@gmod/gbz-base 0.0.1 → 1.1.0

package/README.md

@@ -50,6 +50,27 @@ 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.
 
+## Snarls
+
+A `.gbz.db` built by upstream `gbz-base construct` stores the top-level chains
+of the snarl decomposition as `next` links on the boundary node records (the
+`chains` and `chain_links` tags say how many). The query functions take a
+`snarls` option that uses them the way upstream's `--snarls` and
+`--extend-snarls` do:
+
+- `contained` adds every top-level snarl whose two boundary nodes are both in
+  the subgraph. With `context: 0` an interval query returns only the reference
+  walk, and this is what brings the variation back without a bp radius.
+- `overlapping` also follows a boundary node whose partner lies outside the
+  subgraph, and, when the subgraph holds no chain link at all, walks out to the
+  snarl containing it. The subgraph must be connected, so a node query may give
+  only one node. A snarl can be far larger than the window (a large deletion, a
+  centromere), so set `limit` when using this mode.
+
+`subgraphBetween(db, start, end)` is upstream's `--between`: everything between
+two oriented boundary handles of one chain, with no context. On the command line
+these are `--snarls`, `--extend-snarls` and `--between 129+:160+`.
+
 ## Naming haplotypes
 
 Upstream gbz-base cannot say which haplotype a subgraph path belongs to, so it
@@ -62,9 +83,29 @@ cd tools/haplotype-index && cargo build --release
 ./target/release/gbz-haplotype-index --interval 4096 --from-db graph.gbz.db
 ```
 
-The second form walks the paths through the database's own node records, so
-a database whose GBZ is no longer at hand can still be augmented; the two
-forms write identical tables.
+The second form walks the paths through the database's own node records, so a
+database whose GBZ is no longer at hand can still be augmented; the two forms
+write identical tables. Walking a GBZ uses every core (`--threads`).
+
+With `--output index.db` the tool writes the same tables into a standalone
+companion database instead, and the reader opens the two side by side:
+
+```
+./target/release/gbz-haplotype-index --interval 16384 --output graph.haplotype-index.db graph.gbz
+gbz-base-query https://host/graph.gbz.db --haplotype-index https://host/graph.haplotype-index.db ...
+```
+
+```ts
+const db = await GBZBase.open(new RemoteFile(graphUrl), {
+  haplotypeIndex: new RemoteFile(indexUrl),
+})
+```
+
+This is how a database someone else publishes gets haplotype names without
+anyone rehosting it: HPRC publishes `hprc-v2.1-mc-grch38.gbz.db` (10 GB) beside
+its graphs, and the companion for it is built from the 5 GB GBZ. The companion
+records the graph's path count and the reader refuses one built for a different
+graph.
 
 `HaplotypeSamples` holds one GBWT position every `--interval` bp along every
 path in both orientations, with the path handle and the forward coordinate of
@@ -92,7 +133,7 @@ The test suite requires this library's output to be deep equal to every one of
 them, CIGAR strings included. `generate.sh` regenerates the oracle with an
 upstream binary.
 
-Not ported: snarl extension (`--snarls`, `--between`), GFA output, GAF-base.
+Not ported: GAF-base.
