@gmod/gbz-base 2.2.0 → 2.4.0

package/README.md

@@ -16,7 +16,7 @@ const db = await GBZBase.open(
   new RemoteFile('https://example.org/graph.gbz.db'),
 )
 
-// one record per haplotype fragment crossing the window
+// one record per haplotype crossing the window
 const alignments = await db.getAlignmentsForRange(
   'GRCh38#0#chr6',
   31500000,
@@ -45,13 +45,15 @@ also `snarls`; both resolve haplotype names when the database can. For
 alignments `haplotypes` is `all` or `distinct`, the two outputs that leave
 something to align against the reference.
 
-`context` is the graph context in bp to extend past the window, 100 by default,
-and it shapes the answer rather than padding it: a haplotype's walk ends where
-it leaves the subgraph, so at `context: 0` every bubble cuts a walk into pieces
-and the same window returns several times as many records as it does at 100.
-`limit` caps the subgraph at that many nodes, per fragment. `signal` is an
-`AbortSignal`; a query checks it between range requests, so an abort stops the
-next fetch rather than the one in flight.
+`context` is the graph context in bp to extend past the window, 100 by default.
+It does not decide how many records come back, since the pieces of a walk that
+leaves the subgraph are joined again (see below); it trades nodes read against
+pieces to identify and join. A window inside a snarl much larger than itself
+(MHC class II on the HPRC graph) is 1.1M pieces at `context: 0` and 464 walks at
+1000, three times faster; a window whose private stretches are short bubbles
+costs about the same either way. `limit` caps the subgraph at that many nodes,
+per fragment. `signal` is an `AbortSignal`; a query checks it between range
+requests, so an abort stops the next fetch rather than the one in flight.
 
 ### One returns records, the other a query object
 
@@ -83,7 +85,18 @@ for (const alignment of alignments) {
 }
 ```
 
-`refStart`/`refEnd` are the fragment's span on the reference path you queried.
+A record is one haplotype's passage through the window. Where a haplotype's walk
+leaves the subgraph and comes back (a bubble whose nodes the window does not
+hold, a private insertion), the pieces on either side are identified separately
+and then joined back into one record when they are the same haplotype's
+consecutive fragments, on the same strand and monotone on both the reference and
+the haplotype; the stretch between them becomes the record's insertion and
+deletion, scored the way the diverging stretches inside the window are. Pieces
+that fail those tests (an inversion between them, a tandem repeat mapping both
+to the same reference interval) stay separate records, as do fragments the index
+could not name.
+
+`refStart`/`refEnd` are the record's span on the reference path you queried.
 They run to node boundaries, so a record can begin before the window you asked
 for and end after it. `cigar` is its alignment to that reference, computed like
 upstream: a node-length-weighted LCS, with the diverging stretches scored using
@@ -145,7 +158,9 @@ gbz-base-query https://host/graph.gbz.db --contig chrM --offset 1000 --context 5
 ```
 
 `--stats` reports how many range requests a query made and how many bytes they
-carried.
+carried, and with `--resolve` or `--alignments` how identification went: index
+scans, chains per haplotype, why each chain ended, companion seeks against graph
+record lookups, and fragment lengths against the walk bound.
 
 ## Snarls
 
@@ -209,15 +224,26 @@ path in both orientations, with the path handle and the forward coordinate of
 that node, and `HaplotypeLengths` holds each path's length. The upstream `query`
 binary keeps working on the augmented database.
 
