@gmod/gbz-base 1.0.0 → 2.0.0

package/README.md

@@ -1,45 +1,131 @@
 # @gmod/gbz-base
 
-A pure TypeScript reader for [gbz-base](https://github.com/jltsiren/gbz-base)
-pangenome databases (`.gbz.db`). It answers the same subgraph queries as
-`gbz-base query`, reading only the SQLite pages a query touches, so a
-multi-gigabyte database on an HTTP server is queried through range requests
-without downloading it or compiling anything to WebAssembly.
+[![NPM version](https://img.shields.io/npm/v/@gmod/gbz-base.svg?style=flat-square)](https://npmjs.org/package/@gmod/gbz-base)
+![Build Status](https://img.shields.io/github/actions/workflow/status/GMOD/gbz-base-js/publish.yml?branch=main)
 
-No SQLite library is involved. The reader walks the SQLite b-trees directly
-(rowid lookups, index seeks, overflow chains) and decodes the GBWT node records
-the same way gbwt-rs does. Databases are produced by unmodified upstream
-`gbz-base construct`.
+A pure TypeScript reader for [gbz-base](https://github.com/jltsiren/gbz-base)
+pangenome databases (`.gbz.db`).
 
 ## Usage
 
 ```ts
 import { RemoteFile } from 'generic-filehandle2'
-import { GBZBase, subgraphInInterval } from '@gmod/gbz-base'
+import { GBZBase } from '@gmod/gbz-base'
 
 const db = await GBZBase.open(
   new RemoteFile('https://example.org/graph.gbz.db'),
 )
-const subgraph = await subgraphInInterval(
-  db,
-  { sample: 'GRCh38', contig: 'chr6' },
+
+// one record per haplotype fragment crossing the window
+const alignments = await db.getAlignmentsForRange(
+  'GRCh38#0#chr6',
+  31500000,
+  31501000,
+)
+
+// the same window as a subgraph, for a pangenome view
+const subgraph = await db.getSubgraphForRange(
+  'GRCh38#0#chr6',
   31500000,
   31501000,
-  { context: 0, haplotypes: 'all' },
 )
-const { nodes, edges, paths } = subgraph.toJSON(true)
+const gfa = await subgraph?.toGFA({ names: 'resolved' })
 ```
 
-`paths[0]` is the reference interval, named `GRCh38#0#chr6[start-end]`. Every
-other entry is one haplotype's walk through the subgraph with a `cigar` relative
-to the reference, computed like upstream: a node-length-weighted LCS, with the
-diverging stretches scored using vg's match, mismatch and gap parameters.
+Coordinates are 0-based half-open, and are offsets along the path you named, so
+`('GRCh38#0#chr6', 31500000, 31501000)` is the same window
+`gbz-base query --interval 31500000..31501000` gives.
+
+The path is a PanSN `sample#haplotype#contig` string, or a bare contig for a
+graph whose reference paths have no sample. `{ sample, haplotype, contig }`
+works too, and `parsePathName` is the parser if you want it separately.
+
+Both take `{ context, haplotypes, snarls, limit, signal }` and both resolve
+haplotype names when the database can. `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
+
+`getAlignmentsForRange` hands back data, and spans path fragments — a window
+crossing a boundary queries each fragment and concatenates, which is
+coordinate-correct because a record's `refStart`/`refEnd` are absolute.
+
+`getSubgraphForRange` hands back the `Subgraph` itself, because two disjoint
+fragments do not merge into one graph. It answers for the first fragment
+overlapping the window, clamped to it, and `subgraph.referenceInterval` says
+which interval that was. It is `undefined` when the path is unknown, when no
+fragment overlaps the window, or when the clamped window is empty. Use
+`pathFragmentsForRange` to see the fragments yourself, and `hasPath` to ask
+about a path alone.
+
+A path that exists but was never indexed for random access throws rather than
+returning nothing — that is a database that needs rebuilding, not an empty
+window.
+
+### What an alignment is
+
+```ts
+for (const alignment of alignments) {
+  const { refStart, refEnd, strand, cigar } = alignment
+  if (alignment.resolved) {
+    console.log(alignment.label, alignment.hapStart, alignment.hapEnd)
+  }
+}
+```
+
+`refStart`/`refEnd` are the fragment'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
+vg's match, mismatch and gap parameters. `path` is the walk as node handles,
+`weight` is how many identical haplotypes it stands for, and `start` is its GBWT
+position, which is a property of the graph and so is stable across refetches of
+the same window.
+
+Naming a fragment needs the haplotype index described below, and a database
+without one cannot do it, so the record is a union on `resolved` rather than a
+handful of separately-undefined fields. A resolved one adds the `PathName` as
+`name`, its `HG02723#1#JAHEOU010000100.1[4392999-4393486]` rendering as `label`,
+the `pathHandle`, and `hapStart`/`hapEnd` in that haplotype's own coordinates.
+
+A haplotype whose walk shares no node with the reference has
+`refEnd <= refStart` and an all-insertion CIGAR; those come back like any other,
+to drop or keep as you like.
+
+### Sources
 
