@gmod/hic 1.2.1 → 1.3.1

package/esm/hicFile.js

@@ -1,4 +1,5 @@
 import { inflateRawUnknownSize } from '@gmod/inflate';
+import { SharedReadCache, throwIfAborted } from '@gmod/shared-read-cache';
 import { LocalFile } from 'generic-filehandle2';
 import { binWindow } from "./binWindow.js";
 import BinaryParser from "./binary.js";
@@ -97,21 +98,23 @@ function getNormalizationVectorKey(type, chrIdx, unit, resolution) {
 export class HicFile {
     config;
     file;
-    // Both caches hold the in-flight PROMISE, not the resolved value. A
+    // These caches share the in-flight read, not just its result. A
     // multi-region fetch runs its region pairs concurrently and they share
     // chromosomes, so caching only the result had every concurrent pair miss and
     // re-issue the same reads — measured +12 range requests on a 6-pair fetch.
-    // Same shape as `initPromise`/`normVectorIndexP`, rejection eviction included.
-    normVectorCache = new LRU(NORM_VECTOR_CACHE_SIZE);
-    normalizationTypes = ['NONE'];
-    matrixCache = new LRU(MATRIX_CACHE_SIZE);
+    // `SharedReadCache` cancels a shared read only once every caller waiting on
+    // it has aborted, and drops a rejection so the next caller retries.
+    headerCache = new SharedReadCache();
+    normVectorIndexCache = new SharedReadCache();
+    normVectorCache = new SharedReadCache({ maxSize: NORM_VECTOR_CACHE_SIZE });
+    matrixCache = new SharedReadCache({
+        maxSize: MATRIX_CACHE_SIZE,
+    });
     // 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;
-    normVectorIndexP;
     version = 0;
     genomeId = '';
     footerPosition = 0;
@@ -119,7 +122,6 @@ export class HicFile {
     // carrying none of it ends. Public so a test can cut a real file there to
     // make that second shape.
     normExpectedValueVectorsPosition;
-    normVectorIndex;
     chromosomes = [];
     chromosomeIndexMap = {};
     chrAliasTable = {};
@@ -146,142 +148,133 @@ export class HicFile {
             throw new Error('must supply filehandle, path, or reader');
         }
     }
-    async init() {
-        // Memoize the promise, not a boolean flag: two concurrent callers must
-        // share one header parse rather than both racing readHeaderAndFooter. Clear
-        // it on failure so a later call retries instead of caching a rejected
-        // promise forever.
-        this.initPromise ??= this.readHeaderAndFooter().catch((e) => {
-            this.initPromise = undefined;
-            throw e;
-        });
-        return this.initPromise;
+    async init(opts) {
+        return this.headerCache.get('header', opts?.signal, signal => this.readHeaderAndFooter(signal));
     }
-    async getMetaData() {
-        await this.init();
+    async getMetaData(opts) {
+        await this.init(opts);
         return this.meta;
     }
-    async readHeaderAndFooter() {
-        // `init` clears its memoized promise on failure so a transient read error
-        // retries, and this parse appends as it goes — so a retry has to start from
-        // empty or a failure part-way through the chromosome loop leaves the second
-        // run appending to the first's partial output (duplicate refNames out of
-        // `getRefNames`, a duplicated binsize list out of `getMetaData`).
-        this.chromosomes = [];
-        this.chromosomeIndexMap = {};
-        this.chrAliasTable = {};
-        this.bpResolutions = [];
-        this.masterIndex = {};
-        // Read initial fields magic, version, and footer position
-        let data = await this.file.read(0, 16);
+    // Parsed into locals and committed only at the end: a parse every caller
+    // abandoned can still be running beside the one that replaced it, and a
+    // transient failure part-way through must leave nothing half-written for the
+    // retry to append to.
