npm - @gmod/hic - Versions diffs - 1.3.2 → 2.1.0 - Mend

@gmod/hic 1.3.2 → 2.1.0

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

Files changed (41) hide show

package/README.md +17 -32
package/dist/bufferedFile.js +8 -25
package/dist/bufferedFile.js.map +1 -1
package/dist/hicFile.d.ts +22 -9
package/dist/hicFile.js +218 -175
package/dist/hicFile.js.map +1 -1
package/dist/index.d.ts +1 -1
package/dist/matrixZoomData.d.ts +3 -1
package/dist/matrixZoomData.js +6 -3
package/dist/matrixZoomData.js.map +1 -1
package/dist/normalizationVector.d.ts +3 -1
package/dist/normalizationVector.js +60 -39
package/dist/normalizationVector.js.map +1 -1
package/dist/types.d.ts +16 -0
package/esm/bufferedFile.js +8 -25
package/esm/bufferedFile.js.map +1 -1
package/esm/hicFile.d.ts +22 -9
package/esm/hicFile.js +218 -175
package/esm/hicFile.js.map +1 -1
package/esm/index.d.ts +1 -1
package/esm/matrixZoomData.d.ts +3 -1
package/esm/matrixZoomData.js +6 -3
package/esm/matrixZoomData.js.map +1 -1
package/esm/normalizationVector.d.ts +3 -1
package/esm/normalizationVector.js +60 -39
package/esm/normalizationVector.js.map +1 -1
package/esm/types.d.ts +16 -0
package/package.json +1 -1
package/src/bufferedFile.ts +8 -22
package/src/hicFile.ts +303 -218
package/src/index.ts +1 -0
package/src/matrixZoomData.ts +6 -1
package/src/normalizationVector.ts +77 -43
package/src/types.ts +12 -0
package/dist/lru.d.ts +0 -29
package/dist/lru.js +0 -53
package/dist/lru.js.map +0 -1
package/esm/lru.d.ts +0 -29
package/esm/lru.js +0 -50
package/esm/lru.js.map +0 -1
package/src/lru.ts +0 -75

package/dist/hicFile.js.map CHANGED Viewed

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

@@ -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 { BaseOpts, Chromosome, HicMetadata, HicRegion, ProgressCallback, ProgressOpts, Reader, Zoom, } from './types.ts';
+export type { BaseOpts, Chromosome, ExpectedValues, HicMetadata, HicRegion, ProgressCallback, ProgressOpts, Reader, Zoom, } from './types.ts';

package/dist/matrixZoomData.d.ts CHANGED Viewed

@@ -4,10 +4,12 @@ export default class MatrixZoomData {
     chr1: Chromosome;
     chr2: Chromosome;
     zoom: Zoom;
+    /** the raw contacts summed over the whole map at this binsize */
+    sumCounts: number;
     blockBinCount: number;
     blockColumnCount: number;
     blockIndex: Record<number, BlockIndexEntry>;
-    constructor(chr1: Chromosome, chr2: Chromosome, zoom: Zoom, blockBinCount: number, blockColumnCount: number, blockIndex: Record<number, BlockIndexEntry>);
+    constructor(chr1: Chromosome, chr2: Chromosome, zoom: Zoom, sumCounts: number, blockBinCount: number, blockColumnCount: number, blockIndex: Record<number, BlockIndexEntry>);
     getKey(): string;
     getBlockNumbers(region1: HicRegion, region2: HicRegion, version: number): number[];
     static parseMatrixZoomData(chr1: Chromosome, chr2: Chromosome, dis: BinaryParser): MatrixZoomData;

