@gmod/gbz-base 1.1.0 → 2.1.0

package/README.md

@@ -1,45 +1,133 @@
 # @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' })
+```
+
+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)
+  }
+}
 ```
 
-`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.
+`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. `strand` is `-` when the haplotype runs
+through the window in the opposite direction to the reference, so the same pair
+of paths reports the same strand whichever of the two is the reference. `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:
 
 ```
@@ -104,8 +192,8 @@ const db = await GBZBase.open(new RemoteFile(graphUrl), {
 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.
+records the graph's path and node counts 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
@@ -115,15 +203,28 @@ 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
@@ -141,6 +242,15 @@ node can be placed in order; the Myers-based weighted LCS from gbwt-rs runs only
 for the fragments where that fails (inversions, repeats). The two can pick
 different equal-weight alignments only when the reference walk repeats a node.
 
+One deliberate departure: where a reference walk is stored against node
+orientation (upstream prints "the reference path is not in canonical
+orientation" there), every other walk comes out in the opposite orientation, and
+upstream aligns them handle for handle, giving all-insertion CIGARs against the
+reference despite the nodes being shared. This reader aligns each walk in
+whichever orientation shares more sequence with the reference and reports `-` on
+such records. CHM13 on HPRC chr20 has one such region, right after the fragment
+starting at 30368374.
+
 ## Measured
 
