jbrowse-plugin-graphgenomeviewer 8.2.0 → 8.3.1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "jbrowse-plugin-graphgenomeviewer",
-  "version": "8.2.0",
+  "version": "8.3.1",
   "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": {
@@ -40,7 +40,7 @@
     "@emotion/react": "^11.14.0",
     "@emotion/styled": "^11.14.1",
     "@eslint/js": "^10.0.1",
-    "@jbrowse/bandage-core": "^12.1.1",
+    "@jbrowse/bandage-core": "^12.1.2",
     "@jbrowse/cli": "^4.3.0",
     "@jbrowse/mobx-state-tree": "^6.10.0",
     "@jbrowse/plugin-linear-genome-view": "5.0.0-beta.18",

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 = '8.3.1'

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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package/dist/chunks/chunk-CZI7IP5S.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-VA5U4F23.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-4FPEQQFT.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-BIYQIWDO.js"],
-  "sourcesContent": ["// src/gfa/walkStops.ts\nvar START_STOP_TAG = \"ws\";\nvar END_STOP_TAG = \"we\";\nvar STOP_KINDS = [\"elsewhere\", \"break\", \"end\"];\nvar GAP_CAUSE_TEXT = {\n  missing: \"not in the graph\",\n  elsewhere: \"on nodes filed elsewhere\",\n  unknown: \"gap, cause unknown\",\n  abridged: \"abridged: steps not loaded\",\n  // a walk file's skip row: the haplotype jumps over the window\n  deleted: \"deleted in this haplotype\"\n};\nvar OUTSIDE_TEXT = \"outside the extracted subgraph\";\nfunction gapParts(bp, after, before) {\n  if (!after && !before) {\n    return [{ bp }];\n  }\n  const left = Math.min(after?.trimmed ?? 0, bp);\n  const right = Math.min(before?.trimmed ?? 0, bp - left);\n  let rest = bp - left - right;\n  const lead = after?.kind === \"break\" ? Math.min(after.bp, rest) : 0;\n  rest -= lead;\n  const trail = before?.kind === \"break\" ? Math.min(before.bp, rest) : 0;\n  rest -= trail;\n  const elsewhere = [after, before].find((s) => s?.kind === \"elsewhere\");\n  const parts = [\n    { bp: left },\n    { bp: lead, cause: \"missing\" },\n    elsewhere?.kind === \"elsewhere\" ? { bp: rest, cause: \"elsewhere\", chunk: elsewhere.chunk } : { bp: rest, cause: \"unknown\" },\n    { bp: trail, cause: \"missing\" },\n    { bp: right }\n  ];\n  return parts.filter((part) => part.bp > 0);\n}\nfunction stopAt(table, i) {\n  const bp = table.bp[i];\n  const ref = table.chunkRefs[i];\n  return stopOf(\n    table.kindNames[table.kinds[i]],\n    Number.isNaN(bp) ? void 0 : bp,\n    table.trimmed[i],\n    ref < 0 ? void 0 : { refName: table.chunkRefNames[ref], start: table.chunkStarts[i] }\n  );\n}\nfunction stopOf(kind, bp, trimmed, chunk) {\n  const cut = trimmed > 0 ? { trimmed } : {};\n  if (kind === \"elsewhere\" && chunk) {\n    return { kind, chunk, ...bp === void 0 ? {} : { bp }, ...cut };\n  }\n  if (kind === \"break\" && bp !== void 0) {\n    return { kind, bp, ...chunk ? { chunk } : {}, ...cut };\n  }\n  return kind === \"end\" ? { kind, ...cut } : void 0;\n}\nfunction stopTag(stop) {\n  const parts = [stop.kind];\n  if (\"bp\" in stop && stop.bp !== void 0) {\n    parts.push(`bp=${stop.bp}`);\n  }\n  if (stop.trimmed) {\n    parts.push(`trimmed=${stop.trimmed}`);\n  }\n  if (\"chunk\" in stop && stop.chunk) {\n    parts.push(`chunk=${stop.chunk.refName}:${stop.chunk.start}`);\n  }\n  return parts.join(\",\");\n}\nfunction parseStopTag(value) {\n  const [kind, ...fields] = value.split(\",\");\n  let bp;\n  let trimmed = 0;\n  let chunk;\n  for (const field of fields) {\n    if (field.startsWith(\"bp=\")) {\n      bp = +field.slice(3);\n    } else if (field.startsWith(\"trimmed=\")) {\n      trimmed = +field.slice(8);\n    } else if (field.startsWith(\"chunk=\")) {\n      const at = field.lastIndexOf(\":\");\n      chunk = { refName: field.slice(6, at), start: +field.slice(at + 1) };\n    }\n  }\n  return stopOf(kind, bp, trimmed, chunk);\n}\nfunction stopFields(before, after) {\n  return {\n    ...before ? { before } : {},\n    ...after ? { after } : {}\n  };\n}\nfunction walkStopFields(tags) {\n  const before = tags[START_STOP_TAG];\n  const after = tags[END_STOP_TAG];\n  return stopFields(\n    typeof before === \"string\" ? parseStopTag(before) : void 0,\n    typeof after === \"string\" ? parseStopTag(after) : void 0\n  );\n}\nfunction walkStopTags(walks, p) {\n  const tags = [];\n  for (const [tag, table] of [\n    [START_STOP_TAG, walks.before],\n    [END_STOP_TAG, walks.after]\n  ]) {\n    const stop = table && stopAt(table, p);\n    if (stop) {\n      tags.push(`\t${tag}:Z:${stopTag(stop)}`);\n    }\n  }\n  return tags.join(\"\");\n}\nvar StopColumns = class {\n  constructor() {\n    this.kinds = [];\n    this.bp = [];\n    this.trimmed = [];\n    this.chunkRefs = [];\n    this.chunkStarts = [];\n    this.chunkRefNames = [];\n    this.refIndex = /* @__PURE__ */ new Map();\n  }\n  push(stop) {\n    this.kinds.push(STOP_KINDS.indexOf(stop.kind));\n    this.bp.push(\"bp\" in stop && stop.bp !