@gmod/gbz-base 1.1.0 → 2.0.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +123 -24
- package/dist/cli.js +12 -11
- package/dist/cli.js.map +1 -1
- package/dist/db.d.ts +18 -9
- package/dist/db.js +95 -4
- package/dist/db.js.map +1 -1
- package/dist/index.d.ts +6 -4
- package/dist/index.js +2 -1
- package/dist/index.js.map +1 -1
- package/dist/pathName.d.ts +17 -0
- package/dist/pathName.js +33 -0
- package/dist/pathName.js.map +1 -0
- package/dist/query.d.ts +8 -10
- package/dist/query.js +7 -19
- package/dist/query.js.map +1 -1
- package/dist/sqlite/btree.d.ts +2 -0
- package/dist/sqlite/btree.js +48 -18
- package/dist/sqlite/btree.js.map +1 -1
- package/dist/subgraph.d.ts +25 -12
- package/dist/subgraph.js +33 -16
- package/dist/subgraph.js.map +1 -1
- package/package.json +1 -1
- package/src/cli.ts +19 -13
- package/src/db.ts +153 -13
- package/src/index.ts +12 -10
- package/src/pathName.ts +54 -0
- package/src/query.ts +17 -32
- package/src/sqlite/btree.ts +61 -17
- package/src/subgraph.ts +59 -30
- package/tools/haplotype-index/src/main.rs +13 -5
package/README.md
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# @gmod/gbz-base
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-
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`gbz-base query`, reading only the SQLite pages a query touches, so a
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multi-gigabyte database on an HTTP server is queried through range requests
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without downloading it or compiling anything to WebAssembly.
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[](https://npmjs.org/package/@gmod/gbz-base)
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the same way gbwt-rs does. Databases are produced by unmodified upstream
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`gbz-base construct`.
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A pure TypeScript reader for [gbz-base](https://github.com/jltsiren/gbz-base)
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pangenome databases (`.gbz.db`).
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## Usage
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```ts
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import { RemoteFile } from 'generic-filehandle2'
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import { GBZBase
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import { GBZBase } from '@gmod/gbz-base'
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const db = await GBZBase.open(
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new RemoteFile('https://example.org/graph.gbz.db'),
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)
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// one record per haplotype fragment crossing the window
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const alignments = await db.getAlignmentsForRange(
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'GRCh38#0#chr6',
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31500000,
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31501000,
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{ context: 0, haplotypes: 'all' },
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)
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// the same window as a subgraph, for a pangenome view
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const subgraph = await db.getSubgraphForRange(
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'GRCh38#0#chr6',
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31500000,
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31501000,
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)
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const gfa = await subgraph?.toGFA({ names: 'resolved' })
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```
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Coordinates are 0-based half-open, and are offsets along the path you named, so
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`('GRCh38#0#chr6', 31500000, 31501000)` is the same window
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`gbz-base query --interval 31500000..31501000` gives.
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The path is a PanSN `sample#haplotype#contig` string, or a bare contig for a
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graph whose reference paths have no sample. `{ sample, haplotype, contig }`
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works too, and `parsePathName` is the parser if you want it separately.
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Both take `{ context, haplotypes, snarls, limit, signal }` and both resolve
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haplotype names when the database can. `signal` is an `AbortSignal`; a query
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checks it between range requests, so an abort stops the next fetch rather than
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the one in flight.
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### One returns records, the other a query object
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`getAlignmentsForRange` hands back data, and spans path fragments — a window
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crossing a boundary queries each fragment and concatenates, which is
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coordinate-correct because a record's `refStart`/`refEnd` are absolute.
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`getSubgraphForRange` hands back the `Subgraph` itself, because two disjoint
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fragments do not merge into one graph. It answers for the first fragment
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overlapping the window, clamped to it, and `subgraph.referenceInterval` says
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which interval that was. It is `undefined` when the path is unknown, when no
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fragment overlaps the window, or when the clamped window is empty. Use
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`pathFragmentsForRange` to see the fragments yourself, and `hasPath` to ask
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about a path alone.
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A path that exists but was never indexed for random access throws rather than
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returning nothing — that is a database that needs rebuilding, not an empty
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window.
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### What an alignment is
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```ts
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for (const alignment of alignments) {
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const { refStart, refEnd, strand, cigar } = alignment
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if (alignment.resolved) {
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console.log(alignment.label, alignment.hapStart, alignment.hapEnd)
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}
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}
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```
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`
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`refStart`/`refEnd` are the fragment's span on the reference path you queried.
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They run to node boundaries, so a record can begin before the window you asked
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for and end after it. `cigar` is its alignment to that reference, computed like
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upstream: a node-length-weighted LCS, with the diverging stretches scored using
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vg's match, mismatch and gap parameters. `path` is the walk as node handles,
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`weight` is how many identical haplotypes it stands for, and `start` is its GBWT
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position, which is a property of the graph and so is stable across refetches of
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the same window.
