jbrowse-plugin-graphgenomeviewer 8.7.1 → 8.7.2

package/src/panSNAliases/trackAdapterConfig.ts

@@ -1,5 +1,6 @@
 import { readConfObject } from '@jbrowse/core/configuration'
 import { getSession } from '@jbrowse/core/util'
+import { getConfAssemblyNamesOrNone } from '@jbrowse/core/util/tracks'
 
 import { trackAdapterSnapshot, walkIndexed } from '../graphTrackConfig'
 
@@ -19,12 +20,31 @@ export interface AssemblyAliases {
 // parts name a contig, not a haplotype.
 const PANSN_HAPLOTYPE = /^[^#]+#\d+$/
 
-// The config's `assemblyNameToPanSN` with each assembly's PanSN alias added
-// beneath it: an entry wins for its assembly and for its prefix. Unchanged when
-// no alias qualifies, so such a track keeps its adapter cache key.
+// `HG00621.1`, as HPRC and the hosted configs name a haplotype's assembly, and
+// as a MAF names its rows
+const DOTTED_HAPLOTYPE = /^([^#]+)\.(\d+)$/
+
+function aliasHaplotype({ aliases }: AssemblyAliases) {
+  return aliases.find(a => PANSN_HAPLOTYPE.test(a))
+}
+
+function dottedHaplotype({ name }: AssemblyAliases) {
+  const dotted = DOTTED_HAPLOTYPE.exec(name)
+  return dotted ? `${dotted[1]}#${dotted[2]}` : undefined
+}
+
+// The config's `assemblyNameToPanSN` with each assembly's PanSN haplotype
+// added beneath it, so a lane on that haplotype draws on the assembly and its
+// genes. An entry wins for its assembly and for its prefix, then a
+// `sample#haplotype` alias, then the assembly's own name read as
+// `sample.haplotype`. The anchor's name is never read so, since an accession
+// such as GCA_000001405.15 has that shape and the anchor is the walk file's
+// reference, not one of its lanes. Unchanged when no assembly qualifies, so
+// such a track keeps its adapter cache key.
 export function withPanSNAliases(
   adapterConfig: Record<string, unknown>,
   assemblies: AssemblyAliases[],
+  anchor?: string,
 ) {
   const explicit = (adapterConfig.assemblyNameToPanSN ?? {}) as Record<
     string,
@@ -32,10 +52,22 @@ export function withPanSNAliases(
   >
   const claimed = new Set(Object.values(explicit))
   const fromAliases: Record<string, string> = {}
-  for (const { name, aliases } of assemblies) {
-    const prefix = aliases.find(alias => PANSN_HAPLOTYPE.test(alias))
-    if (prefix !== undefined && !claimed.has(prefix)) {
-      fromAliases[name] = prefix
+  const lanes = assemblies.filter(a => a.name !== anchor)
+  for (const [read, from] of [
+    [aliasHaplotype, assemblies],
+    [dottedHaplotype, lanes],
+  ] as const) {
+    for (const assembly of from) {
+      const prefix = read(assembly)
+      if (
+        prefix !== undefined &&
+        !claimed.has(prefix) &&
+        !(assembly.name in explicit) &&
+        !(assembly.name in fromAliases)
+      ) {
+        fromAliases[assembly.name] = prefix
+        claimed.add(prefix)
+      }
     }
   }
   return Object.keys(fromAliases).length === 0
@@ -46,6 +78,13 @@ export function withPanSNAliases(
       }
 }
 
