jbrowse-plugin-graphgenomeviewer 6.9.2 → 6.10.0

package/dist/chunks/AddTrackWorkflow-OBRE3QJE.js

@@ -0,0 +1,2 @@
+import{a as P,b as N,c as _,f as W}from"./chunk-SS5WD35T.js";import{d as G}from"./chunk-ELLLNUKS.js";import"./chunk-D7FMSRTU.js";import{b as F,j as L,m as T}from"./chunk-TENPGIPX.js";import{g as r}from"./chunk-6OPB7FOJ.js";import{A as E,B as I,E as u,a as S,e as w,f as c,n as R,r as x,s as v,t as M,z as B}from"./chunk-ECD5B2ZM.js";import{b as o,c as b,d as A}from"./chunk-JMBDTNUR.js";var s=JBrowseExports["@jbrowse/core/util/tss-react"],q=t=>s!=null&&t in Object(s)?s[t]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+t+"' from '@jbrowse/core/util/tss-react' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:t});var H=q("makeStyles"),Y=s&&s.__esModule?s.default:s;var K=H()(t=>({paper:{margin:t.spacing(),padding:t.spacing()},field:{marginTop:t.spacing(2)},submit:{marginTop:25,marginBottom:100,display:"block"}})),Q=["RgfaTabixAdapter","GbzBaseSyntenyAdapter","MinigraphBubbleAdapter"],U=A(function({model:a}){let{classes:i}=K(),g=L(a),p=G(a),[n,j]=r("RgfaTabixAdapter"),[l,O]=r(),[f,z]=r(),[y,J]=r(),d=n==="GbzBaseSyntenyAdapter",[k,D]=r(""),[m,V]=r("Pangenome graph"),[C,h]=r();function X(){if(!(!l||!a.assembly))try{h(void 0);let e=m.trim();F({model:a,session:g,conf:W({choice:n,loc:l,indexLoc:f,readsLoc:d?y:void 0,assembly:a.assembly,sample:k,trackId:T({name:e}),name:e})})}catch(e){h(e)}}return b(B,{className:i.paper,children:[C?o(w,{error:C}):null,b(x,{children:[o(M,{children:"File type"}),o(I,{value:n,onChange:e=>{j(e.target.value),h(void 0)},children:Q.map(e=>o(v,{value:e,control:o(E,{}),label:P[e]},e))})]}),o(c,{location:l,name:N[n],rootModel:p,setLocation:O}),o(c,{location:f,name:_[n],rootModel:p,setLocation:z}),d?o(c,{location:y,name:"Path to reads aligned to the graph as GAF (optional; a .gz is read by the .tbi beside it)",rootModel:p,setLocation:J}):null,o(u,{className:i.field,value:k,onChange:e=>{D(e.target.value)},label:"Sample name in the graph",slotProps:{htmlInput:{"data-testid":"graph-sample-input"}},helperText:d?"Optional. The graph's sample for this assembly, e.g. GRCh38 where the assembly is hg38; leave blank when they share a name or the graph has one reference sample":"Optional. The PanSN prefix the graph gives this assembly, e.g. GRCh38 for HPRC's GRCh38#0#chr1; leave blank when the graph's stable names are bare",placeholder:"GRCh38",fullWidth:!0}),o(u,{className:i.field,value:m,helperText:"Track name",slotProps:{htmlInput:{"data-testid":"graph-track-name-input"}},onChange:e=>{V(e.target.value)}}),o(S,{session:g,helperText:"Select assembly to add track to",selected:a.assembly,onChange:e=>{a.setAssembly(e)},fullWidth:!0}),o(R,{variant:"contained",className:i.submit,disabled:!l||!m.trim()||!a.assembly,onClick:X,children:"Submit"})]})}),ie=U;export{ie as default};
+//# sourceMappingURL=AddTrackWorkflow-OBRE3QJE.js.map

package/dist/chunks/AddTrackWorkflow-OBRE3QJE.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["host:@jbrowse/core/util/tss-react", "../../src/GraphAddTrackWorkflow/AddTrackWorkflow.tsx"],