 Any object with `read(length, position)` and `stat()` works as a source, so
 `LocalFile`, `RemoteFile` and `BlobFile` from `generic-filehandle2` all do.
 Pages are fetched in blocks (64 KiB by default, `blockSize` in the open options)
 and cached.
 
+### Lower-level queries
+
+The two above cover the interval query and hide where a contig is stored split
+into path fragments. The four query functions underneath are what
+`gbz-base query` itself does, take a window you have already resolved, and leave
+identification to you:
+
+```ts
+import { subgraphAtOffset, subgraphInInterval } from '@gmod/gbz-base'
+
+const subgraph = await subgraphInInterval(
+  db,
+  { sample: 'GRCh38', contig: 'chr6' },
+  31500000,
+  31501000,
+  { context: 0, haplotypes: 'all' },
+)
+await subgraph.identifyPaths()
+const graph = subgraph.toSubgraphJson({ cigar: true, names: 'resolved' })
+const gfa = await subgraph.toGFA({ cigar: true, names: 'resolved' })
+```
+
+`subgraphAtOffset` and `subgraphAroundNodes` are the other two;
+`subgraphBetween` is described under Snarls. They throw for a window that runs
+past the end of a path fragment, where `getAlignmentsForRange` clamps.
+
 The command line mirrors the upstream tool for the query types it supports:
 
 ```
@@ -50,6 +136,27 @@ 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
@@ -64,7 +171,27 @@ cd tools/haplotype-index && cargo build --release
 
 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.
+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
@@ -74,15 +201,28 @@ 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. `subgraph.alignments()` then gives one
-record per fragment: PanSN name, strand, haplotype interval in that contig's
-coordinates, reference interval, and a CIGAR clipped to the fragment's own
-reference span. `toJSON(cigar, { names: 'resolved' })` names the paths the same
-way. On the command line, `--resolve` and `--alignments`.
+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`.
 
 The tests check every resolved fragment against an independent backward walk
 through the bidirectional GBWT to the path's recorded start position.
 
+## Technical notes
+
+It answers the same subgraph queries as `gbz-base query`, reading only the
+SQLite pages a query touches, so a multi-gigabyte database on an HTTP server is
+queried through range requests without downloading it or compiling anything to
+WebAssembly.
+
+No SQLite library is involved. The reader walks the SQLite b-trees directly
+(rowid lookups, index seeks, overflow chains) and decodes the GBWT node records
+the same way gbwt-rs does. Databases are produced by unmodified upstream
+`gbz-base construct`.
+
 ## Fidelity
 
 `test/data/oracle/` holds JSON written by upstream `gbz-base query` for the
@@ -92,7 +232,7 @@ 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/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 { GBZBase } from "./db.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);
@@ -109,15 +149,23 @@ function parseArgs(argv) {
     }
     return args;
 }
+function alignmentRecord(alignment) {
+    const { start, ...rest } = alignment;
+    return rest.resolved ? { ...rest, name: rest.label, label: undefined } : rest;
+}
 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 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 = {
@@ -125,35 +173,35 @@ export async function main(argv) {
         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 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 && a.hapStart !== undefined && a.hapEnd !== undefined
