jbrowse-plugin-graphgenomeviewer 7.4.2 → 7.4.4

package/dist/chunks/{chunk-MVVXRZXV.js → chunk-JRJHXLGP.js}

@@ -1,2 +1,2 @@
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-//# sourceMappingURL=chunk-MVVXRZXV.js.map
+var o=JBrowseExports["@jbrowse/core/configuration"],t=e=>o!=null&&e in Object(o)?o[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/core/configuration' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),n=t("ConfigurationReference"),r=t("ConfigurationSchema");var i=t("getConf");var a=t("readConfObject");var s=t("setConf");var c=o&&o.__esModule?o.default:o;export{n as a,r as b,i as c,a as d,s as e};
+//# sourceMappingURL=chunk-JRJHXLGP.js.map

package/dist/chunks/{chunk-MVVXRZXV.js.map → chunk-JRJHXLGP.js.map}

@@ -2,6 +2,6 @@
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 }

package/dist/chunks/{chunk-LFTZNUXB.js → chunk-KIYRMZWP.js}

@@ -1,4 +1,4 @@
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-//# sourceMappingURL=chunk-LFTZNUXB.js.map
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package/dist/chunks/{chunk-LFTZNUXB.js.map → chunk-KIYRMZWP.js.map}

@@ -1,6 +1,6 @@
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package/dist/chunks/{chunk-WJGCVNGH.js → chunk-LE43I4PT.js}

@@ -1,4 +1,4 @@
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   "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  // 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-ZPZ7GNBT.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.offsets[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-MUONTMYZ.js

@@ -0,0 +1,2 @@
+import{l as b,m as $,n as S,p as E,q as x,r as T}from"./chunk-FTXDTU27.js";function A(e){let{refName:n,start:t,end:r}=e??{};return typeof n=="string"&&Number.isFinite(t)&&Number.isFinite(r)&&t<r?{refName:n,start:t,end:r}:void 0}function D(e){let n=Number(e);return e!=="auto"&&Number.isFinite(n)?n:"auto"}var w=e=>e.toLocaleString("en-US"),v=({refName:e,start:n,end:t})=>`${e}:${w(n+1)}-${w(t)}`,L=e=>`Forms of ${v(e)}: `;var C={deletion:{svType:"DEL",type:"deletion",alt:"<DEL>"},insertion:{svType:"INS",type:"insertion",alt:"<INS>"},duplication:{svType:"DUP",type:"tandem_duplication",alt:"<DUP:TANDEM>"},replacement:{svType:"CPX",type:"complex_substitution",alt:"<CPX>"},inversion:{svType:"INV",type:"inversion",alt:"<INV>",consequence:"inversion"},shift:{svType:"CPX",type:"complex_structural_alteration",alt:"<CPX>",consequence:"shift"},net:{svType:"CPX",type:"complex_structural_alteration",alt:"<CPX>",consequence:"net"}},_=e=>e.lopsided??(e.delta<0?"deletion":"insertion"),P=e=>C[e.kind].consequence??(_(e)==="deletion"?"loss":"gain"),f=e=>`F${e+1}`,O="other",l=8;function F(e,n){let t=100*e/n;return t>0&&t<1?"<1%":`${Math.round(t)}%`}var d=({forms:e},n)=>e.length>n+1?Math.max(0,n):e.length,m=e=>e.reduce((n,t)=>n+t.members.length,0);function U(e,n=l){let t=d(e,n),r=e.forms.slice(t);return[...e.forms.slice(0,t).map((s,a)=>({name:f(a),label:`${F(s.members.length,e.placed)} \xB7 ${T(s,e)}`,haplotypes:s.members.length,forms:1})),...r.length>0?[{name:O,label:`other forms \xB7 ${F(m(r),e.placed)}`,haplotypes:m(r),forms:r.length}]:[]]}var N=5;function k(e){let n=e.slice(0,N).join(", "),t=e.length-N;return t>0?`${n} and ${t} more`:n}var u=e=>`${e} haplotype${e===1?"":"s"}`;function j(e,n=l){let{abridged:t,unplaced:r,forms:s}=e,a=d(e,n),i=s.slice(a);return[...i.length>0?[`${i.length} smaller forms, ${u(m(i))}, share the empty "other forms" row; maxForms sets how many forms get a row of their own`]:[],...t.length>0?[`${u(t.length)} kept an abridged walk past the forms cut's step budget, which shows as a net change over its span: ${k(t)}`]:[],...r.length>0?[`${u(r.length)} ${r.length===1?"has":"have"} no walk over the pinned window, so no form: ${k(r)}`]:[]]}function V(e,n=l){return Object.fromEntries(e.forms.slice(0,d(e,n)).map((t,r)=>[f(r),"0"]))}function q({copied:e,refStart:n,refEnd:t}){let[r,s]=e??[n,t];return{start:r,end:Math.max(s,r+1)}}var R=(e,n)=>e===n?"1":e===$||e===S?".":"0";function K(e,n=l){let{sites:t,forms:r,placed:s}=e,a=d(e,n);return t.flatMap((i,g)=>i.edge?[]:i.states.flatMap(c=>{if(c.key===b)return[];let h=r.map(o=>x(e,o,g)),y=Object.fromEntries(h.slice(0,a).map((o,p)=>[f(p),R(o,c.key)])),M=m(r.filter((o,p)=>h[p]===c.key));return Object.values(y).includes("1")?c.marks.map((o,p)=>({id:`${g}:${c.key}:${p}`,...q(o),name:E(o),description:`${M} of ${u(s)}`,...C[o.kind],consequence:P(o),mark:o,genotypes:y})):[]}))}export{A as a,D as b,v as c,L as d,l as e,U as f,j as g,V as h,K as i};
+//# sourceMappingURL=chunk-MUONTMYZ.js.map

