jbrowse-plugin-graphgenomeviewer 7.3.0 → 7.3.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "jbrowse-plugin-graphgenomeviewer",
-  "version": "7.3.0",
+  "version": "7.3.2",
   "description": "JBrowse 2 graph genome (pangenome) view: rGFA reference-anchored layouts, the Bandage force-directed engine, and haplotype lanes read from a gbz-base database",
   "license": "GPL-3.0-or-later",
   "repository": {
@@ -32,7 +32,7 @@
     "@jbrowse/core": "5.0.0-beta.11",
     "@jbrowse/display-kit": "5.0.0-beta.11",
     "@jbrowse/display-ui": "5.0.0-beta.11",
-    "@jbrowse/graph-walks": "^2.1.0",
+    "@jbrowse/graph-walks": "^3.1.0",
     "@jbrowse/render-core": "5.0.0-beta.11",
     "@jbrowse/synteny-core": "5.0.0-beta.11"
   },
@@ -40,7 +40,7 @@
     "@emotion/react": "^11.14.0",
     "@emotion/styled": "^11.14.1",
     "@eslint/js": "^10.0.1",
-    "@jbrowse/bandage-core": "^11.4.0",
+    "@jbrowse/bandage-core": "^11.6.1",
     "@jbrowse/cli": "^4.3.0",
     "@jbrowse/mobx-state-tree": "^6.9.0",
     "@jbrowse/plugin-linear-genome-view": "5.0.0-beta.11",

package/src/RgfaTabixAdapter/RgfaTabixAdapter.ts

@@ -90,7 +90,9 @@ export default class RgfaTabixAdapter extends BaseFeatureDataAdapter<RgfaTabixAd
     return refNames.regionBytes(
       regions,
       opts,
-      walks && (start => walks.reader.queryStart(start, opts)),
+      walks &&
+        ((refName, { start, end }) =>
+          walks.reader.queryStart(start, { ...opts, refName, end })),
     )
   }
 

package/src/RgfaTabixAdapter/configSchema.ts

@@ -30,8 +30,8 @@ import type { Instance } from '@jbrowse/mobx-state-tree'
  * `walksUri` takes the prefix of a walk file in place of `uri`, and resolves
  * `<walksUri>.walks.bed.gz` and its `.tbi`. `gfa-to-tabix --walks -o <prefix>`
  * writes one per reference sample, so a track names one as
- * `<prefix>.<sample>`. The adapter reads walk format 3, which gfa-to-tabix
- * writes from 1.1, through @jbrowse/graph-walks. Such a graph's cut carries
+ * `<prefix>.<sample>`. The adapter reads walk format 4, which gfa-to-tabix
+ * writes from 1.2, through @jbrowse/graph-walks. Such a graph's cut carries
  * the haplotypes' walks, and `defaultHaplotypes` names the ones it is cut for
  * until the user picks others.
  *
@@ -48,7 +48,7 @@ import type { Instance } from '@jbrowse/mobx-state-tree'
  * ```js
  * {
  *   type: 'RgfaTabixAdapter',
- *   walksUri: 'https://example.org/hprc-v2.1-mc-grch38.GRCh38',
+ *   walksUri: 'https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38-f4.GRCh38',
  *   assemblyNameToPanSN: { hg38: 'GRCh38' },
  *   defaultHaplotypes: ['HG002', 'HG00733', 'HG02257', 'NA19240'],
  * }
@@ -152,7 +152,7 @@ const RgfaTabixAdapter = ConfigurationSchema(
     ),
     /**
      * #slot
-     * a `gfa-to-tabix --walks` file in walk format 3: per reference chunk,
+     * a `gfa-to-tabix --walks` file in walk format 4: per reference chunk,
      * the reference's path, the ways haplotypes leave it and each haplotype's
      * piece. Unset means the graph has no walks.
      */

package/src/RgfaTabixAdapter/walkFiles.test.ts

@@ -17,9 +17,9 @@ import type { WalkCut } from './walkCut.ts'
 import type { GraphTables } from '@jbrowse/bandage-core/gfa/graphTables'
 
 // chr22 of HPRC v2.1 at base level, one walk file per reference in walk
-// format 3, built under ~/work/scratch/walks-20261008/f3. Skipped where the
+// format 4, built under ~/work/scratch/walks-20261008/f4. Skipped where the
 // files are absent.
-const chr22 = '/home/cdiesh/work/scratch/walks-20261008/f3/chr22'
+const chr22 = '/home/cdiesh/work/scratch/walks-20261008/f4/chr22'
 const present = ['GRCh38', 'CHM13'].every(sample =>
   existsSync(`${chr22}.${sample}.walks.bed.gz`),
 )
@@ -34,27 +34,27 @@ const fixture = (name: string) =>
 //   W HG002   1 chr1 >1>2>7>4>5>6   7 replaces 3
 //   W HG002   2 chr1 >1>2>3>4>8>6   8 replaces 5
 //   W HG00097 1 chr1 >1>2>3>4>5>6
-const headerPrefix = fixture('walks3_header')
+const headerPrefix = fixture('walks4_header')
 
-// walks3_header's walks with the reference named as pggb names a P-line,
+// walks4_header's walks with the reference named as pggb names a P-line,
 // GRCh38#chr1
-const twoPartPrefix = fixture('walks3_twopart')
+const twoPartPrefix = fixture('walks4_twopart')
 
 // An unchopped graph, node 1 spanning 0-2600 and filed under chunk 0 alone:
 //   W GRCh38 0 chr1 >1>2>4
 //   W HG002  1 chr1 >1>3>4   3 replaces 2
-const maxNodePrefix = fixture('walks3_maxnode')
+const maxNodePrefix = fixture('walks4_maxnode')
 
 // Twelve 500 bp reference nodes over chr1:0-6000 in one 10 kb chunk:
 //   W GRCh38  0 chr1 >1>2>3>4>5>6>7>8>9>10>11>12
 //   W HG002   1 chr1 >1>2>3>20>21>9>10>11>12   20 and 21, 2 kb each, replace 4-8
 //   W HG002   2 chr1 >1>2>3>4>5>6>7>8>9>10>11>12
 //   W HG003   1 chr1 >1>2>3>22                 the contig ends on 22, 300 bp
-const rejoinPrefix = fixture('walks3_rejoin')
+const rejoinPrefix = fixture('walks4_rejoin')
 
 // The same graph in 1 kb chunks, whose rows name the chunks their path goes on
 // in: HG002#1 leaves chunk 1000 for 20 and 21 and rejoins at 9, in chunk 4000
-const followPrefix = fixture('walks3_follow')
+const followPrefix = fixture('walks4_follow')
 
 function makeAdapter(prefix: string, slots = {}) {
   const local = (path: string) => ({
@@ -215,7 +215,7 @@ test('a cut for some haplotypes keeps a reference walk named without a haplotype
 
 test('a format 1 walk file is refused, with what to rebuild it with', async () => {
   const cut = makeAdapter(fixture('walks1_header')).getSubgraph(chr1(0, 600))
-  await expect(cut).rejects.toThrow(/rebuild it with gfa-to-tabix 1.1/)
+  await expect(cut).rejects.toThrow(/rebuild it with gfa-to-tabix 1.2/)
 })
 
 test('a cut over walkByteBudget reads no row', async () => {

package/src/RgfaTabixAdapter/walkReader.ts

@@ -87,7 +87,11 @@ export class WalkIndex {
     await getLines(
       this.file,
       refName,
-      await this.reader.queryStart(region.start, opts),
+      await this.reader.queryStart(region.start, {
+        ...opts,
+        refName,
+        end: region.end,
+      }),
       region.end,
       {
         signal: opts.signal,

package/src/WalkTabixSyntenyAdapter/WalkTabixSyntenyAdapter.test.ts

@@ -34,7 +34,7 @@ const fixture = (name: string) =>
 
 function makeAdapter(
   slots: Record<string, unknown> = {},
-  name = 'walks3_header',
+  name = 'walks4_header',
 ) {
   const local = (path: string) => ({
     localPath: path,
@@ -111,7 +111,7 @@ test('a fetch for some haplotypes answers those lanes in the order asked, named
 })
 
 test('a fetch for some haplotypes reads them against a reference walk named without a haplotype', async () => {
-  const found = await feats(makeAdapter({}, 'walks3_twopart'), {
+  const found = await feats(makeAdapter({}, 'walks4_twopart'), {
     haplotypes: ['HG002#1'],
   })
   expect(found.map(summary)).toEqual([
@@ -172,7 +172,7 @@ test('a batch of lane pairs answers each pair what it answers alone', async () =
   expect(batch).toHaveLength(2)
 })
 
-// walks3_lanepairs, a 5.5 kb reference of 2 kb flanks around three 500 bp
+// walks4_lanepairs, a 5.5 kb reference of 2 kb flanks around three 500 bp
 // nodes, in 1 kb chunks:
 //   W GRCh38  0 chr1 >1>2>3>4>5
 //   W HG002   1 chr1 >1>2>3>4>5
@@ -180,7 +180,7 @@ test('a batch of lane pairs answers each pair what it answers alone', async () =
 //   W HG00097 1 chr1 >1>2>6>2>6>2>3>4>5   2 three times, 6 a 30 bp spacer
 test('a lane pair matches through a copy-number array, and draws an inversion between the lanes as a reverse-strand record', async () => {
   const found = await firstValueFrom(
-    makeAdapter({}, 'walks3_lanepairs')
+    makeAdapter({}, 'walks4_lanepairs')
       .getFeatures(
         { ...window, end: 5500 },
         {
@@ -554,7 +554,7 @@ test('a walk turned against the reference for 10 kb or more gains a reverse-stra
 //   W HG00097 1 chr1 >1>2>3>4>5
 test('the anchor window answers a haplotype turned against the reference with a reverse-strand record of the turned stretch', async () => {
   const records = await firstValueFrom(
-    makeAdapter({}, 'walks3_inversion')
+    makeAdapter({}, 'walks4_inversion')
       .getFeatures({ ...window, end: 55_000 }, {})
       .pipe(toArray()),
   )

package/src/WalkTabixSyntenyAdapter/configSchema.ts

@@ -25,14 +25,14 @@ import type { Instance } from '@jbrowse/mobx-state-tree'
  *
  * `walksUri` takes the prefix of one reference's walk file, `<prefix>.<sample>`,
  * and resolves `<walksUri>.walks.bed.gz` and its `.tbi`. The adapter reads walk
- * format 3, which gfa-to-tabix writes from 1.1, through @jbrowse/graph-walks.
+ * format 4, which gfa-to-tabix writes from 1.2, through @jbrowse/graph-walks.
  * Only a window on the anchor is answered.
  *
  * #example
  * ```js
  * {
  *   type: 'WalkTabixSyntenyAdapter',
- *   walksUri: 'https://example.org/hprc-v2.1-mc-grch38.GRCh38',
+ *   walksUri: 'https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38-f4.GRCh38',
  *   assemblyNames: ['hg38'],
  *   assemblyNameToPanSN: { hg38: 'GRCh38' },
  * }
@@ -56,7 +56,7 @@ const WalkTabixSyntenyAdapter = ConfigurationSchema(
     },
     /**
      * #slot
-     * a `gfa-to-tabix --walks` file in walk format 3
+     * a `gfa-to-tabix --walks` file in walk format 4
      */
     walksLocation: fileLocationSlot('/path/to/graph.walks.bed.gz'),
     /**