+    async readHeaderAndFooter(signal) {
+        let data = await this.file.read(0, 16, { signal });
         if (data.byteLength === 0) {
             throw new Error('File content is empty');
         }
         let binaryParser = new BinaryParser(new DataView(data));
         binaryParser.getString(); // magic
-        this.version = binaryParser.getInt();
-        if (this.version < 5) {
-            throw new Error(`Unsupported hic version: ${this.version}`);
-        }
-        this.footerPosition = binaryParser.getLong();
-        // Read footer to determine file position of body section (end of header)
-        await this.readFooter();
-        const bodyPosition = Object.values(this.masterIndex).reduce((min, entry) => Math.min(min, entry.start), Number.MAX_VALUE);
-        data = await this.file.read(16, bodyPosition - 16);
+        const version = binaryParser.getInt();
+        if (version < 5) {
+            throw new Error(`Unsupported hic version: ${version}`);
+        }
+        const footerPosition = binaryParser.getLong();
+        const { masterIndex, normExpectedValueVectorsPosition } = await this.readFooter(version, footerPosition, signal);
+        const bodyPosition = Object.values(masterIndex).reduce((min, entry) => Math.min(min, entry.start), Number.MAX_VALUE);
+        data = await this.file.read(16, bodyPosition - 16, { signal });
         binaryParser = new BinaryParser(new DataView(data));
-        this.genomeId = binaryParser.getString();
-        if (this.version >= 9) {
-            this.normVectorIndexPosition = binaryParser.getLong();
-            this.normVectorIndexSize = binaryParser.getLong();
+        const genomeId = binaryParser.getString();
+        let normVectorIndexPosition = -1;
+        let normVectorIndexSize = -1;
+        if (version >= 9) {
+            normVectorIndexPosition = binaryParser.getLong();
+            normVectorIndexSize = binaryParser.getLong();
         }
         let nAttributes = binaryParser.getInt();
         while (nAttributes-- > 0) {
             binaryParser.getString(); // attribute key
             binaryParser.getString(); // attribute value
         }
+        const chromosomes = [];
+        const chromosomeIndexMap = {};
         let nChrs = binaryParser.getInt();
         let i = 0;
         while (nChrs-- > 0) {
             const chr = {
                 index: i,
                 name: binaryParser.getString(),
-                size: this.version < 9 ? binaryParser.getInt() : binaryParser.getLong(),
+                size: version < 9 ? binaryParser.getInt() : binaryParser.getLong(),
             };
-            this.chromosomes.push(chr);
-            this.chromosomeIndexMap[chr.name] = chr.index;
+            chromosomes.push(chr);
+            chromosomeIndexMap[chr.name] = chr.index;
             i++;
         }
+        const bpResolutions = [];
         let nBpResolutions = binaryParser.getInt();
         while (nBpResolutions-- > 0) {
-            this.bpResolutions.push(binaryParser.getInt());
+            bpResolutions.push(binaryParser.getInt());
         }
-        // Build lookup table for well-known chr aliases
-        for (const chrName of Object.keys(this.chromosomeIndexMap)) {
+        const chrAliasTable = {};
+        for (const chrName of Object.keys(chromosomeIndexMap)) {
             if (chrName.startsWith('chr')) {
-                this.chrAliasTable[chrName.slice(3)] = chrName;
+                chrAliasTable[chrName.slice(3)] = chrName;
             }
             else if (chrName === 'MT') {
-                this.chrAliasTable.chrM = chrName;
+                chrAliasTable.chrM = chrName;
             }
             else {
-                this.chrAliasTable[`chr${chrName}`] = chrName;
+                chrAliasTable[`chr${chrName}`] = chrName;
             }
         }
+        throwIfAborted(signal);
+        this.version = version;
+        this.footerPosition = footerPosition;
+        this.masterIndex = masterIndex;
+        this.normExpectedValueVectorsPosition = normExpectedValueVectorsPosition;
+        this.genomeId = genomeId;