+  "sourcesContent": ["const host = JBrowseExports[\"@jbrowse/core/util/tss-react\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\n            \"This JBrowse does not provide '\" + name + \"' from '\" + \"@jbrowse/core/util/tss-react\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const cx = /* @__PURE__ */ read(\"cx\")\nexport const keyframes = /* @__PURE__ */ read(\"keyframes\")\nexport const makeStyles = /* @__PURE__ */ read(\"makeStyles\")\nexport default host && host.__esModule ? host.default : host", "import { useState } from 'react'\n\nimport { AssemblySelector, ErrorMessage, FileSelector } from '@jbrowse/core/ui'\nimport { addTrackFromWidget, getSession, makeTrackId } from '@jbrowse/core/util'\nimport { makeStyles } from '@jbrowse/core/util/tss-react'\nimport { getRoot } from '@jbrowse/mobx-state-tree'\nimport {\n  Button,\n  FormControl,\n  FormControlLabel,\n  FormLabel,\n  Paper,\n  Radio,\n  RadioGroup,\n  TextField,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport {\n  GRAPH_FILE_FIELDS,\n  GRAPH_FILE_LABELS,\n  GRAPH_INDEX_FIELDS,\n  buildTrackConfig,\n} from './buildTrackConfig'\n\nimport type { GraphFileChoice } from './buildTrackConfig'\nimport type {\n  AbstractRootModel,\n  AddTrackWorkflowModel,\n  FileLocation,\n} from '@jbrowse/core/util'\n\nconst useStyles = makeStyles()(theme => ({\n  paper: {\n    margin: theme.spacing(),\n    padding: theme.spacing(),\n  },\n  field: {\n    marginTop: theme.spacing(2),\n  },\n  submit: {\n    marginTop: 25,\n    marginBottom: 100,\n    display: 'block',\n  },\n}))\n\nconst CHOICES: GraphFileChoice[] = [\n  'RgfaTabixAdapter',\n  'GbzBaseSyntenyAdapter',\n  'MinigraphBubbleAdapter',\n]\n\nconst GraphAddTrackWidget = observer(function GraphAddTrackWidget({\n  model,\n}: {\n  model: AddTrackWorkflowModel\n}) {\n  const { classes } = useStyles()\n  const session = getSession(model)\n  const rootModel = getRoot<AbstractRootModel>(model)\n  const [choice, setChoice] = useState<GraphFileChoice>('RgfaTabixAdapter')\n  const [loc, setLoc] = useState<FileLocation>()\n  const [indexLoc, setIndexLoc] = useState<FileLocation>()\n  const [readsLoc, setReadsLoc] = useState<FileLocation>()\n  const gbz = choice === 'GbzBaseSyntenyAdapter'\n  const [sample, setSample] = useState('')\n  const [trackName, setTrackName] = useState('Pangenome graph')\n  const [error, setError] = useState<unknown>()\n\n  function handleSubmit() {\n    if (!loc || !model.assembly) {\n      return\n    }\n    try {\n      setError(undefined)\n      const name = trackName.trim()\n      addTrackFromWidget({\n        model,\n        session,\n        conf: buildTrackConfig({\n          choice,\n          loc,\n          indexLoc,\n          readsLoc: gbz ? readsLoc : undefined,\n          assembly: model.assembly,\n          sample,\n          trackId: makeTrackId({ name }),\n          name,\n        }),\n      })\n    } catch (e) {\n      setError(e)\n    }\n  }\n\n  return (\n    <Paper className={classes.paper}>\n      {error ? <ErrorMessage error={error} /> : null}\n      <FormControl>\n        <FormLabel>File type</FormLabel>\n        <RadioGroup\n          value={choice}\n          onChange={event => {\n            setChoice(event.target.value as GraphFileChoice)\n            setError(undefined)\n          }}\n        >\n          {CHOICES.map(option => (\n            <FormControlLabel\n              key={option}\n              value={option}\n              control={<Radio />}\n              label={GRAPH_FILE_LABELS[option]}\n            />\n          ))}\n        </RadioGroup>\n      </FormControl>\n      <FileSelector\n        location={loc}\n        name={GRAPH_FILE_FIELDS[choice]}\n        rootModel={rootModel}\n        setLocation={setLoc}\n      />\n      <FileSelector\n        location={indexLoc}\n        name={GRAPH_INDEX_FIELDS[choice]}\n        rootModel={rootModel}\n        setLocation={setIndexLoc}\n      />\n      {gbz ? (\n        <FileSelector\n          location={readsLoc}\n          name=\"Path to reads aligned to the graph as GAF (optional; a .gz is read by the .tbi beside it)\"\n          rootModel={rootModel}\n          setLocation={setReadsLoc}\n        />\n      ) : null}\n      <TextField\n        className={classes.field}\n        value={sample}\n        onChange={event => {\n          setSample(event.target.value)\n        }}\n        label=\"Sample name in the graph\"\n        slotProps={{ htmlInput: { 'data-testid': 'graph-sample-input' } }}\n        helperText={\n          gbz\n            ? \"Optional. The graph's sample for this assembly, e.g. GRCh38 where the assembly is hg38; leave blank when they share a name or the graph has one reference sample\"\n            : \"Optional. The PanSN prefix the graph gives this assembly, e.g. GRCh38 for HPRC's GRCh38#0#chr1; leave blank when the graph's stable names are bare\"\n        }\n        placeholder=\"GRCh38\"\n        fullWidth\n      />\n      <TextField\n        className={classes.field}\n        value={trackName}\n        helperText=\"Track name\"\n        slotProps={{ htmlInput: { 'data-testid': 'graph-track-name-input' } }}\n        onChange={event => {\n          setTrackName(event.target.value)\n        }}\n      />\n      <AssemblySelector\n        session={session}\n        helperText=\"Select assembly to add track to\"\n        selected={model.assembly}\n        onChange={arg => {\n          model.setAssembly(arg)\n        }}\n        fullWidth\n      />\n      <Button\n        variant=\"contained\"\n        className={classes.submit}\n        disabled={!loc || !trackName.trim() || !model.assembly}\n        onClick={handleSubmit}\n      >\n        Submit\n      </Button>\n    </Paper>\n  )\n})\n\nexport default GraphAddTrackWidget\n"],