package/src/WalkTabixSyntenyAdapter/gbzParity.test.ts

@@ -12,10 +12,10 @@ import type { Feature } from '@jbrowse/core/util'
 import type { SyntenyMate } from '@jbrowse/synteny-core'
 
 // chr22 of HPRC v2.1 as a gbz-base database and as gfa-to-tabix's GRCh38
-// walk file in walk format 3, built 2026-10-08 and 2026-10-16. Skipped where
+// walk file in walk format 4, built 2026-10-08 and 2026-10-20. Skipped where
 // the files are absent.
 const dir = '/home/cdiesh/work/scratch/walks-20261008'
-const walkPrefix = `${dir}/f3/chr22.GRCh38`
+const walkPrefix = `${dir}/f4/chr22.GRCh38`
 const present =
   existsSync(`${walkPrefix}.walks.bed.gz`) && existsSync(`${dir}/chr22.gbz.db`)
 

package/src/panSNAliases/panSNAliases.test.ts

@@ -123,11 +123,11 @@ describe("a lanes track anchored on an alias of the window's assembly", () => {
           {
             type: 'WalkTabixSyntenyAdapter',
             walksLocation: local(
-              '../RgfaTabixAdapter/test_data/walks3_header.GRCh38.walks.bed.gz',
+              '../RgfaTabixAdapter/test_data/walks4_header.GRCh38.walks.bed.gz',
             ),
             walksIndex: {
               location: local(
-                '../RgfaTabixAdapter/test_data/walks3_header.GRCh38.walks.bed.gz.tbi',
+                '../RgfaTabixAdapter/test_data/walks4_header.GRCh38.walks.bed.gz.tbi',
               ),
             },
             assemblyNames: ['GRCh38'],

package/src/panSNTabix.ts

@@ -182,12 +182,12 @@ export class PanSNRefNames {
   /**
    * The compressed bytes a read of `regions` fetches from the file, as its
    * index estimates them, for the display's byte gate. `queryStart` moves a
-   * region's start to where the read begins.
+   * window's start to where the read begins.
    */
   async regionBytes(
     regions: Region[],
     opts: BaseOptions = {},
-    queryStart = async (start: number) => start,
+    queryStart = async (_refName: string, region: Region) => region.start,
   ) {
     const spans = []
     for (const region of regions) {
@@ -195,7 +195,7 @@ export class PanSNRefNames {
       if (refName !== undefined) {
         spans.push({
           refName,
-          start: await queryStart(region.start),
+          start: await queryStart(refName, region),
           end: region.end,
         })
       }

package/src/version.ts

@@ -1 +1 @@
-export const version = '7.3.0'
+export const version = '7.3.2'

