jbrowse-plugin-graphgenomeviewer 8.2.0 → 8.3.1

package/dist/chunks/{chunk-OGXVDZPS.js → chunk-DSKPOCCE.js}

@@ -1,4 +1,4 @@
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 `)){let n=fe(e);n&&s.push(n)}return s}var ce=/:(\d+)|=([A-Za-z]+)|\*[a-zA-Z]([a-zA-Z])|\+([A-Za-z]+)|-([A-Za-z]+)|~[a-z]{2}(\d+)[a-z]{2}/g;function Ae(t){let s=[];for(let e of t.matchAll(ce))e[1]!==void 0?s.push({op:"match",length:+e[1]}):e[2]!==void 0?s.push({op:"match",length:e[2].length}):e[3]!==void 0?s.push({op:"substitution",seq:e[3].toUpperCase()}):e[4]!==void 0?s.push({op:"insertion",seq:e[4].toUpperCase()}):e[5]!==void 0?s.push({op:"deletion",length:e[5].length}):e[6]!==void 0&&s.push({op:"match",length:+e[6]});return s}export{F as a,U as b,de as c,H as d,pe as e,me as f,Ne as g,fe as h,we as i,Ae as j};
-//# sourceMappingURL=chunk-OGXVDZPS.js.map
+//# sourceMappingURL=chunk-DSKPOCCE.js.map

package/dist/chunks/{chunk-OGXVDZPS.js.map → chunk-DSKPOCCE.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-5ORP7EFJ.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-JQVS4DRW.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-5OJZV6YT.js"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.2/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-5ORP7EFJ.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.2/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-JQVS4DRW.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.2/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-5OJZV6YT.js"],
   "sourcesContent": ["import {\n  addTo\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  isBackbone\n} from \"./chunk-RJWPJCIB.js\";\nimport {\n  isGenericSample,\n  panSNContig,\n  panSNHaplotype,\n  panSNSample\n} from \"./chunk-2JL2JVZ2.js\";\n\n// src/reference.ts\nvar WELL_KNOWN_SAMPLES = /* @__PURE__ */ new Map([\n  [\"hg38\", \"GRCh38\"],\n  [\"hg19\", \"GRCh37\"],\n  [\"hs1\", \"CHM13\"],\n  [\"t2t-chm13\", \"CHM13\"],\n  [\"chm13v2\", \"CHM13\"]\n]);\nfunction wellKnownSample(assemblyName) {\n  return WELL_KNOWN_SAMPLES.get(assemblyName.toLowerCase());\n}\nfunction sampleOf(refName) {\n  const sample = refName.includes(\"#\") ? panSNSample(refName) : void 0;\n  return sample === void 0 || isGenericSample(sample) ? void 0 : sample;\n}\nfunction haplotypeOf(refName) {\n  return panSNHaplotype(refName) ?? panSNSample(refName);\n}\nfunction graphHaplotypes(graph) {\n  const refNames = new Set((graph.anchorPaths ?? []).map((p) => p.name));\n  for (const node of graph.nodes) {\n    if (node.stable) {\n      refNames.add(node.stable.refName);\n    }\n  }\n  const bySample = /* @__PURE__ */ new Map();\n  for (const refName of refNames) {\n    const sample = sampleOf(refName);\n    if (sample !== void 0) {\n      addTo(bySample, sample, haplotypeOf(refName));\n    }\n  }\n  return bySample;\n}\nfunction backboneFrom(contigs, haplotypes) {\n  const samples = new Set(contigs.map((c) => sampleOf(c.refName)));\n  const [sample] = samples;\n  if (samples.size !