jbrowse-plugin-graphgenomeviewer 8.8.2 → 9.0.0

package/dist/chunks/chunk-QUDJ7AM3.js

@@ -1,2 +0,0 @@
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-//# sourceMappingURL=chunk-QUDJ7AM3.js.map

package/dist/chunks/chunk-QUDJ7AM3.js.map

@@ -1,7 +0,0 @@
-{
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-  "sources": ["jbrowse-host:@jbrowse/core/configuration"],
-  "sourcesContent": ["const host = JBrowseExports[\"@jbrowse/core/configuration\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\"This JBrowse does not provide '\" + name + \"' from '\" + \"@jbrowse/core/configuration\" + \"' to plugins: \" + \"GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\")\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const ConfigurationReference = /* @__PURE__ */ read(\"ConfigurationReference\")\nexport const ConfigurationSchema = /* @__PURE__ */ read(\"ConfigurationSchema\")\nexport const ConfigurationSchemaUnion = /* @__PURE__ */ read(\"ConfigurationSchemaUnion\")\nexport const DEFAULT_FORMAT_DETAILS_DEPTH = /* @__PURE__ */ read(\"DEFAULT_FORMAT_DETAILS_DEPTH\")\nexport const FormatAboutConfigSchemaFactory = /* @__PURE__ */ read(\"FormatAboutConfigSchemaFactory\")\nexport const FormatDetailsConfigSchemaFactory = /* @__PURE__ */ read(\"FormatDetailsConfigSchemaFactory\")\nexport const applyConfSettings = /* @__PURE__ */ read(\"applyConfSettings\")\nexport const applyRetiredSpellings = /* @__PURE__ */ read(\"applyRetiredSpellings\")\nexport const arraySlotUnion = /* @__PURE__ */ read(\"arraySlotUnion\")\nexport const bamIndexFields = /* @__PURE__ */ read(\"bamIndexFields\")\nexport const bamIndexSchema = /* @__PURE__ */ read(\"bamIndexSchema\")\nexport const canonicalSpelling = /* @__PURE__ */ read(\"canonicalSpelling\")\nexport const declaredSnapshot = /* @__PURE__ */ read(\"declaredSnapshot\")\nexport const evaluateForFeature = /* @__PURE__ */ read(\"evaluateForFeature\")\nexport const evaluateJexl = /* @__PURE__ */ read(\"evaluateJexl\")\nexport const expandTabixShorthand = /* @__PURE__ */ read(\"expandTabixShorthand\")\nexport const expandUriShorthand = /* @__PURE__ */ read(\"expandUriShorthand\")\nexport const fillIndexType = /* @__PURE__ */ 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read(\"mergeFormatCallbacks\")\nexport const parsePlot = /* @__PURE__ */ read(\"parsePlot\")\nexport const partitionAdvanced = /* @__PURE__ */ read(\"partitionAdvanced\")\nexport const plotKeysOf = /* @__PURE__ */ read(\"plotKeysOf\")\nexport const plotList = /* @__PURE__ */ read(\"plotList\")\nexport const plotOf = /* @__PURE__ */ read(\"plotOf\")\nexport const plotWrites = /* @__PURE__ */ read(\"plotWrites\")\nexport const preProcessConfigSnapshot = /* @__PURE__ */ read(\"preProcessConfigSnapshot\")\nexport const preProcessSnapshotWith = /* @__PURE__ */ read(\"preProcessSnapshotWith\")\nexport const readConfObject = /* @__PURE__ */ read(\"readConfObject\")\nexport const readConfigValue = /* @__PURE__ */ read(\"readConfigValue\")\nexport const refusingUndeclaredKeys = /* @__PURE__ */ read(\"refusingUndeclaredKeys\")\nexport const requestedIndexType = /* @__PURE__ */ read(\"requestedIndexType\")\nexport const requirementProblems = /* @__PURE__ */ read(\"requirementProblems\")\nexport const setConf = /* @__PURE__ */ read(\"setConf\")\nexport const shorthandTargets = /* @__PURE__ */ read(\"shorthandTargets\")\nexport const shorthandTargetsOf = /* @__PURE__ */ read(\"shorthandTargetsOf\")\nexport const slotChoices = /* @__PURE__ */ read(\"slotChoices\")\nexport const slotValueRefusal = /* @__PURE__ */ read(\"slotValueRefusal\")\nexport const tabixIndexFields = /* @__PURE__ */ read(\"tabixIndexFields\")\nexport const tabixIndexSchema = /* @__PURE__ */ read(\"tabixIndexSchema\")\nexport const tabixIndexSnapshot = /* @__PURE__ */ read(\"tabixIndexSnapshot\")\nexport const toCallbackValue = /* @__PURE__ */ read(\"toCallbackValue\")\nexport const toFixedValue = /* @__PURE__ */ read(\"toFixedValue\")\nexport const writesWholeAt = /* @__PURE__ */ read(\"writesWholeAt\")\nexport default host && host.__esModule ? host.default : host"],
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package/dist/chunks/chunk-T7LVVBTT.js