package/dist/chunks/GbzBaseSyntenyAdapter-FXMGIM7Z.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.4.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-TUQKGAK3.js", "../../src/GbzBaseSyntenyAdapter/companion.ts", "../../src/gaf/gafFile.ts", "../../src/GbzBaseSyntenyAdapter/GbzBaseSyntenyAdapter.ts"],
-  "sourcesContent": ["import {\n  GBZ_CUT_DEFAULTS,\n  NoReferenceSampleError,\n  aliasedSample,\n  cutWindowGFA,\n  haplotypeWanted,\n  referencePathQuery,\n  referenceSamplesOf\n} from \"./chunk-NMWQUFPF.js\";\nimport {\n  panSNSample\n} from \"./chunk-4XWZNPQ2.js\";\n\n// src/gbzCut.ts\nimport { GBZBase } from \"@gmod/gbz-base\";\nvar HPRC_GBZ = {\n  db: \"https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/release2/minigraph-cactus/v2.1/hprc-v2.1-mc-grch38/hprc-v2.1-mc-grch38.gbz.db\",\n  index: \"https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38.haplotype-index.f3.db\"\n};\nfunction gbzLocations({ db, index }) {\n  return db === \"hprc\" ? { db: HPRC_GBZ.db, index: index ?? HPRC_GBZ.index } : { db, index };\n}\nfunction haplotypeIndexBeside(db) {\n  const GBZ_DB = /\\.gbz\\.db$/i;\n  return GBZ_DB.test(db) ? db.replace(GBZ_DB, \".haplotype-index.db\") : void 0;\n}\nfunction parseRegion(text) {\n  const m = /^\\s*([^:\\s]+):([\\d,]+)-([\\d,]+)\\s*$/.exec(text);\n  if (!m) {\n    throw new Error(\n      `\"${text}\" is not a region like chr6:160,614,798-160,647,758`\n    );\n  }\n  const n = (s) => Number(s.replaceAll(\",\", \"\"));\n  const region = { refName: m[1], start: n(m[2]), end: n(m[3]) };\n  if (region.end <= region.start) {\n    throw new Error(`\"${text}\" ends at or before it starts`);\n  }\n  return region;\n}\nasync function openGbz(db, index) {\n  const base = await GBZBase.open({ source: db, haplotypeIndex: index });\n  return { base, referenceSamples: await referenceSamplesOf(base) };\n}\nfunction referenceSample(ref, samples) {\n  if (ref) {\n    return aliasedSample(panSNSample(ref), samples) ?? ref;\n  }\n  const first = samples[0];\n  if (first === void 0) {\n    throw new NoReferenceSampleError(\"\", samples);\n  }\n  return first;\n}\nasync function cutGbzRegion({ base, referenceSamples }, src, signal) {\n  const region = parseRegion(src.region);\n  const sample = referenceSample(src.referenceSample, referenceSamples);\n  const query = await referencePathQuery(base, sample, region.refName);\n  if (!query) {\n    throw new Error(`${sample} has no indexed path named ${region.refName}`);\n  }\n  signal?.throwIfAborted();\n  const wanted = src.haplotypes?.length ? src.haplotypes : void 0;\n  const text = await cutWindowGFA(base, query, region.start, region.end, {\n    context: src.context ?? GBZ_CUT_DEFAULTS.context,\n    snarls: src.snarls ?? GBZ_CUT_DEFAULTS.snarls,\n    limit: GBZ_CUT_DEFAULTS.limit,\n    signal,\n    keep: wanted ? (name) => haplotypeWanted(name, wanted) : void 0\n  });\n  return { text, region, sample };\n}\n\nexport {\n  HPRC_GBZ,\n  gbzLocations,\n  haplotypeIndexBeside,\n  parseRegion,\n  openGbz,\n  cutGbzRegion\n};\n", "import { haplotypeIndexBeside } from '@jbrowse/bandage-core/gbzCut'\nimport { openLocation } from '@jbrowse/core/util/io'\n\nimport { locationName, readsSiblings, renamed } from '../locationName'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { FileLocation } from '@jbrowse/core/util/types'\n\nexport function siblingCompanion(gbzDb: FileLocation) {\n  return readsSiblings(gbzDb) && haplotypeIndexBeside(locationName(gbzDb))\n    ? renamed(gbzDb, name => haplotypeIndexBeside(name)!)\n    : undefined\n}\n\n// 404 is a missing file, and so is 403 from a bucket that does not let a\n// reader list it; anything else leaves the file's presence unknown\nfunction isMissing(error: unknown) {\n  return (\n    error instanceof Error &&\n    (/\\bHTTP 40[34]\\b/.test(error.message) ||\n      (error as { code?: unknown }).code === 'ENOENT')\n  )\n}\n\n// `unreadable` is why a companion that may be there could not be checked, such\n// as a network error, or a server that answers a missing file without CORS\nexport async function findCompanion(\n  gbzDb: FileLocation,\n  pluginManager?: PluginManager,\n): Promise<{ location?: FileLocation; unreadable?: string }> {\n  const candidate = siblingCompanion(gbzDb)\n  if (!candidate) {\n    return {}\n  }\n  try {\n    await openLocation(candidate, pluginManager).stat()\n    return { location: candidate }\n  } catch (error) {\n    return isMissing(error) ? {} : { unreadable: String(error) }\n  }\n}\n", "import { unzip } from '@gmod/bgzf-filehandle'\nimport { parseGaf, parseGafLine } from '@jbrowse/bandage-core/gaf/parseGaf'\nimport { cachedSetup } from '@jbrowse/core/data_adapters/BaseAdapter'\n\nimport type { TabixIndexedFile } from '@gmod/tabix'\nimport type { GafRecord } from '@jbrowse/bandage-core/gaf/parseGaf'\n\ninterface WholeFile {\n  stat(): Promise<{ size: number }>\n  readFile(opts?: { signal?: AbortSignal }): Promise<Uint8Array>\n}\n\nexport interface GafReads {\n  records: GafRecord[]\n  // reads over the nodes before sampling\n  total: number\n}\n\n// The tube map lays reads out on the main thread at about 40 ms per thousand\nexport const MAX_READS = 5000\n\n// An unindexed GAF is read whole, once, into the worker\nconst MAX_UNINDEXED_BYTES = 50 * 2 ** 20\n\nexport class UnindexedGafTooLargeError extends Error {\n  override name = 'UnindexedGafTooLargeError'\n\n  constructor(size: number) {\n    super(\n      `this GAF is ${(size / 2 ** 20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`,\n    )\n  }\n}\n\n// Evenly spaced, so a pileup thins out rather than losing its right half\nfunction sample(records: GafRecord[], max: number) {\n  if (records.length <= max) {\n    return records\n  }\n  const stride = records.length / max\n  return Array.from({ length: max }, (_, k) => records[Math.floor(k * stride)]!)\n}\n\nconst touches = (record: GafRecord, names: ReadonlySet<string>) =>\n  record.path.some(step => names.has(step.name))\n\n// A GAF over a graph's segments: bgzipped and indexed with `tabix -p gaf`,\n// which keys each line by its lowest and highest node id and so needs numeric\n// segment names, or plain or gzipped and read whole.\nexport class GafFile {\n  // Shared by every window, so the signal is cachedSetup's own, which aborts\n  // once no caller is left waiting\n  private whole = cachedSetup({\n    setup: async ({ signal }) => {\n      const { size } = await this.file.stat()\n      if (size > MAX_UNINDEXED_BYTES) {\n        throw new UnindexedGafTooLargeError(size)\n      }\n      const bytes = await this.file.readFile({ signal })\n      const text = new TextDecoder().decode(\n        bytes[0] === 0x1f && bytes[1] === 0x8b ? await unzip(bytes) : bytes,\n      )\n      return parseGaf(text)\n    },\n  })\n\n  constructor(\n    private file: WholeFile,\n    private tabix?: TabixIndexedFile,\n  ) {}\n\n  private async readIndexed(\n    tabix: TabixIndexedFile,\n    names: ReadonlySet<string>,\n    signal?: AbortSignal,\n  ) {\n    let lo = Infinity\n    let hi = -Infinity\n    for (const name of names) {\n      const id = Number(name)\n      if (Number.isInteger(id)) {\n        lo = Math.min(lo, id)\n        hi = Math.max(hi, id)\n      }\n    }\n    const records: GafRecord[] = []\n    if (lo <= hi) {\n      // a GAF index ignores the refName, and getLines keeps a read whose node\n      // ids span min..max when min < end && max >= start, hence hi + 1\n      await tabix.getLines('{node}', lo, hi + 1, {\n        signal,\n        lineCallback: line => {\n          const record = parseGafLine(line)\n          if (record && touches(record, names)) {\n            records.push(record)\n          }\n        },\n      })\n    }\n    return records\n  }\n\n  async readsOver(\n    names: ReadonlySet<string>,\n    { signal }: { signal?: AbortSignal } = {},\n  ): Promise<GafReads> {\n    const records = this.tabix\n      ? await this.readIndexed(this.tabix, names, signal)\n      : (await this.whole({ signal })).filter(r => touches(r, names))\n    return { records: sample(records, MAX_READS), total: records.length }\n  }\n}\n", "import { GBZBase, SubgraphLimitError } from '@gmod/gbz-base'\nimport {\n  NodeLimitError,\n  cutWindowTables,\n  haplotypePrefix,\n  haplotypeWanted,\n  nodeLimitError,\n  referencePathQuery,\n  referenceSamplesOf,\n  resolveReferenceSample,\n} from '@jbrowse/bandage-core/gbzWindow'\nimport {\n  assemblyByPanSNPrefix,\n  panSNMatchesPrefix,\n  resolvePanSNPrefix,\n} from '@jbrowse/bandage-core/pansn'\nimport { cachedSetup } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { getBpDisplayStr, updateStatus } from '@jbrowse/core/util'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\n\nimport { findCompanion } from './companion.ts'\nimport { walkCutFor } from '../RgfaTabixAdapter/walkCut.ts'\nimport { GafFile } from '../gaf/gafFile.ts'\nimport { locationIsSet } from '../locationName.ts'\nimport { openTabixSlot } from '../panSNTabix.ts'\nimport { ComparativeAdapterBase } from '../synteny/ComparativeAdapterBase.ts'\nimport SyntenyFeature from '../synteny/SyntenyFeature.ts'\nimport {\n  laneAssemblyName,\n  lanePairsStatus,\n  requestedPairs,\n} from '../synteny/lanePairs.ts'\nimport { laneZoomNotice } from '../synteny/laneZoomNotice.ts'\nimport { matchFeature } from '../synteny/matchFeature.ts'\n\nimport type { GbzBaseSyntenyAdapterConfig } from './configSchema.ts'\nimport type { SubgraphAdapterOptions } from '../GetSubgraph.ts'\nimport type { GafReads } from '../gaf/gafFile.ts'\nimport type { LaneFeatureOptions, LanePair } from '../synteny/lanePairs.ts'\nimport type {\n  HaplotypeAlignment,\n  HaplotypeRef,\n  PairAlignment,\n  PathName,\n  PathQuery,\n  Subgraph,\n} from '@gmod/gbz-base'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util'\nimport type { FileLocation, Region } from '@jbrowse/core/util/types'\n\nexport class NoHaplotypeIndexError extends Error {\n  override name = 'NoHaplotypeIndexError'\n\n  constructor(unreadable?: string) {\n    super(\n      unreadable === undefined\n        ? 'no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation'\n        : `the haplotype index beside the graph database could not be checked (${unreadable}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`,\n    )\n  }\n}\n\ninterface GbzHaplotype {\n  prefix: string\n  sample: string\n  haplotype: number\n  contigs: string[]\n  isReference: boolean\n}\n\n/**\n * One lane the header declares, in the shape MultiWaySyntenyDisplay's lane\n * picker reads: `name` is the lane's assembly name, the same string the\n * fetched features' mates carry, `label` its PanSN prefix and `group` its\n * sample, so a diploid sample's two lanes sit together\n */\ninterface GbzHeaderLane {\n  name: string\n  label: string\n  group: string\n}\n\nexport { PairTargetError } from '../synteny/lanePairs.ts'\n\nclass HaplotypeWindowError extends Error {\n  override name = 'HaplotypeWindowError'\n\n  constructor(assemblyName: string, anchor: string) {\n    super(\n      `the graph is cut on its reference, ${anchor}; a window on ${assemblyName} has no reference coordinates to cut at. Open the graph from a ${anchor} view, and find this haplotype's lane there`,\n    )\n  }\n}\n\ntype ResolvedAlignment = Extract<HaplotypeAlignment, { resolved: true }>\n\n/**\n * The id of one haplotype fragment: the walk's GBWT position at its first node\n * in the window, which is a property of the graph, so the same fragment gets\n * the same id on a refetch of the same window and the display's hover and\n * selection survive it. `clipToRegion` suffixes the window.\n */\nfunction fragmentId(name: PathName, alignment: ResolvedAlignment) {\n  return `${haplotypePrefix(name)}#${name.contig}@${alignment.start.node}.${alignment.start.offset}`\n}\n\nfunction fragmentFeature({\n  alignment,\n  assemblyName,\n  refName,\n  lane,\n}: {\n  alignment: ResolvedAlignment\n  assemblyName: string\n  refName: string\n  lane: string\n}) {\n  const { refStart, refEnd, strand, cigar } = alignment\n  if (refEnd <= refStart) {\n    return undefined\n  } else {\n    const { name, hapStart, hapEnd } = alignment\n    const id = fragmentId(name, alignment)\n    const data: SimpleFeatureSerialized = {\n      uniqueId: id,\n      assemblyName,\n      refName,\n      start: refStart,\n      end: refEnd,\n      type: 'match',\n      strand: strand === '-' ? -1 : 1,\n      CIGAR: cigar,\n      syntenyId: id,\n      mate: {\n        refName: name.contig,\n        start: hapStart,\n        end: hapEnd,\n        assemblyName: lane,\n      },\n    }\n    return new SyntenyFeature(data)\n  }\n}\n\n// gbz-base writes the CIGAR along the target, which is the side a JBrowse\n// feature is, so it passes through unchanged\nfunction pairFeature({\n  pair,\n  lane,\n  mateLane,\n}: {\n  pair: PairAlignment\n  lane: string\n  mateLane: string\n}) {\n  return matchFeature({\n    target: {\n      name: `${haplotypePrefix(pair.target)}#${pair.target.contig}`,\n      assemblyName: lane,\n      refName: pair.target.contig,\n      start: pair.targetStart,\n      end: pair.targetEnd,\n    },\n    query: {\n      name: `${haplotypePrefix(pair.query)}#${pair.query.contig}`,\n      assemblyName: mateLane,\n      refName: pair.query.contig,\n      start: pair.queryStart,\n      end: pair.queryEnd,\n    },\n    strand: pair.strand,\n    cigar: pair.cigar,\n    matches: pair.matches,\n    columns: pair.columns,\n  })\n}\n\n// The longest detour a pair cut widens its context to take in\nconst BRIDGE_MAX_BP = 120_000\n\n/**\n * The widest gap, up to `BRIDGE_MAX_BP`, between two pieces of one kept walk:\n * a haplotype that left the cut's nodes for sequence the reference lacks and\n * came back. Two kept haplotypes that share that sequence only align across it\n * once its nodes are in the cut.\n */\nexport function widestWalkGap(subgraphs: Subgraph[], kept: Set<string>) {\n  const byPath = new Map<string, [number, number][]>()\n  for (const subgraph of subgraphs) {\n    for (const { name, start, end } of subgraph.walkSpans()) {\n      const prefix = haplotypePrefix(name)\n      if (kept.has(prefix)) {\n        const key = `${prefix}#${name.contig}`\n        const spans = byPath.get(key)\n        if (spans) {\n          spans.push([start, end])\n        } else {\n          byPath.set(key, [[start, end]])\n        }\n      }\n    }\n  }\n  let widest = 0\n  for (const spans of byPath.values()) {\n    spans.sort((a, b) => a[0] - b[0])\n    for (let i = 1; i < spans.length; i++) {\n      const gap = spans[i]![0] - spans[i - 1]![1]\n      if (gap > 0 && gap <= BRIDGE_MAX_BP) {\n        widest = Math.max(widest, gap)\n      }\n    }\n  }\n  return widest\n}\n\n// A window past the node limit fails as a zoom-in notice naming a span that\n// fits\nfunction zoomInNotice(error: unknown, what: string) {\n  if (error instanceof NodeLimitError) {\n    error.message = `Zoom in to about ${getBpDisplayStr(error.fitsBp)} to see ${what}`\n  }\n  return error\n}\n\nconst laneLimitNotice = (error: unknown, nodeLimit: number, windowBp: number) =>\n  laneZoomNotice(\n    zoomInNotice(nodeLimitError(error, nodeLimit, windowBp) ?? error, 'lanes'),\n    windowBp,\n  )\n\n// gbz-base reads whole bp; a view asks at fractional ones\nconst wholeBp = (region: Region) => ({\n  ...region,\n  start: Math.floor(region.start),\n  end: Math.ceil(region.end),\n})\n\nexport default class GbzBaseSyntenyAdapter extends ComparativeAdapterBase<GbzBaseSyntenyAdapterConfig> {\n  private graph = cachedSetup({\n    label: 'Opening pangenome database',\n    setup: async () => {\n      const gbzDb: FileLocation = this.getConf('gbzDbLocation')\n      const configured: FileLocation = this.getConf('haplotypeIndexLocation')\n      const companion = locationIsSet(configured)\n        ? { location: configured }\n        : await findCompanion(gbzDb, this.pluginManager)\n      const indexLocation = companion.location\n      const db = await GBZBase.open({\n        source: openLocation(gbzDb, this.pluginManager),\n        haplotypeIndex: indexLocation\n          ? openLocation(indexLocation, this.pluginManager)\n          : undefined,\n      })\n      const anchor = this.getConf('assemblyNames')[0]\n      if (anchor === undefined) {\n        throw new Error(\n          'GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as',\n        )\n      }\n      const referenceSamples = await referenceSamplesOf(db)\n      const referenceSample = resolveReferenceSample({\n        configured: this.getConf('referenceSample'),\n        anchorPrefix: resolvePanSNPrefix(this, anchor),\n        referenceSamples,\n      })\n      return {\n        db,\n        anchor,\n        referenceSample,\n        referenceSamples,\n        unreadableIndex: companion.unreadable,\n      }\n    },\n  })\n\n  /**\n   * The indexed reference path a window on `refName` resolves against, or\n   * undefined when the reference sample has no indexed path by that contig.