@gmod/bam 8.2.0 → 8.3.1

package/dist/indexFile.d.ts

@@ -22,14 +22,11 @@ export declare function memoizeByRefId<T>(getIndices: (refId: number) => T | und
 export default abstract class IndexFile<TParsed extends ParsedIndexBase = ParsedIndexBase> {
     filehandle: GenericFilehandle;
     renameRefSeq: (s: string) => string;
-    private parseP?;
     /**
-     * The signal `parseP` was started under, while it is still in flight. The
-     * index is parsed once and shared by every query against the file, so without
-     * this the first query to arrive would own a read all the others depend on —
-     * see {@link parse}.
+     * The parsed index, as a shared read — see {@link parse}. One entry, never
+     * evicted, which is what a memo is.
      */
-    private parseSignal?;
+    private parseCache;
     constructor({ filehandle, renameRefSeq, }: {
         filehandle: GenericFilehandle;
         renameRefSeq?: (a: string) => string;
@@ -42,6 +39,7 @@ export default abstract class IndexFile<TParsed extends ParsedIndexBase = Parsed
     }[]>;
     protected abstract reg2bins(min: number, max: number): readonly (readonly [number, number])[];
     protected abstract getLowestChunk(refIndex: RefIndex, min: number): OffsetCoords | undefined;
+    protected abstract getHighestChunk(refIndex: RefIndex, max: number): number | undefined;
     blocksForRange(refId: number, min: number, max: number, opts?: BaseOpts): Promise<Chunk[]>;
     /**
      * Parse the index, or join the parse already running.
@@ -49,26 +47,50 @@ export default abstract class IndexFile<TParsed extends ParsedIndexBase = Parsed
      * The index is downloaded and parsed once for the life of this object, so it
      * is the one read here that is shared between queries — and therefore the one
      * place a cancellation can leak from the query that asked for it to a query
-     * that did not. `_parse` hands `opts` straight to `filehandle.readFile`, so
-     * without this the first query to arrive owns a read every other query
-     * depends on: when it pans away, every concurrent query fails with its abort.
+     * that did not. `_parse` hands `opts` straight to `filehandle.readFile`, so a
+     * bare memoized promise makes the first query to arrive the owner of a read
+     * every other query depends on: when it pans away, every concurrent query
+     * fails with its abort.
      *
-     * A caller that joined someone else's parse and saw it fail because *they*
-     * aborted starts over rather than inheriting the failure — once, then
-     * propagates. Bounding it at one attempt is what jbrowse's
-     * `RemoteFileWithRangeCache.joinChunk` does with the same retry one layer
-     * down, and for the reason it gives: the pathological case becomes one
-     * duplicate parse rather than a recursion whose depth depends on how the
-     * aborts interleave.
+     * The same cache the chunk reads use, for the same reason and with the same
+     * rule: the parse runs under a signal of its own and is cancelled only once
+     * every caller waiting on it has given up, so one query's abort is reported
+     * to that query alone. A rejection is dropped rather than cached, so a
+     * transient failure does not poison the index for the life of the file.
      *
-     * A retry rather than the reference count `_cachedChunkFeatures` uses, for
-     * the reason `@gmod/cram` gives for the same split in `CraiIndex`: the index
-     * is parsed once for the life of the object, so there is no repeated waste to
-     * recover, and this is a dozen lines against restructuring the memo.
+     * The fill is per call rather than on the cache so that the caller who starts
+     * the parse has its `onProgress` reach `filehandle.readFile` — the index is a
+     * whole-file read, and a determinate "downloading index" bar is what that
+     * callback exists for.
      */
-    parse(opts?: BaseOpts, retried?: boolean): Promise<TParsed>;
-    private startParse;
+    parse(opts?: BaseOpts): Promise<TParsed>;
     lineCount(refId: number, opts?: BaseOpts): Promise<number>;
     hasRefSeq(seqId: number, opts?: BaseOpts): Promise<boolean>;
+    /**
+     * Compressed bytes a `getRecordsForRange` over these regions is expected to
+     * download, from the index alone.
+     *
+     * Per region this is `chunksLikelyRead`, not every chunk `blocksForRange`
+     * returns: the difference is the whole point on a long-read file, where a
+     * narrow window inherits every chunk of every overlapping bin and reads a
+     * handful of them. Measured on a 40x ONT BAM (COLO829BL, chr3), summing all
+     * chunks against the bytes the same query really pulls:
+     *
+     * | window | all chunks | actually read | this estimate |
+     * | ------ | ---------- | ------------- | ------------- |
+     * | 380bp  | 43.5MB     | 7.8MB         | 7.8MB         |
+     * | 3.4kb  | 43.5MB     | 7.8MB         | 7.8MB         |
+     * | 100kb  | 46.6MB     | 10.4MB        | 10.4MB        |
+     * | 2Mb    | 155.9MB    | 155.9MB       | 123.8MB       |
+     *
+     * A caller gating on this — jbrowse's "too much data" banner is the one that
+     * exists — was being told 5.6x the truth on exactly the windows a reader
+     * spends their time in, and cannot answer it by zooming: every window narrower
+     * than a linear-index interval resolves to the same chunks and so to the same
+     * number.
+     *
+     * Still summed over merged chunks rather than per region, so two regions
+     * sharing a chunk are charged for it once.
+     */
     estimatedBytesForRegions(regions: Region[], opts?: BaseOpts): Promise<number>;
 }

