jbrowse-plugin-graphgenomeviewer 6.1.2 → 6.1.3

package/dist/chunks/chunk-5AOGDAVJ.js

@@ -0,0 +1,2 @@
+import{N as u,T as w,W as S,ca as k,fa as D}from"./chunk-SZTJRDEL.js";import{a as y,b as A,c as N,d as R}from"./chunk-TYJTJGPO.js";import{b as c}from"./chunk-FY3BTKY4.js";var m=[{value:0,label:"Fastest"},{value:1,label:"Fast"},{value:2,label:"Default"},{value:3,label:"Fine"},{value:4,label:"Best"}];var L=c(A(),1),o=c(R(),1),b=c(N(),1),G=c(D(),1),e=c(y(),1),C=(0,G.makeStyles)()({section:{marginBottom:24},formControl:{minWidth:200}});function s({warn:l=!1,children:n}){return(0,e.jsx)(o.Typography,{variant:"caption",color:l?"warning.main":"text.secondary",children:n})}var T=(0,b.observer)(function({model:n}){return n.hasGraph&&!n.usesLayoutEngine?(0,e.jsx)(s,{warn:!0,children:"No effect on this layout: only the force-directed layout is drawn by the engine that reads this."}):null});function g({label:l,checked:n,onChange:t,children:p}){let{classes:i}=C();return(0,e.jsxs)("div",{className:i.section,children:[(0,e.jsx)(o.FormControlLabel,{control:(0,e.jsx)(o.Switch,{checked:n,onChange:d=>{t(d.target.checked)}}),label:l}),p]})}function h({label:l,value:n,options:t,testId:p,sx:i,onChange:d}){let{classes:r}=C();return(0,e.jsxs)(o.FormControl,{className:r.formControl,sx:i,children:[(0,e.jsx)(o.InputLabel,{children:l}),(0,e.jsx)(o.Select,{value:n,label:l,"data-testid":p,onChange:a=>{d(a.target.value)},children:t.map(({value:a,label:v,description:f})=>(0,e.jsx)(o.MenuItem,{value:a,children:f?(0,e.jsx)(o.Tooltip,{title:f,placement:"right",children:(0,e.jsx)("span",{children:v})}):v},a))})]})}var I=l=>l.map(({trackId:n,name:t})=>({value:n,label:t})),P=(0,b.observer)(function(n){let{model:t,open:p,onClose:i,children:d}=n,{classes:r}=C();return(0,e.jsxs)(L.Dialog,{open:p,onClose:i,title:"Graph settings",children:[(0,e.jsxs)(o.DialogContent,{children:[(0,e.jsx)("div",{className:r.section,children:(0,e.jsxs)(o.FormControl,{fullWidth:!0,children:[(0,e.jsx)(o.FormLabel,{component:"legend",children:"Layout quality"}),(0,e.jsx)(o.RadioGroup,{value:t.layoutQuality,onChange:a=>{t.setLayoutQuality(parseInt(a.target.value)),t.recomputeLayout()},children:m.map(a=>(0,e.jsx)(o.FormControlLabel,{value:a.value,control:(0,e.jsx)(o.Radio,{}),label:a.label},a.value))}),(0,e.jsx)(s,{children:"FMMM's iteration budget, the same scale Bandage exposes. 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+//# sourceMappingURL=chunk-5AOGDAVJ.js.map

package/dist/chunks/chunk-5AOGDAVJ.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@7.3.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-K5SIJGAE.js", "../../src/GraphGenomeView/components/GraphSettingsDialog.tsx"],
+  "sourcesContent": ["// src/layoutQualities.ts\nvar LAYOUT_QUALITIES = [\n  { value: 0, label: \"Fastest\" },\n  { value: 1, label: \"Fast\" },\n  { value: 2, label: \"Default\" },\n  { value: 3, label: \"Fine\" },\n  { value: 4, label: \"Best\" }\n];\n\nexport {\n  LAYOUT_QUALITIES\n};\n", "import type { ReactNode } from 'react'\n\nimport { BUBBLE_SPREADS } from '@jbrowse/bandage-core/bubbleSpreads'\nimport { COLOR_SCHEMES } from '@jbrowse/bandage-core/colorSchemes'\nimport { LAYOUT_QUALITIES } from '@jbrowse/bandage-core/layoutQualities'\nimport { NODE_WIDTHS } from '@jbrowse/bandage-core/nodeWidths'\nimport { MAX_PATH_COLORS } from '@jbrowse/bandage-core/pathColors'\nimport { Dialog } from '@jbrowse/core/ui'\nimport {\n  Button,\n  DialogActions,\n  DialogContent,\n  FormControl,\n  FormControlLabel,\n  FormLabel,\n  InputLabel,\n  MenuItem,\n  Radio,\n  RadioGroup,\n  Select,\n  Switch,\n  Tooltip,\n  Typography,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport type { GraphPaneModel } from '../model'\nimport type { SxProps } from '@mui/material'\n\nconst useStyles = makeStyles()({\n  section: {\n    marginBottom: 24,\n  },\n  formControl: {\n    minWidth: 200,\n  },\n})\n\nfunction Caption({\n  warn = false,\n  children,\n}: {\n  warn?: boolean\n  children: ReactNode\n}) {\n  return (\n    <Typography\n      variant=\"caption\"\n      color={warn ? 