jbrowse-plugin-graphgenomeviewer 8.2.0 → 8.3.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "jbrowse-plugin-graphgenomeviewer",
-  "version": "8.2.0",
+  "version": "8.3.0",
   "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": {

package/src/GraphAddTrackWorkflow/buildTrackConfig.test.ts

@@ -270,6 +270,24 @@ describe('buildTrackConfig', () => {
       expect(conf.adapter).not.toHaveProperty('coarse.aboveBpPerPx')
     })
 
+    it('reads a format 2 tier as its one file', () => {
+      const conf = buildTrackConfig({
+        ...args,
+        manifest: { tier: { ...tier, format: 2 } },
+      })
+      expect(conf.adapter).toMatchObject({
+        coarse: {
+          foldBelowBp: 10000,
+          graphLocation: at('hprc.fold10000.graph.bed.gz'),
+          graphIndex: {
+            indexType: 'TBI',
+            location: at('hprc.fold10000.graph.bed.gz.tbi'),
+          },
+        },
+      })
+      expect(conf.adapter).not.toHaveProperty('coarse.segmentsLocation')
+    })
+
     it('maps the assembly onto its reference unless the user named one', () => {
       const reference = { reference: 'GRCh38' }
       expect(

package/src/GraphAddTrackWorkflow/buildTrackConfig.ts

@@ -94,6 +94,16 @@ function coarseTier(
   if (!tier) {
     return {}
   }
+  if (tier.format === 2) {
+    const graph = besideSegments(loc, `${tier.prefix}${GRAPH_SUFFIX}`)
+    return {
+      coarse: {
+        foldBelowBp: tier.foldBelowBp,
+        graphLocation: graph,
+        graphIndex: siblingIndex(graph, indexLoc),
+      },
+    }
+  }
   const segs = besideSegments(loc, `${tier.prefix}${SEGMENTS_SUFFIX}`)
   const links = besideSegments(loc, `${tier.prefix}.links.bed.gz`)
   return {

package/src/GraphAddTrackWorkflow/graphManifest.test.ts

@@ -49,6 +49,18 @@ test('reads the reference and tier, ignoring unknown fields', () => {
   })
 })
 
+test('reads a format 2 tier', () => {
+  expect(
+    parse({
+      ...manifest,
+      tier: { prefix: 'out.fold10000', foldBelowBp: 10000, format: 2 },
+    }),
+  ).toEqual({
+    reference: 'GRCh38',
+    tier: { prefix: 'out.fold10000', foldBelowBp: 10000, format: 2 },
+  })
+})
+
 test('a null reference, tier and companions leave those out', () => {
   expect(
     parse({

package/src/GraphAddTrackWorkflow/graphManifest.ts

@@ -15,7 +15,9 @@ import type { FileLocation } from '@jbrowse/core/util'
 // Open track reads
 export interface GraphManifest {
   reference?: string
-  tier?: { prefix: string; foldBelowBp: number }
+  // `format: 2` when the tier is one `<prefix>.graph.bed.gz`, as gfa-to-tabix
+  // 2 writes it, rather than a segments and links pair
+  tier?: { prefix: string; foldBelowBp: number; format?: 2 }
 }
 
 const FETCH_TIMEOUT_MS = 5000
@@ -67,7 +69,13 @@ export function parseGraphManifest(text: string): GraphManifest | undefined {
   return {
     ...(typeof reference === 'string' ? { reference: reference.trim() } : {}),
     ...(isTier(tier)
-      ? { tier: { prefix: tier.prefix, foldBelowBp: tier.foldBelowBp } }
+      ? {
+          tier: {
+            prefix: tier.prefix,
+            foldBelowBp: tier.foldBelowBp,
+            ...(tier.format === 2 ? { format: 2 as const } : {}),
+          },
+        }
       : {}),
   }
 }

package/src/version.ts

@@ -1 +1 @@
-export const version = '8.2.0'
+export const version = '8.3.0'