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Naming a fragment needs the haplotype index described below, and a database
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without one cannot do it, so the record is a union on `resolved` rather than a
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handful of separately-undefined fields. A resolved one adds the `PathName` as
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`name`, its `HG02723#1#JAHEOU010000100.1[4392999-4393486]` rendering as `label`,
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the `pathHandle`, and `hapStart`/`hapEnd` in that haplotype's own coordinates.
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A haplotype whose walk shares no node with the reference has
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`refEnd <= refStart` and an all-insertion CIGAR; those come back like any other,
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to drop or keep as you like.
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### Sources
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Any object with `read(length, position)` and `stat()` works as a source, so
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`LocalFile`, `RemoteFile` and `BlobFile` from `generic-filehandle2` all do.
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Pages are fetched in blocks (64 KiB by default, `blockSize` in the open options)
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and cached.
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### Lower-level queries
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The two above cover the interval query and hide where a contig is stored split
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into path fragments. The four query functions underneath are what
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`gbz-base query` itself does, take a window you have already resolved, and leave
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identification to you:
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```ts
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import { subgraphAtOffset, subgraphInInterval } from '@gmod/gbz-base'
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const subgraph = await subgraphInInterval(
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db,
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{ sample: 'GRCh38', contig: 'chr6' },
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31500000,
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31501000,
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{ context: 0, haplotypes: 'all' },
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)
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await subgraph.identifyPaths()
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const graph = subgraph.toSubgraphJson({ cigar: true, names: 'resolved' })
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const gfa = await subgraph.toGFA({ cigar: true, names: 'resolved' })
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```
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`subgraphAtOffset` and `subgraphAroundNodes` are the other two;
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`subgraphBetween` is described under Snarls. They throw for a window that runs
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past the end of a path fragment, where `getAlignmentsForRange` clamps.
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The command line mirrors the upstream tool for the query types it supports:
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```
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At query time `subgraph.identifyPaths()` loads the samples for the window's node
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range in one index scan, chains each haplotype's fragments to the next through
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the private nodes between them, and walks at most one interval past the window
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for a chain that met no sample inside it.
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for a chain that met no sample inside it. This is what fills in the `resolved`
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half of a feature: PanSN name, haplotype interval in that contig's coordinates,