-At query time `subgraph.identifyPaths()` loads the samples for the window's node
-range in one index scan, chains each haplotype's fragments to the next through
-the private nodes between them, and walks at most one interval past the window
-for a chain that met no sample inside it. This is what fills in the `resolved`
-half of a feature: PanSN name, haplotype interval in that contig's coordinates,
-and the path handle. `getAlignmentsForRange` and `getSubgraphForRange` run it
-for you when the database has the tables; on the lower-level path you call it
-yourself before `alignments()` or `toSubgraphJson({ names: 'resolved' })`. On
-the command line, `--resolve` and `--alignments`.
+At query time `subgraph.identifyPaths()` loads the samples for the window's
+nodes with one index scan per run of consecutive node ids (a window whose nodes
+sit in far-apart id ranges, as a tandem repeat's do, is not one scan across the
+gap), chains each haplotype's fragments to the next through the private nodes
+between them, and for a chain that met no sample inside the window walks on
+until it finds one, up to four intervals past the last fragment it linked. This
+is what fills in the `resolved` half of a feature: PanSN name, haplotype
+interval in that contig's coordinates, and the path handle.
+`getAlignmentsForRange` and `getSubgraphForRange` run it for you when the
+database has the tables; on the lower-level path you call it yourself before
+`alignments()` or `toSubgraphJson({ names: 'resolved' })`. On the command line,
+`--resolve` and `--alignments`.
+
+A named walk in GFA or JSON output lists its steps in the haplotype's own
+direction, whichever twin of the walk the extraction kept, so `start..end` and
+the steps agree as the W line spec requires. `keepHaplotypes(name => ...)`
+narrows an identified subgraph to the reference walk and the walks whose PanSN
+name the predicate accepts, dropping every node only the other walks visited; on
+the command line `--keep SAMPLE` or `--keep SAMPLE#HAP` (repeatable). This is
+how a cut for a chosen set of haplotypes is written once and drawn as it is.
 
 The tests check every resolved fragment against an independent backward walk
 through the bidirectional GBWT to the path's recorded start position.

package/dist/cli.js

@@ -19,11 +19,21 @@ const USAGE = `Usage: gbz-base-query [options] graph.gbz.db
   --cigar              output CIGAR strings for the haplotypes
   --format FMT         json (default) or gfa
   --resolve            name haplotypes from the HaplotypeSamples table
-  --alignments         print one alignment record per haplotype fragment instead of the subgraph
+  --keep NAME          keep only the walks of this sample or sample#haplotype (may repeat; implies --resolve)
+  --alignments         print one alignment record per haplotype instead of the subgraph
   --haplotype-index F  companion database written by gbz-haplotype-index --output
   --block-size INT     bytes fetched per range request (default: 65536)
   --stats              print fetch statistics to stderr
 `;
+const HAPLOTYPE_OUTPUTS = [
+    'all',
+    'distinct',
+    'reference-only',
+    'none',
+];
+function isHaplotypeOutput(text) {
+    return HAPLOTYPE_OUTPUTS.some(output => output === text);
+}
 function parseHandle(text) {
     const orientation = text.endsWith('-') ? 'reverse' : 'forward';
     const digits = /[+-]$/.test(text) ? text.slice(0, -1) : text;
@@ -43,6 +53,7 @@ function parseArgs(argv) {
         cigar: false,
         format: 'json',
         resolve: false,
+        keep: [],
         alignments: false,
         blockSize: 65536,
         stats: false,
@@ -102,15 +113,24 @@ function parseArgs(argv) {
             case '--limit':
                 args.limit = Number(next(i++));
                 break;
-            case '--haplotypes':
-                args.haplotypes = next(i++);
+            case '--haplotypes': {
+                const output = next(i++);
+                if (!isHaplotypeOutput(output)) {
+                    throw new Error(`--haplotypes must be one of `);