+function canonicalName(assemblies: AssemblyAliases[], name: string) {
+  return (
+    assemblies.find(a => a.name === name || a.aliases.includes(name))?.name ??
+    name
+  )
+}
+
 // The config's `assemblyNames` and `assemblyNameToPanSN` keys by each
 // assembly's canonical name, the name a window arrives with. An alias renamed
 // here still resolves to itself as a PanSN prefix. Unchanged when every name is
@@ -54,9 +93,7 @@ export function withCanonicalAssemblyNames(
   adapterConfig: Record<string, unknown>,
   assemblies: AssemblyAliases[],
 ) {
-  const canonical = (name: string) =>
-    assemblies.find(a => a.name === name || a.aliases.includes(name))?.name ??
-    name
+  const canonical = (name: string) => canonicalName(assemblies, name)
   const names = (adapterConfig.assemblyNames ?? []) as string[]
   const explicit = (adapterConfig.assemblyNameToPanSN ?? {}) as Record<
     string,
@@ -113,8 +150,10 @@ export function trackAdapterConfig(
       aliases: readConfObject(conf, 'aliases'),
     }),
   )
+  const [anchor] = getConfAssemblyNamesOrNone(track)
   return withPanSNAliases(
     withCanonicalAssemblyNames(adapterConfig, assemblies),
     assemblies,
+    anchor === undefined ? undefined : canonicalName(assemblies, anchor),
   )
 }

package/src/version.ts

@@ -1 +1 @@
-export const version = '8.7.1'
+export const version = '8.7.2'

package/dist/chunks/AddTrackWorkflow-IOPTETLH.js

@@ -1,2 +0,0 @@
-import{b as J,c as D,d as V,e as X,f as q,h as K}from"./chunk-CGPYVMGQ.js";import"./chunk-TMM73K4C.js";import"./chunk-6VNDP3UB.js";import"./chunk-D6TY2QEG.js";import{d as M,e as P}from"./chunk-FLKXKTS2.js";import{b as w,h as v,j as A,m as x}from"./chunk-TC265JAP.js";import{i as o}from"./chunk-J2PN6CG3.js";import{A as O,B as j,C as z,F as h,a as H,f as E,g as c,o as B,s as N,t as W,u as _}from"./chunk-WE7DQVXF.js";import{b as a,c as f,d as I}from"./chunk-DUU6T2I5.js";var n=JBrowseExports["@jbrowse/core/util/tss-react"],oe=s=>n!=null&&s in Object(n)?n[s]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+s+"' from '@jbrowse/core/util/tss-react' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:s});var Q=oe("makeStyles"),ie=n&&n.__esModule?n.default:n;var se=Q()(s=>({paper:{margin:s.spacing(),padding:s.spacing()},field:{marginTop:s.spacing(2)},submit:{marginTop:25,marginBottom:100,display:"block"}})),re=["RgfaTabixAdapter","RgfaTabixWalks","GbzBaseSyntenyAdapter","MinigraphBubbleAdapter"],ne=I(function({model:t}){let{classes:i}=se(),y=A(t),d=M(t),[r,U]=o("RgfaTabixAdapter"),[l,Y]=o(),[k,G]=o(),[T,Z]=o(),m=r==="GbzBaseSyntenyAdapter",u=r==="RgfaTabixWalks",[C,$]=o(""),[R,ee]=o(""),[b,ae]=o("Pangenome graph"),[S,g]=o(),[F,L]=o(!1);async function te(){if(!l||!t.assembly)return;g(void 0),L(!0);let e=r==="RgfaTabixAdapter"?await J(l,v(t).pluginManager):void 0;if(L(!1),!