+  "mappings": "mYAAA,IAAMA,EAAO,eAAe,8BAA8B,EACpDC,EAAOC,GACXF,GAAQ,MAAQE,KAAQ,OAAOF,CAAI,EAC/BA,EAAKE,CAAI,EACT,OAAO,OACL,UAAY,CACV,MAAM,IAAI,MACR,kCAAoCA,EAAO,8IAC7C,CACF,EACA,CAAE,mBAAoBA,CAAK,CAC7B,EAGC,IAAMC,EAA6BC,EAAK,YAAY,EACpDC,EAAQC,GAAQA,EAAK,WAAaA,EAAK,QAAUA,ECiBxD,IAAMC,EAAYC,EAAW,EAAEC,IAAU,CACvC,MAAO,CACL,OAAQA,EAAM,QAAQ,EACtB,QAASA,EAAM,QAAQ,CACzB,EACA,MAAO,CACL,UAAWA,EAAM,QAAQ,CAAC,CAC5B,EACA,OAAQ,CACN,UAAW,GACX,aAAc,IACd,QAAS,OACX,CACF,EAAE,EAEIC,EAA6B,CACjC,mBACA,wBACA,wBACF,EAEMC,EAAsBC,EAAS,SAA6B,CAChE,MAAAC,CACF,EAEG,CACD,GAAM,CAAE,QAAAC,CAAQ,EAAIP,EAAU,EACxBQ,EAAUC,EAAWH,CAAK,EAC1BI,EAAYC,EAA2BL,CAAK,EAC5C,CAACM,EAAQC,CAAS,EAAIC,EAA0B,kBAAkB,EAClE,CAACC,EAAKC,CAAM,EAAIF,EAAuB,EACvC,CAACG,EAAUC,CAAW,EAAIJ,EAAuB,EACjD,CAACK,EAAUC,CAAW,EAAIN,EAAuB,EACjDO,EAAMT,IAAW,wBACjB,CAACU,EAAQC,CAAS,EAAIT,EAAS,EAAE,EACjC,CAACU,EAAWC,CAAY,EAAIX,EAAS,iBAAiB,EACtD,CAACY,EAAOC,CAAQ,EAAIb,EAAkB,EAE5C,SAASc,GAAe,CACtB,GAAI,GAACb,GAAO,CAACT,EAAM,UAGnB,GAAI,CACFqB,EAAS,MAAS,EAClB,IAAME,EAAOL,EAAU,KAAK,EAC5BM,EAAmB,CACjB,MAAAxB,EACA,QAAAE,EACA,KAAMuB,EAAiB,CACrB,OAAAnB,EACA,IAAAG,EACA,SAAAE,EACA,SAAUI,EAAMF,EAAW,OAC3B,SAAUb,EAAM,SAChB,OAAAgB,EACA,QAASU,EAAY,CAAE,KAAAH,CAAK,CAAC,EAC7B,KAAAA,CACF,CAAC,CACH,CAAC,CACH,OAAS,EAAG,CACVF,EAAS,CAAC,CACZ,CACF,CAEA,OACEM,EAACC,EAAA,CAAM,UAAW3B,EAAQ,MACvB,UAAAmB,EAAQS,EAACC,EAAA,CAAa,MAAOV,EAAO,EAAK,KAC1CO,EAACI,EAAA,CACC,UAAAF,EAACG,EAAA,CAAU,qBAAS,EACpBH,EAACI,EAAA,CACC,MAAO3B,EACP,SAAU4B,GAAS,CACjB3B,EAAU2B,EAAM,OAAO,KAAwB,EAC/Cb,EAAS,MAAS,CACpB,EAEC,SAAAxB,EAAQ,IAAIsC,GACXN,EAACO,EAAA,CAEC,MAAOD,EACP,QAASN,EAACQ,EAAA,EAAM,EAChB,MAAOC,EAAkBH,CAAM,GAH1BA,CAIP,CACD,EACH,GACF,EACAN,EAACU,EAAA,CACC,SAAU9B,EACV,KAAM+B,EAAkBlC,CAAM,EAC9B,UAAWF,EACX,YAAaM,EACf,EACAmB,EAACU,EAAA,CACC,SAAU5B,EACV,KAAM8B,EAAmBnC,CAAM,EAC/B,UAAWF,EACX,YAAaQ,EACf,EACCG,EACCc,EAACU,EAAA,CACC,SAAU1B,EACV,KAAK,4FACL,UAAWT,EACX,YAAaU,EACf,EACE,KACJe,EAACa,EAAA,CACC,UAAWzC,EAAQ,MACnB,MAAOe,EACP,SAAUkB,GAAS,CACjBjB,EAAUiB,EAAM,OAAO,KAAK,CAC9B,EACA,MAAM,2BACN,UAAW,CAAE,UAAW,CAAE,cAAe,oBAAqB,CAAE,EAChE,WACEnB,EACI,mKACA,qJAEN,YAAY,SACZ,UAAS,GACX,EACAc,EAACa,EAAA,CACC,UAAWzC,EAAQ,MACnB,MAAOiB,EACP,WAAW,aACX,UAAW,CAAE,UAAW,CAAE,cAAe,wBAAyB,CAAE,EACpE,SAAUgB,GAAS,CACjBf,EAAae,EAAM,OAAO,KAAK,CACjC,EACF,EACAL,EAACc,EAAA,CACC,QAASzC,EACT,WAAW,kCACX,SAAUF,EAAM,SAChB,SAAU4C,GAAO,CACf5C,EAAM,YAAY4C,CAAG,CACvB,EACA,UAAS,GACX,EACAf,EAACgB,EAAA,CACC,QAAQ,YACR,UAAW5C,EAAQ,OACnB,SAAU,CAACQ,GAAO,CAACS,EAAU,KAAK,GAAK,CAAClB,EAAM,SAC9C,QAASsB,EACV,kBAED,GACF,CAEJ,CAAC,EAEMwB,GAAQhD",
+  "names": ["host", "read", "name", "makeStyles", "read", "tss_react_default", "host", "useStyles", "makeStyles", "theme", "CHOICES", "GraphAddTrackWidget", "observer", "model", "classes", "session", "getSession", "rootModel", "getRoot", "choice", "setChoice", "useState", "loc", "setLoc", "indexLoc", "setIndexLoc", "readsLoc", "setReadsLoc", "gbz", "sample", "setSample", "trackName", "setTrackName", "error", "setError", "handleSubmit", "name", "addTrackFromWidget", "buildTrackConfig", "makeTrackId", "jsxs", "Paper", "jsx", "ErrorMessage", "FormControl", "FormLabel", "RadioGroup", "event", "option", "FormControlLabel", "Radio", "GRAPH_FILE_LABELS", "FileSelector", "GRAPH_FILE_FIELDS", "GRAPH_INDEX_FIELDS", "TextField", "AssemblySelector", "arg", "Button", "AddTrackWorkflow_default"]
+}

package/dist/chunks/ChooseSamplesDialog-75F3KRRG.js

