@gmod/gbz-base 1.1.0 → 2.0.0

package/dist/query.js

@@ -1,26 +1,16 @@
-import { GENERIC_SAMPLE } from "./db.js";
+import { pathNameFor } from "./pathName.js";
 import { Subgraph } from "./subgraph.js";
-function pathName(query, fragment) {
-    return {
-        sample: query.sample ?? GENERIC_SAMPLE,
-        contig: query.contig,
-        haplotype: query.haplotype ?? 0,
-        fragment,
-    };
-}
 export async function subgraphAtOffset(db, query, offset, opts = {}) {
-    const subgraph = new Subgraph(db);
-    subgraph.limit = opts.limit;
-    const reference = await subgraph.pathPosition(pathName(query, offset));
+    const subgraph = new Subgraph(db, opts);
+    const reference = await subgraph.pathPosition(pathNameFor(query, offset));
     await subgraph.aroundPosition(reference.position.handle, reference.position.nodeOffset, opts.context ?? 100);
     await subgraph.extractSnarls(opts.snarls ?? 'none');
     subgraph.extractPaths(reference, opts.haplotypes ?? 'all');
     return subgraph;
 }
 export async function subgraphInInterval(db, query, start, end, opts = {}) {
-    const subgraph = new Subgraph(db);
-    subgraph.limit = opts.limit;
-    const reference = await subgraph.pathPosition(pathName(query, start));
+    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');
@@ -35,8 +25,7 @@ export async function subgraphAroundNodes(db, nodes, opts = {}) {
     if (snarls === 'overlapping' && nodes.length > 1) {
         throw new Error('Overlapping snarls cannot be extracted for a node-based query with multiple nodes');
     }
-    const subgraph = new Subgraph(db);
-    subgraph.limit = opts.limit;
+    const subgraph = new Subgraph(db, opts);
     await subgraph.aroundNodes(nodes, opts.context ?? 100);
     await subgraph.extractSnarls(snarls);
     subgraph.extractPaths(undefined, haplotypes);
@@ -47,8 +36,7 @@ export async function subgraphBetween(db, start, end, opts = {}) {
     if (haplotypes === 'reference-only') {
         throw new Error('Cannot output a reference path in a node-based query');
     }
-    const subgraph = new Subgraph(db);
-    subgraph.limit = opts.limit;
+    const subgraph = new Subgraph(db, opts);
     await subgraph.betweenNodes(start, end);
     subgraph.extractPaths(undefined, haplotypes);
     return subgraph;

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,MAAM,eAAe,CAAA;AAgBxC,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,MAAM,SAAS,GAAG,MAAM,QAAQ,CAAC,YAAY,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC,CAAA;IACxE,MAAM,QAAQ,CAAC,cAAc,CAC3B,SAAS,CAAC,QAAQ,EAClB,GAAG,GAAG,KAAK,EACX,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,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

@@ -3,6 +3,7 @@ import type { SqlValue } from './record.ts';
 export declare class BTree {
     private readonly usable;
     private pager;
+    private decodedIndexPages;
     constructor(pager: Pager, reservedBytes: number);
     private localPayloadSize;
     private payload;
@@ -12,6 +13,7 @@ export declare class BTree {
         rowid: number;
         values: SqlValue[];
     }>;
+    private decodedCells;
     private indexCell;
     indexScanFrom(root: number, low: number[]): AsyncGenerator<SqlValue[]>;
     indexSeekLE(root: number, key: number[]): Promise<SqlValue[] | undefined>;