package/dist/matrixZoomData.js CHANGED Viewed

@@ -5,13 +5,16 @@ class MatrixZoomData {
     chr1;
     chr2;
     zoom;
+    /** the raw contacts summed over the whole map at this binsize */
+    sumCounts;
     blockBinCount;
     blockColumnCount;
     blockIndex;
-    constructor(chr1, chr2, zoom, blockBinCount, blockColumnCount, blockIndex) {
+    constructor(chr1, chr2, zoom, sumCounts, blockBinCount, blockColumnCount, blockIndex) {
         this.chr1 = chr1;
         this.chr2 = chr2;
         this.zoom = zoom;
+        this.sumCounts = sumCounts;
         this.blockBinCount = blockBinCount;
         this.blockColumnCount = blockColumnCount;
         this.blockIndex = blockIndex;
@@ -74,7 +77,7 @@ class MatrixZoomData {
     static parseMatrixZoomData(chr1, chr2, dis) {
         const unit = dis.getString();
         const zoomIndex = dis.getInt();
-        dis.getFloat(); // sumCounts
+        const sumCounts = dis.getFloat();
         dis.getFloat(); // occupiedCellCount
         dis.getFloat(); // stdDev
         dis.getFloat(); // percent95
@@ -89,7 +92,7 @@ class MatrixZoomData {
             const size = dis.getInt();
             blockIndex[blockNumber] = { filePosition, size };
         }
-        return new MatrixZoomData(chr1, chr2, { index: zoomIndex, unit, binSize }, blockBinCount, blockColumnCount, blockIndex);
+        return new MatrixZoomData(chr1, chr2, { index: zoomIndex, unit, binSize }, sumCounts, blockBinCount, blockColumnCount, blockIndex);
     }
 }
 exports.default = MatrixZoomData;

package/dist/matrixZoomData.js.map CHANGED Viewed

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

@@ -6,5 +6,7 @@ export default class NormalizationVector {
     private nValues;
     private dataType;
     constructor(file: Reader, filePosition: number, nValues: number, dataType: number);
-    getValues(start: number, end: number, opts?: BaseOpts): Promise<Float64Array<ArrayBufferLike>>;
+    getValues(start: number, end: number, opts?: BaseOpts): Promise<Float64Array>;
+    private readRange;
+    private readValues;
 }

package/dist/normalizationVector.js CHANGED Viewed

@@ -6,6 +6,8 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const binary_ts_1 = __importDefault(require("./binary.js"));
 const DOUBLE = 8;
 class NormalizationVector {
+    // Holds the in-flight read, so the two concurrent `getValues` calls of a
+    // same-chromosome pair share one read instead of both missing.
     cache;
     file;
     filePosition;
@@ -18,48 +20,67 @@ class NormalizationVector {
         this.dataType = dataType;
     }
     async getValues(start, end, opts) {
-        // The read below clamps to `nValues`, so the cache can never cover past it.
-        // Compare against the clamped bound or a request that runs off the end of
-        // the vector — reachable when the assembly's refseq is longer than the size
-        // the `.hic` recorded for that chromosome — leaves `end > cache.end` true
-        // forever, and every call re-reads the same range from the file.
+        // The read clamps to `nValues`, so the cache can never cover past it.
+        // Comparing against the clamped bound keeps a request running off the end
+        // of the vector (an assembly refseq longer than the `.hic` recorded) from
+        // missing forever.
         const wanted = Math.min(end, this.nValues);
-        if (!this.cache || start < this.cache.start || wanted > this.cache.end) {
-            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;
-            // 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, opts)
-                : 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++) {
-                values[i] =
-                    this.dataType === DOUBLE ? parser.getDouble() : parser.getFloat();
+        let cache = this.cache;
+        const joined = !!cache && start >= cache.start && wanted <= cache.end;
+        if (!cache || !joined) {
+            cache = this.readRange(start, end, opts);
+            this.cache = cache;
+            const pending = cache;
+            pending.values.catch(() => {
+                if (this.cache === pending) {
+                    this.cache = undefined;
+                }
+            });
+        }
+        let values;
+        try {
+            values = await cache.values;
+        }
+        catch (e) {
+            // The pair that started a joined read passed its own signal, so that
+            // pair aborting says nothing about this caller.
+            if (!joined || opts?.signal?.aborted) {
+                throw e;
             }
-            this.cache = { start: adjustedStart, end: adjustedEnd, values };
+            return this.getValues(start, end, opts);
+        }
+        // A view, not a copy. Both this and `subarray` clamp a request running past
+        // the end; an out-of-range index reads undefined, the product goes NaN, and
+        // the record filter drops it.
+        const sliceStart = start - cache.start;
+        return values.subarray(sliceStart, sliceStart + (end - start));
+    }
+    readRange(start, end, opts) {
+        const adjustedEnd = Math.min(this.nValues, end + 1000);
+        // Clamped against `adjustedEnd` too, or a window starting past the vector
+        // gives a negative read length, which the reader turns into a RangeError
+        // instead of the empty answer the caller handles.
+        const adjustedStart = Math.min(Math.max(0, start - 1000), adjustedEnd);
+        const n = adjustedEnd - adjustedStart;
+        return {
+            start: adjustedStart,
+            end: adjustedEnd,
+            values: this.readValues(adjustedStart, n, opts),
+        };
+    }
+    async readValues(start, n, opts) {
+        // A zero-length range request on a remote file is still a round trip.
+        if (n <= 0) {
+            return new Float64Array(0);
+        }
+        const data = await this.file.read(this.filePosition + start * this.dataType, n * this.dataType, opts);
+        const parser = new binary_ts_1.default(new DataView(data));
+        const values = new Float64Array(n);
+        for (let i = 0; i < n; i++) {
+            values[i] =
+                this.dataType === DOUBLE ? parser.getDouble() : parser.getFloat();
         }
-        // A view, not a copy: the caller only reads it, and a fetch asks for one of
-        // these per chromosome per region pair. Both this and `slice` clamp a
-        // request running past the end to what exists, which the caller already
-        // handles — an out-of-range index reads undefined, making the product NaN,
-        // which the record filter drops.
-        const sliceStart = start - this.cache.start;
-        return this.cache.values.subarray(sliceStart, sliceStart + (end - start));
+        return values;
     }
 }
 exports.default = NormalizationVector;

