jbrowse-plugin-graphgenomeviewer 8.3.1 → 8.3.3

package/dist/chunks/{chunk-WA7FCDLQ.js.map → chunk-DXJSOZY2.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../src/graphTrackConfig.ts", "../../src/GraphGenomeView/trackFeatures.ts", "../../src/GraphGenomeView/repeats/repeatFeatures.ts", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.2/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-EQDQ7P4Y.js", "../../src/GraphGenomeView/genes/geneFeatures.ts", "host:tss-react/mui"],
+  "sources": ["../../src/graphTrackConfig.ts", "../../src/GraphGenomeView/trackFeatures.ts", "../../src/GraphGenomeView/repeats/repeatFeatures.ts", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.2.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-EQDQ7P4Y.js", "../../src/GraphGenomeView/genes/geneFeatures.ts", "host:tss-react/mui"],
   "sourcesContent": ["import {\n  getConfAssemblyNamesOrNone,\n  toTrackConfigEntry,\n} from '@jbrowse/core/util/tracks'\n\nimport { snapshotNamesFile } from './locationName.ts'\n\nimport type { AnyTrackConfig } from '@jbrowse/core/configuration'\n\nfunction isStringArray(value: unknown): value is string[] {\n  return Array.isArray(value) && value.every(item => typeof item === 'string')\n}\n\n// The assemblies the track names after its reference, which is what core's\n// MultiWaySyntenyDisplay opens a lane-declaring source on.\nexport function trackLanes(track: AnyTrackConfig) {\n  const lanes = getConfAssemblyNamesOrNone(track).slice(1)\n  return lanes.length > 0 ? lanes : undefined\n}\n\n// Whether a track names a walk file, by the `walksUri` shorthand as written\n// or the location it expands to: an rGFA track may, and a\n// WalkTabixSyntenyAdapter one does\nexport function walkIndexed(adapterConfig: Record<string, unknown>) {\n  return (\n    adapterConfig.type === 'WalkTabixSyntenyAdapter' ||\n    (adapterConfig.type === 'RgfaTabixAdapter' &&\n      ((typeof adapterConfig.walksUri === 'string' &&\n        adapterConfig.walksUri !== '') ||\n        snapshotNamesFile(adapterConfig.walksLocation)))\n  )\n}\n\n// Whether a track's cut reads `haplotypes`: a GBZ cut does, and so does an\n// rGFA one with a walk file\nexport function cutsByHaplotype(adapterConfig: Record<string, unknown>) {\n  return (\n    adapterConfig.type === 'GbzBaseSyntenyAdapter' || walkIndexed(adapterConfig)\n  )\n}\n\n// The haplotypes a walk-indexed track's config names to cut for until the\n// user picks others\nexport function configHaplotypes(adapterConfig: Record<string, unknown>) {\n  const { defaultHaplotypes } = adapterConfig\n  return walkIndexed(adapterConfig) &&\n    isStringArray(defaultHaplotypes) &&\n    defaultHaplotypes.length > 0\n    ? defaultHaplotypes\n    : undefined\n}\n\n// A graph is cut on the first assembly its track names, the rule\n// GbzBaseSyntenyAdapter states for its anchor. Every other assembly the track\n// names holds its sequence as rank>0 alleles off that reference's backbone, so\n// a window on one has no reference coordinates to frame the cut by.\nexport function graphReferenceAssembly(track: AnyTrackConfig) {\n  return getConfAssemblyNamesOrNone(track)[0]\n}\n\n// A track's adapter config, from a live node or a session's frozen entry\nexport function trackAdapterSnapshot(track: AnyTrackConfig) {\n  return toTrackConfigEntry(track).adapter as Record<string, unknown>\n}\n\nexport function offReferenceProblem(\n  referenceAssembly: string | undefined,\n  assemblyName: string,\n) {\n  return referenceAssembly === undefined || referenceAssembly === assemblyName\n    ? undefined\n    : `The graph is cut on its reference, ${referenceAssembly}: open it from a view of ${referenceAssembly}`\n}\n", "import type { Feature } from '@jbrowse/core/util'\n\nexport type FeatureLike = Feature | Record<string, unknown>\n\nexport function ownField(f: FeatureLike, name: string): unknown {\n  return typeof (f as Feature).get === 'function'\n    ? (f as Feature).get(name)\n    : (f as Record<string, unknown>)[name]\n}\n\nexport interface TrackChoice {\n  trackId: string\n  name?: string\n  adapterType: string\n}\n\nexport function namedTrack<T extends TrackChoice>(tracks: T[], named: string) {\n  return tracks.find(t => t.trackId === named)\n}\n\n// what a track-name hint such as /repeat|tandem/ is matched against\nexport function trackLabel(t: TrackChoice) {\n  return `${t.trackId} ${t.name ?? ''}`\n}\n", "import { namedTrack, ownField, trackLabel } from '../trackFeatures'\n\nimport type { FeatureLike, TrackChoice } from '../trackFeatures'\n\nexport interface RepeatCall {\n  bp: number\n  // TRGT's `SD`. Zero means the allele is a copy of the one the reads did\n  // support, so its length states nothing about a second haplotype; absent\n  // where the genotyper writes no such field.