@gmod/bam 9.0.0 → 10.0.0

package/README.md

@@ -36,10 +36,12 @@ const bam = new BamFile({
 
 Over HTTP it is worth putting
 [`@gmod/range-cache-filehandle`](https://github.com/GMOD/range-cache-filehandle)
-underneath the filehandle. It caches what it reads in 256 KiB chunks and turns
-the chunks a read is missing into one request per contiguous run, so the
-scattered index and data reads a query makes arrive as a couple of fetches
-rather than dozens. `bamFilehandle` and `baiFilehandle` accept any
+underneath the filehandle. A query fetches the index once, then reads the
+records as a handful of byte ranges spread through the BAM —
+[this visualizer](https://cmdcolin.github.io/bam_index_visualizer) draws that
+pattern for a file of your choosing. The cache serves those ranges out of 256
+KiB chunks, so neighboring ranges share a request and later queries reuse what
+is already fetched. `bamFilehandle` and `baiFilehandle` accept any
 generic-filehandle2 object, so it drops straight in:
 
 ```typescript
@@ -77,10 +79,11 @@ for await (const records of streamBamRecords({ bamUrl: 'unsorted.bam' })) {
 }
 ```
 
-It reads the file a window at a time rather than all at once, so a 1GB BAM
-streams through in bounded memory. A standalone function rather than a `BamFile`
-method, so that streaming alone leaves `BAI`/`CSI` and the chunk cache out of
-your bundle. See [docs/api.md](docs/api.md) for `onHeader` and the window size.
+`streamBamRecords` reads the file a window at a time rather than all at once, so
+a 1GB BAM streams through in bounded memory. It is a standalone function rather
+than a `BamFile` method, so that streaming alone leaves `BAI`/`CSI` and the
+chunk cache out of your bundle. See [docs/api.md](docs/api.md) for `onHeader`
+and the window size.
 
 ## Mismatches
 
@@ -109,17 +112,17 @@ for (const record of await bam.getRecordsForRange('ctgA', 0, 50000)) {
 
 `code` is a CIGAR char code, to compare against the exported `MISMATCH_SUBST`,
 `MISMATCH_INSERTION`, … constants, and `record.forEachMismatch(cb, opts?)`
-reports the same set while allocating nothing per difference. What those two
-fields say, with that read walked through them:
+reports the same set while allocating nothing per difference. What the two
+fields mean, with that read walked through them:
 [docs/cigar-and-md.md](docs/cigar-and-md.md).
 
 Substitutions need either an `MD` tag on the read or the reference bases, which
-is what `fetchReferenceSequence` is doing above — most aligners leave `MD` off,
-and a query calls it only when one of its reads needs it. Without it, a read
-lacking `MD` still reports its indels and clips but no substitutions — nothing
-in the record says where they are. [docs/api.md](docs/api.md#mismatches) has the
-field meanings, and what to do about reads that run past the region you are
-looking at.
+`fetchReferenceSequence` supplies above — most aligners leave `MD` off, and a
+query calls it only when one of its reads needs it. Without it, `getMismatches`
+still returns indels and clips for a read lacking `MD`, but no substitutions —
+the record does not contain their positions.
+[docs/api.md](docs/api.md#mismatches) has the field meanings, and what to do
+about reads that run past the region you are looking at.
 
 ## How a query flows
 
@@ -154,7 +157,7 @@ const bam = new BamFile({
 Safe to pass unconditionally: `getSharedWorkerPool()` returns `undefined` under
 node, or anywhere the host forbids Workers, which keeps the in-process path. No
 cross-origin isolation needed. bam-js never creates a pool on its own — the
-thread budget belongs to the consumer. Worker counts, lifecycle and benchmarks:
+consumer controls the thread budget. Worker counts, lifecycle and benchmarks:
 [bgzf-filehandle's worker pool docs](https://github.com/GMOD/bgzf-filehandle/blob/main/docs/worker-pool.md).
 