== 1 || sample === void 0) {\n    return { contigs, prefixes: [], named: false };\n  }\n  const own = new Set(contigs.map((c) => haplotypeOf(c.refName)));\n  const unique = [...haplotypes.get(sample) ?? []].every((h) => own.has(h));\n  const shared = new Set(contigs.map((c) => panSNHaplotype(c.refName)));\n  const [haplotype] = shared;\n  return {\n    contigs,\n    prefixes: [\n      ...unique ? [sample] : [],\n      ...shared.size === 1 && haplotype ? [haplotype] : []\n    ],\n    named: true\n  };\n}\nfunction graphBackbone(graph) {\n  const spans = /* @__PURE__ */ new Map();\n  for (const node of graph.nodes) {\n    if (isBackbone(node)) {\n      const { refName, start } = node.stable;\n      const end = start + node.length;\n      const span = spans.get(refName);\n      if (span) {\n        span.start = Math.min(span.start, start);\n        span.end = Math.max(span.end, end);\n      } else {\n        spans.set(refName, {\n          refName,\n          contig: panSNContig(refName),\n          start,\n          end\n        });\n      }\n    }\n  }\n  const contigs = [...spans.values()];\n  return contigs.length ? backboneFrom(contigs, graphHaplotypes(graph)) : void 0;\n}\nfunction referenceLabel(graph, region) {\n  const backbone = graphBackbone(graph);\n  const contig = region ? panSNContig(region.refName) : backbone?.contigs.length === 1 ? backbone.contigs[0].contig : void 0;\n  const sample = backbone?.named ? panSNSample(backbone.contigs[0].refName) : void 0;\n  return contig && (sample ? `${sample} ${contig}` : contig);\n}\nfunction backboneAssembly(backbone, assemblies) {\n  const names = (a) => [a.name, ...a.aliases ?? []];\n  const naming = (prefix) => (a) => names(a).some((n) => n.toLowerCase() === prefix.toLowerCase());\n  const prefixes = [...backbone?.prefixes ?? []].reverse();\n  const sample = backbone?.prefixes.find((p) => !p.includes(\"#\"))?.toLowerCase();\n  for (const prefix of prefixes) {\n    const assembly = assemblies.find(naming(prefix));\n    if (assembly) {\n      return assembly;\n    }\n  }\n  return sample === void 0 ? void 0 : assemblies.find(\n    (a) => names(a).some((n) => wellKnownSample(n)?.toLowerCase() === sample)\n  );\n}\nfunction assemblyWalk(graph, assembly) {\n  const haplotypes = graphHaplotypes(graph);\n  return graph.anchorPaths?.find(\n    (walk) => backboneAssembly(\n      backboneFrom(\n        [\n          {\n            refName: walk.name,\n            contig: panSNContig(walk.name),\n            start: walk.start,\n            end: walk.start + walk.length\n          }\n        ],\n        haplotypes\n      ),\n      [assembly]\n    )\n  );\n}\nfunction contigNames(contig) {\n  const bare = contig.replace(/^chr/i, \"\");\n  const forms = !bare ? [] : /^(M|MT)$/i.test(bare) ? [\"M\", \"MT\"] : [bare];\n  return [.../* @__PURE__ */ new Set([contig, ...forms.flatMap((f) => [f, `chr${f}`])])];\n}\nfunction refNameBinding(refNames, aliases = {}) {\n  const exact = new Set(refNames);\n  const byName = /* @__PURE__ */ new Map();\n  for (const refName of exact) {\n    const contig = panSNContig(refName);\n    const alias = aliases[contig];\n    for (const name of /* @__PURE__ */ new Set([\n      ...contigNames(contig),\n      ...alias ? [alias] : []\n    ])) {\n      byName.set(name, byName.has(name) ? void 0 : refName);\n    }\n  }\n  return (name) => exact.has(name) ? name : byName.get(name);\n}\nfunction featuresOnBackbone(features, backbone, aliases) {\n  const bind = refNameBinding(\n    backbone.contigs.map((c) => c.refName),\n    aliases\n  );\n  return features.flatMap((f) => {\n    const refName = bind(f.refName);\n    return refName === void 0 ? [] : [refName === f.refName ? f : { ...f, refName }];\n  });\n}\n\nexport {\n  WELL_KNOWN_SAMPLES,\n  