\n  spanningReads?: number\n  // the PanSN haplotype a phased genotype puts this allele on\n  haplotype?: number\n}\n\n// A tandem repeat array as the walk rows need it: its span on the reference,\n// which is what the bars measure between, and its unit length, which is what\n// they tile by. Read off whatever repeat annotation the session has, since the\n// tools all state the same two facts under different names: VCF 4.5's\n// `<CNV:TR>` allele gives `RUL` and `RUS` (one entry per repeat sequence,\n// grouped by `RN`), UCSC simpleRepeat and TRF give `period` and the consensus\n// `sequence`, TRGT gives `MOTIFS` and `TRID`, ExpansionHunter `RU` and `REPID`,\n// HipSTR and GangSTR `PERIOD`, vamos its `motifs`. A VCF record's INFO is\n// searched as well as its top level, and a list's first entry is the unit the\n// bars tile by: for a compound array that is the first repeat sequence, which\n// is the expanding one at every such locus in the common catalogues.\nexport interface RepeatArray {\n  key: string\n  name: string\n  refName: string\n  start: number\n  end: number\n  unit: number\n  motif?: string\n  // Each sample's genotyped alleles, from a genotyper's per-sample `AL`\n  // (TRGT) or a genotype over VCF 4.5 <CNV:TR> alleles; absent from a\n  // catalogue.\n  calls?: Record<string, RepeatCall[]>\n}\n\nexport const REPEAT_ADAPTER_TYPES = new Set([\n  'BedAdapter',\n  'BedTabixAdapter',\n  'BigBedAdapter',\n  'VcfAdapter',\n  'VcfTabixAdapter',\n])\n\nexport const REPEAT_TRACK_HINT =\n  /repeat|tandem|\\bstr\\b|vntr|trf|trgt|vamos|expansion|microsat/i\n\nexport function pickRepeatTrack<T extends TrackChoice>(\n  tracks: T[],\n  named: string,\n) {\n  const chosen = named ? namedTrack(tracks, named) : undefined\n  if (chosen) {\n    return chosen\n  }\n  const candidates = tracks.filter(t => REPEAT_ADAPTER_TYPES.has(t.adapterType))\n  return candidates.find(t => REPEAT_TRACK_HINT.test(trackLabel(t)))\n}\n\n// A TRGT repeat catalogue is a BED whose name column packs the record:\n// `ID=HTT;MOTIFS=CAG,CCG;STRUC=(CAG)nCAACAG(CCG)n`. Read as fields when it\n// has that shape.\nconst PACKED_NAME = /^\\w+=[^;]*(;\\w+=[^;]*)*$/\n\nfunction packedName(f: FeatureLike) {\n  const name = ownField(f, 'name')\n  if (typeof name !== 'string' || !PACKED_NAME.test(name)) {\n    return undefined\n  }\n  return Object.fromEntries(\n    name.split(';').map(pair => {\n      const i = pair.indexOf('=')\n      return [pair.slice(0, i), pair.slice(i + 1)]\n    }),\n  )\n}\n\n// A field at the feature's top level, in a VCF record's INFO, or in a packed\n// name column, in that order.\nfunction field(f: FeatureLike, name: string): unknown {\n  const top = ownField(f, name)\n  if (top !== undefined) {\n    return top\n  }\n  const info = ownField(f, 'INFO') as Record<string, unknown> | undefined\n  return info?.[name] ?? packedName(f)?.[name]\n}\n\nconst MOTIF_FIELDS = [\n  'RUS',\n  'MOTIFS',\n  'RU',\n  'motifs',\n  'motif',\n  'sequence',\n  'consensus',\n]\nconst PERIOD_FIELDS = [\n  'RUL',\n  'period',\n  'PERIOD',\n  'consensusSize',\n  'unit',\n  'unitLength',\n]\nconst NAME_FIELDS = ['TRID', 'REPID', 'VARID', 'ID', 'name', 'id']\n\n// The first entry of a list-valued field, whether it arrived parsed or as\n// the comma-joined text a VCF INFO or a BED column holds; VCF's missing \".\"\n// counts as absent.\nfunction first(f: FeatureLike, names: string[]) {\n  for (const name of names) {\n    const value = field(f, name)\n    const one = String((Array.isArray(value) ? value[0] : value) ?? '')\n      .split(',')[0]!\n      .trim()\n    if (one !== '' && one !== '.') {\n      return one\n    }\n  }\n  return undefined\n}\n\nconst IUPAC = /^[ACGTURYSWKMBDHVN]+$/i\n\n// The unit in bp: a stated period, else the length of the first motif.\nexport function repeatUnitOf(f: FeatureLike) {\n  const period = Number(first(f, PERIOD_FIELDS))\n  if (Number.isFinite(period) && period > 0) {\n    return Math.round(period)\n  }\n  const motif = first(f, MOTIF_FIELDS)\n  return motif && IUPAC.test(motif) ? motif.length : undefined\n}\n\n// A per-sample list field, parsed or as the comma-joined text a VCF column\n// holds. A missing entry stays missing: read as 0, an absent `SD` would make\n// every allele of every genotyper that writes no such field unspanned.\nfunction numbers(value: unknown) {\n  const raw: unknown[] = Array.isArray(value)\n    ? value\n    : String(value ?? '').split(',')\n  return raw.map(one => {\n    const n =\n      one === '' || one === null || one === undefined ? NaN : Number(one)\n    return Number.isFinite(n) ? n : undefined\n  })\n}\n\nfunction strings(value: unknown) {\n  const raw: unknown[] = Array.isArray(value)\n    ? value\n    : String(value ?? '').split(',')\n  return raw.map(one => {\n    const text = String(one ?? '').trim()\n    return text === '' || text === '.' ? undefined : text\n  })\n}\n\nconst TANDEM_REPEAT = '<CNV:TR>'\n\n// Each ALT allele's length, off VCF 4.5's flattened list-of-lists: RN says how\n// many RUS/RUL/RUC/RB entries each allele takes, and the allele's bases are\n// its runs' RB, or unit length times count where RB is missing. An allele that\n// is not <CNV:TR>, or has a run stating neither, has none.\nfunction tandemAlleleBp(f: FeatureLike) {\n  const alts = strings(ownField(f, 'ALT'))\n  if (!alts.includes(TANDEM_REPEAT)) {\n    return undefined\n  }\n  const rn = numbers(field(f, 'RN'))\n  const rus = strings(field(f, 'RUS'))\n  const rul = numbers(field(f, 'RUL'))\n  const ruc = numbers(field(f, 'RUC'))\n  const rb = numbers(field(f, 'RB'))\n  let k = 0\n  return alts.map((alt, i) => {\n    const n = rn[i] ?? (alt === TANDEM_REPEAT ? 