@gmod/hic 1.1.0 → 1.2.1

package/README.md

@@ -37,6 +37,18 @@ records.bin2 // Int32Array of bin indices along region2
 records.counts // Float32Array of contact counts
 ```
 
+Both reading methods take an optional trailing `{ onProgress }`, called
+`(current, total)` as the work lands, so a loading indicator can show a bar
+rather than a spinner. The unit is the block for a contact fetch and the
+expected-value chunk for the normalization-index walk — the slow part of opening
+a pre-v9 file. See [docs/api.md](docs/api.md#progress).
+
+```js
+await hic.getContactRecords('KR', region, region, 'BP', 2_500_000, {
+  onProgress: (current, total) => showBar(current / total),
+})
+```
+
 In the browser, or for a file over HTTP, pass a `filehandle` from
 [`generic-filehandle2`](https://www.npmjs.com/package/generic-filehandle2)
 instead of a `path`:

package/dist/hicFile.d.ts

@@ -2,7 +2,7 @@ import Matrix from './matrix.ts';
 import NormalizationVector from './normalizationVector.ts';
 import type { ContactRecords } from './contactRecords.ts';
 import type MatrixZoomData from './matrixZoomData.ts';
-import type { BlockIndexEntry, HicMetadata, HicRegion, Reader } from './types.ts';
+import type { BlockIndexEntry, HicMetadata, HicRegion, ProgressOpts, Reader } from './types.ts';
 import type { GenericFilehandle } from 'generic-filehandle2';
 /**
  * Prefix of the error thrown when a region pair has no matrix at the requested
@@ -65,13 +65,13 @@ export declare class HicFile {
     private readFooter;
     getMatrix(chrIdx1: number, chrIdx2: number): Promise<Matrix | undefined>;
     private readMatrix;
-    getContactRecords(normalization: string, region1: HicRegion, region2: HicRegion, units: string, binsize: number): Promise<{
+    getContactRecords(normalization: string, region1: HicRegion, region2: HicRegion, units: string, binsize: number, opts?: ProgressOpts): Promise<{
         records: ContactRecords;
         appliedNormalization: string;
         transposed: boolean;
     }>;
     private getNormVectors;
-    getBlocks(region1: HicRegion, region2: HicRegion, binSize: number): Promise<(Block | undefined)[]>;
+    getBlocks(region1: HicRegion, region2: HicRegion, binSize: number, opts?: ProgressOpts): Promise<(Block | undefined)[]>;
     readBlock(blockNumber: number, zd: MatrixZoomData): Promise<Block | undefined>;
     /**
      * Decode one block's records straight into typed arrays.
@@ -85,9 +85,9 @@ export declare class HicFile {
     private parseBlockRecords;
     getNormalizationVector(type: string, chr: string, unit: string, binSize: number): Promise<NormalizationVector | undefined>;
     private readNormalizationVector;
-    getNormVectorIndex(): Promise<Record<string, BlockIndexEntry> | undefined>;
+    getNormVectorIndex(opts?: ProgressOpts): Promise<Record<string, BlockIndexEntry> | undefined>;
     private loadNormVectorIndex;
-    getNormalizationOptions(): Promise<string[]>;
+    getNormalizationOptions(opts?: ProgressOpts): Promise<string[]>;
     private readNormVectorIndex;
     private readNormExpectedValuesAndNormVectorIndex;
     private skipExpectedValues;

package/dist/hicFile.js

@@ -286,7 +286,7 @@ 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)];
@@ -326,7 +326,10 @@ 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
@@ -427,7 +430,7 @@ 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);
@@ -463,7 +466,27 @@ 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);
@@ -614,7 +637,7 @@ class HicFile {
         const filePosition = this.version < 9 ? idx.filePosition + 4 : idx.filePosition + 8;
         return new normalizationVector_ts_1.default(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
@@ -629,7 +652,10 @@ 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;
             });
@@ -637,7 +663,7 @@ 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) {
@@ -655,7 +681,7 @@ 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
@@ -669,10 +695,10 @@ 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) {
@@ -688,10 +714,10 @@ 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.
