@gmod/gbz-base 1.0.0 → 2.0.0

package/dist/db.js

@@ -1,8 +1,10 @@
 import { ENDMARKER, nodeId, nodeOrientation } from "./gbwt/node.js";
 import { GbwtRecord, decompressEdges } from "./gbwt/record.js";
 import { decodeSequence, encodedSequenceLength } from "./gbwt/sequence.js";
+import { graphNameFromTags } from "./graphName.js";
+import { formatPathName, pathNameFor, toPathQuery } from "./pathName.js";
+import { subgraphInInterval } from "./query.js";
 import { SqliteDatabase } from "./sqlite/database.js";
-export const GENERIC_SAMPLE = '_gbwt_ref';
 export const SCHEMA_VERSION = 'GBZ-base version 4';
 export class SchemaVersionError extends Error {
     name = 'SchemaVersionError';
@@ -14,9 +16,6 @@ export class SchemaVersionError extends Error {
         this.found = found;
     }
 }
-export function formatPathName(name, end) {
-    return `${name.sample}#${name.haplotype}#${name.contig}[${name.fragment}-${end}]`;
-}
 export class GbzRecord {
     sequenceLen;
     handle;
@@ -91,33 +90,52 @@ function rowToPath(rowid, values) {
         isIndexed: num(values[9], 'Paths.is_indexed') !== 0,
     };
 }
+async function readTags(sqlite) {
+    const tags = new Map();
+    for await (const { values } of sqlite.scan('Tags')) {
+        tags.set(str(values[0], 'Tags.key'), str(values[1], 'Tags.value'));
+    }
+    return tags;
+}
 export class GBZBase {
     tagCache;
     pathCache;
+    indexTags;
     sqlite;
-    constructor(sqlite) {
+    index;
+    constructor(sqlite, index) {
         this.sqlite = sqlite;
+        this.index = index;
     }
     static async open(source, opts = {}) {
-        const sqlite = await SqliteDatabase.open(source, opts);
+        const { haplotypeIndex, ...pagerOptions } = opts;
+        const sqlite = await SqliteDatabase.open(source, pagerOptions);
         for (const table of ['Tags', 'Nodes', 'Paths', 'ReferenceIndex']) {
             sqlite.rootPage(table);
         }
-        const db = new GBZBase(sqlite);
+        const index = haplotypeIndex
+            ? await SqliteDatabase.open(haplotypeIndex, pagerOptions)
+            : sqlite;
+        const db = new GBZBase(sqlite, index);
         const version = await db.tag('version');
         if (version !== SCHEMA_VERSION) {
             throw new SchemaVersionError(version);
         }
+        if (haplotypeIndex) {
+            for (const table of ['Tags', 'HaplotypeSamples', 'HaplotypeLengths']) {
+                index.rootPage(table);
+            }
+            db.indexTags = await readTags(index);
+            const indexed = db.indexTags.get('haplotype_index_paths');
+            const paths = await db.tag('paths');
+            if (indexed !== paths) {
+                throw new Error(`haplotype index was built for ${indexed ?? 'an unknown number of'} paths but the graph has ${paths}`);
+            }
+        }
         return db;
     }
     tags() {
-        this.tagCache ??= (async () => {
-            const tags = new Map();
-            for await (const { values } of this.sqlite.scan('Tags')) {
-                tags.set(str(values[0], 'Tags.key'), str(values[1], 'Tags.value'));
-            }
-            return tags;
-        })();
+        this.tagCache ??= readTags(this.sqlite);
         return this.tagCache;
     }
     async tag(key) {
@@ -155,11 +173,130 @@ export class GBZBase {
     async pathsForSample(sample) {
         return (await this.paths()).filter(p => p.name.sample === sample);
     }
+    async pathsNamed(ref) {
+        const name = pathNameFor(toPathQuery(ref), 0);
+        return (await this.paths())
+            .filter(p => p.name.sample === name.sample &&
+            p.name.contig === name.contig &&
+            p.name.haplotype === name.haplotype)
+            .sort((a, b) => a.name.fragment - b.name.fragment);
+    }
+    async hasPath(ref) {
+        return (await this.pathsNamed(ref)).length > 0;
+    }
+    pathLengths = new Map();
+    pathLength(handle) {
+        let length = this.pathLengths.get(handle);
+        if (!length) {
+            length = this.walkPathLength(handle);
+            this.pathLengths.set(handle, length);
+            length.catch(() => this.pathLengths.delete(handle));
+        }
+        return length;
+    }
+    async walkPathLength(handle) {
+        const indexed = this.hasHaplotypeIndex
+            ? await this.haplotypeLength(handle)
+            : undefined;
+        if (indexed === undefined) {
+            const last = await this.indexedPosition(handle, Number.MAX_SAFE_INTEGER);
+            if (!last) {
+                const path = await this.getPath(handle);
+                throw new Error(`Path ${path ? formatPathName(path.name, path.name.fragment) : handle} has not been indexed for random access`);
+            }
+            let length = last.pathOffset;
+            let pos = last.pos;
+            for (;;) {
+                const record = await this.getRecord(pos.node);
+                if (!record) {
+                    throw new Error(`Node ${pos.node} does not exist in the graph`);
+                }
+                length += record.sequenceLen;
+                const next = record.gbwt().lf(pos.offset);
+                if (!next || next.node === ENDMARKER) {
+                    return length;