+        this.normVectorIndexPosition = normVectorIndexPosition;
+        this.normVectorIndexSize = normVectorIndexSize;
+        this.chromosomes = chromosomes;
+        this.chromosomeIndexMap = chromosomeIndexMap;
+        this.bpResolutions = bpResolutions;
+        this.chrAliasTable = chrAliasTable;
         this.meta = {
-            version: this.version,
-            genome: this.genomeId,
-            chromosomes: this.chromosomes,
-            resolutions: this.bpResolutions,
+            version,
+            genome: genomeId,
+            chromosomes,
+            resolutions: bpResolutions,
         };
     }
-    async readFooter() {
-        const skip = this.version < 9 ? 8 : 12;
-        let data = await this.file.read(this.footerPosition, skip);
+    async readFooter(version, footerPosition, signal) {
+        const skip = version < 9 ? 8 : 12;
+        let data = await this.file.read(footerPosition, skip, { signal });
         let binaryParser = new BinaryParser(new DataView(data));
         // Total size, master index + expected values
-        const nBytes = this.version < 9 ? binaryParser.getInt() : binaryParser.getLong();
+        const nBytes = version < 9 ? binaryParser.getInt() : binaryParser.getLong();
         let nEntries = binaryParser.getInt();
         // Estimate the size of the master index. String key length is unknown, be
         // conservative (100 bytes).
         const miSize = nEntries * (100 + 64 + 32);
-        data = await this.file.read(this.footerPosition + skip, Math.min(miSize, nBytes));
+        data = await this.file.read(footerPosition + skip, Math.min(miSize, nBytes), { signal });
         binaryParser = new BinaryParser(new DataView(data));
+        const masterIndex = {};
         while (nEntries-- > 0) {
             const key = binaryParser.getString();
             const pos = binaryParser.getLong();
             const size = binaryParser.getInt();
-            this.masterIndex[key] = { start: pos, size };
+            masterIndex[key] = { start: pos, size };
         }
         // Normalized expected values start after the expected values
-        if (this.version > 5) {
-            const s = this.version < 9 ? 4 : 8;
-            this.normExpectedValueVectorsPosition = this.footerPosition + s + nBytes;
-        }
+        const normExpectedValueVectorsPosition = version > 5 ? footerPosition + (version < 9 ? 4 : 8) + nBytes : undefined;
+        return { masterIndex, normExpectedValueVectorsPosition };
     }
-    async getMatrix(chrIdx1, chrIdx2) {
-        const key = Matrix.getKey(chrIdx1, chrIdx2);
-        let p = this.matrixCache.get(key);
-        if (!p) {
-            p = this.readMatrix(chrIdx1, chrIdx2).catch((e) => {
-                this.matrixCache.delete(key);
-                throw e;
-            });
-            this.matrixCache.set(key, p);
-        }
-        return p;
+    async getMatrix(chrIdx1, chrIdx2, opts) {
+        await this.init(opts);
+        return this.matrixCache.get(Matrix.getKey(chrIdx1, chrIdx2), opts?.signal, signal => this.readMatrix(chrIdx1, chrIdx2, signal));
     }
-    async readMatrix(chrIdx1, chrIdx2) {
-        await this.init();
+    async readMatrix(chrIdx1, chrIdx2, signal) {
         const idx = this.masterIndex[Matrix.getKey(chrIdx1, chrIdx2)];
         let matrix;
         if (idx) {
-            const data = await this.file.read(idx.start, idx.size);
+            const data = await this.file.read(idx.start, idx.size, { signal });
             matrix = Matrix.parseMatrix(data, this.chromosomes);
         }
         return matrix;
     }
     async getContactRecords(normalization, region1, region2, units, binsize, opts) {
-        await this.init();
+        await this.init(opts);
         const idx1 = this.chromosomeIndexMap[this.getFileChrName(region1.chr)];
         const idx2 = this.chromosomeIndexMap[this.getFileChrName(region2.chr)];
         // A `.hic` stores only `bin1 <= bin2`, so a query whose x window sits to the
@@ -319,12 +312,13 @@ export class HicFile {
         // resolved once per pair rather than per block, each paired with the bin
         // offset its values start at.