@@ -1,2 +0,0 @@
-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

@@ -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, 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' ? 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-}

package/dist/chunks/chunk-ZBFIEBO6.js

@@ -1,2 +0,0 @@
-import{a as B}from"./chunk-APSXG7SV.js";import{h as b,i as o,k as f,z as m}from"./chunk-GLSUAMGV.js";import{h as u}from"./chunk-KBOVZ3GI.js";var O={steps:"walkStepBudget",bytes:"walkByteBudget"},y=64,k=class{constructor(e,t){this.file=e;this.adapter=t;this.reader=new f(e)}async haplotypeNames(e={}){let{haplotypes:t}=await this.reader.header(e);return t.length>0?t:void 0}budgets(){return{stepBudget:this.adapter.getConf("walkStepBudget"),byteBudget:this.adapter.getConf("walkByteBudget"),budgetNames:O}}async subgraph(e,t,{signal:i,haplotypes:d,walkRows:s,expand:r,expandSamples:n}){let g=this.budgets(),p=o(d?.map(a=>u(this.adapter,a)),e),l=s&&p&&(d?.length??0)<=y?p:void 0,c=s&&n?.length&&n.length<=y?o(n.map(a=>u(this.adapter,a)),e):void 0,h=r?.length?a=>r.includes(a):void 0,{graph:w,kept:A,fragments:S,skips:x}=await this.reader.cut(e,t,{...g,stepBudget:s?1/0:g.stepBudget,signal:i,keep:p,...l||c||h?{expand:a=>!!l?.(a)||!!c?.(a)||!!h?.(a)}:{}});return B(w.tables(A,S,x),t,s)}async referenceNodes(e,t,i){let d=[];await m(this.file,e,await this.reader.queryStart(t.start,{...i,refName:e,end:t.end}),t.end,{signal:i.signal,lineCallback:r=>{let n=r.split("	");n[3]==="ref"&&d.push(n)}});let s=new Set;return b(d).filter(r=>r.refName!==e||r.end<=t.start||r.start>=t.end||s.has(r.id)?!1:(s.add(r.id),!0))}};export{k as a};
-//# sourceMappingURL=chunk-ZBFIEBO6.js.map