package/dist/indexFile.js

@@ -4,6 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.memoizeByRefId = memoizeByRefId;
+const shared_read_cache_1 = require("@gmod/shared-read-cache");
 const quick_lru_1 = __importDefault(require("@jbrowse/quick-lru"));
 const util_ts_1 = require("./util.js");
 // SYNC: ~/src/gmod/tabix-js/src/util.ts memoizeByRefId
@@ -28,14 +29,11 @@ function memoizeByRefId(getIndices, maxSize = 5) {
 class IndexFile {
     filehandle;
     renameRefSeq;
-    parseP;
     /**
-     * The signal `parseP` was started under, while it is still in flight. The
-     * index is parsed once and shared by every query against the file, so without
-     * this the first query to arrive would own a read all the others depend on —
-     * see {@link parse}.
+     * The parsed index, as a shared read — see {@link parse}. One entry, never
+     * evicted, which is what a memo is.
      */
-    parseSignal;
+    parseCache = new shared_read_cache_1.SharedReadCache({});
     constructor({ filehandle, renameRefSeq = (n) => n, }) {
         this.filehandle = filehandle;
         this.renameRefSeq = renameRefSeq;
@@ -67,68 +65,32 @@ class IndexFile {
         }
         return (0, util_ts_1.optimizeChunks)(chunks, this.getLowestChunk(ba, min));
     }
-    // SYNC: ~/src/gmod/tabix-js/src/indexFile.ts parse — same owner-signal
-    // tracking and one-attempt retry, and the same reasoning below.
+    // SYNC: ~/src/gmod/tabix-js/src/indexFile.ts parse — same shape and the same
+    // reasoning below.
     /**
      * Parse the index, or join the parse already running.
      *
      * The index is downloaded and parsed once for the life of this object, so it
      * is the one read here that is shared between queries — and therefore the one
      * place a cancellation can leak from the query that asked for it to a query
-     * that did not. `_parse` hands `opts` straight to `filehandle.readFile`, so
-     * without this the first query to arrive owns a read every other query
-     * depends on: when it pans away, every concurrent query fails with its abort.
+     * that did not. `_parse` hands `opts` straight to `filehandle.readFile`, so a
+     * bare memoized promise makes the first query to arrive the owner of a read
+     * every other query depends on: when it pans away, every concurrent query
+     * fails with its abort.
      *
-     * A caller that joined someone else's parse and saw it fail because *they*
-     * aborted starts over rather than inheriting the failure — once, then
-     * propagates. Bounding it at one attempt is what jbrowse's
-     * `RemoteFileWithRangeCache.joinChunk` does with the same retry one layer
-     * down, and for the reason it gives: the pathological case becomes one
-     * duplicate parse rather than a recursion whose depth depends on how the
-     * aborts interleave.
+     * The same cache the chunk reads use, for the same reason and with the same
+     * rule: the parse runs under a signal of its own and is cancelled only once
+     * every caller waiting on it has given up, so one query's abort is reported
+     * to that query alone. A rejection is dropped rather than cached, so a
+     * transient failure does not poison the index for the life of the file.
      *
-     * A retry rather than the reference count `_cachedChunkFeatures` uses, for
-     * the reason `@gmod/cram` gives for the same split in `CraiIndex`: the index
-     * is parsed once for the life of the object, so there is no repeated waste to
-     * recover, and this is a dozen lines against restructuring the memo.
+     * The fill is per call rather than on the cache so that the caller who starts
+     * the parse has its `onProgress` reach `filehandle.readFile` — the index is a
+     * whole-file read, and a determinate "downloading index" bar is what that
+     * callback exists for.
      */
-    async parse(opts = {}, retried = false) {