== void 0 ? stop.bp : NaN);\n    this.trimmed.push(stop.trimmed ?? 0);\n    const chunk = \"chunk\" in stop ? stop.chunk : void 0;\n    if (chunk) {\n      let ref = this.refIndex.get(chunk.refName);\n      if (ref === void 0) {\n        ref = this.chunkRefNames.length;\n        this.refIndex.set(chunk.refName, ref);\n        this.chunkRefNames.push(chunk.refName);\n      }\n      this.chunkRefs.push(ref);\n      this.chunkStarts.push(chunk.start);\n    } else {\n      this.chunkRefs.push(-1);\n      this.chunkStarts.push(NaN);\n    }\n  }\n  table() {\n    return {\n      kinds: Uint8Array.from(this.kinds),\n      kindNames: [...STOP_KINDS],\n      bp: Float64Array.from(this.bp),\n      trimmed: Float64Array.from(this.trimmed),\n      chunkRefs: Int32Array.from(this.chunkRefs),\n      chunkStarts: Float64Array.from(this.chunkStarts),\n      chunkRefNames: this.chunkRefNames\n    };\n  }\n};\n\nexport {\n  START_STOP_TAG,\n  END_STOP_TAG,\n  GAP_CAUSE_TEXT,\n  OUTSIDE_TEXT,\n  gapParts,\n  stopAt,\n  stopTag,\n  parseStopTag,\n  stopFields,\n  walkStopFields,\n  walkStopTags,\n  StopColumns\n};\n", "import {\n  stopAt,\n  stopFields,\n  walkStopTags\n} from \"./chunk-VA5U4F23.js\";\nimport {\n  PathVisits\n} from \"./chunk-BEUTROKU.js\";\nimport {\n  panSNFields,\n  panSNSample\n} from \"./chunk-2JL2JVZ2.js\";\n\n// src/gfa/graphTables.ts\nfunction pLineName(name, start, end) {\n  return start === 0 ? name : `${name}:${start}-${end}`;\n}\nfunction tablePath(w, p) {\n  const walkName = w.names[p];\n  const fields = panSNFields(walkName);\n  const start = w.starts[p];\n  const steps = w.abridgedSteps?.[p] ?? Number.NaN;\n  const abridged = Number.isNaN(steps) ? {} : { abridged: { steps, bp: w.abridgedBp?.[p] ?? 0 } };\n  return fields ? {\n    name: `${fields.sample}#${fields.haplotype}#${fields.contig}`,\n    start,\n    ...fields,\n    ...stopFields(\n      w.before && stopAt(w.before, p),\n      w.after && stopAt(w.after, p)\n    ),\n    ...abridged\n  } : { name: pLineName(walkName, start, w.ends[p]), start };\n}\nfunction namesByList(lists, names, listCount, pathNames) {\n  const starts = new Int32Array(listCount + 1);\n  for (const list of lists) {\n    starts[list + 1]++;\n  }\n  for (let i = 0; i < listCount; i++) {\n    starts[i + 1] += starts[i];\n  }\n  const fill = starts.slice(0, listCount);\n  const grouped = new Int32Array(lists.length);\n  lists.forEach((list, i) => {\n    grouped[fill[list]++] = names[i];\n  });\n  const listed = new Int32Array(pathNames.length).fill(-1);\n  return Array.from({ length: listCount }, (_, list) => {\n    const out = [];\n    for (let i = starts[list]; i < starts[list + 1]; i++) {\n      const k = grouped[i];\n      if (listed[k] !== list) {\n        listed[k] = list;\n        out.push(pathNames[k]);\n      }\n    }\n    return out;\n  });\n}\nfunction tableNodeIds({ nodes: n, links: l, walks: w }, traversals) {\n  const canonical = new Uint8Array(n.names.length);\n  const claim = (node, reversed) => {\n    if (canonical[node] === 0) {\n      canonical[node] = reversed ? 2 : 1;\n    }\n  };\n  for (let i = 0; i < l.from.length; i++) {\n    claim(l.from[i], l.strands[i] & 1);\n    claim(l.to[i], l.strands[i] & 2);\n  }\n  const stepCount = w.offsets[w.names.length] ?? 