@gmod/gbz-base 1.0.0 → 1.1.0

package/dist/graphName.js

@@ -0,0 +1,83 @@
+function parseRelationships(field, what) {
+    const relationships = new Map();
+    if (field !== undefined) {
+        for (const rel of field.split(';')) {
+            const parts = rel.split(',');
+            const [from, to] = parts;
+            if (parts.length !== 2 || !from || !to) {
+                throw new Error(`Invalid ${what} relationship: ${rel}`);
+            }
+            let targets = relationships.get(from);
+            if (!targets) {
+                targets = new Set();
+                relationships.set(from, targets);
+            }
+            targets.add(to);
+        }
+    }
+    return relationships;
+}
+export function graphNameFromTags(tags) {
+    return {
+        name: tags.get('pggname'),
+        subgraph: parseRelationships(tags.get('subgraph'), 'subgraph'),
+        translation: parseRelationships(tags.get('translation'), 'translation'),
+    };
+}
+function merge(into, from) {
+    for (const [key, values] of from) {
+        let targets = into.get(key);
+        if (!targets) {
+            targets = new Set();
+            into.set(key, targets);
+        }
+        for (const value of values) {
+            targets.add(value);
+        }
+    }
+}
+export function subgraphName(name, parent) {
+    const result = {
+        name,
+        subgraph: new Map(),
+        translation: new Map(),
+    };
+    if (parent.name !== undefined) {
+        result.subgraph.set(name, new Set([parent.name]));
+        merge(result.subgraph, parent.subgraph);
+        merge(result.translation, parent.translation);
+    }
+    return result;
+}
+function sortedEntries(relationships) {
+    return [...relationships.entries()]
+        .sort(([a], [b]) => (a < b ? -1 : a > b ? 1 : 0))
+        .flatMap(([from, tos]) => [...tos].sort().map(to => [from, to]));
+}
+export function gfaHeaderLines(graphName) {
+    const lines = [];
+    if (graphName.name !== undefined) {
+        lines.push(`H\tNM:Z:${graphName.name}`);
+    }
+    for (const [subgraph, supergraph] of sortedEntries(graphName.subgraph)) {
+        lines.push(`H\tSG:Z:${subgraph},${supergraph}`);
+    }
+    for (const [from, to] of sortedEntries(graphName.translation)) {
+        lines.push(`H\tTL:Z:${from},${to}`);
+    }
+    return lines;
+}
+export async function sha256Hex(chunks) {
+    const total = chunks.reduce((sum, chunk) => sum + chunk.length, 0);
+    const bytes = new Uint8Array(total);
+    let offset = 0;
+    for (const chunk of chunks) {
+        bytes.set(chunk, offset);
+        offset += chunk.length;
+    }
+    const digest = await globalThis.crypto.subtle.digest('SHA-256', bytes);
+    return [...new Uint8Array(digest)]
+        .map(byte => byte.toString(16).padStart(2, '0'))
+        .join('');
+}
+//# sourceMappingURL=graphName.js.map

package/dist/graphName.js.map

@@ -0,0 +1 @@
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package/dist/index.d.ts

@@ -1,11 +1,12 @@
 export { GBZBase, GENERIC_SAMPLE, GbzRecord, SCHEMA_VERSION, SchemaVersionError, formatPathName, } from './db.ts';
-export type { GbzPath, HaplotypeSample, PathName } from './db.ts';
+export type { GbzPath, HaplotypeSample, OpenOptions, PathName } from './db.ts';
 export type { ByteSource } from './filehandle.ts';
 export type { Pos } from './gbwt/record.ts';
 export { Subgraph } from './subgraph.ts';
-export type { HaplotypeAlignment, HaplotypeOutput, PathIdentity, PathPosition, ReferencePath, SubgraphJson, SubgraphPath, ToJsonOptions, } from './subgraph.ts';
-export { subgraphAroundNodes, subgraphAtOffset, subgraphInInterval, } from './query.ts';
+export type { HaplotypeAlignment, HaplotypeOutput, PathIdentity, PathPosition, ReferencePath, SnarlOutput, SubgraphJson, SubgraphPath, ToJsonOptions, } from './subgraph.ts';
+export { subgraphAroundNodes, subgraphAtOffset, subgraphBetween, subgraphInInterval, } from './query.ts';
 export type { PathQuery, QueryOptions } from './query.ts';
 export { SqliteDatabase } from './sqlite/database.ts';
+export type { GraphName } from './graphName.ts';
 export { weightedLcs } from './lcs.ts';
 export * as nodes from './gbwt/node.ts';

package/dist/index.js

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

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,OAAO,EACP,cAAc,EACd,SAAS,EACT,cAAc,EACd,kBAAkB,EAClB,cAAc,GACf,MAAM,SAAS,CAAA;AAIhB,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAWxC,OAAO,EACL,mBAAmB,EACnB,gBAAgB,EAChB,kBAAkB,GACnB,MAAM,YAAY,CAAA;AAEnB,OAAO,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAA;AACrD,OAAO,EAAE,WAAW,EAAE,MAAM,UAAU,CAAA;AACtC,OAAO,KAAK,KAAK,MAAM,gBAAgB,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,OAAO,EACP,cAAc,EACd,SAAS,EACT,cAAc,EACd,kBAAkB,EAClB,cAAc,GACf,MAAM,SAAS,CAAA;AAIhB,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAYxC,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.d.ts