package/dist/normalizationVector.js.map CHANGED Viewed

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

@@ -56,6 +56,22 @@ export interface BlockIndexEntry {
     filePosition: number;
     size: number;
 }
+/**
+ * The expected contact count for one region pair, the denominator of
+ * observed/expected. Within a chromosome it depends only on the distance in
+ * bins, so it is the expected-value vector's entries over the distances the
+ * pair spans: `values[|bin2 - bin1| - firstDistance]`, already divided by the
+ * chromosome's scale factor and holding the vector's last value past its end.
+ * Between chromosomes it is one number, the map's average contact.
+ */
+export type ExpectedValues = {
+    kind: 'intra';
+    firstDistance: number;
+    values: Float64Array;
+} | {
+    kind: 'inter';
+    average: number;
+};
 export interface HicMetadata {
     version: number;
     genome: string;

package/esm/bufferedFile.js CHANGED Viewed

@@ -33,33 +33,16 @@ export default class BufferedFile {
             const sliceStart = start - bufferStart;
             result = buf.slice(sliceStart, sliceStart + length);
         }
-        else if (buf && start < bufferStart && end > bufferStart) {
-            // Overlap left (unexpected in straw); we don't adjust the buffer
-            const l1 = bufferStart - start;
-            const a1 = await this.file.read(position, l1, opts);
-            const l2 = length - l1;
-            if (l2 > 0) {
-                result = concatBuffers(a1, buf.slice(0, l2));
-            }
-            else {
-                result = a1;
-            }
-        }
-        else if (buf && start < bufferEnd && end > bufferEnd) {
-            // Overlap right
+        else if (buf && start >= bufferStart && start < bufferEnd) {
+            // Overlap right. The expected-values walk only moves forward, so a
+            // request starting before the buffer takes the fresh read below.
             const l1 = bufferEnd - start;
             const a1 = buf.slice(this.bufferLength - l1, this.bufferLength);
-            const l2 = length - l1;
-            if (l2 > 0) {
-                const next = await this.file.read(bufferEnd, this.size, opts);
-                this.buffer = next;
-                this.bufferStart = bufferEnd;
-                this.bufferLength = next.byteLength;
-                result = concatBuffers(a1, next.slice(0, l2));
-            }
-            else {
-                result = a1;
-            }
+            const next = await this.file.read(bufferEnd, this.size, opts);
+            this.buffer = next;
+            this.bufferStart = bufferEnd;
+            this.bufferLength = next.byteLength;
+            result = concatBuffers(a1, next.slice(0, length - l1));
         }
         else {
             // No overlap with buffer

package/esm/bufferedFile.js.map CHANGED Viewed

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package/esm/hicFile.d.ts CHANGED Viewed

