jbrowse-plugin-graphgenomeviewer 8.3.1 → 8.3.2

package/dist/chunks/{chunk-B2MJV7HN.js → chunk-OMF5XFKR.js}

@@ -1,2 +1,2 @@
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package/dist/chunks/{chunk-B2MJV7HN.js.map → chunk-OMF5XFKR.js.map}

@@ -1,6 +1,6 @@
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-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.2/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-2JL2JVZ2.js"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@12.2.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-2JL2JVZ2.js"],
   "sourcesContent": ["// src/pansn.ts\nvar SEP = \"#\";\nfunction panSNSample(refName) {\n  return refName.split(SEP)[0];\n}\nvar GENERIC_SAMPLES = /* @__PURE__ */ new Set([\"_gbwt_ref\"]);\nfunction isGenericSample(sample) {\n  return GENERIC_SAMPLES.has(sample);\n}\nfunction panSNHaplotype(refName) {\n  const parts = refName.split(SEP);\n  return parts.length >= 3 ? `${parts[0]}${SEP}${parts[1]}` : void 0;\n}\nfunction panSNContig(refName) {\n  const parts = refName.split(SEP);\n  return parts.length >= 3 ? parts.slice(2).join(SEP) : parts.length === 2 ? parts[1] : refName;\n}\nfunction panSNFields(name) {\n  const [sample = \"\", haplotype = \"\", ...contig] = name.split(SEP);\n  return contig.length > 0 ? { sample, haplotype: +haplotype, contig: contig.join(SEP) } : void 0;\n}\nfunction parsePanSN(refName) {\n  const parts = refName.split(SEP);\n  const haplotype = parts.length >= 2 && parts[1] !== \"\" ? Number(parts[1]) : Number.NaN;\n  return {\n    sample: parts[0],\n    haplotype: Number.isFinite(haplotype) ? haplotype : void 0\n  };\n}\nfunction panSNMatchesPrefix(refName, prefix) {\n  return prefix !== void 0 && (refName === prefix || refName.startsWith(prefix + SEP));\n}\nfunction assemblyNameToPanSN(adapter) {\n  return adapter.getConf(\"assemblyNameToPanSN\") ?? {};\n}\nfunction resolvePanSNPrefix(adapter, name) {\n  return name === void 0 ? void 0 : assemblyNameToPanSN(adapter)[name] ?? name;\n}\nvar asmByPrefixCache = /* @__PURE__ */ new WeakMap();\nfunction assemblyByPanSNPrefix(adapter) {\n  let out = asmByPrefixCache.get(adapter);\n  if (out === void 0) {\n    const map = assemblyNameToPanSN(adapter);\n    out = {};\n    for (const asm of /* @__PURE__ */ new Set([\n      ...Object.keys(map),\n      ...adapter.getConf(\"assemblyNames\")\n    ])) {\n      out[map[asm] ?? asm] = asm;\n    }\n    asmByPrefixCache.set(adapter, out);\n  }\n  return out;\n}\n\nexport {\n  panSNSample,\n  isGenericSample,\n  panSNHaplotype,\n  panSNContig,\n  panSNFields,\n  parsePanSN,\n  panSNMatchesPrefix,\n  resolvePanSNPrefix,\n  assemblyByPanSNPrefix\n};\n"],
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package/dist/chunks/{chunk-PEE2MP7K.js → chunk-TNEXOJ5F.js}

@@ -1,2 +1,2 @@
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+//# sourceMappingURL=chunk-TNEXOJ5F.js.map

package/dist/chunks/{chunk-PEE2MP7K.js.map → chunk-TNEXOJ5F.js.map}

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+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@12.2.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-FX4RDMDN.js"],
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package/dist/chunks/chunk-VP6AGIRF.js

@@ -0,0 +1,2 @@
+import{a as B}from"./chunk-EINURNZ6.js";import{h as b,i as o,k as f,z as m}from"./chunk-JTOW3TOE.js";import{h as u}from"./chunk-OMF5XFKR.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};
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package/dist/chunks/chunk-VP6AGIRF.js.map

@@ -0,0 +1,7 @@
+{
+  "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"]
+}