\n   */\n  private async referenceQuery(\n    refName: string,\n    opts: BaseOptions,\n  ): Promise<PathQuery | undefined> {\n    const { db, referenceSample } = await this.graph(opts)\n    return referencePathQuery(db, referenceSample, refName)\n  }\n\n  /**\n   * Every haplotype the graph carries a walk for, `sample#haplotype` with its\n   * contigs, from the Paths scan the adapter already makes; the lane picker's\n   * source list. Reference samples are included and flagged.\n   */\n  async getHaplotypes(opts: BaseOptions = {}): Promise<GbzHaplotype[]> {\n    const { db, referenceSamples } = await this.graph(opts)\n    const byPrefix = new Map<string, GbzHaplotype>()\n    for (const path of await db.paths()) {\n      const prefix = haplotypePrefix(path.name)\n      const entry = byPrefix.get(prefix)\n      if (entry) {\n        if (!entry.contigs.includes(path.name.contig)) {\n          entry.contigs.push(path.name.contig)\n        }\n      } else {\n        byPrefix.set(prefix, {\n          prefix,\n          sample: path.name.sample,\n          haplotype: path.name.haplotype,\n          contigs: [path.name.contig],\n          isReference: referenceSamples.includes(path.name.sample),\n        })\n      }\n    }\n    return [...byPrefix.values()]\n  }\n\n  /**\n   * `lanes` is every haplotype but the reference sample's own, which is the\n   * anchor rather than a lane, declared up front so the display can offer the\n   * whole graph's haplotypes before a fetch has placed any of them.\n   */\n  async getHeader(opts: BaseOptions = {}) {\n    const { anchor, referenceSample } = await this.graph(opts)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    const lanes: GbzHeaderLane[] = []\n    for (const haplotype of await this.getHaplotypes(opts)) {\n      if (haplotype.sample !== referenceSample) {\n        lanes.push({\n          name: laneAssemblyName(asmByPrefix, haplotype.prefix),\n          label: haplotype.prefix,\n          group: haplotype.sample,\n        })\n      }\n    }\n    return {\n      hasCoarseTier: false,\n      anchorAssemblyName: anchor,\n      lanes,\n    }\n  }\n\n  async getRefNames(opts: BaseOptions = {}) {\n    const { db, anchor, referenceSample } = await this.graph(opts)\n    const { assemblyName } = opts\n    const prefix =\n      assemblyName === anchor\n        ? undefined\n        : resolvePanSNPrefix(this, assemblyName)\n    const contigs = (await db.paths())\n      .filter(path =>\n        assemblyName === anchor\n          ? path.isIndexed && path.name.sample === referenceSample\n          : panSNMatchesPrefix(haplotypePrefix(path.name), prefix),\n      )\n      .map(path => path.name.contig)\n    return [...new Set(contigs)]\n  }\n\n  /**\n   * The predicate gbz-base builds a window for, from the lanes a fetch asks\n   * for. With a companion whose stray rows cover the window gbz-base walks\n   * only the wanted haplotypes; otherwise it names every walk and keeps the\n   * ones the predicate accepts, and throws rather than guess when a walk has\n   * no name. Either way a cut holds those walks, the reference, and the nodes\n   * they visit. Undefined when every haplotype is wanted.\n   */\n  //\n  // `targetPrefix` is a pairwise view's one lane, and it belongs in here: left\n  // to filter what came back, it handed gbz-base no predicate, and every\n  // haplotype in the graph was walked for one to be kept.\n  private keepPredicate(\n    haplotypes: string[] | undefined,\n    targetPrefix?: string,\n  ) {\n    const wantedPrefixes =\n      haplotypes === undefined || haplotypes.length === 0\n        ? undefined\n        : haplotypes.map(lane => resolvePanSNPrefix(this, lane))\n    return wantedPrefixes === undefined && targetPrefix === undefined\n      ? undefined\n      : (name: PathName) =>\n          haplotypeWanted(name, wantedPrefixes) &&\n          (targetPrefix === undefined ||\n            panSNMatchesPrefix(haplotypePrefix(name), targetPrefix))\n  }\n\n  /**\n   * The graph view's cut of the window, as tables: the reference walk, every\n   * top-level snarl contained in it, and one walk per haplotype, PanSN-named\n   * when the database (or its companion) carries the haplotype index and\n   * `unknown#N` otherwise. The reference walk is the first, which is the one\n   * the view anchors on by default. With `haplotypes` the walks are that\n   * set's and the nodes those walks visit, the reference walk kept. With\n   * `walkRows` the rows' runs come along, as on a walk-file cut.\n   *\n   * Only a window on the anchor can be cut: a haplotype lane's coordinates\n   * are its own contig's, and the graph is indexed for random access on the\n   * reference sample's paths alone.\n   */\n  async getSubgraph(region: Region, opts: SubgraphAdapterOptions = {}) {\n    const { signal } = opts\n    const { db, anchor, referenceSample, unreadableIndex } = await this.graph({\n      signal,\n    })\n    const { assemblyName, refName, start, end } = wholeBp(region)\n    if (assemblyName !== anchor) {\n      throw new HaplotypeWindowError(assemblyName, anchor)\n    }\n    const query = await this.referenceQuery(refName, { signal })\n    if (!query) {\n      throw new Error(\n        `${referenceSample} has no indexed path ${refName} in this graph`,\n      )\n    }\n    const keep = this.keepPredicate(opts.haplotypes)\n    if (keep !== undefined && !db.hasHaplotypeIndex) {\n      throw new NoHaplotypeIndexError(unreadableIndex)\n    }\n    const cut = await cutWindowTables(db, query, start, end, {\n      context: this.getConf('context'),\n      snarls: opts.snarls ?? this.getConf('subgraphSnarls'),\n      limit: this.getConf('nodeLimit'),\n      signal: opts.signal,\n      keep,\n    }).catch((error: unknown) => {\n      throw zoomInNotice(error, 'the graph')\n    })\n    return typeof cut === 'string'\n      ? cut\n      : walkCutFor(cut, { start, end }, opts.walkRows)\n  }\n\n  private gaf = cachedSetup({\n    label: 'Opening reads',\n    setup: async () => {\n      const location: FileLocation = this.getConf('readsLocation')\n      const index: FileLocation = this.getConf(['readsIndex', 'location'])\n      return locationIsSet(location)\n        ? new GafFile(\n            openLocation(location, this.pluginManager),\n            locationIsSet(index)\n              ? openTabixSlot(this, ['readsLocation'], ['readsIndex'])\n              : undefined,\n          )\n        : undefined\n    },\n  })\n\n  /**\n   * The reads over a cut's segments, from `readsLocation`, sampled down to\n   * what the tube map lays out at interactive speed\n   */\n  async getReads(\n    nodeNames: string[],\n    opts: BaseOptions = {},\n  ): Promise<GafReads> {\n    const gaf = await this.gaf(opts)\n    return gaf\n      ? gaf.readsOver(new Set(nodeNames), opts)\n      : { records: [], total: 0 }\n  }\n\n  private async laneHaplotypes(\n    assemblyName: string,\n    opts: BaseOptions,\n  ): Promise<HaplotypeRef[]> {\n    const prefix = resolvePanSNPrefix(this, assemblyName)\n    return (await this.getHaplotypes(opts)).filter(haplotype =>\n      panSNMatchesPrefix(haplotype.prefix, prefix),\n    )\n  }\n\n  private async anchorFeatures(region: Region, opts: LaneFeatureOptions) {\n    const { db } = await this.graph(opts)\n    const { assemblyName, refName, start, end } = region\n    const targetPrefix = resolvePanSNPrefix(this, opts.targetAssemblyName)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    const keep = this.keepPredicate(opts.haplotypes, targetPrefix)\n    const query = await this.referenceQuery(refName, opts)\n    const nodeLimit: number = this.getConf('nodeLimit')\n    const alignments = query\n      ? await updateStatus(\n          `Reading graph ${refName}:${start.toLocaleString()}-${end.toLocaleString()}`,\n          opts.statusCallback,\n          () =>\n            db\n              .getAlignments({\n                path: query,\n                start,\n                end,\n                context: this.getConf('context'),\n                haplotypes: 'all',\n                limit: nodeLimit,\n                signal: opts.signal,\n                keep,\n              })\n              .catch((error: unknown) => {\n                throw laneLimitNotice(error, nodeLimit, end - start)\n              }),\n        )\n      : []\n    return alignments.flatMap(alignment => {\n      const feature = alignment.resolved\n        ? fragmentFeature({\n            alignment,\n            assemblyName,\n            refName,\n            lane: laneAssemblyName(\n              asmByPrefix,\n              haplotypePrefix(alignment.name),\n            ),\n          })\n        : undefined\n      return feature === undefined ? [] : [feature]\n    })\n  }\n\n  /**\n   * Each pair's two lanes cut out of the anchor window alone, all pairs in one\n   * cut, and each walk of a pair's query lane aligned to each walk of its\n   * target lane on the nodes both visit, with no base compared. A pair's\n   * records sit on its query lane's contigs, the lane the display draws on top.\n   *\n   * Whether the index has anchor rows changes only how fast gbz-base finds\n   * the walks: both routes cut the same pieces.\n   */\n  private async pairFeatures(\n    region: Region,\n    pairs: LanePair[],\n    opts: LaneFeatureOptions,\n  ) {\n    const { db } = await this.graph(opts)\n    const { refName, start, end } = region\n    const sides = await Promise.all(\n      pairs.map(async pair => ({\n        pair,\n        featureSide: await this.laneHaplotypes(pair.queryAssemblyName, opts),\n        mateSide: await this.laneHaplotypes(pair.targetAssemblyName, opts),\n      })),\n    )\n    const answerable = sides.filter(\n      ({ featureSide, mateSide }) =>\n        featureSide.length > 0 && mateSide.length > 0,\n    )\n    const kept = new Set(\n      answerable.flatMap(({ featureSide, mateSide }) =>\n        [...featureSide, ...mateSide].map(haplotypePrefix),\n      ),\n    )\n    const query = await this.referenceQuery(refName, opts)\n    const nodeLimit: number = this.getConf('nodeLimit')\n    const baseContext: number = this.getConf('context')\n    const cut = (path: PathQuery, context: number) =>\n      db.getSubgraphs({\n        path,\n        start,\n        end,\n        context,\n        snarls: this.getConf('subgraphSnarls'),\n        haplotypes: 'all',\n        limit: nodeLimit,\n        signal: opts.signal,\n        keep: name => kept.has(haplotypePrefix(name)),\n      })\n    // a cut past the node limit for the wider context keeps the first one\n    const bridged = async (path: PathQuery) => {\n      const subgraphs = await cut(path, baseContext).catch((error: unknown) => {\n        throw laneLimitNotice(error, nodeLimit, end - start)\n      })\n      const gap = widestWalkGap(subgraphs, kept)\n      const context = Math.ceil(gap / 2) + 2000\n      return gap > 0 && context > baseContext\n        ? cut(path, context).catch((error: unknown) => {\n            if (error instanceof SubgraphLimitError) {\n              return subgraphs\n            }\n            throw error\n          })\n        : subgraphs\n    }\n    const subgraphs =\n      query && answerable.length > 0\n        ? await updateStatus(lanePairsStatus(pairs), opts.statusCallback, () =>\n            bridged(query),\n          )\n        : []\n    return subgraphs.flatMap(subgraph =>\n      answerable.flatMap(({ pair, featureSide, mateSide }) =>\n        featureSide.flatMap(target =>\n          mateSide.flatMap(mate =>\n            subgraph\n              .pairAlignments({ target, query: mate, bases: false })\n              .map(alignment =>\n                pairFeature({\n                  pair: alignment,\n                  lane: pair.queryAssemblyName,\n                  mateLane: pair.targetAssemblyName,\n                }),\n              ),\n          ),\n        ),\n      ),\n    )\n  }\n\n  getFeatures(asked: Region, opts: LaneFeatureOptions = {}) {\n    const region = wholeBp(asked)\n    return ObservableCreate<Feature>(async observer => {\n      const { db, anchor, unreadableIndex } = await this.graph(opts)\n      if (!db.hasHaplotypeIndex) {\n        throw new NoHaplotypeIndexError(unreadableIndex)\n      }\n      // the graph is indexed on its reference alone, so a window on a\n      // haplotype lane has no answer: a lane pair is read inside the anchor's\n      if (region.assemblyName === anchor) {\n        const pairs = requestedPairs(opts)\n        const features =\n          pairs.length > 0\n            ? await this.pairFeatures(region, pairs, opts)\n            : await this.anchorFeatures(region, opts)\n        for (const feature of features) {\n          observer.next(feature)\n        }\n      }\n      observer.complete()\n    }, opts.signal)\n  }\n}\n"],
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-  "names": ["haplotypeIndexBeside", "db", "GBZ_DB", "siblingCompanion", "gbzDb", "readsSiblings", "haplotypeIndexBeside", "locationName", "renamed", "name", "isMissing", "error", "findCompanion", "pluginManager", "candidate", "openLocation", "MAX_READS", "MAX_UNINDEXED_BYTES", "UnindexedGafTooLargeError", "size", "sample", "records", "max", "stride", "_", "k", "touches", "record", "names", "step", "GafFile", "file", "tabix", "cachedSetup", "signal", "bytes", "text", "unzip", "parseGaf", "lo", "hi", "name", "id", "line", "parseGafLine", "r", "NoHaplotypeIndexError", "unreadable", "HaplotypeWindowError", "assemblyName", "anchor", "fragmentId", "name", "alignment", "haplotypePrefix", "fragmentFeature", "refName", "lane", "refStart", "refEnd", "strand", "cigar", "hapStart", "hapEnd", "id", "data", "SyntenyFeature", "pairFeature", "pair", "mateLane", "matchFeature", "BRIDGE_MAX_BP", "widestWalkGap", "subgraphs", "kept", "byPath", "subgraph", "start", "end", "prefix", "key", "spans", "widest", "a", "b", "i", "gap", "zoomInNotice", "error", "what", "NodeLimitError", "getBpDisplayStr", "laneLimitNotice", "nodeLimit", "windowBp", "laneZoomNotice", "nodeLimitError", "wholeBp", "region", "GbzBaseSyntenyAdapter", "ComparativeAdapterBase", "cachedSetup", "gbzDb", "configured", "companion", "locationIsSet", "findCompanion", "indexLocation", "db", "GBZBase", "openLocation", "referenceSamples", "referenceSamplesOf", "referenceSample", "resolveReferenceSample", "resolvePanSNPrefix", "location", "index", "GafFile", "openTabixSlot", "opts", "referencePathQuery", "byPrefix", "path", "entry", "asmByPrefix", "assemblyByPanSNPrefix", "lanes", "haplotype", "laneAssemblyName", "contigs", "panSNMatchesPrefix", "haplotypes", "targetPrefix", "wantedPrefixes", "haplotypeWanted", "signal", "unreadableIndex", "query", "keep", "cut", "cutWindowTables", "walkCutFor", "nodeNames", "gaf", "updateStatus", "feature", "pairs", "answerable", "featureSide", "mateSide", "baseContext", "context", "bridged", "SubgraphLimitError", "lanePairsStatus", "target", "mate", "asked", "ObservableCreate", "observer", "requestedPairs", "features"]
-}