'warning.main' : 'text.secondary'}\n    >\n      {children}\n    </Typography>\n  )\n}\n\n// Layout quality and bubble spread are the engine's inputs, and an anchored\n// layout places a node from its coordinates without reaching it. Left enabled\n// so the force layout can be set up before switching to it.\nconst EngineOnly = observer(function EngineOnly({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  return model.hasGraph && !model.usesLayoutEngine ? (\n    <Caption warn>\n      No effect on this layout: only the force-directed layout is drawn by the\n      engine that reads this.\n    </Caption>\n  ) : null\n})\n\nfunction SettingSwitch({\n  label,\n  checked,\n  onChange,\n  children,\n}: {\n  label: string\n  checked: boolean\n  onChange: (checked: boolean) => void\n  children?: ReactNode\n}) {\n  const { classes } = useStyles()\n  return (\n    <div className={classes.section}>\n      <FormControlLabel\n        control={\n          <Switch\n            checked={checked}\n            onChange={e => {\n              onChange(e.target.checked)\n            }}\n          />\n        }\n        label={label}\n      />\n      {children}\n    </div>\n  )\n}\n\n// One dropdown setting; an option's description is its tooltip\nfunction SettingSelect<T extends string>({\n  label,\n  value,\n  options,\n  testId,\n  sx,\n  onChange,\n}: {\n  label: string\n  value: T\n  options: readonly { value: T; label: string; description?: string }[]\n  testId?: string\n  sx?: SxProps\n  onChange: (value: T) => void\n}) {\n  const { classes } = useStyles()\n  return (\n    <FormControl className={classes.formControl} sx={sx}>\n      <InputLabel>{label}</InputLabel>\n      <Select\n        value={value}\n        label={label}\n        data-testid={testId}\n        onChange={e => {\n          onChange(e.target.value as T)\n        }}\n      >\n        {options.map(({ value, label, description }) => (\n          <MenuItem key={value} value={value}>\n            {description ? (\n              <Tooltip title={description} placement=\"right\">\n                <span>{label}</span>\n              </Tooltip>\n            ) : (\n              label\n            )}\n          </MenuItem>\n        ))}\n      </Select>\n    </FormControl>\n  )\n}\n\nconst trackOptions = (tracks: { trackId: string; name: string }[]) =>\n  tracks.map(({ trackId, name }) => ({ value: trackId, label: name }))\n\n// `children` is the host's own section, between node width and colour\nconst GraphSettingsDialog = observer(function GraphSettingsDialog(props: {\n  model: GraphPaneModel\n  open: boolean\n  onClose: () => void\n  children?: ReactNode\n}) {\n  const { model, open, onClose, children } = props\n  const { classes } = useStyles()\n\n  return (\n    <Dialog open={open} onClose={onClose} title=\"Graph settings\">\n      <DialogContent>\n        <div className={classes.section}>\n          <FormControl fullWidth>\n            <FormLabel component=\"legend\">Layout quality</FormLabel>\n            <RadioGroup\n              value={model.layoutQuality}\n              onChange={e => {\n                model.setLayoutQuality(parseInt(e.target.value))\n                void model.recomputeLayout()\n              }}\n            >\n              {LAYOUT_QUALITIES.map(q => (\n                <FormControlLabel\n                  key={q.value}\n                  value={q.value}\n                  control={<Radio />}\n                  label={q.label}\n                />\n              ))}\n            </RadioGroup>\n            <Caption>\n              FMMM&apos;s iteration budget, the same scale Bandage exposes.