wellKnownSample,\n  graphBackbone,\n  referenceLabel,\n  backboneAssembly,\n  assemblyWalk,\n  contigNames,\n  refNameBinding,\n  featuresOnBackbone\n};\n", "import {\n  END_STOP_TAG,\n  START_STOP_TAG,\n  StopColumns,\n  parseStopTag\n} from \"./chunk-VA5U4F23.js\";\nimport {\n  Column\n} from \"./chunk-BEUTROKU.js\";\n\n// src/gfa/gfaTables.ts\nvar GT = 62;\nvar LT = 60;\nvar TAB = 9;\nvar ZERO = 48;\nvar NINE = 57;\nvar TABLE_TAG = /^(?:LN:i|SN:Z|SO:i|SR:i):/;\nvar UNTABLED_RECORD = /^[PEOUFG]\\t/;\nvar trimCR = (line) => line.endsWith(\"\\r\") ? line.slice(0, -1) : line;\nfunction stepColumns() {\n  return {\n    nodes: new Column(new Int32Array(1 << 16)),\n    reversed: new Column(new Uint8Array(1 << 16))\n  };\n}\nvar SegmentIndex = class {\n  constructor() {\n    this.names = [];\n    this.byName = /* @__PURE__ */ new Map();\n    // ids that are plain decimal, so a walk step finds its segment without\n    // slicing a string out of the body\n    this.byNumber = /* @__PURE__ */ new Map();\n  }\n  has(name) {\n    return this.byName.has(name);\n  }\n  add(name) {\n    const i = this.names.length;\n    this.byName.set(name, i);\n    this.names.push(name);\n    const n = +name;\n    if (Number.isSafeInteger(n) && String(n) === name) {\n      this.byNumber.set(n, i);\n    }\n    return i;\n  }\n  of(name) {\n    return this.byName.get(name) ?? this.add(name);\n  }\n  ofNumber(n) {\n    return this.byNumber.get(n);\n  }\n};\nfunction readSegment(line) {\n  const [, name, sequence = \"*\", ...tags] = line.split(\"\t\");\n  if (!name || /^\\d+$/.test(sequence)) {\n    return void 0;\n  }\n  let length = sequence === \"*\" ? 0 : sequence.length;\n  let refName;\n  let start;\n  let rank;\n  for (const tag of tags) {\n    if (!TABLE_TAG.test(tag)) {\n      return void 0;\n    }\n    const value = tag.slice(5);\n    const key = tag.slice(0, 2);\n    if (key === \"LN\") {\n      length = +value;\n    } else if (key === \"SN\") {\n      refName = value;\n    } else if (key === \"SO\") {\n      start = +value;\n    } else {\n      rank = +value;\n    }\n  }\n  const stable = refName !== void 0 && start !== void 0 && rank !== void 0 ? { refName, start, rank } : void 0;\n  return { name, length, stable };\n}\nfunction readWalkBody(line, from, segments, steps) {\n  let reversed = 0;\n  let start = -1;\n  let value = 0;\n  let decimal = true;\n  const finish = (end) => {\n    if (start >= 0 && end > start) {\n      const node = decimal && end - start < 16 && (end - start === 1 || line.charCodeAt(start) !== ZERO) ? segments.ofNumber(value) : void 0;\n      steps.nodes.push(node ?? segments.of(line.slice(start, end)));\n      steps.reversed.push(reversed);\n    }\n  };\n  let i = from;\n  for (; i < line.length; i++) {\n    const ch = line.charCodeAt(i);\n    if (ch === GT || ch === LT) {\n      finish(i);\n      reversed = ch === LT ? 