(!P(t)||!t.assembly))try{let p=b.trim();w({model:t,session:y,conf:K({choice:r,loc:l,indexLoc:k,readsLoc:m?T:void 0,manifest:e,assembly:t.assembly,sample:C,haplotypes:u?q(R):void 0,trackId:x({name:p}),name:p})})}catch(p){g(p)}}return f(O,{className:i.paper,children:[S?a(E,{error:S}):null,f(N,{children:[a(_,{children:"File type"}),a(z,{value:r,onChange:e=>{U(e.target.value),G(void 0),g(void 0)},children:re.map(e=>a(W,{value:e,control:a(j,{}),label:D[e]},e))})]}),a(c,{location:l,name:V[r],rootModel:d,setLocation:Y}),a(c,{location:k,name:X[r],rootModel:d,setLocation:G}),m?a(c,{location:T,name:"Path to reads aligned to the graph as GAF (optional; a .gz is read by the .tbi beside it)",rootModel:d,setLocation:Z}):null,a(h,{className:i.field,value:C,onChange:e=>{$(e.target.value)},label:"Sample name in the graph",slotProps:{htmlInput:{"data-testid":"graph-sample-input"}},helperText:m?"Optional. The graph's sample for this assembly, e.g. GRCh38 where the assembly is hg38; leave blank when they share a name or the graph has one reference sample":u?"Optional. The PanSN sample this assembly is in the graph; blank takes it from the file name, GRCh38 in chr22.GRCh38.walks.bed.gz":"Optional. The PanSN prefix the graph gives this assembly, e.g. GRCh38 for HPRC's GRCh38#0#chr1; leave blank when the graph's stable names are bare",placeholder:"GRCh38",fullWidth:!0}),u?a(h,{className:i.field,value:R,onChange:e=>{ee(e.target.value)},label:"Haplotypes",slotProps:{htmlInput:{"data-testid":"graph-haplotypes-input"}},helperText:"Optional. The haplotypes the track cuts for until you pick others in its menu, as PanSN names separated by commas (HG002#1, or HG002 for both); blank is every haplotype in the file",placeholder:"HG002, HG00733",fullWidth:!0}):null,a(h,{className:i.field,value:b,label:"Track name",slotProps:{htmlInput:{"data-testid":"graph-track-name-input"}},onChange:e=>{ae(e.target.value)}}),a(H,{session:y,helperText:"Select assembly to add track to",selected:t.assembly,onChange:e=>{t.setAssembly(e)},fullWidth:!0}),a(B,{variant:"contained",className:i.submit,disabled:!l||!b.trim()||!t.assembly||F,onClick:()=>{te()},children:F?"Reading graph.json\u2026":"Submit"})]})}),ye=ne;export{ye as default};
-//# sourceMappingURL=AddTrackWorkflow-IOPTETLH.js.map