package/dist/chunks/RgfaTabixAdapter-O3NMNRZ2.js

@@ -1,2 +0,0 @@
-import{a as b}from"./chunk-YKSUKPYY.js";import"./chunk-JCAZTNYG.js";import{a as N}from"./chunk-KOB7YIMR.js";import"./chunk-YBLNN5FU.js";import"./chunk-6KUHGRHU.js";import"./chunk-6MUBJVBG.js";import{b as g,h as c,i as u,j as h,k as w,p as m,q as k,r as x}from"./chunk-B2EP6FOQ.js";import"./chunk-YBLNN5FU.js";import"./chunk-MVVXRZXV.js";import"./chunk-7HWHWPRW.js";import{d}from"./chunk-IKJZPPOA.js";import"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{a as p,o as f}from"./chunk-TENPGIPX.js";var l=class extends g{constructor(){super(...arguments);this.fine=this.openIndex([])}static{this.capabilities=["getFeatures","getRefNames"]}openIndex(e){let t=m(this,[...e,"segmentsLocation"],[...e,"segmentsIndex"]),s=m(this,[...e,"linksLocation"],[...e,"linksIndex"]),n=this.getConf("walksLocation"),i=e.length===0&&d(n)?new b(m(this,["walksLocation"],["walksIndex"]),this):void 0;return{segments:t,links:s,walks:i,refNames:new x(i?.file??t,this)}}async getHaplotypeNames(e={}){return this.fine.walks?.haplotypeNames(e)}index(e="fine"){return e==="fine"?this.fine:(this.coarse??=this.openIndex(["coarse"]),this.coarse)}async getRefNames(e={}){return this.fine.refNames.assemblyRefNames(e)}async getRegionByteSize(e,t={}){let{walks:s,refNames:n}=this.fine;return n.regionBytes(e,t,s&&(i=>s.reader.queryStart(i,t)))}async hasDataForRefName(){return!0}getFeatures(e,t={}){return N(async s=>{let n=await this.fine.refNames.resolveMapped(e,t);if(n!==void 0){let{walks:i}=this.fine,a=r=>{s.next(r)};await(i?this.walkFeatures(i,n,e,t,a):this.segmentFeatures(n,e,t,a))}s.complete()},t.signal)}async walkFeatures(e,t,s,n,i){let a=await f("Downloading walks",n.statusCallback,()=>e.referenceNodes(t,s,n));for(let r of a){let o=String(r.id);i(new p({uniqueId:o,refName:s.refName,start:r.start,end:r.end,name:o,type:"segment",rank:0,stableName:r.refName}))}}async segmentFeatures(e,t,s,n){await f("Downloading segments",s.statusCallback,()=>w(this.fine.segments,e,t.start,t.end,{signal:s.signal,lineCallback:i=>{let{segment:a,anchored:r}=c(i);if(r&&a.refName!==e)return;let o=u(a);n(new p({uniqueId:a.id,refName:t.refName,start:a.start,end:a.end,name:a.id,type:"segment",rank:a.rank,stableName:a.refName,...o&&{samples:o,sampleCount:o.length}}))}}))}async getSubgraph(e,t={}){let{hops:s,signal:n,tier:i}=t,a=this.index(i),r=await a.refNames.resolve(e,{signal:n});if(r===void 0)throw new Error(k(e));return a.walks?a.walks.subgraph(r,e,t):h(a,{refName:r,start:e.start,end:e.end},{hops:s,signal:n})}};export{l as default};
-//# sourceMappingURL=RgfaTabixAdapter-O3NMNRZ2.js.map