1 : 0;\n      start = i + 1;\n      value = 0;\n      decimal = true;\n    } else if (ch === TAB) {\n      break;\n    } else if (decimal && ch >= ZERO && ch <= NINE) {\n      value = value * 10 + ch - ZERO;\n    } else {\n      decimal = false;\n    }\n  }\n  finish(i);\n  return i;\n}\nfunction walkFields(line) {\n  const fields = [];\n  let at = 0;\n  while (fields.length < 6) {\n    const tab = line.indexOf(\"\t\", at);\n    if (tab === -1) {\n      return void 0;\n    }\n    fields.push(line.slice(at, tab));\n    at = tab + 1;\n  }\n  const [, sample, haplotype, contig, start, end] = fields;\n  return sample && haplotype && contig && start && end && at < line.length ? { sample, haplotype, contig, start, end, body: at } : void 0;\n}\nfunction gfaTables(text) {\n  const lines = text.split(\"\\n\");\n  const segments = new SegmentIndex();\n  const lengths = [];\n  const refs = [];\n  const starts = [];\n  const ranks = [];\n  const refNames = [];\n  const refIndex = /* @__PURE__ */ new Map();\n  for (const raw of lines) {\n    if (UNTABLED_RECORD.test(raw)) {\n      return void 0;\n    }\n    if (raw.startsWith(\"S\t\")) {\n      const s = readSegment(trimCR(raw));\n      if (!s || segments.has(s.name)) {\n        return void 0;\n      }\n      segments.add(s.name);\n      lengths.push(s.length);\n      let ref = -1;\n      if (s.stable) {\n        ref = refIndex.get(s.stable.refName) ?? refNames.length;\n        if (ref === refNames.length) {\n          refNames.push(s.stable.refName);\n          refIndex.set(s.stable.refName, ref);\n        }\n      }\n      refs.push(ref);\n      starts.push(s.stable?.start ?? 0);\n      ranks.push(s.stable?.rank ?? 0);\n    }\n  }\n  const from = [];\n  const to = [];\n  const strands = [];\n  const names = [];\n  const walkStarts = [];\n  const walkEnds = [];\n  const offsets = [0];\n  const steps = stepColumns();\n  const before = new StopColumns();\n  const after = new StopColumns();\n  for (const raw of lines) {\n    if (raw.startsWith(\"L\t\")) {\n      const [, source, strand1, target, strand2] = trimCR(raw).split(\"\t\");\n      if (source && target && strand2) {\n        from.push(segments.of(source));\n        to.push(segments.of(target));\n        strands.push((strand1 === \"-\" ? 1 : 0) | (strand2 === \"-\" ? 2 : 0));\n      }\n    } else if (raw.startsWith(\"W\t\")) {\n      const line = trimCR(raw);\n      const w = walkFields(line);\n      if (w) {\n        names.push(`${w.sample}#${w.haplotype}#${w.contig}`);\n        walkStarts.push(w.start === \"*\" ? 0 : +w.start);\n        walkEnds.push(w.end === \"*\" ? -1 : +w.end);\n        const end = readWalkBody(line, w.body, segments, steps);\n        const tags = walkTags(line, end);\n        if (tags === void 0) {\n          return void 0;\n        }\n        if (tags.before) {\n          before.push(tags.before);\n        }\n        if (tags.after) {\n          after.push(tags.after);\n        }\n        if (steps.nodes.length === offsets.at(-1)) {\n          return void 0;\n        }\n        offsets.push(steps.nodes.length);\n      }\n    }\n  }\n  if ([before.kinds.length, after.kinds.length].some(\n    (n) => n > 0 && n < names.length\n  )) {\n    return void 0;\n  }\n  return {\n    nodes: {\n      names: segments.names,\n      lengths: Int32Array.from(lengths),\n      refs: Int32Array.from(refs),\n      starts: Float64Array.from(starts),\n      ranks: Int32Array.from(ranks),\n      refNames\n    },\n    links: {\n      from: Int32Array.from(from),\n      to: Int32Array.from(to),\n      strands: Uint8Array.from(strands)\n    },\n    walks: {\n      names,\n      starts: Float64Array.from(walkStarts),\n      ends: Float64Array.from(walkEnds),\n      offsets: Int32Array.from(offsets),\n      steps: steps.nodes.data.slice(0, steps.nodes.length),\n      reversed: steps.reversed.data.slice(0, steps.reversed.length),\n      ...stopColumns(names.length, before, after)\n    }\n  };\n}\nfunction walkTags(line, from) {\n  const out = {};\n  for (const tag of from < line.length ? line.slice(from + 1).split(\"\t\") : []) {\n    const value = tag.slice(5);\n    if (tag.startsWith(`${START_STOP_TAG}:Z:`)) {\n      out.before = parseStopTag(value);\n      if (!out.before) {\n        return void 0;\n      }\n    } else if (tag.startsWith(`${END_STOP_TAG}:Z:`)) {\n      out.after = parseStopTag(value);\n      if (!out.after) {\n        return void 0;\n      }\n    }\n  }\n  return out;\n}\nfunction stopColumns(walks, before, after) {\n  return {\n    ...before.kinds.length === walks && walks > 0 ? { before: before.table() } : {},\n    ...after.kinds.length === walks && walks > 0 ? { after: after.table() } : {}\n  };\n}\n\nexport {\n  gfaTables\n};\n", "// src/gaf/parseGaf.ts\nvar STEP = /([><])([^><]+)/g;\nfunction parseGafPath(column) {\n  if (!column.startsWith(\">\") && !column.startsWith(\"<\")) {\n    return void 0;\n  }\n  const steps = [];\n  for (const [, arrow, name] of column.matchAll(STEP)) {\n    steps.push({ name, strand: arrow === \">\" ? \"+\" : \"-\" });\n  }\n  return steps;\n}\nfunction parseGafLine(text) {\n  const line = text.trimEnd();\n  const columns = line.split(\"\t\");\n  if (columns.length < 12 || line.startsWith(\"#\")) {\n    return void 0;\n  }\n  const path = parseGafPath(columns[5]);\n  if (!path) {\n    return void 0;\n  }\n  let cs;\n  let secondary = false;\n  for (let i = 12; i < columns.length; i++) {\n    const tag = columns[i];\n    if (tag.startsWith(\"cs:Z:\")) {\n      cs = tag.slice(5);\n    } else if (tag === \"tp:A:S\") {\n      secondary = true;\n    }\n  }\n  return {\n    name: columns[0],\n    queryLength: +columns[1],\n    queryStart: +columns[2],\n    queryEnd: +columns[3],\n    strand: columns[4] === \"-\" ? \"-\" : \"+\",\n    path,\n    pathLength: +columns[6],\n    pathStart: +columns[7],\n    pathEnd: +columns[8],\n    matches: +columns[9],\n    blockLength: +columns[10],\n    mappingQuality: +columns[11],\n    secondary,\n    ...cs === void 0 ? {} : { cs }\n  };\n}\nfunction parseGaf(text) {\n  const records = [];\n  for (const line of text.split(\"\\n\")) {\n    const record = parseGafLine(line);\n    if (record) {\n      records.push(record);\n    }\n  }\n  return records;\n}\nvar CS_OP = /:(\\d+)|=([A-Za-z]+)|\\*[a-zA-Z]([a-zA-Z])|\\+([A-Za-z]+)|-([A-Za-z]+)|~[a-z]{2}(\\d+)[a-z]{2}/g;\nfunction parseCs(cs) {\n  const ops = [];\n  for (const m of cs.matchAll(CS_OP)) {\n    if (m[1] !== void 0) {\n      ops.push({ op: \"match\", length: +m[1] });\n    } else if (m[2] !== void 0) {\n      ops.push({ op: \"match\", length: m[2].length });\n    } else if (m[3] !== void 0) {\n      ops.push({ op: \"substitution\", seq: m[3].toUpperCase() });\n    } else if (m[4] !== void 0) {\n      ops.push({ op: \"insertion\", seq: m[4].toUpperCase() });\n    } else if (m[5] !== void 0) {\n      ops.push({ op: \"deletion\", length: m[5].length });\n    } else if (m[6] !== void 0) {\n      ops.push({ op: \"match\", length: +m[6] });\n    }\n  }\n  return ops;\n}\n\nexport {\n  parseGafPath,\n  parseGafLine,\n  parseGaf,\n  parseCs\n};\n"],
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package/dist/chunks/{chunk-UHV6XIDG.js → chunk-EKGY6PG2.js}

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