package/dist/chunks/chunk-CGPYVMGQ.js

@@ -1,2 +0,0 @@
-import{c as y}from"./chunk-TMM73K4C.js";import{a as p,b as f,c as x,d as A,h as a,i as g,j as d}from"./chunk-6VNDP3UB.js";import{a as T}from"./chunk-D6TY2QEG.js";var z=5e3;function G(e){return typeof e=="string"&&/^[\w+-][\w.+-]*$/.test(e)}function F(e){return e==null}function M(e){return typeof e=="object"&&e!==null&&!Array.isArray(e)}function L(e){return M(e)&&G(e.prefix)&&typeof e.foldBelowBp=="number"&&Number.isFinite(e.foldBelowBp)&&e.foldBelowBp>0}function P(e){let n;try{n=JSON.parse(e)}catch{return}if(!M(n)||n.schema!==1)return;let{reference:t,tier:i,index:r,contig:o,bubbles:s,alleles:l}=n;if((F(t)||typeof t=="string"&&t.trim()!=="")&&(F(i)||L(i))&&[r,o,s,l].every(k=>F(k)||G(k)))return{...typeof t=="string"?{reference:t.trim()}:{},...L(i)?{tier:{prefix:i.prefix,foldBelowBp:i.foldBelowBp,...i.format===2?{format:2}:{}}}:{}}}function u(e,n){return d(e,t=>t.replace(/[^/\\]*$/,n))}function R(e){let n=a(e);return[p,f].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 d(e,i=>`${i.slice(0,-t.length)}${n}`)}function _(e){return N(e)?B(e,".graph.json"):void 0}async function X(e,n){let t=_(e);if(t)try{let i=await T(t,n).readFile({encoding:"utf8",signal:AbortSignal.timeout(z)});return P(i)}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)"},w="Path to tabix index (optional; the sibling .tbi is assumed, a .csi is recognised by name)",Z={RgfaTabixAdapter:w,RgfaTabixWalks:w,GbzBaseSyntenyAdapter:"Path to the haplotype index (optional; graph.haplotype-index.db beside the database is assumed)",MinigraphBubbleAdapter:w};function h(e,n){return d(e,t=>t+n)}function C(e){if(!a(e).endsWith(p))throw new Error(`Expected a segments BED ending in ${p}, got ${a(e)}`);return B(e,".links.bed.gz")}function b(e,n){return n?{location:n,indexType:y(a(n),"CSI","TBI")}:{location:h(e,".tbi"),indexType:"TBI"}}function c(e,n){return n!==void 0&&y(a(n),"CSI","TBI")==="CSI"?{location:h(e,".csi"),indexType:"CSI"}:{location:h(e,".tbi"),indexType:"TBI"}}function S(e,n){let t=n.trim();return t&&e?{assemblyNameToPanSN:{[e]:t}}:{}}function E(e,n,t){if(!t)return{};if(t.format===2){let o=u(e,`${t.prefix}${f}`);return{coarse:{foldBelowBp:t.foldBelowBp,graphLocation:o,graphIndex:c(o,n)}}}let i=u(e,`${t.prefix}${p}`),r=u(e,`${t.prefix}.links.bed.gz`);return{coarse:{foldBelowBp:t.foldBelowBp,segmentsLocation:i,segmentsIndex:c(i,n),linksLocation:r,linksIndex:c(r,n)}}}function I(e,n,t){let i=t===e?void 0:t;return S(e,n.trim()||i||"")}function $(e){return e?{readsLocation:e,...a(e).endsWith(".gz")&&g(e)?{readsIndex:{location:h(e,".tbi")}}:{}}:{}}function q(e){return e.split(/[\s,]+/).filter(n=>n!=="")}function W({choice:e,loc:n,indexLoc:t,readsLoc:i,manifest:r,assembly:o,sample:s,haplotypes:l=[]}){if(e==="RgfaTabixWalks"){if(!a(n).endsWith(x))throw new Error(`Expected a walk file ending in ${x}, got ${a(n)}`);return{type:"RgfaTabixAdapter",walksLocation:n,walksIndex:b(n,t),...I(o,s,A(n)),...l.length>0?{defaultHaplotypes:l}:{}}}if(e==="GbzBaseSyntenyAdapter")return{type:"GbzBaseSyntenyAdapter",gbzDbLocation:n,...t?{haplotypeIndexLocation:t}:{},...$(i),...S(o,s)};if(e==="MinigraphBubbleAdapter")return{type:"MinigraphBubbleAdapter",bubblesLocation:n,index:b(n,t),...S(o,s)};if(a(n).endsWith(f))return{type:"RgfaTabixAdapter",graphLocation:n,graphIndex:b(n,t),...I(o,s,r?.reference),...E(n,t,r?.tier)};let m=C(n);return{type:"RgfaTabixAdapter",segmentsLocation:n,segmentsIndex:b(n,t),linksLocation:m,linksIndex:c(m,t),...I(o,s,r?.reference),...E(n,t,r?.tier)}}function Q(e){let{choice:n,assembly:t,trackId:i,name:r}=e;return{type:n==="MinigraphBubbleAdapter"?"FeatureTrack":"GraphTrack",trackId:i,name:r,assemblyNames:[t],adapter:W(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,W as g,Q as h};
-//# sourceMappingURL=chunk-CGPYVMGQ.js.map

