@gmod/gbz-base 1.1.0 → 2.1.0

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.
Files changed (30) hide show
  1. package/README.md +136 -26
  2. package/dist/cli.js +12 -11
  3. package/dist/cli.js.map +1 -1
  4. package/dist/db.d.ts +18 -9
  5. package/dist/db.js +100 -4
  6. package/dist/db.js.map +1 -1
  7. package/dist/index.d.ts +6 -4
  8. package/dist/index.js +2 -1
  9. package/dist/index.js.map +1 -1
  10. package/dist/pathName.d.ts +17 -0
  11. package/dist/pathName.js +33 -0
  12. package/dist/pathName.js.map +1 -0
  13. package/dist/query.d.ts +8 -10
  14. package/dist/query.js +7 -19
  15. package/dist/query.js.map +1 -1
  16. package/dist/sqlite/btree.d.ts +2 -0
  17. package/dist/sqlite/btree.js +48 -18
  18. package/dist/sqlite/btree.js.map +1 -1
  19. package/dist/subgraph.d.ts +28 -13
  20. package/dist/subgraph.js +91 -37
  21. package/dist/subgraph.js.map +1 -1
  22. package/package.json +1 -1
  23. package/src/cli.ts +19 -13
  24. package/src/db.ts +160 -13
  25. package/src/index.ts +12 -10
  26. package/src/pathName.ts +54 -0
  27. package/src/query.ts +17 -32
  28. package/src/sqlite/btree.ts +61 -17
  29. package/src/subgraph.ts +117 -52
  30. package/tools/haplotype-index/src/main.rs +33 -16
package/dist/subgraph.js.map CHANGED
@@ -1 +1 @@
1
- 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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@gmod/gbz-base",
3
- "version": "1.1.0",
3
+ "version": "2.1.0",
4
4
  "description": "Pure TypeScript reader for gbz-base pangenome databases (.gbz.db) with random access over HTTP range requests",
5
5
  "license": "MIT",
6
6
  "packageManager": "pnpm@11.15.1",
package/src/cli.ts CHANGED
@@ -1,6 +1,6 @@
1
1
  import { LocalFile, RemoteFile } from 'generic-filehandle2'
2
2
 
3
- import { GBZBase, formatPathName } from './db.ts'
3
+ import { GBZBase } from './db.ts'
4
4
  import { encodeNode } from './gbwt/node.ts'
5
5
  import {
6
6
  subgraphAroundNodes,
@@ -9,7 +9,11 @@ import {
9
9
  subgraphInInterval,
10
10
  } from './query.ts'
11
11
 
12
- import type { HaplotypeOutput, SnarlOutput } from './subgraph.ts'
12
+ import type {
13
+ HaplotypeAlignment,
14
+ HaplotypeOutput,
15
+ SnarlOutput,
16
+ } from './subgraph.ts'
13
17
 
14
18
  const USAGE = `Usage: gbz-base-query [options] graph.gbz.db
15
19
 
@@ -183,6 +187,11 @@ function parseArgs(argv: string[]): Args {
183
187
  return args
184
188
  }
185
189
 