-        (0, util_ts_1.throwIfAborted)(opts.signal);
-        const pending = this.parseP;
-        if (!pending) {
-            return this.startParse(opts);
-        }
-        // read before awaiting: the owner is forgotten as soon as the parse settles
-        const ownerSignal = this.parseSignal;
-        try {
-            return await pending;
-        }
-        catch (e) {
-            if (retried || !ownerSignal?.aborted || opts.signal?.aborted) {
-                throw e;
-            }
-            return this.parse(opts, true);
-        }
-    }
-    startParse(opts) {
-        const pending = this._parse(opts);
-        this.parseP = pending;
-        this.parseSignal = opts.signal;
-        // Drop a rejection rather than keeping it, so one transient failure does not
-        // poison the index for the lifetime of the file. Both branches are
-        // identity-checked so a retry started after this settles is not cleared by
-        // the attempt it already replaced.
-        pending.then(() => {
-            if (this.parseP === pending) {
-                this.parseSignal = undefined;
-            }
-        }, () => {
-            if (this.parseP === pending) {
-                this.parseP = undefined;
-                this.parseSignal = undefined;
-            }
-        });
-        return pending;
+    parse(opts = {}) {
+        return this.parseCache.get('index', opts.signal, signal => this._parse({ ...opts, signal }));
     }
     async lineCount(refId, opts) {
         const indexData = await this.parse(opts);
@@ -138,8 +100,41 @@ class IndexFile {
         const indexData = await this.parse(opts);
         return !!indexData.indices(seqId);
     }
+    /**
+     * Compressed bytes a `getRecordsForRange` over these regions is expected to
+     * download, from the index alone.
+     *
+     * Per region this is `chunksLikelyRead`, not every chunk `blocksForRange`
+     * returns: the difference is the whole point on a long-read file, where a
+     * narrow window inherits every chunk of every overlapping bin and reads a
+     * handful of them. Measured on a 40x ONT BAM (COLO829BL, chr3), summing all
+     * chunks against the bytes the same query really pulls:
+     *
+     * | window | all chunks | actually read | this estimate |
+     * | ------ | ---------- | ------------- | ------------- |
+     * | 380bp  | 43.5MB     | 7.8MB         | 7.8MB         |
+     * | 3.4kb  | 43.5MB     | 7.8MB         | 7.8MB         |
+     * | 100kb  | 46.6MB     | 10.4MB        | 10.4MB        |
+     * | 2Mb    | 155.9MB    | 155.9MB       | 123.8MB       |
+     *
+     * A caller gating on this — jbrowse's "too much data" banner is the one that
+     * exists — was being told 5.6x the truth on exactly the windows a reader
+     * spends their time in, and cannot answer it by zooming: every window narrower
+     * than a linear-index interval resolves to the same chunks and so to the same
+     * number.
+     *
+     * Still summed over merged chunks rather than per region, so two regions
+     * sharing a chunk are charged for it once.
+     */
     async estimatedBytesForRegions(regions, opts) {
-        const blockResults = await Promise.all(regions.map(r => this.blocksForRange(r.refId, r.start, r.end, opts)));
+        const indexData = await this.parse(opts);
+        const blockResults = await Promise.all(regions.map(async (r) => {
+            const chunks = await this.blocksForRange(r.refId, r.start, r.end, opts);
+            const refIndex = indexData.indices(r.refId);
+            return refIndex
+                ? (0, util_ts_1.chunksLikelyRead)(chunks, this.getHighestChunk(refIndex, r.end))
+                : chunks;
+        }));
         // Deduplicate and merge overlapping blocks across all regions
         const mergedBlocks = (0, util_ts_1.optimizeChunks)(blockResults.flat());
         let total = 0;