@@ -0,0 +1,2 @@
+import{a as i}from"./chunk-5JXGPUTF.js";import"./chunk-6OPB7FOJ.js";import"./chunk-ECD5B2ZM.js";import{b as a,d as s}from"./chunk-JMBDTNUR.js";var t=s(function({model:o,onClose:p}){let{samples:l}=o.walkRowSampleChoices;return a(i,{title:"Choose samples",label:"Samples",testId:"graph-choose-samples",caption:`${l.length.toLocaleString()} samples in this cut. Their walks show in pairs, in the order picked.`,options:l,initial:o.walkRowSamples??[],confirmLabel:e=>e.length>0?"Show these samples":"Show every sample",onPick:e=>{o.setWalkRowSamples(e.length>0?e:void 0)},onClose:p})}),h=t;export{h as default};
+//# sourceMappingURL=ChooseSamplesDialog-75F3KRRG.js.map

package/dist/chunks/{ChooseSamplesDialog-GWMJ7B5D.js.map → ChooseSamplesDialog-75F3KRRG.js.map}

@@ -2,6 +2,6 @@
   "version": 3,
   "sources": ["../../src/GraphGenomeView/components/ChooseSamplesDialog.tsx"],
   "sourcesContent": ["import { observer } from 'mobx-react'\n\nimport PickNamesDialog from './PickNamesDialog'\n\nimport type { GraphPaneModel } from '../model'\n\ntype SamplePicker = Pick<\n  GraphPaneModel,\n  'walkRowSampleChoices' | 'walkRowSamples' | 'setWalkRowSamples'\n>\n\n// Which samples' walks walk rows show\nconst ChooseSamplesDialog = observer(function ChooseSamplesDialog({\n  model,\n  onClose,\n}: {\n  model: SamplePicker\n  onClose: () => void\n}) {\n  const { samples } = model.walkRowSampleChoices\n  return (\n    <PickNamesDialog\n      title=\"Choose samples\"\n      label=\"Samples\"\n      testId=\"graph-choose-samples\"\n      caption={`${samples.length.toLocaleString()} samples in this cut. Their walks show in pairs, in the order picked.`}\n      options={samples}\n      initial={model.walkRowSamples ?? []}\n      confirmLabel={picked =>\n        picked.length > 0 ? 'Show these samples' : 'Show every sample'\n      }\n      onPick={picked => {\n        model.setWalkRowSamples(picked.length > 0 ? picked : undefined)\n      }}\n      onClose={onClose}\n    />\n  )\n})\n\nexport default ChooseSamplesDialog\n"],
-  "mappings": "uLAAA,IAAAA,EAAyB,SAqBrB,IAAAC,EAAA,SATEC,KAAsB,YAAS,SAA6B,CAChE,MAAAC,EACA,QAAAC,CACF,EAGG,CACD,GAAM,CAAE,QAAAC,CAAQ,EAAIF,EAAM,qBAC1B,SACE,OAACG,EAAA,CACC,MAAM,iBACN,MAAM,UACN,OAAO,uBACP,QAAS,GAAGD,EAAQ,OAAO,eAAe,CAAC,wEAC3C,QAASA,EACT,QAASF,EAAM,gBAAkB,CAAC,EAClC,aAAcI,GACZA,EAAO,OAAS,EAAI,qBAAuB,oBAE7C,OAAQA,GAAU,CAChBJ,EAAM,kBAAkBI,EAAO,OAAS,EAAIA,EAAS,MAAS,CAChE,EACA,QAASH,EACX,CAEJ,CAAC,EAEMI,EAAQN",
-  "names": ["import_mobx_react", "import_jsx_runtime", "ChooseSamplesDialog", "model", "onClose", "samples", "PickNamesDialog", "picked", "ChooseSamplesDialog_default"]
+  "mappings": "+IAYA,IAAMA,EAAsBC,EAAS,SAA6B,CAChE,MAAAC,EACA,QAAAC,CACF,EAGG,CACD,GAAM,CAAE,QAAAC,CAAQ,EAAIF,EAAM,qBAC1B,OACEG,EAACC,EAAA,CACC,MAAM,iBACN,MAAM,UACN,OAAO,uBACP,QAAS,GAAGF,EAAQ,OAAO,eAAe,CAAC,wEAC3C,QAASA,EACT,QAASF,EAAM,gBAAkB,CAAC,EAClC,aAAcK,GACZA,EAAO,OAAS,EAAI,qBAAuB,oBAE7C,OAAQA,GAAU,CAChBL,EAAM,kBAAkBK,EAAO,OAAS,EAAIA,EAAS,MAAS,CAChE,EACA,QAASJ,EACX,CAEJ,CAAC,EAEMK,EAAQR",