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and the path handle. `getAlignmentsForRange` and `getSubgraphForRange` run it
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for you when the database has the tables; on the lower-level path you call it
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yourself before `alignments()` or `toSubgraphJson({ names: 'resolved' })`. On
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the command line, `--resolve` and `--alignments`.
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The tests check every resolved fragment against an independent backward walk
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through the bidirectional GBWT to the path's recorded start position.
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## Technical notes
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It answers the same subgraph queries as `gbz-base query`, reading only the
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SQLite pages a query touches, so a multi-gigabyte database on an HTTP server is
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queried through range requests without downloading it or compiling anything to
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WebAssembly.
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No SQLite library is involved. The reader walks the SQLite b-trees directly
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(rowid lookups, index seeks, overflow chains) and decodes the GBWT node records
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the same way gbwt-rs does. Databases are produced by unmodified upstream
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`gbz-base construct`.
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## Fidelity
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`test/data/oracle/` holds JSON written by upstream `gbz-base query` for the
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package/dist/cli.js
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import { LocalFile, RemoteFile } from 'generic-filehandle2';
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import { GBZBase
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import { GBZBase } from "./db.js";
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import { encodeNode } from "./gbwt/node.js";
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import { subgraphAroundNodes, subgraphAtOffset, subgraphBetween, subgraphInInterval, } from "./query.js";
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const USAGE = `Usage: gbz-base-query [options] graph.gbz.db
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}
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return args;
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}
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function alignmentRecord(alignment) {
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const { start, ...rest } = alignment;
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return rest.resolved ? { ...rest, name: rest.label, label: undefined } : rest;
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}
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export async function main(argv) {
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const args = parseArgs(argv);
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const open = (file) => /^https?:\/\//.test(file) ? new RemoteFile(file) : new LocalFile(file);
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}
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const names = args.resolve ? 'resolved' : 'anonymous';
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const output = args.alignments
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? subgraph.alignments().map(
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name: a.name && a.hapStart !== undefined && a.hapEnd !== undefined
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? formatPathName({ ...a.name, fragment: a.hapStart }, a.hapEnd)
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: undefined,
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start: undefined,
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}))
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: subgraph.toJSON(args.cigar, { names });
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? subgraph.alignments().map(alignmentRecord)