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+{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;;;;AA8BA,wCAkBC;AAhDD,+DAAyD;AACzD,mEAAyC;AAEzC,uCAA4D;AAwB5D,uDAAuD;AACvD,6EAA6E;AAC7E,2CAA2C;AAC3C,SAAgB,cAAc,CAC5B,UAA4C,EAC5C,OAAO,GAAG,CAAC;IAEX,MAAM,KAAK,GAAG,IAAI,mBAAQ,CAAY,EAAE,OAAO,EAAE,CAAC,CAAA;IAClD,OAAO,CAAC,KAAa,EAAE,EAAE;QACvB,yEAAyE;QACzE,sDAAsD;QACtD,MAAM,MAAM,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;QAC/B,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;YACzB,OAAO,MAAM,CAAA;QACf,CAAC;QACD,MAAM,MAAM,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;QAChC,IAAI,MAAM,EAAE,CAAC;YACX,KAAK,CAAC,GAAG,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QAC1B,CAAC;QACD,OAAO,MAAM,CAAA;IACf,CAAC,CAAA;AACH,CAAC;AAED,MAA8B,SAAS;IAG9B,UAAU,CAAmB;IAC7B,YAAY,CAAuB;IAE1C;;;OAGG;IACK,UAAU,GAAG,IAAI,mCAAe,CAAkB,EAAE,CAAC,CAAA;IAE7D,YAAY,EACV,UAAU,EACV,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIhC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;IAClC,CAAC;IAkCD,KAAK,CAAC,cAAc,CAClB,KAAa,EACb,GAAW,EACX,GAAW,EACX,OAAiB,EAAE;QAEnB,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;YACZ,GAAG,GAAG,CAAC,CAAA;QACT,CAAC;QACD,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACnC,IAAI,CAAC,EAAE,EAAE,CAAC;YACR,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,eAAe,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;QAC/C,IAAI,eAAe,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACjC,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,MAAM,GAAY,EAAE,CAAA;QAC1B,MAAM,EAAE,QAAQ,EAAE,GAAG,EAAE,CAAA;QACvB,KAAK,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC,IAAI,eAAe,EAAE,CAAC;YAC3C,KAAK,IAAI,GAAG,GAAG,KAAK,EAAE,GAAG,IAAI,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC;gBACxC,MAAM,SAAS,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;gBAC/B,IAAI,SAAS,EAAE,CAAC;oBACd,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;wBACjD,MAAM,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAE,CAAC,CAAA;oBAC5B,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;QACD,OAAO,IAAA,wBAAc,EAAC,MAAM,EAAE,IAAI,CAAC,cAAc,CAAC,EAAE,EAAE,GAAG,CAAC,CAAC,CAAA;IAC7D,CAAC;IAED,6EAA6E;IAC7E,mBAAmB;IACnB;;;;;;;;;;;;;;;;;;;;;OAqBG;IACH,KAAK,CAAC,OAAiB,EAAE;QACvB,OAAO,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,OAAO,EAAE,IAAI,CAAC,MAAM,EAAE,MAAM,CAAC,EAAE,CACxD,IAAI,CAAC,MAAM,CAAC,EAAE,GAAG,IAAI,EAAE,MAAM,EAAE,CAAC,CACjC,CAAA;IACH,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,IAAe;QAC5C,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,OAAO,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,KAAK,EAAE,SAAS,IAAI,CAAC,CAAA;IACxD,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,IAAe;QAC5C,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,OAAO,CAAC,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;IACnC,CAAC;IAED;;;;;;;;;;;;;;;;;;;;;;;;;OAyBG;IACH,KAAK,CAAC,wBAAwB,CAAC,OAAiB,EAAE,IAAe;QAC/D,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,YAAY,GAAG,MAAM,OAAO,CAAC,GAAG,CACpC,OAAO,CAAC,GAAG,CAAC,KAAK,EAAC,CAAC,EAAC,EAAE;YACpB,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;YACvE,MAAM,QAAQ,GAAG,SAAS,CAAC,OAAO,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;YAC3C,OAAO,QAAQ;gBACb,CAAC,CAAC,IAAA,0BAAgB,EAAC,MAAM,EAAE,IAAI,CAAC,eAAe,CAAC,QAAQ,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC;gBACjE,CAAC,CAAC,MAAM,CAAA;QACZ,CAAC,CAAC,CACH,CAAA;QAED,8DAA8D;QAC9D,MAAM,YAAY,GAAG,IAAA,wBAAc,EAAC,YAAY,CAAC,IAAI,EAAE,CAAC,CAAA;QAExD,IAAI,KAAK,GAAG,CAAC,CAAA;QACb,KAAK,MAAM,KAAK,IAAI,YAAY,EAAE,CAAC;YACjC,KAAK,IAAI,KAAK,CAAC,WAAW,EAAE,CAAA;QAC9B,CAAC;QACD,OAAO,KAAK,CAAA;IACd,CAAC;CACF;AA/KD,4BA+KC"}