\n              Higher is slower: on a thousand-node cut the top setting is\n              seconds rather than tenths.\n            </Caption>\n            <EngineOnly model={model} />\n          </FormControl>\n        </div>\n\n        <SettingSwitch\n          label=\"Draw paths\"\n          checked={model.drawPaths}\n          onChange={draw => {\n            model.setDrawPaths(draw)\n          }}\n        >\n          <Caption>\n            Color each node and connector by the paths through it, one lane per\n            path in legend order, so a path that skips a node leaves its lane\n            empty\n          </Caption>\n          {model.drawPaths && !model.effectiveDrawPaths ? (\n            <Caption warn>\n              {model.pathCount > MAX_PATH_COLORS\n                ? `Off: ${model.pathCount.toLocaleString()} paths is past the ${MAX_PATH_COLORS} this can tell apart`\n                : 'Off: this graph states no paths'}\n            </Caption>\n          ) : null}\n        </SettingSwitch>\n\n        <SettingSwitch\n          label=\"Mark bubbles\"\n          checked={model.showBubbles}\n          onChange={show => {\n            model.setShowBubbles(show)\n          }}\n        >\n          <Caption>\n            A halo along the nodes of each bubble, labelled by what it is, with\n            the label opening the bubble on its own\n          </Caption>\n        </SettingSwitch>\n\n        <SettingSwitch\n          label=\"Genes on the backbone\"\n          checked={model.showGenes}\n          onChange={show => {\n            model.setShowGenes(show)\n          }}\n        >\n          <Caption>\n            Exons along the reference nodes that carry them and each gene's name\n            at its midpoint, from the assembly's annotation track\n          </Caption>\n          {model.geneTrackChoices.length > 1 ? (\n            <SettingSelect\n              label=\"Gene track\"\n              value={model.geneTrack?.trackId ?? ''}\n              options={trackOptions(model.geneTrackChoices)}\n              testId=\"graph-gene-track-select\"\n              sx={{ mt: 1 }}\n              onChange={trackId => {\n                model.setGeneTrackId(trackId)\n                void model.reloadGenes()\n              }}\n            />\n          ) : null}\n          {model.repeatTrackChoices.length > 1 ? (\n            <SettingSelect\n              label=\"Repeat track\"\n              value={model.repeatTrack?.trackId ?? ''}\n              options={trackOptions(model.repeatTrackChoices)}\n              testId=\"graph-repeat-track-select\"\n              sx={{ mt: 1 }}\n              onChange={trackId => {\n                model.setRepeatTrackId(trackId)\n                void model.reloadRepeats()\n              }}\n            />\n          ) : null}\n        </SettingSwitch>\n\n        {model.anchorPaths.length > 1 ? (\n          <div className={classes.section}>\n            <SettingSelect\n              label=\"Reference path\"\n              value={model.activeReferencePath ?? ''}\n              options={model.anchorPaths.map(({ name }) => ({\n                value: name,\n                label: name,\n              }))}\n              testId=\"graph-reference-path-select\"\n              onChange={name => {\n                model.setReferencePath(name)\n                void model.recomputeLayout()\n              }}\n            />\n            <Caption>\n              Which path the anchored layouts draw x against. A GFA with no rGFA\n              tags states its coordinates only in its paths, and marks none of\n              them as the reference.