@@ -724,7 +750,7 @@ 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_ts_1.default({ file: this.file, size: 256000 });
         const data = await file.read(start, INT);
@@ -740,9 +766,17 @@ class HicFile {
         }
         const binaryParser = new binary_ts_1.default(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 binary_ts_1.default(new DataView(buf));
             parser.getString(); // type
@@ -755,11 +789,22 @@ 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/dist/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/dist/normalizationVector.js

@@ -25,11 +25,26 @@ class NormalizationVector {
         // forever, and every call re-reads the same range from the file.
         const wanted = Math.min(end, this.nValues);
         if (!this.cache || start < this.cache.start || wanted > this.cache.end) {
-            const adjustedStart = Math.max(0, start - 1000);
             const adjustedEnd = Math.min(this.nValues, end + 1000);
+            // Clamped against `adjustedEnd`, and not merely against zero, or a window
+            // starting past the vector produces a NEGATIVE `n` — and a negative read
+            // length reaches the reader as `new Uint8Array(-8)`, a RangeError that
+            // fails the whole fetch instead of the empty answer the caller below
+            // already handles. The padding is what sets how far past is far enough:
+            // more than 1000 bins, which at a fine binsize is not far at all.
+            //
+            // Reachable exactly where the comment above says: the assembly's refseq
+            // is longer than the size the `.hic` recorded for that chromosome, so a
+            // view of the tail of it asks for bins the vector never had.
+            const adjustedStart = Math.min(Math.max(0, start - 1000), adjustedEnd);
             const startPosition = this.filePosition + adjustedStart * this.dataType;
             const n = adjustedEnd - adjustedStart;
-            const data = await this.file.read(startPosition, n * this.dataType);
+            // Nothing to read when the window is entirely past the vector, and on a
+            // remote file a zero-length range request is still a round trip — one per
+            // region pair, on every fetch, for as long as the view stays there.
+            const data = n > 0
+                ? await this.file.read(startPosition, n * this.dataType)
+                : new ArrayBuffer(0);
             const parser = new binary_ts_1.default(new DataView(data));
             const values = new Float64Array(n);
             for (let i = 0; i < n; i++) {

package/dist/normalizationVector.js.map

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package/dist/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/esm/hicFile.d.ts

@@ -2,7 +2,7 @@ import Matrix from './matrix.ts';
 import NormalizationVector from './normalizationVector.ts';
 import type { ContactRecords } from './contactRecords.ts';
 import type MatrixZoomData from './matrixZoomData.ts';
-import type { BlockIndexEntry, HicMetadata, HicRegion, Reader } from './types.ts';
+import type { BlockIndexEntry, HicMetadata, HicRegion, ProgressOpts, Reader } from './types.ts';
 import type { GenericFilehandle } from 'generic-filehandle2';
 /**
  * Prefix of the error thrown when a region pair has no matrix at the requested
@@ -65,13 +65,13 @@ export declare class HicFile {
     private readFooter;
     getMatrix(chrIdx1: number, chrIdx2: number): Promise<Matrix | undefined>;
     private readMatrix;
-    getContactRecords(normalization: string, region1: HicRegion, region2: HicRegion, units: string, binsize: number): Promise<{
+    getContactRecords(normalization: string, region1: HicRegion, region2: HicRegion, units: string, binsize: number, opts?: ProgressOpts): Promise<{
         records: ContactRecords;
         appliedNormalization: string;
         transposed: boolean;
     }>;
     private getNormVectors;
-    getBlocks(region1: HicRegion, region2: HicRegion, binSize: number): Promise<(Block | undefined)[]>;
+    getBlocks(region1: HicRegion, region2: HicRegion, binSize: number, opts?: ProgressOpts): Promise<(Block | undefined)[]>;
     readBlock(blockNumber: number, zd: MatrixZoomData): Promise<Block | undefined>;
     /**
      * Decode one block's records straight into typed arrays.
@@ -85,9 +85,9 @@ export declare class HicFile {
     private parseBlockRecords;
     getNormalizationVector(type: string, chr: string, unit: string, binSize: number): Promise<NormalizationVector | undefined>;
     private readNormalizationVector;
-    getNormVectorIndex(): Promise<Record<string, BlockIndexEntry> | undefined>;
+    getNormVectorIndex(opts?: ProgressOpts): Promise<Record<string, BlockIndexEntry> | undefined>;
     private loadNormVectorIndex;
-    getNormalizationOptions(): Promise<string[]>;
+    getNormalizationOptions(opts?: ProgressOpts): Promise<string[]>;
     private readNormVectorIndex;
     private readNormExpectedValuesAndNormVectorIndex;
     private skipExpectedValues;

package/esm/hicFile.js

@@ -280,7 +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)];
@@ -320,7 +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
@@ -421,7 +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);
@@ -457,7 +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);
@@ -608,7 +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
@@ -623,7 +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;
             });
@@ -631,7 +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) {
@@ -649,7 +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
@@ -663,10 +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) {
@@ -682,10 +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.