package/dist/sqlite/btree.js

@@ -3,8 +3,16 @@ const INTERIOR_INDEX = 0x02;
 const INTERIOR_TABLE = 0x05;
 const LEAF_INDEX = 0x0a;
 const LEAF_TABLE = 0x0d;
+function readUint16(page, offset) {
+    return page[offset] * 256 + page[offset + 1];
+}
+function readUint32(page, offset) {
+    return (page[offset] * 16777216 +
+        page[offset + 1] * 65536 +
+        page[offset + 2] * 256 +
+        page[offset + 3]);
+}
 function readHeader(page, start) {
-    const view = new DataView(page.buffer, page.byteOffset, page.byteLength);
     const type = page[start];
     if (type !== INTERIOR_INDEX &&
         type !== INTERIOR_TABLE &&
@@ -15,22 +23,19 @@ function readHeader(page, start) {
     const interior = type === INTERIOR_INDEX || type === INTERIOR_TABLE;
     return {
         type,
-        cellCount: view.getUint16(start + 3),
-        rightChild: interior ? view.getUint32(start + 8) : 0,
+        cellCount: readUint16(page, start + 3),
+        rightChild: interior ? readUint32(page, start + 8) : 0,
         cellPointers: start + (interior ? 12 : 8),
     };
 }
 function cellOffset(page, header, index) {
-    const view = new DataView(page.buffer, page.byteOffset, page.byteLength);
-    return view.getUint16(header.cellPointers + 2 * index);
-}
-function readUint32(page, offset) {
-    const view = new DataView(page.buffer, page.byteOffset, page.byteLength);
-    return view.getUint32(offset);
+    return readUint16(page, header.cellPointers + 2 * index);
 }
+const MAX_DECODED_INDEX_PAGES = 4096;
 export class BTree {
     usable;
     pager;
+    decodedIndexPages = new Map();
     constructor(pager, reservedBytes) {
         this.pager = pager;
         this.usable = pager.pageSize - reservedBytes;
@@ -143,12 +148,37 @@ export class BTree {
             }
         }
     }
-    async indexCell(page, header, index) {
-        const offset = cellOffset(page, header, index);
-        const interior = header.type === INTERIOR_INDEX;
-        const [size, afterSize] = readVarint(page, interior ? offset + 4 : offset);
-        const values = decodeRecord(await this.payload(page, afterSize, size, true));
-        return { values, leftChild: interior ? readUint32(page, offset) : 0 };
+    decodedCells(pageNumber, header) {
+        let cells = this.decodedIndexPages.get(pageNumber);
+        if (cells) {
+            this.decodedIndexPages.delete(pageNumber);
+        }
+        else {
+            cells = new Array(header.cellCount);
+            if (this.decodedIndexPages.size >= MAX_DECODED_INDEX_PAGES) {
+                const oldest = this.decodedIndexPages.keys().next().value;
+                if (oldest !== undefined) {
+                    this.decodedIndexPages.delete(oldest);
+                }
+            }
+        }
+        this.decodedIndexPages.set(pageNumber, cells);
+        return cells;
+    }
+    async indexCell(pageNumber, page, header, index) {
+        const cells = this.decodedCells(pageNumber, header);
+        let cell = cells[index];
+        if (!cell) {
+            const offset = cellOffset(page, header, index);
+            const interior = header.type === INTERIOR_INDEX;
+            const [size, afterSize] = readVarint(page, interior ? offset + 4 : offset);
+            cell = {
+                values: decodeRecord(await this.payload(page, afterSize, size, true)),
+                leftChild: interior ? readUint32(page, offset) : 0,
+            };
+            cells[index] = cell;
+        }
+        return cell;
     }
     async *indexScanFrom(root, low) {
         const { page, header } = await this.pageAt(root);
@@ -156,7 +186,7 @@ export class BTree {
         let high = header.cellCount;
         while (first < high) {
             const mid = (first + high) >> 1;
-            const cell = await this.indexCell(page, header, mid);
+            const cell = await this.indexCell(root, page, header, mid);
             if (compareKey(cell.values, low) < 0) {
                 first = mid + 1;
             }
@@ -165,7 +195,7 @@ export class BTree {
             }
         }
         for (let i = first; i < header.cellCount; i++) {
-            const cell = await this.indexCell(page, header, i);
+            const cell = await this.indexCell(root, page, header, i);
             if (header.type === INTERIOR_INDEX) {
                 yield* this.indexScanFrom(cell.leftChild, low);
             }
@@ -185,7 +215,7 @@ export class BTree {
             let child = 0;
             while (low < high) {
                 const mid = (low + high) >> 1;
-                const cell = await this.indexCell(page, header, mid);
+                const cell = await this.indexCell(pageNumber, page, header, mid);
                 if (compareKey(cell.values, key) <= 0) {
                     best = cell.values;
                     low = mid + 1;