0;\n  for (let s = 0; s < stepCount; s++) {\n    const node = w.steps[s];\n    claim(node, w.reversed[s]);\n    if (traversals) {\n      traversals[node]++;\n    }\n  }\n  return n.names.map(\n    (segment, i) => `${segment}${canonical[i] === 2 ? \"-\" : \"+\"}`\n  );\n}\nfunction graphFromTables({ nodes: n, links: l, walks: w }, name = \"Imported GFA\") {\n  const count = n.names.length;\n  const declared = n.lengths.length;\n  const drawnWalks = [];\n  for (let p = 0; p < w.names.length; p++) {\n    if (w.offsets[p + 1] > w.offsets[p]) {\n      drawnWalks.push(p);\n    }\n  }\n  const traversals = new Int32Array(count);\n  const ids = tableNodeIds({ nodes: n, links: l, walks: w }, traversals);\n  const nodes = [];\n  for (let i = 0; i < declared; i++) {\n    const ref = n.refs[i];\n    nodes.push({\n      id: ids[i],\n      name: n.names[i],\n      length: n.lengths[i],\n      depth: Math.max(traversals[i], 1),\n      stable: ref < 0 ? void 0 : {\n        refName: n.refNames[ref],\n        start: n.starts[i],\n        rank: n.ranks[i]\n      },\n      samples: void 0\n    });\n  }\n  const edges = [];\n  const neighbours = new Array(count);\n  const pairList = (a, b) => {\n    const near = neighbours[a];\n    if (near) {\n      for (let j = 0; j < near.length; j += 2) {\n        if (near[j] === b) {\n          return near[j + 1];\n        }\n      }\n    }\n    return void 0;\n  };\n  const addPair = (a, b, list) => {\n    const near = neighbours[a];\n    if (near) {\n      near.push(b, list);\n    } else {\n      neighbours[a] = [b, list];\n    }\n  };\n  const edgeLists = [];\n  let lists = 0;\n  for (let i = 0; i < l.from.length; i++) {\n    const a = l.from[i];\n    const b = l.to[i];\n    edges.push({\n      from: ids[a],\n      to: ids[b],\n      fromStrand: l.strands[i] & 1 ? \"-\" : \"+\",\n      toStrand: l.strands[i] & 2 ? \"-\" : \"+\"\n    });\n    let list = pairList(a, b);\n    if (list === void 0) {\n      list = lists++;\n      addPair(a, b, list);\n      addPair(b, a, list);\n    }\n    edgeLists.push(list);\n  }\n  const adjacency = new Int32Array(count + 1);\n  for (let a = 0; a < count; a++) {\n    adjacency[a + 1] = adjacency[a] + (neighbours[a]?.length ?? 0) / 2;\n  }\n  const adjacentNode = new Int32Array(adjacency[count]);\n  const adjacentList = new Int32Array(adjacency[count]);\n  neighbours.forEach((near, a) => {\n    for (let j = 0; j < near.length; j += 2) {\n      adjacentNode[adjacency[a] + j / 2] = near[j];\n      adjacentList[adjacency[a] + j / 2] = near[j + 1];\n    }\n  });\n  const listOf = (a, b) => {\n    for (let j = adjacency[a]; j < adjacency[a + 1]; j++) {\n      if (adjacentNode[j] === b) {\n        return adjacentList[j];\n      }\n    }\n    return -1;\n  };\n  const nameIndex = /* @__PURE__ */ new Map();\n  const pathNames = [];\n  const crossedList = new Int32Array(w.offsets[w.names.length] ?? 0);\n  const crossedName = new Int32Array(crossedList.length);\n  let crossings = 0;\n  const lastWalk = new Int32Array(lists).fill(-1);\n  const paths = [];\n  const anchorPaths = [];\n  const totalSteps = w.offsets[w.names.length] ?? 0;\n  const visitPath = new Int32Array(totalSteps);\n  const visitStart = new Float64Array(totalSteps);\n  const visitReversed = new Uint8Array(totalSteps);\n  const fill = new Int32Array(count).fill(-1);\n  const visitOrder = [];\n  const blocks = [0];\n  const pathSamples = [];\n  const edgeNameIndex = /* @__PURE__ */ new Map();\n  const edgeNames = [];\n  for (const p of drawnWalks) {\n    const head = tablePath(w, p);\n    const { start, name: pathName } = head;\n    const visitName = head.sample === void 0 ? w.names[p] : pathName;\n    let named = nameIndex.get(visitName);\n    if (named === void 0) {\n      named = pathNames.length;\n      nameIndex.set(visitName, named);\n      pathNames.push(visitName);\n      pathSamples.push(panSNSample(visitName));\n    }\n    let edgeNamed = edgeNameIndex.get(pathName);\n    if (edgeNamed === void 0) {\n      edgeNamed = edgeNames.length;\n      edgeNameIndex.set(pathName, edgeNamed);\n      edgeNames.push(pathName);\n    }\n    const visitSample = pathSamples[named];\n    const first = w.offsets[p];\n    const nodeIds = new Array(w.offsets[p + 1] - first);\n    let pos = start;\n    let prev = -1;\n    for (let s = first; s < w.offsets[p + 1]; s++) {\n      const node = w.steps[s];\n      nodeIds[s - first] = ids[node];\n      if (fill[node] === -1) {\n        fill[node] = blocks.at(-1);\n        blocks.push(fill[node] + traversals[node]);\n        visitOrder.push(node);\n      }\n      const at = fill[node]++;\n      visitPath[at] = named;\n      visitStart[at] = pos;\n      visitReversed[at] = w.reversed[s];\n      pos += node < declared ? n.lengths[node] : 0;\n      if (prev >= 0) {\n        const list = listOf(prev, node);\n        if (list >= 0 && lastWalk[list] !