 
 CIGARs are computed by matching each shared node to its earliest usable
 occurrence on the reference walk, which is weight-optimal whenever every shared

package/bin/query.js

@@ -2,6 +2,8 @@
 import { main } from '../dist/cli.js'
 
 main(process.argv.slice(2)).catch(error => {
-  process.stderr.write(`${error instanceof Error ? error.message : String(error)}\n`)
+  process.stderr.write(
+    `${error instanceof Error ? error.message : String(error)}\n`,
+  )
   process.exit(1)
 })

package/dist/cli.js

@@ -1,6 +1,7 @@
 import { LocalFile, RemoteFile } from 'generic-filehandle2';
 import { GBZBase, formatPathName } from "./db.js";
-import { subgraphAroundNodes, subgraphAtOffset, subgraphInInterval } from "./query.js";
+import { encodeNode } from "./gbwt/node.js";
+import { subgraphAroundNodes, subgraphAtOffset, subgraphBetween, subgraphInInterval, } from "./query.js";
 const USAGE = `Usage: gbz-base-query [options] graph.gbz.db
 
   --sample STR         sample name (default: generic path)
@@ -9,23 +10,38 @@ const USAGE = `Usage: gbz-base-query [options] graph.gbz.db
   -o, --offset INT     sequence offset
   -i, --interval A..B  half-open sequence interval
   -n, --node INT       node identifier (may repeat)
+  -b, --between A:B    subgraph between two chain boundary handles, each INT[+-]
   --context INT        context length in bp (default: 100)
+  --snarls             extend the subgraph with contained top-level snarls
+  --extend-snarls      extend the subgraph with overlapping top-level snarls
   --limit INT          safety limit for the number of nodes
   --haplotypes SEL     all, distinct, reference-only or none (default: all)
   --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
+  --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
 `;
+function parseHandle(text) {
+    const orientation = text.endsWith('-') ? 'reverse' : 'forward';
+    const digits = /[+-]$/.test(text) ? text.slice(0, -1) : text;
+    if (!/^\d+$/.test(digits)) {
+        throw new Error(`Failed to parse oriented node ${text}`);
+    }
+    return encodeNode(Number(digits), orientation);
+}
 function parseArgs(argv) {
     const args = {
         file: '',
         haplotype: 0,
         nodes: [],
         context: 100,
+        snarls: 'none',
         haplotypes: 'all',
         cigar: false,
+        format: 'json',
         resolve: false,
         alignments: false,
         blockSize: 65536,
@@ -64,9 +80,25 @@ function parseArgs(argv) {
             case '--node':
                 args.nodes.push(Number(next(i++)));
                 break;
+            case '-b':
+            case '--between': {
+                const [a, b, extra] = next(i++).split(':');
+                if (a === undefined || b === undefined || extra !== undefined) {
+                    throw new Error(`--between needs two oriented nodes, like 14+:17-`);
+                }
+                args.between = [parseHandle(a), parseHandle(b)];
+                break;
+            }
             case '--context':
                 args.context = Number(next(i++));
                 break;
+            case '--snarls':
+                args.snarls =
+                    args.snarls === 'overlapping' ? 'overlapping' : 'contained';
+                break;
+            case '--extend-snarls':
+                args.snarls = 'overlapping';
+                break;
             case '--limit':
                 args.limit = Number(next(i++));
                 break;
@@ -86,12 +118,20 @@ function parseArgs(argv) {
             case '--block-size':
                 args.blockSize = Number(next(i++));
                 break;
+            case '--haplotype-index':
+                args.haplotypeIndex = next(i++);
+                break;
             case '--stats':
                 args.stats = true;
                 break;
-            case '--format':
-                next(i++);
+            case '--format': {
+                const format = next(i++);
+                if (format !== 'json' && format !== 'gfa') {
+                    throw new Error(`Unknown output format ${format}`);
+                }
+                args.format = format;