package/dist/sqlite/btree.js.map

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

@@ -1,6 +1,7 @@
-import type { GBZBase, PathName } from './db.ts';
+import type { GBZBase } from './db.ts';
 import type { Orientation } from './gbwt/node.ts';
 import type { Pos } from './gbwt/record.ts';
+import type { PathName } from './pathName.ts';
 export type HaplotypeOutput = 'all' | 'distinct' | 'reference-only' | 'none';
 export type SnarlOutput = 'none' | 'contained' | 'overlapping';
 export interface PathPosition {
@@ -43,12 +44,8 @@ export interface SubgraphJson {
     }[];
     paths: SubgraphPath[];
 }
-export interface HaplotypeAlignment {
-    pathHandle: number | undefined;
-    name: PathName | undefined;
+export interface AlignmentSpan {
     strand: '+' | '-';
-    hapStart: number | undefined;
-    hapEnd: number | undefined;
     refStart: number;
     refEnd: number;
     cigar: string;
@@ -56,8 +53,23 @@ export interface HaplotypeAlignment {
     path: number[];
     start: Pos;
 }
-export interface ToJsonOptions {
-    names?: 'anonymous' | 'resolved';
+export type HaplotypeAlignment = AlignmentSpan & ({
+    resolved: true;
+    name: PathName;
+    label: string;
+    pathHandle: number;
+    hapStart: number;
+    hapEnd: number;
+} | {
+    resolved: false;
+});
+export interface SubgraphOutputOptions {
+    cigar?: boolean | undefined;
+    names?: 'anonymous' | 'resolved' | undefined;
+}
+export interface SubgraphOptions {
+    limit?: number | undefined;
+    signal?: AbortSignal | undefined;
 }
 export declare class Subgraph {
     private records;
@@ -68,7 +80,6 @@ export declare class Subgraph {
     private refInterval;
     private refIndexCache;
     private refPrefixCache;
-    limit: number | undefined;
     readonly stats: {
         orderedAlignments: number;
         lcsAlignments: number;
@@ -76,7 +87,9 @@ export declare class Subgraph {
         identificationFetches: number;
     };
     private db;
-    constructor(db: GBZBase);
+    private readonly limit;
+    private readonly signal;
+    constructor(db: GBZBase, opts?: SubgraphOptions);
     get nodeCount(): number;
     get pathCount(): number;
     get referenceInterval(): {
@@ -127,6 +140,6 @@ export declare class Subgraph {
     alignments(): HaplotypeAlignment[];
     private canonicalEdges;
     stableName(): Promise<string>;
-    toGFA(cigar: boolean, opts?: ToJsonOptions): Promise<string>;
-    toJSON(cigar: boolean, opts?: ToJsonOptions): SubgraphJson;
+    toGFA(opts?: SubgraphOutputOptions): Promise<string>;
+    toSubgraphJson(opts?: SubgraphOutputOptions): SubgraphJson;
 }