@@ -1,9 +1,10 @@
 import { Subgraph } from './subgraph.ts';
 import type { GBZBase } from './db.ts';
-import type { HaplotypeOutput } from './subgraph.ts';
+import type { HaplotypeOutput, SnarlOutput } from './subgraph.ts';
 export interface QueryOptions {
     context?: number;
     haplotypes?: HaplotypeOutput;
+    snarls?: SnarlOutput;
     limit?: number;
 }
 export interface PathQuery {
@@ -14,3 +15,4 @@ export interface PathQuery {
 export declare function subgraphAtOffset(db: GBZBase, query: PathQuery, offset: number, opts?: QueryOptions): Promise<Subgraph>;
 export declare function subgraphInInterval(db: GBZBase, query: PathQuery, start: number, end: number, opts?: QueryOptions): Promise<Subgraph>;
 export declare function subgraphAroundNodes(db: GBZBase, nodes: number[], opts?: QueryOptions): Promise<Subgraph>;
+export declare function subgraphBetween(db: GBZBase, start: number, end: number, opts?: Pick<QueryOptions, 'haplotypes' | 'limit'>): Promise<Subgraph>;

package/dist/query.js

@@ -13,6 +13,7 @@ export async function subgraphAtOffset(db, query, offset, opts = {}) {
     subgraph.limit = opts.limit;
     const reference = await subgraph.pathPosition(pathName(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;
 }
@@ -21,17 +22,34 @@ export async function subgraphInInterval(db, query, start, end, opts = {}) {
     subgraph.limit = opts.limit;
     const reference = await subgraph.pathPosition(pathName(query, start));
     await subgraph.aroundInterval(reference.position, end - start, opts.context ?? 100);
+    await subgraph.extractSnarls(opts.snarls ?? 'none');
     subgraph.extractPaths(reference, opts.haplotypes ?? 'all');
     return subgraph;
 }
 export async function subgraphAroundNodes(db, nodes, opts = {}) {
     const haplotypes = opts.haplotypes ?? 'all';
+    const snarls = opts.snarls ?? 'none';
     if (haplotypes === 'reference-only') {
         throw new Error('Cannot output a reference path in a node-based query');
     }
+    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;
     await subgraph.aroundNodes(nodes, opts.context ?? 100);
+    await subgraph.extractSnarls(snarls);
+    subgraph.extractPaths(undefined, haplotypes);
+    return subgraph;
+}
+export async function subgraphBetween(db, start, end, opts = {}) {
+    const haplotypes = opts.haplotypes ?? 'all';
+    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;
+    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,cAAc,EAAE,MAAM,SAAS,CAAA;AACxC,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAkBxC,SAAS,QAAQ,CAAC,KAAgB,EAAE,QAAgB;IAClD,OAAO;QACL,MAAM,EAAE,KAAK,CAAC,MAAM,IAAI,cAAc;QACtC,MAAM,EAAE,KAAK,CAAC,MAAM;QACpB,SAAS,EAAE,KAAK,CAAC,SAAS,IAAI,CAAC;QAC/B,QAAQ;KACT,CAAA;AACH,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,gBAAgB,CACpC,EAAW,EACX,KAAgB,EAChB,MAAc,EACd,OAAqB,EAAE;IAEvB,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,EAAE,CAAC,CAAA;IACjC,QAAQ,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,CAAA;IAC3B,MAAM,SAAS,GAAG,MAAM,QAAQ,CAAC,YAAY,CAAC,QAAQ,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC,CAAA;IACtE,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,CAAC,CAAA;IACjC,QAAQ,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,CAAA;IAC3B,MAAM,SAAS,GAAG,MAAM,QAAQ,CAAC,YAAY,CAAC,QAAQ,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC,CAAA;IACrE,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,CAAC,CAAA;IACjC,QAAQ,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,CAAA;IAC3B,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,OAAmD,EAAE;IAErD,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,CAAC,CAAA;IACjC,QAAQ,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,CAAA;IAC3B,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.js

@@ -132,10 +132,15 @@ export class BTree {
             }
         }
         else {
+            const children = [];
             for (let i = 0; i < header.cellCount; i++) {
-                yield* this.tableScan(readUint32(page, cellOffset(page, header, i)));
+                children.push(readUint32(page, cellOffset(page, header, i)));
+            }
+            children.push(header.rightChild);
+            this.pager.prefetch(children);
+            for (const child of children) {
+                yield* this.tableScan(child);
             }
-            yield* this.tableScan(header.rightChild);
         }
     }
     async indexCell(page, header, index) {

package/dist/sqlite/btree.js.map

@@ -1 +1 @@
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package/dist/sqlite/pager.d.ts