package/dist/util.d.ts

@@ -25,6 +25,46 @@ export interface BaseOpts {
      */
     onProgress?: (bytesDownloaded: number, totalBytes?: number) => void;
 }
+export { throwIfAborted } from '@gmod/shared-read-cache';
+export declare const MAX_CONCURRENT_CHUNK_READS = 6;
+/**
+ * The prefix of `chunks` a query is expected to actually read, for callers that
+ * want to forecast a query's cost without running it.
+ *
+ * `blocksForRange` returns every chunk of every bin overlapping the query, at
+ * every level of the binning scheme, minus the ones the linear index puts
+ * entirely before it. On a long-read file that is wildly more than the query
+ * reads: a coarse bin's chunks run to the end of the bin's span, so a 380bp
+ * window on a deep ONT BAM resolves to 90 chunks / 43.5MB, of which
+ * `getRecordsForRange` reads 6 / 7.8MB before the early stop fires.
+ *
+ * Two bounds, and the answer is the larger:
+ *
+ * - `upperBoundBlockPosition` — the file offset past which a chunk holds no
+ *   record the query wants, from the linear index one window beyond the query
+ *   end. Chunks come back sorted by `minv`, so the ones under it are a prefix.
+ * - `MAX_CONCURRENT_CHUNK_READS` — the first batch is read unconditionally, so
+ *   no query ever costs less than that however tight the upper bound is.
+ *
+ * **This is a forecast, not a bound the reader obeys**, and it is deliberately
+ * only used to describe a query rather than to answer one. The upper bound is
+ * an approximation: a record starting before the query end can sit at a higher
+ * offset than the linear-index entry past it (a long read reaching into the
+ * next window pins that entry low), so pruning a fetch this way would drop
+ * records. A forecast that is occasionally 20% under warns slightly early;
+ * a fetch that is occasionally short returns wrong data.
+ *
+ * An EMPTY prefix is that pin at its worst — the bound has landed at or before
+ * the query's own first chunk, so it orders nothing — and the answer there is
+ * every chunk rather than the batch floor. Without it this returns the floor on
+ * a file whose features are long against the linear-index interval, which is
+ * where the same forecast really does go wrong: ported to tabix-js and measured
+ * on the 1000 Genomes SV callset, whose 1.4Mb deletions pin the entry at the
+ * data start, it forecast 0.04MB against the 0.22MB the query read. On this
+ * corpus the fallback costs one fixture's win (chr22_nanopore, whose 10kb
+ * window keeps summing all 22 chunks) and no accuracy anywhere else.
+ */
+export declare function chunksLikelyRead(chunks: Chunk[], upperBoundBlockPosition?: number): Chunk[];
 /**
  * Merge and order the chunks a query resolved to.
  *
@@ -35,7 +75,6 @@ export interface BaseOpts {
  * underneath you. (The Chunk objects themselves are never mutated; a merged
  * span produces a new instance.)
  */
-export { throwIfAborted } from '@gmod/shared-read-cache';
 export declare function optimizeChunks(chunks: Chunk[], lowest?: OffsetCoords): Chunk[];
 export declare function parsePseudoBin(bytes: Uint8Array, offset: number): {
     lineCount: number;