                 break;
+            }
             case '-h':
             case '--help':
                 process.stdout.write(USAGE);
@@ -111,30 +151,56 @@ function parseArgs(argv) {
 }
 export async function main(argv) {
     const args = parseArgs(argv);
-    const source = /^https?:\/\//.test(args.file) ? new RemoteFile(args.file) : new LocalFile(args.file);
-    const db = await GBZBase.open(source, { blockSize: args.blockSize });
-    const opts = { context: args.context, haplotypes: args.haplotypes, ...(args.limit === undefined ? {} : { limit: args.limit }) };
-    const query = { contig: args.contig ?? '', haplotype: args.haplotype, ...(args.sample === undefined ? {} : { sample: args.sample }) };
-    const subgraph = args.nodes.length > 0
-        ? await subgraphAroundNodes(db, args.nodes, opts)
-        : args.interval
-            ? await subgraphInInterval(db, query, args.interval[0], args.interval[1], opts)
-            : args.offset !== undefined
-                ? await subgraphAtOffset(db, query, args.offset, opts)
-                : undefined;
+    const open = (file) => /^https?:\/\//.test(file) ? new RemoteFile(file) : new LocalFile(file);
+    const db = await GBZBase.open(open(args.file), {
+        blockSize: args.blockSize,
+        ...(args.haplotypeIndex === undefined
+            ? {}
+            : { haplotypeIndex: open(args.haplotypeIndex) }),
+    });
+    const opts = {
+        context: args.context,
+        haplotypes: args.haplotypes,
+        snarls: args.snarls,
+        ...(args.limit === undefined ? {} : { limit: args.limit }),
+    };
+    const query = {
+        contig: args.contig ?? '',
+        haplotype: args.haplotype,
+        ...(args.sample === undefined ? {} : { sample: args.sample }),
+    };
+    const subgraph = args.between
+        ? await subgraphBetween(db, args.between[0], args.between[1], opts)
+        : args.nodes.length > 0
+            ? await subgraphAroundNodes(db, args.nodes, opts)
+            : args.interval
+                ? await subgraphInInterval(db, query, args.interval[0], args.interval[1], opts)
+                : args.offset !== undefined
+                    ? await subgraphAtOffset(db, query, args.offset, opts)
+                    : undefined;
     if (!subgraph) {
-        throw new Error('Query type must be specified using --offset, --interval or --node');
+        throw new Error('Query type must be specified using --offset, --interval, --node or --between');
     }
     if (args.resolve) {
         await subgraph.identifyPaths();
     }
+    const names = args.resolve ? 'resolved' : 'anonymous';
     const output = args.alignments
-        ? subgraph.alignments().map(a => ({ ...a, name: a.name ? formatPathName(a.name, a.name.fragment) : undefined, start: undefined }))
-        : subgraph.toJSON(args.cigar, { names: args.resolve ? 'resolved' : 'anonymous' });
-    process.stdout.write(`${JSON.stringify(output)}\n`);
+        ? subgraph.alignments().map(a => ({
+            ...a,
+            name: a.name && a.hapStart !== undefined && a.hapEnd !== undefined
+                ? formatPathName({ ...a.name, fragment: a.hapStart }, a.hapEnd)
+                : undefined,
+            start: undefined,
+        }))
+        : subgraph.toJSON(args.cigar, { names });
+    process.stdout.write(args.format === 'gfa' && !args.alignments
+        ? await subgraph.toGFA(args.cigar, { names })
+        : `${JSON.stringify(output)}\n`);
     if (args.stats) {
         const { fetches, bytesFetched } = db.sqlite.pager;
-        const { orderedAlignments, lcsAlignments, identificationSteps, identificationFetches } = subgraph.stats;
+        const { orderedAlignments, lcsAlignments, identificationSteps, identificationFetches, } = subgraph.stats;
         process.stderr.write(`Subgraph contains ${subgraph.nodeCount} nodes and ${subgraph.pathCount} paths; ${fetches} fetches, ${bytesFetched} bytes; ${orderedAlignments} ordered + ${lcsAlignments} lcs alignments; identification ${identificationSteps} steps, ${identificationFetches} lookups\n`);
     }
 }
+//# sourceMappingURL=cli.js.map

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package/dist/db.d.ts