@@ -13,7 +13,12 @@ export declare class Pager {
     readonly pageSize: number;
     private fileSize;
     constructor(source: ByteSource, pageSize: number, fileSize: number, opts?: PagerOptions);
+    private read;
     seed(index: number, bytes: Uint8Array): void;
     private block;
+    prefetch(pageNumbers: number[]): void;
+    private fetchRun;
+    private forgetOnFailure;
+    private evict;
     page(pageNumber: number): Promise<Uint8Array<ArrayBufferLike>>;
 }

package/dist/sqlite/pager.js

@@ -15,6 +15,23 @@ export class Pager {
         this.blockSize = Math.max(pageSize, Math.ceil(requested / pageSize) * pageSize);
         this.maxBlocks = opts.maxBlocks ?? 256;
     }
+    async read(length, start) {
+        let attempt = 0;
+        for (;;) {
+            try {
+                const bytes = await this.source.read(length, start);
+                this.bytesFetched += bytes.length;
+                return bytes;
+            }
+            catch (error) {
+                attempt += 1;
+                if (attempt >= 3) {
+                    throw error;
+                }
+                await new Promise(resolve => setTimeout(resolve, 200 * attempt));
+            }
+        }
+    }
     seed(index, bytes) {
         if (bytes.length ===
             Math.min(this.blockSize, this.fileSize - index * this.blockSize)) {
@@ -30,19 +47,59 @@ export class Pager {
         }
         const start = index * this.blockSize;
         const length = Math.min(this.blockSize, this.fileSize - start);
-        const pending = this.source.read(length, start).then(bytes => {
-            this.bytesFetched += bytes.length;
-            return bytes;
-        });
+        const pending = this.read(length, start);
         this.fetches += 1;
         this.blocks.set(index, pending);
-        if (this.blocks.size > this.maxBlocks) {
+        this.forgetOnFailure(pending, [index]);
+        this.evict();
+        return pending;
+    }
+    prefetch(pageNumbers) {
+        const wanted = [
+            ...new Set(pageNumbers.map(pageNumber => Math.floor(((pageNumber - 1) * this.pageSize) / this.blockSize))),
+        ]
+            .filter(index => !this.blocks.has(index))
+            .sort((a, b) => a - b);
+        let runStart = 0;
+        while (runStart < wanted.length) {
+            let runEnd = runStart + 1;
+            while (runEnd < wanted.length &&
+                wanted[runEnd] === wanted[runEnd - 1] + 1) {
+                runEnd += 1;
+            }
+            this.fetchRun(wanted[runStart], runEnd - runStart);
+            runStart = runEnd;
+        }
+    }
+    fetchRun(firstIndex, count) {
+        const start = firstIndex * this.blockSize;
+        const length = Math.min(count * this.blockSize, this.fileSize - start);
+        const pending = this.read(length, start);
+        this.fetches += 1;
+        const indexes = [];
+        for (let i = 0; i < count; i++) {
+            const within = i * this.blockSize;
+            indexes.push(firstIndex + i);
+            this.blocks.set(firstIndex + i, pending.then(bytes => bytes.subarray(within, within + this.blockSize)));
+        }
+        this.forgetOnFailure(pending, indexes);
+        this.evict();
+    }
+    forgetOnFailure(pending, indexes) {
+        pending.catch(() => {
+            for (const index of indexes) {
+                this.blocks.delete(index);
+            }
+        });
+    }
+    evict() {
+        while (this.blocks.size > this.maxBlocks) {
             const oldest = this.blocks.keys().next().value;
-            if (oldest !== undefined) {
-                this.blocks.delete(oldest);
+            if (oldest === undefined) {
+                break;
             }
+            this.blocks.delete(oldest);
         }
-        return pending;
     }
     async page(pageNumber) {
         const offset = (pageNumber - 1) * this.pageSize;

package/dist/sqlite/pager.js.map

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

@@ -2,6 +2,7 @@ import type { GBZBase, PathName } from './db.ts';
 import type { Orientation } from './gbwt/node.ts';
 import type { Pos } from './gbwt/record.ts';
 export type HaplotypeOutput = 'all' | 'distinct' | 'reference-only' | 'none';
+export type SnarlOutput = 'none' | 'contained' | 'overlapping';
 export interface PathPosition {
     seqOffset: number;
     handle: number;
@@ -105,6 +106,12 @@ export declare class Subgraph {
         removed: number;
     }>;
     private insertContext;
+    betweenNodes(start: number, end: number): Promise<number>;
+    extractSnarls(snarls: SnarlOutput): Promise<number>;
+    private overlappingSnarls;
+    private isSnarlEntryInSubgraph;
+    private recordReader;
+    private findCoveringSnarl;
     extractPaths(reference: ReferencePath | undefined, output: HaplotypeOutput): void;
     private distinctPaths;
     identifyPaths(): Promise<void>;
@@ -118,5 +125,8 @@ export declare class Subgraph {
     private edits;
     alignToRef(pathIndex: number): string | undefined;
     alignments(): HaplotypeAlignment[];
+    private canonicalEdges;
+    stableName(): Promise<string>;
+    toGFA(cigar: boolean, opts?: ToJsonOptions): Promise<string>;
     toJSON(cigar: boolean, opts?: ToJsonOptions): SubgraphJson;
 }