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

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/WalkFormsAdapter/pinned.ts", "../../src/WalkFormsAdapter/formRows.ts"],
+  "sourcesContent": ["export interface Pinned {\n  refName: string\n  start: number\n  end: number\n}\n\nexport type FloorBp = number | 'auto'\n\nexport function pinnedOf(value: unknown): Pinned | undefined {\n  const { refName, start, end } = (value ?? {}) as Partial<Pinned>\n  return typeof refName === 'string' &&\n    Number.isFinite(start) &&\n    Number.isFinite(end) &&\n    start! < end!\n    ? { refName, start: start!, end: end! }\n    : undefined\n}\n\nexport function floorOf(value: unknown): FloorBp {\n  const n = Number(value)\n  return value !== 'auto' && Number.isFinite(n) ? n : 'auto'\n}\n\nconst n = (x: number) => x.toLocaleString('en-US')\n\n// 1-based and closed, as a locus box reads\nexport const pinnedLocus = ({ refName, start, end }: Pinned) =>\n  `${refName}:${n(start + 1)}-${n(end)}`\n\n// Names the window in each warning toast, so a re-pin or floor change can take\n// the old ones down\nexport const warningPrefix = (pinned: Pinned) =>\n  `Forms of ${pinnedLocus(pinned)}: `\n", "import {\n  NO_CALL_STATE,\n  RARER_STATE,\n  REFERENCE_STATE,\n  formStateAt,\n  formTag,\n  markTag,\n} from '@jbrowse/graph-walks'\n\nimport type { Mark, MarkKind, StructuralForms } from '@jbrowse/graph-walks'\n\nexport const CONSEQUENCES = [\n  'loss',\n  'gain',\n  'shift',\n  'inversion',\n  'net',\n] as const\n\nexport type Consequence = (typeof CONSEQUENCES)[number]\n\n// `svType` in core's vocabulary (UNIVERSAL_FIELD_PRESETS) and `type` as a\n// Sequence Ontology term, which VcfFeature gives `<DUP:TANDEM>` too\nconst KINDS: Record<\n  MarkKind,\n  { svType: string; type: string; alt: string; consequence?: Consequence }\n> = {\n  deletion: { svType: 'DEL', type: 'deletion', alt: '<DEL>' },\n  insertion: { svType: 'INS', type: 'insertion', alt: '<INS>' },\n  duplication: {\n    svType: 'DUP',\n    type: 'tandem_duplication',\n    alt: '<DUP:TANDEM>',\n  },\n  replacement: { svType: 'CPX', type: 'complex_substitution', alt: '<CPX>' },\n  inversion: {\n    svType: 'INV',\n    type: 'inversion',\n    alt: '<INV>',\n    consequence: 'inversion',\n  },\n  shift: {\n    svType: 'CPX',\n    type: 'complex_structural_alteration',\n    alt: '<CPX>',\n    consequence: 'shift',\n  },\n  net: {\n    svType: 'CPX',\n    type: 'complex_structural_alteration',\n    alt: '<CPX>',\n    consequence: 'net',\n  },\n}\n\n// A lopsided replacement colours by the side graph-walks names, which its net\n// sign agrees with; any other change by its net sign\nconst sideOf = (m: Mark) =>\n  m.lopsided ?? (m.delta < 0 ? 'deletion' : 'insertion')\n\nconst consequenceOf = (m: Mark): Consequence =>\n  KINDS[m.kind].consequence ?? (sideOf(m) === 'deletion' ? 'loss' : 'gain')\n\nexport const formName = (i: number) => `F${i + 1}`\n\nexport const OTHER_FORMS = 'other'\n\nexport const DEFAULT_MAX_FORMS = 8\n\nfunction percent(n: number, of: number) {\n  const p = (100 * n) / of\n  return p > 0 && p < 1 ? '<1%' : `${Math.round(p)}%`\n}\n\n// The forms drawn as rows of their own, largest first; one more than\n// `maxForms` gets its own row rather than an \"other forms\" row\nconst shownCount = ({ forms }: StructuralForms, maxForms: number) =>\n  forms.length > maxForms + 1 ? Math.max(0, maxForms) : forms.length\n\nconst sum = (forms: StructuralForms['forms']) =>\n  forms.reduce((n, f) => n + f.members.length, 0)\n\n/**\n * One row per form, largest first, labelled \"66% \u00B7 del 18.4kb\". Past\n * `maxForms` the rest share one empty \"other forms\" row. A row's `forms`\n * counts the forms it holds, so the rows sum to the window's forms.