@@ -718,7 +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);
@@ -734,9 +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
@@ -749,11 +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

package/esm/hicFile.js.map

@@ -1 +1 @@
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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/normalizationVector.js

@@ -20,11 +20,26 @@ export default class NormalizationVector {
         // forever, and every call re-reads the same range from the file.
         const wanted = Math.min(end, this.nValues);
         if (!this.cache || start < this.cache.start || wanted > this.cache.end) {
-            const adjustedStart = Math.max(0, start - 1000);
             const adjustedEnd = Math.min(this.nValues, end + 1000);
+            // Clamped against `adjustedEnd`, and not merely against zero, or a window
+            // starting past the vector produces a NEGATIVE `n` — and a negative read
+            // length reaches the reader as `new Uint8Array(-8)`, a RangeError that
+            // fails the whole fetch instead of the empty answer the caller below
+            // already handles. The padding is what sets how far past is far enough:
+            // more than 1000 bins, which at a fine binsize is not far at all.
+            //
+            // Reachable exactly where the comment above says: the assembly's refseq
+            // is longer than the size the `.hic` recorded for that chromosome, so a
+            // view of the tail of it asks for bins the vector never had.
+            const adjustedStart = Math.min(Math.max(0, start - 1000), adjustedEnd);
             const startPosition = this.filePosition + adjustedStart * this.dataType;
             const n = adjustedEnd - adjustedStart;
-            const data = await this.file.read(startPosition, n * this.dataType);
+            // Nothing to read when the window is entirely past the vector, and on a
+            // remote file a zero-length range request is still a round trip — one per
+            // region pair, on every fetch, for as long as the view stays there.
+            const data = n > 0
+                ? await this.file.read(startPosition, n * this.dataType)
+                : new ArrayBuffer(0);
             const parser = new BinaryParser(new DataView(data));
             const values = new Float64Array(n);
             for (let i = 0; i < n; i++) {

package/esm/normalizationVector.js.map

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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": "1.1.0",
+  "version": "1.2.1",
   "packageManager": "pnpm@11.15.1",
   "description": "Read .hic contact matrix files in node or the browser",
   "license": "MIT",

package/src/hicFile.ts

@@ -16,6 +16,8 @@ import type {
   Chromosome,
   HicMetadata,
   HicRegion,
+  ProgressCallback,
+  ProgressOpts,
   Reader,
 } from './types.ts'
 import type { GenericFilehandle } from 'generic-filehandle2'
@@ -380,6 +382,7 @@ export class HicFile {
     region2: HicRegion,
     units: string,
     binsize: number,
+    opts?: ProgressOpts,
   ) {
     await this.init()
 
@@ -425,7 +428,10 @@ 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
@@ -555,7 +561,12 @@ export class HicFile {
     return result
   }
 
-  async getBlocks(region1: HicRegion, region2: HicRegion, binSize: number) {
+  async getBlocks(
+    region1: HicRegion,
+    region2: HicRegion,
+    binSize: number,
+    opts?: ProgressOpts,
+  ) {
     const blockKey = (blockNumber: number, zd: MatrixZoomData) =>
       `${zd.getKey()}_${blockNumber}`
 
@@ -595,10 +606,28 @@ export class HicFile {
           }
         }
 
+        // 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(blockNumber =>
-            this.readBlock(blockNumber, zd),
-          ),
+          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) {
@@ -778,7 +807,7 @@ export class HicFile {
     return new NormalizationVector(this.file, filePosition, nValues, dataType)
   }
 
-  async getNormVectorIndex() {
+  async getNormVectorIndex(opts?: ProgressOpts) {
     // 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
@@ -793,18 +822,21 @@ 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: unknown) => {
-          this.normVectorIndexP = undefined
-          throw 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: unknown) => {
+        this.normVectorIndexP = undefined
+        throw e
+      })
       await this.normVectorIndexP
     }
     return this.normVectorIndex
   }
 
-  private async loadNormVectorIndex() {
+  private async loadNormVectorIndex(onProgress?: ProgressCallback) {
     // 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) {
@@ -820,7 +852,7 @@ 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
         // arrives here. hic-straw's own IO threw a 416 for a read past EOF and
@@ -834,10 +866,10 @@ export class HicFile {
     }
   }
 
-  async getNormalizationOptions() {
+  async getNormalizationOptions(opts?: ProgressOpts) {
     // 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
   }
 
@@ -855,11 +887,14 @@ export class HicFile {
 
   // Used when the position of the norm vector index is unknown: read through
   // the expected values to find the index.