         const [norm, blocks] = await Promise.all([
-            this.getNormVectors(normalization, r1, r2, units, binsize),
+            this.getNormVectors(normalization, r1, r2, units, binsize, opts),
             // 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),
         ]);
+        throwIfAborted(opts?.signal);
         // 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
         // rather than nest in it, so the true count isn't known without either this
@@ -402,21 +396,22 @@ export class HicFile {
             transposed: transpose,
         };
     }
-    async getNormVectors(normalization, r1, r2, units, binsize) {
+    async getNormVectors(normalization, r1, r2, units, binsize, opts) {
+        const signalOpts = { signal: opts?.signal };
         let result;
         if (normalization && normalization !== 'NONE') {
             const chr1 = this.getFileChrName(r1.chr);
             const chr2 = this.getFileChrName(r2.chr);
             const offset1 = Math.floor(r1.start / binsize);
             const offset2 = Math.floor(r2.start / binsize);
-            const nv1 = await this.getNormalizationVector(normalization, chr1, units, binsize);
+            const nv1 = await this.getNormalizationVector(normalization, chr1, units, binsize, signalOpts);
             const nv2 = chr1 === chr2
                 ? nv1
-                : await this.getNormalizationVector(normalization, chr2, units, binsize);
+                : await this.getNormalizationVector(normalization, chr2, units, binsize, signalOpts);
             if (nv1 && nv2) {
                 result = {
-                    v1: await nv1.getValues(offset1, Math.ceil(r1.end / binsize)),
-                    v2: await nv2.getValues(offset2, Math.ceil(r2.end / binsize)),
+                    v1: await nv1.getValues(offset1, Math.ceil(r1.end / binsize), signalOpts),
+                    v2: await nv2.getValues(offset2, Math.ceil(r2.end / binsize), signalOpts),
                     offset1,
                     offset2,
                 };
@@ -426,7 +421,7 @@ export class HicFile {
     }
     async getBlocks(region1, region2, binSize, opts) {
         const blockKey = (blockNumber, zd) => `${zd.getKey()}_${blockNumber}`;
-        await this.init();
+        await this.init(opts);
         const chr1 = this.getFileChrName(region1.chr);
         const chr2 = this.getFileChrName(region2.chr);
         const idx1 = this.chromosomeIndexMap[chr1];
@@ -443,7 +438,8 @@ export class HicFile {
             // .hic files store no inter-chromosomal maps, and a multi-region view asks
             // for every pair. Answering with no blocks, rather than warning once per
             // pair per fetch, leaves that for the caller to notice or ignore.
-            const matrix = await this.getMatrix(idx1, idx2);
+            const signalOpts = { signal: opts?.signal };
+            const matrix = await this.getMatrix(idx1, idx2, signalOpts);
             if (matrix) {
                 const zd = matrix.getZoomData(binSize);
                 if (!zd) {
@@ -476,7 +472,7 @@ export class HicFile {
                 // 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);
+                    const block = await this.readBlock(blockNumber, zd, signalOpts);
                     done++;
                     onProgress?.(done, blockNumbers.length);
                     return block;
@@ -491,11 +487,14 @@ export class HicFile {
         }
         return blocks;
     }
-    async readBlock(blockNumber, zd) {
+    async readBlock(blockNumber, zd, opts) {
         const idx = zd.blockIndex[blockNumber];
         let block;
         if (idx) {
-            const data = await this.file.read(idx.filePosition, idx.size);
+            const data = await this.file.read(idx.filePosition, idx.size, {
+                signal: opts?.signal,
+            });
+            throwIfAborted(opts?.signal);
             // `.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.