 ## Usage with htsget
@@ -184,15 +187,15 @@ const bam = new HtsgetFile({
 })
 ```
 
-That `fetch` serves the ticket request _and_ the data-block urls the ticket
-points at, which may live on a third-party host — so only attach credentials to
-hosts you trust.
+The `fetch` you pass makes both the ticket request and the data-block requests
+the ticket points at, and those data-block URLs may be on a third-party host —
+so only attach credentials to hosts you trust.
 
 ## Docs
 
 - [docs/api.md](docs/api.md) — every constructor option, method and `BamRecord`
   field, plus custom record classes
-- [docs/cigar-and-md.md](docs/cigar-and-md.md) — what `CIGAR` and `MD` say, and
+- [docs/cigar-and-md.md](docs/cigar-and-md.md) — what `CIGAR` and `MD` mean, and
   how the walk reads mismatches out of them
 - [docs/dataflow.md](docs/dataflow.md) — how a query flows, and where wasm sits
 - [docs/optimizations.md](docs/optimizations.md) — why each step of that path

package/dist/bai.d.ts

@@ -14,6 +14,8 @@ export interface IndexCovEntry {
     score: number;
 }
 export default class BAI extends IndexFile<BaiParsed> {
+    protected minShift: number;
+    protected depth: number;
     _parse(opts: BaseOpts): Promise<BaiParsed>;
     indexCov(seqId: number, start?: number, end?: number, opts?: BaseOpts): Promise<IndexCovEntry[]>;
     protected reg2bins(min: number, max: number): readonly [readonly [0, 0], readonly [number, number], readonly [number, number], readonly [number, number], readonly [number, number], readonly [number, number]];

package/dist/bai.js

@@ -61,6 +61,22 @@ function roundUp(n, multiple) {
     const rem = n % multiple;
     return rem === 0 ? n : n - rem + multiple;
 }
+/**
+ * Older samtools leaves 0:0 in linear-index windows no read overlaps. htslib
+ * fills interior ones from the next entry on load (`hts.c`, "fill missing
+ * values"); this also fills leading ones, which htslib leaves at 0. Either
+ * way the entry stays a lower bound, since no record overlaps that window.
+ * Left as 0, a leading entry scores its whole absolute file offset in
+ * `indexCov`, and `getLowestChunk` falls back to the start of the file.
+ */
+function fillLinearGaps(blocks, data) {
+    for (let j = blocks.length - 2; j >= 0; j--) {
+        if (blocks[j] === 0 && data[j] === 0) {
+            blocks[j] = blocks[j + 1];
+            data[j] = data[j + 1];
+        }
+    }
+}
 // Compute bin ranges that overlap [beg, end). Each level's first-bin offset
 // is (8^L - 1) / 7. See SAMv1.pdf §5.1.1 for the binning derivation.
 function reg2bins(beg, end) {
@@ -88,6 +104,8 @@ function reg2bins(beg, end) {
     ];
 }
 class BAI extends indexFile_ts_1.default {
+    minShift = BAI_LINEAR_SHIFT;
+    depth = BAI_DEPTH;
     async _parse(opts) {
         const bytes = await this.filehandle.readFile(opts);
         const dataView = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);
@@ -184,6 +202,7 @@ class BAI extends indexFile_ts_1.default {
                 linearDataPositions[j] = (bytes[curr + 1] << 8) | bytes[curr];
                 curr += 8;
             }
+            fillLinearGaps(linearBlockPositions, linearDataPositions);
             (0, util_ts_1.clampChunkEnds)(Object.values(binIndex).flat(), linearBlockPositions);
             return {
                 binIndex,

package/dist/bai.js.map

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package/dist/bamFile.js

@@ -204,7 +204,7 @@ class BamFile {
         const parsed = (0, util_ts_1.parseRefSeqs)(uncba, headLen + 8, this.renameRefSeq);
         let samHeader;
         if (parsed) {
-            const headerText = new TextDecoder('utf8').decode(uncba.subarray(8, 8 + headLen));
+            const headerText = (0, util_ts_1.decodeHeaderText)(uncba, headLen);
             this.header = headerText;
             this.chrToIndex = parsed.chrToIndex;
             this.indexToChr = parsed.indexToChr;
@@ -266,7 +266,7 @@ class BamFile {
         if (chrId === undefined || !this.index) {
             return [];
         }
-        const chunks = await this.index.blocksForRange(chrId, min - 1, max, opts);