+                }
+                pos = next;
+            }
+        }
+        return indexed;
+    }
+    async pathFragmentsForRange(ref, start, end) {
+        if (end <= start) {
+            return [];
+        }
+        const ordered = await this.pathsNamed(ref);
+        const covering = ordered.filter(p => p.name.fragment <= start).slice(-1);
+        const within = ordered.filter(p => p.name.fragment > start && p.name.fragment < end);
+        const fragments = await Promise.all([...covering, ...within].map(async (path) => ({
+            path,
+            start: path.name.fragment,
+            end: path.name.fragment + (await this.pathLength(path.handle)),
+        })));
+        return fragments.filter(f => start < f.end);
+    }
+    async subgraphForFragment(fragment, start, end, opts) {
+        const lo = Math.max(start, fragment.start);
+        const hi = Math.min(end, fragment.end);
+        let subgraph;
+        if (hi > lo) {
+            const { sample, contig, haplotype } = fragment.path.name;
+            subgraph = await subgraphInInterval(this, { sample, contig, haplotype }, lo, hi, opts);
+            const haplotypes = opts.haplotypes ?? 'all';
+            const named = haplotypes === 'all' || haplotypes === 'distinct';
+            if (this.hasHaplotypeIndex && named) {
+                await subgraph.identifyPaths();
+            }
+        }
+        return subgraph;
+    }
+    async getSubgraphForRange(ref, start, end, opts = {}) {
+        const [fragment] = await this.pathFragmentsForRange(ref, start, end);
+        return fragment
+            ? this.subgraphForFragment(fragment, start, end, opts)
+            : undefined;
+    }
+    async getAlignmentsForRange(ref, start, end, opts = {}) {
+        const result = [];
+        for (const fragment of await this.pathFragmentsForRange(ref, start, end)) {
+            const subgraph = await this.subgraphForFragment(fragment, start, end, opts);
+            if (subgraph) {
+                result.push(...subgraph.alignments());
+            }
+        }
+        return result;
+    }
+    async graphName() {
+        const gbzTags = new Map();
+        for (const [key, value] of await this.tags()) {
+            if (key.startsWith('gbz_')) {
+                gbzTags.set(key.slice('gbz_'.length), value);
+            }
+        }
+        let name = {
+            name: undefined,
+            subgraph: new Map(),
+            translation: new Map(),
+        };
+        try {
+            name = graphNameFromTags(gbzTags);
+        }
+        catch {
+            // upstream falls back to an empty name when the tags do not parse
+        }
+        return name;
+    }
+    async hasChainLinks() {
+        const links = await this.tag('chain_links');
+        return links !== undefined && Number(links) > 0;
+    }
     get hasHaplotypeIndex() {
-        return (this.sqlite.has('HaplotypeSamples') && this.sqlite.has('HaplotypeLengths'));
+        return (this.index.has('HaplotypeSamples') && this.index.has('HaplotypeLengths'));
     }
     async haplotypeSampleInterval() {
-        const value = await this.tag('haplotype_index_interval');
+        const value = this.indexTags
+            ? this.indexTags.get('haplotype_index_interval')
+            : await this.tag('haplotype_index_interval');
         return value === undefined ? undefined : Number(value);
     }
     sampleFromRow(values) {
@@ -175,7 +312,7 @@ export class GBZBase {
     }
     async haplotypeSamplesInRange(minHandle, maxHandle) {
         const samples = [];
-        for await (const key of this.sqlite.indexScanFrom('HaplotypeSamples', [
+        for await (const key of this.index.indexScanFrom('HaplotypeSamples', [
             minHandle,
             0,
         ])) {
@@ -183,7 +320,7 @@ export class GBZBase {
             if (node > maxHandle) {
                 break;
             }
-            const row = await this.sqlite.byRowid('HaplotypeSamples', num(key[2], 'HaplotypeSamples rowid'));
+            const row = await this.index.byRowid('HaplotypeSamples', num(key[2], 'HaplotypeSamples rowid'));
             if (row) {
                 samples.push(this.sampleFromRow(row));
             }
@@ -191,18 +328,15 @@ export class GBZBase {
         return samples;
     }
     async haplotypeSampleAt(node, offset) {
-        const key = await this.sqlite.indexSeekLE('HaplotypeSamples', [
-            node,
-            offset,
-        ]);
+        const key = await this.index.indexSeekLE('HaplotypeSamples', [node, offset]);
         if (key?.[0] !== node || key[1] !== offset) {
             return undefined;
         }
-        const row = await this.sqlite.byRowid('HaplotypeSamples', num(key[2], 'HaplotypeSamples rowid'));
+        const row = await this.index.byRowid('HaplotypeSamples', num(key[2], 'HaplotypeSamples rowid'));
         return row ? this.sampleFromRow(row) : undefined;
     }
     async haplotypeLength(pathHandle) {
-        const row = await this.sqlite.byRowid('HaplotypeLengths', pathHandle);
+        const row = await this.index.byRowid('HaplotypeLengths', pathHandle);
         return row ? num(row[1], 'HaplotypeLengths.length') : undefined;
     }
     async indexedPosition(pathHandle, pathOffset) {

