jbrowse-plugin-graphgenomeviewer 8.8.2 → 9.0.0

package/dist/chunks/chunk-CJ4VON23.js

@@ -0,0 +1,2 @@
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U.endRow(),V?.endRow(),ye({name:a,...Ce(a)},m,F)},X=pe(ae),{axis:f}=X,A=f?{start:f.start,end:f.start+X.bp+X.gapBp}:E,g=[...ce.values()].map((a,m)=>({meta:pe(a,A),row:m+1})),B=new Set(ce.keys());for(let[a,m]of ie)B.has(a)||g.push({meta:Ge(a,m,A),row:g.length+1});let Z=[X,...g.map(a=>a.meta)];if(new Set(Z.map(a=>a.label)).size<Z.length)for(let a of Z)a.label=gt(a.name)??a.label;g.sort((a,m)=>Number(m.meta.complete)-Number(a.meta.complete)||m.meta.bp-a.meta.bp||a.meta.label.localeCompare(m.meta.label));let K=[0,...g.map(a=>a.row)],{offsets:me,columns:We}=U.reorder(K,[be,be,be,a=>new Uint8Array(a),be]),[Ae,xe,Se,Pe,ee]=We;return{origin:E?E.start:D(Ne)??0,rows:[X,...g.map(a=>a.meta)],offsets:me,start:Ae,bp:xe,referenceStart:Se,flags:Pe,near:ee,visits:V&&Xt(V,K,p)}}function Vt(e,t){let r=new Map;if(e)for(let s=0;s<e.names.length;s++){let o=bt(e,s),i=ve(o.name).name;if(i!==t){let b=r.get(i);b?b.push(o):r.set(i,[o])}}for(let s of r.values())s.sort((o,i)=>o.hapStart-i.hapStart);return r}function Xt(e,t,r){let{offsets:s,columns:o}=e.reorder(t,[w=>new Int32Array(w),be,be,w=>new Uint8Array(w)]),[i,b,l,p]=o;return{offsets:s,node:i,start:b,bp:l,onReference:p,names:r}}function Zt(e,t){let r=e.flags[t],s={start:e.start[t],bp:e.bp[t],onReference:(r&Qe)!==0};if(r&Be){s.gap=!0;let o=Pt[r>>It&7];o&&(s.cause=o);let i=e.near[t];Number.isNaN(i)||(s.near=i)}else s.referenceStart=Number.isNaN(e.referenceStart[t])?void 0:e.referenceStart[t];return r&St&&(s.reversed=!0),s}function zt(e,t){let r=[];for(let s=e.offsets[t];s<e.offsets[t+1];s++)r.push({node:e.names[e.node[s]],start:e.start[s],bp:e.bp[s],onReference:e.onReference[s]===1});return r}function fs(e,t){let r=e.rows.map((s,o)=>{let i=[];for(let b=e.offsets[o];b<e.offsets[o+1];b++)i.push(Zt(e,b));return{...s,runs:i,visits:e.visits&&zt(e.visits,o)}});return{origin:e.origin,unit:t,reference:r[0],rows:r.slice(1)}}export{bt as a,Dt as b,_e as c,Le as d,Ke as e,Kt as f,Ut as g,qt as h,Jt as i,Nt as j,qe as k,ts as l,Gt as m,cs as n,fs as o};
+//# sourceMappingURL=chunk-CJ4VON23.js.map

package/dist/chunks/chunk-CJ4VON23.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@13.1.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-NPDW3JAD.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@13.1.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-DBLRFSET.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@13.1.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-WWQI7LPU.js"],
+  "sourcesContent": ["// src/gfa/departures.ts\nfunction departureAt(t, k) {\n  return {\n    name: t.names[k],\n    hapStart: t.hapStarts[k],\n    ownBp: t.ownBp[k],\n    missingBp: t.missingBp[k],\n    leavePos: t.leavePos[k],\n    leaveReversed: t.leaveReversed[k] === 1,\n    leavePasses: t.leavePasses[k],\n    rejoinPos: t.rejoinPos[k],\n    rejoinReversed: t.rejoinReversed[k] === 1,\n    rejoinPasses: t.rejoinPasses[k],\n    fromSteps: t.fromSteps[k] === 1\n  };\n}\nfunction departureTable(departures = []) {\n  return {\n    names: departures.map((d) => d.name),\n    hapStarts: Float64Array.from(departures, (d) => d.hapStart),\n    ownBp: Float64Array.from(departures, (d) => d.ownBp),\n    missingBp: Float64Array.from(departures, (d) => d.missingBp),\n    leavePos: Float64Array.from(departures, (d) => d.leavePos),\n    leaveReversed: Uint8Array.from(departures, (d) => d.leaveReversed ? 1 : 0),\n    leavePasses: Int32Array.from(departures, (d) => d.leavePasses),\n    rejoinPos: Float64Array.from(departures, (d) => d.rejoinPos),\n    rejoinReversed: Uint8Array.from(\n      departures,\n      (d) => d.rejoinReversed ? 1 : 0\n    ),\n    rejoinPasses: Int32Array.from(departures, (d) => d.rejoinPasses),\n    fromSteps: Uint8Array.from(departures, (d) => d.fromSteps ? 1 : 0),\n    offsets: new Int32Array(departures.length + 1),\n    steps: new Int32Array(0),\n    reversed: new Uint8Array(0)\n  };\n}\nfunction departureKind(d) {\n  return d.leaveReversed !== d.rejoinReversed ? \"switch\" : d.leavePos === d.rejoinPos ? \"adjacent\" : (d.leaveReversed ? d.rejoinPos > d.leavePos : d.rejoinPos < d.leavePos) ? \"back\" : \"forward\";\n}\nfunction placementChoice(d) {\n  return d.leavePasses > 1 || d.rejoinPasses > 1;\n}\nfunction departureSpan(d) {\n  return {\n    start: Math.min(d.leavePos, d.rejoinPos),\n    end: Math.max(d.leavePos, d.rejoinPos)\n  };\n}\nfunction roughBp(bp) {\n  return bp >= 1e6 ? `${Number((bp / 1e6).toPrecision(2))} Mb` : bp >= 1e3 ? `${Number((bp / 1e3).toPrecision(2))} kb` : `${bp} bp`;\n}\nfunction departureText(d, reference = \"the reference\") {\n  const { start, end } = departureSpan(d);\n  const apart = roughBp(end - start);\n  const kind = departureKind(d);\n  const ends = kind === \"forward\" ? `no step on ${reference} across ${apart}` : kind === \"back\" ? `rejoins ${reference} ${apart} back` : kind === \"switch\" ? `rejoins ${reference} on the other strand, ${apart} away` : `between adjacent steps on ${reference}`;\n  return [\n    ends,\n    `${roughBp(d.ownBp)} of its own`,\n    ...d.missingBp > 0 ? [`${roughBp(d.missingBp)} not in the graph`] : [],\n    ...placementChoice(d) ? [PLACEMENT_CHOICE_TEXT] : []\n  ].join(\" \\xB7 \");\n}\nvar PLACEMENT_CHOICE_TEXT = \"placement choice\";\nvar GAP_CAUSE_TEXT = {\n  missing: \"not in the graph\",\n  elsewhere: \"on nodes filed elsewhere\",\n  own: \"of its own, not read\",\n  abridged: \"abridged: steps not loaded\",\n  // a row of departures alone: the haplotype has no step on the reference\n  // across the window, which says nothing of what it carries instead\n  departure: \"no step on the reference\"\n};\nvar OUTSIDE_TEXT = \"outside the extracted subgraph\";\nfunction gapParts(from, to, trimmed, departures) {\n  const bp = to - from;\n  const inside = departures.filter((d) => d.hapStart >= from && d.hapStart + d.ownBp <= to).sort((a, b) => a.hapStart - b.hapStart);\n  const first = inside[0];\n  return first ? splitGap(from, to, trimmed, inside, first) : [{ bp }];\n}\nfunction splitGap(from, to, trimmed, inside, first) {\n  const bp = to - from;\n  const left = Math.min(trimmed.after ?? 0, bp);\n  const right = Math.min(trimmed.before ?? 0, bp - left);\n  const between = bp - left - right;\n  const missing = Math.min(\n    inside.reduce((sum, d) => sum + d.missingBp, 0),\n    between\n  );\n  const spans = inside.length === 1 && first.hapStart === from && first.hapStart + first.ownBp === to;\n  const rest = spans ? { bp: between - missing, cause: \"own\" } : {\n    bp: between - missing,\n    cause: \"elsewhere\",\n    near: first.hapStart === from ? first.rejoinPos : first.leavePos\n  };\n  const parts = [\n    { bp: left },\n    { bp: missing, cause: \"missing\" },\n    rest,\n    { bp: right }\n  ];\n  return parts.filter((part) => part.bp > 0);\n}\n\nexport {\n  departureAt,\n  departureTable,\n  departureKind,\n  placementChoice,\n  departureSpan,\n  roughBp,\n  departureText,\n  PLACEMENT_CHOICE_TEXT,\n  GAP_CAUSE_TEXT,\n  OUTSIDE_TEXT,\n  gapParts\n};\n", "import {\n  PathVisits\n} from \"./chunk-BEUTROKU.js\";\nimport {\n  panSNFields,\n  panSNSample\n} from \"./chunk-2JL2JVZ2.js\";\n\n// src/gfa/graphTables.ts\nfunction pLineName(name, start, end) {\n  return start === 0 ? name : `${name}:${start}-${end}`;\n}\nfunction tablePath(w, p) {\n  const walkName = w.names[p];\n  const fields = panSNFields(walkName);\n  const start = w.starts[p];\n  const steps = w.abridgedSteps?.[p] ?? Number.NaN;\n  const abridged = Number.isNaN(steps) ? {} : { abridged: { steps, bp: w.abridgedBp?.[p] ?? 0 } };\n  const trimmedBefore = w.trimmedBefore?.[p];\n  const trimmedAfter = w.trimmedAfter?.[p];\n  return fields ? {\n    name: `${fields.sample}#${fields.haplotype}#${fields.contig}`,\n    start,\n    ...fields,\n    ...trimmedBefore === void 0 ? {} : { trimmedBefore },\n    ...trimmedAfter === void 0 ? {} : { trimmedAfter },\n    ...abridged\n  } : { name: pLineName(walkName, start, w.ends[p]), start };\n}\nfunction namesByList(lists, names, listCount, pathNames) {\n  const starts = new Int32Array(listCount + 1);\n  for (const list of lists) {\n    starts[list + 1]++;\n  }\n  for (let i = 0; i < listCount; i++) {\n    starts[i + 1] += starts[i];\n  }\n  const fill = starts.slice(0, listCount);\n  const grouped = new Int32Array(lists.length);\n  lists.forEach((list, i) => {\n    grouped[fill[list]++] = names[i];\n  });\n  const listed = new Int32Array(pathNames.length).fill(-1);\n  return Array.from({ length: listCount }, (_, list) => {\n    const out = [];\n    for (let i = starts[list]; i < starts[list + 1]; i++) {\n      const k = grouped[i];\n      if (listed[k] !== list) {\n        listed[k] = list;\n        out.push(pathNames[k]);\n      }\n    }\n    return out;\n  });\n}\nfunction tableNodeIds({ nodes: n, links: l, walks: w }, traversals) {\n  const canonical = new Uint8Array(n.names.length);\n  const claim = (node, reversed) => {\n    if (canonical[node] === 0) {\n      canonical[node] = reversed ? 2 : 1;\n    }\n  };\n  for (let i = 0; i < l.from.length; i++) {\n    claim(l.from[i], l.strands[i] & 1);\n    claim(l.to[i], l.strands[i] & 2);\n  }\n  const stepCount = w.offsets[w.names.length] ?? 0;\n  for (let s = 0; s < stepCount; s++) {\n    const node = w.steps[s];\n    claim(node, w.reversed[s]);\n    if (traversals) {\n      traversals[node]++;\n    }\n  }\n  return n.names.map(\n    (segment, i) => `${segment}${canonical[i] === 2 ? \"-\" : \"+\"}`\n  );\n}\nfunction graphFromTables({ nodes: n, links: l, walks: w, departures }, name = \"Imported GFA\") {\n  const count = n.names.length;\n  const declared = n.lengths.length;\n  const drawnWalks = [];\n  for (let p = 0; p < w.names.length; p++) {\n    if (w.offsets[p + 1] > w.offsets[p]) {\n      drawnWalks.push(p);\n    }\n  }\n  const traversals = new Int32Array(count);\n  const ids = tableNodeIds({ nodes: n, links: l, walks: w }, traversals);\n  const nodes = [];\n  for (let i = 0; i < declared; i++) {\n    const ref = n.refs[i];\n    nodes.push({\n      id: ids[i],\n      name: n.names[i],\n      length: n.lengths[i],\n      depth: Math.max(traversals[i], 1),\n      stable: ref < 0 ? void 0 : {\n        refName: n.refNames[ref],\n        start: n.starts[i],\n        rank: n.ranks[i]\n      },\n      samples: void 0\n    });\n  }\n  const edges = [];\n  const neighbours = new Array(count);\n  const pairList = (a, b) => {\n    const near = neighbours[a];\n    if (near) {\n      for (let j = 0; j < near.length; j += 2) {\n        if (near[j] === b) {\n          return near[j + 1];\n        }\n      }\n    }\n    return void 0;\n  };\n  const addPair = (a, b, list) => {\n    const near = neighbours[a];\n    if (near) {\n      near.push(b, list);\n    } else {\n      neighbours[a] = [b, list];\n    }\n  };\n  const edgeLists = [];\n  let lists = 0;\n  for (let i = 0; i < l.from.length; i++) {\n    const a = l.from[i];\n    const b = l.to[i];\n    edges.push({\n      from: ids[a],\n      to: ids[b],\n      fromStrand: l.strands[i] & 1 ? \"-\" : \"+\",\n      toStrand: l.strands[i] & 2 ? \"-\" : \"+\"\n    });\n    let list = pairList(a, b);\n    if (list === void 0) {\n      list = lists++;\n      addPair(a, b, list);\n      addPair(b, a, list);\n    }\n    edgeLists.push(list);\n  }\n  const adjacency = new Int32Array(count + 1);\n  for (let a = 0; a < count; a++) {\n    adjacency[a + 1] = adjacency[a] + (neighbours[a]?.length ?? 0) / 2;\n  }\n  const adjacentNode = new Int32Array(adjacency[count]);\n  const adjacentList = new Int32Array(adjacency[count]);\n  neighbours.forEach((near, a) => {\n    for (let j = 0; j < near.length; j += 2) {\n      adjacentNode[adjacency[a] + j / 2] = near[j];\n      adjacentList[adjacency[a] + j / 2] = near[j + 1];\n    }\n  });\n  const listOf = (a, b) => {\n    for (let j = adjacency[a]; j < adjacency[a + 1]; j++) {\n      if (adjacentNode[j] === b) {\n        return adjacentList[j];\n      }\n    }\n    return -1;\n  };\n  const nameIndex = /* @__PURE__ */ new Map();\n  const pathNames = [];\n  const crossedList = new Int32Array(w.offsets[w.names.length] ?? 0);\n  const crossedName = new Int32Array(crossedList.length);\n  let crossings = 0;\n  const lastWalk = new Int32Array(lists).fill(-1);\n  const paths = [];\n  const anchorPaths = [];\n  const totalSteps = w.offsets[w.names.length] ?? 0;\n  const visitPath = new Int32Array(totalSteps);\n  const visitStart = new Float64Array(totalSteps);\n  const visitReversed = new Uint8Array(totalSteps);\n  const fill = new Int32Array(count).fill(-1);\n  const visitOrder = [];\n  const blocks = [0];\n  const pathSamples = [];\n  const edgeNameIndex = /* @__PURE__ */ new Map();\n  const edgeNames = [];\n  for (const p of drawnWalks) {\n    const head = tablePath(w, p);\n    const { start, name: pathName } = head;\n    const visitName = head.sample === void 0 ? w.names[p] : pathName;\n    let named = nameIndex.get(visitName);\n    if (named === void 0) {\n      named = pathNames.length;\n      nameIndex.set(visitName, named);\n      pathNames.push(visitName);\n      pathSamples.push(panSNSample(visitName));\n    }\n    let edgeNamed = edgeNameIndex.get(pathName);\n    if (edgeNamed === void 0) {\n      edgeNamed = edgeNames.length;\n      edgeNameIndex.set(pathName, edgeNamed);\n      edgeNames.push(pathName);\n    }\n    const visitSample = pathSamples[named];\n    const first = w.offsets[p];\n    const nodeIds = new Array(w.offsets[p + 1] - first);\n    let pos = start;\n    let prev = -1;\n    for (let s = first; s < w.offsets[p + 1]; s++) {\n      const node = w.steps[s];\n      nodeIds[s - first] = ids[node];\n      if (fill[node] === -1) {\n        fill[node] = blocks.at(-1);\n        blocks.push(fill[node] + traversals[node]);\n        visitOrder.push(node);\n      }\n      const at = fill[node]++;\n      visitPath[at] = named;\n      visitStart[at] = pos;\n      visitReversed[at] = w.reversed[s];\n      pos += node < declared ? n.lengths[node] : 0;\n      if (prev >= 0) {\n        const list = listOf(prev, node);\n        if (list >= 0 && lastWalk[list] !== p) {\n          lastWalk[list] = p;\n          crossedList[crossings] = list;\n          crossedName[crossings++] = edgeNamed;\n        }\n      }\n      prev = node;\n    }\n    paths.push({ ...head, nodeIds });\n    anchorPaths.push({\n      name: visitName,\n      sample: visitSample,\n      start,\n      length: pos - start\n    });\n  }\n  const listNames = namesByList(\n    crossedList.subarray(0, crossings),\n    crossedName,\n    lists,\n    edgeNames\n  );\n  edges.forEach((edge, i) => {\n    const names = listNames[edgeLists[i]];\n    if (names.length > 0) {\n      edge.pathIds = names;\n    }\n  });\n  const walked = drawnWalks.length > 0;\n  return {\n    name,\n    nodes,\n    edges,\n    paths: walked ? paths : void 0,\n    anchorPaths: walked ? anchorPaths : void 0,\n    pathVisits: walked ? new PathVisits({\n      segments: visitOrder.map((node) => n.names[node]),\n      offsets: Int32Array.from(blocks),\n      path: visitPath.subarray(0, blocks.at(-1)),\n      start: visitStart.subarray(0, blocks.at(-1)),\n      reversed: visitReversed.subarray(0, blocks.at(-1)),\n      paths: pathNames,\n      samples: pathSamples\n    }) : void 0,\n    anchoredBy: nodes.some((node) => node.stable) ? \"tags\" : void 0,\n    ...departures.names.length > 0 ? { departures } : {}\n  };\n}\nfunction graphTablesGFA({\n  nodes,\n  links,\n  walks\n}) {\n  const { names } = nodes;\n  const lines = [\"H\tVN:Z:1.1\"];\n  for (let i = 0; i < nodes.lengths.length; i++) {\n    const ref = nodes.refs[i];\n    const stable = ref < 0 ? \"\" : `\tSN:Z:${nodes.refNames[ref]}\tSO:i:${nodes.starts[i]}\tSR:i:${nodes.ranks[i]}`;\n    lines.push(`S\t${names[i]}\t*\tLN:i:${nodes.lengths[i]}${stable}`);\n  }\n  for (let i = 0; i < links.from.length; i++) {\n    const strands = links.strands[i];\n    lines.push(\n      `L\t${names[links.from[i]]}\t${strands & 1 ? \"-\" : \"+\"}\t${names[links.to[i]]}\t${strands & 2 ? \"-\" : \"+\"}\t0M`\n    );\n  }\n  for (let p = 0; p < walks.names.length; p++) {\n    const name = walks.names[p];\n    const fields = panSNFields(name);\n    const start = walks.starts[p];\n    const end = walks.ends[p];\n    const steps = [];\n    for (let s = walks.offsets[p]; s < walks.offsets[p + 1]; s++) {\n      steps.push([names[walks.steps[s]], walks.reversed[s]]);\n    }\n    lines.push(\n      fields ? `W\t${fields.sample}\t${fields.haplotype}\t${fields.contig}\t${start}\t${end}\t${steps.map(([id, rev]) => (rev ? \"<\" : \">\") + id).join(\"\")}` : `P\t${pLineName(name, start, end)}\t${steps.map(([id, rev]) => id + (rev ? \"-\" : \"+\")).join(\",\")}\t*`\n    );\n  }\n  return lines.join(\"\\n\");\n}\n\nexport {\n  tablePath,\n  tableNodeIds,\n  graphFromTables,\n  graphTablesGFA\n};\n", "import {\n  tableNodeIds,\n  tablePath\n} from \"./chunk-DBLRFSET.js\";\nimport {\n  departureAt,\n  departureSpan,\n  gapParts,\n  placementChoice\n} from \"./chunk-NPDW3JAD.js\";\nimport {\n  pathOrigin\n} from \"./chunk-QBI6SC74.js\";\nimport {\n  groupBy\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  panSNContig,\n  panSNFields,\n  panSNHaplotype,\n  panSNSample\n} from \"./chunk-2JL2JVZ2.js\";\n\n// src/layout/walkRowRuns.ts\nvar RUN_ON_REFERENCE = 1;\nvar RUN_REVERSED = 2;\nvar RUN_GAP = 4;\nvar GAP_CAUSES = [\n  void 0,\n  \"missing\",\n  \"elsewhere\",\n  \"own\",\n  \"abridged\",\n  \"departure\"\n];\nvar CAUSE_SHIFT = 3;\nvar causeFlags = (cause) => GAP_CAUSES.indexOf(cause) << CAUSE_SHIFT;\nfunction referenceOf(names, referencePath, rankZero) {\n  return referencePath !== void 0 && names.includes(referencePath) ? referencePath : names.find((n) => rankZero.has(n)) ?? names[0];\n}\nfunction referenceWalkName(graph) {\n  return referenceOf(\n    (graph.paths ?? []).map((p) => pathOrigin(p.name).name),\n    graph.referencePath,\n    new Set(\n      graph.nodes.flatMap(\n        (n) => n.stable?.rank === 0 ? [n.stable.refName] : []\n      )\n    )\n  );\n}\nvar namesReference = (reference) => {\n  const contig = reference && panSNContig(reference);\n  return (name) => name !== void 0 && (name === reference || name === contig);\n};\nfunction graphPieces(graph) {\n  const index = /* @__PURE__ */ new Map();\n  const names = [];\n  const lengths = [];\n  const indexOf = (id) => {\n    let i = index.get(id);\n    if (i === void 0) {\n      i = names.length;\n      index.set(id, i);\n      names.push(id);\n      lengths.push(0);\n    }\n    return i;\n  };\n  const reference = referenceWalkName(graph);\n  const onReferenceContig = namesReference(reference);\n  const stable = /* @__PURE__ */ new Map();\n  for (const node of graph.nodes) {\n    const i = indexOf(node.id);\n    lengths[i] = node.length;\n    if (node.stable?.rank === 0 && onReferenceContig(node.stable.refName)) {\n      stable.set(i, node.stable.start);\n    }\n  }\n  const heads = graph.paths ?? [];\n  const from = new Int32Array(heads.length);\n  const to = new Int32Array(heads.length);\n  const steps = [];\n  heads.forEach((path, p) => {\n    from[p] = steps.length;\n    for (const id of path.nodeIds) {\n      steps.push(indexOf(id));\n    }\n    to[p] = steps.length;\n  });\n  return {\n    heads,\n    from,\n    to,\n    steps: Int32Array.from(steps),\n    lengths: Int32Array.from(lengths),\n    names,\n    reference,\n    stableStart: (node) => stable.get(node) ?? Number.NaN,\n    departures: graph.departures\n  };\n}\nfunction tablePieces(tables, referencePath, visits) {\n  const { nodes: n, walks: w } = tables;\n  const kept = [];\n  for (let p = 0; p < w.names.length; p++) {\n    if (w.offsets[p + 1] > w.offsets[p]) {\n      kept.push(p);\n    }\n  }\n  const heads = kept.map((p) => tablePath(w, p));\n  const rankZero = /* @__PURE__ */ new Set();\n  for (let i = 0; i < n.lengths.length; i++) {\n    if (n.refs[i] >= 0 && n.ranks[i] === 0) {\n      rankZero.add(n.refNames[n.refs[i]]);\n    }\n  }\n  const reference = referenceOf(\n    heads.map((h) => pathOrigin(h.name).name),\n    referencePath,\n    rankZero\n  );\n  const onReferenceContig = namesReference(reference);\n  return {\n    heads,\n    from: Int32Array.from(kept, (p) => w.offsets[p]),\n    to: Int32Array.from(kept, (p) => w.offsets[p + 1]),\n    steps: w.steps,\n    lengths: n.lengths,\n    // a visit names its node as the Graph does, which costs a pass over the\n    // steps\n    names: visits ? tableNodeIds(tables) : n.names,\n    reference,\n    stableStart: (node) => node < n.lengths.length && n.ranks[node] === 0 && onReferenceContig(n.refNames[n.refs[node]]) ? n.starts[node] : Number.NaN,\n    departures: tables.departures\n  };\n}\nfunction sampleOf(path) {\n  return path.sample ?? panSNSample(path.name);\n}\nfunction labelOf(path) {\n  return path.haplotype !== void 0 && path.sample !== void 0 ? `${path.sample}#${path.haplotype}` : sampleOf(path);\n}\nvar Columns = class {\n  constructor(width) {\n    this.offsets = [0];\n    this.values = Array.from({ length: width }, () => []);\n  }\n  get length() {\n    return this.values[0].length;\n  }\n  push(a, b, c, d, e) {\n    const v = this.values;\n    v[0].push(a);\n    v[1].push(b);\n    v[2].push(c);\n    v[3].push(d);\n    if (e !