+        const chunks = await this.index.blocksForRange(chrId, min, max, opts);
         return this._fetchChunkFeatures(chunks, chrId, chr, min, max, opts);
     }
     /**
@@ -501,38 +501,30 @@ class BamFile {
         // make the count NaN.
         const readNameCounts = new Map();
         const readIds = new Set();
+        const names = new Array(records.length);
         for (let i = 0, l = records.length; i < l; i++) {
             const r = records[i];
             const name = r.name;
+            names[i] = name;
             readNameCounts.set(name, (readNameCounts.get(name) ?? 0) + 1);
             readIds.add(r.fileOffset);
         }
         const matePromises = [];
         for (let i = 0, l = records.length; i < l; i++) {
             const f = records[i];
-            const name = f.name;
             if (this.index &&
-                readNameCounts.get(name) === 1 &&
+                readNameCounts.get(names[i]) === 1 &&
                 (pairAcrossChr ||
                     (f.next_refid === chrId &&
                         Math.abs(f.start - f.next_pos) < maxInsertSize))) {
                 matePromises.push(this.index.blocksForRange(f.next_refid, f.next_pos, f.next_pos + 1, opts));
             }
         }
-        const map = new Map();
-        const res = await Promise.all(matePromises);
-        for (let i = 0, l = res.length; i < l; i++) {
-            const chunks = res[i];
-            for (let j = 0, jl = chunks.length; j < jl; j++) {
-                const m = chunks[j];
-                // Key on the virtual-offset span — the same key _cachedChunkFeatures
-                // uses. Chunk.toString() also folds in `bin` and fetchedSize(), which
-                // keeps two chunks covering an identical span apart here even though
-                // the cache below collapses them, so their records came back twice.
-                map.set(chunkCacheKey(m), m);
-            }
-        }
-        const mateChunks = [...map.values()];
+        // Each mate's lookup is merged on its own, so two of them can resolve to
+        // different spans over the same records. Merging the union again makes
+        // them disjoint, which is what keeps a mate in the overlap from coming
+        // back once per span.
+        const mateChunks = (0, util_ts_1.optimizeChunks)((await Promise.all(matePromises)).flat());
         // Bounded for the reason ADR 0008 bounds the main query path: a viewAsPairs
         // query over a busy region resolves to many distinct mate chunks, and an
         // unbounded fan-out inflates every one of them at once. Same inline pool
@@ -611,7 +603,7 @@ class BamFile {
         const hasDpositions = dpositions.length > 0;
         const hasCpositions = cpositions.length > 0;
         while (blockStart + 4 < ba.length) {
-            const blockSize = dataView.getInt32(blockStart, true);
+            const blockSize = (0, util_ts_1.readBlockSize)(dataView, blockStart);
             const blockEnd = blockStart + 4 + blockSize - 1;
             if (hasDpositions) {
                 const target = blockStart + chunk.minv.dataPosition;

package/dist/bamFile.js.map

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

@@ -1,11 +1,17 @@
-import Chunk from './chunk.ts';
 import IndexFile from './indexFile.ts';
 import { VirtualOffset } from './virtualOffset.ts';
+import type { ParsedIndexBase, RefIndex } from './indexFile.ts';
 import type { BaseOpts } from './util.ts';
-export default class CSI extends IndexFile {
+interface CsiRefIndex extends RefIndex {
+    loffsets: Map<number, VirtualOffset>;
+}
+interface CsiParsed extends ParsedIndexBase<CsiRefIndex> {
+    csi: true;
+}
+export default class CSI extends IndexFile<CsiParsed> {
     private maxBinNumber;
-    private depth;
-    private minShift;
+    protected depth: number;
+    protected minShift: number;
     indexCov(): Promise<never[]>;
     parseAuxData(bytes: Uint8Array, offset: number): {
         refNameToId: Record<string, number>;
@@ -22,31 +28,15 @@ export default class CSI extends IndexFile {
         format: string;
         formatFlags: number;
     };
-    _parse(opts: BaseOpts): Promise<{