package/dist/util.js

@@ -3,7 +3,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.throwIfAborted = void 0;
+exports.MAX_CONCURRENT_CHUNK_READS = exports.throwIfAborted = void 0;
+exports.chunksLikelyRead = chunksLikelyRead;
 exports.optimizeChunks = optimizeChunks;
 exports.parsePseudoBin = parsePseudoBin;
 exports.clampChunkEnds = clampChunkEnds;
@@ -14,6 +15,70 @@ exports.concatUint8Array = concatUint8Array;
 exports.appendInRange = appendInRange;
 const chunk_ts_1 = __importDefault(require("./chunk.js"));
 const virtualOffset_ts_1 = require("./virtualOffset.js");
+// Re-exported so the internal import path stays './util.ts'. The
+// implementation moved to @gmod/shared-read-cache, which needs it anyway --
+// every consumer of that package was carrying an identical copy.
+var shared_read_cache_1 = require("@gmod/shared-read-cache");
+Object.defineProperty(exports, "throwIfAborted", { enumerable: true, get: function () { return shared_read_cache_1.throwIfAborted; } });
+// How many of a query's chunks to read at once. Six is the HTTP/1.1 per-host
+// connection cap browsers enforce, so going much above it buys nothing on the
+// transport that matters and only widens peak memory.
+//
+// It is also the SMALLEST number of chunks any query reads, because
+// `_fetchChunkFeatures` checks its early stop once, after this first batch
+// (ADR 0010) — which is what `chunksLikelyRead` below is built on.
+exports.MAX_CONCURRENT_CHUNK_READS = 6;
+/**
+ * The prefix of `chunks` a query is expected to actually read, for callers that
+ * want to forecast a query's cost without running it.
+ *
+ * `blocksForRange` returns every chunk of every bin overlapping the query, at
+ * every level of the binning scheme, minus the ones the linear index puts
+ * entirely before it. On a long-read file that is wildly more than the query
+ * reads: a coarse bin's chunks run to the end of the bin's span, so a 380bp
+ * window on a deep ONT BAM resolves to 90 chunks / 43.5MB, of which
+ * `getRecordsForRange` reads 6 / 7.8MB before the early stop fires.
+ *
+ * Two bounds, and the answer is the larger:
+ *
+ * - `upperBoundBlockPosition` — the file offset past which a chunk holds no
+ *   record the query wants, from the linear index one window beyond the query
+ *   end. Chunks come back sorted by `minv`, so the ones under it are a prefix.
+ * - `MAX_CONCURRENT_CHUNK_READS` — the first batch is read unconditionally, so
+ *   no query ever costs less than that however tight the upper bound is.
+ *
+ * **This is a forecast, not a bound the reader obeys**, and it is deliberately
+ * only used to describe a query rather than to answer one. The upper bound is
+ * an approximation: a record starting before the query end can sit at a higher
+ * offset than the linear-index entry past it (a long read reaching into the
+ * next window pins that entry low), so pruning a fetch this way would drop
+ * records. A forecast that is occasionally 20% under warns slightly early;
+ * a fetch that is occasionally short returns wrong data.
+ *
+ * An EMPTY prefix is that pin at its worst — the bound has landed at or before
+ * the query's own first chunk, so it orders nothing — and the answer there is
+ * every chunk rather than the batch floor. Without it this returns the floor on
+ * a file whose features are long against the linear-index interval, which is
+ * where the same forecast really does go wrong: ported to tabix-js and measured
+ * on the 1000 Genomes SV callset, whose 1.4Mb deletions pin the entry at the
+ * data start, it forecast 0.04MB against the 0.22MB the query read. On this
+ * corpus the fallback costs one fixture's win (chr22_nanopore, whose 10kb
+ * window keeps summing all 22 chunks) and no accuracy anywhere else.
+ */
+function chunksLikelyRead(chunks, upperBoundBlockPosition) {
+    if (upperBoundBlockPosition === undefined ||
+        chunks.length <= exports.MAX_CONCURRENT_CHUNK_READS) {
+        return chunks;
+    }
+    let n = 0;
+    while (n < chunks.length &&
+        chunks[n].minv.blockPosition < upperBoundBlockPosition) {
+        n++;
+    }
+    return n === 0 || n >= chunks.length
+        ? chunks
+        : chunks.slice(0, Math.max(n, exports.MAX_CONCURRENT_CHUNK_READS));
+}
 /**
  * Merge and order the chunks a query resolved to.
  *
@@ -24,11 +89,6 @@ const virtualOffset_ts_1 = require("./virtualOffset.js");
  * underneath you. (The Chunk objects themselves are never mutated; a merged
  * span produces a new instance.)
  */
-// Re-exported so the internal import path stays './util.ts'. The
-// implementation moved to @gmod/shared-read-cache, which needs it anyway --
-// every consumer of that package was carrying an identical copy.
-var shared_read_cache_1 = require("@gmod/shared-read-cache");
-Object.defineProperty(exports, "throwIfAborted", { enumerable: true, get: function () { return shared_read_cache_1.throwIfAborted; } });
 function optimizeChunks(chunks, lowest) {
     const n = chunks.length;
     if (n === 0) {