\n            </Caption>\n          </div>\n        ) : null}\n\n        <div className={classes.section}>\n          <SettingSelect\n            label=\"Bubble spread\"\n            value={model.bubbleSpread}\n            options={BUBBLE_SPREADS}\n            testId=\"graph-bubble-spread-select\"\n            onChange={spread => {\n              model.setBubbleSpread(spread)\n              void model.recomputeLayout()\n            }}\n          />\n          <Caption>\n            How far the force layout opens a bubble. A pangenome allele is a few\n            bp, so at Bandage&apos;s own scale both arms land inside one node\n            thickness and the graph draws as a rope.\n          </Caption>\n          <EngineOnly model={model} />\n        </div>\n\n        <div className={classes.section}>\n          <SettingSelect\n            label=\"Node width\"\n            value={model.nodeWidth}\n            options={NODE_WIDTHS}\n            testId=\"graph-node-width-select\"\n            onChange={width => {\n              model.setNodeWidth(width)\n            }}\n          />\n          <Caption>\n            Bandage&apos;s depth as width. 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+}

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+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@7.3.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-WSIFAZU7.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@7.3.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-RAKOB6IV.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@7.3.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-LTUWJKHD.js"],
   "sourcesContent": ["// src/gbzJoin.ts\nvar UNKNOWN_SAMPLE = \"unknown\";\nfunction parseWalk(line) {\n  const fields = line.split(\"\t\");\n  return {\n    fields,\n    name: fields.slice(1, 4).join(\"\t\"),\n    start: +fields[4],\n    end: +fields[5]\n  };\n}\nvar stepsOf = (walk) => walk.fields[6].match(/[<>][^<>]+/g) ?? [];\nfunction segmentLengths(lines) {\n  const lengths = /* @__PURE__ */ new Map();\n  for (const line of lines) {\n    if (line.startsWith(\"S\t\")) {\n      const [, id, sequence, ...tags] = line.split(\"\t\");\n      const ln = tags.find((tag) => tag.startsWith(\"LN:i:\"));\n      lengths.set(\n        id,\n        sequence === \"*\" && ln ? +ln.slice(\"LN:i:\".length) : sequence.length\n      );\n    }\n  }\n  return lengths;\n}\nfunction extend(a, b, lengths) {\n  if (b.end <= a.end) {\n    return a;\n  }\n  const steps = stepsOf(b);\n  let pos = b.start;\n  for (const [i, step] of steps.entries()) {\n    if (pos === a.end) {\n      const fields = [...a.fields];\n      fields[5] = String(b.end);\n      fields[6] = a.fields[6] + steps.slice(i).join(\"\");\n      return { ...a, fields, end: b.end };\n    }\n    const length = lengths.get(step.slice(1));\n    if (pos > a.end || length === void 0) {\n      return void 0;\n    }\n    pos += length;\n  }\n  return void 0;\n}\nfunction joinPieces(pieces, lengths, startsPath) {\n  const joined = [];\n  for (const piece of pieces.sort((a, b) => a.start - b.start)) {\n    const last = joined.at(-1);\n    const [, sample, haplotype, contig] = piece.fields;\n    const joins = last !== void 0 && (piece.start < last.end || piece.start === last.end && !startsPath(sample, +haplotype, contig, piece.start));\n    const extended = joins ? extend(last, piece, lengths) : void 0;\n    if (extended) {\n      joined[joined.length - 1] = extended;\n    } else {\n      joined.push(piece);\n    }\n  }\n  return joined;\n}\nvar flip = (sign) => sign === \"+\" ? \"-\" : \"+\";\nfunction* stepLinks(walk) {\n  const steps = stepsOf(walk).map((step) => ({\n    id: step.slice(1),\n    sign: step.startsWith(\">\") ? \"+\" : \"-\"\n  }));\n  for (let i = 1; i < steps.length; i++) {\n    const a = steps[i - 1];\n    const b = steps[i];\n    yield {\n      forward: `L\t${a.id}\t${a.sign}\t${b.id}\t${b.sign}\t0M`,\n      reverse: `L\t${b.id}\t${flip(b.sign)}\t${a.id}\t${flip(a.sign)}\t0M`\n    };\n  }\n}\nfunction joinCuts(gfas, startsPath) {\n  if (gfas.length <= 1) {\n    return gfas[0] ?? \"\";\n  }\n  const cuts = gfas.map((gfa) => gfa.split(\"\\n\").filter((line) => line !