\n */\nexport function formSources(\n  result: StructuralForms,\n  maxForms = DEFAULT_MAX_FORMS,\n) {\n  const shown = shownCount(result, maxForms)\n  const rest = result.forms.slice(shown)\n  return [\n    ...result.forms.slice(0, shown).map((f, i) => ({\n      name: formName(i),\n      label: `${percent(f.members.length, result.placed)} \u00B7 ${formTag(f, result)}`,\n      haplotypes: f.members.length,\n      forms: 1,\n    })),\n    ...(rest.length > 0\n      ? [\n          {\n            name: OTHER_FORMS,\n            label: `other forms \u00B7 ${percent(sum(rest), result.placed)}`,\n            haplotypes: sum(rest),\n            forms: rest.length,\n          },\n        ]\n      : []),\n  ]\n}\n\nconst LISTED_NAMES = 5\n\nfunction names(haplotypes: string[]) {\n  const listed = haplotypes.slice(0, LISTED_NAMES).join(', ')\n  const more = haplotypes.length - LISTED_NAMES\n  return more > 0 ? `${listed} and ${more} more` : listed\n}\n\nconst haplotypeCount = (n: number) => `${n} haplotype${n === 1 ? '' : 's'}`\n\nexport function formWarnings(\n  result: StructuralForms,\n  maxForms = DEFAULT_MAX_FORMS,\n) {\n  const { abridged, unplaced, forms } = result\n  const shown = shownCount(result, maxForms)\n  const rest = forms.slice(shown)\n  return [\n    ...(rest.length > 0\n      ? [\n          `${rest.length} smaller forms, ${haplotypeCount(sum(rest))}, share the empty \"other forms\" row; maxForms sets how many forms get a row of their own`,\n        ]\n      : []),\n    ...(abridged.length > 0\n      ? [\n          `${haplotypeCount(abridged.length)} kept an abridged walk past the forms cut's step budget, which shows as a net change over its span: ${names(abridged)}`,\n        ]\n      : []),\n    ...(unplaced.length > 0\n      ? [\n          `${haplotypeCount(unplaced.length)} ${unplaced.length === 1 ? 'has' : 'have'} no walk over the pinned window, so no form: ${names(unplaced)}`,\n        ]\n      : []),\n  ]\n}\n\n// Genotype `0` in every form with a row of its own\nexport function referenceGenotypes(\n  result: StructuralForms,\n  maxForms = DEFAULT_MAX_FORMS,\n): Record<string, string> {\n  return Object.fromEntries(\n    result.forms\n      .slice(0, shownCount(result, maxForms))\n      .map((_, j) => [formName(j), '0']),\n  )\n}\n\nexport interface FormVariant {\n  id: string\n  start: number\n  end: number\n  name: string\n  description: string\n  type: string\n  svType: string\n  consequence: Consequence\n  alt: string\n  mark: Mark\n  genotypes: Record<string, string>\n}\n\n// A duplication draws over the stretch it copies rather than its zero-width\n// junction, as a VCF `<DUP>` spans its copy\nfunction drawnSpan({ copied, refStart, refEnd }: Mark) {\n  const [start, end] = copied ?? 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+  "names": ["pinnedOf", "value", "refName", "start", "end", "floorOf", "n", "x", "pinnedLocus", "warningPrefix", "pinned", "KINDS", "sideOf", "m", "consequenceOf", "formName", "i", "OTHER_FORMS", "DEFAULT_MAX_FORMS", "percent", "n", "of", "p", "shownCount", "forms", "maxForms", "sum", "f", "formSources", "result", "shown", "rest", "formTag", "LISTED_NAMES", "names", "haplotypes", "listed", "more", "haplotypeCount", "formWarnings", "abridged", "unplaced", "referenceGenotypes", "_", "j", "drawnSpan", "copied", "refStart", "refEnd", "start", "end", "genotypeOf", "formState", "state", "NO_CALL_STATE", "RARER_STATE", "formVariants", "sites", "placed", "site", "s", "REFERENCE_STATE", "states", "formStateAt", "genotypes", "carriers", "mark", "k", "markTag"]
+}

