile } from 'generic-filehandle2';
-import { inflate } from 'pako-esm2';
 import { binWindow } from "./binWindow.js";
 import BinaryParser from "./binary.js";
 import BufferedFile from "./bufferedFile.js";
@@ -67,6 +67,11 @@ const BLOCK_CACHE_MAX_ENTRIES = 1024;
 // binsize. Measured on the file above: 0.05 MB at 2.5 Mb, 0.23 MB at 100 kb. So
 // the entry cap now tracks the working set and this tracks the memory, instead
 // of one number answering both badly. See LRU's WeightOpts.
+//
+// This is the one capacity here a caller can override (`blockCacheMaxBytes`),
+// because it is the only one that bounds MEMORY. The two entry caps below are
+// working-set sizes derived from how many region pairs a fetch runs at once,
+// which the library knows and the caller would only have to rederive.
 const BLOCK_CACHE_MAX_BYTES = 128 * 1024 * 1024;
 // One entry per (chrIdx1, chrIdx2), so the working set is the pair count.
 // 512 covers a 31-region view; human whole-genome is 300. A matrix holds the
@@ -100,10 +105,9 @@ export class HicFile {
     normVectorCache = new LRU(NORM_VECTOR_CACHE_SIZE);
     normalizationTypes = ['NONE'];
     matrixCache = new LRU(MATRIX_CACHE_SIZE);
-    blockCache = new LRU(BLOCK_CACHE_MAX_ENTRIES, {
-        maxBytes: BLOCK_CACHE_MAX_BYTES,
-        weigh: blockCacheWeight,
-    });
+    // Assigned in the constructor rather than here, since its byte budget is
+    // configurable and a field initializer cannot see `config`.
+    blockCache;
     normVectorIndexPosition = -1;
     normVectorIndexSize = -1;
     initPromise;
@@ -123,8 +127,12 @@ export class HicFile {
     masterIndex = {};
     meta;
     constructor(config) {
-        const { filehandle, path, reader } = config;
+        const { filehandle, path, reader, blockCacheMaxBytes } = config;
         this.config = config;
+        this.blockCache = new LRU(BLOCK_CACHE_MAX_ENTRIES, {
+            maxBytes: blockCacheMaxBytes ?? BLOCK_CACHE_MAX_BYTES,
+            weigh: blockCacheWeight,
+        });
         if (reader) {
             this.file = reader;
         }
@@ -272,7 +280,7 @@ export class HicFile {
         }
         return matrix;
     }
-    async getContactRecords(normalization, region1, region2, units, binsize) {
+    async getContactRecords(normalization, region1, region2, units, binsize, opts) {
         await this.init();
         const idx1 = this.chromosomeIndexMap[this.getFileChrName(region1.chr)];
         const idx2 = this.chromosomeIndexMap[this.getFileChrName(region2.chr)];
@@ -312,7 +320,10 @@ export class HicFile {
         // offset its values start at.
         const [norm, blocks] = await Promise.all([
             this.getNormVectors(normalization, r1, r2, units, binsize),
-            this.getBlocks(r1, r2, binsize),
+            // The measurable half of the pair: blocks are counted and the two norm
+            // vectors are not, because the vector chain is two hops whatever the
+            // query and the block chain is the one that grows with the region.
+            this.getBlocks(r1, r2, binsize, opts),
         ]);
         // Sum of the blocks' record counts bounds the survivors, so the output is
         // allocated once and filled by a write cursor. Blocks overlap the window
@@ -413,7 +424,7 @@ export class HicFile {
         }
         return result;
     }
-    async getBlocks(region1, region2, binSize) {
+    async getBlocks(region1, region2, binSize, opts) {
         const blockKey = (blockNumber, zd) => `${zd.getKey()}_${blockNumber}`;
         await this.init();
         const chr1 = this.getFileChrName(region1.chr);
@@ -449,7 +460,27 @@ export class HicFile {
                         blockNumbersToQuery.push(num);
                     }
                 }
-                const newBlocks = await Promise.all(blockNumbersToQuery.map(blockNumber => this.readBlock(blockNumber, zd)));
+                // Cached blocks are already done, not absent: a pan that reuses most
+                // of its blocks reads most of the way along rather than restarting at
+                // zero, which is what the bar should say — the work left is the reads.