package/dist/chunks/RgfaTabixAdapter-O3NMNRZ2.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../src/RgfaTabixAdapter/RgfaTabixAdapter.ts"],
-  "sourcesContent": ["import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { SimpleFeature, updateStatus } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { parseSegmentRow, rgfaCut, segmentSamples } from '@jbrowse/graph-walks'\n\nimport { locationIsSet } from '../locationName.ts'\nimport {\n  PanSNRefNames,\n  openTabixSlot,\n  unmappedRegionMessage,\n} from '../panSNTabix.ts'\nimport { getLines } from '../tabixRange.ts'\nimport { WalkIndex } from './walkReader.ts'\n\nimport type { RgfaTabixAdapterConfig } from './configSchema.ts'\nimport type { SubgraphAdapterOptions, SubgraphTier } from '../GetSubgraph.ts'\nimport type { WalkCut } from './walkCut.ts'\nimport type { TabixIndexedFile } from '@gmod/tabix'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { FileLocation, Region } from '@jbrowse/core/util/types'\n\ninterface GraphIndex {\n  segments: TabixIndexedFile\n  links: TabixIndexedFile\n  walks?: WalkIndex\n  refNames: PanSNRefNames\n}\n\nexport default class RgfaTabixAdapter extends BaseFeatureDataAdapter<RgfaTabixAdapterConfig> {\n  public static capabilities = ['getFeatures', 'getRefNames']\n\n  private readonly fine = this.openIndex([])\n  private coarse: GraphIndex | undefined\n\n  // refNames off the SEGMENT index: it is the one that names every stable\n  // sequence the graph is anchored to, where the link index only names those a\n  // link touches. A walk-indexed graph's walk file names the same sequences,\n  // and it has no segment file.\n  private openIndex(under: string[]): GraphIndex {\n    const segments = openTabixSlot(\n      this,\n      [...under, 'segmentsLocation'],\n      [...under, 'segmentsIndex'],\n    )\n    const links = openTabixSlot(\n      this,\n      [...under, 'linksLocation'],\n      [...under, 'linksIndex'],\n    )\n    const walksLocation: FileLocation = this.getConf('walksLocation')\n    const walks =\n      under.length === 0 && locationIsSet(walksLocation)\n        ? new WalkIndex(\n            openTabixSlot(this, ['walksLocation'], ['walksIndex']),\n            this,\n          )\n        : undefined\n    return {\n      segments,\n      links,\n      walks,\n      refNames: new PanSNRefNames(walks?.file ?? segments, this),\n    }\n  }\n\n  /**\n   * The haplotypes a walk-indexed graph's header names, `sample#haplotype`\n   * in byte order, or undefined when it names none\n   */\n  async getHaplotypeNames(opts: BaseOptions = {}) {\n    return this.fine.walks?.haplotypeNames(opts)\n  }\n\n  private index(tier: SubgraphTier = 'fine') {\n    if (tier === 'fine') {\n      return this.fine\n    }\n    this.coarse ??= this.openIndex(['coarse'])\n    return this.coarse\n  }\n\n  async getRefNames(opts: BaseOptions = {}) {\n    return this.fine.refNames.assemblyRefNames(opts)\n  }\n\n  // getFeatures reads a walk file from the chunk before the window\n  async getRegionByteSize(regions: Region[], opts: BaseOptions = {}) {\n    const { walks, refNames } = this.fine\n    return refNames.regionBytes(\n      regions,\n      opts,\n      walks && (start => walks.reader.queryStart(start, opts)),\n    )\n  }\n\n  public async hasDataForRefName() {\n    return true\n  }\n\n  getFeatures(query: Region, opts: BaseOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      const tabixRefName = await this.fine.refNames.resolveMapped(query, opts)\n      if (tabixRefName !== undefined) {\n        const { walks } = this.fine\n        const emit = (feature: Feature) => {\n          observer.next(feature)\n        }\n        await (walks\n          ? this.walkFeatures(walks, tabixRefName, query, opts, emit)\n          : this.segmentFeatures(tabixRefName, query, opts, emit))\n      }\n      observer.complete()\n    }, opts.signal)\n  }\n\n  // A walk-indexed graph's reference nodes are its ref rows' steps\n  private async walkFeatures(\n    walks: WalkIndex,\n    tabixRefName: string,\n    query: Region,\n    opts: BaseOptions,\n    emit: (feature: Feature) => void,\n  ) {\n    const nodes = await updateStatus(\n      'Downloading walks',\n      opts.statusCallback,\n      () => walks.referenceNodes(tabixRefName, query, opts),\n    )\n    for (const node of nodes) {\n      const id = String(node.id)\n      emit(\n        new SimpleFeature({\n          uniqueId: id,\n          refName: query.refName,\n          start: node.start,\n          end: node.end,\n          name: id,\n          type: 'segment',\n          rank: 0,\n          stableName: node.refName,\n        }),\n      )\n    }\n  }\n\n  private async segmentFeatures(\n    tabixRefName: string,\n    query: Region,\n    opts: BaseOptions,\n    emit: (feature: Feature) => void,\n  ) {\n    await updateStatus('Downloading segments', opts.statusCallback, () =>\n      getLines(this.fine.segments, tabixRefName, query.start, query.end, {\n        signal: opts.signal,\n        lineCallback: line => {\n          const { segment, anchored } = parseSegmentRow(line)\n          // An anchored index also returns the alleles under the region,\n          // which lie on other stable sequences and have no place on this one\n          if (anchored && segment.refName !== tabixRefName) {\n            return\n          }\n          // `samples` lists the haplotypes whose paths visit the segment and\n          // `sampleCount` counts them. A lane's color reads the count, and\n          // a count in jexl would otherwise rely on `.length` resolving\n          // through a member access on an array.\n          const samples = segmentSamples(segment)\n          emit(\n            new SimpleFeature({\n              uniqueId: segment.id,\n              refName: query.refName,\n              start: segment.start,\n              end: segment.end,\n              name: segment.id,\n              type: 'segment',\n              rank: segment.rank,\n              stableName: segment.refName,\n              ...(samples && { samples, sampleCount: samples.length }),\n            }),\n          )\n        },\n      }),\n    )\n  }\n\n  // The graph around a region for GraphGenomeView: GFA text (rgfaCut), or a\n  // walk-indexed graph's tables (WalkIndex.subgraph). `tier: 'coarse'` reads\n  // the `coarse` pair instead, the same way.\n  async getSubgraph(\n    region: Region,\n    opts: SubgraphAdapterOptions = {},\n  ): Promise<string | WalkCut> {\n    const { hops, signal, tier } = opts\n    const index = this.index(tier)\n    const tabixRefName = await index.refNames.resolve(region, { signal })\n    if (tabixRefName === undefined) {\n      throw new Error(unmappedRegionMessage(region))\n    }\n    if (index.walks) {\n      return index.walks.subgraph(tabixRefName, region, opts)\n    }\n    return rgfaCut(\n      index,\n      { refName: tabixRefName, start: region.start, end: region.end },\n      { hops, signal },\n    )\n  }\n}\n"],
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he(r.map((a,c)=>a+(s[c]-a)*n))}function mn(t,e){let[n,o,r]=Tt(t,e).map(Math.round);return`rgb(${n}, ${o}, ${r})`}function ht(t,e){let[n,o,r]=Tt(t,e).map(Math.round);return p(n,o,r,255)}function ue({field:t,scheme:e},n){return t==="walk"?ht(e,dn):n===void 0?pn:ht(e,n)}var pn=It;function de({field:t,scheme:e}){let n=(o,r)=>({offset:o,color:mn(e,r),abgr:ht(e,r)});return t==="walk"?[n(0,dn)]:Array.from({length:7},(o,r)=>n(r/6,r/6))}export{In as a,Tn as b,p as c,zt as d,me as e,j as f,pe as g,An as h,Ee as i,vn as j,xe as k,Jt as l,Pe as m,St as n,De as o,Fe as p,Qn as q,Zn as r,He as s,un as t,wt as u,ie as v,ue as w,pn as x,de as y};
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