-  private async readNormExpectedValuesAndNormVectorIndex() {
+  private async readNormExpectedValuesAndNormVectorIndex(
+    onProgress?: ProgressCallback,
+  ) {
     await this.init()
     if (this.normExpectedValueVectorsPosition !== undefined) {
       const nviStart = await this.skipExpectedValues(
         this.normExpectedValueVectorsPosition,
+        onProgress,
       )
       let byteCount = INT
 
@@ -897,7 +932,10 @@ export class HicFile {
 
   // Used when the position of the norm vector index is unknown: skip the
   // normalized expected values to find the index.
-  private async skipExpectedValues(start: number) {
+  private async skipExpectedValues(
+    start: number,
+    onProgress?: ProgressCallback,
+  ) {
     const version = this.version
     const file = new BufferedFile({ file: this.file, size: 256000 })
     const data = await file.read(start, INT)
@@ -914,12 +952,17 @@ export class HicFile {
     const binaryParser = new BinaryParser(new DataView(data))
     const nEntries = binaryParser.getInt() // Total # of expected value chunks
 
-    const parseNext = async (
-      chunkStart: number,
-      remaining: number,
-    ): Promise<number> => {
+    // 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: number) => {
       let chunkSize = 0
-      const p0 = chunkStart
 
       let buf = await file.read(chunkStart, 500)
       let parser = new BinaryParser(new DataView(buf))
@@ -935,12 +978,23 @@ export class HicFile {
       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
   }
 
   private parseNormVectorEntry(binaryParser: BinaryParser) {

package/src/index.ts

@@ -7,6 +7,8 @@ export type {
   Chromosome,
   HicMetadata,
   HicRegion,
+  ProgressCallback,
+  ProgressOpts,
   Reader,
   Zoom,
 } from './types.ts'

package/src/normalizationVector.ts

@@ -33,11 +33,27 @@ export default class NormalizationVector {
     // forever, and every call re-reads the same range from the file.
     const wanted = Math.min(end, this.nValues)
     if (!this.cache || start < this.cache.start || wanted > this.cache.end) {
-      const adjustedStart = Math.max(0, start - 1000)
       const adjustedEnd = Math.min(this.nValues, end + 1000)
+      // Clamped against `adjustedEnd`, and not merely against zero, or a window
+      // starting past the vector produces a NEGATIVE `n` — and a negative read
+      // length reaches the reader as `new Uint8Array(-8)`, a RangeError that
+      // fails the whole fetch instead of the empty answer the caller below
+      // already handles. The padding is what sets how far past is far enough:
+      // more than 1000 bins, which at a fine binsize is not far at all.
+      //
+      // Reachable exactly where the comment above says: the assembly's refseq
+      // is longer than the size the `.hic` recorded for that chromosome, so a
+      // view of the tail of it asks for bins the vector never had.
+      const adjustedStart = Math.min(Math.max(0, start - 1000), adjustedEnd)
       const startPosition = this.filePosition + adjustedStart * this.dataType
       const n = adjustedEnd - adjustedStart
-      const data = await this.file.read(startPosition, n * this.dataType)
+      // Nothing to read when the window is entirely past the vector, and on a
+      // remote file a zero-length range request is still a round trip — one per
+      // region pair, on every fetch, for as long as the view stays there.
+      const data =
+        n > 0
+          ? await this.file.read(startPosition, n * this.dataType)
+          : new ArrayBuffer(0)
       const parser = new BinaryParser(new DataView(data))
       const values = new Float64Array(n)
       for (let i = 0; i < n; i++) {

package/src/types.ts

@@ -9,6 +9,31 @@ 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