+                }
+                args.haplotypes = output;
                 break;
+            }
             case '--cigar':
                 args.cigar = true;
                 break;
             case '--resolve':
                 args.resolve = true;
                 break;
+            case '--keep':
+                args.keep.push(next(i++));
+                args.resolve = true;
+                break;
             case '--alignments':
                 args.alignments = true;
                 args.resolve = true;
@@ -149,6 +169,36 @@ function parseArgs(argv) {
     }
     return args;
 }
+const CHAIN_ENDS = [
+    'in-fragment sample',
+    'identified sibling',
+    'out-of-window sample',
+    'bound',
+    'endmarker',
+    'cycle',
+];
+function identificationReport(stats) {
+    const { chains, fragmentLengths, interval, scans } = stats;
+    const resolved = chains.filter(c => c.pathHandle !== undefined);
+    const haplotypes = new Set(resolved.map(c => c.pathHandle)).size;
+    const unresolved = chains.filter(c => c.pathHandle === undefined);
+    const unresolvedFragments = unresolved.reduce((n, c) => n + c.fragments, 0);
+    const sum = (pick) => chains.reduce((n, c) => n + pick(c), 0);
+    const ends = CHAIN_ENDS.map(end => `${end} ${chains.filter(c => c.end === end).length}`).join(', ');
+    const bound = 4 * interval;
+    const overBound = fragmentLengths.filter(len => len > bound).length;
+    const maxLen = fragmentLengths.reduce((a, b) => Math.max(a, b), 0);
+    const scannedNodes = scans.reduce((n, [a, b]) => n + ((b - a) >> 1) + 1, 0);
+    const scanned = `${scans.length} index scans over ${scannedNodes} nodes for ${stats.windowSamples} samples`;
+    return [
+        `identification: interval ${interval}; ${scanned}`,
+        `  ${fragmentLengths.length} fragments in ${chains.length} chains for ${haplotypes} haplotypes (${resolved.length - haplotypes} chains beyond one per haplotype; ${unresolved.length} chains / ${unresolvedFragments} fragments unresolved)`,
+        `  chain ends: ${ends}`,
+        `  sibling links ${sum(c => c.fragments - 1)}; out-of-window steps ${sum(c => c.steps)}, ${sum(c => c.reentries)} re-entering the subgraph, ${sum(c => c.twinLandings)} on a discarded twin's start`,
+        `  companion seeks ${stats.companionSeeks} (${stats.companionMisses} misses); graph record lookups ${stats.graphLookups}, ${stats.graphFetches} fetched`,
+        `  fragment length max ${maxLen}, ${overBound} over the ${bound} bp bound`,
+    ].join('\n');
+}
 function alignmentRecord(alignment) {
     const { start, ...rest } = alignment;
     return rest.resolved ? { ...rest, name: rest.label, label: undefined } : rest;
@@ -188,6 +238,11 @@ export async function main(argv) {
     if (args.resolve) {
         await subgraph.identifyPaths();
     }
+    if (args.keep.length > 0) {
+        const wanted = args.keep.map(text => text.split('#'));
+        subgraph.keepHaplotypes(name => wanted.some(([sample, haplotype]) => sample === name.sample &&
+            (haplotype === undefined || Number(haplotype) === name.haplotype)));
+    }
     const names = args.resolve ? 'resolved' : 'anonymous';
     const output = args.alignments
         ? subgraph.alignments().map(alignmentRecord)
@@ -202,6 +257,9 @@ export async function main(argv) {
             : ` (haplotype index: ${db.index.pager.fetches} fetches, ${db.index.pager.bytesFetched} bytes)`;
         const { orderedAlignments, lcsAlignments, identificationSteps, identificationFetches, } = subgraph.stats;
         process.stderr.write(`Subgraph contains ${subgraph.nodeCount} nodes and ${subgraph.pathCount} paths; ${fetches} fetches, ${bytesFetched} bytes${index}; ${orderedAlignments} ordered + ${lcsAlignments} lcs alignments; identification ${identificationSteps} steps, ${identificationFetches} lookups\n`);
+        if (args.resolve) {
+            process.stderr.write(`${identificationReport(subgraph.stats.identification)}\n`);
+        }
     }
 }
 //# sourceMappingURL=cli.js.map