+  "names": ["ChooseSamplesDialog", "observer", "model", "onClose", "samples", "jsx", "PickNamesDialog", "picked", "ChooseSamplesDialog_default"]
 }

package/dist/chunks/ChooseWalksDialog-L23LYMKI.js

@@ -0,0 +1,2 @@
+import{a as t}from"./chunk-5JXGPUTF.js";import"./chunk-6OPB7FOJ.js";import"./chunk-ECD5B2ZM.js";import{b as l,d as i}from"./chunk-JMBDTNUR.js";var h=i(function({model:o,onClose:s}){let{walkChoices:a}=o;return l(t,{title:"Choose haplotypes",label:"Haplotypes",testId:"graph-choose-walks",caption:`${a.length.toLocaleString()} haplotypes in this cut. The ones picked are highlighted in this order, and the rest fades.`,options:a.map(e=>e.name),initial:o.walkLayers.map(e=>e.walk),optionLabel:e=>o.walkLabel(e),confirmLabel:e=>e.length>0?"Highlight these":"Clear highlights",onPick:e=>{o.liftWalks(e)},onClose:s})}),k=h;export{k as default};
+//# sourceMappingURL=ChooseWalksDialog-L23LYMKI.js.map

package/dist/chunks/{ChooseWalksDialog-6HVVZMFD.js.map → ChooseWalksDialog-L23LYMKI.js.map}

@@ -2,6 +2,6 @@
   "version": 3,
   "sources": ["../../src/GraphGenomeView/components/ChooseWalksDialog.tsx"],
   "sourcesContent": ["import { observer } from 'mobx-react'\n\nimport PickNamesDialog from './PickNamesDialog'\n\nimport type { GraphPaneModel } from '../model'\n\ntype WalkPicker = Pick<\n  GraphPaneModel,\n  'walkChoices' | 'walkLayers' | 'walkLabel' | 'liftWalks'\n>\n\n// Which haplotypes to highlight, for a graph with more walks than a menu can\n// list\nconst ChooseWalksDialog = observer(function ChooseWalksDialog({\n  model,\n  onClose,\n}: {\n  model: WalkPicker\n  onClose: () => void\n}) {\n  const { walkChoices } = model\n  return (\n    <PickNamesDialog\n      title=\"Choose haplotypes\"\n      label=\"Haplotypes\"\n      testId=\"graph-choose-walks\"\n      caption={`${walkChoices.length.toLocaleString()} haplotypes in this cut. The ones picked are highlighted in this order, and the rest fades.`}\n      options={walkChoices.map(c => c.name)}\n      initial={model.walkLayers.map(l => l.walk)}\n      optionLabel={name => model.walkLabel(name)}\n      confirmLabel={picked =>\n        picked.length > 0 ? 'Highlight these' : 'Clear highlights'\n      }\n      onPick={picked => {\n        model.liftWalks(picked)\n      }}\n      onClose={onClose}\n    />\n  )\n})\n\nexport default ChooseWalksDialog\n"],
-  "mappings": "uLAAA,IAAAA,EAAyB,SAsBrB,IAAAC,EAAA,SATEC,KAAoB,YAAS,SAA2B,CAC5D,MAAAC,EACA,QAAAC,CACF,EAGG,CACD,GAAM,CAAE,YAAAC,CAAY,EAAIF,EACxB,SACE,OAACG,EAAA,CACC,MAAM,oBACN,MAAM,aACN,OAAO,qBACP,QAAS,GAAGD,EAAY,OAAO,eAAe,CAAC,8FAC/C,QAASA,EAAY,IAAIE,GAAKA,EAAE,IAAI,EACpC,QAASJ,EAAM,WAAW,IAAIK,GAAKA,EAAE,IAAI,EACzC,YAAaC,GAAQN,EAAM,UAAUM,CAAI,EACzC,aAAcC,GACZA,EAAO,OAAS,EAAI,kBAAoB,mBAE1C,OAAQA,GAAU,CAChBP,EAAM,UAAUO,CAAM,CACxB,EACA,QAASN,EACX,CAEJ,CAAC,EAEMO,EAAQT",
-  "names": ["import_mobx_react", "import_jsx_runtime", "ChooseWalksDialog", "model", "onClose", "walkChoices", "PickNamesDialog", "c", "l", "name", "picked", "ChooseWalksDialog_default"]