+                //
+                // A query covering no blocks at all reports nothing rather than `0, 0`:
+                // there is no fraction in it, and a caller dividing would get NaN.
+                const { onProgress } = opts ?? {};
+                let done = blocks.length;
+                if (blockNumbers.length > 0) {
+                    onProgress?.(done, blockNumbers.length);
+                }
+                // Still one `Promise.all`, so every block is still issued in one wave:
+                // what a remote file pays is round-trip DEPTH, and counting the
+                // completions must not turn one wave into a queue. `readChainDepth`
+                // pins that.
+                const newBlocks = await Promise.all(blockNumbersToQuery.map(async (blockNumber) => {
+                    const block = await this.readBlock(blockNumber, zd);
+                    done++;
+                    onProgress?.(done, blockNumbers.length);
+                    return block;
+                }));
                 for (const block of newBlocks) {
                     if (block) {
                         this.blockCache.set(blockKey(block.blockNumber, zd), block);
@@ -465,7 +496,12 @@ export class HicFile {
         let block;
         if (idx) {
             const data = await this.file.read(idx.filePosition, idx.size);
-            const plain = inflate(new Uint8Array(data), {});
+            // `.subarray(2)` drops the zlib header: libdeflate's raw-deflate path is
+            // the fast one, and a `.hic` records only a block's *compressed* size, so
+            // there is no known output size to hand the exact-size entry point.
+            // `inflateRawUnknownSize` guesses 4x the input, which clears this
+            // format's ~2.3x ratio in one pass.
+            const plain = await inflateRawUnknownSize(new Uint8Array(data).subarray(2));
             const parser = new BinaryParser(new DataView(plain.buffer, plain.byteOffset, plain.byteLength));
             // Total records in the block, whatever encoding follows — so every branch
             // below knows its exact (or, for the dense encoding, upper-bound) size
@@ -595,7 +631,7 @@ export class HicFile {
         const filePosition = this.version < 9 ? idx.filePosition + 4 : idx.filePosition + 8;
         return new NormalizationVector(this.file, filePosition, nValues, dataType);
     }
-    async getNormVectorIndex() {
+    async getNormVectorIndex(opts) {
         // Before the version gate, not after it: `version` is 0 until the header is
         // parsed, so calling this first — which `getNormalizationOptions` on its own
         // does — answered "no index" for every file rather than for a v5 one. A
@@ -610,7 +646,10 @@ export class HicFile {
             // sequential range reads, only to rediscover there is nothing there.
             // Cleared on failure (like `init`) so a transient read error retries
             // rather than caching a rejection forever.
-            this.normVectorIndexP ??= this.loadNormVectorIndex().catch((e) => {
+            // The walk runs once, so its progress belongs to the call that performs
+            // it: a caller joining an in-flight or finished load is not waiting on
+            // reads and is told nothing, which is the truth rather than a silence.
+            this.normVectorIndexP ??= this.loadNormVectorIndex(opts?.onProgress).catch((e) => {
                 this.normVectorIndexP = undefined;
                 throw e;
             });
@@ -618,7 +657,7 @@ export class HicFile {
         }
         return this.normVectorIndex;
     }
-    async loadNormVectorIndex() {
+    async loadNormVectorIndex(onProgress) {
         // If we know the position of the norm vector index, read it directly.
         // This is the case for hic v9 files.
         if (this.normVectorIndexPosition > 0 && this.normVectorIndexSize > 0) {
@@ -636,7 +675,7 @@ export class HicFile {
         }
         else {
             try {
-                await this.readNormExpectedValuesAndNormVectorIndex();
+                await this.readNormExpectedValuesAndNormVectorIndex(onProgress);
             }
             catch (e) {
                 // Not "expected if the file has no norm vectors" — that case never
@@ -650,10 +689,10 @@ export class HicFile {
             }
         }
     }
-    async getNormalizationOptions() {
+    async getNormalizationOptions(opts) {
         // Normalization options are computed as a side effect of loading the
         // index. A bit ugly but alternatives are worse.