-        refNameToId?: Record<string, number> | undefined;
-        refIdToName?: string[] | undefined;
-        columnNumbers?: {
-            ref: number;
-            start: number;
-            end: number;
-        } | undefined;
-        coordinateType?: string | undefined;
-        metaValue?: number | undefined;
-        metaChar?: string | undefined;
-        skipLines?: number | undefined;
-        format?: string | undefined;
-        formatFlags?: number | undefined;
-        firstDataLine: VirtualOffset | undefined;
-        indices: (refId: number) => {
-            binIndex: Record<number, Chunk[]>;
-            stats: {
-                lineCount: number;
-            } | undefined;
-        } | undefined;
-        refCount: number;
-        csi: boolean;
-    }>;
-    protected getLowestChunk(): VirtualOffset;
+    _parse(opts: BaseOpts): Promise<CsiParsed>;
+    /**
+     * CSI has no linear index, but each bin's `loffset` is the linear-index entry
+     * at the bin's first window (htslib's `update_loff`), so the finest bin at or
+     * left of `min` bounds the query from below the way BAI's linear index does.
+     * Walks left through siblings and then up to the parent, as `hts_itr_query`
+     * does for CSI.
+     */
+    protected getLowestChunk(refIndex: CsiRefIndex, min: number): VirtualOffset;
     protected getHighestChunk(): undefined;
     /**
      * calculate the list of bins that may overlap with region [beg,end)
@@ -55,3 +45,4 @@ export default class CSI extends IndexFile {
      */
     protected reg2bins(beg: number, end: number): (readonly [number, number])[];
 }
+export {};

package/dist/csi.js

@@ -101,7 +101,7 @@ class CSI extends indexFile_ts_1.default {
         }
         this.minShift = dataView.getInt32(4, true);
         this.depth = dataView.getInt32(8, true);
-        this.maxBinNumber = ((1 << ((this.depth + 1) * 3)) - 1) / 7;
+        this.maxBinNumber = (8 ** (this.depth + 1) - 1) / 7;
         const maxBinNumber = this.maxBinNumber;
         const auxLength = dataView.getInt32(12, true);
         // A tabix-only branch, which is why parseAuxData and the parseNameBytes it
@@ -136,10 +136,10 @@ class CSI extends indexFile_ts_1.default {
                     curr += 28 + 16;
                 }
                 else {
-                    // A bin's loffset is the smallest virtual offset of any record in it,
-                    // so the minimum over loffsets is already the minimum over the bin's
-                    // chunks — one read per bin instead of one per chunk. Checked against
-                    // every .csi in test/data: same answer on all 19.
+                    // A bin's loffset is the linear-index entry at its first window, so
+                    // the smallest over every bin is the first record's offset — one
+                    // read per bin instead of one per chunk. Checked against every .csi
+                    // in test/data: same answer on all 19.
                     firstDataLine = (0, util_ts_1.minVirtualOffset)(bytes, curr, 1, firstDataLine);
                     curr += 8; // loffset
                     const chunkCount = dataView.getInt32(curr, true);
@@ -156,6 +156,7 @@ class CSI extends indexFile_ts_1.default {
             const binCount = dataView.getInt32(curr, true);
             curr += 4;
             const binIndex = {};
+            const loffsets = new Map();
             let pseudoBinStats;
             for (let j = 0; j < binCount; j++) {
                 const bin = dataView.getUint32(curr, true);
@@ -165,7 +166,8 @@ class CSI extends indexFile_ts_1.default {
                     curr += 28 + 16;
                 }
                 else {
-                    curr += 8; // skip loffset; firstDataLine was computed in the first pass
+                    loffsets.set(bin, (0, virtualOffset_ts_1.fromBytes)(bytes, curr));
+                    curr += 8;
                     const chunkCount = dataView.getInt32(curr, true);
                     curr += 4;
                     const chunks = new Array(chunkCount);
@@ -182,6 +184,7 @@ class CSI extends indexFile_ts_1.default {