== p) {\n          lastWalk[list] = p;\n          crossedList[crossings] = list;\n          crossedName[crossings++] = edgeNamed;\n        }\n      }\n      prev = node;\n    }\n    paths.push({ ...head, nodeIds });\n    anchorPaths.push({\n      name: visitName,\n      sample: visitSample,\n      start,\n      length: pos - start\n    });\n  }\n  const listNames = namesByList(\n    crossedList.subarray(0, crossings),\n    crossedName,\n    lists,\n    edgeNames\n  );\n  edges.forEach((edge, i) => {\n    const names = listNames[edgeLists[i]];\n    if (names.length > 0) {\n      edge.pathIds = names;\n    }\n  });\n  const walked = drawnWalks.length > 0;\n  return {\n    name,\n    nodes,\n    edges,\n    paths: walked ? paths : void 0,\n    anchorPaths: walked ? anchorPaths : void 0,\n    pathVisits: walked ? new PathVisits({\n      segments: visitOrder.map((node) => n.names[node]),\n      offsets: Int32Array.from(blocks),\n      path: visitPath.subarray(0, blocks.at(-1)),\n      start: visitStart.subarray(0, blocks.at(-1)),\n      reversed: visitReversed.subarray(0, blocks.at(-1)),\n      paths: pathNames,\n      samples: pathSamples\n    }) : void 0,\n    anchoredBy: nodes.some((node) => node.stable) ? \"tags\" : void 0\n  };\n}\nfunction graphTablesGFA({ nodes, links, walks }) {\n  const { names } = nodes;\n  const lines = [\"H\tVN:Z:1.1\"];\n  for (let i = 0; i < nodes.lengths.length; i++) {\n    const ref = nodes.refs[i];\n    const stable = ref < 0 ? \"\" : `\tSN:Z:${nodes.refNames[ref]}\tSO:i:${nodes.starts[i]}\tSR:i:${nodes.ranks[i]}`;\n    lines.push(`S\t${names[i]}\t*\tLN:i:${nodes.lengths[i]}${stable}`);\n  }\n  for (let i = 0; i < links.from.length; i++) {\n    const strands = links.strands[i];\n    lines.push(\n      `L\t${names[links.from[i]]}\t${strands & 1 ? \"-\" : \"+\"}\t${names[links.to[i]]}\t${strands & 2 ? \"-\" : \"+\"}\t0M`\n    );\n  }\n  for (let p = 0; p < walks.names.length; p++) {\n    const name = walks.names[p];\n    const fields = panSNFields(name);\n    const start = walks.starts[p];\n    const end = walks.ends[p];\n    const steps = [];\n    for (let s = walks.offsets[p]; s < walks.offsets[p + 1]; s++) {\n      steps.push([names[walks.steps[s]], walks.reversed[s]]);\n    }\n    lines.push(\n      fields ? `W\t${fields.sample}\t${fields.haplotype}\t${fields.contig}\t${start}\t${end}\t${steps.map(([id, rev]) => (rev ? \"<\" : \">\") + id).join(\"\")}${walkStopTags(walks, p)}` : `P\t${pLineName(name, start, end)}\t${steps.map(([id, rev]) => id + (rev ? \"-\" : \"+\")).join(\",\")}\t*`\n    );\n  }\n  return lines.join(\"\\n\");\n}\n\nexport {\n  tablePath,\n  tableNodeIds,\n  graphFromTables,\n  graphTablesGFA\n};\n", "import {\n  tableNodeIds,\n  tablePath\n} from \"./chunk-4FPEQQFT.js\";\nimport {\n  gapParts\n} from \"./chunk-VA5U4F23.js\";\nimport {\n  pathOrigin\n} from \"./chunk-BRH73RCH.js\";\nimport {\n  groupBy\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  panSNContig,\n  panSNFields,\n  panSNHaplotype,\n  panSNSample\n} from \"./chunk-2JL2JVZ2.js\";\n\n// src/layout/walkRowRuns.ts\nvar RUN_ON_REFERENCE = 1;\nvar RUN_REVERSED = 2;\nvar RUN_GAP = 4;\nvar GAP_CAUSES = [\n  void 0,\n  \"missing\",\n  \"elsewhere\",\n  \"unknown\",\n  \"abridged\",\n  \"deleted\"\n];\nvar CAUSE_SHIFT = 3;\nvar causeFlags = (cause) => GAP_CAUSES.indexOf(cause) << CAUSE_SHIFT;\nfunction referenceOf(names, referencePath, rankZero) {\n  return referencePath !== void 0 && names.includes(referencePath) ? referencePath : names.find((n) => rankZero.has(n)) ?? names[0];\n}\nfunction referenceWalkName(graph) {\n  return referenceOf(\n    (graph.paths ?? []).map((p) => pathOrigin(p.name).name),\n    graph.referencePath,\n    new Set(\n      graph.nodes.flatMap(\n        (n) => n.stable?.rank === 0 ? [n.stable.refName] : []\n      )\n    )\n  );\n}\nfunction graphPieces(graph) {\n  const index = /* @__PURE__ */ new Map();\n  const names = [];\n  const lengths = [];\n  const indexOf = (id) => {\n    let i = index.get(id);\n    if (i === void 0) {\n      i = names.length;\n      index.set(id, i);\n      names.push(id);\n      lengths.push(0);\n    }\n    return i;\n  };\n  for (const node of graph.nodes) {\n    lengths[indexOf(node.id)] = node.length;\n  }\n  const heads = graph.paths ?? [];\n  const from = new Int32Array(heads.length);\n  const to = new Int32Array(heads.length);\n  const steps = [];\n  heads.forEach((path, p) => {\n    from[p] = steps.length;\n    for (const id of path.nodeIds) {\n      