@@ -1,7 +1,8 @@
-import type { ByteSource } from './filehandle.ts';
 import { GbwtRecord } from './gbwt/record.ts';
-import type { Pos } from './gbwt/record.ts';
 import { SqliteDatabase } from './sqlite/database.ts';
+import type { ByteSource } from './filehandle.ts';
+import type { Pos } from './gbwt/record.ts';
+import type { GraphName } from './graphName.ts';
 import type { PagerOptions } from './sqlite/pager.ts';
 export interface PathName {
     sample: string;
@@ -12,8 +13,8 @@ export interface PathName {
 export declare const GENERIC_SAMPLE = "_gbwt_ref";
 export declare const SCHEMA_VERSION = "GBZ-base version 4";
 export declare class SchemaVersionError extends Error {
-    readonly found: string | undefined;
     name: string;
+    readonly found: string | undefined;
     constructor(found: string | undefined);
 }
 export declare function formatPathName(name: PathName, end: number): string;
@@ -32,12 +33,12 @@ export interface GbzPath {
     isIndexed: boolean;
 }
 export declare class GbzRecord {
+    readonly sequenceLen: number;
     readonly handle: number;
     readonly edges: Pos[];
     readonly bwt: Uint8Array;
     readonly encodedSequence: Uint8Array;
     readonly next: number | undefined;
-    readonly sequenceLen: number;
     private decoded;
     constructor(handle: number, edges: Pos[], bwt: Uint8Array, encodedSequence: Uint8Array, next: number | undefined);
     get id(): number;
@@ -46,12 +47,17 @@ export declare class GbzRecord {
     successors(): number[];
     gbwt(): GbwtRecord;
 }
+export interface OpenOptions extends PagerOptions {
+    haplotypeIndex?: ByteSource;
+}
 export declare class GBZBase {
-    readonly sqlite: SqliteDatabase;
     private tagCache;
     private pathCache;
+    private indexTags;
+    readonly sqlite: SqliteDatabase;
+    private readonly index;
     private constructor();
-    static open(source: ByteSource, opts?: PagerOptions): Promise<GBZBase>;
+    static open(source: ByteSource, opts?: OpenOptions): Promise<GBZBase>;
     tags(): Promise<Map<string, string>>;
     tag(key: string): Promise<string | undefined>;
     getRecord(handle: number): Promise<GbzRecord | undefined>;
@@ -59,6 +65,8 @@ export declare class GBZBase {
     getPath(handle: number): Promise<GbzPath | undefined>;
     findPath(name: PathName): Promise<GbzPath | undefined>;
     pathsForSample(sample: string): Promise<GbzPath[]>;
+    graphName(): Promise<GraphName>;
+    hasChainLinks(): Promise<boolean>;
     get hasHaplotypeIndex(): boolean;
     haplotypeSampleInterval(): Promise<number | undefined>;
     private sampleFromRow;

package/dist/db.js

@@ -1,12 +1,13 @@
-import { GbwtRecord, decompressEdges } from "./gbwt/record.js";
 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 { SqliteDatabase } from "./sqlite/database.js";
 export const GENERIC_SAMPLE = '_gbwt_ref';
 export const SCHEMA_VERSION = 'GBZ-base version 4';
 export class SchemaVersionError extends Error {
-    found;
     name = 'SchemaVersionError';
+    found;
     constructor(found) {
         super(found === undefined
             ? `not a gbz-base database: its Tags table has no version`
@@ -18,12 +19,12 @@ export function formatPathName(name, end) {
     return `${name.sample}#${name.haplotype}#${name.contig}[${name.fragment}-${end}]`;
 }
 export class GbzRecord {
+    sequenceLen;
     handle;
     edges;
     bwt;
     encodedSequence;
     next;
-    sequenceLen;
     decoded;
     constructor(handle, edges, bwt, encodedSequence, next) {
         this.handle = handle;
@@ -74,8 +75,14 @@ function blob(value, what) {
 function rowToPath(rowid, values) {
     return {
         handle: rowid,
-        fwStart: { node: num(values[1], 'Paths.fw_node'), offset: num(values[2], 'Paths.fw_offset') },
-        revStart: { node: num(values[3], 'Paths.rev_node'), offset: num(values[4], 'Paths.rev_offset') },
+        fwStart: {
+            node: num(values[1], 'Paths.fw_node'),
+            offset: num(values[2], 'Paths.fw_offset'),
+        },
+        revStart: {
+            node: num(values[3], 'Paths.rev_node'),
+            offset: num(values[4], 'Paths.rev_offset'),
