@gmod/hic 1.3.1 → 2.0.0

package/dist/hicFile.js.map

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

@@ -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

@@ -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

@@ -1 +1 @@
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package/esm/bufferedFile.js

@@ -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

@@ -1 +1 @@
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+{"version":3,"file":"bufferedFile.js","sourceRoot":"","sources":["../src/bufferedFile.ts"],"names":[],"mappings":"AAEA,SAAS,aAAa,CAAC,OAAoB,EAAE,OAAoB;IAC/D,MAAM,GAAG,GAAG,IAAI,UAAU,CAAC,OAAO,CAAC,UAAU,GAAG,OAAO,CAAC,UAAU,CAAC,CAAA;IACnE,GAAG,CAAC,GAAG,CAAC,IAAI,UAAU,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,CAAA;IACnC,GAAG,CAAC,GAAG,CAAC,IAAI,UAAU,CAAC,OAAO,CAAC,EAAE,OAAO,CAAC,UAAU,CAAC,CAAA;IACpD,OAAO,GAAG,CAAC,MAAM,CAAA;AACnB,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,YAAY;IACvB,IAAI,CAAQ;IACZ,IAAI,CAAQ;IACZ,WAAW,GAAG,CAAC,CAAA;IACf,YAAY,GAAG,CAAC,CAAA;IAChB,MAAM,CAAyB;IAEvC,YAAY,IAAqC;QAC/C,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC,IAAI,CAAA;QACrB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC,IAAI,IAAI,KAAK,CAAA;IAChC,CAAC;IAED,KAAK,CAAC,IAAI,CACR,QAAgB,EAChB,MAAc,EACd,IAAe;QAEf,MAAM,KAAK,GAAG,QAAQ,CAAA;QACtB,MAAM,GAAG,GAAG,QAAQ,GAAG,MAAM,CAAA;QAC7B,MAAM,WAAW,GAAG,IAAI,CAAC,WAAW,CAAA;QACpC,MAAM,SAAS,GAAG,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,YAAY,CAAA;QACtD,MAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAA;QAEvB,IAAI,MAAmB,CAAA;QACvB,IAAI,MAAM,GAAG,IAAI,CAAC,IAAI,EAAE,CAAC;YACvB,uEAAuE;YACvE,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;YACvB,IAAI,CAAC,WAAW,GAAG,CAAC,CAAA;YACpB,IAAI,CAAC,YAAY,GAAG,CAAC,CAAA;YACrB,MAAM,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,MAAM,EAAE,IAAI,CAAC,CAAA;QACvD,CAAC;aAAM,IAAI,GAAG,IAAI,KAAK,IAAI,WAAW,IAAI,GAAG,IAAI,SAAS,EAAE,CAAC;YAC3D,+BAA+B;YAC/B,MAAM,UAAU,GAAG,KAAK,GAAG,WAAW,CAAA;YACtC,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,UAAU,EAAE,UAAU,GAAG,MAAM,CAAC,CAAA;QACrD,CAAC;aAAM,IAAI,GAAG,IAAI,KAAK,IAAI,WAAW,IAAI,KAAK,GAAG,SAAS,EAAE,CAAC;YAC5D,mEAAmE;YACnE,iEAAiE;YACjE,MAAM,EAAE,GAAG,SAAS,GAAG,KAAK,CAAA;YAC5B,MAAM,EAAE,GAAG,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,YAAY,GAAG,EAAE,EAAE,IAAI,CAAC,YAAY,CAAC,CAAA;YAC/D,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,IAAI,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC7D,IAAI,CAAC,MAAM,GAAG,IAAI,CAAA;YAClB,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;YAC5B,IAAI,CAAC,YAAY,GAAG,IAAI,CAAC,UAAU,CAAA;YACnC,MAAM,GAAG,aAAa,CAAC,EAAE,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,MAAM,GAAG,EAAE,CAAC,CAAC,CAAA;QACxD,CAAC;aAAM,CAAC;YACN,yBAAyB;YACzB,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,IAAI,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC5D,IAAI,CAAC,MAAM,GAAG,IAAI,CAAA;YAClB,IAAI,CAAC,WAAW,GAAG,QAAQ,CAAA;YAC3B,IAAI,CAAC,YAAY,GAAG,IAAI,CAAC,UAAU,CAAA;YACnC,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,MAAM,CAAC,CAAA;QAChC,CAAC;QACD,OAAO,MAAM,CAAA;IACf,CAAC;CACF"}

package/esm/hicFile.d.ts

@@ -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;
 }
@@ -37,7 +36,7 @@ interface Block {
     records: ContactRecords;
 }
 export declare class HicFile {
-    private config;
+    private nvi;
     private file;
     private headerCache;
     private normVectorIndexCache;
@@ -52,7 +51,6 @@ export declare class HicFile {
     normExpectedValueVectorsPosition: number | undefined;
     private chromosomes;
     private chromosomeIndexMap;
-    private chrAliasTable;
     private bpResolutions;
     private masterIndex;
     private meta;
@@ -63,7 +61,7 @@ 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 +79,7 @@ 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;
@@ -91,6 +89,5 @@ export declare class HicFile {
     private readNormExpectedValuesAndNormVectorIndex;
     private skipExpectedValues;
     private parseNormVectorEntry;
-    getFileChrName(chrAlias: string): string;
 }
 export {};