package/dist/chunks/chunk-5FNGR33G.js

@@ -1,2 +0,0 @@
-import{c as m}from"./chunk-3VGXCEMQ.js";import{a as p,b as l,c as h,d as A,h as a,i as g,j as d}from"./chunk-6VNDP3UB.js";import{a as T}from"./chunk-OGQ6OQDN.js";var z=5e3;function G(e){return typeof e=="string"&&/^[\w+-][\w.+-]*$/.test(e)}function x(e){return e==null}function M(e){return typeof e=="object"&&e!==null&&!Array.isArray(e)}function L(e){return M(e)&&G(e.prefix)&&typeof e.foldBelowBp=="number"&&Number.isFinite(e.foldBelowBp)&&e.foldBelowBp>0}function P(e){let n;try{n=JSON.parse(e)}catch{return}if(!M(n)||n.schema!==1)return;let{reference:i,tier:t,index:r,contig:o,bubbles:s,alleles:f}=n;if((x(i)||typeof i=="string"&&i.trim()!=="")&&(x(t)||L(t))&&[r,o,s,f].every(I=>x(I)||G(I)))return{...typeof i=="string"?{reference:i.trim()}:{},...L(t)?{tier:{prefix:t.prefix,foldBelowBp:t.foldBelowBp}}:{}}}function y(e,n){return d(e,i=>i.replace(/[^/\\]*$/,n))}function R(e){let n=a(e);return[p,l].find(i=>n.endsWith(i))}function N(e){return g(e)&&R(e)!==void 0}function F(e,n){let i=R(e)??p;return d(e,t=>`${t.slice(0,-i.length)}${n}`)}function _(e){return N(e)?F(e,".graph.json"):void 0}async function X(e,n){let i=_(e);if(i)try{let t=await T(i,n).readFile({encoding:"utf8",signal:AbortSignal.timeout(z)});return P(t)}catch{return}}var J={RgfaTabixAdapter:"Indexed GFA (gfa-to-tabix .segs.bed.gz or .graph.bed.gz)",RgfaTabixWalks:"Haplotype walks (.walks.bed.gz)",GbzBaseSyntenyAdapter:"GBZ database (.gbz.db)",MinigraphBubbleAdapter:"Minigraph bubbles (tabix BED)"},K={RgfaTabixAdapter:"Path to segments BED (.segs.bed.gz from gfa-to-tabix; the .links.bed.gz, its index and any .graph.json are read beside it), or format 2's .graph.bed.gz",RgfaTabixWalks:"Path to a walk file (<prefix>.<sample>.walks.bed.gz from gfa-to-tabix --walks, for the sample this assembly is)",GbzBaseSyntenyAdapter:"Path to the .gbz.db written by gbz-base construct",MinigraphBubbleAdapter:"Path to bubbles BED (.bed.gz from gfatools bubble)"},B="Path to tabix index (optional; the sibling .tbi is assumed, a .csi is recognised by name)",Z={RgfaTabixAdapter:B,RgfaTabixWalks:B,GbzBaseSyntenyAdapter:"Path to the haplotype index (optional; graph.haplotype-index.db beside the database is assumed)",MinigraphBubbleAdapter:B};function b(e,n){return d(e,i=>i+n)}function C(e){if(!a(e).endsWith(p))throw new Error(`Expected a segments BED ending in ${p}, got ${a(e)}`);return F(e,".links.bed.gz")}function u(e,n){return n?