== void 0) {\n      v[4].push(e);\n    }\n  }\n  endRow() {\n    this.offsets.push(this.length);\n  }\n  // the rows in `order`, column i in the array `make[i]` makes\n  reorder(order, make) {\n    const offsets = new Uint32Array(order.length + 1);\n    order.forEach((row, i) => {\n      offsets[i + 1] = offsets[i] + this.offsets[row + 1] - this.offsets[row];\n    });\n    const columns = make.map((m, c) => {\n      const from = this.values[c];\n      const out = m(this.length);\n      let at = 0;\n      for (const row of order) {\n        for (let k = this.offsets[row]; k < this.offsets[row + 1]; k++) {\n          out[at++] = from[k];\n        }\n      }\n      return out;\n    });\n    return { offsets, columns };\n  }\n};\nvar float64 = (n) => new Float64Array(n);\nfunction walkRowRuns(source, region, o = {}) {\n  const {\n    heads,\n    from,\n    to,\n    steps: all,\n    lengths,\n    names,\n    reference,\n    stableStart,\n    departures\n  } = \"walks\" in source ? tablePieces(source, o.referencePath, o.visits) : graphPieces(source);\n  const declared = lengths.length;\n  const lengthOf = (node) => node < declared ? lengths[node] : 0;\n  const nameOf = (p) => pathOrigin(heads[p].name).name;\n  const startOf = (p) => heads[p].start;\n  const byStart = (a, b) => (startOf(a) ?? 0) - (startOf(b) ?? 0);\n  const pieceIds = heads.map((_, p) => p);\n  const referencePieces = pieceIds.filter((p) => nameOf(p) === reference).sort(byStart);\n  const first = referencePieces[0];\n  const others = pieceIds.filter((p) => nameOf(p) !== reference);\n  const departuresOf = departuresByWalk(departures, reference);\n  if (first === void 0 || others.length === 0 && departuresOf.size === 0) {\n    return void 0;\n  }\n  const walks = groupBy(others, nameOf);\n  const spanStart = new Float64Array(names.length).fill(Number.NaN);\n  const spanEnd = new Float64Array(names.length);\n  const revisits = /* @__PURE__ */ new Map();\n  let flankEnd = -Infinity;\n  let flankStart = Infinity;\n  let referenceLo = Infinity;\n  let referenceHi = -Infinity;\n  const cut = region && region.end > region.start ? region : void 0;\n  for (const piece of referencePieces) {\n    let pos = startOf(piece) ?? 0;\n    for (let s = from[piece], stop = to[piece]; s < stop; s++) {\n      const node = all[s];\n      const len = lengthOf(node);\n      if (!Number.isNaN(spanStart[node])) {\n        const starts = revisits.get(node);\n        if (starts) {\n          starts.push(pos);\n        } else {\n          revisits.set(node, [spanStart[node], pos]);\n        }\n      } else {\n        spanStart[node] = pos;\n        spanEnd[node] = pos + len;\n        referenceLo = Math.min(referenceLo, pos);\n        referenceHi = Math.max(referenceHi, pos + len);\n        if (cut) {\n          if (pos + len <= cut.start) {\n            flankEnd = Math.max(flankEnd, pos + len);\n          }\n          if (pos >= cut.end) {\n            flankStart = Math.min(flankStart, pos);\n          }\n        }\n      }\n      pos += len;\n    }\n  }\n  const flanked = cut === void 0 || flankEnd > -Infinity && flankStart < Infinity;\n  const runs = new Columns(5);\n  const visits = o.visits ? new Columns(4) : void 0;\n  let steps = new Int32Array(0);\n  let stepStart = new Float64Array(0);\n  const departureRuns = (own, bar2) => {\n    const spans = own.map(departureSpan).sort((a, b) => a.start - b.start);\n    const base = bar2?.start ?? spans[0]?.start ?? 0;\n    const merged = [];\n    for (const span of spans) {\n      const start2 = bar2 ? Math.max(span.start, bar2.start) : span.start;\n      const end = bar2 ? Math.min(span.end, bar2.end) : span.end;\n      const last = merged.at(-1);\n      if (end > start2) {\n        if (last && start2 <= last.end) {\n          last.end = Math.max(last.end, end);\n        } else {\n          merged.push({ start: start2, end });\n        }\n      }\n    }\n    let gapBp = 0;\n    for (const { start: start2, end } of merged) {\n      runs.push(\n        start2 - base,\n        end - start2,\n        Number.NaN,\n        RUN_GAP | causeFlags(\"departure\"),\n        Number.NaN\n      );\n      gapBp += end - start2;\n    }\n    return gapBp;\n  };\n  const steplessMeta = (head, own, gapBp) => ({\n    name: head.name,\n    label: labelOf(head),\n    sample: sampleOf(head),\n    haplotype: head.haplotype,\n    bp: 0,\n    offReferenceBp: own.reduce((sum, d) => sum + d.ownBp, 0),\n    gapBp,\n    complete: true,\n    stop: void 0,\n    axis: void 0,\n    departures: own,\n    stepless: true,\n    ...own.some(placementChoice) ? { placementChoice: true } : {}\n  });\n  const rowOf = (pieces, bar2) => {\n    const head = heads[pieces[0]];\n    const own = departuresOf.get(nameOf(pieces[0])) ?? [];\n    const extents = [];\n    const ordered = [...pieces].sort(byStart);\n    let count = ordered.length - 1;\n    let abridgedSteps = 0;\n    for (const piece of ordered) {\n      count += to[piece] - from[piece] + (heads[piece].abridged ? 1 : 0);\n      abridgedSteps += heads[piece].abridged?.steps ?? 