steps.push(indexOf(id));\n    }\n    to[p] = steps.length;\n  });\n  return {\n    heads,\n    from,\n    to,\n    steps: Int32Array.from(steps),\n    lengths: Int32Array.from(lengths),\n    names,\n    reference: referenceWalkName(graph)\n  };\n}\nfunction tablePieces(tables, referencePath, visits) {\n  const { nodes: n, walks: w } = tables;\n  const kept = [];\n  for (let p = 0; p < w.names.length; p++) {\n    if (w.offsets[p + 1] > w.offsets[p]) {\n      kept.push(p);\n    }\n  }\n  const heads = kept.map((p) => tablePath(w, p));\n  const rankZero = /* @__PURE__ */ new Set();\n  for (let i = 0; i < n.lengths.length; i++) {\n    if (n.refs[i] >= 0 && n.ranks[i] === 0) {\n      rankZero.add(n.refNames[n.refs[i]]);\n    }\n  }\n  return {\n    heads,\n    from: Int32Array.from(kept, (p) => w.offsets[p]),\n    to: Int32Array.from(kept, (p) => w.offsets[p + 1]),\n    steps: w.steps,\n    lengths: n.lengths,\n    // a visit names its node as the Graph does, which costs a pass over the\n    // steps\n    names: visits ? tableNodeIds(tables) : n.names,\n    reference: referenceOf(\n      heads.map((h) => pathOrigin(h.name).name),\n      referencePath,\n      rankZero\n    )\n  };\n}\nfunction sampleOf(path) {\n  return path.sample ?? panSNSample(path.name);\n}\nfunction labelOf(path) {\n  return path.haplotype !== void 0 && path.sample !== void 0 ? `${path.sample}#${path.haplotype}` : sampleOf(path);\n}\nvar Columns = class {\n  constructor(width) {\n    this.offsets = [0];\n    this.values = Array.from({ length: width }, () => []);\n  }\n  get length() {\n    return this.values[0].length;\n  }\n  push(a, b, c, d, e) {\n    const v = this.values;\n    v[0].push(a);\n    v[1].push(b);\n    v[2].push(c);\n    v[3].push(d);\n    if (e !== void 0) {\n      v[4].push(e);\n    }\n  }\n  endRow() {\n    this.offsets.push(this.length);\n  }\n  // the rows in `order`, column i in the array `make[i]` makes\n  reorder(order, make) {\n    const offsets = new Uint32Array(order.length + 1);\n    order.forEach((row, i) => {\n      offsets[i + 1] = offsets[i] + this.offsets[row + 1] - this.offsets[row];\n    });\n    const columns = make.map((m, c) => {\n      const from = this.values[c];\n      const out = m(this.length);\n      let at = 0;\n      for (const row of order) {\n        for (let k = this.offsets[row]; k < this.offsets[row + 1]; k++) {\n          out[at++] = from[k];\n        }\n      }\n      return out;\n    });\n    return { offsets, columns };\n  }\n};\nvar float64 = (n) => new Float64Array(n);\nfunction walkRowRuns(source, region, o = {}) {\n  const {\n    heads,\n    from,\n    to,\n    steps: all,\n    lengths,\n    names,\n    reference\n  } = \"walks\" in source ? tablePieces(source, o.referencePath, o.visits) : graphPieces(source);\n  const declared = lengths.length;\n  const lengthOf = (node) => node < declared ? lengths[node] : 0;\n  const nameOf = (p) => pathOrigin(heads[p].name).name;\n  const startOf = (p) => heads[p].start;\n  const byStart = (a, b) => (startOf(a) ?? 0) - (startOf(b) ?? 0);\n  const pieceIds = heads.map((_, p) => p);\n  const referencePieces = pieceIds.filter((p) => nameOf(p) === reference).sort(byStart);\n  const first = referencePieces[0];\n  const others = pieceIds.filter((p) => nameOf(p) !== reference);\n  const skips = \"walks\" in source ? source.skips : void 0;\n  if (first === void 0 || others.length === 0 && !skips?.names.length) {\n    return void 0;\n  }\n  const walks = groupBy(others, nameOf);\n  const spanStart = new Float64Array(names.length).fill(Number.NaN);\n  const spanEnd = new Float64Array(names.length);\n  const revisits = /* @__PURE__ */ new Map();\n  let flankEnd = -Infinity;\n  let flankStart = Infinity;\n  const cut = region && region.end > region.start ? region : void 0;\n  for (const piece of referencePieces) {\n    let pos = startOf(piece) ?? 