package/dist/chunks/chunk-ZBFIEBO6.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../src/RgfaTabixAdapter/walkReader.ts"],
-  "sourcesContent": ["import { resolvePanSNPrefix } from '@jbrowse/bandage-core/pansn'\nimport { WalkReader, referenceNodes, walksKept } from '@jbrowse/graph-walks'\n\nimport { getLines } from '../tabixRange.ts'\nimport { walkCutFor } from './walkCut.ts'\n\nimport type { SubgraphAdapterOptions } from '../GetSubgraph.ts'\nimport type { TabixIndexedFile } from '@gmod/tabix'\nimport type {\n  BaseFeatureDataAdapter,\n  BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\n\n// The zoom-in notices name the config slots that set the budgets\nexport const BUDGET_SLOTS = {\n  steps: 'walkStepBudget',\n  bytes: 'walkByteBudget',\n}\n\n// Walk rows read a list of haplotypes, or of the samples they show, this long or\n// shorter in full where format 5 abridged it; a longer list, or every\n// haplotype, keeps the abridged rows\nexport const EXPAND_NAMED_MAX = 64\n\n/**\n * A walk file and the answers both walk-indexed adapters give from it,\n * RgfaTabixAdapter and WalkTabixSyntenyAdapter, whose schemas declare the\n * budget slots. @jbrowse/graph-walks reads and cuts the file.\n */\nexport class WalkIndex {\n  readonly reader: WalkReader\n\n  constructor(\n    readonly file: TabixIndexedFile,\n    private adapter: BaseFeatureDataAdapter,\n  ) {\n    this.reader = new WalkReader(file)\n  }\n\n  /**\n   * The haplotypes the header names, `sample#haplotype` in byte order, or\n   * undefined when it names none\n   */\n  async haplotypeNames(opts: BaseOptions = {}) {\n    const { haplotypes } = await this.reader.header(opts)\n    return haplotypes.length > 0 ? haplotypes : undefined\n  }\n\n  budgets() {\n    return {\n      stepBudget: this.adapter.getConf('walkStepBudget') as number,\n      byteBudget: this.adapter.getConf('walkByteBudget') as number,\n      budgetNames: BUDGET_SLOTS,\n    }\n  }\n\n  /**\n   * The graph display's cut of a window: the reference walk, the walks of\n   * `haplotypes` (every walk when unset), and the nodes and links they visit,\n   * with the haplotypes whose deletion spans the window as `skips`, which walk\n   * rows draw. Walk rows draw runs, so the step budget spares them, and read a\n   * short list of named walks in full where format 5 abridged them.\n   */\n  async subgraph(\n    refName: string,\n    region: { start: number; end: number },\n    {\n      signal,\n      haplotypes,\n      walkRows,\n      expand,\n      expandSamples,\n    }: SubgraphAdapterOptions,\n  ) {\n    const budgets = this.budgets()\n    const keep = walksKept(\n      haplotypes?.map(lane => resolvePanSNPrefix(this.adapter, lane)),\n      refName,\n    )\n    const named =\n      walkRows && keep && (haplotypes?.length ?? 0) <= EXPAND_NAMED_MAX\n        ? keep\n        : undefined\n    const shown =\n      walkRows &&\n      expandSamples?.length &&\n      expandSamples.length <= EXPAND_NAMED_MAX\n        ? walksKept(\n            expandSamples.map(s => resolvePanSNPrefix(this.adapter, s)),\n            refName,\n          )\n        : undefined\n    const asked = expand?.length\n      ? (name: string) => expand.includes(name)\n      : undefined\n    const { graph, kept, fragments, skips } = await this.reader.cut(\n      refName,\n      region,\n      {\n        ...budgets,\n        stepBudget: walkRows ? Infinity : budgets.stepBudget,\n        signal,\n        keep,\n        ...(named || shown || asked\n          ? {\n              expand: (name: string) =>\n                !!named?.(name) || !!shown?.(name) || !!asked?.(name),\n            }\n          : {}),\n      },\n    )\n    return walkCutFor(graph.tables(kept, fragments, skips), region, walkRows)\n  }\n\n  /**\n   * The reference nodes overlapping a window, from the ref rows of its\n   * chunks. A row's tabix interval is its chunk's first base, and gfa-to-tabix\n   * files a node crossing in from a chunk before under that chunk, so the read\n   * starts at queryStart.\n   */\n  async referenceNodes(\n    refName: string,\n    region: { start: number; end: number },\n    opts: BaseOptions,\n  ) {\n    const refRows: string[][] = []\n    await getLines(\n      this.file,\n      refName,\n      await this.reader.queryStart(region.start, {\n        ...opts,\n        refName,\n        end: region.end,\n      }),\n      region.end,\n      {\n        signal: opts.signal,\n        lineCallback: line => {\n          const cols = line.split('\\t')\n          if (cols[3] === 'ref') {\n            refRows.push(cols)\n          }\n        },\n      },\n    )\n    const seen = new Set<number>()\n    return referenceNodes(refRows).filter(node => {\n      if (\n        node.refName !== refName ||\n        node.end <= region.start ||\n        node.start >= region.end ||\n        seen.has(node.id)\n      ) {\n        return false\n      }\n      seen.add(node.id)\n      return true\n    })\n  }\n}\n"],
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-  "names": ["BUDGET_SLOTS", "EXPAND_NAMED_MAX", "WalkIndex", "file", "adapter", "WalkReader", "opts", "haplotypes", "refName", "region", "signal", "walkRows", "expand", "expandSamples", "budgets", "keep", "walksKept", "lane", "resolvePanSNPrefix", "named", "shown", "s", "asked", "name", "graph", "kept", "fragments", "skips", "walkCutFor", "refRows", "getLines", "line", "cols", "seen", "referenceNodes", "node"]
-}