190
+ function alignmentRecord(alignment: HaplotypeAlignment) {
191
+ const { start, ...rest } = alignment
192
+ return rest.resolved ? { ...rest, name: rest.label, label: undefined } : rest
193
+ }
194
+
186
195
  export async function main(argv: string[]) {
187
196
  const args = parseArgs(argv)
188
197
  const open = (file: string) =>
@@ -229,22 +238,19 @@ export async function main(argv: string[]) {
229
238
  }
230
239
  const names = args.resolve ? 'resolved' : 'anonymous'
231
240
  const output = args.alignments
232
- ? subgraph.alignments().map(a => ({
233
- ...a,
234
- name:
235
- a.name && a.hapStart !== undefined && a.hapEnd !== undefined
236
- ? formatPathName({ ...a.name, fragment: a.hapStart }, a.hapEnd)
237
- : undefined,
238
- start: undefined,
239
- }))
240
- : subgraph.toJSON(args.cigar, { names })
241
+ ? subgraph.alignments().map(alignmentRecord)
242
+ : subgraph.toSubgraphJson({ cigar: args.cigar, names })
241
243
  process.stdout.write(
242
244
  args.format === 'gfa' && !args.alignments
243
- ? await subgraph.toGFA(args.cigar, { names })
245
+ ? await subgraph.toGFA({ cigar: args.cigar, names })
244
246
  : `${JSON.stringify(output)}\n`,
245
247
  )
246
248
  if (args.stats) {
247
249
  const { fetches, bytesFetched } = db.sqlite.pager
250
+ const index =
251
+ db.index === db.sqlite
252
+ ? ''
253
+ : ` (haplotype index: ${db.index.pager.fetches} fetches, ${db.index.pager.bytesFetched} bytes)`
248
254
  const {
249
255
  orderedAlignments,
250
256
  lcsAlignments,
@@ -252,7 +258,7 @@ export async function main(argv: string[]) {
252
258
  identificationFetches,
253
259
  } = subgraph.stats
254
260
  process.stderr.write(
255
- `Subgraph contains ${subgraph.nodeCount} nodes and ${subgraph.pathCount} paths; ${fetches} fetches, ${bytesFetched} bytes; ${orderedAlignments} ordered + ${lcsAlignments} lcs alignments; identification ${identificationSteps} steps, ${identificationFetches} lookups\n`,
261
+ `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`,
256
262
  )
257
263
  }
258
264
  }
package/src/db.ts CHANGED
@@ -2,24 +2,27 @@ import { ENDMARKER, nodeId, nodeOrientation } from './gbwt/node.ts'
2
2
  import { GbwtRecord, decompressEdges } from './gbwt/record.ts'
3
3
  import { decodeSequence, encodedSequenceLength } from './gbwt/sequence.ts'
4
4
  import { graphNameFromTags } from './graphName.ts'
5
+ import { formatPathName, pathNameFor, toPathQuery } from './pathName.ts'
6
+ import { subgraphInInterval } from './query.ts'
5
7
  import { SqliteDatabase } from './sqlite/database.ts'
6
8
 
7
9
  import type { ByteSource } from './filehandle.ts'
8
10
  import type { Pos } from './gbwt/record.ts'
9
11
  import type { GraphName } from './graphName.ts'
12
+ import type { PathName, PathRef } from './pathName.ts'
13
+ import type { QueryOptions } from './query.ts'
10
14
  import type { PagerOptions } from './sqlite/pager.ts'
11
15
  import type { SqlValue } from './sqlite/record.ts'
16
+ import type { HaplotypeAlignment, Subgraph } from './subgraph.ts'
12
17
 
13
- export interface PathName {
14
- sample: string
15
- contig: string
16
- haplotype: number
17
- fragment: number
18
- }
19
-
20
- export const GENERIC_SAMPLE = '_gbwt_ref'
21
18
  export const SCHEMA_VERSION = 'GBZ-base version 4'
22
19
 
20
+ export interface PathFragment {
21
+ path: GbzPath
22
+ start: number
23
+ end: number
24
+ }
25
+
23
26
  export class SchemaVersionError extends Error {
24
27
  override name = 'SchemaVersionError'
25
28
 
@@ -35,10 +38,6 @@ export class SchemaVersionError extends Error {
35
38
  }
36
39
  }
37
40
 
38
- export function formatPathName(name: PathName, end: number) {
39
- return `${name.sample}#${name.haplotype}#${name.contig}[${name.fragment}-${end}]`
40
- }
41
-
42
41
  export interface HaplotypeSample {
43
42
  node: number
44
43
  offset: number
@@ -164,7 +163,7 @@ export class GBZBase {
164
163
  private indexTags: Map<string, string> | undefined
165
164
 
166
165
  readonly sqlite: SqliteDatabase
167
- private readonly index: SqliteDatabase
166
+ readonly index: SqliteDatabase
168
167
 
169
168
  private constructor(sqlite: SqliteDatabase, index: SqliteDatabase) {
170
169
  this.sqlite = sqlite
@@ -197,6 +196,13 @@ export class GBZBase {
197
196
  `haplotype index was built for ${indexed ?? 'an unknown number of'} paths but the graph has ${paths}`,
198
197
  )
199
198
  }
199
+ const indexedNodes = db.indexTags.get('haplotype_index_nodes')
200
+ const nodes = await db.tag('nodes')
201
+ if (indexedNodes !== undefined && indexedNodes !== nodes) {
202
+ throw new Error(
203
+ `haplotype index was built for a graph with ${indexedNodes} nodes but this one has ${nodes}`,
204
+ )
205
+ }
200
206
  }
201
207
  return db
202
208
  }
@@ -256,6 +262,147 @@ export class GBZBase {
256
262
  return (await this.paths()).filter(p => p.name.sample === sample)
257
263
  }
258
264
 