0;\n    for (let s = from[piece], stop = to[piece]; s < stop; s++) {\n      const node = all[s];\n      const len = lengthOf(node);\n      if (!Number.isNaN(spanStart[node])) {\n        const starts = revisits.get(node);\n        if (starts) {\n          starts.push(pos);\n        } else {\n          revisits.set(node, [spanStart[node], pos]);\n        }\n      } else {\n        spanStart[node] = pos;\n        spanEnd[node] = pos + len;\n        if (cut) {\n          if (pos + len <= cut.start) {\n            flankEnd = Math.max(flankEnd, pos + len);\n          }\n          if (pos >= cut.end) {\n            flankStart = Math.min(flankStart, pos);\n          }\n        }\n      }\n      pos += len;\n    }\n  }\n  const flanked = cut === void 0 || flankEnd > -Infinity && flankStart < Infinity;\n  const runs = new Columns(5);\n  const chunks = [];\n  const chunkIndex = /* @__PURE__ */ new Map();\n  const chunkOf = (chunk2) => {\n    if (!chunk2) {\n      return -1;\n    }\n    const key = `${chunk2.refName}:${chunk2.start}`;\n    let i = chunkIndex.get(key);\n    if (i === void 0) {\n      i = chunks.length;\n      chunkIndex.set(key, i);\n      chunks.push(chunk2);\n    }\n    return i;\n  };\n  const visits = o.visits ? new Columns(4) : void 0;\n  let steps = new Int32Array(0);\n  let stepStart = new Float64Array(0);\n  const rowOf = (pieces) => {\n    const head = heads[pieces[0]];\n    const ordered = [...pieces].sort(byStart);\n    let count = ordered.length - 1;\n    let abridgedSteps = 0;\n    for (const piece of ordered) {\n      count += to[piece] - from[piece] + (heads[piece].abridged ? 1 : 0);\n      abridgedSteps += heads[piece].abridged?.steps ?? 0;\n    }\n    if (count > steps.length) {\n      steps = new Int32Array(count * 2);\n      stepStart = new Float64Array(count * 2);\n    }\n    let length = 0;\n    let unplaced = false;\n    let end;\n    let previous;\n    const partsAt = /* @__PURE__ */ new Map();\n    let owed = 0;\n    for (const piece of ordered) {\n      const start2 = startOf(piece);\n      const jump = start2 === void 0 || end === void 0 ? 0 : start2 - end;\n      if (start2 === void 0 || jump < 0) {\n        unplaced = true;\n      }\n      if (jump < 0 && heads[previous].abridged) {\n        owed -= jump;\n      }\n      const covered = Math.min(owed, Math.max(jump, 0));\n      owed -= covered;\n      const gap = jump - covered;\n      if (gap > 0) {\n        partsAt.set(\n          length,\n          gapParts(\n            gap,\n            previous === void 0 ? void 0 : heads[previous].after,\n            heads[piece].before\n          )\n        );\n        steps[length] = -gap;\n        stepStart[length++] = end;\n      }\n      let pos = start2 ?? 0;\n      const abridged = heads[piece].abridged;\n      for (let s = from[piece], stop2 = to[piece]; s < stop2; s++) {\n        const node = all[s];\n        const bp3 = abridged ? abridged.bp - (pos - (start2 ?? 0)) - lengthOf(node) : 0;\n        if (bp3 > 0 && s === stop2 - 1 && s > from[piece]) {\n          partsAt.set(length, [{ bp: bp3, cause: \"abridged\" }]);\n          steps[length] = -bp3;\n          stepStart[length++] = pos;\n          pos += bp3;\n        }\n        steps[length] = node;\n        stepStart[length++] = pos;\n        pos += lengthOf(node);\n      }\n      end = start2 === void 0 ? void 0 : pos;\n      previous = piece;\n    }\n    const onReference = (i) => i >= 0 && i < length && steps[i] >= 0 && !Number.isNaN(spanStart[steps[i]]);\n    const stepEnd = (i) => {\n      const id = steps[i];\n      return stepStart[i] + (id < 0 ? -id : lengthOf(id));\n    };\n    const partialSide = (i0, i1) => {\n      const flank = i0 >= 0 ? i0 : i1;\n      let near = -1;\n      for (let d = 1; near < 0 && d < length; d++) {\n        near = [flank - d, flank + d].find(onReference) ?? -1;\n      }\n      if (near < 0) {\n        return void 0;\n      }\n      const forward = near > flank === spanStart[steps[near]] > spanStart[steps[flank]];\n      const after = forward === (flank === i0);\n      const last2 = after ? length - 1 : 0;\n      const contigEnds = onReference(last2);\n      const stop2 = {\n        contigEnds,\n        shortBp: contigEnds ? Math.max(\n          0,\n          cut.start - spanEnd[steps[last2]],\n          spanStart[steps[last2]] - cut.end\n        ) : 0\n      };\n      return {\n        stop: stop2,\n        lo: after ? flank + 1 : 0,\n        hi: after ? length : flank,\n        backward: !forward,\n        axisStart: forward ? after ? stepEnd(flank) : stepStart[0] : after ? stepEnd(length - 1) : stepStart[flank]\n      };\n    };\n    let lo = 0;\n    let hi = length;\n    let backward = false;\n    let complete = true;\n    let flankFrom = -1;\n    let flankTo = -1;\n    let axisStart;\n    let stop;\n    const trimAbridged = (inner, bp3) => {\n      const parts = partsAt.get(inner);\n      const gap = parts?.[0];\n      if (bp3 <= 0 || gap?.cause !