== \"\"));\n  const ofType = (cut, type) => cut.filter((line) => line.startsWith(`${type}\t`));\n  const lengths = segmentLengths(cuts.flat());\n  let unknownOffset = 0;\n  const walksByCut = cuts.map((cut) => {\n    const walks2 = ofType(cut, \"W\").map(parseWalk);\n    const offset = unknownOffset;\n    for (const walk of walks2.filter((w) => w.fields[1] === UNKNOWN_SAMPLE)) {\n      const haplotype = +walk.fields[2] + offset;\n      walk.fields[2] = String(haplotype);\n      walk.name = walk.fields.slice(1, 4).join(\"\t\");\n      unknownOffset = Math.max(unknownOffset, haplotype);\n    }\n    return walks2;\n  });\n  const byName = /* @__PURE__ */ new Map();\n  for (const walk of [\n    ...walksByCut.flatMap((walks2) => walks2.slice(0, 1)),\n    ...walksByCut.flatMap((walks2) => walks2.slice(1))\n  ]) {\n    const pieces = byName.get(walk.name);\n    if (pieces) {\n      pieces.push(walk);\n    } else {\n      byName.set(walk.name, [walk]);\n    }\n  }\n  const walks = [...byName.values()].flatMap(\n    (pieces) => joinPieces(pieces, lengths, startsPath)\n  );\n  const links = new Set(cuts.flatMap((cut) => ofType(cut, \"L\")));\n  for (const walk of walks) {\n    for (const link of stepLinks(walk)) {\n      if (!links.has(link.forward) && !links.has(link.reverse)) {\n        links.add(link.forward);\n      }\n    }\n  }\n  const lines = /* @__PURE__ */ new Set([\n    ...ofType(cuts[0], \"H\"),\n    ...cuts.flatMap((cut) => ofType(cut, \"S\")),\n    ...links,\n    ...walks.map((walk) => walk.fields.join(\"\t\"))\n  ]);\n  return `${[...lines].join(\"\\n\")}\n`;\n}\n\nexport {\n  joinCuts\n};\n", "import {\n  isGenericSample,\n  panSNContig,\n  panSNHaplotype,\n  panSNSample\n} from \"./chunk-BPLIXMH7.js\";\nimport {\n  isBackbone\n} from \"./chunk-FYQWPEEY.js\";\n\n// src/reference.ts\nvar WELL_KNOWN_SAMPLES = /* @__PURE__ */ new Map([\n  [\"hg38\", \"GRCh38\"],\n  [\"hg19\", \"GRCh37\"],\n  [\"hs1\", \"CHM13\"],\n  [\"t2t-chm13\", \"CHM13\"],\n  [\"chm13v2\", \"CHM13\"]\n]);\nfunction wellKnownSample(assemblyName) {\n  return WELL_KNOWN_SAMPLES.get(assemblyName.toLowerCase());\n}\nfunction sampleOf(refName) {\n  const sample = refName.includes(\"#\") ? panSNSample(refName) : void 0;\n  return sample === void 0 || isGenericSample(sample) ? void 0 : sample;\n}\nfunction haplotypeOf(refName) {\n  return panSNHaplotype(refName) ?? panSNSample(refName);\n}\nfunction graphHaplotypes(graph) {\n  const refNames = new Set((graph.anchorPaths ?? []).map((p) => p.name));\n  for (const node of graph.nodes) {\n    if (node.stable) {\n      refNames.add(node.stable.refName);\n    }\n  }\n  const bySample = /* @__PURE__ */ new Map();\n  for (const refName of refNames) {\n    const sample = sampleOf(refName);\n    if (sample !== void 0) {\n      const haplotypes = bySample.get(sample) ?? bySample.set(sample, /* @__PURE__ */ new Set()).get(sample);\n      haplotypes.add(haplotypeOf(refName));\n    }\n  }\n  return bySample;\n}\nfunction backboneFrom(contigs, haplotypes) {\n  const samples = new Set(contigs.map((c) => sampleOf(c.refName)));\n  const [sample] = samples;\n  if (samples.size !