package/dist/cli.js.map

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package/dist/db.d.ts

@@ -63,6 +63,7 @@ export declare class GBZBase {
     static open(source: ByteSource, opts?: OpenOptions): Promise<GBZBase>;
     tags(): Promise<Map<string, string>>;
     tag(key: string): Promise<string | undefined>;
+    prefetchRecords(lo: number, hi: number): Promise<void>;
     getRecord(handle: number): Promise<GbzRecord | undefined>;
     paths(): Promise<GbzPath[]>;
     getPath(handle: number): Promise<GbzPath | undefined>;

package/dist/db.js

@@ -146,6 +146,9 @@ export class GBZBase {
     async tag(key) {
         return (await this.tags()).get(key);
     }
+    prefetchRecords(lo, hi) {
+        return this.sqlite.prefetchRows('Nodes', lo, hi);
+    }
     async getRecord(handle) {
         const row = await this.sqlite.byRowid('Nodes', handle);
         if (!row) {

package/dist/db.js.map

@@ -1 +1 @@
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package/dist/gbwt/node.d.ts

@@ -13,3 +13,4 @@ export declare function entryOrientation(side: NodeSide): Orientation;
 export declare function exitOrientation(side: NodeSide): Orientation;
 export declare function edgeIsCanonical(from: number, to: number): boolean;
 export declare function pathIsCanonical(path: number[]): boolean;
+export declare function pathEndsAreCanonical(first: number | undefined, last: number | undefined): boolean;

package/dist/gbwt/node.js

@@ -37,8 +37,9 @@ export function edgeIsCanonical(from, to) {
         : toId >= fromId;
 }
 export function pathIsCanonical(path) {
-    const first = path[0];
-    const last = path[path.length - 1];
+    return pathEndsAreCanonical(path[0], path[path.length - 1]);
+}
+export function pathEndsAreCanonical(first, last) {
     if (first === undefined || last === undefined) {
         return true;
     }

package/dist/gbwt/node.js.map

@@ -1 +1 @@
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+{"version":3,"file":"node.js","sourceRoot":"","sources":["../../src/gbwt/node.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,SAAS,GAAG,CAAC,CAAA;AAI1B,MAAM,UAAU,UAAU,CAAC,EAAU,EAAE,WAAwB;IAC7D,OAAO,CAAC,GAAG,EAAE,GAAG,CAAC,WAAW,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AACrD,CAAC;AAED,MAAM,UAAU,MAAM,CAAC,MAAc;IACnC,OAAO,IAAI,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;AAC/B,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,MAAc;IAC5C,OAAO,MAAM,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,CAAA;AACjD,CAAC;AAED,MAAM,UAAU,SAAS,CAAC,MAAc;IACtC,OAAO,MAAM,GAAG,CAAC,KAAK,CAAC,CAAA;AACzB,CAAC;AAED,MAAM,UAAU,QAAQ,CAAC,MAAc;IACrC,OAAO,MAAM,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAA;AACnD,CAAC;AAID,MAAM,UAAU,QAAQ,CAAC,IAAc;IACrC,OAAO,IAAI,KAAK,MAAM,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAA;AAC3C,CAAC;AAED,MAAM,UAAU,SAAS,CAAC,WAAwB;IAChD,OAAO,WAAW,KAAK,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,OAAO,CAAA;AACrD,CAAC;AAED,MAAM,UAAU,QAAQ,CAAC,WAAwB;IAC/C,OAAO,WAAW,KAAK,SAAS,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAA;AACrD,CAAC;AAED,MAAM,UAAU,gBAAgB,CAAC,IAAc;IAC7C,OAAO,IAAI,KAAK,MAAM,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,CAAA;AAChD,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,IAAc;IAC5C,OAAO,IAAI,KAAK,OAAO,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,CAAA;AACjD,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,IAAY,EAAE,EAAU;IACtD,MAAM,MAAM,GAAG,MAAM,CAAC,IAAI,CAAC,CAAA;IAC3B,MAAM,IAAI,GAAG,MAAM,CAAC,EAAE,CAAC,CAAA;IACvB,OAAO,SAAS,CAAC,IAAI,CAAC;QACpB,CAAC,CAAC,IAAI,GAAG,MAAM,IAAI,CAAC,IAAI,KAAK,MAAM,IAAI,CAAC,SAAS,CAAC,EAAE,CAAC,CAAC;QACtD,CAAC,CAAC,IAAI,IAAI,MAAM,CAAA;AACpB,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,IAAc;IAC5C,OAAO,oBAAoB,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAA;AAC7D,CAAC;AAED,MAAM,UAAU,oBAAoB,CAClC,KAAyB,EACzB,IAAwB;IAExB,IAAI,KAAK,KAAK,SAAS,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;QAC9C,OAAO,IAAI,CAAA;IACb,CAAC;IACD,OAAO,SAAS,CAAC,KAAK,CAAC,KAAK,SAAS,CAAC,IAAI,CAAC;QACzC,CAAC,CAAC,CAAC,SAAS,CAAC,KAAK,CAAC;QACnB,CAAC,CAAC,eAAe,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;AAClC,CAAC"}