1 : 0)\n    let bp = 0\n    let known = 0\n    for (let j = 0; j < n; j++, k++) {\n      const motif = rus[k]\n      const unitLength =\n        rul[k] ?? (motif && IUPAC.test(motif) ? motif.length : undefined)\n      const count = ruc[k]\n      const runBp =\n        rb[k] ??\n        (unitLength && count !== undefined\n          ? Math.round(unitLength * count)\n          : undefined)\n      if (runBp !== undefined) {\n        bp += runBp\n        known++\n      }\n    }\n    return alt === TANDEM_REPEAT && n > 0 && known === n ? bp : undefined\n  })\n}\n\n// A sample's alleles through its genotype: 0 is the reference's, an index\n// past it the ALT allele's. A phased genotype's k-th allele is PanSN\n// haplotype k, the order vg deconstruct writes an assembly's haplotypes in.\nfunction genotyped(\n  gt: string | undefined,\n  alleleBp: (number | undefined)[],\n  referenceBp: number,\n) {\n  const phased = gt?.includes('|')\n  return (gt ?? '').split(/[/|]/).flatMap((index, k): RepeatCall[] => {\n    const i = index === '' ? NaN : Number(index)\n    const bp = i > 0 ? alleleBp[i - 1] : referenceBp\n    if (!Number.isInteger(i) || bp === undefined) {\n      return []\n    }\n    return [{ bp, ...(phased ? { haplotype: k + 1 } : {}) }]\n  })\n}\n\nfunction callsOf(\n  f: FeatureLike,\n  alleleBp: (number | undefined)[] | undefined,\n  referenceBp: number,\n) {\n  const samples = ownField(f, 'samples') as\n    Record<string, Record<string, unknown>> | undefined\n  const called: Record<string, RepeatCall[]> = {}\n  for (const [sample, fields] of Object.entries(samples ?? {})) {\n    const reads = numbers(fields.SD)\n    const lengths = numbers(fields.AL).flatMap((bp, i) =>\n      bp !== undefined && bp > 0\n        ? [reads[i] === undefined ? { bp } : { bp, spanningReads: reads[i] }]\n        : [],\n    )\n    const calls =\n      lengths.length > 0 || !alleleBp\n        ? lengths\n        : genotyped(strings(fields.GT)[0], alleleBp, referenceBp)\n    if (calls.length > 0) {\n      called[sample] = calls\n    }\n  }\n  return Object.keys(called).length > 0 ? called : undefined\n}\n\n// A <CNV:TR> record's POS is the base before the array and SVLEN the\n// reference allele's length, while a VCF feature starts at that padding base.\nfunction spanOf(f: FeatureLike, tandem: boolean) {\n  const start = field(f, 'start') as number\n  const end = field(f, 'end') as number\n  const svlen = numbers(field(f, 'SVLEN'))[0]\n  return tandem && svlen !== undefined\n    ? { start: start + 1, end: start + 1 + svlen }\n    : { start, end }\n}\n\nexport function repeatArraysFrom(features: FeatureLike[]): RepeatArray[] {\n  const arrays: RepeatArray[] = []\n  for (const f of features) {\n    const alleleBp = tandemAlleleBp(f)\n    const { start, end } = spanOf(f, alleleBp !== undefined)\n    const unit = repeatUnitOf(f)\n    if (!(end > start) || unit === undefined) {\n      continue\n    }\n    const refName = field(f, 'refName') as string\n    const motif = first(f, MOTIF_FIELDS)\n    const stated = first(f, NAME_FIELDS)\n    arrays.push({\n      key: `${refName}:${start}-${end}`,\n      name:\n        (stated && !PACKED_NAME.test(stated) ? stated : undefined) ??\n        (motif && motif.length <= 12\n          ? `(${motif})n`\n          : `${refName}:${(start + 1).toLocaleString('en-US')}-${end.toLocaleString('en-US')}`),\n      refName,\n      start,\n      end,\n      unit,\n      motif,\n      calls: callsOf(f, alleleBp, end - start),\n    })\n  }\n  return arrays.sort((a, b) => a.start - b.start)\n}\n", "// src/genes/geneFiles.ts\nvar GENE_TYPE = /(gene|gene_segment|RNA|transcript)$/i;\nvar isGene = (type) => GENE_TYPE.test(type) || type === \"CDS\" || type === \"exon\";\nfunction mergedIntervals(intervals) {\n  const out = [];\n  for (const iv of [...intervals].sort((a, b) => a.start - b.start)) {\n    const last = out.at(-1);\n    if (last && iv.start <= last.end) {\n      last.end = Math.max(last.end, iv.end);\n    } else {\n      out.push({ ...iv });\n    }\n  }\n  return out;\n}\nfunction strandOf(s) {\n  return s === \"+\" ? 1 : s === \"-\" ? -1 : 0;\n}\nfunction unescape(value) {\n  try {\n    return decodeURIComponent(value);\n  } catch {\n    return value;\n  }\n}\nfunction attributes(column) {\n  const out = /* @__PURE__ */ new Map();\n  for (const pair of column.split(\";\")) {\n    const eq = pair.indexOf(\"=\");\n    if (eq > 0) {\n      out.set(pair.slice(0, eq).trim(), unescape(pair.slice(eq + 1).trim()));\n    }\n  }\n  return out;\n}\nfunction gff3Row(line) {\n  const cols = line.split(\"\t\");\n  const start = Number(cols[3]);\n  const end = Number(cols[4]);\n  if (cols.length < 9 || !Number.isInteger(start) || !Number.isInteger(end)) {\n    return void 0;\n  }\n  return {\n    refName: cols[0],\n    type: cols[2],\n    start: start - 1,\n    end,\n    strand: strandOf(cols[6]),\n    attrs: attributes(cols[8])\n  };\n}\nfunction genesFromGff3Lines(lines) {\n  const rows = [];\n  for (const line of lines) {\n    if (line.startsWith(\"##FASTA\")) {\n      break;\n    }\n    const row = line.startsWith(\"#\") ? void 0 : gff3Row(line);\n    if (row) {\n      rows.push(row);\n    }\n  }\n  