package/dist/chunks/chunk-CGPYVMGQ.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  // `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\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 ${locationName(loc)}`,\n    )\n  }\n  return segmentsSibling(loc, '.links.bed.gz')\n}\n\nfunction tabixIndex(loc: FileLocation, indexLoc: FileLocation | undefined) {\n  return indexLoc\n    ? {\n        location: indexLoc,\n        indexType: makeIndexType(locationName(indexLoc), 'CSI', 'TBI'),\n      }\n    : { location: sibling(loc, '.tbi'), indexType: 'TBI' }\n}\n\n// The links file's index is assumed beside it, of the kind the segments' is.\nfunction siblingIndex(loc: FileLocation, indexLoc: FileLocation | undefined) {\n  const csi =\n    indexLoc !== undefined &&\n    makeIndexType(locationName(indexLoc), 'CSI', 'TBI') === 'CSI'\n  return csi\n    ? { location: sibling(loc, '.csi'), indexType: 'CSI' }\n    : { location: sibling(loc, '.tbi'), indexType: 'TBI' }\n}\n\n// none for a guessed config, which knows no assembly yet; see withWalkReference\nfunction panSN(assembly: string, sample: string) {\n  const name = sample.trim()\n  return name && assembly ? { assemblyNameToPanSN: { [assembly]: name } } : {}\n}\n\nfunction coarseTier(\n  loc: FileLocation,\n  indexLoc: FileLocation | undefined,\n  tier: GraphManifest['tier'],\n) {\n  if (!tier) {\n    return {}\n  }\n  if (tier.format === 2) {\n    const graph = besideSegments(loc, `${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') {\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' ? 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t=this.walkLift?.referenceDomain;return t&&{...t,name:e.graphRegion?.refName}},get walkLabels(){return je(this.walkChoices)},walkLabel(t){return this.walkLabels.get(t)??t},get liftPaintsOffReference(){return!!this.walkLift?.walks.some(t=>t.encoding.field!=="walk"&&[...t.colors.values()].includes(po))},get liftedWalksLabel(){let t=this.walkLift?.walks??[];return t.length===1?this.walkLabel(t[0].name):"these walks"},get effectiveColorScheme(){return e.layoutResult?.tubeMap&&(this.tubeMapReads||e.chosenColorScheme==="auto")?"uniform":Oe(e.chosenColorScheme,e.graph)},get tubeMapReads(){let t=e.layoutResult;return!t?.tubeMapPanels&&(t?.tubeMap?.layout.reads.length??0)>0},get colorSchemeLock(){return this.walkLift?{value:"By walk",why:"Each highlighted haplotype colours its own lane: set it under Haplotypes, Color highlighted..."}:this.tubeMapReads?{value:"By strand",why:"Reads take the reds and blues, so the tube map leaves its nodes clear"}:void 0},get nodePositions(){return e.layoutResult?.nodePositions},get labelsNodeSizes(){return!e.layoutResult?.tubeMap&&!this.walkLift},get alleleDeletions(){return e.layoutResult?.alleleDeletions??