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: subgraph.toSubgraphJson({ cigar: args.cigar, names });
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process.stdout.write(args.format === 'gfa' && !args.alignments
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? await subgraph.toGFA(args.cigar,
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? await subgraph.toGFA({ cigar: args.cigar, names })
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: `${JSON.stringify(output)}\n`);
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if (args.stats) {
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const { fetches, bytesFetched } = db.sqlite.pager;
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const index = db.index === db.sqlite
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? ''
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: ` (haplotype index: ${db.index.pager.fetches} fetches, ${db.index.pager.bytesFetched} bytes)`;
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const { orderedAlignments, lcsAlignments, identificationSteps, identificationFetches, } = subgraph.stats;
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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`);
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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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}
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}
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//# sourceMappingURL=cli.js.map
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package/dist/cli.js.map
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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,
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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
CHANGED
|
@@ -3,21 +3,21 @@ import { SqliteDatabase } from './sqlite/database.ts';
|
|
|
3
3
|
import type { ByteSource } from './filehandle.ts';
|
|
4
4
|
import type { Pos } from './gbwt/record.ts';
|
|
5
5
|
import type { GraphName } from './graphName.ts';
|
|
6
|
+
import type { PathName, PathRef } from './pathName.ts';
|
|
7
|
+
import type { QueryOptions } from './query.ts';
|
|
6
8
|
import type { PagerOptions } from './sqlite/pager.ts';
|
|
7
|
-
|
|
8
|
-
sample: string;
|
|
9
|
-
contig: string;
|
|
10
|
-
haplotype: number;
|
|
11
|
-
fragment: number;
|
|
12
|
-
}
|
|
13
|
-
export declare const GENERIC_SAMPLE = "_gbwt_ref";
|
|
9
|
+
import type { HaplotypeAlignment, Subgraph } from './subgraph.ts';
|
|
14
10
|
export declare const SCHEMA_VERSION = "GBZ-base version 4";
|
|
11
|
+
export interface PathFragment {
|
|
12
|
+
path: GbzPath;
|
|
13
|
+
start: number;
|
|
14
|
+
end: number;
|
|
15
|
+
}
|
|
15
16
|
export declare class SchemaVersionError extends Error {
|
|
16
17
|
name: string;
|
|
17
18
|
readonly found: string | undefined;
|
|
18
19
|
constructor(found: string | undefined);
|
|
19
20
|
}
|
|
20
|
-
export declare function formatPathName(name: PathName, end: number): string;
|
|
21
21
|
export interface HaplotypeSample {
|
|
22
22
|
node: number;
|
|
23
23
|
offset: number;
|
|
@@ -55,7 +55,7 @@ export declare class GBZBase {
|
|
|
55
55
|
private pathCache;
|
|
56
56
|
private indexTags;
|
|
57
57
|
readonly sqlite: SqliteDatabase;
|
|
58
|
-
|
|
58
|
+
readonly index: SqliteDatabase;
|
|
59
59
|
private constructor();
|
|
60
60
|
static open(source: ByteSource, opts?: OpenOptions): Promise<GBZBase>;
|
|
61
61
|
tags(): Promise<Map<string, string>>;
|
|
@@ -65,6 +65,15 @@ export declare class GBZBase {
|
|
|
65
65
|
getPath(handle: number): Promise<GbzPath | undefined>;
|
|
66
66
|
findPath(name: PathName): Promise<GbzPath | undefined>;
|
|
67
67
|
pathsForSample(sample: string): Promise<GbzPath[]>;
|
|
68
|
+
private pathsNamed;
|
|
69
|
+
hasPath(ref: PathRef): Promise<boolean>;
|
|
70
|
+
private pathLengths;
|
|
71
|
+
pathLength(handle: number): Promise<number>;
|
|
72
|
+
private walkPathLength;
|
|
73
|
+
pathFragmentsForRange(ref: PathRef, start: number, end: number): Promise<PathFragment[]>;
|
|
74
|
+
private subgraphForFragment;
|
|
75
|
+
getSubgraphForRange(ref: PathRef, start: number, end: number, opts?: QueryOptions): Promise<Subgraph | undefined>;
|
|
76
|
+
getAlignmentsForRange(ref: PathRef, start: number, end: number, opts?: QueryOptions): Promise<HaplotypeAlignment[]>;
|
|
68
77
|
graphName(): Promise<GraphName>;
|
|
69
78
|
hasChainLinks(): Promise<boolean>;
|
|