package/dist/util.js.map

@@ -1 +1 @@
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package/esm/bai.d.ts

@@ -21,5 +21,6 @@ export default class BAI extends IndexFile<BaiParsed> {
         blockPosition: number;
         dataPosition: number;
     } | undefined;
+    protected getHighestChunk(refIndex: BaiRefIndex, max: number): number | undefined;
 }
 export {};

package/esm/bai.js

@@ -223,5 +223,20 @@ export default class BAI extends IndexFile {
                 dataPosition: linearDataPositions[i],
             };
     }
+    // The linear-index entry one window PAST the query: the smallest file offset
+    // of any record overlapping the window after it. Records the query wants are
+    // overwhelmingly below it, which is what makes it a usable forecast — but not
+    // a bound, because a long read reaching into that next window pins the entry
+    // at ITS offset, and records starting later (still before the query end) sit
+    // above it. chunksLikelyRead says why an estimate may use it and a fetch may
+    // not.
+    //
+    // undefined past the end of the linear index, i.e. for a query running to the
+    // end of the reference, where there is no next window to bound anything with.
+    getHighestChunk(refIndex, max) {
+        const { linearBlockPositions } = refIndex;
+        const i = (max >> BAI_LINEAR_SHIFT) + 1;
+        return i < linearBlockPositions.length ? linearBlockPositions[i] : undefined;
+    }
 }
 //# sourceMappingURL=bai.js.map

package/esm/bai.js.map

@@ -1 +1 @@
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