[]},get deletionRoutes(){return e.layoutResult?.deletionRoutes},get stranded(){return e.layoutResult?.stranded},get pixelRows(){return e.layoutResult?.pixelRows??!1},get zoomPercent(){return`${(e.scale*100).toFixed(1)}%`},get isDefaultViewport(){return e.scale===1&&e.translateX===0&&e.translateY===0}})).views(e=>({get derivedBubbles(){return e.graph?kt(e.graph):[]},get openBubbleInsides(){let{graph:t}=e;return t?e.openBubbles.map(n=>kt(He(t,me(n)),n).filter(o=>!o.covering)):[]},get openBubble(){return e.openBubbles.at(-1)},get openBubbleFocus(){let t=this.openBubble,{graph:n}=e;if(!t||!n)return;let o=new Set(me(t)),r=new Set(n.nodes.filter(s=>o.has(s.name)).map(s=>s.id)),a=new Set;return n.edges.forEach((s,i)=>{r.has(s.from)&&r.has(s.to)&&a.add(i)}),{walks:[],nodeIds:r,edgeIndexes:a,names:new Set}},get drawnHighlight(){return e.walkLift??this.openBubbleFocus},bubbleIsOpen(t){return e.openBubbles.some(n=>st(n,t))},bubbleFaded({bubble:t,nodeIds:n}){let o=e.walkLift,r=this.openBubbleFocus;return o?!n.some(a=>o.nodeIds.has(a)):!!r&&!this.bubbleIsOpen(t)&&!n.every(a=>r.nodeIds.has(a))}})).views(e=>({get bubbles(){let t=e.indexBubbles?.length?e.indexBubbles:e.derivedBubbles,n=new Set(t.map(it));return[...t,...e.openBubbleInsides.flat().filter(o=>!n.has(it(o))&&n.add(it(o)))]},get foldNote(){let t=e.foldedBelowBp;return t===void 0?void 0:`variants under ${Yn(t)} folded into the reference`}})).views(e=>({get cutHaplotypes(){},get sourceAdapter(){let t=e.sourceTrack;return t?dr(e,t):void 0},get sourceTrackId(){return e.sourceTrack?.trackId},get sessionTracks(){let t=U(e);return t.tracks.map(n=>({trackId:n.trackId,name:Wn(n,t),adapterType:Qe(n).type,assemblies:en(t,n)}))}})).views(e=>({get assemblyTrackChoices(){let t=e.graphRegion,n=t&&Qt(U(e),t.assemblyName);return 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rowVisitsNeeded(){return e.chosenLayoutMode==="walkrows"&&(e.walkRibbons||e.layerSet.has("walkBlocks")||e.walkRowOrder==="shared")},assemblySpellings(t){let{assemblyManager:n}=U(e),o=n.has(t)?n.get(t):void 0,r=e.sourceAdapter?.assemblyNameToPanSN??{},a=[t,...o?[o.name,...o.aliases]:[]];return{name:t,aliases:[...a,...a.flatMap(s=>r[s]??[])]}},get drawsLoadedReference(){let t=e.graph;return t?.anchoredBy==="tags"||t?.referencePath!==void 0&&t.referencePath===e.loadedReferencePath}})).views(e=>({get geneAssembly(){let t=e.graphRegion;return t?e.assemblySpellings(t.assemblyName):void 0},get geneLaneFilter(){let t=e.containingView;if(!t)return;let n=nr(t,e.geneTrack?.trackId);return n.length?new Dr({filters:n,jexl:Nn(e).pluginManager.jexl}):void 0},get geneFeatures(){let t=e.geneTrackFeatures,n=this.geneLaneFilter;return t?or(n?t.filter(o=>n.passes(o)):t):void 0},get backboneGenes(){let{backbone:t}=e,{geneAssembly:n,geneFeatures:o}=this,r=e.drawsLoadedReference||n!==void 0&&In(t,[n])!==void 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t=e.sourceAdapter?.samplesTsvLocation;return t&&Cn(t)?t:void 0},get walkRowGroupFields(){return Lo(e.walkRowSampleTable)},get tubeMapColoring(){let t=e.tubeMapColorBy,n=e.walkRowSampleTable;if(!t||!n||!this.walkRowGroupFields.includes(t))return;let o=Bo(t,n),r=(e.graph?.paths??[]).map(a=>de(a.name).name).filter(a=>a!==e.graph?.referencePath);return{field:t,valueOf:o,palette:Eo(r.map(o)),unvalued:r.some(a=>o(a)==="")}},get tableGroupBy(){let t=e.walkRowGroupBy,n=e.walkRowSampleTable;return t&&n&&this.walkRowGroupFields.includes(t.field)?{groupBy:t,table:n}:void 0},get tubeMapPanelSplit(){let{field:t,sort:n}=e.facetSetting,o=this.tableGroupBy;return t!==""?{by:t,sort:n}:o?{by:"column",...o.groupBy,table:o.table}:void 0},get keptCohortRows(){let t=this.cohortWalkRows,n=t&&Me(t.rows,e.walkRowSamples);if(!t||!n||e.walkRowOrder!