+  "mappings": "+IAaA,IAAMA,EAAoBC,EAAS,SAA2B,CAC5D,MAAAC,EACA,QAAAC,CACF,EAGG,CACD,GAAM,CAAE,YAAAC,CAAY,EAAIF,EACxB,OACEG,EAACC,EAAA,CACC,MAAM,oBACN,MAAM,aACN,OAAO,qBACP,QAAS,GAAGF,EAAY,OAAO,eAAe,CAAC,8FAC/C,QAASA,EAAY,IAAIG,GAAKA,EAAE,IAAI,EACpC,QAASL,EAAM,WAAW,IAAIM,GAAKA,EAAE,IAAI,EACzC,YAAaC,GAAQP,EAAM,UAAUO,CAAI,EACzC,aAAcC,GACZA,EAAO,OAAS,EAAI,kBAAoB,mBAE1C,OAAQA,GAAU,CAChBR,EAAM,UAAUQ,CAAM,CACxB,EACA,QAASP,EACX,CAEJ,CAAC,EAEMQ,EAAQX",
+  "names": ["ChooseWalksDialog", "observer", "model", "onClose", "walkChoices", "jsx", "PickNamesDialog", "c", "l", "name", "picked", "ChooseWalksDialog_default"]
 }

package/dist/chunks/GbzBaseSyntenyAdapter-WPRJGI7E.js

@@ -0,0 +1,8 @@
+import{a as Gr,b as ot,c as zr,d as jr,e as Ur}from"./chunk-X4NNWAXW.js";import{a as Nn,b as Tn}from"./chunk-NU53CDGF.js";import{f as _s,g as qr,h as ye,i as Mn,j as Pn,k as St,l as kn,m as _n,o as On}from"./chunk-R4DSKZ5P.js";import"./chunk-PR5YUSXN.js";import{a as ze}from"./chunk-OGQ6OQDN.js";import"./chunk-YBLNN5FU.js";import{e as bt,f as Ge,g as Rn}from"./chunk-XKN5LH2Z.js";import"./chunk-E7J6SB5P.js";import{b as Br,c as Hr,d as Dr}from"./chunk-D7FMSRTU.js";import{a as Lr,c as Fr,e as $r,o as Cn}from"./chunk-TENPGIPX.js";function be(r,e){return 2*r+(e==="reverse"?1:0)}function O(r){return Math.floor(r/2)}function je(r){return r%2===0?"forward":"reverse"}function j(r){return r%2===1}function re(r){return r%2===0?r+1:r-1}function Wr(r){return r==="left"?"right":"left"}function It(r){return r==="forward"?"left":"right"}function vt(r){return r==="forward"?"right":"left"}function Vr(r){return r==="left"?"forward":"reverse"}function Qr(r){return r==="right"?"forward":"reverse"}function Ue(r,e){let t=O(r),n=O(e);return j(r)?n>t||n===t&&!j(e):n>=t}function st(r){return Le(r[0],r[r.length-1])}function Le(r,e){return r===void 0||e===void 0?!0:j(r)===j(e)?!j(r):Ue(r,e)}var it=class{offset=0;bytes;constructor(e){this.bytes=e}get done(){return this.offset>=this.bytes.length}byte(){let e=this.bytes[this.offset];if(e!==void 0)return this.offset+=1,e}int(){let e=1,t=0;for(;this.offset<this.bytes.length;){let n=this.bytes[this.offset];if(this.offset+=1,t+=(n&127)*e,e*=128,(n&128)===0)return t}}},Yr=255,Os=256,Et=class{source;sigma;threshold;constructor(e,t){this.source=new it(e),this.sigma=t===0?Number.MAX_SAFE_INTEGER:t,this.threshold=this.sigma<Yr?Math.floor(Os/this.sigma):0}next(){if(this.sigma>=Yr){let o=this.source.int(),s=this.source.int();return o===void 0||s===void 0?void 0:{value:o,len:s+1}}let e=this.source.byte();if(e===void 0)return;let t=e%this.sigma,n=Math.floor(e/this.sigma)+1;if(n===this.threshold){let o=this.source.int();if(o===void 0)return;n+=o}return{value:t,len:n}}*[Symbol.iterator](){for(let e=this.next();e!