package/dist/index.d.ts

@@ -4,8 +4,8 @@ export { GENERIC_SAMPLE, formatPathName, parsePathName } from './pathName.ts';
 export type { PathName, PathQuery, PathRef } from './pathName.ts';
 export type { ByteSource } from './filehandle.ts';
 export type { Pos } from './gbwt/record.ts';
-export { Subgraph } from './subgraph.ts';
-export type { AlignmentSpan, HaplotypeAlignment, HaplotypeOutput, PathIdentity, PathPosition, ReferencePath, SnarlOutput, SubgraphJson, SubgraphOptions, SubgraphOutputOptions, SubgraphPath, } from './subgraph.ts';
+export { Subgraph, SubgraphLimitError } from './subgraph.ts';
+export type { AlignmentSpan, ChainEnd, ChainRecord, HaplotypeAlignment, HaplotypeOutput, IdentificationStats, PathIdentity, PathPosition, ReferencePath, SnarlOutput, SubgraphJson, SubgraphOptions, SubgraphOutputOptions, SubgraphPath, } from './subgraph.ts';
 export { subgraphAroundNodes, subgraphAtOffset, subgraphBetween, subgraphInInterval, } from './query.ts';
 export type { QueryOptions } from './query.ts';
 export { SqliteDatabase } from './sqlite/database.ts';

package/dist/index.js

@@ -1,6 +1,6 @@
 export { GBZBase, GbzRecord, SCHEMA_VERSION, SchemaVersionError } from "./db.js";
 export { GENERIC_SAMPLE, formatPathName, parsePathName } from "./pathName.js";
-export { Subgraph } from "./subgraph.js";
+export { Subgraph, SubgraphLimitError } from "./subgraph.js";
 export { subgraphAroundNodes, subgraphAtOffset, subgraphBetween, subgraphInInterval, } from "./query.js";
 export { SqliteDatabase } from "./sqlite/database.js";
 export { weightedLcs } from "./lcs.js";

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,SAAS,EAAE,cAAc,EAAE,kBAAkB,EAAE,MAAM,SAAS,CAAA;AAQhF,OAAO,EAAE,cAAc,EAAE,cAAc,EAAE,aAAa,EAAE,MAAM,eAAe,CAAA;AAI7E,OAAO,EAAE,QAAQ,EAAE,kBAAkB,EAAE,MAAM,eAAe,CAAA;AAiB5D,OAAO,EACL,mBAAmB,EACnB,gBAAgB,EAChB,eAAe,EACf,kBAAkB,GACnB,MAAM,YAAY,CAAA;AAEnB,OAAO,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAA;AAErD,OAAO,EAAE,WAAW,EAAE,MAAM,UAAU,CAAA;AACtC,OAAO,KAAK,KAAK,MAAM,gBAAgB,CAAA"}

package/dist/query.js

@@ -1,5 +1,5 @@
 import { pathNameFor } from "./pathName.js";
-import { Subgraph } from "./subgraph.js";
+import { Subgraph, SubgraphLimitError } from "./subgraph.js";
 export async function subgraphAtOffset(db, query, offset, opts = {}) {
     const subgraph = new Subgraph(db, opts);
     const reference = await subgraph.pathPosition(pathNameFor(query, offset));
@@ -10,10 +10,21 @@ export async function subgraphAtOffset(db, query, offset, opts = {}) {
 }
 export async function subgraphInInterval(db, query, start, end, opts = {}) {
     const subgraph = new Subgraph(db, opts);
-    const reference = await subgraph.pathPosition(pathNameFor(query, start));
-    await subgraph.aroundInterval(reference.position, end - start, opts.context ?? 100);
-    await subgraph.extractSnarls(opts.snarls ?? 'none');
-    subgraph.extractPaths(reference, opts.haplotypes ?? 'all');
+    try {
+        const reference = await subgraph.pathPosition(pathNameFor(query, start));
+        await subgraph.prefetchReferenceWalk(reference, end - start);
+        await subgraph.aroundInterval(reference.position, end - start, opts.context ?? 100);
+        await subgraph.extractSnarls(opts.snarls ?? 'none');
+        subgraph.extractPaths(reference, opts.haplotypes ?? 'all');
+    }
+    catch (error) {
+        throw error instanceof SubgraphLimitError && error.windowBp === undefined
+            ? new SubgraphLimitError(error.limit, {
+                windowBp: end - start,
+                walkedBp: subgraph.referenceWalkedBp ?? 0,
+            })
+            : error;
+    }
     return subgraph;
 }
 export async function subgraphAroundNodes(db, nodes, opts = {}) {