0;\n    }\n    if (count > steps.length) {\n      steps = new Int32Array(count * 2);\n      stepStart = new Float64Array(count * 2);\n    }\n    let length = 0;\n    let unplaced = false;\n    let end;\n    let previous;\n    const partsAt = /* @__PURE__ */ new Map();\n    let owed = 0;\n    for (const piece of ordered) {\n      const start2 = startOf(piece);\n      const jump = start2 === void 0 || end === void 0 ? 0 : start2 - end;\n      if (start2 === void 0 || jump < 0) {\n        unplaced = true;\n      }\n      if (jump < 0 && heads[previous].abridged) {\n        owed -= jump;\n      }\n      const covered = Math.min(owed, Math.max(jump, 0));\n      owed -= covered;\n      const gap = jump - covered;\n      if (gap > 0) {\n        partsAt.set(\n          length,\n          gapParts(\n            start2 - gap,\n            start2,\n            {\n              after: heads[previous].trimmedAfter,\n              before: heads[piece].trimmedBefore\n            },\n            own\n          )\n        );\n        steps[length] = -gap;\n        stepStart[length++] = end;\n      }\n      let pos = start2 ?? 0;\n      const abridged = heads[piece].abridged;\n      for (let s = from[piece], stop2 = to[piece]; s < stop2; s++) {\n        const node = all[s];\n        const bp3 = abridged ? abridged.bp - (pos - (start2 ?? 0)) - lengthOf(node) : 0;\n        if (bp3 > 0 && s === stop2 - 1 && s > from[piece]) {\n          partsAt.set(length, [{ bp: bp3, cause: \"abridged\" }]);\n          steps[length] = -bp3;\n          stepStart[length++] = pos;\n          pos += bp3;\n        }\n        steps[length] = node;\n        stepStart[length++] = pos;\n        pos += lengthOf(node);\n      }\n      end = start2 === void 0 ? void 0 : pos;\n      if (start2 !== void 0) {\n        extents.push([start2, pos]);\n      }\n      previous = piece;\n    }\n    const onReference = (i) => i >= 0 && i < length && steps[i] >= 0 && !Number.isNaN(spanStart[steps[i]]);\n    const stepEnd = (i) => {\n      const id = steps[i];\n      return stepStart[i] + (id < 0 ? -id : lengthOf(id));\n    };\n    const endOf = (after) => {\n      const last2 = after ? length - 1 : 0;\n      const edge = after ? stepEnd(last2) : stepStart[last2];\n      return {\n        last: last2,\n        departure: own.find(\n          (d) => after ? d.hapStart === edge : d.hapStart + d.ownBp === edge\n        ),\n        trimmed: after ? heads[ordered.at(-1)].trimmedAfter : heads[ordered[0]].trimmedBefore\n      };\n    };\n    const flankForward = (flank, rightward) => {\n      let near2 = -1;\n      for (let d = 1; near2 < 0 && d < length; d++) {\n        near2 = [flank - d, flank + d].find(onReference) ?? -1;\n      }\n      const tail = endOf(true);\n      const lead = endOf(false);\n      return near2 >= 0 ? near2 > flank === spanStart[steps[near2]] > spanStart[steps[flank]] : length > 1 ? void 0 : tail.departure ? !tail.departure.leaveReversed : lead.departure ? !lead.departure.rejoinReversed : (!tail.trimmed || !!lead.trimmed) === rightward;\n    };\n    const partialSide = (i0, i1, inside) => {\n      const flank = i0 >= 0 ? i0 : i1;\n      const rightward = flank === i0;\n      const forward = flankForward(flank, rightward);\n      const after = forward === rightward;\n      const { last: last2, departure, trimmed } = endOf(after);\n      const contigEnds = onReference(last2) && !departure && !trimmed;\n      const stop2 = {\n        contigEnds,\n        shortBp: contigEnds ? Math.max(\n          0,\n          cut.start - spanEnd[steps[last2]],\n          spanStart[steps[last2]] - cut.end\n        ) : 0,\n        ...departure ? {\n          goesOn: {\n            departure,\n            near: after ? departure.rejoinPos : departure.leavePos\n          }\n        } : {}\n      };\n      const skip = inside ? 0 : 1;\n      const from2 = after === inside ? stepStart[flank] : stepEnd(flank);\n      return forward === void 0 ? void 0 : {\n        stop: stop2,\n        lo: after ? flank + skip : 0,\n        hi: after ? length : flank + 1 - skip,\n        backward: !forward,\n        axisStart: forward ? after ? from2 : stepStart[0] : after ? stepEnd(length - 1) : from2\n      };\n    };\n    let lo = 0;\n    let hi = length;\n    let backward = false;\n    let complete = true;\n    let flankFrom = -1;\n    let flankTo = -1;\n    let axisStart;\n    let stop;\n    const trimAbridged = (inner, bp3) => {\n      const parts = partsAt.get(inner);\n      const gap = parts?.[0];\n      if (bp3 <= 0 || gap?.cause !== \"abridged\") {\n        return 0;\n      }\n      const trimmed = Math.min(bp3, gap.bp);\n      partsAt.set(\n        inner,\n        gap.bp > trimmed ? [{ ...gap, bp: gap.bp - trimmed }] : []\n      );\n      steps[inner] += trimmed;\n      return trimmed;\n    };\n    const abridgedAt = (i) => partsAt.get(i)?.