-        await this.getNormVectorIndex();
+        await this.getNormVectorIndex(opts);
         return this.normalizationTypes;
     }
     async readNormVectorIndex(range) {
@@ -669,10 +708,10 @@ export class HicFile {
     }
     // Used when the position of the norm vector index is unknown: read through
     // the expected values to find the index.
-    async readNormExpectedValuesAndNormVectorIndex() {
+    async readNormExpectedValuesAndNormVectorIndex(onProgress) {
         await this.init();
         if (this.normExpectedValueVectorsPosition !== undefined) {
-            const nviStart = await this.skipExpectedValues(this.normExpectedValueVectorsPosition);
+            const nviStart = await this.skipExpectedValues(this.normExpectedValueVectorsPosition, onProgress);
             let byteCount = INT;
             let data = await this.file.read(nviStart, INT);
             // Possible if there are no norm vectors. A legal v8 file, though uncommon.
@@ -705,7 +744,7 @@ export class HicFile {
     }
     // Used when the position of the norm vector index is unknown: skip the
     // normalized expected values to find the index.
-    async skipExpectedValues(start) {
+    async skipExpectedValues(start, onProgress) {
         const version = this.version;
         const file = new BufferedFile({ file: this.file, size: 256000 });
         const data = await file.read(start, INT);
@@ -721,9 +760,17 @@ export class HicFile {
         }
         const binaryParser = new BinaryParser(new DataView(data));
         const nEntries = binaryParser.getInt(); // Total # of expected value chunks
-        const parseNext = async (chunkStart, remaining) => {
+        // Skip one chunk, answering where the next one starts.
+        //
+        // Its two reads land a whole expected-value vector apart — one per bin of
+        // the genome, so tens of MB at a fine binsize — which is further than the
+        // buffer reaches. On a remote file that is two round trips per chunk that
+        // nothing can merge, and it is why this walk, not the index it is looking
+        // for, is the slow part of opening a pre-v9 file. It is also why the chunk
+        // is the unit worth counting: `nEntries` of them, known before the first
+        // read, each costing about the same.
+        const skipChunk = async (chunkStart) => {
             let chunkSize = 0;
-            const p0 = chunkStart;
             let buf = await file.read(chunkStart, 500);
             let parser = new BinaryParser(new DataView(buf));
             parser.getString(); // type
@@ -736,11 +783,22 @@ export class HicFile {
             const nChrScaleFactors = parser.getInt();
             chunkSize +=
                 INT + nChrScaleFactors * (INT + (version < 9 ? DOUBLE : FLOAT));
-            return remaining - 1 === 0
-                ? p0 + chunkSize
-                : parseNext(p0 + chunkSize, remaining - 1);
+            return chunkStart + chunkSize;
         };
-        return nEntries === 0 ? start + INT : parseNext(start + INT, nEntries);
+        // A loop rather than the tail recursion this was, because the position is
+        // the only thing carried between chunks and a counter now rides along with
+        // it. Chunks must be walked in order — each one's size is only known once
+        // the one before it has been parsed — so the awaits are sequential by
+        // nature, not by oversight.