package/dist/subgraph.js

@@ -1,7 +1,7 @@
-import { formatPathName } from "./db.js";
 import { ENDMARKER, edgeIsCanonical, encodeNode, entryOrientation, entrySide, exitOrientation, exitSide, flipNode, flipSide, isReverse, nodeId, nodeOrientation, pathIsCanonical, } from "./gbwt/node.js";
 import { gfaHeaderLines, sha256Hex, subgraphName } from "./graphName.js";
 import { weightedLcs } from "./lcs.js";
+import { formatPathName } from "./pathName.js";
 function sideBefore(a, b) {
     return (a[0] < b[0] ||
         (a[0] === b[0] && (a[1] < b[1] || (a[1] === b[1] && a[2] < b[2]))));
@@ -67,7 +67,6 @@ export class Subgraph {
     refInterval;
     refIndexCache;
     refPrefixCache;
-    limit;
     stats = {
         orderedAlignments: 0,
         lcsAlignments: 0,
@@ -75,8 +74,12 @@ export class Subgraph {
         identificationFetches: 0,
     };
     db;
-    constructor(db) {
+    limit;
+    signal;
+    constructor(db, opts = {}) {
         this.db = db;
+        this.limit = opts.limit;
+        this.signal = opts.signal;
     }
     get nodeCount() {
         return this.records.size / 2;
@@ -110,6 +113,7 @@ export class Subgraph {
         return [...this.records.keys()].sort((a, b) => a - b);
     }
     async addNode(id) {
+        this.signal?.throwIfAborted();
         if (this.limit !== undefined && this.nodeCount >= this.limit) {
             throw new Error(`Subgraph size limit of ${this.limit} nodes exceeded`);
         }
@@ -608,6 +612,7 @@ export class Subgraph {
             let current = start;
             let pos;
             while (anchor === undefined) {
+                this.signal?.throwIfAborted();
                 if (current !== undefined) {
                     if (visited.has(current)) {
                         break;
@@ -886,23 +891,16 @@ export class Subgraph {
                 last -= 1;
             }
             const identity = info.identity;
-            const strand = info.path.some(handle => isReverse(handle)) &&
+            const walkStrand = info.path.some(handle => isReverse(handle)) &&
                 !info.path.some(handle => !isReverse(handle))
                 ? '-'
                 : '+';
-            result.push({
-                pathHandle: identity?.pathHandle,
-                name: identity?.name,
+            const span = {
                 strand: identity
                     ? identity.orientation === 'forward'
                         ? '+'
                         : '-'
-                    : strand,
-                hapStart: identity
-                    ? identity.name.fragment + identity.hapStart
-                    : undefined,
-                hapEnd: identity ? identity.name.fragment + identity.hapEnd : undefined,
-                start: info.positions[0],
+                    : walkStrand,
                 refStart: reference.start + leading,
                 refEnd: reference.start + refTotal - trailing,
                 cigar: edits
@@ -911,7 +909,24 @@ export class Subgraph {
                     .join(''),
                 weight: info.weight,
                 path: info.path,
-            });
+                start: info.positions[0],
+            };
+            if (identity) {
+                const hapStart = identity.name.fragment + identity.hapStart;
+                const hapEnd = identity.name.fragment + identity.hapEnd;
+                result.push({
+                    ...span,
+                    resolved: true,
+                    name: identity.name,
+                    label: formatPathName({ ...identity.name, fragment: hapStart }, hapEnd),
+                    pathHandle: identity.pathHandle,
+                    hapStart,
+                    hapEnd,
+                });
+            }
+            else {
+                result.push({ ...span, resolved: false });
+            }
         });
         return result;
     }
@@ -950,7 +965,8 @@ export class Subgraph {
         }
         return sha256Hex(chunks);
     }
-    async toGFA(cigar, opts = {}) {
+    async toGFA(opts = {}) {
+        const cigar = opts.cigar ?? false;
         const lines = [
             this.refPath ? `H\tVN:Z:1.1\tRS:Z:${this.refPath.sample}` : 'H\tVN:Z:1.1',
             ...gfaHeaderLines(subgraphName(await this.stableName(), await this.db.graphName())),
@@ -1000,7 +1016,8 @@ export class Subgraph {
         });
         return `${lines.join('\n')}\n`;
     }
-    toJSON(cigar, opts = {}) {
+    toSubgraphJson(opts = {}) {
+        const cigar = opts.cigar ?? false;
         const handles = this.sortedHandles();
         const nodes = handles
             .filter(handle => !isReverse(handle))