{location:n,indexType:m(a(n),"CSI","TBI")}:{location:b(e,".tbi"),indexType:"TBI"}}function k(e,n){return n!==void 0&&m(a(n),"CSI","TBI")==="CSI"?{location:b(e,".csi"),indexType:"CSI"}:{location:b(e,".tbi"),indexType:"TBI"}}function w(e,n){let i=n.trim();return i&&e?{assemblyNameToPanSN:{[e]:i}}:{}}function E(e,n,i){if(!i)return{};let t=y(e,`${i.prefix}${p}`),r=y(e,`${i.prefix}.links.bed.gz`);return{coarse:{foldBelowBp:i.foldBelowBp,segmentsLocation:t,segmentsIndex:k(t,n),linksLocation:r,linksIndex:k(r,n)}}}function S(e,n,i){let t=i===e?void 0:i;return w(e,n.trim()||t||"")}function W(e){return e?{readsLocation:e,...a(e).endsWith(".gz")&&g(e)?{readsIndex:{location:b(e,".tbi")}}:{}}:{}}function q(e){return e.split(/[\s,]+/).filter(n=>n!=="")}function D({choice:e,loc:n,indexLoc:i,readsLoc:t,manifest:r,assembly:o,sample:s,haplotypes:f=[]}){if(e==="RgfaTabixWalks"){if(!a(n).endsWith(h))throw new Error(`Expected a walk file ending in ${h}, got ${a(n)}`);return{type:"RgfaTabixAdapter",walksLocation:n,walksIndex:u(n,i),...S(o,s,A(n)),...f.length>0?{defaultHaplotypes:f}:{}}}if(e==="GbzBaseSyntenyAdapter")return{type:"GbzBaseSyntenyAdapter",gbzDbLocation:n,...i?{haplotypeIndexLocation:i}:{},...W(t),...w(o,s)};if(e==="MinigraphBubbleAdapter")return{type:"MinigraphBubbleAdapter",bubblesLocation:n,index:u(n,i),...w(o,s)};if(a(n).endsWith(l))return{type:"RgfaTabixAdapter",graphLocation:n,graphIndex:u(n,i),...S(o,s,r?.reference),...E(n,i,r?.tier)};let c=C(n);return{type:"RgfaTabixAdapter",segmentsLocation:n,segmentsIndex:u(n,i),linksLocation:c,linksIndex:k(c,i),...S(o,s,r?.reference),...E(n,i,r?.tier)}}function Q(e){let{choice:n,assembly:i,trackId:t,name:r}=e;return{type:n==="MinigraphBubbleAdapter"?"FeatureTrack":"GraphTrack",trackId:t,name:r,assemblyNames:[i],adapter:D(e),...n==="RgfaTabixAdapter"||n==="RgfaTabixWalks"?{displayDefaults:{labels:{name:{show:!1},description:{show:!1}}}}:{}}}export{N as a,X as b,J as c,K as d,Z as e,q as f,D as g,Q as h};
-//# sourceMappingURL=chunk-5FNGR33G.js.map