const parentOf = /* @__PURE__ */ new Map();\n  for (const { attrs } of rows) {\n    const id = attrs.get(\"ID\");\n    const parent = attrs.get(\"Parent\")?.split(\",\")[0];\n    if (id && parent) {\n      parentOf.set(id, parent);\n    }\n  }\n  const rootOf = (row) => {\n    let id = row.attrs.get(\"Parent\")?.split(\",\")[0] ?? row.attrs.get(\"ID\");\n    if (!id) {\n      return row.attrs.get(\"gene_id\");\n    }\n    const seen = /* @__PURE__ */ new Set();\n    while (id && parentOf.has(id) && !seen.has(id)) {\n      seen.add(id);\n      id = parentOf.get(id);\n    }\n    return id;\n  };\n  const groups = /* @__PURE__ */ new Map();\n  rows.forEach((row, i) => {\n    const root = rootOf(row) ?? `#${i}`;\n    const key = `${row.refName}\t${root}`;\n    const group = groups.get(key) ?? groups.set(key, { rows: [] }).get(key);\n    group.rows.push(row);\n    if (!row.attrs.has(\"Parent\") && !group.top) {\n      group.top = row;\n    }\n  });\n  const genes = [];\n  for (const [key, { top, rows: rows2 }] of groups) {\n    if (top && !isGene(top.type)) {\n      continue;\n    }\n    const first = top ?? rows2[0];\n    const start = top?.start ?? Math.min(...rows2.map((r) => r.start));\n    const end = top?.end ?? Math.max(...rows2.map((r) => r.end));\n    const a = first.attrs;\n    const spans = (type) => rows2.filter((r) => r.type === type).map((r) => ({ start: r.start, end: r.end }));\n    const exons = spans(\"exon\");\n    const coding = spans(\"CDS\");\n    const transcribed = rows2.some(\n      (r) => r !== top && r.type !== \"exon\" && r.type !== \"CDS\"\n    );\n    genes.push({\n      name: a.get(\"Name\") ?? a.get(\"gene_name\") ?? a.get(\"gene\") ?? a.get(\"gene_id\") ?? key.split(\"\t\")[1],\n      refName: first.refName,\n      start,\n      end,\n      strand: first.strand,\n      // A range read holds only the rows over its window, so a gene with\n      // transcripts but no exon or CDS there is intronic in it. Only a gene\n      // with no transcripts, as a bacterium's gene and CDS, is one exon.\n      exons: exons.length ? mergedIntervals(exons) : transcribed ? mergedIntervals(coding) : [{ start, end }]\n    });\n  }\n  return genes;\n}\nfunction mergeOverlappingByName(genes) {\n  const out = [];\n  const open = /* @__PURE__ */ new Map();\n  for (const g of [...genes].sort((a, b) => a.start - b.start)) {\n    const key = `${g.refName}\t${g.strand}\t${g.name}`;\n    const last = open.get(key);\n    if (last && g.start < last.end) {\n      last.end = Math.max(last.end, g.end);\n      last.exons = mergedIntervals([...last.exons, ...g.exons]);\n    } else {\n      const gene = { ...g, exons: mergedIntervals(g.exons) };\n      out.push(gene);\n      open.set(key, gene);\n    }\n  }\n  return out;\n}\nvar BED_HEADER = /^(#|track\\s|browser\\s)/;\nfunction genesFromBed(text) {\n  const rows = [];\n  for (const line of text.split(\"\\n\")) {\n    const cols = line.replace(/\\r$/, \"\").split(\"\t\");\n    const start = Number(cols[1]);\n    const end = Number(cols[2]);\n    if (BED_HEADER.test(line) || cols.length < 3 || !Number.isInteger(start) || !(end > start)) {\n      continue;\n    }\n    const refName = cols[0];\n    const name = cols[3] && cols[3] !== \".\" ? cols[3] : `${refName}:${start + 1}-${end}`;\n    const sizes = cols[10]?.split(\",\").filter((s) => s !== \"\").map(Number);\n    const starts = cols[11]?.split(\",\").filter((s) => s !== \"\").map(Number);\n    const blocks = sizes?.length && sizes.length === starts?.length ? sizes.map((size, i) => ({\n      start: start + starts[i],\n      end: start + starts[i] + size\n    })) : [{ start, end }];\n    rows.push({\n      name,\n      refName,\n      start,\n      end,\n      strand: strandOf(cols[5]),\n      exons: blocks\n    });\n  }\n  return mergeOverlappingByName(rows);\n}\nfunction sniffedFormat(text) {\n  const first = text.split(\"\\n\", 1e3).find((l) => l.trim() !== \"\" && !BED_HEADER.test(l));\n  const cols = first?.split(\"\t\") ?? [];\n  return /^\\d+$/.test(cols[1] ?? \"\") && /^\\d+$/.test(cols[2] ?? \"\") ? \"bed\" : \"gff3\";\n}\nfunction genesFromText(text, format = sniffedFormat(text)) {\n  return format === \"bed\" ? genesFromBed(text) : genesFromGff3Lines(text.split(/\\r?\\n/));\n}\n\nexport {\n  mergedIntervals,\n  genesFromGff3Lines,\n  mergeOverlappingByName,\n  genesFromBed,\n  genesFromText\n};\n", "import {\n  mergeOverlappingByName,\n  mergedIntervals,\n} from '@jbrowse/bandage-core/genes/geneFiles'\nimport { readConfObject } from '@jbrowse/core/configuration'\n\nimport { REPEAT_TRACK_HINT } from '../repeats/repeatFeatures'\nimport { namedTrack, ownField, trackLabel } from '../trackFeatures'\n\nimport type { FeatureLike, TrackChoice } from '../trackFeatures'\nimport type { GeneModel } from '@jbrowse/bandage-core/genes/genePins'\nimport type { AnyConfigurationModel } from '@jbrowse/core/configuration'\n\n// The adapters whose tracks hold gene models, in the order the session's\n// tracks are searched when no track is named.