package/dist/chunks/{chunk-SFYSQ52W.js → chunk-OJWBLPPH.js}

@@ -1,2 +1,2 @@
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-//# sourceMappingURL=chunk-SFYSQ52W.js.map
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+//# sourceMappingURL=chunk-OJWBLPPH.js.map

package/dist/chunks/{chunk-JSRGX4TC.js → chunk-P3FBI5ML.js}

@@ -1,2 +1,2 @@
 function o(t){return t===void 0||t==="*"?void 0:t}function s(t){let e=t.split("	");return{refName:e[0],start:+e[1],end:+e[2],segmentCount:+e[3],pathCount:+e[4],inversion:e[5]==="1",shortestAlleleLength:+e[6],longestAlleleLength:+e[7],segments:e[11],shortestAllele:o(e[12]),longestAllele:o(e[13])}}function u(t,e){return t.key!==void 0||e.key!==void 0?t.key===e.key:t.refName===e.refName&&t.start===e.start&&t.end===e.end}function i(t){return t.key??`${t.refName}:${t.start}-${t.end}`}function b(t){let{shortestAlleleLength:e,longestAlleleLength:n}=t;return e===n?`${n.toLocaleString()} bp`:`${e.toLocaleString()}-${n.toLocaleString()} bp`}var r=2147483647;function a(t){let{pathCount:e,segmentCount:n,inversion:l}=t;return[`${n} segments`,e===r?"more paths than gfatools counts":`up to ${e.toLocaleString()} paths`,...l?["inversion"]:[]].join(", ")}export{s as a,u as b,i as c,b as d,r as e,a as f};
-//# sourceMappingURL=chunk-JSRGX4TC.js.map
+//# sourceMappingURL=chunk-P3FBI5ML.js.map

package/dist/chunks/{chunk-JSRGX4TC.js.map → chunk-P3FBI5ML.js.map}

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 {
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+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.9.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-FX4RDMDN.js"],
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package/dist/chunks/chunk-QV7SSOMJ.js

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+import{l as o}from"./chunk-G53BI7VK.js";function u(a,r,e){return e?{...a,walkRowRuns:o(a,r)}:a}export{u as a};
+//# sourceMappingURL=chunk-QV7SSOMJ.js.map

package/dist/chunks/chunk-S333HOG5.js

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