jbrowse-plugin-graphgenomeviewer 8.7.1 → 8.7.2

package/dist/chunks/{chunk-6V6OOEYK.js → chunk-OS52UJIX.js}

@@ -1,2 +1,2 @@
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+//# sourceMappingURL=chunk-OS52UJIX.js.map

package/dist/chunks/chunk-T7LVVBTT.js

@@ -0,0 +1,2 @@
+import{c as F}from"./chunk-TMM73K4C.js";import{a as p,b as d,c as y,d as T,h as r,i as g,j as f}from"./chunk-6VNDP3UB.js";import{a as I}from"./chunk-D6TY2QEG.js";var W=5e3;function G(e){return typeof e=="string"&&/^[\w+-][\w.+-]*$/.test(e)}function k(e){return e==null}function M(e){return typeof e=="object"&&e!==null&&!Array.isArray(e)}function L(e){return M(e)&&G(e.prefix)&&typeof e.foldBelowBp=="number"&&Number.isFinite(e.foldBelowBp)&&e.foldBelowBp>0}function P(e){let n;try{n=JSON.parse(e)}catch{return}if(!M(n)||n.schema!==1)return;let{reference:t,tier:i,index:a,contig:o,bubbles:s,alleles:l}=n;if((k(t)||typeof t=="string"&&t.trim()!=="")&&(k(i)||L(i))&&[a,o,s,l].every(A=>k(A)||G(A)))return{...typeof t=="string"?{reference:t.trim()}:{},...L(i)?{tier:{prefix:i.prefix,foldBelowBp:i.foldBelowBp,...i.format===2?{format:2}:{}}}:{}}}function b(e,n){return f(e,t=>t.replace(/[^/\\]*$/,n))}function R(e){let n=r(e);return[p,d].find(t=>n.endsWith(t))}function N(e){return g(e)&&R(e)!==void 0}function B(e,n){let t=R(e)??p;return f(e,i=>`${i.slice(0,-t.length)}${n}`)}function _(e){return N(e)?B(e,".graph.json"):void 0}async function j(e,n){let t=_(e);if(t)try{let i=await I(t,n).readFile({encoding:"utf8",signal:AbortSignal.timeout(W)});return P(i)}catch{return}}var J={RgfaTabixAdapter:"Indexed GFA (gfa-to-tabix .segs.bed.gz or .graph.bed.gz)",RgfaTabixWalks:"Haplotype walks without lanes (.walks.bed.gz)",WalkTabixSyntenyAdapter:"Haplotype walks (.walks.bed.gz)",GbzBaseSyntenyAdapter:"GBZ database (.gbz.db)",MinigraphBubbleAdapter:"Minigraph bubbles (tabix BED)"},E="Path to a walk file (<prefix>.<sample>.walks.bed.gz from gfa-to-tabix --walks, for the sample this assembly is)",Z={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:E,WalkTabixSyntenyAdapter:E,GbzBaseSyntenyAdapter:"Path to the .gbz.db written by gbz-base construct",MinigraphBubbleAdapter:"Path to bubbles BED (.bed.gz from gfatools bubble)"},u="Path to tabix index (optional; the sibling .tbi is assumed, a .csi is recognised by name)",q={RgfaTabixAdapter:u,RgfaTabixWalks:u,WalkTabixSyntenyAdapter:u,GbzBaseSyntenyAdapter:"Path to the haplotype index (optional; graph.haplotype-index.db beside the database is assumed)",MinigraphBubbleAdapter:u};function x(e,n){return f(e,t=>t+n)}function C(e){if(!r(e).endsWith(p))throw new Error(`Expected a segments BED ending in ${p}, got ${r(e)}`);return B(e,".links.bed.gz")}function c(e,n){return n?