[0]?.cause === \"abridged\";\n    const placeStart = (i) => {\n      const id = steps[i];\n      if (id < 0 || partsAt.has(i)) {\n        return Number.NaN;\n      }\n      return Number.isNaN(spanStart[id]) && (abridgedAt(i - 1) || abridgedAt(i + 1)) ? stableStart(id) : spanStart[id];\n    };\n    const stopsInside = (i0, i1, inside) => {\n      complete = false;\n      const side = i0 >= 0 || i1 >= 0 ? partialSide(i0, i1, inside) : void 0;\n      if (side) {\n        ;\n        ({ lo, hi, backward, axisStart, stop } = side);\n      }\n    };\n    let leftTrim = 0;\n    let rightTrim = 0;\n    if (cut && flanked) {\n      let i0 = -1;\n      let i1 = -1;\n      let bestEnd = -Infinity;\n      let bestStart = Infinity;\n      for (let i = 0; i < length; i++) {\n        const start2 = placeStart(i);\n        if (!Number.isNaN(start2)) {\n          const end2 = start2 + lengthOf(steps[i]);\n          if (end2 <= cut.start && end2 > bestEnd) {\n            bestEnd = end2;\n            i0 = i;\n          }\n          if (start2 >= cut.end && start2 < bestStart) {\n            bestStart = start2;\n            i1 = i;\n          }\n        }\n      }\n      if (i0 < 0 || i1 < 0) {\n        stopsInside(i0, i1, false);\n      } else {\n        lo = Math.min(i0, i1) + 1;\n        hi = Math.max(i0, i1);\n        backward = i0 > i1;\n        flankFrom = i0;\n        flankTo = i1;\n        const inward = backward ? -1 : 1;\n        leftTrim = trimAbridged(i0 + inward, flankEnd - bestEnd);\n        rightTrim = trimAbridged(i1 - inward, bestStart - flankStart);\n      }\n    } else if (cut && ordered.some(\n      (p) => heads[p].trimmedBefore !== void 0 || heads[p].trimmedAfter !== void 0\n    )) {\n      let i0 = -1;\n      let i1 = -1;\n      for (let i = 0; i < length; i++) {\n        const start2 = placeStart(i);\n        if (i0 < 0 && start2 === referenceLo) {\n          i0 = i;\n        }\n        if (i1 < 0 && start2 + lengthOf(steps[i]) === referenceHi) {\n          i1 = i;\n        }\n      }\n      if (i0 < 0 || i1 < 0) {\n        stopsInside(i0, i1, true);\n      }\n    }\n    const stepless = bar2 !== void 0 && lo >= hi && own.some((d) => {\n      const span = departureSpan(d);\n      return span.start < bar2.end && span.end > bar2.start;\n    });\n    const contig = head.contig ?? panSNContig(pathOrigin(head.name).name);\n    const axis2 = unplaced || length === 0 ? void 0 : axisStart !== void 0 ? { contig, start: axisStart, reversed: backward } : flankFrom < 0 ? { contig, start: stepStart[0], reversed: false } : flankFrom < flankTo ? {\n      contig,\n      start: stepEnd(flankFrom) + leftTrim,\n      reversed: false\n    } : {\n      contig,\n      start: stepStart[flankFrom] - leftTrim,\n      reversed: true\n    };\n    let bp2 = 0;\n    let offReferenceBp = 0;\n    let gapBp = 0;\n    let step = 0;\n    let last = -1;\n    let lastFlags = 0;\n    let lastRef = Number.NaN;\n    let cursor = Number.NaN;\n    const placeOf = (id) => {\n      const starts = revisits.get(id);\n      if (!starts || Number.isNaN(cursor)) {\n        return spanStart[id];\n      }\n      const len = lengthOf(id);\n      let best = starts[0];\n      let bestGap = Infinity;\n      for (const start2 of starts) {\n        const gap = Math.min(\n          Math.abs(start2 - cursor),\n          Math.abs(start2 + len - cursor)\n        );\n        if (gap < bestGap) {\n          best = start2;\n          bestGap = gap;\n        }\n      }\n      return best;\n    };\n    const [, runBp, runRef, runFlags] = runs.values;\n    for (let k = lo; k < hi; k++) {\n      const index = backward ? hi - 1 - (k - lo) : k;\n      const id = steps[index];\n      const parts = partsAt.get(index);\n      if (parts) {\n        for (const part of backward ? [...parts].reverse() : parts) {\n          runs.push(\n            bp2,\n            part.bp,\n            Number.NaN,\n            RUN_GAP | causeFlags(part.cause),\n            part.near ?? Number.NaN\n          );\n          bp2 += part.bp;\n        }\n        last = runs.length - 1;\n        lastFlags = RUN_GAP;\n        lastRef = Number.NaN;\n        gapBp += -id;\n        step = 0;\n        continue;\n      }\n      const len = lengthOf(id);\n      const at = placeOf(id);\n      const on = !Number.isNaN(at);\n      visits?.push(id, bp2, len, on ? 1 : 0);\n      const placed = last >= 0 && !Number.isNaN(lastRef);\n      const forward = on && placed && step >= 0 && lastRef + (runBp[last] ?? 0) === at;\n      const back = on && placed && step <= 0 && at + len === lastRef;\n      if (!on && last >= 0 && !(lastFlags & (RUN_ON_REFERENCE | RUN_GAP))) {\n        runBp[last] += len;\n      } else if (forward || back) {\n        runBp[last] += len;\n        if (!forward) {\n          lastRef = at;\n          runRef[last] = at;\n          lastFlags |= RUN_REVERSED;\n          runFlags[last] = lastFlags;\n        }\n        step = forward ? 1 : -1;\n      } else {\n        lastFlags = on ? RUN_ON_REFERENCE : 0;\n        lastRef = on ? at : Number.NaN;\n        runs.push(bp2, len, lastRef, lastFlags, Number.NaN);\n        last = runs.length - 1;\n        step = 0;\n      }\n      bp2 += len;\n      if (on) {\n        cursor = step < 0 ? at : at + len;\n      } else {\n        offReferenceBp += len;\n      }\n    }\n    const departureGapBp = stepless ? departureRuns(own, bar2) : 0;\n    runs.endRow();\n    visits?.endRow();\n    const undrawn = own.filter(\n      (d) => !extents.some(([a, b]) => d.hapStart > a && d.hapStart + d.ownBp < b)\n    );\n    return stepless ? steplessMeta(head, own, departureGapBp) : {\n      name: head.name,\n      label: labelOf(head),\n      sample: sampleOf(head),\n      haplotype: head.haplotype,\n      bp: bp2,\n      offReferenceBp,\n      gapBp,\n      complete,\n      