== \"abridged\") {\n        return 0;\n      }\n      const trimmed = Math.min(bp3, gap.bp);\n      partsAt.set(\n        inner,\n        gap.bp > trimmed ? [{ ...gap, bp: gap.bp - trimmed }] : []\n      );\n      steps[inner] += trimmed;\n      return trimmed;\n    };\n    let leftTrim = 0;\n    let rightTrim = 0;\n    if (cut && flanked) {\n      let i0 = -1;\n      let i1 = -1;\n      let bestEnd = -Infinity;\n      let bestStart = Infinity;\n      for (let i = 0; i < length; i++) {\n        const id = steps[i];\n        if (id >= 0 && !Number.isNaN(spanStart[id])) {\n          if (spanEnd[id] <= cut.start && spanEnd[id] > bestEnd) {\n            bestEnd = spanEnd[id];\n            i0 = i;\n          }\n          if (spanStart[id] >= cut.end && spanStart[id] < bestStart) {\n            bestStart = spanStart[id];\n            i1 = i;\n          }\n        }\n      }\n      if (i0 < 0 || i1 < 0) {\n        complete = false;\n        const inside = i0 >= 0 || i1 >= 0 ? partialSide(i0, i1) : void 0;\n        if (inside) {\n          ;\n          ({ lo, hi, backward, axisStart, stop } = inside);\n        }\n      } else {\n        lo = Math.min(i0, i1) + 1;\n        hi = Math.max(i0, i1);\n        backward = i0 > i1;\n        flankFrom = i0;\n        flankTo = i1;\n        const inward = backward ? -1 : 1;\n        leftTrim = trimAbridged(i0 + inward, flankEnd - spanEnd[steps[i0]]);\n        rightTrim = trimAbridged(\n          i1 - inward,\n          spanStart[steps[i1]] - flankStart\n        );\n      }\n    }\n    const contig = head.contig ?? panSNContig(pathOrigin(head.name).name);\n    const axis = unplaced || length === 0 ? void 0 : axisStart !== void 0 ? { contig, start: axisStart, reversed: backward } : flankFrom < 0 ? { contig, start: stepStart[0], reversed: false } : flankFrom < flankTo ? {\n      contig,\n      start: stepEnd(flankFrom) + leftTrim,\n      reversed: false\n    } : {\n      contig,\n      start: stepStart[flankFrom] - leftTrim,\n      reversed: true\n    };\n    let bp2 = 0;\n    let offReferenceBp = 0;\n    let gapBp = 0;\n    let step = 0;\n    let last = -1;\n    let lastFlags = 0;\n    let lastRef = Number.NaN;\n    let cursor = Number.NaN;\n    const placeOf = (id) => {\n      const starts = revisits.get(id);\n      if (!starts || Number.isNaN(cursor)) {\n        return spanStart[id];\n      }\n      const len = lengthOf(id);\n      let best = starts[0];\n      let bestGap = Infinity;\n      for (const start2 of starts) {\n        const gap = Math.min(\n          Math.abs(start2 - cursor),\n          Math.abs(start2 + len - cursor)\n        );\n        if (gap < bestGap) {\n          best = start2;\n          bestGap = gap;\n        }\n      }\n      return best;\n    };\n    const [, runBp, runRef, runFlags] = runs.values;\n    for (let k = lo; k < hi; k++) {\n      const index = backward ? hi - 1 - (k - lo) : k;\n      const id = steps[index];\n      const parts = partsAt.get(index);\n      if (parts) {\n        for (const part of backward ? [...parts].reverse() : parts) {\n          runs.push(\n            bp2,\n            part.bp,\n            Number.NaN,\n            RUN_GAP | causeFlags(part.cause),\n            chunkOf(part.chunk)\n          );\n          bp2 += part.bp;\n        }\n        last = runs.length - 1;\n        lastFlags = RUN_GAP;\n        lastRef = Number.NaN;\n        gapBp += -id;\n        step = 0;\n        continue;\n      }\n      const len = lengthOf(id);\n      const at = placeOf(id);\n      const on = !Number.isNaN(at);\n      visits?.push(id, bp2, len, on ? 1 : 0);\n      const placed = last >= 0 && !Number.isNaN(lastRef);\n      const forward = on && placed && step >= 0 && lastRef + (runBp[last] ?? 0) === at;\n      const back = on && placed && step <= 0 && at + len === lastRef;\n      if (!on && last >= 0 && !(lastFlags & (RUN_ON_REFERENCE | RUN_GAP))) {\n        runBp[last] += len;\n      } else if (forward || back) {\n        runBp[last] += len;\n        if (!forward) {\n          lastRef = at;\n          runRef[last] = at;\n          lastFlags |= RUN_REVERSED;\n          runFlags[last] = lastFlags;\n        }\n        step = forward ? 