=="shared")return n;let o=[t.reference,...n];return yn(o).filter(r=>r>0).map(r=>o[r])},get walkRowGroups(){let t=this.keptCohortRows,n=this.tableGroupBy;return t&&n?Po(t,n.table,n.groupBy):void 0},get walkRowBars(){let t=this.cohortWalkRows,n=this.keptCohortRows;return t&&n?{...t,rows:this.walkRowGroups?.rows??n}:void 0},get walkRowList(){let t=this.walkRowBars;return t?[t.reference,...t.rows]:[]},get walkRowRibbons(){let t=this.walkRowGroups?.sections??[];return e.walkRibbons&&e.rowVisitsNeeded&&this.walkRowBars?kn(this.walkRowList).filter(({row:n})=>Xt(t,n)===Xt(t,n+1)):void 0},get sharedBlocks(){return e.layerSet.has("walkBlocks")&&e.rowVisitsNeeded&&this.walkRowBars?Rn(this.walkRowList):void 0},get drawsNodes(){return Y(e.drawnLayoutMode??e.chosenLayoutMode).drawsNodes},get genePins(){Te(e.positionsVersion);let t=e.layoutResult?.nodePositions,n=[...e.backboneGenes??[],...e.ownGeneFeatures??[]];return e.showGenes&&this.drawsNodes&&e.graph&&n.length>0&&t?Be(e.graph,n,t):[]},get bubbleHalos(){Te(e.positionsVersion);let t=e.layoutResult?.nodePositions,n=e.showBubbles?e.bubbles:e.hoveredBubble?[e.hoveredBubble]:[];return n.length===0||!this.drawsNodes||!e.graph||!t?[]:pn(e.graph,n,t,e.repeatArrays)},get referenceRamp(){return e.effectiveColorScheme==="reference-position"?e.drawnReferenceRamp:void 0},get assemblyNames(){let t=e.graphRegion;return t?[t.assemblyName]:[]},get axisScale(){return rt(e.scale,e.pixelRows)},get scaleX(){return this.axisScale.scaleX},get scaleY(){return this.axisScale.scaleY}})).views(e=>({get screenTransform(){return{scaleX:e.scaleX,scaleY:e.scaleY,translateX:e.translateX,translateY:e.translateY}},toScreen(t){return{x:t.x*e.scaleX+e.translateX,y:t.y*e.scaleY+e.translateY}},get deletionDrawing(){return e.graph?Ve(e.graph,e.allDeletions,e.showDeletionEdges):void 0},get deletions(){return this.deletionDrawing?.shown??[]},get deletionEdgeIndexes(){return this.deletionDrawing?.bypassed},get hiddenEdgeIndexes(){return this.deletionDrawing?.hidden},get referenceRampDomain(){let t=e.referenceRamp;return t?{start:t.start,end:t.start+t.span}:void 0},get paintsNodeColors(){return 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n&&e.graph&&e.chosenHover!=="off"?kr(e.graph,n,e.assemblyResolver,e.graphRegion?.assemblyName):[]}}));var ea=Qr.views(e=>({get walkStripShown(){return nn({walkStrip:e.walkStrip,mode:{drawsNodes:e.modeDrawsNodes},drawsPicture:!!e.layoutResult?.tubeMap||!!e.walkRowBars,walks:e.graph?.paths?.length??0,host:!!e.host})},get walkStripRows(){let t=this.walkStripShown?e.cutWalkRows:void 0;return t?{...t,rows:Me(t.rows,e.walkRowSamples)}:void 0},get walkStripFrame(){let t=this.walkStripRows;if(t)return Ie(t,{width:e.paneWidth})},cutsWholeWalksIn(t,n=e.walkStrip){let o=Y(t);return e.sourceAdapter?.type==="GbzBaseSyntenyAdapter"&&on(o,{walkStrip:n&&o.drawsNodes,host:!!e.host})},get cutsWholeWalks(){return this.cutsWholeWalksIn(e.chosenLayoutMode)},get walkStripMarks(){let t=this.walkStripRows,n=e.hoveredNode??e.selectedNode,o=n===null?void 0:e.nodeById?.get(n);return t&&o&&e.graph?rn(e.graph,[t.reference,...t.rows],o):[]},rowLocation(t,n){let o={sample:t.sample,haplotype:t.haplotype===void 0?void 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