stop,\n      axis: axis2,\n      ...abridgedSteps > 0 ? { abridgedSteps } : {},\n      ...leftTrim + rightTrim > 0 ? { estimated: true } : {},\n      ...undrawn.length > 0 ? { departures: undrawn } : {},\n      ...own.some(placementChoice) ? { placementChoice: true } : {}\n    };\n  };\n  const steplessRowOf = (name, own, bar2) => {\n    const gapBp = departureRuns(own, bar2);\n    runs.endRow();\n    visits?.endRow();\n    return steplessMeta({ name, ...panSNFields(name) }, own, gapBp);\n  };\n  const referenceRow = rowOf(referencePieces);\n  const { axis } = referenceRow;\n  const bar = axis ? {\n    start: axis.start,\n    end: axis.start + referenceRow.bp + referenceRow.gapBp\n  } : cut;\n  const rows = [...walks.values()].map((pieces, i) => ({\n    meta: rowOf(pieces, bar),\n    row: i + 1\n  }));\n  const drawn = new Set(walks.keys());\n  for (const [name, own] of departuresOf) {\n    if (!drawn.has(name)) {\n      rows.push({\n        meta: steplessRowOf(name, own, bar),\n        row: rows.length + 1\n      });\n    }\n  }\n  const metas = [referenceRow, ...rows.map((r) => r.meta)];\n  if (new Set(metas.map((m) => m.label)).size < metas.length) {\n    for (const meta of metas) {\n      meta.label = panSNHaplotype(meta.name) ?? meta.label;\n    }\n  }\n  rows.sort(\n    (a, b) => Number(b.meta.complete) - Number(a.meta.complete) || b.meta.bp - a.meta.bp || a.meta.label.localeCompare(b.meta.label)\n  );\n  const order = [0, ...rows.map((r) => r.row)];\n  const { offsets, columns } = runs.reorder(order, [\n    float64,\n    float64,\n    float64,\n    (n) => new Uint8Array(n),\n    float64\n  ]);\n  const [start, bp, referenceStart, flags, near] = columns;\n  return {\n    origin: cut ? cut.start : startOf(first) ?? 0,\n    rows: [referenceRow, ...rows.map((r) => r.meta)],\n    offsets,\n    start,\n    bp,\n    referenceStart,\n    flags,\n    near,\n    visits: visits && visitColumns(visits, order, names)\n  };\n}\nfunction departuresByWalk(table, reference) {\n  const byWalk = /* @__PURE__ */ new Map();\n  if (table) {\n    for (let k = 0; k < table.names.length; k++) {\n      const d = departureAt(table, k);\n      const name = pathOrigin(d.name).name;\n      if (name !== reference) {\n        const list = byWalk.get(name);\n        if (list) {\n          list.push(d);\n        } else {\n          byWalk.set(name, [d]);\n        }\n      }\n    }\n  }\n  for (const list of byWalk.values()) {\n    list.sort((a, b) => a.hapStart - b.hapStart);\n  }\n  return byWalk;\n}\nfunction visitColumns(visits, order, names) {\n  const { offsets, columns } = visits.reorder(order, [\n    (n) => new Int32Array(n),\n    float64,\n    float64,\n    (n) => new Uint8Array(n)\n  ]);\n  const [node, start, bp, onReference] = columns;\n  return { offsets, node, start, bp, onReference, names };\n}\nfunction runAt(t, k) {\n  const f = t.flags[k];\n  const run = {\n    start: t.start[k],\n    bp: t.bp[k],\n    onReference: (f & RUN_ON_REFERENCE) !== 0\n  };\n  if (f & RUN_GAP) {\n    run.gap = true;\n    const cause = GAP_CAUSES[f >> CAUSE_SHIFT & 7];\n    if (cause) {\n      run.cause = cause;\n    }\n    const near = t.near[k];\n    if (!Number.isNaN(near)) {\n      run.near = near;\n    }\n  } else {\n    run.referenceStart = Number.isNaN(t.referenceStart[k]) ? void 0 : t.referenceStart[k];\n  }\n  if (f & RUN_REVERSED) {\n    run.reversed = true;\n  }\n  return run;\n}\nfunction visitsOf(v, row) {\n  const out = [];\n  for (let k = v.offsets[row]; k < v.offsets[row + 1]; k++) {\n    out.push({\n      node: v.names[v.node[k]],\n      start: v.start[k],\n      bp: v.bp[k],\n      onReference: v.onReference[k] === 1\n    });\n  }\n  return out;\n}\nfunction walkRowsOf(t, unit) {\n  const rows = t.rows.map((meta, i) => {\n    const runs = [];\n    for (let k = t.offsets[i]; k < t.offsets[i + 1]; k++) {\n      runs.push(runAt(t, k));\n    }\n    return {\n      ...meta,\n      runs,\n      visits: t.visits && visitsOf(t.visits, i)\n    };\n  });\n  return { origin: t.origin, unit, reference: rows[0], rows: rows.slice(1) };\n}\n\nexport {\n  referenceWalkName,\n  walkRowRuns,\n  runAt,\n  walkRowsOf\n};\n"],
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+}

package/dist/chunks/{chunk-AGUEPVOR.js → chunk-FQI75MV6.js}

@@ -1,2 +1,2 @@
 function o(n,{refRefNameMap:f={},queryRefNameMap:m={}}={}){let r=[];for(let e of n){let t=e.get("mate");if(t){let a=e.get("refName");r.push({refRefName:f[a]??a,queryRefName:m[t.refName]??t.refName,refStart:e.get("start"),refEnd:e.get("end"),queryStart:t.start,queryEnd:t.end,strand:e.get("strand")??1})}}return r}export{o as a};
-//# sourceMappingURL=chunk-AGUEPVOR.js.map
+//# sourceMappingURL=chunk-FQI75MV6.js.map

package/dist/chunks/{chunk-AGUEPVOR.js.map → chunk-FQI75MV6.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+synteny-core@5.0.0-beta.19_@emotion+react@11.14.0_@types+react@19.3.0_react@19_eb34fd01d29d05a1c3ac8167d41484d7/node_modules/@jbrowse/synteny-core/esm/extractAlignmentData.js"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+synteny-core@5.0.0-beta.20_@emotion+react@11.14.0_@types+react@19.3.0_react@19_56a3e322b5b3da42dc5bccc6b71729c9/node_modules/@jbrowse/synteny-core/esm/extractAlignmentData.js"],
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