+        if (nEntries > 0) {
+            onProgress?.(0, nEntries);
+        }
+        let position = start + INT;
+        for (let done = 0; done < nEntries; done++) {
+            position = await skipChunk(position);
+            onProgress?.(done + 1, nEntries);
+        }
+        return position;
     }
     parseNormVectorEntry(binaryParser) {
         const type = binaryParser.getString(); // 15

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package/esm/index.d.ts

@@ -2,4 +2,4 @@ export { HicFile, NO_DATA_FOR_RESOLUTION } from './hicFile.ts';
 export { readerFromFilehandle } from './reader.ts';
 export type { HicConfig } from './hicFile.ts';
 export type { ContactRecords } from './contactRecords.ts';
-export type { Chromosome, HicMetadata, HicRegion, Reader, Zoom, } from './types.ts';
+export type { Chromosome, HicMetadata, HicRegion, ProgressCallback, ProgressOpts, Reader, Zoom, } from './types.ts';

package/esm/types.d.ts

@@ -8,6 +8,29 @@
 export interface Reader {
     read: (position: number, length: number) => Promise<ArrayBuffer>;
 }
+/**
+ * Progress within one phase: `current` of `total` units done, called as the
+ * phase advances and once with `current` 0 before it starts, so a caller can
+ * show a determinate bar from the first moment rather than after the first
+ * unit lands.
+ *
+ * The unit is whatever that phase measures — expected-value chunks for the
+ * normalization-index walk, blocks for a contact fetch — and a caller renders
+ * `current / total` without needing to know which. `total` never changes within
+ * a call, and `current` never goes backwards.
+ *
+ * A phase with nothing to do does not call this at all, rather than calling it
+ * with a `total` of 0 that a caller could only divide by.
+ */
+export type ProgressCallback = (current: number, total: number) => void;
+/**
+ * Progress reporting for one call. Per call rather than per file: progress
+ * belongs to the operation a caller is waiting on, and a file-wide callback
+ * could not say which of several concurrent fetches it was describing.
+ */
+export interface ProgressOpts {
+    onProgress?: ProgressCallback;
+}
 export interface Chromosome {
     index: number;
     name: string;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/hic",
-  "version": "1.0.0",
+  "version": "1.2.0",
   "packageManager": "pnpm@11.15.1",
   "description": "Read .hic contact matrix files in node or the browser",
   "license": "MIT",
@@ -27,6 +27,7 @@
   ],
   "scripts": {
     "test": "vitest",
+    "test:pack": "./scripts/test-pack.sh",
     "clean": "rimraf dist esm",
     "format": "prettier --write .",
     "format:check": "prettier --check .",
@@ -36,10 +37,13 @@
     "build:esm": "tsc --outDir esm",
     "build:es5": "tsc --module commonjs --moduleResolution bundler --outDir dist",
     "postbuild:es5": "echo '{\"type\": \"commonjs\"}' > dist/package.json",
-    "preversion": "pnpm lint && pnpm format:check && pnpm typecheck && pnpm test --run && pnpm build",
+    "preversion": "pnpm lint && pnpm format:check && pnpm typecheck && pnpm test --run && pnpm build && pnpm test:pack",
     "postversion": "git push --follow-tags",
     "build": "pnpm build:esm && pnpm build:es5",
     "coverage": "pnpm test --coverage",
+    "benchonly": "vitest bench",
+    "bench:cache": "node --experimental-strip-types scripts/bench-cache.ts",
+    "bench:requests": "node --experimental-strip-types scripts/bench-requests.ts",
     "version": "git-cliff --tag v$npm_package_version --unreleased --prepend CHANGELOG.md && git add CHANGELOG.md"
   },
   "keywords": [
@@ -51,16 +55,18 @@
     "biojs"
   ],
   "dependencies": {
-    "generic-filehandle2": "^2.3.1",
-    "pako-esm2": "^2.0.2"
+    "@gmod/inflate": "^1.0.0",
+    "generic-filehandle2": "^2.3.1"
   },
   "devDependencies": {
     "@eslint/js": "^10.0.1",
+    "@gmod/range-cache-filehandle": "^1.0.2",
     "@types/node": "^25.9.5",
     "@vitest/coverage-v8": "^4.1.10",
     "eslint": "^10.8.0",
     "eslint-plugin-import-x": "^4.17.1",
     "git-cliff": "^2.13.1",
+    "pako-esm2": "^2.0.2",
     "prettier": "^3.9.6",
     "rimraf": "^6.1.3",
     "typescript": "^6.0.3",