+        },
         name: {
             sample: str(values[5], 'Paths.sample'),
             contig: str(values[6], 'Paths.contig'),
@@ -85,33 +92,52 @@ 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 {
-    sqlite;
     tagCache;
     pathCache;
-    constructor(sqlite) {
+    indexTags;
+    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) {
@@ -149,11 +175,37 @@ export class GBZBase {
     async pathsForSample(sample) {
         return (await this.paths()).filter(p => p.name.sample === sample);
     }
+    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) {
@@ -161,18 +213,23 @@ export class GBZBase {
             node: num(values[0], 'HaplotypeSamples.node_handle'),
             offset: num(values[1], 'HaplotypeSamples.node_offset'),
             pathHandle: num(values[2], 'HaplotypeSamples.path_handle'),
-            orientation: num(values[3], 'HaplotypeSamples.orientation') === 0 ? 'forward' : 'reverse',
+            orientation: num(values[3], 'HaplotypeSamples.orientation') === 0
+                ? 'forward'
+                : 'reverse',
             pathOffset: num(values[4], 'HaplotypeSamples.path_offset'),
         };
     }
     async haplotypeSamplesInRange(minHandle, maxHandle) {
         const samples = [];
-        for await (const key of this.sqlite.indexScanFrom('HaplotypeSamples', [minHandle, 0])) {
+        for await (const key of this.index.indexScanFrom('HaplotypeSamples', [
+            minHandle,
+            0,
+        ])) {
             const node = num(key[0], 'HaplotypeSamples.node_handle');
             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));
             }
@@ -180,20 +237,23 @@ export class GBZBase {
         return samples;
     }
     async haplotypeSampleAt(node, offset) {
-        const key = await this.sqlite.indexSeekLE('HaplotypeSamples', [node, offset]);
-        if (!key || key[0] !== node || key[1] !== 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) {
-        const key = await this.sqlite.indexSeekLE('ReferenceIndex', [pathHandle, pathOffset]);
-        if (!key || key[0] !== pathHandle) {
+        const key = await this.sqlite.indexSeekLE('ReferenceIndex', [
+            pathHandle,
+            pathOffset,
+        ]);
+        if (key?.[0] !== pathHandle) {
             return undefined;
         }
         const row = await this.sqlite.byRowid('ReferenceIndex', num(key[2], 'ReferenceIndex rowid'));
@@ -202,7 +262,11 @@ export class GBZBase {
         }
         return {
             pathOffset: num(row[1], 'ReferenceIndex.path_offset'),
-            pos: { node: num(row[2], 'ReferenceIndex.node_handle'), offset: num(row[3], 'ReferenceIndex.node_offset') },
+            pos: {
+                node: num(row[2], 'ReferenceIndex.node_handle'),
+                offset: num(row[3], 'ReferenceIndex.node_offset'),
+            },
         };
     }
 }
+//# sourceMappingURL=db.js.map

package/dist/db.js.map

@@ -0,0 +1 @@
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package/dist/filehandle.js

@@ -1 +1,2 @@
 export {};
+//# sourceMappingURL=filehandle.js.map

package/dist/filehandle.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"filehandle.js","sourceRoot":"","sources":["../src/filehandle.ts"],"names":[],"mappings":""}

package/dist/gbwt/bytecode.d.ts

@@ -1,6 +1,6 @@
 export declare class ByteCodeReader {
-    private bytes;
     offset: number;
+    private bytes;
     constructor(bytes: Uint8Array);
     get done(): boolean;
     byte(): number | undefined;

package/dist/gbwt/bytecode.js

@@ -1,6 +1,6 @@
 export class ByteCodeReader {
-    bytes;
     offset = 0;
+    bytes;
     constructor(bytes) {
         this.bytes = bytes;
     }
@@ -39,13 +39,16 @@ export class RunReader {
     constructor(bytes, sigma) {
         this.source = new ByteCodeReader(bytes);
         this.sigma = sigma === 0 ? Number.MAX_SAFE_INTEGER : sigma;
-        this.threshold = this.sigma < RLE_THRESHOLD ? Math.floor(RLE_UNIVERSE / this.sigma) : 0;
+        this.threshold =
+            this.sigma < RLE_THRESHOLD ? Math.floor(RLE_UNIVERSE / this.sigma) : 0;
     }
     next() {
         if (this.sigma >= RLE_THRESHOLD) {