265
+ private async pathsNamed(ref: PathRef) {
266
+ const name = pathNameFor(toPathQuery(ref), 0)
267
+ return (await this.paths())
268
+ .filter(
269
+ p =>
270
+ p.name.sample === name.sample &&
271
+ p.name.contig === name.contig &&
272
+ p.name.haplotype === name.haplotype,
273
+ )
274
+ .sort((a, b) => a.name.fragment - b.name.fragment)
275
+ }
276
+
277
+ async hasPath(ref: PathRef) {
278
+ return (await this.pathsNamed(ref)).length > 0
279
+ }
280
+
281
+ private pathLengths = new Map<number, Promise<number>>()
282
+
283
+ pathLength(handle: number) {
284
+ let length = this.pathLengths.get(handle)
285
+ if (!length) {
286
+ length = this.walkPathLength(handle)
287
+ this.pathLengths.set(handle, length)
288
+ length.catch(() => this.pathLengths.delete(handle))
289
+ }
290
+ return length
291
+ }
292
+
293
+ private async walkPathLength(handle: number) {
294
+ const indexed = this.hasHaplotypeIndex
295
+ ? await this.haplotypeLength(handle)
296
+ : undefined
297
+ if (indexed === undefined) {
298
+ const last = await this.indexedPosition(handle, Number.MAX_SAFE_INTEGER)
299
+ if (!last) {
300
+ const path = await this.getPath(handle)
301
+ throw new Error(
302
+ `Path ${path ? formatPathName(path.name, path.name.fragment) : handle} has not been indexed for random access`,
303
+ )
304
+ }
305
+ let length = last.pathOffset
306
+ let pos = last.pos
307
+ for (;;) {
308
+ const record = await this.getRecord(pos.node)
309
+ if (!record) {
310
+ throw new Error(`Node ${pos.node} does not exist in the graph`)
311
+ }
312
+ length += record.sequenceLen
313
+ const next = record.gbwt().lf(pos.offset)
314
+ if (!next || next.node === ENDMARKER) {
315
+ return length
316
+ }
317
+ pos = next
318
+ }
319
+ }
320
+ return indexed
321
+ }
322
+
323
+ async pathFragmentsForRange(
324
+ ref: PathRef,
325
+ start: number,
326
+ end: number,
327
+ ): Promise<PathFragment[]> {
328
+ if (end <= start) {
329
+ return []
330
+ }
331
+ const ordered = await this.pathsNamed(ref)
332
+ const covering = ordered.filter(p => p.name.fragment <= start).slice(-1)
333
+ const within = ordered.filter(
334
+ p => p.name.fragment > start && p.name.fragment < end,
335
+ )
336
+ const fragments = await Promise.all(
337
+ [...covering, ...within].map(async path => ({
338
+ path,
339
+ start: path.name.fragment,
340
+ end: path.name.fragment + (await this.pathLength(path.handle)),
341
+ })),
342
+ )
343
+ return fragments.filter(f => start < f.end)
344
+ }
345
+
346
+ private async subgraphForFragment(
347
+ fragment: PathFragment,
348
+ start: number,
349
+ end: number,
350
+ opts: QueryOptions,
351
+ ) {
352
+ const lo = Math.max(start, fragment.start)
353
+ const hi = Math.min(end, fragment.end)
354
+ let subgraph: Subgraph | undefined
355
+ if (hi > lo) {
356
+ const { sample, contig, haplotype } = fragment.path.name
357
+ subgraph = await subgraphInInterval(
358
+ this,
359
+ { sample, contig, haplotype },
360
+ lo,
361
+ hi,
362
+ opts,
363
+ )
364
+ const haplotypes = opts.haplotypes ?? 'all'
365
+ const named = haplotypes === 'all' || haplotypes === 'distinct'
366
+ if (this.hasHaplotypeIndex && named) {
367
+ await subgraph.identifyPaths()
368
+ }
369
+ }
370
+ return subgraph
371
+ }
372
+
373
+ async getSubgraphForRange(
374
+ ref: PathRef,
375
+ start: number,
376
+ end: number,
377
+ opts: QueryOptions = {},
378
+ ) {
379
+ const [fragment] = await this.pathFragmentsForRange(ref, start, end)
380
+ return fragment
381
+ ? this.subgraphForFragment(fragment, start, end, opts)
382
+ : undefined
383
+ }
384
+
385
+ async getAlignmentsForRange(
386
+ ref: PathRef,