70
79
|
get hasHaplotypeIndex(): boolean;
|
package/dist/db.js
CHANGED
|
@@ -2,8 +2,9 @@ import { ENDMARKER, nodeId, nodeOrientation } from "./gbwt/node.js";
|
|
|
2
2
|
import { GbwtRecord, decompressEdges } from "./gbwt/record.js";
|
|
3
3
|
import { decodeSequence, encodedSequenceLength } from "./gbwt/sequence.js";
|
|
4
4
|
import { graphNameFromTags } from "./graphName.js";
|
|
5
|
+
import { formatPathName, pathNameFor, toPathQuery } from "./pathName.js";
|
|
6
|
+
import { subgraphInInterval } from "./query.js";
|
|
5
7
|
import { SqliteDatabase } from "./sqlite/database.js";
|
|
6
|
-
export const GENERIC_SAMPLE = '_gbwt_ref';
|
|
7
8
|
export const SCHEMA_VERSION = 'GBZ-base version 4';
|
|
8
9
|
export class SchemaVersionError extends Error {
|
|
9
10
|
name = 'SchemaVersionError';
|
|
@@ -15,9 +16,6 @@ export class SchemaVersionError extends Error {
|
|
|
15
16
|
this.found = found;
|
|
16
17
|
}
|
|
17
18
|
}
|
|
18
|
-
export function formatPathName(name, end) {
|
|
19
|
-
return `${name.sample}#${name.haplotype}#${name.contig}[${name.fragment}-${end}]`;
|
|
20
|
-
}
|
|
21
19
|
export class GbzRecord {
|
|
22
20
|
sequenceLen;
|
|
23
21
|
handle;
|
|
@@ -175,6 +173,99 @@ export class GBZBase {
|
|
|
175
173
|
async pathsForSample(sample) {
|
|
176
174
|
return (await this.paths()).filter(p => p.name.sample === sample);
|
|
177
175
|
}
|
|
176
|
+
async pathsNamed(ref) {
|
|
177
|
+
const name = pathNameFor(toPathQuery(ref), 0);
|
|
178
|
+
return (await this.paths())
|
|
179
|
+
.filter(p => p.name.sample === name.sample &&
|
|
180
|
+
p.name.contig === name.contig &&
|
|
181
|
+
p.name.haplotype === name.haplotype)
|
|
182
|
+
.sort((a, b) => a.name.fragment - b.name.fragment);
|
|
183
|
+
}
|
|
184
|
+
async hasPath(ref) {
|
|
185
|
+
return (await this.pathsNamed(ref)).length > 0;
|
|
186
|
+
}
|
|
187
|
+
pathLengths = new Map();
|
|
188
|
+
pathLength(handle) {
|
|
189
|
+
let length = this.pathLengths.get(handle);
|
|
190
|
+
if (!length) {
|
|
191
|
+
length = this.walkPathLength(handle);
|
|
192
|
+
this.pathLengths.set(handle, length);
|
|
193
|
+
length.catch(() => this.pathLengths.delete(handle));
|
|
194
|
+
}
|
|
195
|
+
return length;
|
|
196
|
+
}
|
|
197
|
+
async walkPathLength(handle) {
|
|
198
|
+
const indexed = this.hasHaplotypeIndex
|
|
199
|
+
? await this.haplotypeLength(handle)
|
|
200
|
+
: undefined;
|
|
201
|
+
if (indexed === undefined) {
|
|
202
|
+
const last = await this.indexedPosition(handle, Number.MAX_SAFE_INTEGER);
|
|
203
|
+
if (!last) {
|
|
204
|
+
const path = await this.getPath(handle);
|
|
205
|
+
throw new Error(`Path ${path ? formatPathName(path.name, path.name.fragment) : handle} has not been indexed for random access`);
|
|
206
|
+
}
|
|
207
|
+
let length = last.pathOffset;
|
|
208
|
+
let pos = last.pos;
|
|
209
|
+
for (;;) {
|
|
210
|
+
const record = await this.getRecord(pos.node);
|
|
211
|
+
if (!record) {
|
|
212
|
+
throw new Error(`Node ${pos.node} does not exist in the graph`);
|
|
213
|
+
}
|
|
214
|
+
length += record.sequenceLen;
|
|
215
|
+
const next = record.gbwt().lf(pos.offset);
|
|
216
|
+
if (!next || next.node === ENDMARKER) {
|
|
217
|
+
return length;
|
|
218
|
+
}
|
|
219
|
+
pos = next;
|
|
220
|
+
}
|
|
221
|
+
}
|
|
222
|
+
return indexed;
|
|
223
|
+
}
|
|
224
|
+
async pathFragmentsForRange(ref, start, end) {
|
|
225
|
+
if (end <= start) {
|
|
226
|
+
return [];
|
|
227
|
+
}
|
|
228
|
+
const ordered = await this.pathsNamed(ref);
|
|
229
|
+
const covering = ordered.filter(p => p.name.fragment <= start).slice(-1);
|
|
230
|
+
const within = ordered.filter(p => p.name.fragment > start && p.name.fragment < end);
|
|
231
|
+
const fragments = await Promise.all([...covering, ...within].map(async (path) => ({
|
|
232
|
+
path,
|
|
233
|
+
start: path.name.fragment,
|
|
234
|
+
end: path.name.fragment + (await this.pathLength(path.handle)),
|
|
235
|
+
})));
|
|
236
|
+
return fragments.filter(f => start < f.end);
|
|
237
|
+
}
|
|
238
|
+
async subgraphForFragment(fragment, start, end, opts) {
|
|
239
|
+
const lo = Math.max(start, fragment.start);
|
|
240
|
+
const hi = Math.min(end, fragment.end);
|
|
241
|
+
let subgraph;
|
|
242
|
+
if (hi > lo) {
|
|
243
|
+
const { sample, contig, haplotype } = fragment.path.name;
|
|
244
|
+
subgraph = await subgraphInInterval(this, { sample, contig, haplotype }, lo, hi, opts);
|
|
245
|
+
const haplotypes = opts.haplotypes ?? 'all';
|
|
246
|
+