\nexport const GENE_ADAPTER_TYPES = new Set([\n  'Gff3TabixAdapter',\n  'Gff3Adapter',\n  'BedTabixAdapter',\n  'BedAdapter',\n  'GtfTabixAdapter',\n  'GtfAdapter',\n  'BigBedAdapter',\n  'NCListAdapter',\n])\n\nconst GENE_TRACK_HINT = /gene|refseq|gencode|ensembl|annotation/i\n\n// A BED track is as often peaks or repeats as genes, so one counts only where\n// its name says it is annotation\nconst BED_ADAPTER_TYPES = new Set(['BedTabixAdapter', 'BedAdapter'])\n\n// Which of the session's tracks to read genes from: the named one while the\n// assembly has it (a saved pick can name a track since removed), else the\n// first gene-bearing track on the assembly whose name says it is annotation,\n// else the first non-BED gene-bearing track. A track whose name says repeats is\n// never picked unnamed, as \"RepeatMasker annotation\" would be.\nexport function pickGeneTrack<T extends TrackChoice>(\n  tracks: T[],\n  named: string,\n) {\n  const chosen = named ? namedTrack(tracks, named) : undefined\n  if (chosen) {\n    return chosen\n  }\n  const candidates = tracks.filter(\n    t =>\n      GENE_ADAPTER_TYPES.has(t.adapterType) &&\n      !REPEAT_TRACK_HINT.test(trackLabel(t)),\n  )\n  return (\n    candidates.find(t => GENE_TRACK_HINT.test(trackLabel(t))) ??\n    candidates.find(t => !BED_ADAPTER_TYPES.has(t.adapterType))\n  )\n}\n\nconst TE_TRACK_HINT = /\\bTEs?\\b|transpos/i\n\n// What a walk row's boxes are, for the key: TEs where the annotation track's\n// name says so, else genes\nexport function annotationNoun(track: TrackChoice | undefined) {\n  return track && TE_TRACK_HINT.test(trackLabel(track)) ? 'TE' : 'gene'\n}\n\ninterface LaneView {\n  tracks?: readonly {\n    configuration: AnyConfigurationModel\n    displays: readonly { configuration: AnyConfigurationModel }[]\n  }[]\n}\n\n// The `filter` of the gene track's lane in the view the graph is drawn in, so\n// the chips name what the lane draws. None where the view shows no such lane,\n// or has no tracks, as a graph genome view of its own.\nexport function laneFilters(view: object, trackId: string | undefined) {\n  const lane = (view as LaneView).tracks?.find(\n    t => readConfObject(t.configuration, 'trackId') === trackId,\n  )?.displays[0]\n  return lane\n    ? ((readConfObject(lane.configuration, 'filter') as string[] | undefined) ??\n        [])\n    : []\n}\n\n// Records spanning a whole sequence, the types the GFF3 adapter declines to\n// widen a fetch for. RefSeq opens every molecule with a `region` named\n// ANONYMOUS.\nconst WHOLE_SEQUENCE_TYPES = new Set([\n  'chromosome',\n  'region',\n  'contig',\n  'supercontig',\n  'scaffold',\n])\n\n// JBrowse's BED parser splits a coding BED12 block into CDS and UTR parts and\n// keeps `exon` for non-coding ones, so all of them are exon\nconst EXON_PARTS = new Set([\n  'exon',\n  'CDS',\n  'five_prime_UTR',\n  'three_prime_UTR',\n  'UTR',\n])\n\nfunction exonsOf(f: FeatureLike, into: { start: number; end: number }[]) {\n  const type = ownField(f, 'type')\n  if (typeof type === 'string' && EXON_PARTS.has(type)) {\n    into.push({\n      start: ownField(f, 'start') as number,\n      end: ownField(f, 'end') as number,\n    })\n  }\n  const children = ownField(f, 'subfeatures') as FeatureLike[] | undefined\n  for (const child of children ?? []) {\n    exonsOf(child, into)\n  }\n}\n\n// Genes from a track's features: every top-level feature but a whole-sequence\n// record, named by the first of gene_name, name, gene and gene_id it carries,\n// with the exons found anywhere under it merged. A feature with no exons is one exon,\n// its whole span. A BED track gives one feature per transcript, so a name's\n// overlapping features merge, while its copies down the contig stay apart.\n// UCSC's ncbiRefSeq.gff gene records carry their symbol only as gene_id. 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package/dist/chunks/{chunk-NAC3EXT4.js → chunk-ELO4G2TG.js}

@@ -1,2 +1,2 @@
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-//# sourceMappingURL=chunk-NAC3EXT4.js.map
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+//# sourceMappingURL=chunk-ELO4G2TG.js.map

package/dist/chunks/{chunk-NAC3EXT4.js.map → chunk-ELO4G2TG.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-BSOZW3FC.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.2/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-HOAIOEI7.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.2/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-RJWPJCIB.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.2/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-BEUTROKU.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.2/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-BRH73RCH.js"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@12.2.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-BSOZW3FC.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.2.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-HOAIOEI7.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.2.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-RJWPJCIB.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.2.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-BEUTROKU.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.2.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-BRH73RCH.js"],