387
+ start: number,
388
+ end: number,
389
+ opts: QueryOptions = {},
390
+ ) {
391
+ const result: HaplotypeAlignment[] = []
392
+ for (const fragment of await this.pathFragmentsForRange(ref, start, end)) {
393
+ const subgraph = await this.subgraphForFragment(
394
+ fragment,
395
+ start,
396
+ end,
397
+ opts,
398
+ )
399
+ if (subgraph) {
400
+ result.push(...subgraph.alignments())
401
+ }
402
+ }
403
+ return result
404
+ }
405
+
259
406
  async graphName() {
260
407
  const gbzTags = new Map<string, string>()
261
408
  for (const [key, value] of await this.tags()) {
package/src/index.ts CHANGED
@@ -1,16 +1,17 @@
1
- export {
2
- GBZBase,
3
- GENERIC_SAMPLE,
4
- GbzRecord,
5
- SCHEMA_VERSION,
6
- SchemaVersionError,
7
- formatPathName,
1
+ export { GBZBase, GbzRecord, SCHEMA_VERSION, SchemaVersionError } from './db.ts'
2
+ export type {
3
+ GbzPath,
4
+ HaplotypeSample,
5
+ OpenOptions,
6
+ PathFragment,
8
7
  } from './db.ts'
9
- export type { GbzPath, HaplotypeSample, OpenOptions, PathName } from './db.ts'
8
+ export { GENERIC_SAMPLE, formatPathName, parsePathName } from './pathName.ts'
9
+ export type { PathName, PathQuery, PathRef } from './pathName.ts'
10
10
  export type { ByteSource } from './filehandle.ts'
11
11
  export type { Pos } from './gbwt/record.ts'
12
12
  export { Subgraph } from './subgraph.ts'
13
13
  export type {
14
+ AlignmentSpan,
14
15
  HaplotypeAlignment,
15
16
  HaplotypeOutput,
16
17
  PathIdentity,
@@ -18,8 +19,9 @@ export type {
18
19
  ReferencePath,
19
20
  SnarlOutput,
20
21
  SubgraphJson,
22
+ SubgraphOptions,
23
+ SubgraphOutputOptions,
21
24
  SubgraphPath,
22
- ToJsonOptions,
23
25
  } from './subgraph.ts'
24
26
  export {
25
27
  subgraphAroundNodes,
@@ -27,7 +29,7 @@ export {
27
29
  subgraphBetween,
28
30
  subgraphInInterval,
29
31
  } from './query.ts'
30
- export type { PathQuery, QueryOptions } from './query.ts'
32
+ export type { QueryOptions } from './query.ts'
31
33
  export { SqliteDatabase } from './sqlite/database.ts'
32
34
  export type { GraphName } from './graphName.ts'
33
35
  export { weightedLcs } from './lcs.ts'
package/src/pathName.ts ADDED
@@ -0,0 +1,54 @@
1
+ export interface PathName {
2
+ sample: string
3
+ contig: string
4
+ haplotype: number
5
+ fragment: number
6
+ }
7
+
8
+ export interface PathQuery {
9
+ sample?: string
10
+ contig: string
11
+ haplotype?: number
12
+ }
13
+
14
+ export type PathRef = string | PathQuery
15
+
16
+ export const GENERIC_SAMPLE = '_gbwt_ref'
17
+
18
+ export function formatPathName(name: PathName, end: number) {
19
+ return `${name.sample}#${name.haplotype}#${name.contig}[${name.fragment}-${end}]`
20
+ }
21
+
22
+ const PAN_SN = /^([^#]+)#(\d+)#([^#]+?)(?:\[\d+-\d+\])?$/
23
+ const BARE_CONTIG = /^([^#]+?)(?:\[\d+-\d+\])?$/
24
+
25
+ export function parsePathName(name: string): PathQuery {
26
+ const panSn = PAN_SN.exec(name)
27
+ if (panSn) {
28
+ return {
29
+ sample: panSn[1]!,
30
+ haplotype: Number(panSn[2]),
31
+ contig: panSn[3]!,
32
+ }
33
+ }
34
+ const bare = BARE_CONTIG.exec(name)
35
+ if (bare) {
36
+ return { contig: bare[1]! }
37
+ }
38
+ throw new Error(
39
+ `"${name}" is not a path name; expected "sample#haplotype#contig" or a bare contig`,
40
+ )
41
+ }
42
+
43
+ export function toPathQuery(ref: PathRef) {
44
+ return typeof ref === 'string' ? parsePathName(ref) : ref
45
+ }
46
+
47
+ export function pathNameFor(query: PathQuery, fragment: number): PathName {
48
+ return {
49
+ sample: query.sample ?? GENERIC_SAMPLE,
50
+ contig: query.contig,
51
+ haplotype: query.haplotype ?? 0,
52
+ fragment,
53
+ }
54
+ }