{location:n,indexType:F(r(n),"CSI","TBI")}:{location:x(e,".tbi"),indexType:"TBI"}}function h(e,n){return n!==void 0&&F(r(n),"CSI","TBI")==="CSI"?{location:x(e,".csi"),indexType:"CSI"}:{location:x(e,".tbi"),indexType:"TBI"}}function w(e,n){let t=n.trim();return t&&e?{assemblyNameToPanSN:{[e]:t}}:{}}function z(e,n,t){if(!t)return{};if(t.format===2){let o=b(e,`${t.prefix}${d}`);return{coarse:{foldBelowBp:t.foldBelowBp,graphLocation:o,graphIndex:h(o,n)}}}let i=b(e,`${t.prefix}${p}`),a=b(e,`${t.prefix}.links.bed.gz`);return{coarse:{foldBelowBp:t.foldBelowBp,segmentsLocation:i,segmentsIndex:h(i,n),linksLocation:a,linksIndex:h(a,n)}}}function S(e,n,t){let i=t===e?void 0:t;return w(e,n.trim()||i||"")}function $(e){return e?{readsLocation:e,...r(e).endsWith(".gz")&&g(e)?{readsIndex:{location:x(e,".tbi")}}:{}}:{}}function Q(e){return e.split(/[\s,]+/).filter(n=>n!=="")}function D({choice:e,loc:n,indexLoc:t,readsLoc:i,manifest:a,assembly:o,sample:s,haplotypes:l=[]}){if(e==="RgfaTabixWalks"||e==="WalkTabixSyntenyAdapter"){if(!r(n).endsWith(y))throw new Error(`Expected a walk file ending in ${y}, got ${r(n)}`);return{type:e==="RgfaTabixWalks"?"RgfaTabixAdapter":e,walksLocation:n,walksIndex:c(n,t),...S(o,s,T(n)),...l.length>0?{defaultHaplotypes:l}:{}}}if(e==="GbzBaseSyntenyAdapter")return{type:"GbzBaseSyntenyAdapter",gbzDbLocation:n,...t?{haplotypeIndexLocation:t}:{},...$(i),...w(o,s)};if(e==="MinigraphBubbleAdapter")return{type:"MinigraphBubbleAdapter",bubblesLocation:n,index:c(n,t),...w(o,s)};if(r(n).endsWith(d))return{type:"RgfaTabixAdapter",graphLocation:n,graphIndex:c(n,t),...S(o,s,a?.reference),...z(n,t,a?.tier)};let m=C(n);return{type:"RgfaTabixAdapter",segmentsLocation:n,segmentsIndex:c(n,t),linksLocation:m,linksIndex:h(m,t),...S(o,s,a?.reference),...z(n,t,a?.tier)}}function V(e){let{choice:n,assembly:t,trackId:i,name:a}=e;return{type:n==="MinigraphBubbleAdapter"?"FeatureTrack":"GraphTrack",trackId:i,name:a,assemblyNames:[t],adapter:D(e),...n==="RgfaTabixAdapter"||n==="RgfaTabixWalks"?{displayDefaults:{labels:{name:{show:!1},description:{show:!1}}}}:{}}}export{N as a,j as b,J as c,Z as d,q as e,Q as f,D as g,V as h};
+//# sourceMappingURL=chunk-T7LVVBTT.js.map