package/dist/chunks/chunk-5FNGR33G.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../src/GraphAddTrackWorkflow/graphManifest.ts", "../../src/GraphAddTrackWorkflow/buildTrackConfig.ts"],
-  "sourcesContent": ["import { openLocation } from '@jbrowse/core/util/io'\n\nimport {\n  GRAPH_SUFFIX,\n  SEGMENTS_SUFFIX,\n  locationName,\n  readsSiblings,\n  renamed,\n} from '../locationName'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { FileLocation } from '@jbrowse/core/util'\n\n// The part of `<prefix>.graph.json`, written by `gfa-to-tabix build`, that\n// Open track reads\nexport interface GraphManifest {\n  reference?: string\n  tier?: { prefix: string; foldBelowBp: number }\n}\n\nconst FETCH_TIMEOUT_MS = 5000\n\n// A bare file name beside the manifest: no directory, scheme or leading dot\nfunction isSiblingName(name: unknown): name is string {\n  return typeof name === 'string' && /^[\\w+-][\\w.+-]*$/.test(name)\n}\n\nfunction isAbsent(value: unknown) {\n  return value === undefined || value === null\n}\n\nfunction isPlainRecord(value: unknown): value is Record<string, unknown> {\n  return typeof value === 'object' && value !== null && !Array.isArray(value)\n}\n\nfunction isTier(tier: unknown): tier is NonNullable<GraphManifest['tier']> {\n  return (\n    isPlainRecord(tier) &&\n    isSiblingName(tier.prefix) &&\n    typeof tier.foldBelowBp === 'number' &&\n    Number.isFinite(tier.foldBelowBp) &&\n    tier.foldBelowBp > 0\n  )\n}\n\nexport function parseGraphManifest(text: string): GraphManifest | undefined {\n  let json: unknown\n  try {\n    json = JSON.parse(text)\n  } catch {\n    return undefined\n  }\n  if (!isPlainRecord(json) || json.schema !== 1) {\n    return undefined\n  }\n  const { reference, tier, index, contig, bubbles, alleles } = json\n  const valid =\n    (isAbsent(reference) ||\n      (typeof reference === 'string' && reference.trim() !== '')) &&\n    (isAbsent(tier) || isTier(tier)) &&\n    [index, contig, bubbles, alleles].every(\n      f => isAbsent(f) || isSiblingName(f),\n    )\n  if (!valid) {\n    return undefined\n  }\n  return {\n    ...(typeof reference === 'string' ? { reference: reference.trim() } : {}),\n    ...(isTier(tier)\n      ? { tier: { prefix: tier.prefix, foldBelowBp: tier.foldBelowBp } }\n      : {}),\n  }\n}\n\n// A file the manifest names, in the directory of the segments file opened\nexport function besideSegments(segs: FileLocation, fileName: string) {\n  return renamed(segs, name => name.replace(/[^/\\\\]*$/, fileName))\n}\n\n// The suffix of a gfa-to-tabix index file: format 1's segments BED or format\n// 2's graph BED\nfunction indexSuffix(loc: FileLocation) {\n  const name = locationName(loc)\n  return [SEGMENTS_SUFFIX, GRAPH_SUFFIX].find(suffix => name.endsWith(suffix))\n}\n\n// A segments BED, or format 2's graph BED, the rest of the index and the\n// manifest can be found beside\nexport function isGraphIndexLocation(loc: FileLocation) {\n  return readsSiblings(loc) && indexSuffix(loc) !== undefined\n}\n\n// `<prefix><suffix>` beside `<prefix>.segs.bed.gz` or `<prefix>.graph.bed.gz`\nexport function segmentsSibling(segs: FileLocation, suffix: string) {\n  const own = indexSuffix(segs) ?? SEGMENTS_SUFFIX\n  return renamed(segs, name => `${name.slice(0, -own.length)}${suffix}`)\n}\n\nexport function manifestLocation(segs: FileLocation) {\n  return isGraphIndexLocation(segs)\n    ? segmentsSibling(segs, '.graph.json')\n    : undefined\n}\n\n// Undefined for a manifest that is missing, unreadable or not schema 1, so\n// Open track falls back to the files beside the segments alone\nexport async function readGraphManifest(\n  segs: FileLocation,\n  pluginManager?: PluginManager,\n) {\n  const loc = manifestLocation(segs)\n  if (!loc) {\n    return undefined\n  }\n  try {\n    const text = await openLocation(loc, pluginManager).readFile({\n      encoding: 'utf8',\n      signal: AbortSignal.timeout(FETCH_TIMEOUT_MS),\n    })\n    return parseGraphManifest(text)\n  } catch {\n    return undefined\n  }\n}\n", "import { makeIndexType } from '@jbrowse/core/util/tracks'\n\nimport { besideSegments, segmentsSibling } from './graphManifest'\nimport {\n  GRAPH_SUFFIX,\n  SEGMENTS_SUFFIX,\n  WALKS_SUFFIX,\n  locationName,\n  readsSiblings,\n  renamed,\n  walkFileSample,\n} from '../locationName'\n\nimport type { GraphManifest } from './graphManifest'\nimport type { FileLocation } from '@jbrowse/core/util'\n\n// 'RgfaTabixWalks' is an RgfaTabixAdapter read from a walk file\nexport type GraphFileChoice =\n  | 'RgfaTabixAdapter'\n  | 'RgfaTabixWalks'\n  | 'GbzBaseSyntenyAdapter'\n  | 'MinigraphBubbleAdapter'\n\nexport const GRAPH_FILE_LABELS: Record<GraphFileChoice, string> = {\n  RgfaTabixAdapter: 'Indexed GFA (gfa-to-tabix .segs.bed.gz or .graph.bed.gz)',\n  RgfaTabixWalks: 'Haplotype walks (.walks.bed.gz)',\n  GbzBaseSyntenyAdapter: 'GBZ database (.gbz.db)',\n  MinigraphBubbleAdapter: 'Minigraph bubbles (tabix BED)',\n}\n\nexport const GRAPH_FILE_FIELDS: Record<GraphFileChoice, string> = {\n  RgfaTabixAdapter:\n    \"Path to segments BED (.segs.bed.gz from gfa-to-tabix; the .links.bed.gz, its index and any .graph.json are read beside it), or format 2's .graph.bed.gz\",\n  RgfaTabixWalks:\n    'Path to a walk file (<prefix>.<sample>.walks.bed.gz from gfa-to-tabix --walks, for the sample this assembly is)',\n  GbzBaseSyntenyAdapter: 'Path to the .gbz.db written by gbz-base construct',\n  MinigraphBubbleAdapter: 'Path to bubbles BED (.bed.gz from gfatools bubble)',\n}\n\nconst TABIX_INDEX_FIELD =\n  'Path to tabix index (optional; the sibling .tbi is assumed, a .csi is recognised by name)'\n\nexport const GRAPH_INDEX_FIELDS: Record<GraphFileChoice, string> = {\n  RgfaTabixAdapter: TABIX_INDEX_FIELD,\n  RgfaTabixWalks: TABIX_INDEX_FIELD,\n  GbzBaseSyntenyAdapter:\n    'Path to the haplotype index (optional; graph.haplotype-index.db beside the database is assumed)',\n  MinigraphBubbleAdapter: TABIX_INDEX_FIELD,\n}\n\nfunction sibling(loc: FileLocation, suffix: string) {\n  return renamed(loc, name => name + suffix)\n}\n\nfunction linksLocation(loc: FileLocation) {\n  if (!locationName(loc).endsWith(SEGMENTS_SUFFIX)) {\n    throw new Error(\n      `Expected a segments BED ending in ${SEGMENTS_SUFFIX}, got ${locationName(loc)}`,\n    )\n  }\n  return segmentsSibling(loc, '.links.bed.gz')\n}\n\nfunction tabixIndex(loc: FileLocation, indexLoc: FileLocation | undefined) {\n  return indexLoc\n    ? {\n        location: indexLoc,\n        indexType: makeIndexType(locationName(indexLoc), 'CSI', 'TBI'),\n      }\n    : { location: sibling(loc, '.tbi'), indexType: 'TBI' }\n}\n\n// The links file's index is assumed beside it, of the kind the segments' is.\nfunction siblingIndex(loc: FileLocation, indexLoc: FileLocation | undefined) {\n  const csi =\n    indexLoc !== undefined &&\n    makeIndexType(locationName(indexLoc), 'CSI', 'TBI') === 'CSI'\n  return csi\n    ? { location: sibling(loc, '.csi'), indexType: 'CSI' }\n    : { location: sibling(loc, '.tbi'), indexType: 'TBI' }\n}\n\n// none for a guessed config, which knows no assembly yet; see withWalkReference\nfunction panSN(assembly: string, sample: string) {\n  const name = sample.trim()\n  return name && assembly ? { assemblyNameToPanSN: { [assembly]: name } } : {}\n}\n\nfunction coarseTier(\n  loc: FileLocation,\n  indexLoc: FileLocation | undefined,\n  tier: GraphManifest['tier'],\n) {\n  if (!tier) {\n    return {}\n  }\n  const segs = besideSegments(loc, `${tier.prefix}${SEGMENTS_SUFFIX}`)\n  const links = besideSegments(loc, `${tier.prefix}.links.bed.gz`)\n  return {\n    coarse: {\n      foldBelowBp: tier.foldBelowBp,\n      segmentsLocation: segs,\n      segmentsIndex: siblingIndex(segs, indexLoc),\n      linksLocation: links,\n      linksIndex: siblingIndex(links, indexLoc),\n    },\n  }\n}\n\n// The user's sample wins; the reference the graph's files name (a manifest's,\n// or a walk file's own) stands in when blank\nfunction referencePanSN(\n  assembly: string,\n  sample: string,\n  reference: string | undefined,\n) {\n  const fromManifest = reference === assembly ? undefined : reference\n  return panSN(assembly, sample.trim() || fromManifest || '')\n}\n\n// a bgzipped GAF is read by its tabix index, a plain one whole\nfunction readsConfig(readsLoc: FileLocation | undefined) {\n  return readsLoc\n    ? {\n        readsLocation: readsLoc,\n        ...