package/dist/query.js.map

@@ -1 +1 @@
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+{"version":3,"file":"query.js","sourceRoot":"","sources":["../src/query.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,eAAe,CAAA;AAC3C,OAAO,EAAE,QAAQ,EAAE,kBAAkB,EAAE,MAAM,eAAe,CAAA;AAgB5D,MAAM,CAAC,KAAK,UAAU,gBAAgB,CACpC,EAAW,EACX,KAAgB,EAChB,MAAc,EACd,OAAqB,EAAE;IAEvB,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;IACvC,MAAM,SAAS,GAAG,MAAM,QAAQ,CAAC,YAAY,CAAC,WAAW,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC,CAAA;IACzE,MAAM,QAAQ,CAAC,cAAc,CAC3B,SAAS,CAAC,QAAQ,CAAC,MAAM,EACzB,SAAS,CAAC,QAAQ,CAAC,UAAU,EAC7B,IAAI,CAAC,OAAO,IAAI,GAAG,CACpB,CAAA;IACD,MAAM,QAAQ,CAAC,aAAa,CAAC,IAAI,CAAC,MAAM,IAAI,MAAM,CAAC,CAAA;IACnD,QAAQ,CAAC,YAAY,CAAC,SAAS,EAAE,IAAI,CAAC,UAAU,IAAI,KAAK,CAAC,CAAA;IAC1D,OAAO,QAAQ,CAAA;AACjB,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,kBAAkB,CACtC,EAAW,EACX,KAAgB,EAChB,KAAa,EACb,GAAW,EACX,OAAqB,EAAE;IAEvB,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;IACvC,IAAI,CAAC;QACH,MAAM,SAAS,GAAG,MAAM,QAAQ,CAAC,YAAY,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC,CAAA;QACxE,MAAM,QAAQ,CAAC,qBAAqB,CAAC,SAAS,EAAE,GAAG,GAAG,KAAK,CAAC,CAAA;QAC5D,MAAM,QAAQ,CAAC,cAAc,CAC3B,SAAS,CAAC,QAAQ,EAClB,GAAG,GAAG,KAAK,EACX,IAAI,CAAC,OAAO,IAAI,GAAG,CACpB,CAAA;QACD,MAAM,QAAQ,CAAC,aAAa,CAAC,IAAI,CAAC,MAAM,IAAI,MAAM,CAAC,CAAA;QACnD,QAAQ,CAAC,YAAY,CAAC,SAAS,EAAE,IAAI,CAAC,UAAU,IAAI,KAAK,CAAC,CAAA;IAC5D,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,MAAM,KAAK,YAAY,kBAAkB,IAAI,KAAK,CAAC,QAAQ,KAAK,SAAS;YACvE,CAAC,CAAC,IAAI,kBAAkB,CAAC,KAAK,CAAC,KAAK,EAAE;gBAClC,QAAQ,EAAE,GAAG,GAAG,KAAK;gBACrB,QAAQ,EAAE,QAAQ,CAAC,iBAAiB,IAAI,CAAC;aAC1C,CAAC;YACJ,CAAC,CAAC,KAAK,CAAA;IACX,CAAC;IACD,OAAO,QAAQ,CAAA;AACjB,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,mBAAmB,CACvC,EAAW,EACX,KAAe,EACf,OAAqB,EAAE;IAEvB,MAAM,UAAU,GAAG,IAAI,CAAC,UAAU,IAAI,KAAK,CAAA;IAC3C,MAAM,MAAM,GAAG,IAAI,CAAC,MAAM,IAAI,MAAM,CAAA;IACpC,IAAI,UAAU,KAAK,gBAAgB,EAAE,CAAC;QACpC,MAAM,IAAI,KAAK,CAAC,sDAAsD,CAAC,CAAA;IACzE,CAAC;IACD,IAAI,MAAM,KAAK,aAAa,IAAI,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACjD,MAAM,IAAI,KAAK,CACb,mFAAmF,CACpF,CAAA;IACH,CAAC;IACD,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;IACvC,MAAM,QAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,IAAI,CAAC,OAAO,IAAI,GAAG,CAAC,CAAA;IACtD,MAAM,QAAQ,CAAC,aAAa,CAAC,MAAM,CAAC,CAAA;IACpC,QAAQ,CAAC,YAAY,CAAC,SAAS,EAAE,UAAU,CAAC,CAAA;IAC5C,OAAO,QAAQ,CAAA;AACjB,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,eAAe,CACnC,EAAW,EACX,KAAa,EACb,GAAW,EACX,OAA8D,EAAE;IAEhE,MAAM,UAAU,GAAG,IAAI,CAAC,UAAU,IAAI,KAAK,CAAA;IAC3C,IAAI,UAAU,KAAK,gBAAgB,EAAE,CAAC;QACpC,MAAM,IAAI,KAAK,CAAC,sDAAsD,CAAC,CAAA;IACzE,CAAC;IACD,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;IACvC,MAAM,QAAQ,CAAC,YAAY,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;IACvC,QAAQ,CAAC,YAAY,CAAC,SAAS,EAAE,UAAU,CAAC,CAAA;IAC5C,OAAO,QAAQ,CAAA;AACjB,CAAC"}