package/dist/chunks/chunk-T7LVVBTT.js.map

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+{
+  "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  // `format: 2` when the tier is one `<prefix>.graph.bed.gz`, as gfa-to-tabix\n  // 2 writes it, rather than a segments and links pair\n  tier?: { prefix: string; foldBelowBp: number; format?: 2 }\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.+-]*$/.test(name)\n}\n\nfunction isAbsent(value: unknown) {\n  return value === undefined || value === null\n}\n\nfunction isPlainRecord(value: unknown): value is Record<string, unknown> {\n  return typeof value === 'object' && value !== null && !Array.isArray(value)\n}\n\nfunction isTier(tier: unknown): tier is NonNullable<GraphManifest['tier']> {\n  return (\n    isPlainRecord(tier) &&\n    isSiblingName(tier.prefix) &&\n    typeof tier.foldBelowBp === 'number' &&\n    Number.isFinite(tier.foldBelowBp) &&\n    tier.foldBelowBp > 0\n  )\n}\n\nexport function parseGraphManifest(text: string): GraphManifest | undefined {\n  let json: unknown\n  try {\n    json = JSON.parse(text)\n  } catch {\n    return undefined\n  }\n  if (!isPlainRecord(json) || json.schema !== 1) {\n    return undefined\n  }\n  const { reference, tier, index, contig, bubbles, alleles } = json\n  const valid =\n    (isAbsent(reference) ||\n      (typeof reference === 'string' && reference.trim() !== '')) &&\n    (isAbsent(tier) || isTier(tier)) &&\n    [index, contig, bubbles, alleles].every(\n      f => isAbsent(f) || isSiblingName(f),\n    )\n  if (!valid) {\n    return undefined\n  }\n  return {\n    ...(typeof reference === 'string' ? { reference: reference.trim() } : {}),\n    ...(isTier(tier)\n      ? {\n          tier: {\n            prefix: tier.prefix,\n            foldBelowBp: tier.foldBelowBp,\n            ...(tier.format === 2 ? { format: 2 as const } : {}),\n          },\n        }\n      : {}),\n  }\n}\n\n// A file the manifest names, in the directory of the segments file opened\nexport function besideSegments(segs: FileLocation, fileName: string) {\n  return renamed(segs, name => name.replace(/[^/\\\\]*$/, 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, which draws\n// the graph without haplotype lanes\nexport type GraphFileChoice =\n  | 'RgfaTabixAdapter'\n  | 'RgfaTabixWalks'\n  | 'WalkTabixSyntenyAdapter'\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 without lanes (.walks.bed.gz)',\n  WalkTabixSyntenyAdapter: 'Haplotype walks (.walks.bed.gz)',\n  GbzBaseSyntenyAdapter: 'GBZ database (.gbz.db)',\n  MinigraphBubbleAdapter: 'Minigraph bubbles (tabix BED)',\n}\n\nconst WALKS_FIELD =\n  'Path to a walk file (<prefix>.<sample>.walks.bed.gz from gfa-to-tabix --walks, for the sample this assembly is)'\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: WALKS_FIELD,\n  WalkTabixSyntenyAdapter: WALKS_FIELD,\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  WalkTabixSyntenyAdapter: 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 ${locationName(loc)}`,\n    )\n  }\n  return segmentsSibling(loc, '.links.bed.gz')\n}\n\nfunction tabixIndex(loc: FileLocation, indexLoc: FileLocation | undefined) {\n  return indexLoc\n    ? {\n        location: indexLoc,\n        indexType: makeIndexType(locationName(indexLoc), 'CSI', 'TBI'),\n      }\n    : { location: sibling(loc, '.tbi'), indexType: 'TBI' }\n}\n\n// The links file's index is assumed beside it, of the kind the segments' is.\nfunction siblingIndex(loc: FileLocation, indexLoc: FileLocation | undefined) {\n  const csi =\n    indexLoc !== undefined &&\n    makeIndexType(locationName(indexLoc), 'CSI', 'TBI') === 'CSI'\n  return csi\n    ? { location: sibling(loc, '.csi'), indexType: 'CSI' }\n    : { location: sibling(loc, '.tbi'), indexType: 'TBI' }\n}\n\n// none for a guessed config, which knows no assembly yet; see withWalkReference\nfunction panSN(assembly: string, sample: string) {\n  const name = sample.trim()\n  return name && assembly ? { assemblyNameToPanSN: { [assembly]: name } } : {}\n}\n\nfunction coarseTier(\n  loc: FileLocation,\n  indexLoc: FileLocation | undefined,\n  tier: GraphManifest['tier'],\n) {\n  if (!tier) {\n    return {}\n  }\n  if (tier.format === 2) {\n    const graph = besideSegments(loc, `${tier.prefix}${GRAPH_SUFFIX}`)\n    return {\n      coarse: {\n        foldBelowBp: tier.foldBelowBp,\n        graphLocation: graph,\n        graphIndex: siblingIndex(graph, indexLoc),\n      },\n    }\n  }\n  const segs = besideSegments(loc, `${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' || choice === 'WalkTabixSyntenyAdapter') {\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: choice === 'RgfaTabixWalks' ? 'RgfaTabixAdapter' : choice,\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' ? 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+}