const named = haplotypes === 'all' || haplotypes === 'distinct';
|
|
247
|
+
if (this.hasHaplotypeIndex && named) {
|
|
248
|
+
await subgraph.identifyPaths();
|
|
249
|
+
}
|
|
250
|
+
}
|
|
251
|
+
return subgraph;
|
|
252
|
+
}
|
|
253
|
+
async getSubgraphForRange(ref, start, end, opts = {}) {
|
|
254
|
+
const [fragment] = await this.pathFragmentsForRange(ref, start, end);
|
|
255
|
+
return fragment
|
|
256
|
+
? this.subgraphForFragment(fragment, start, end, opts)
|
|
257
|
+
: undefined;
|
|
258
|
+
}
|
|
259
|
+
async getAlignmentsForRange(ref, start, end, opts = {}) {
|
|
260
|
+
const result = [];
|
|
261
|
+
for (const fragment of await this.pathFragmentsForRange(ref, start, end)) {
|
|
262
|
+
const subgraph = await this.subgraphForFragment(fragment, start, end, opts);
|
|
263
|
+
if (subgraph) {
|
|
264
|
+
result.push(...subgraph.alignments());
|
|
265
|
+
}
|
|
266
|
+
}
|
|
267
|
+
return result;
|
|
268
|
+
}
|
|
178
269
|
async graphName() {
|
|
179
270
|
const gbzTags = new Map();
|
|
180
271
|
for (const [key, value] of await this.tags()) {
|
package/dist/db.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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AC,IAAI,CAAA;YACxD,QAAQ,GAAG,MAAM,kBAAkB,CACjC,IAAI,EACJ,EAAE,MAAM,EAAE,MAAM,EAAE,SAAS,EAAE,EAC7B,EAAE,EACF,EAAE,EACF,IAAI,CACL,CAAA;YACD,MAAM,UAAU,GAAG,IAAI,CAAC,UAAU,IAAI,KAAK,CAAA;YAC3C,MAAM,KAAK,GAAG,UAAU,KAAK,KAAK,IAAI,UAAU,KAAK,UAAU,CAAA;YAC/D,IAAI,IAAI,CAAC,iBAAiB,IAAI,KAAK,EAAE,CAAC;gBACpC,MAAM,QAAQ,CAAC,aAAa,EAAE,CAAA;YAChC,CAAC;QACH,CAAC;QACD,OAAO,QAAQ,CAAA;IACjB,CAAC;IAED,KAAK,CAAC,mBAAmB,CACvB,GAAY,EACZ,KAAa,EACb,GAAW,EACX,OAAqB,EAAE;QAEvB,MAAM,CAAC,QAAQ,CAAC,GAAG,MAAM,IAAI,CAAC,qBAAqB,CAAC,GAAG,EAAE,KAAK,EAAE,GAAG,CAAC,CAAA;QACpE,OAAO,QAAQ;YACb,CAAC,CAAC,IAAI,CAAC,mBAAmB,CAAC,QAAQ,EAAE,KAAK,EAAE,GAAG,EAAE,IAAI,CAAC;YACtD,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,KAAK,CAAC,qBAAqB,CACzB,GAAY,EACZ,KAAa,EACb,GAAW,EACX,OAAqB,EAAE;QAEvB,MAAM,MAAM,GAAyB,EAAE,CAAA;QACvC,KAAK,MAAM,QAAQ,IAAI,MAAM,IAAI,CAAC,qBAAqB,CAAC,GAAG,EAAE,KAAK,EAAE,GAAG,CAAC,EAAE,CAAC;YACzE,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,mBAAmB,CAC7C,QAAQ,EACR,KAAK,EACL,GAAG,EACH,IAAI,CACL,CAAA;YACD,IAAI,QAAQ,EAAE,CAAC;gBACb,MAAM,CAAC,IAAI,CAAC,GAAG,QAAQ,CAAC,UAAU,EAAE,CAAC,CAAA;YACvC,CAAC;QACH,CAAC;QACD,OAAO,MAAM,CAAA;IACf,CAAC;IAED,KAAK,CAAC,SAAS;QACb,MAAM,OAAO,GAAG,IAAI,GAAG,EAAkB,CAAA;QACzC,KAAK,MAAM,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,MAAM,IAAI,CAAC,IAAI,EAAE,EAAE,CAAC;YAC7C,IAAI,GAAG,CAAC,UAAU,CAAC,MAAM,CAAC,EAAE,CAAC;gBAC3B,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,KAAK,CAAC,CAAA;YAC9C,CAAC;QACH,CAAC;QACD,IAAI,IAAI,GAAc;YACpB,IAAI,EAAE,SAAS;YACf,QAAQ,EAAE,IAAI,GAAG,EAAE;YACnB,WAAW,EAAE,IAAI,GAAG,EAAE;SACvB,CAAA;QACD,IAAI,CAAC;YACH,IAAI,GAAG,iBAAiB,CAAC,OAAO,CAAC,CAAA;QACnC,CAAC;QAAC,MAAM,CAAC;YACP,kEAAkE;QACpE,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,KAAK,CAAC,aAAa;QACjB,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,aAAa,CAAC,CAAA;QAC3C,OAAO,KAAK,KAAK,SAAS,IAAI,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;IACjD,CAAC;IAED,IAAI,iBAAiB;QACnB,OAAO,CACL,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,kBAAkB,CAAC,IAAI,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,kBAAkB,CAAC,CACzE,CAAA;IACH,CAAC;IAED,KAAK,CAAC,uBAAuB;QAC3B,MAAM,KAAK,GAAG,IAAI,CAAC,SAAS;YAC1B,CAAC,CAAC,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,0BAA0B,CAAC;YAChD,CAAC,CAAC,MAAM,IAAI,CAAC,GAAG,CAAC,0BAA0B,CAAC,CAAA;QAC9C,OAAO,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;IACxD,CAAC;IAEO,aAAa,CAAC,MAAkB;QACtC,OAAO;YACL,IAAI,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,8BAA8B,CAAC;YACpD,MAAM,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,8BAA8B,CAAC;YACtD,UAAU,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,8BAA8B,CAAC;YAC1D,WAAW,EACT,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,8BAA8B,CAAC,KAAK,CAAC;gBAClD,CAAC,CAAC,SAAS;gBACX,CAAC,CAAC,SAAS;YACf,UAAU,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,8BAA8B,CAAC;SAC3D,CAAA;IACH,CAAC;IAED,KAAK,CAAC,uBAAuB,CAAC,SAAiB,EAAE,SAAiB;QAChE,MAAM,OAAO,GAAsB,EAAE,CAAA;QACrC,IAAI,KAAK,EAAE,MAAM,GAAG,IAAI,IAAI,CAAC,KAAK,CAAC,aAAa,CAAC,kBAAkB,EAAE;YACnE,SAAS;YACT,CAAC;SACF,CAAC,EAAE,CAAC;YACH,MAAM,IAAI,GAAG,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,8BAA8B,CAAC,CAAA;YACxD,IAAI,IAAI,GAAG,SAAS,EAAE,CAAC;gBACrB,MAAK;YACP,CAAC;YACD,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,OAAO,CAClC,kBAAkB,EAClB,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,wBAAwB,CAAC,CACtC,CAAA;YACD,IAAI,GAAG,EAAE,CAAC;gBACR,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,aAAa,CAAC,GAAG,CAAC,CAAC,CAAA;YACvC,CAAC;QACH,CAAC;QACD,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,KAAK,CAAC,iBAAiB,CAAC,IAAY,EAAE,MAAc;QAClD,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,kBAAkB,EAAE,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC,CAAA;QAC5E,IAAI,GAAG,EAAE,CAAC,CAAC,CAAC,KAAK,IAAI,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,MAAM,EAAE,CAAC;YAC3C,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,OAAO,CAClC,kBAAkB,EAClB,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,wBAAwB,CAAC,CACtC,CAAA;QACD,OAAO,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IAClD,CAAC;IAED,KAAK,CAAC,eAAe,CAAC,UAAkB;QACtC,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,kBAAkB,EAAE,UAAU,CAAC,CAAA;QACpE,OAAO,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,yBAAyB,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IACjE,CAAC;IAED,KAAK,CAAC,eAAe,CACnB,UAAkB,EAClB,UAAkB;QAElB,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,gBAAgB,EAAE;YAC1D,UAAU;YACV,UAAU;SACX,CAAC,CAAA;QACF,IAAI,GAAG,EAAE,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE,CAAC;YAC5B,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,OAAO,CACnC,gBAAgB,EAChB,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,sBAAsB,CAAC,CACpC,CAAA;QACD,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,MAAM,IAAI,KAAK,CAAC,uDAAuD,CAAC,CAAA;QAC1E,CAAC;QACD,OAAO;YACL,UAAU,EAAE,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,4BAA4B,CAAC;YACrD,GAAG,EAAE;gBACH,IAAI,EAAE,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,4BAA4B,CAAC;gBAC/C,MAAM,EAAE,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,4BAA4B,CAAC;aAClD;SACF,CAAA;IACH,CAAC;CACF"}
|
package/dist/index.d.ts
CHANGED
|
@@ -1,11 +1,13 @@
|
|
|
1
|
-
export { GBZBase,
|
|
2
|
-
export type { GbzPath, HaplotypeSample, OpenOptions,
|
|
1
|
+
export { GBZBase, GbzRecord, SCHEMA_VERSION, SchemaVersionError } from './db.ts';
|
|
2
|
+
export type { GbzPath, HaplotypeSample, OpenOptions, PathFragment, } from './db.ts';
|
|
3
|
+
export { GENERIC_SAMPLE, formatPathName, parsePathName } from './pathName.ts';
|
|
4
|
+
export type { PathName, PathQuery, PathRef } from './pathName.ts';
|
|
3
5
|
export type { ByteSource } from './filehandle.ts';
|
|
4
6
|
export type { Pos } from './gbwt/record.ts';
|
|
5
7
|
export { Subgraph } from './subgraph.ts';
|
|
6
|
-
export type { HaplotypeAlignment, HaplotypeOutput, PathIdentity, PathPosition, ReferencePath, SnarlOutput, SubgraphJson,
|
|
8
|
+
export type { AlignmentSpan, HaplotypeAlignment, HaplotypeOutput, PathIdentity, PathPosition, ReferencePath, SnarlOutput, SubgraphJson, SubgraphOptions, SubgraphOutputOptions, SubgraphPath, } from './subgraph.ts';
|
|
7
9
|
export { subgraphAroundNodes, subgraphAtOffset, subgraphBetween, subgraphInInterval, } from './query.ts';
|
|
8
|
-
export type {
|
|
10
|
+
export type { QueryOptions } from './query.ts';
|
|
9
11
|
export { SqliteDatabase } from './sqlite/database.ts';
|
|
10
12
|
export type { GraphName } from './graphName.ts';
|
|
11
13
|
export { weightedLcs } from './lcs.ts';
|
package/dist/index.js
CHANGED
|
@@ -1,4 +1,5 @@
|
|
|
1
|
-
export { GBZBase,
|
|
1
|
+
export { GBZBase, GbzRecord, SCHEMA_VERSION, SchemaVersionError } from "./db.js";
|
|
2
|
+
export { GENERIC_SAMPLE, formatPathName, parsePathName } from "./pathName.js";
|
|
2
3
|
export { Subgraph } from "./subgraph.js";
|
|
3
4
|
export { subgraphAroundNodes, subgraphAtOffset, subgraphBetween, subgraphInInterval, } from "./query.js";
|
|
4
5
|
export { SqliteDatabase } from "./sqlite/database.js";
|
package/dist/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,
|
|
1
|
+
{"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"}
|
|
@@ -0,0 +1,17 @@
|
|
|
1
|
+
export interface PathName {
|
|
2
|
+
sample: string;
|
|
3
|
+
contig: string;
|
|
4
|
+
haplotype: number;
|
|
5
|
+
fragment: number;
|
|
6
|
+
}
|
|
7
|
+
export interface PathQuery {
|
|
8
|
+
sample?: string;
|
|
9
|
+
contig: string;
|
|
10
|
+
haplotype?: number;
|
|
11
|
+
}
|
|
12
|
+
export type PathRef = string | PathQuery;
|
|
13
|
+
export declare const GENERIC_SAMPLE = "_gbwt_ref";
|
|
14
|
+
export declare function formatPathName(name: PathName, end: number): string;
|
|
15
|
+
export declare function parsePathName(name: string): PathQuery;