package/dist/sqlite/btree.d.ts

@@ -4,10 +4,14 @@ export declare class BTree {
     private readonly usable;
     private pager;
     private decodedIndexPages;
+    private tableDepths;
     constructor(pager: Pager, reservedBytes: number);
     private localPayloadSize;
     private payload;
     private pageAt;
+    private tableDepth;
+    private childIndexFor;
+    prefetchRowidRange(root: number, lo: number, hi: number): Promise<void>;
     tableRowid(root: number, rowid: number): Promise<SqlValue[] | undefined>;
     tableScan(root: number): AsyncGenerator<{
         rowid: number;

package/dist/sqlite/btree.js

@@ -32,10 +32,12 @@ function cellOffset(page, header, index) {
     return readUint16(page, header.cellPointers + 2 * index);
 }
 const MAX_DECODED_INDEX_PAGES = 4096;
+const PREFETCH_PAGE_LIMIT = 4096;
 export class BTree {
     usable;
     pager;
     decodedIndexPages = new Map();
+    tableDepths = new Map();
     constructor(pager, reservedBytes) {
         this.pager = pager;
         this.usable = pager.pageSize - reservedBytes;
@@ -77,6 +79,70 @@ export class BTree {
         const page = await this.pager.page(pageNumber);
         return { page, header: readHeader(page, pageNumber === 1 ? 100 : 0) };
     }
+    tableDepth(root, towards) {
+        let depth = this.tableDepths.get(root);
+        if (!depth) {
+            depth = (async () => {
+                let pageNumber = root;
+                for (let level = 0;; level++) {
+                    const { page, header } = await this.pageAt(pageNumber);
+                    if (header.type === LEAF_TABLE) {
+                        return level;
+                    }
+                    if (header.type !== INTERIOR_TABLE) {
+                        throw new Error('SQLite table b-tree contains an index page');
+                    }
+                    const child = this.childIndexFor(page, header, towards);
+                    pageNumber =
+                        child === header.cellCount
+                            ? header.rightChild
+                            : readUint32(page, cellOffset(page, header, child));
+                }
+            })();
+            this.tableDepths.set(root, depth);
+            depth.catch(() => this.tableDepths.delete(root));
+        }
+        return depth;
+    }
+    childIndexFor(page, header, rowid) {
+        let low = 0;
+        let high = header.cellCount;
+        while (low < high) {
+            const mid = (low + high) >> 1;
+            const [key] = readVarint(page, cellOffset(page, header, mid) + 4);
+            if (key < rowid) {
+                low = mid + 1;
+            }
+            else {
+                high = mid;
+            }
+        }
+        return low;
+    }
+    async prefetchRowidRange(root, lo, hi) {
+        const leafLevel = await this.tableDepth(root, lo);
+        let pages = [root];
+        for (let level = 0; level < leafLevel; level++) {
+            const decoded = await Promise.all(pages.map(n => this.pageAt(n)));
+            const children = [];
+            decoded.forEach(({ page, header }, i) => {
+                const from = i === 0 ? this.childIndexFor(page, header, lo) : 0;
+                const to = i === decoded.length - 1
+                    ? this.childIndexFor(page, header, hi)
+                    : header.cellCount;
+                for (let c = from; c <= to; c++) {
+                    children.push(c === header.cellCount
+                        ? header.rightChild
+                        : readUint32(page, cellOffset(page, header, c)));
+                }
+            });
+            if (children.length > PREFETCH_PAGE_LIMIT) {
+                return;
+            }
+            this.pager.prefetch(children);
+            pages = children;
+        }
+    }
     async tableRowid(root, rowid) {
         let pageNumber = root;
         for (;;) {

package/dist/sqlite/btree.js.map

@@ -1 +1 @@
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