1 : -1;\n      } else {\n        lastFlags = on ? RUN_ON_REFERENCE : 0;\n        lastRef = on ? at : Number.NaN;\n        runs.push(bp2, len, lastRef, lastFlags, -1);\n        last = runs.length - 1;\n        step = 0;\n      }\n      bp2 += len;\n      if (on) {\n        cursor = step < 0 ? at : at + len;\n      } else {\n        offReferenceBp += len;\n      }\n    }\n    runs.endRow();\n    visits?.endRow();\n    return {\n      name: head.name,\n      label: labelOf(head),\n      sample: sampleOf(head),\n      haplotype: head.haplotype,\n      bp: bp2,\n      offReferenceBp,\n      gapBp,\n      complete,\n      stop,\n      axis,\n      ...abridgedSteps > 0 ? { abridgedSteps } : {},\n      ...leftTrim + rightTrim > 0 ? { estimated: true } : {}\n    };\n  };\n  const skipRowOf = (name, start2, end) => {\n    const from2 = cut ? Math.max(start2, cut.start) : start2;\n    const bp2 = (cut ? Math.min(end, cut.end) : end) - from2;\n    runs.push(\n      from2 - (cut ? cut.start : start2),\n      bp2,\n      Number.NaN,\n      RUN_GAP | causeFlags(\"deleted\"),\n      -1\n    );\n    runs.endRow();\n    visits?.endRow();\n    const head = { name, ...panSNFields(name) };\n    return {\n      name,\n      label: labelOf(head),\n      sample: sampleOf(head),\n      haplotype: head.haplotype,\n      bp: 0,\n      offReferenceBp: 0,\n      gapBp: bp2,\n      complete: true,\n      stop: void 0,\n      axis: void 0\n    };\n  };\n  const referenceRow = rowOf(referencePieces);\n  const rows = [...walks.values()].map((pieces, i) => ({\n    meta: rowOf(pieces),\n    row: i + 1\n  }));\n  const drawn = new Set(walks.keys());\n  skips?.names.forEach((name, k) => {\n    const contig = pathOrigin(name).name;\n    if (!drawn.has(contig)) {\n      drawn.add(contig);\n      rows.push({\n        meta: skipRowOf(contig, skips.starts[k], skips.ends[k]),\n        row: rows.length + 1\n      });\n    }\n  });\n  const metas = [referenceRow, ...rows.map((r) => r.meta)];\n  if (new Set(metas.map((m) => m.label)).size < metas.length) {\n    for (const meta of metas) {\n      meta.label = panSNHaplotype(meta.name) ?? meta.label;\n    }\n  }\n  rows.sort(\n    (a, b) => Number(b.meta.complete) - Number(a.meta.complete) || b.meta.bp - a.meta.bp || a.meta.label.localeCompare(b.meta.label)\n  );\n  const order = [0, ...rows.map((r) => r.row)];\n  const { offsets, columns } = runs.reorder(order, [\n    float64,\n    float64,\n    float64,\n    (n) => new Uint8Array(n),\n    (n) => new Int32Array(n)\n  ]);\n  const [start, bp, referenceStart, flags, chunk] = columns;\n  return {\n    origin: cut ? cut.start : startOf(first) ?? 0,\n    rows: [referenceRow, ...rows.map((r) => r.meta)],\n    offsets,\n    start,\n    bp,\n    referenceStart,\n    flags,\n    chunk,\n    chunks,\n    visits: visits && visitColumns(visits, order, names)\n  };\n}\nfunction visitColumns(visits, order, names) {\n  const { offsets, columns } = visits.reorder(order, [\n    (n) => new Int32Array(n),\n    float64,\n    float64,\n    (n) => new Uint8Array(n)\n  ]);\n  const [node, start, bp, onReference] = columns;\n  return { offsets, node, start, bp, onReference, names };\n}\nfunction runAt(t, k) {\n  const f = t.flags[k];\n  const run = {\n    start: t.start[k],\n    bp: t.bp[k],\n    onReference: (f & RUN_ON_REFERENCE) !== 0\n  };\n  if (f & RUN_GAP) {\n    run.gap = true;\n    const cause = GAP_CAUSES[f >> CAUSE_SHIFT & 7];\n    if (cause) {\n      run.cause = cause;\n    }\n    const chunk = t.chunks[t.chunk[k]];\n    if (chunk) {\n      run.chunk = chunk;\n    }\n  } else {\n    run.referenceStart = Number.isNaN(t.referenceStart[k]) ? void 0 : t.referenceStart[k];\n  }\n  if (f & RUN_REVERSED) {\n    run.reversed = true;\n  }\n  return run;\n}\nfunction visitsOf(v, row) {\n  const out = [];\n  for (let k = v.offsets[row]; k < v.offsets[row + 1]; k++) {\n    out.push({\n      node: v.names[v.node[k]],\n      start: v.start[k],\n      bp: v.bp[k],\n      onReference: v.onReference[k] === 1\n    });\n  }\n  return out;\n}\nfunction walkRowsOf(t, unit) {\n  const rows = t.rows.map((meta, i) => {\n    const runs = [];\n    for (let k = t.offsets[i]; k < t.offsets[i + 1]; k++) {\n      runs.push(runAt(t, k));\n    }\n    return {\n      ...meta,\n      runs,\n      visits: t.visits && visitsOf(t.visits, i)\n    };\n  });\n  return { origin: t.origin, unit, reference: rows[0], rows: rows.slice(1) };\n}\n\nexport {\n  referenceWalkName,\n  walkRowRuns,\n  runAt,\n  walkRowsOf\n};\n"],
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package/dist/chunks/chunk-HAAABGE7.js

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