== 1 || sample === void 0) {\n    return { contigs, prefixes: [], named: false };\n  }\n  const own = new Set(contigs.map((c) => haplotypeOf(c.refName)));\n  const unique = [...haplotypes.get(sample) ?? []].every((h) => own.has(h));\n  const shared = new Set(contigs.map((c) => panSNHaplotype(c.refName)));\n  const [haplotype] = shared;\n  return {\n    contigs,\n    prefixes: [\n      ...unique ? [sample] : [],\n      ...shared.size === 1 && haplotype ? [haplotype] : []\n    ],\n    named: true\n  };\n}\nfunction graphBackbone(graph) {\n  const spans = /* @__PURE__ */ new Map();\n  for (const node of graph.nodes) {\n    if (isBackbone(node)) {\n      const { refName, start } = node.stable;\n      const end = start + node.length;\n      const span = spans.get(refName);\n      if (span) {\n        span.start = Math.min(span.start, start);\n        span.end = Math.max(span.end, end);\n      } else {\n        spans.set(refName, {\n          refName,\n          contig: panSNContig(refName),\n          start,\n          end\n        });\n      }\n    }\n  }\n  const contigs = [...spans.values()];\n  return contigs.length ? backboneFrom(contigs, graphHaplotypes(graph)) : void 0;\n}\nfunction referenceLabel(graph, region) {\n  const backbone = graphBackbone(graph);\n  const contig = region ? panSNContig(region.refName) : backbone?.contigs.length === 1 ? backbone.contigs[0].contig : void 0;\n  const sample = backbone?.named ? panSNSample(backbone.contigs[0].refName) : void 0;\n  return contig && (sample ? `${sample} ${contig}` : contig);\n}\nfunction backboneAssembly(backbone, assemblies) {\n  const names = (a) => [a.name, ...a.aliases ?? []];\n  const naming = (prefix) => (a) => names(a).some((n) => n.toLowerCase() === prefix.toLowerCase());\n  const prefixes = [...backbone?.prefixes ?? []].reverse();\n  const sample = backbone?.prefixes.find((p) => !p.includes(\"#\"))?.toLowerCase();\n  for (const prefix of prefixes) {\n    const assembly = assemblies.find(naming(prefix));\n    if (assembly) {\n      return assembly;\n    }\n  }\n  return sample === void 0 ? void 0 : assemblies.find(\n    (a) => names(a).some((n) => wellKnownSample(n)?.toLowerCase() === sample)\n  );\n}\nfunction assemblyWalk(graph, assembly) {\n  const haplotypes = graphHaplotypes(graph);\n  return graph.anchorPaths?.find(\n    (walk) => backboneAssembly(\n      backboneFrom(\n        [\n          {\n            refName: walk.name,\n            contig: panSNContig(walk.name),\n            start: walk.start,\n            end: walk.start + walk.length\n          }\n        ],\n        haplotypes\n      ),\n      [assembly]\n    )\n  );\n}\nfunction contigNames(contig) {\n  const bare = contig.replace(/^chr/i, \"\");\n  const forms = !bare ? [] : /^(M|MT)$/i.test(bare) ? [\"M\", \"MT\"] : [bare];\n  return [.../* @__PURE__ */ new Set([contig, ...forms.flatMap((f) => [f, `chr${f}`])])];\n}\nfunction refNameBinding(refNames, aliases = {}) {\n  const exact = new Set(refNames);\n  const byName = /* @__PURE__ */ new Map();\n  for (const refName of exact) {\n    const contig = panSNContig(refName);\n    const alias = aliases[contig];\n    for (const name of /* @__PURE__ */ new Set([\n      ...contigNames(contig),\n      ...alias ? [alias] : []\n    ])) {\n      byName.set(name, byName.has(name) ? void 0 : refName);\n    }\n  }\n  return (name) => exact.has(name) ? name : byName.get(name);\n}\nfunction featuresOnBackbone(features, backbone, aliases) {\n  const bind = refNameBinding(\n    backbone.contigs.map((c) => c.refName),\n    aliases\n  );\n  return features.flatMap((f) => {\n    const refName = bind(f.refName);\n    return refName === void 0 ? [] : [refName === f.refName ? f : { ...f, refName }];\n  });\n}\n\nexport {\n  WELL_KNOWN_SAMPLES,\n  wellKnownSample,\n  graphBackbone,\n  referenceLabel,\n  backboneAssembly,\n  assemblyWalk,\n  contigNames,\n  refNameBinding,\n  featuresOnBackbone\n};\n", "import {\n  joinCuts\n} from \"./chunk-WSIFAZU7.js\";\nimport {\n  wellKnownSample\n} from \"./chunk-RAKOB6IV.js\";\nimport {\n  panSNMatchesPrefix,\n  panSNSample\n} from \"./chunk-BPLIXMH7.js\";\n\n// src/gbzWindow.ts\nvar NoReferenceSampleError = class extends Error {\n  constructor(anchor, referenceSamples) {\n    super(\n      referenceSamples.length === 0 ? `the graph names no reference sample (gbwt_reference_samples) and the anchor \"${anchor}\" maps to none; set referenceSample` : `the anchor \"${anchor}\" is none of the graph's reference samples (${referenceSamples.join(\", \")}); set referenceSample or map it through assemblyNameToPanSN`\n    );\n    this.name = \"NoReferenceSampleError\";\n  }\n};\nvar NodeLimitError = class extends Error {\n  constructor(limit, windowBp, fitsBp) {\n    super(\n      `this ${windowBp.toLocaleString()} bp window reads more than nodeLimit (${limit.toLocaleString()}) graph nodes; zoom in to about ${fitsBp.toLocaleString()} bp or raise nodeLimit`\n    );\n    this.fitsBp = fitsBp;\n    this.name = \"NodeLimitError\";\n    this.regionTooLarge = true;\n  }\n};\nfunction haplotypePrefix(name) {\n  return `${name.sample}#${name.haplotype}`;\n}\nfunction haplotypeWanted(name, wanted) {\n  const prefix = haplotypePrefix(name);\n  return wanted === void 0 || wanted.some((candidate) => panSNMatchesPrefix(prefix, candidate));\n}\nasync function referenceSamplesOf(db) {\n  return (await db.tag(\"gbwt_reference_samples\") ?? \"\").split(/\\s+/).filter((sample) => sample !== \"\");\n}\nfunction aliasedSample(anchorSample, referenceSamples) {\n  const lower = anchorSample.toLowerCase();\n  const alias = wellKnownSample(anchorSample)?.toLowerCase();\n  return referenceSamples.find((s) => s === anchorSample) ?? referenceSamples.find((s) => s.toLowerCase() === lower) ?? referenceSamples.find((s) => s.toLowerCase() === alias);\n}\nfunction resolveReferenceSample({\n  configured,\n  anchorPrefix,\n  referenceSamples\n}) {\n  if (configured !== \"\") {\n    return configured;\n  }\n  const sample = aliasedSample(panSNSample(anchorPrefix), referenceSamples) ?? (referenceSamples.length === 1 ? referenceSamples[0] : void 0);\n  if (sample === void 0) {\n    throw new NoReferenceSampleError(anchorPrefix, referenceSamples);\n  }\n  return sample;\n}\nasync function referencePathQuery(db, referenceSample, refName) {\n  const path = (await db.paths()).find(\n    (p) => p.isIndexed && p.name.sample === referenceSample && p.name.contig === refName\n  );\n  return path ? {\n    sample: path.name.sample,\n    contig: refName,\n    haplotype: path.name.haplotype\n  } : void 0;\n}\nfunction nodeLimitError(error, limit, windowBp) {\n  const isLimit = error instanceof Error && (error.name === \"SubgraphLimitError\" || /^Subgraph size limit of \\d+ nodes exceeded/.test(error.message));\n  if (!isLimit) {\n    return void 0;\n  } else {\n    const walked = error.walkedBp;\n    const fits = typeof walked === \"number\" && walked > 0 ? Math.floor(walked * 0.8) : Math.floor(windowBp / 2);\n    return new NodeLimitError(limit, windowBp, Math.max(fits, 1));\n  }\n}\nvar GBZ_CUT_DEFAULTS = {\n  context: 1e3,\n  snarls: \"contained\",\n  limit: 1e5\n};\nasync function cutWindowGFA(db, query, start, end, opts) {\n  if (!query) {\n    return \"\";\n  }\n  const subgraphs = await db.getSubgraphs({ ...opts, path: query, start, end, haplotypes: \"all\" }).catch((error) => {\n    throw nodeLimitError(error, opts.limit, end - start) ?? error;\n  });\n  const paths = await db.paths();\n  return joinCuts(\n    await Promise.all(subgraphs.map((subgraph) => subgraph.toGFA())),\n    (sample, haplotype, contig, at) => paths.some(\n      ({ name }) => name.sample === sample && name.haplotype === haplotype && name.contig === contig && name.fragment === at\n    )\n  );\n}\n\nexport {\n  NoReferenceSampleError,\n  NodeLimitError,\n  haplotypePrefix,\n  haplotypeWanted,\n  referenceSamplesOf,\n  resolveReferenceSample,\n  referencePathQuery,\n  nodeLimitError,\n  GBZ_CUT_DEFAULTS,\n  cutWindowGFA\n};\n"],
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package/dist/chunks/{chunk-U3XWI3ON.js → chunk-EAK4DAP4.js}

@@ -1,3 +1,3 @@
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