|
|
16
|
+
export declare function toPathQuery(ref: PathRef): PathQuery;
|
|
17
|
+
export declare function pathNameFor(query: PathQuery, fragment: number): PathName;
|
package/dist/pathName.js
ADDED
|
@@ -0,0 +1,33 @@
|
|
|
1
|
+
export const GENERIC_SAMPLE = '_gbwt_ref';
|
|
2
|
+
export function formatPathName(name, end) {
|
|
3
|
+
return `${name.sample}#${name.haplotype}#${name.contig}[${name.fragment}-${end}]`;
|
|
4
|
+
}
|
|
5
|
+
const PAN_SN = /^([^#]+)#(\d+)#([^#]+?)(?:\[\d+-\d+\])?$/;
|
|
6
|
+
const BARE_CONTIG = /^([^#]+?)(?:\[\d+-\d+\])?$/;
|
|
7
|
+
export function parsePathName(name) {
|
|
8
|
+
const panSn = PAN_SN.exec(name);
|
|
9
|
+
if (panSn) {
|
|
10
|
+
return {
|
|
11
|
+
sample: panSn[1],
|
|
12
|
+
haplotype: Number(panSn[2]),
|
|
13
|
+
contig: panSn[3],
|
|
14
|
+
};
|
|
15
|
+
}
|
|
16
|
+
const bare = BARE_CONTIG.exec(name);
|
|
17
|
+
if (bare) {
|
|
18
|
+
return { contig: bare[1] };
|
|
19
|
+
}
|
|
20
|
+
throw new Error(`"${name}" is not a path name; expected "sample#haplotype#contig" or a bare contig`);
|
|
21
|
+
}
|
|
22
|
+
export function toPathQuery(ref) {
|
|
23
|
+
return typeof ref === 'string' ? parsePathName(ref) : ref;
|
|
24
|
+
}
|
|
25
|
+
export function pathNameFor(query, fragment) {
|
|
26
|
+
return {
|
|
27
|
+
sample: query.sample ?? GENERIC_SAMPLE,
|
|
28
|
+
contig: query.contig,
|
|
29
|
+
haplotype: query.haplotype ?? 0,
|
|
30
|
+
fragment,
|
|
31
|
+
};
|
|
32
|
+
}
|
|
33
|
+
//# sourceMappingURL=pathName.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"pathName.js","sourceRoot":"","sources":["../src/pathName.ts"],"names":[],"mappings":"AAeA,MAAM,CAAC,MAAM,cAAc,GAAG,WAAW,CAAA;AAEzC,MAAM,UAAU,cAAc,CAAC,IAAc,EAAE,GAAW;IACxD,OAAO,GAAG,IAAI,CAAC,MAAM,IAAI,IAAI,CAAC,SAAS,IAAI,IAAI,CAAC,MAAM,IAAI,IAAI,CAAC,QAAQ,IAAI,GAAG,GAAG,CAAA;AACnF,CAAC;AAED,MAAM,MAAM,GAAG,0CAA0C,CAAA;AACzD,MAAM,WAAW,GAAG,4BAA4B,CAAA;AAEhD,MAAM,UAAU,aAAa,CAAC,IAAY;IACxC,MAAM,KAAK,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;IAC/B,IAAI,KAAK,EAAE,CAAC;QACV,OAAO;YACL,MAAM,EAAE,KAAK,CAAC,CAAC,CAAE;YACjB,SAAS,EAAE,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;YAC3B,MAAM,EAAE,KAAK,CAAC,CAAC,CAAE;SAClB,CAAA;IACH,CAAC;IACD,MAAM,IAAI,GAAG,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;IACnC,IAAI,IAAI,EAAE,CAAC;QACT,OAAO,EAAE,MAAM,EAAE,IAAI,CAAC,CAAC,CAAE,EAAE,CAAA;IAC7B,CAAC;IACD,MAAM,IAAI,KAAK,CACb,IAAI,IAAI,2EAA2E,CACpF,CAAA;AACH,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,GAAY;IACtC,OAAO,OAAO,GAAG,KAAK,QAAQ,CAAC,CAAC,CAAC,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;AAC3D,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,KAAgB,EAAE,QAAgB;IAC5D,OAAO;QACL,MAAM,EAAE,KAAK,CAAC,MAAM,IAAI,cAAc;QACtC,MAAM,EAAE,KAAK,CAAC,MAAM;QACpB,SAAS,EAAE,KAAK,CAAC,SAAS,IAAI,CAAC;QAC/B,QAAQ;KACT,CAAA;AACH,CAAC"}
|
package/dist/query.d.ts
CHANGED
|
@@ -1,18 +1,16 @@
|
|
|
1
1
|
import { Subgraph } from './subgraph.ts';
|
|
2
2
|
import type { GBZBase } from './db.ts';
|
|
3
|
+
import type { PathQuery } from './pathName.ts';
|
|
3
4
|
import type { HaplotypeOutput, SnarlOutput } from './subgraph.ts';
|
|
5
|
+
export type { PathQuery } from './pathName.ts';
|
|
4
6
|
export interface QueryOptions {
|
|
5
|
-
context?: number;
|
|
6
|
-
haplotypes?: HaplotypeOutput;
|
|
7
|
-
snarls?: SnarlOutput;
|
|
8
|
-
limit?: number;
|
|
9
|
-
|
|
10
|
-
export interface PathQuery {
|
|
11
|
-
sample?: string;
|
|
12
|
-
contig: string;
|
|
13
|
-
haplotype?: number;
|
|
7
|
+
context?: number | undefined;
|
|
8
|
+
haplotypes?: HaplotypeOutput | undefined;
|
|
9
|
+
snarls?: SnarlOutput | undefined;
|
|
10
|
+
limit?: number | undefined;
|
|
11
|
+
signal?: AbortSignal | undefined;
|
|
14
12
|
}
|
|
15
13
|
export declare function subgraphAtOffset(db: GBZBase, query: PathQuery, offset: number, opts?: QueryOptions): Promise<Subgraph>;
|
|
16
14
|
export declare function subgraphInInterval(db: GBZBase, query: PathQuery, start: number, end: number, opts?: QueryOptions): Promise<Subgraph>;
|
|
17
15
|
export declare function subgraphAroundNodes(db: GBZBase, nodes: number[], opts?: QueryOptions): Promise<Subgraph>;
|
|
18
|
-
export declare function subgraphBetween(db: GBZBase, start: number, end: number, opts?: Pick<QueryOptions, 'haplotypes' | 'limit'>): Promise<Subgraph>;
|
|
16
|
+
export declare function subgraphBetween(db: GBZBase, start: number, end: number, opts?: Pick<QueryOptions, 'haplotypes' | 'limit' | 'signal'>): Promise<Subgraph>;
|