 Against a 134 MB HPRC chr20 `.gbz.db` served over HTTPS,

package/dist/cli.js

@@ -1,5 +1,5 @@
 import { LocalFile, RemoteFile } from 'generic-filehandle2';
-import { GBZBase, formatPathName } from "./db.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
@@ -149,6 +149,10 @@ 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 open = (file) => /^https?:\/\//.test(file) ? new RemoteFile(file) : new LocalFile(file);
@@ -186,21 +190,18 @@ export async function main(argv) {
     }
     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 });
+        ? subgraph.alignments().map(alignmentRecord)
+        : subgraph.toSubgraphJson({ cigar: args.cigar, names });
     process.stdout.write(args.format === 'gfa' && !args.alignments
-        ? await subgraph.toGFA(args.cigar, { names })
+        ? 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`);
     }
 }
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+{"version":3,"file":"cli.js","sourceRoot":"","sources":["../src/cli.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAA;AAE3D,OAAO,EAAE,OAAO,EAAE,MAAM,SAAS,CAAA;AACjC,OAAO,EAAE,UAAU,EAAE,MAAM,gBAAgB,CAAA;AAC3C,OAAO,EACL,mBAAmB,EACnB,gBAAgB,EAChB,eAAe,EACf,kBAAkB,GACnB,MAAM,YAAY,CAAA;AAQnB,MAAM,KAAK,GAAG;;;;;;;;;;;;;;;;;;;;;CAqBb,CAAA;AAwBD,SAAS,WAAW,CAAC,IAAY;IAC/B,MAAM,WAAW,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,CAAA;IAC9D,MAAM,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;IAC5D,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,EAAE,CAAC;QAC1B,MAAM,IAAI,KAAK,CAAC,iCAAiC,IAAI,EAAE,CAAC,CAAA;IAC1D,CAAC;IACD,OAAO,UAAU,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,WAAW,CAAC,CAAA;AAChD,CAAC;AAED,SAAS,SAAS,CAAC,IAAc;IAC/B,MAAM,IAAI,GAAS;QACjB,IAAI,EAAE,EAAE;QACR,SAAS,EAAE,CAAC;QACZ,KAAK,EAAE,EAAE;QACT,OAAO,EAAE,GAAG;QACZ,MAAM,EAAE,MAAM;QACd,UAAU,EAAE,KAAK;QACjB,KAAK,EAAE,KAAK;QACZ,MAAM,EAAE,MAAM;QACd,OAAO,EAAE,KAAK;QACd,UAAU,EAAE,KAAK;QACjB,SAAS,EAAE,KAAK;QAChB,KAAK,EAAE,KAAK;KACb,CAAA;IACD,MAAM,IAAI,GAAG,CAAC,CAAS,EAAE,EAAE;QACzB,MAAM,KAAK,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;QACzB,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,MAAM,IAAI,KAAK,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAA;QAC7C,CAAC;QACD,OAAO,KAAK,CAAA;IACd,CAAC,CAAA;IACD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACrC,MAAM,GAAG,GAAG,IAAI,CAAC,CAAC,CAAE,CAAA;QACpB,QAAQ,GAAG,EAAE,CAAC;YACZ,KAAK,UAAU;gBACb,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,CAAC,EAAE,CAAC,CAAA;gBACvB,MAAK;YACP,KAAK,UAAU;gBACb,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,CAAC,EAAE,CAAC,CAAA;gBACvB,MAAK;YACP,KAAK,aAAa;gBAChB,IAAI,CAAC,SAAS,GAAG,MAAM,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;gBAClC,MAAK;YACP,KAAK,IAAI,CAAC;YACV,KAAK,UAAU;gBACb,IAAI,CAAC,MAAM,GAAG,MAAM,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;gBAC/B,MAAK;YACP,KAAK,IAAI,CAAC;YACV,KAAK,YAAY,CAAC,CAAC,CAAC;gBAClB,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;gBACpC,IAAI,CAAC,QAAQ,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,MAAM,CAAC,CAAC,CAAC,CAAC,CAAA;gBACtC,MAAK;YACP,CAAC;YACD,KAAK,IAAI,CAAC;YACV,KAAK,QAAQ;gBACX,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;gBAClC,MAAK;YACP,KAAK,IAAI,CAAC;YACV,KAAK,WAAW,CAAC,CAAC,CAAC;gBACjB,MAAM,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,CAAC,GAAG,IAAI,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;gBAC1C,IAAI,CAAC,KAAK,SAAS,IAAI,CAAC,KAAK,SAAS,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;oBAC9D,MAAM,IAAI,KAAK,CAAC,kDAAkD,CAAC,CAAA;gBACrE,CAAC;gBACD,IAAI,CAAC,OAAO,GAAG,CAAC,WAAW,CAAC,CAAC,CAAC,EAAE,WAAW,CAAC,CAAC,CAAC,CAAC,CAAA;gBAC/C,MAAK;YACP,CAAC;YACD,KAAK,WAAW;gBACd,IAAI,CAAC,OAAO,GAAG,MAAM,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;gBAChC,MAAK;YACP,KAAK,UAAU;gBACb,IAAI,CAAC,MAAM;oBACT,IAAI,CAAC,MAAM,KAAK,aAAa,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,WAAW,CAAA;gBAC7D,MAAK;YACP,KAAK,iBAAiB;gBACpB,IAAI,CAAC,MAAM,GAAG,aAAa,CAAA;gBAC3B,MAAK;YACP,KAAK,SAAS;gBACZ,IAAI,CAAC,KAAK,GAAG,MAAM,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;gBAC9B,MAAK;YACP,KAAK,cAAc;gBACjB,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,CAAC,EAAE,CAAoB,CAAA;gBAC9C,MAAK;YACP,KAAK,SAAS;gBACZ,IAAI,CAAC,KAAK,GAAG,IAAI,CAAA;gBACjB,MAAK;YACP,KAAK,WAAW;gBACd,IAAI,CAAC,OAAO,GAAG,IAAI,CAAA;gBACnB,MAAK;YACP,KAAK,cAAc;gBACjB,IAAI,CAAC,UAAU,GAAG,IAAI,CAAA;gBACtB,IAAI,CAAC,OAAO,GAAG,IAAI,CAAA;gBACnB,MAAK;YACP,KAAK,cAAc;gBACjB,IAAI,CAAC,SAAS,GAAG,MAAM,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;gBAClC,MAAK;YACP,KAAK,mBAAmB;gBACtB,IAAI,CAAC,cAAc,GAAG,IAAI,CAAC,CAAC,EAAE,CAAC,CAAA;gBAC/B,MAAK;YACP,KAAK,SAAS;gBACZ,IAAI,CAAC,KAAK,GAAG,IAAI,CAAA;gBACjB,MAAK;YACP,KAAK,UAAU,CAAC,CAAC,CAAC;gBAChB,MAAM,MAAM,GAAG,IAAI,CAAC,CAAC,EAAE,CAAC,CAAA;gBACxB,IAAI,MAAM,KAAK,MAAM,IAAI,MAAM,KAAK,KAAK,EAAE,CAAC;oBAC1C,MAAM,IAAI,KAAK,CAAC,yBAAyB,MAAM,EAAE,CAAC,CAAA;gBACpD,CAAC;gBACD,IAAI,CAAC,MAAM,GAAG,MAAM,CAAA;gBACpB,MAAK;YACP,CAAC;YACD,KAAK,IAAI,CAAC;YACV,KAAK,QAAQ;gBACX,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;gBAC3B,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;gBACf,MAAK;YACP;gBACE,IAAI,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;oBACxB,MAAM,IAAI,KAAK,CAAC,kBAAkB,GAAG,EAAE,CAAC,CAAA;gBAC1C,CAAC;gBACD,IAAI,CAAC,IAAI,GAAG,GAAG,CAAA;QACnB,CAAC;IACH,CAAC;IACD,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAC;QACf,MAAM,IAAI,KAAK,CAAC,KAAK,CAAC,CAAA;IACxB,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC;AAED,SAAS,eAAe,CAAC,SAA6B;IACpD,MAAM,EAAE,KAAK,EAAE,GAAG,IAAI,EAAE,GAAG,SAAS,CAAA;IACpC,OAAO,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE,GAAG,IAAI,EAAE,IAAI,EAAE,IAAI,CAAC,KAAK,EAAE,KAAK,EAAE,SAAS,EAAE,CAAC,CAAC,CAAC,IAAI,CAAA;AAC/E,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,IAAI,CAAC,IAAc;IACvC,MAAM,IAAI,GAAG,SAAS,CAAC,IAAI,CAAC,CAAA;IAC5B,MAAM,IAAI,GAAG,CAAC,IAAY,EAAE,EAAE,CAC5B,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,SAAS,CAAC,IAAI,CAAC,CAAA;IACxE,MAAM,EAAE,GAAG,MAAM,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE;QAC7C,SAAS,EAAE,IAAI,CAAC,SAAS;QACzB,GAAG,CAAC,IAAI,CAAC,cAAc,KAAK,SAAS;YACnC,CAAC,CAAC,EAAE;YACJ,CAAC,CAAC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package/dist/db.d.ts