   "sourcesContent": ["// src/util/groups.ts\nfunction pushTo(map, key, value) {\n  const list = map.get(key);\n  if (list) {\n    list.push(value);\n  } else {\n    map.set(key, [value]);\n  }\n}\nfunction addTo(map, key, value) {\n  const set = map.get(key);\n  if (set) {\n    set.add(value);\n  } else {\n    map.set(key, /* @__PURE__ */ new Set([value]));\n  }\n}\nfunction groupBy(items, keyOf) {\n  const groups = /* @__PURE__ */ new Map();\n  for (const item of items) {\n    pushTo(groups, keyOf(item), item);\n  }\n  return groups;\n}\n\nexport {\n  pushTo,\n  addTo,\n  groupBy\n};\n", "// src/util/partitionPoint.ts\nfunction partitionPoint(n, pred) {\n  let lo = 0;\n  let hi = n;\n  while (lo < hi) {\n    const mid = lo + hi >> 1;\n    if (pred(mid)) {\n      lo = mid + 1;\n    } else {\n      hi = mid;\n    }\n  }\n  return lo;\n}\n\nexport {\n  partitionPoint\n};\n", "import {\n  partitionPoint\n} from \"./chunk-HOAIOEI7.js\";\n\n// src/anchoredNodes.ts\nvar REFERENCE_RANK = 0;\nfunction isAnchored(node) {\n  return node.stable !== void 0;\n}\nfunction isBackbone(node) {\n  return node.stable?.rank === REFERENCE_RANK;\n}\nfunction isOffReference(node) {\n  return node.stable !== void 0 && node.stable.rank > REFERENCE_RANK;\n}\nfunction backboneNodes(graph) {\n  return graph.nodes.filter(isBackbone);\n}\nfunction overlapsWindow(node, window) {\n  return node.stable.start < window.end && node.stable.start + node.length > window.start;\n}\nfunction backbonePositions(backbone) {\n  const positions = {};\n  for (const node of backbone) {\n    positions[node.id] = [\n      { x: node.stable.start, y: 0 },\n      { x: node.stable.start + node.length, y: 0 }\n    ];\n  }\n  return positions;\n}\nfunction firstNodeAtOrAfter(nodes, bp) {\n  return partitionPoint(nodes.length, (i) => nodes[i].stable.start < bp);\n}\nfunction backboneSpan(backbone) {\n  let min = Infinity;\n  let max = -Infinity;\n  for (const node of backbone) {\n    min = Math.min(min, node.stable.start);\n    max = Math.max(max, node.stable.start + node.length);\n  }\n  return max - min;\n}\nfunction referenceSpan(backbone, region) {\n  return region && region.end > region.start ? region.end - region.start : backboneSpan(backbone);\n}\n\nexport {\n  REFERENCE_RANK,\n  isAnchored,\n  isBackbone,\n  isOffReference,\n  backboneNodes,\n  overlapsWindow,\n  backbonePositions,\n  firstNodeAtOrAfter,\n  backboneSpan,\n  referenceSpan\n};\n", "// src/pathVisits.ts\nvar PathVisits = class {\n  constructor(columns) {\n    this.segments = columns.segments;\n    this.offsets = columns.offsets;\n    this.path = columns.path;\n    this.start = columns.start;\n    this.reversed = columns.reversed;\n    this.paths = columns.paths;\n    this.samples = columns.samples;\n    this.slots = new Map(this.segments.map((s, i) => [s, i]));\n  }\n  static from(entries) {\n    const builder = new PathVisitsBuilder();\n    for (const [segment, visits] of entries) {\n      builder.declare(segment);\n      for (const v of visits) {\n        builder.add(segment, v.path, v.sample, v.start, v.strand === \"-\");\n      }\n    }\n    return builder.build();\n  }\n  get size() {\n    return this.segments.length;\n  }\n  // the segment's index into `segments` and `offsets`, -1 when unvisited\n  slot(segment) {\n    return this.slots.get(segment) ?? -1;\n  }\n  pathIndex(path) {\n    return this.paths.indexOf(path);\n  }\n  // the first of `slot`'s visits by path `p`, -1 for none\n  firstBy(slot, p) {\n    for (let i = this.offsets[slot]; i < this.offsets[slot + 1]; i++) {\n      if (this.path[i] === p) {\n        return i;\n      }\n    }\n    return -1;\n  }\n  // the visit of `slot` on the path first in name order, at its lowest offset\n  // there: where gfa-to-tabix places a segment the reference doesn't visit, so\n  // both place it alike whatever order the file lists its paths in\n  firstByName(slot) {\n    let best = this.offsets[slot];\n    for (let i = best + 1; i < this.offsets[slot + 1]; i++) {\n      const a = this.paths[this.path[i]];\n      const b = this.paths[this.path[best]];\n      if (a < b || a === b && this.start[i] < this.start[best]) {\n        best = i;\n      }\n    }\n    return best;\n  }\n  // Paths' steps replayed in walk order against their visits: the k-th call\n  // for one path and segment answers that path's k-th visit there, -1 past\n  // its last. A walk in pieces lists its pieces in path order, so replaying\n  // the pieces in order reads each step's own visit.\n  replay() {\n    const cursor = /* @__PURE__ */ new Map();\n    return (slot, p) => {\n      if (slot < 0 || p < 0) {\n        return -1;\n      }\n      const key = slot * this.paths.length + p;\n      const end = this.offsets[slot + 1];\n      let at = cursor.get(key) ?? this.offsets[slot];\n      while (at < end && this.path[at] !