@@ -590,41 +589,34 @@ export class HicFile {
         }
         throw new Error(`Unknown block type: ${type}`);
     }
-    async getNormalizationVector(type, chr, unit, binSize) {
-        await this.init();
+    async getNormalizationVector(type, chr, unit, binSize, opts) {
+        await this.init(opts);
         const chrIdx = this.chromosomeIndexMap[this.getFileChrName(chr)];
         if (chrIdx === undefined) {
             return undefined;
         }
         const key = getNormalizationVectorKey(type, chrIdx, unit, binSize);
-        // Caching the promise is what keeps concurrent region pairs sharing one
-        // vector: a chromosome appears in every pair it takes part in, so with a
+        // Sharing the in-flight read is what keeps concurrent region pairs sharing
+        // one vector: a chromosome appears in every pair it takes part in, so with a
         // result-only cache each of those pairs missed while the first was still in
         // flight and read the header again — and then held its own
         // `NormalizationVector`, whose value cache is per instance, so the whole
         // vector was re-read too.
-        let p = this.normVectorCache.get(key);
-        if (!p) {
-            // A file with no vectors at all, or none for this (type, chr, unit,
-            // binsize), simply answers undefined and the caller falls back to raw
-            // counts. hic-straw warns to the console here; that fires once per
-            // chromosome per region pair per fetch, and the console is the wrong place
-            // for it anyway — `getContactRecords` reports the normalization it
-            // actually applied instead.
-            p = this.readNormalizationVector(key).catch((e) => {
-                this.normVectorCache.delete(key);
-                throw e;
-            });
-            this.normVectorCache.set(key, p);
-        }
-        return p;
+        //
+        // A file with no vectors at all, or none for this (type, chr, unit,
+        // binsize), simply answers undefined and the caller falls back to raw
+        // counts. hic-straw warns to the console here; that fires once per
+        // chromosome per region pair per fetch, and the console is the wrong place
+        // for it anyway — `getContactRecords` reports the normalization it actually
+        // applied instead.
+        return this.normVectorCache.get(key, opts?.signal, signal => this.readNormalizationVector(key, signal));
     }
-    async readNormalizationVector(key) {
-        const idx = (await this.getNormVectorIndex())?.[key];
+    async readNormalizationVector(key, signal) {
+        const idx = (await this.getNormVectorIndex({ signal }))?.[key];
         if (!idx) {
             return undefined;
         }
-        const data = await this.file.read(idx.filePosition, 8);
+        const data = await this.file.read(idx.filePosition, 8, { signal });
         const parser = new BinaryParser(new DataView(data));
         const nValues = this.version < 9 ? parser.getInt() : parser.getLong();
         const dataType = this.version < 9 ? DOUBLE : FLOAT;
@@ -632,52 +624,47 @@ export class HicFile {
         return new NormalizationVector(this.file, filePosition, nValues, dataType);
     }
     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
-        // caller that reads metadata first never sees it.
-        await this.init();
-        if (this.version >= 6) {
-            // Memoize the *attempt*, not just a populated result. A legal (if
-            // uncommon) v8 file with no norm vectors leaves `normVectorIndex`
-            // undefined, and the old `!this.normVectorIndex` guard then re-ran the
-            // discovery on every call — two calls per region pair per fetch, each
-            // walking the whole normalized-expected-values section with a chain of
-            // 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.
-            // 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;
-            });
-            await this.normVectorIndexP;
+        return (await this.getParsedNormVectorIndex(opts))?.entries;
+    }
+    async getParsedNormVectorIndex(opts) {
+        // await init() before the version gate, not after: this class defaults
+        // `version` to 0, so checking it before the header is parsed would answer
+        // "no index" for every file rather than for a v5 one.