             const value = this.source.int();
             const len = this.source.int();
-            return value === undefined || len === undefined ? undefined : { value, len: len + 1 };
+            return value === undefined || len === undefined
+                ? undefined
+                : { value, len: len + 1 };
         }
         const byte = this.source.byte();
         if (byte === undefined) {
@@ -68,3 +71,4 @@ export class RunReader {
         }
     }
 }
+//# sourceMappingURL=bytecode.js.map

package/dist/gbwt/bytecode.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"bytecode.js","sourceRoot":"","sources":["../../src/gbwt/bytecode.ts"],"names":[],"mappings":"AAAA,MAAM,OAAO,cAAc;IACzB,MAAM,GAAG,CAAC,CAAA;IACF,KAAK,CAAY;IAEzB,YAAY,KAAiB;QAC3B,IAAI,CAAC,KAAK,GAAG,KAAK,CAAA;IACpB,CAAC;IAED,IAAI,IAAI;QACN,OAAO,IAAI,CAAC,MAAM,IAAI,IAAI,CAAC,KAAK,CAAC,MAAM,CAAA;IACzC,CAAC;IAED,IAAI;QACF,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QACrC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,IAAI,CAAC,MAAM,IAAI,CAAC,CAAA;QAChB,OAAO,KAAK,CAAA;IACd,CAAC;IAED,GAAG;QACD,IAAI,KAAK,GAAG,CAAC,CAAA;QACb,IAAI,MAAM,GAAG,CAAC,CAAA;QACd,OAAO,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC;YACvC,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,CAAE,CAAA;YACtC,IAAI,CAAC,MAAM,IAAI,CAAC,CAAA;YAChB,MAAM,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,GAAG,KAAK,CAAA;YAChC,KAAK,IAAI,GAAG,CAAA;YACZ,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;gBACzB,OAAO,MAAM,CAAA;YACf,CAAC;QACH,CAAC;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;CACF;AAOD,MAAM,aAAa,GAAG,GAAG,CAAA;AACzB,MAAM,YAAY,GAAG,GAAG,CAAA;AAExB,MAAM,OAAO,SAAS;IACZ,MAAM,CAAgB;IACtB,KAAK,CAAQ;IACb,SAAS,CAAQ;IAEzB,YAAY,KAAiB,EAAE,KAAa;QAC1C,IAAI,CAAC,MAAM,GAAG,IAAI,cAAc,CAAC,KAAK,CAAC,CAAA;QACvC,IAAI,CAAC,KAAK,GAAG,KAAK,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,gBAAgB,CAAC,CAAC,CAAC,KAAK,CAAA;QAC1D,IAAI,CAAC,SAAS;YACZ,IAAI,CAAC,KAAK,GAAG,aAAa,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,YAAY,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC1E,CAAC;IAED,IAAI;QACF,IAAI,IAAI,CAAC,KAAK,IAAI,aAAa,EAAE,CAAC;YAChC,MAAM,KAAK,GAAG,IAAI,CAAC,MAAM,CAAC,GAAG,EAAE,CAAA;YAC/B,MAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAC,GAAG,EAAE,CAAA;YAC7B,OAAO,KAAK,KAAK,SAAS,IAAI,GAAG,KAAK,SAAS;gBAC7C,CAAC,CAAC,SAAS;gBACX,CAAC,CAAC,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,GAAG,CAAC,EAAE,CAAA;QAC7B,CAAC;QACD,MAAM,IAAI,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,CAAA;QAC/B,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;YACvB,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,MAAM,KAAK,GAAG,IAAI,GAAG,IAAI,CAAC,KAAK,CAAA;QAC/B,IAAI,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QAC3C,IAAI,GAAG,KAAK,IAAI,CAAC,SAAS,EAAE,CAAC;YAC3B,MAAM,KAAK,GAAG,IAAI,CAAC,MAAM,CAAC,GAAG,EAAE,CAAA;YAC/B,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;gBACxB,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,GAAG,IAAI,KAAK,CAAA;QACd,CAAC;QACD,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,CAAA;IACvB,CAAC;IAED,CAAC,CAAC,MAAM,CAAC,QAAQ,CAAC;QAChB,KAAK,IAAI,GAAG,GAAG,IAAI,CAAC,IAAI,EAAE,EAAE,GAAG,KAAK,SAAS,EAAE,GAAG,GAAG,IAAI,CAAC,IAAI,EAAE,EAAE,CAAC;YACjE,MAAM,GAAG,CAAA;QACX,CAAC;IACH,CAAC;CACF"}

package/dist/gbwt/node.js

@@ -32,7 +32,9 @@ export function exitOrientation(side) {
 export function edgeIsCanonical(from, to) {
     const fromId = nodeId(from);
     const toId = nodeId(to);
-    return isReverse(from) ? toId > fromId || (toId === fromId && !isReverse(to)) : toId >= fromId;
+    return isReverse(from)
+        ? toId > fromId || (toId === fromId && !isReverse(to))
+        : toId >= fromId;
 }
 export function pathIsCanonical(path) {
     const first = path[0];
@@ -40,5 +42,8 @@ export function pathIsCanonical(path) {
     if (first === undefined || last === undefined) {
         return true;
     }
-    return isReverse(first) === isReverse(last) ? !isReverse(first) : edgeIsCanonical(first, last);
+    return isReverse(first) === isReverse(last)
+        ? !isReverse(first)
+        : edgeIsCanonical(first, last);
 }
+//# sourceMappingURL=node.js.map