@@ -3,21 +3,21 @@ 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;
@@ -55,7 +55,7 @@ export declare class GBZBase {
     private pathCache;
     private indexTags;
     readonly sqlite: SqliteDatabase;
-    private readonly index;
+    readonly index: SqliteDatabase;
     private constructor();
     static open(source: ByteSource, opts?: OpenOptions): Promise<GBZBase>;
     tags(): Promise<Map<string, string>>;
@@ -65,6 +65,15 @@ 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;

package/dist/db.js

@@ -2,8 +2,9 @@ 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';
@@ -15,9 +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;
@@ -133,6 +131,11 @@ export class GBZBase {
             if (indexed !== paths) {
                 throw new Error(`haplotype index was built for ${indexed ?? 'an unknown number of'} paths but the graph has ${paths}`);
             }
+            const indexedNodes = db.indexTags.get('haplotype_index_nodes');
+            const nodes = await db.tag('nodes');
+            if (indexedNodes !== undefined && indexedNodes !== nodes) {
+                throw new Error(`haplotype index was built for a graph with ${indexedNodes} nodes but this one has ${nodes}`);
+            }
         }
         return db;
     }
@@ -175,6 +178,99 @@ 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()) {

package/dist/db.js.map

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package/dist/index.d.ts

@@ -1,11 +1,13 @@
-export { GBZBase, GENERIC_SAMPLE, GbzRecord, SCHEMA_VERSION, SchemaVersionError, formatPathName, } from './db.ts';
-export type { GbzPath, HaplotypeSample, OpenOptions, 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, SnarlOutput, SubgraphJson, SubgraphPath, ToJsonOptions, } from './subgraph.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 { PathQuery, QueryOptions } 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';

package/dist/index.js

@@ -1,4 +1,5 @@
-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, subgraphBetween, subgraphInInterval, } from "./query.js";
 export { SqliteDatabase } from "./sqlite/database.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;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"}
+{"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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