(locationName(readsLoc).endsWith('.gz') && readsSiblings(readsLoc)\n          ? { readsIndex: { location: sibling(readsLoc, '.tbi') } }\n          : {}),\n      }\n    : {}\n}\n\n// Names typed as a list, by comma or space\nexport function parseHaplotypes(text: string) {\n  return text.split(/[\\s,]+/).filter(name => name !== '')\n}\n\nexport function buildAdapterConfig({\n  choice,\n  loc,\n  indexLoc,\n  readsLoc,\n  manifest,\n  assembly,\n  sample,\n  haplotypes = [],\n}: {\n  choice: GraphFileChoice\n  loc: FileLocation\n  indexLoc: FileLocation | undefined\n  // a GBZ track's GAF reads, which no other choice takes\n  readsLoc?: FileLocation\n  // the `.graph.json` beside an rGFA segments file\n  manifest?: GraphManifest\n  assembly: string\n  sample: string\n  // a walk file's haplotypes to cut for until the user picks others\n  haplotypes?: string[]\n}) {\n  if (choice === 'RgfaTabixWalks') {\n    if (!locationName(loc).endsWith(WALKS_SUFFIX)) {\n      throw new Error(\n        `Expected a walk file ending in ${WALKS_SUFFIX}, got ${locationName(loc)}`,\n      )\n    }\n    return {\n      type: 'RgfaTabixAdapter',\n      walksLocation: loc,\n      walksIndex: tabixIndex(loc, indexLoc),\n      ...referencePanSN(assembly, sample, walkFileSample(loc)),\n      ...(haplotypes.length > 0 ? { defaultHaplotypes: haplotypes } : {}),\n    }\n  }\n  if (choice === 'GbzBaseSyntenyAdapter') {\n    return {\n      type: 'GbzBaseSyntenyAdapter',\n      gbzDbLocation: loc,\n      ...(indexLoc ? { haplotypeIndexLocation: indexLoc } : {}),\n      ...readsConfig(readsLoc),\n      ...panSN(assembly, sample),\n    }\n  }\n  if (choice === 'MinigraphBubbleAdapter') {\n    return {\n      type: 'MinigraphBubbleAdapter',\n      bubblesLocation: loc,\n      index: tabixIndex(loc, indexLoc),\n      ...panSN(assembly, sample),\n    }\n  }\n  if (locationName(loc).endsWith(GRAPH_SUFFIX)) {\n    return {\n      type: 'RgfaTabixAdapter',\n      graphLocation: loc,\n      graphIndex: tabixIndex(loc, indexLoc),\n      ...referencePanSN(assembly, sample, manifest?.reference),\n      ...coarseTier(loc, indexLoc, manifest?.tier),\n    }\n  }\n  const links = linksLocation(loc)\n  return {\n    type: 'RgfaTabixAdapter',\n    segmentsLocation: loc,\n    segmentsIndex: tabixIndex(loc, indexLoc),\n    linksLocation: links,\n    linksIndex: siblingIndex(links, indexLoc),\n    ...referencePanSN(assembly, sample, manifest?.reference),\n    ...coarseTier(loc, indexLoc, manifest?.tier),\n  }\n}\n\nexport function buildTrackConfig(args: {\n  choice: GraphFileChoice\n  loc: FileLocation\n  indexLoc: FileLocation | undefined\n  readsLoc?: FileLocation\n  manifest?: GraphManifest\n  assembly: string\n  sample: string\n  haplotypes?: string[]\n  trackId: string\n  name: string\n}) {\n  const { choice, assembly, trackId, name } = args\n  return {\n    type: choice === 'MinigraphBubbleAdapter' ? 'FeatureTrack' : 'GraphTrack',\n    trackId,\n    name,\n    assemblyNames: [assembly],\n    adapter: buildAdapterConfig(args),\n    ...(choice === 'RgfaTabixAdapter' || choice === 'RgfaTabixWalks'\n      ? {\n          displayDefaults: {\n            labels: { name: { show: false }, description: { show: false } },\n          },\n        }\n      : {}),\n  }\n}\n"],
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-}