+        await this.init(opts);
+        if (this.version < 6) {
+            return undefined;
         }
-        return this.normVectorIndex;
+        // Memoize the *attempt*, not just a populated result. A legal (if uncommon)
+        // v8 file with no norm vectors has no index, and re-running the discovery
+        // on every call cost two calls per region pair per fetch, each walking the
+        // whole normalized-expected-values section with a chain of sequential range
+        // reads, only to rediscover there is nothing there.
+        //
+        // The walk runs once, so its progress belongs to the call that performs
+        // it: the fill is per call, so a caller joining an in-flight or finished
+        // load is not waiting on reads and is told nothing.
+        return this.normVectorIndexCache.get('nvi', opts?.signal, signal => this.loadNormVectorIndex({ signal, onProgress: opts?.onProgress }));
     }
-    async loadNormVectorIndex(onProgress) {
-        // If we know the position of the norm vector index, read it directly.
-        // This is the case for hic v9 files.
+    async loadNormVectorIndex(opts) {
         if (this.normVectorIndexPosition > 0 && this.normVectorIndexSize > 0) {
-            await this.readNormVectorIndex({
+            return this.readNormVectorIndex({
                 start: this.normVectorIndexPosition,
                 size: this.normVectorIndexSize,
-            });
+            }, opts.signal);
         }
         else if (this.config.nvi) {
             const nviArray = decodeURIComponent(this.config.nvi).split(',');
-            await this.readNormVectorIndex({
+            return this.readNormVectorIndex({
                 start: parseInt(nviArray[0]),
                 size: parseInt(nviArray[1]),
-            });
+            }, opts.signal);
         }
         else {
             try {
-                await this.readNormExpectedValuesAndNormVectorIndex(onProgress);
+                return await this.readNormExpectedValuesAndNormVectorIndex(opts);
             }
             catch (e) {
+                throwIfAborted(opts.signal);
                 // Not "expected if the file has no norm vectors" — that case never
                 // arrives here. hic-straw's own IO threw a 416 for a read past EOF and
                 // this caught it; `generic-filehandle2` deliberately turns a 416 into an
@@ -686,41 +673,41 @@ export class HicFile {
                 // the read side owns that case now, and anything reaching here is a real
                 // failure worth printing.
                 console.error(e);
+                return undefined;
             }
         }
     }
     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(opts);
-        return this.normalizationTypes;
+        return (await this.getParsedNormVectorIndex(opts))?.types ?? ['NONE'];
     }
-    async readNormVectorIndex(range) {
-        await this.init();
-        const data = await this.file.read(range.start, range.size);
+    async readNormVectorIndex(range, signal) {
+        const data = await this.file.read(range.start, range.size, { signal });
         const binaryParser = new BinaryParser(new DataView(data));
-        this.normVectorIndex = {};
+        const index = { entries: {}, types: ['NONE'] };
         let nEntries = binaryParser.getInt();
         while (nEntries-- > 0) {
-            this.parseNormVectorEntry(binaryParser);
+            this.parseNormVectorEntry(binaryParser, index);
         }
-        return this.normVectorIndex;
+        return index;
     }
     // Used when the position of the norm vector index is unknown: read through
     // the expected values to find the index.
-    async readNormExpectedValuesAndNormVectorIndex(onProgress) {
-        await this.init();
+    async readNormExpectedValuesAndNormVectorIndex(opts) {
+        const { signal } = opts;
+        let index;
         if (this.normExpectedValueVectorsPosition !== undefined) {
-            const nviStart = await this.skipExpectedValues(this.normExpectedValueVectorsPosition, onProgress);
+            const nviStart = await this.skipExpectedValues(this.normExpectedValueVectorsPosition, opts);
             let byteCount = INT;
-            let data = await this.file.read(nviStart, INT);
+            let data = await this.file.read(nviStart, INT, { signal });
             // Possible if there are no norm vectors. A legal v8 file, though uncommon.