-                ? formatPathName({ ...a.name, fragment: a.hapStart }, a.hapEnd)
-                : undefined,
-            start: undefined,
-        }))
-        : subgraph.toJSON(args.cigar, {
-            names: args.resolve ? 'resolved' : 'anonymous',
-        });
-    process.stdout.write(`${JSON.stringify(output)}\n`);
+        ? subgraph.alignments().map(alignmentRecord)
+        : subgraph.toSubgraphJson({ cigar: args.cigar, names });
+    process.stdout.write(args.format === 'gfa' && !args.alignments
+        ? await subgraph.toGFA({ cigar: args.cigar, names })
+        : `${JSON.stringify(output)}\n`);
     if (args.stats) {
         const { fetches, bytesFetched } = db.sqlite.pager;
+        const index = db.index === db.sqlite
+            ? ''
+            : ` (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; ${orderedAlignments} ordered + ${lcsAlignments} lcs alignments; identification ${identificationSteps} steps, ${identificationFetches} lookups\n`);
+        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`);
     }
 }
 //# sourceMappingURL=cli.js.map

package/dist/cli.js.map

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

@@ -2,21 +2,22 @@ import { GbwtRecord } 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 { PathName, PathRef } from './pathName.ts';
+import type { QueryOptions } from './query.ts';
 import type { PagerOptions } from './sqlite/pager.ts';
-export interface PathName {
-    sample: string;
-    contig: string;
-    haplotype: number;
-    fragment: number;
-}
-export declare const GENERIC_SAMPLE = "_gbwt_ref";
+import type { HaplotypeAlignment, Subgraph } from './subgraph.ts';
 export declare const SCHEMA_VERSION = "GBZ-base version 4";
+export interface PathFragment {
+    path: GbzPath;
+    start: number;
+    end: number;
+}
 export declare class SchemaVersionError extends Error {
     name: string;
     readonly found: string | undefined;
     constructor(found: string | undefined);
 }
-export declare function formatPathName(name: PathName, end: number): string;
 export interface HaplotypeSample {
     node: number;
     offset: number;
@@ -46,12 +47,17 @@ export declare class GbzRecord {
     successors(): number[];
     gbwt(): GbwtRecord;
 }
+export interface OpenOptions extends PagerOptions {
+    haplotypeIndex?: ByteSource;
+}
 export declare class GBZBase {
     private tagCache;
     private pathCache;
+    private indexTags;
     readonly sqlite: SqliteDatabase;
+    readonly index: SqliteDatabase;
     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 +65,17 @@ export declare class GBZBase {
     getPath(handle: number): Promise<GbzPath | undefined>;
     findPath(name: PathName): Promise<GbzPath | undefined>;
     pathsForSample(sample: string): Promise<GbzPath[]>;
+    private pathsNamed;
+    hasPath(ref: PathRef): Promise<boolean>;
+    private pathLengths;
+    pathLength(handle: number): Promise<number>;
+    private walkPathLength;
+    pathFragmentsForRange(ref: PathRef, start: number, end: number): Promise<PathFragment[]>;
+    private subgraphForFragment;
+    getSubgraphForRange(ref: PathRef, start: number, end: number, opts?: QueryOptions): Promise<Subgraph | undefined>;
+    getAlignmentsForRange(ref: PathRef, start: number, end: number, opts?: QueryOptions): Promise<HaplotypeAlignment[]>;
+    graphName(): Promise<GraphName>;
+    hasChainLinks(): Promise<boolean>;
     get hasHaplotypeIndex(): boolean;
     haplotypeSampleInterval(): Promise<number | undefined>;
     private sampleFromRow;