package/dist/db.js.map

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package/dist/gbwt/record.d.ts

@@ -14,5 +14,9 @@ export declare class GbwtRecord {
     private edgeTo;
     offsetTo(pos: Pos): number | undefined;
     predecessorAt(i: number): number | undefined;
+    decompressArrays(): {
+        nodes: Int32Array<ArrayBuffer>;
+        offsets: Int32Array<ArrayBuffer>;
+    };
     decompress(): Pos[];
 }

package/dist/gbwt/record.js

@@ -123,6 +123,28 @@ export class GbwtRecord {
         }
         return undefined;
     }
+    decompressArrays() {
+        const offsets = this.edges.map(e => e.offset);
+        let total = 0;
+        for (const run of this.runs()) {
+            total += run.len;
+        }
+        const nodes = new Int32Array(total);
+        const nextOffsets = new Int32Array(total);
+        let i = 0;
+        for (const run of this.runs()) {
+            const edge = this.edge(run.value);
+            let offset = offsets[run.value];
+            for (let k = 0; k < run.len; k++) {
+                nodes[i] = edge.node;
+                nextOffsets[i] = offset;
+                offset += 1;
+                i += 1;
+            }
+            offsets[run.value] = offset;
+        }
+        return { nodes, offsets: nextOffsets };
+    }
     decompress() {
         const offsets = this.edges.map(e => e.offset);
         const result = [];

package/dist/gbwt/record.js.map

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

@@ -0,0 +1,9 @@
+export interface GraphName {
+    name: string | undefined;
+    subgraph: Map<string, Set<string>>;
+    translation: Map<string, Set<string>>;
+}
+export declare function graphNameFromTags(tags: Map<string, string>): GraphName;
+export declare function subgraphName(name: string, parent: GraphName): GraphName;
+export declare function gfaHeaderLines(graphName: GraphName): string[];
+export declare function sha256Hex(chunks: Uint8Array[]): Promise<string>;