             if (data.byteLength !== 0) {
                 const binaryParser = new BinaryParser(new DataView(data));
                 const nEntries = binaryParser.getInt();
                 const sizeEstimate = nEntries * 30;
-                data = await this.file.read(nviStart + byteCount, sizeEstimate);
-                this.normVectorIndex = {};
+                data = await this.file.read(nviStart + byteCount, sizeEstimate, {
+                    signal,
+                });
+                const found = { entries: {}, types: ['NONE'] };
                 const processEntries = async (remaining, buf) => {
                     const parser = new BinaryParser(new DataView(buf));
                     let n = remaining;
@@ -729,25 +716,31 @@ export class HicFile {
                             n++; // Reset counter as entry is not processed
                             byteCount += parser.position;
                             const est = Math.max(1000, n * 30);
-                            const more = await this.file.read(nviStart + byteCount, est);
+                            const more = await this.file.read(nviStart + byteCount, est, {
+                                signal,
+                            });
                             await processEntries(n, more);
                             return;
                         }
-                        this.parseNormVectorEntry(parser);
+                        this.parseNormVectorEntry(parser, found);
                     }
                     byteCount += parser.position;
                 };
                 await processEntries(nEntries, data);
+                throwIfAborted(signal);
                 this.config.nvi = `${nviStart},${byteCount}`;
+                index = found;
             }
         }
+        return index;
     }
     // Used when the position of the norm vector index is unknown: skip the
     // normalized expected values to find the index.
-    async skipExpectedValues(start, onProgress) {
+    async skipExpectedValues(start, opts) {
+        const { signal, onProgress } = opts;
         const version = this.version;
         const file = new BufferedFile({ file: this.file, size: 256000 });
-        const data = await file.read(start, INT);
+        const data = await file.read(start, INT, { signal });
         // A file with no normalization at all ends where this section would start,
         // so the count this is about to read is past EOF. That is the same "no norm
         // vectors" case `readNormExpectedValuesAndNormVectorIndex` guards its own
@@ -771,14 +764,14 @@ export class HicFile {
         // read, each costing about the same.
         const skipChunk = async (chunkStart) => {
             let chunkSize = 0;
-            let buf = await file.read(chunkStart, 500);
+            let buf = await file.read(chunkStart, 500, { signal });
             let parser = new BinaryParser(new DataView(buf));
             parser.getString(); // type
             parser.getString(); // unit
             parser.getInt(); // binSize
             const nValues = version < 9 ? parser.getInt() : parser.getLong();
             chunkSize += parser.position + nValues * (version < 9 ? DOUBLE : FLOAT);
-            buf = await file.read(chunkStart + chunkSize, INT);
+            buf = await file.read(chunkStart + chunkSize, INT, { signal });
             parser = new BinaryParser(new DataView(buf));
             const nChrScaleFactors = parser.getInt();
             chunkSize +=
@@ -800,7 +793,7 @@ export class HicFile {
         }
         return position;
     }
-    parseNormVectorEntry(binaryParser) {
+    parseNormVectorEntry(binaryParser, index) {
         const type = binaryParser.getString(); // 15
         const chrIdx = binaryParser.getInt(); // 4
         const unit = binaryParser.getString(); // 3
@@ -808,10 +801,10 @@ export class HicFile {
         const filePosition = binaryParser.getLong(); // 8
         const sizeInBytes = this.version < 9 ? binaryParser.getInt() : binaryParser.getLong(); // 4:8
         const key = `${type}_${chrIdx}_${unit}_${binSize}`;
-        if (!this.normalizationTypes.includes(type)) {
-            this.normalizationTypes.push(type);
+        if (!index.types.includes(type)) {
+            index.types.push(type);
         }
-        this.normVectorIndex[key] = { filePosition, size: sizeInBytes };
+        index.entries[key] = { filePosition, size: sizeInBytes };
     }
     getFileChrName(chrAlias) {
         return this.chrAliasTable[chrAlias] ?? chrAlias;