== p) {\n        at++;\n      }\n      cursor.set(key, at + 1);\n      return at < end ? at : -1;\n    };\n  }\n  // the visits of paths `keepPath` accepts, at segments `keepSegment` does\n  filter(keepPath, keepSegment = () => true) {\n    const kept = this.paths.map(keepPath);\n    const builder = new PathVisitsBuilder();\n    this.segments.forEach((segment, s) => {\n      if (!keepSegment(segment)) {\n        return;\n      }\n      const slot = builder.declare(segment);\n      for (let i = this.offsets[s]; i < this.offsets[s + 1]; i++) {\n        const p = this.path[i];\n        if (kept[p]) {\n          builder.addAt(\n            slot,\n            builder.pathOf(this.paths[p], this.samples[p]),\n            this.start[i],\n            this.reversed[i] === 1\n          );\n        }\n      }\n    });\n    return builder.build();\n  }\n  strand(i) {\n    return this.reversed[i] ? \"-\" : \"+\";\n  }\n  visit(i) {\n    const p = this.path[i];\n    return {\n      path: this.paths[p],\n      sample: this.samples[p],\n      start: this.start[i],\n      strand: this.strand(i)\n    };\n  }\n  visitsAt(slot) {\n    const out = [];\n    for (let i = this.offsets[slot]; i < this.offsets[slot + 1]; i++) {\n      out.push(this.visit(i));\n    }\n    return out;\n  }\n  get(segment) {\n    const slot = this.slot(segment);\n    return slot < 0 ? void 0 : this.visitsAt(slot);\n  }\n  has(segment) {\n    return this.slots.has(segment);\n  }\n  keys() {\n    return this.segments[Symbol.iterator]();\n  }\n  *values() {\n    for (let s = 0; s < this.segments.length; s++) {\n      yield this.visitsAt(s);\n    }\n  }\n  *entries() {\n    for (let s = 0; s < this.segments.length; s++) {\n      yield [this.segments[s], this.visitsAt(s)];\n    }\n  }\n  [Symbol.iterator]() {\n    return this.entries();\n  }\n};\nvar Column = class {\n  constructor(data) {\n    this.data = data;\n    this.length = 0;\n  }\n  push(value) {\n    if (this.length === this.data.length) {\n      const grown = new this.data.constructor(\n        this.data.length * 2\n      );\n      grown.set(this.data);\n      this.data = grown;\n    }\n    this.data[this.length++] = value;\n  }\n};\nvar PathVisitsBuilder = class {\n  constructor() {\n    this.segments = [];\n    this.slots = /* @__PURE__ */ new Map();\n    this.paths = [];\n    this.samples = [];\n    this.pathIndex = /* @__PURE__ */ new Map();\n    this.slot = new Column(new Int32Array(1024));\n    this.path = new Column(new Int32Array(1024));\n    this.start = new Column(new Float64Array(1024));\n    this.reversed = new Column(new Uint8Array(1024));\n  }\n  // a segment's place in iteration order, though it has no visits yet\n  declare(segment) {\n    let s = this.slots.get(segment);\n    if (s === void 0) {\n      s = this.segments.length;\n      this.slots.set(segment, s);\n      this.segments.push(segment);\n    }\n    return s;\n  }\n  // a path's index, so a caller adding many of its visits names it once\n  pathOf(path, sample) {\n    let p = this.pathIndex.get(path);\n    if (p === void 0) {\n      p = this.paths.length;\n      this.pathIndex.set(path, p);\n      this.paths.push(path);\n      this.samples.push(sample);\n    }\n    return p;\n  }\n  add(segment, path, sample, start, reversed) {\n    this.addAt(\n      this.declare(segment),\n      this.pathOf(path, sample),\n      start,\n      reversed\n    );\n  }\n  addAt(slot, path, start, reversed) {\n    this.slot.push(slot);\n    this.path.push(path);\n    this.start.push(start);\n    this.reversed.push(reversed ? 1 : 0);\n  }\n  build() {\n    const n = this.slot.length;\n    const segments = this.segments.length;\n    const offsets = new Int32Array(segments + 1);\n    const slot = this.slot.data;\n    for (let i = 0; i < n; i++) {\n      offsets[slot[i] + 1]++;\n    }\n    for (let s = 0; s < segments; s++) {\n      offsets[s + 1] += offsets[s];\n    }\n    const fill = offsets.slice(0, segments);\n    const path = new Int32Array(n);\n    const start = new Float64Array(n);\n    const reversed = new Uint8Array(n);\n    for (let i = 0; i < n; i++) {\n      const at = fill[slot[i]]++;\n      path[at] = this.path.data[i];\n      start[at] = this.start.data[i];\n      reversed[at] = this.reversed.data[i];\n    }\n    return new PathVisits({\n      segments: this.segments,\n      offsets,\n      path,\n      start,\n      reversed,\n      paths: this.paths,\n      samples: this.samples\n    });\n  }\n};\n\nexport {\n  PathVisits,\n  Column,\n  PathVisitsBuilder\n};\n", "import {\n  PathVisitsBuilder\n} from \"./chunk-BEUTROKU.js\";\nimport {\n  groupBy\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  REFERENCE_RANK\n} from \"./chunk-RJWPJCIB.js\";\nimport {\n  panSNSample\n} from \"./chunk-2JL2JVZ2.js\";\n\n// src/pathAnchoring.ts\nvar RANGE_SUFFIX = /:(\\d+)-\\d+$/;\nvar VG_FRAGMENT = /^([^#]*#[^#]*#[^#[]*)#(\\d+)(?:\\[(\\d+)-\\d+\\])?$/;\nvar VG_SUBRANGE = /\\[(\\d+)-\\d+\\]$/;\nfunction pathOrigin(pathName) {\n  const fragment = VG_FRAGMENT.exec(pathName);\n  if (fragment) {\n    return { name: fragment[1], start: +fragment[2] + +(fragment[3] ?? 