             (0, util_ts_1.clampChunkEnds)(Object.values(binIndex).flat());
             return {
                 binIndex,
+                loffsets,
                 stats: pseudoBinStats,
             };
         }
@@ -193,11 +196,25 @@ class CSI extends indexFile_ts_1.default {
             ...aux,
         };
     }
-    // CSI has no linear index — every refId starts from the beginning of file.
-    getLowestChunk() {
-        return ZERO_OFFSET;
+    /**
+     * CSI has no linear index, but each bin's `loffset` is the linear-index entry
+     * at the bin's first window (htslib's `update_loff`), so the finest bin at or
+     * left of `min` bounds the query from below the way BAI's linear index does.
+     * Walks left through siblings and then up to the parent, as `hts_itr_query`
+     * does for CSI.
+     */
+    getLowestChunk(refIndex, min) {
+        const { loffsets } = refIndex;
+        const leaves = 8 ** this.depth;
+        let bin = (leaves - 1) / 7 +
+            Math.min(Math.floor(min / 2 ** this.minShift), leaves - 1);
+        while (bin > 0 && !loffsets.has(bin)) {
+            const parent = Math.floor((bin - 1) / 8);
+            bin = bin > parent * 8 + 1 ? bin - 1 : parent;
+        }
+        return loffsets.get(bin) ?? ZERO_OFFSET;
     }
-    // ...and so there is nothing to bound the far end of a query with either, so
+    // No linear index means nothing to forecast the far end of a query with, so
     // estimatedBytesForRegions keeps summing every chunk on a CSI-indexed file.
     getHighestChunk() {
         return undefined;

package/dist/csi.js.map

@@ -1 +1 @@
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+{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,2DAA6C;AAE7C,0DAA8B;AAC9B,+DAA0D;AAC1D,uCAKkB;AAClB,yDAA6D;AAK7D,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,MAAM,WAAW,GAAG,IAAI,gCAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;AAE3C,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,CAAC,IAAI,IAAI,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,IAAI,IAAI,CAAC,CAAA;AACpC,CAAC;AAUD,MAAqB,GAAI,SAAQ,sBAAoB;IAC3C,YAAY,GAAG,CAAC,CAAA;IACd,KAAK,GAAG,CAAC,CAAA;IACT,QAAQ,GAAG,CAAC,CAAA;IAEtB,uEAAuE;IACvE,iEAAiE;IACjE,KAAK,CAAC,QAAQ;QACZ,OAAO,EAAE,CAAA;IACX,CAAC;IAED,YAAY,CAAC,KAAiB,EAAE,MAAc;QAC5C,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAA;QACD,MAAM,WAAW,GAAG,QAAQ,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QACpD,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACnE,MAAM,MAAM,GAAG,CAAC,SAAS,EAAE,KAAK,EAAE,KAAK,CAAC,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QAC3D,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;QACrE,CAAC;QACD,MAAM,aAAa,GAAG;YACpB,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YACxC,KAAK,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YAC1C,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC;SAC1C,CAAA;QACD,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;QAChE,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,iBAAiB,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QAE9D,OAAO;YACL,aAAa;YACb,cAAc;YACd,SAAS;YACT,QAAQ;YACR,SAAS;YACT,MAAM;YACN,WAAW;YACX,GAAG,IAAA,wBAAc,EACf,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,EAC5D,IAAI,CAAC,YAAY,CAClB;SACF,CAAA;IACH,CAAC;IAED,4BAA4B;IAC5B,KAAK,CAAC,MAAM,CAAC,IAAc;QACzB,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QACnD,MAAM,KAAK,GAAG,MAAM,IAAA,uBAAK,EAAC,MAAM,CAAC,CAAA;QAEjC,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAA;QACD,yEAAyE;QACzE,sEAAsE;QACtE,MAAM,KAAK,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACzC,IAAI,KAAK,KAAK,UAAU,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;YACjD,oDAAoD;YACpD,MAAM,IAAI,KAAK,CAAC,kBAAkB,KAAK,EAAE,CAAC,CAAA;QAC5C,CAAC;QAED,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC1C,IAAI,CAAC,KAAK,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACvC,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QACnD,MAAM,YAAY,GAAG,IAAI,CAAC,YAAY,CAAA;QACtC,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAC7C,2EAA2E;QAC3E,yEAAyE;QACzE,2EAA2E;QAC3E,wEAAwE;QACxE,wEAAwE;QACxE,uEAAuE;QACvE,+DAA+D;QAC/D,EAAE;QACF,iEAAiE;QACjE,yEAAyE;QACzE,mEAAmE;QACnE,oEAAoE;QACpE,sEAAsE;QACtE,iEAAiE;QACjE,MAAM,GAAG,GAAG,SAAS,IAAI,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;QACtE,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,GAAG,SAAS,EAAE,IAAI,CAAC,CAAA;QAExD,mEAAmE;QACnE,+CAA+C;QAC/C,IAAI,IAAI,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;QAC7B,IAAI,aAAwC,CAAA;QAC5C,MAAM,OAAO,GAAG,EAAc,CAAA;QAC9B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;YAClC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAClB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,IAAI,CAAC,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC;oBAC5B,IAAI,IAAI,EAAE,GAAG,EAAE,CAAA;gBACjB,CAAC;qBAAM,CAAC;oBACN,oEAAoE;oBACpE,iEAAiE;oBACjE,oEAAoE;oBACpE,uCAAuC;oBACvC,aAAa,GAAG,IAAA,0BAAgB,EAAC,KAAK,EAAE,IAAI,EAAE,CAAC,EAAE,aAAa,CAAC,CAAA;oBAC/D,IAAI,IAAI,CAAC,CAAA,CAAC,UAAU;oBACpB,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;oBAChD,IAAI,IAAI,CAAC,GAAG,EAAE,GAAG,UAAU,CAAA;gBAC7B,CAAC;YACH,CAAC;QACH,CAAC;QAED,SAAS,UAAU,CAAC,KAAa;YAC/B,IAAI,IAAI,GAAG,OAAO,CAAC,KAAK,CAAC,CAAA;YACzB,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;gBACvB,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,oBAAoB;YACpB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,IAAI,CAAC,CAAA;YACT,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAC5C,MAAM,QAAQ,GAAG,IAAI,GAAG,EAAyB,CAAA;YACjD,IAAI,cAAc,CAAA;YAClB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,GAAG,YAAY,EAAE,CAAC;oBACvB,cAAc,GAAG,IAAA,wBAAc,EAAC,KAAK,EAAE,IAAI,GAAG,EAAE,CAAC,CAAA;oBACjD,IAAI,IAAI,EAAE,GAAG,EAAE,CAAA;gBACjB,CAAC;qBAAM,CAAC;oBACN,QAAQ,CAAC,GAAG,CAAC,GAAG,EAAE,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAA;oBACzC,IAAI,IAAI,CAAC,CAAA;oBACT,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;oBAChD,IAAI,IAAI,CAAC,CAAA;o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package/dist/indexFile.d.ts

@@ -19,6 +19,23 @@ export interface ParsedIndexBase<R extends RefIndex = RefIndex> {
     indices: (refId: number) => R | undefined;
 }
 export declare function memoizeByRefId<T>(getIndices: (refId: number) => T | undefined, maxSize?: number): (refId: number) => T | undefined;
+/**
+ * The virtual offset past which a coordinate-sorted file holds nothing
+ * overlapping `[.., end)`, from the binning index alone: htslib's `max_off`
+ * (`hts_itr_query` in hts.c).
+ *
+ * Walk right from the finest bin after the one holding `end - 1`, stepping up
+ * to the parent at every first child, so each bin visited begins at or past
+ * `end` and never overlaps the query. Every record in such a bin starts at or
+ * past `end`, so the first chunk of the first bin that exists is a record past
+ * the query, and in a sorted file so is every record after it.
+ *
+ * A bound, unlike the linear-index forecast in `chunksLikelyRead`: it rests on
+ * the same sort order `appendInRange` and the early stop already assume, and
+ * cannot drop a record they would keep. See ADR 0023 for why the caller drops
+ * whole merged chunks with it rather than trimming them.
+ */
+export declare function maxOffset(binIndex: Record<number, Chunk[]>, end: number, minShift: number, depth: number): import("./virtualOffset.ts").Offset | undefined;
 export default abstract class IndexFile<TParsed extends ParsedIndexBase = ParsedIndexBase> {
     filehandle: GenericFilehandle;
     renameRefSeq: (s: string) => string;
@@ -37,6 +54,8 @@ export default abstract class IndexFile<TParsed extends ParsedIndexBase = Parsed
         end: number;
         score: number;
     }[]>;
+    protected abstract minShift: number;
+    protected abstract depth: number;
     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;
@@ -87,7 +106,8 @@ export default abstract class IndexFile<TParsed extends ParsedIndexBase = Parsed
      * 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.
+     * number. The table predates `max_off` (ADR 0023), which now drops most of
+     * the gap between the first two columns from `blocksForRange` itself.
      *
      * Still summed over merged chunks rather than per region, so two regions
      * sharing a chunk are charged for it once.