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 +1,14 @@
-export { GBZBase, GENERIC_SAMPLE, GbzRecord, SCHEMA_VERSION, SchemaVersionError, formatPathName, } from './db.ts';
-export type { GbzPath, HaplotypeSample, PathName } from './db.ts';
+export { GBZBase, GbzRecord, SCHEMA_VERSION, SchemaVersionError } from './db.ts';
+export type { GbzPath, HaplotypeSample, OpenOptions, PathFragment, } from './db.ts';
+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 { HaplotypeAlignment, HaplotypeOutput, PathIdentity, PathPosition, ReferencePath, SubgraphJson, SubgraphPath, ToJsonOptions, } from './subgraph.ts';
-export { subgraphAroundNodes, subgraphAtOffset, subgraphInInterval, } from './query.ts';
-export type { PathQuery, QueryOptions } from './query.ts';
+export type { AlignmentSpan, HaplotypeAlignment, HaplotypeOutput, 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';
+export type { GraphName } from './graphName.ts';
 export { weightedLcs } from './lcs.ts';
 export * as nodes from './gbwt/node.ts';

package/dist/index.js

@@ -1,6 +1,7 @@
-export { GBZBase, GENERIC_SAMPLE, GbzRecord, SCHEMA_VERSION, SchemaVersionError, formatPathName, } from "./db.js";
+export { GBZBase, GbzRecord, SCHEMA_VERSION, SchemaVersionError } from "./db.js";
+export { GENERIC_SAMPLE, formatPathName, parsePathName } from "./pathName.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 @@
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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;AAOhF,OAAO,EAAE,cAAc,EAAE,cAAc,EAAE,aAAa,EAAE,MAAM,eAAe,CAAA;AAI7E,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAcxC,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/pathName.d.ts

@@ -0,0 +1,17 @@
+export interface PathName {
+    sample: string;
+    contig: string;
+    haplotype: number;
+    fragment: number;
+}
+export interface PathQuery {
+    sample?: string;
+    contig: string;
+    haplotype?: number;
+}
+export type PathRef = string | PathQuery;
+export declare const GENERIC_SAMPLE = "_gbwt_ref";
+export declare function formatPathName(name: PathName, end: number): string;
+export declare function parsePathName(name: string): PathQuery;
+export declare function toPathQuery(ref: PathRef): PathQuery;
+export declare function pathNameFor(query: PathQuery, fragment: number): PathName;

package/dist/pathName.js

@@ -0,0 +1,33 @@
+export const GENERIC_SAMPLE = '_gbwt_ref';
+export function formatPathName(name, end) {
+    return `${name.sample}#${name.haplotype}#${name.contig}[${name.fragment}-${end}]`;
+}
+const PAN_SN = /^([^#]+)#(\d+)#([^#]+?)(?:\[\d+-\d+\])?$/;
+const BARE_CONTIG = /^([^#]+?)(?:\[\d+-\d+\])?$/;
+export function parsePathName(name) {
+    const panSn = PAN_SN.exec(name);
+    if (panSn) {
+        return {
+            sample: panSn[1],
+            haplotype: Number(panSn[2]),
+            contig: panSn[3],
+        };
+    }
+    const bare = BARE_CONTIG.exec(name);
+    if (bare) {
+        return { contig: bare[1] };
+    }
+    throw new Error(`"${name}" is not a path name; expected "sample#haplotype#contig" or a bare contig`);
+}
+export function toPathQuery(ref) {
+    return typeof ref === 'string' ? parsePathName(ref) : ref;
+}
+export function pathNameFor(query, fragment) {
+    return {
+        sample: query.sample ?? GENERIC_SAMPLE,
+        contig: query.contig,
+        haplotype: query.haplotype ?? 0,
+        fragment,
+    };
+}
+//# sourceMappingURL=pathName.js.map

package/dist/pathName.js.map

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

@@ -1,16 +1,16 @@
 import { Subgraph } from './subgraph.ts';
 import type { GBZBase } from './db.ts';
-import type { HaplotypeOutput } from './subgraph.ts';
+import type { PathQuery } from './pathName.ts';
+import type { HaplotypeOutput, SnarlOutput } from './subgraph.ts';
+export type { PathQuery } from './pathName.ts';
 export interface QueryOptions {
-    context?: number;
-    haplotypes?: HaplotypeOutput;
-    limit?: number;
-}
-export interface PathQuery {
-    sample?: string;
-    contig: string;
-    haplotype?: number;
+    context?: number | undefined;
+    haplotypes?: HaplotypeOutput | undefined;
+    snarls?: SnarlOutput | undefined;
+    limit?: number | undefined;
+    signal?: AbortSignal | undefined;
 }
 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' | 'signal'>): Promise<Subgraph>;