0) };\n  }\n  const match = RANGE_SUFFIX.exec(pathName) ?? VG_SUBRANGE.exec(pathName);\n  return match ? { name: pathName.slice(0, match.index), start: +match[1] } : { name: pathName, start: 0 };\n}\nfunction surveyPaths(paths, lengthOf) {\n  const anchorPaths = [];\n  const visits = new PathVisitsBuilder();\n  for (const path of paths) {\n    const sample = panSNSample(path.name);\n    const p = visits.pathOf(path.name, sample);\n    let pos = path.start;\n    for (const step of path.steps) {\n      visits.addAt(visits.declare(step.id), p, pos, step.strand === \"-\");\n      pos += lengthOf(step.id);\n    }\n    anchorPaths.push({\n      name: path.name,\n      sample,\n      start: path.start,\n      length: pos - path.start\n    });\n  }\n  return { anchorPaths, pathVisits: visits.build() };\n}\nfunction chooseReferencePath(anchorPaths, preferred) {\n  const named = anchorPaths.find(\n    (p) => p.sample === preferred || p.name === preferred\n  );\n  return named ?? anchorPaths[0];\n}\nvar OFF_REFERENCE_RANK = 1;\nfunction anchorNode(node, visits, reference, samplesOf) {\n  const slot = visits.slot(node.name);\n  if (slot < 0 || visits.offsets[slot] === visits.offsets[slot + 1]) {\n    return node;\n  }\n  const own = visits.firstBy(slot, reference);\n  const anchor = own >= 0 ? own : visits.firstByName(slot);\n  return {\n    ...node,\n    stable: {\n      refName: visits.paths[visits.path[anchor]],\n      start: visits.start[anchor],\n      rank: own >= 0 ? REFERENCE_RANK : OFF_REFERENCE_RANK,\n      strand: visits.strand(anchor)\n    },\n    samples: samplesOf(slot)\n  };\n}\nfunction sampleSorter(visits) {\n  const sorted = [...new Set(visits.samples)].sort();\n  const rank = new Map(sorted.map((sample, i) => [sample, i]));\n  const pathRank = Int32Array.from(visits.samples, (s) => rank.get(s));\n  const seen = new Uint8Array(sorted.length);\n  const ranks = new Int32Array(sorted.length);\n  return (slot) => {\n    let n = 0;\n    for (let i = visits.offsets[slot]; i < visits.offsets[slot + 1]; i++) {\n      const r = pathRank[visits.path[i]];\n      if (seen[r] === 0) {\n        seen[r] = 1;\n        ranks[n++] = r;\n      }\n    }\n    let out;\n    if (n === sorted.length) {\n      out = sorted;\n      seen.fill(0);\n    } else if (n * 8 < sorted.length) {\n      const found = ranks.subarray(0, n);\n      found.forEach((r) => seen[r] = 0);\n      out = Array.from(found.sort(), (r) => sorted[r]);\n    } else {\n      out = [];\n      for (let r = 0; r < sorted.length; r++) {\n        if (seen[r] === 1) {\n          seen[r] = 0;\n          out.push(sorted[r]);\n        }\n      }\n    }\n    return out;\n  };\n}\nfunction anchorFromPaths(graph, preferred) {\n  const { anchorPaths, pathVisits } = graph;\n  const reference = anchorPaths && pathVisits ? chooseReferencePath(anchorPaths, preferred) : void 0;\n  if (!reference || !anchorPaths || !pathVisits) {\n    return graph;\n  }\n  const samplesOf = sampleSorter(pathVisits);\n  const referenceIndex = pathVisits.pathIndex(reference.name);\n  return {\n    ...graph,\n    nodes: graph.nodes.map(\n      (node) => anchorNode(node, pathVisits, referenceIndex, samplesOf)\n    ),\n    anchoredBy: \"paths\",\n    referencePath: reference.name\n  };\n}\nfunction anchorGraph(graph, preferred) {\n  if (graph.anchoredBy !== \"tags\") {\n    return anchorFromPaths(graph, preferred);\n  }\n  const referencePath = taggedReferencePath(graph);\n  return referencePath ? { ...graph, referencePath } : graph;\n}\nfunction taggedReferencePath(graph) {\n  const refName = graph.nodes.find((n) => n.stable?.rank === 0)?.stable?.refName;\n  return refName !== void 0 && graph.anchorPaths?.some((p) => p.name === refName) ? refName : void 0;\n}\nfunction trimOrigins(graph, kept) {\n  if (!graph.anchorPaths) {\n    return void 0;\n  }\n  const lengthOf = new Map(graph.nodes.map((n) => [n.id, n.length]));\n  const bp = (ids, end = ids.length) => {\n    let sum = 0;\n    for (let i = 0; i < end; i++) {\n      sum += lengthOf.get(ids[i]) ?? 0;\n    }\n    return sum;\n  };\n  const byOrigin = groupBy(graph.paths ?? [], (p) => pathOrigin(p.name).name);\n  return graph.anchorPaths.map((o) => {\n    const pieces = byOrigin.get(o.name);\n    const path = pieces?.length === 1 ? pieces[0] : void 0;\n    const stretch = path && kept.get(path.name);\n    return path && stretch ? {\n      ...o,\n      start: o.start + bp(path.nodeIds, stretch.first),\n      length: bp(stretch.nodeIds)\n    } : o;\n  });\n}\nfunction referenceVisitStarts(graph) {\n  const { pathVisits } = graph;\n  const cache = /* @__PURE__ */ new Map();\n  return (node) => {\n    let starts = cache.get(node.id);\n    if (!starts) {\n      starts = [];\n      const slot = pathVisits ? pathVisits.slot(node.name) : -1;\n      const p = slot >= 0 ? pathVisits.pathIndex(node.stable.refName) : -1;\n      if (p >= 0) {\n        for (let i = pathVisits.offsets[slot]; i < pathVisits.offsets[slot + 1]; i++) {\n          if (pathVisits.path[i] === p) {\n            starts.push(pathVisits.start[i]);\n          }\n        }\n      }\n      if (starts.length < 2) {\n        starts = [node.stable.start];\n      }\n      cache.set(node.id, starts);\n    }\n    return starts;\n  };\n}\n\nexport {\n  pathOrigin,\n  surveyPaths,\n  chooseReferencePath,\n  anchorFromPaths,\n  anchorGraph,\n  trimOrigins,\n  referenceVisitStarts\n};\n"],
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package/dist/chunks/{chunk-PEE2MP7K.js → chunk-JBQSIRNH.js}

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

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package/dist/chunks/{chunk-EKGY6PG2.js → chunk-MBGXXS3Z.js}

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