@@ -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 { BaseOpts, BlockIndexEntry, HicMetadata, HicRegion, ProgressOpts, Reader } from './types.ts';
+import type { BaseOpts, BlockIndexEntry, ExpectedValues, 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
@@ -27,8 +27,7 @@ export interface HicConfig {
     /**
      * Ceiling on the decompressed contacts the block cache holds, in bytes.
      * Defaults to 128 MB. Lower it where the budget is tight and re-reading is
-     * cheaper than the memory; raising it buys nothing once a fetch's working set
-     * fits, since the entry cap bounds the cache too.
+     * cheaper than the memory.
      */
     blockCacheMaxBytes?: number;
 }
@@ -37,10 +36,11 @@ interface Block {
     records: ContactRecords;
 }
 export declare class HicFile {
-    private config;
+    private nvi;
     private file;
     private headerCache;
     private normVectorIndexCache;
+    private expectedSectionCache;
     private normVectorCache;
     private matrixCache;
     private blockCache;
@@ -49,10 +49,10 @@ export declare class HicFile {
     private version;
     private genomeId;
     private footerPosition;
+    private expectedValuesPosition;
     normExpectedValueVectorsPosition: number | undefined;
     private chromosomes;
     private chromosomeIndexMap;
-    private chrAliasTable;
     private bpResolutions;
     private masterIndex;
     private meta;
@@ -63,7 +63,7 @@ export declare class HicFile {
     private readFooter;
     getMatrix(chrIdx1: number, chrIdx2: number, opts?: BaseOpts): Promise<Matrix | undefined>;
     private readMatrix;
-    getContactRecords(normalization: string, region1: HicRegion, region2: HicRegion, units: string, binsize: number, opts?: ProgressOpts): Promise<{
+    getContactRecords(normalization: string, region1: HicRegion, region2: HicRegion, binsize: number, opts?: ProgressOpts): Promise<{
         records: ContactRecords;
         appliedNormalization: string;
         transposed: boolean;
@@ -81,7 +81,7 @@ export declare class HicFile {
      * of the session, so it is worth one memcpy not to pin an oversized buffer.
      */
     private parseBlockRecords;
-    getNormalizationVector(type: string, chr: string, unit: string, binSize: number, opts?: BaseOpts): Promise<NormalizationVector | undefined>;
+    getNormalizationVector(type: string, chr: string, binSize: number, opts?: BaseOpts): Promise<NormalizationVector | undefined>;
     private readNormalizationVector;
     getNormVectorIndex(opts?: ProgressOpts): Promise<Record<string, BlockIndexEntry> | undefined>;
     private getParsedNormVectorIndex;
@@ -89,8 +89,21 @@ export declare class HicFile {
     getNormalizationOptions(opts?: ProgressOpts): Promise<string[]>;
     private readNormVectorIndex;
     private readNormExpectedValuesAndNormVectorIndex;
-    private skipExpectedValues;
+    /**
+     * The expected count for a region pair at `binsize`, the denominator of
+     * observed/expected, as straw computes it. `normalization` must be the one
+     * the pair's records carry (`getContactRecords`' `appliedNormalization`),
+     * since each normalization has its own vector. Undefined where the file has
+     * no expected value for it: no vector at this binsize, or a version 5 file
+     * asked for a normalized one.
+     *
+     * Within a chromosome the vector is read for only the distances the pair
+     * spans. Between chromosomes straw divides by the map's average contact, the
+     * raw `sumCounts` over its bins, whatever the normalization.
+     */
+    getExpectedValues(normalization: string, region1: HicRegion, region2: HicRegion, binsize: number, opts?: ProgressOpts): Promise<ExpectedValues | undefined>;
+    private getExpectedSection;
+    private walkExpectedSection;
     private parseNormVectorEntry;
-    getFileChrName(chrAlias: string): string;
 }
 export {};