==void 0;e=this.next())yield e}};function Kr(r){let e=new it(r),t=e.int();if(t===void 0||t===0)return[];let n=[],o=0;for(let s=0;s<t;s++){let i=e.int(),a=e.int();if(i===void 0||a===void 0)throw new Error("GBWT edge list ends early");o+=i,n.push({node:o,offset:a})}return n}var At=class{edges;bwt;constructor(e,t){this.edges=e,this.bwt=t}runs(){return new Et(this.bwt,this.edges.length)}edge(e){let t=this.edges[e];if(t===void 0)throw new Error(`GBWT run refers to edge rank ${e} of ${this.edges.length}`);return t}lf(e){let t=this.edges.map(o=>o.offset),n=0;for(let o of this.runs()){let s=this.edge(o.value),i=t[o.value];if(n+o.len>e)return s.node===0?void 0:{node:s.node,offset:i+(e-n)};t[o.value]=i+o.len,n+=o.len}}edgeTo(e){let t=0,n=this.edges.length;for(;t<n;){let o=t+n>>1,s=this.edges[o];if(s.node===e)return o;s.node<e?t=o+1:n=o}}offsetTo(e){if(e.node===0)return;let t=this.edgeTo(e.node);if(t===void 0)return;let n=this.edges[t].offset;if(n>e.offset)return;let o=0;for(let s of this.runs())if(o+=s.len,s.value===t&&(n+=s.len,n>e.offset))return o-(n-e.offset)}predecessorAt(e){let t=this.edges.map(o=>({node:o.node===0?0:re(o.node),count:0}));for(let o of this.runs()){let s=t[o.value];s&&(s.count+=o.len)}for(let o=1;o<t.length;o++){let s=t[o-1],i=t[o];O(s.node)===O(i.node)&&(t[o-1]=i,t[o]=s)}let n=0;for(let o of t)if(n+=o.count,n>e)return o.node===0?void 0:o.node}decompressArrays(){let e=this.edges.map(i=>i.offset),t=0;for(let i of this.runs())t+=i.len;let n=new Int32Array(t),o=new Int32Array(t),s=0;for(let i of this.runs()){let a=this.edge(i.value),f=e[i.value];for(let c=0;c<i.len;c++)n[s]=a.node,o[s]=f,f+=1,s+=1;e[i.value]=f}return{nodes:n,offsets:o}}decompress(){let e=this.edges.map(n=>n.offset),t=[];for(let n of this.runs()){let o=this.edge(n.value);for(let s=0;s<n.len;s++)t.push({node:o.node,offset:e[n.value]}),e[n.value]=e[n.value]+1}return t}};var Ns=["","A","C","G","T","N"];function Xr(r){let e=r[r.length-1];if(e===void 0)return 0;let t=e,n=0;for(let o=0;o<3&&t%6!==0;o++)t=Math.floor(t/6),n+=1;return 3*(r.length-1)+n}function Zr(r){let e="";for(let t of r){let n=t;for(let o=0;o<3;o++){let s=Ns[n%6];if(s==="")return e;n=Math.floor(n/6),e+=s}}return e}var Ts={A:"T",C:"G",G:"C",T:"A",N:"N"};function Ct(r){let e="";for(let t=r.length-1;t>=0;t--)e+=Ts[r[t]]??"N";return e}var Ls=Uint32Array.from([1116352408,1899447441,3049323471,3921009573,961987163,1508970993,2453635748,2870763221,3624381080,310598401,607225278,1426881987,1925078388,2162078206,2614888103,3248222580,3835390401,4022224774,264347078,604807628,770255983,1249150122,1555081692,1996064986,2554220882,2821834349,2952996808,3210313671,3336571891,3584528711,113926993,338241895,666307205,773529912,1294757372,1396182291,1695183700,1986661051,2177026350,2456956037,2730485921,2820302411,3259730800,3345764771,3516065817,3600352804,4094571909,275423344,430227734,506948616,659060556,883997877,958139571,1322822218,1537002063,1747873779,1955562222,2024104815,2227730452,2361852424,2428436474,2756734187,3204031479,3329325298]),ve=(r,e)=>r>>>e|r<<32-e;function Jr(r){let e=Math.ceil((r.length+9)/64),t=new Uint8Array(e*64);t.set(r),t[r.length]=128;let n=new DataView(t.buffer),o=r.length*8;n.setUint32(t.length-8,Math.floor(o/2**32)),n.setUint32(t.length-4,o>>>0);let s=Uint32Array.from([1779033703,3144134277,1013904242,2773480762,1359893119,2600822924,528734635,1541459225]),i=new Uint32Array(64);for(let c=0;c<e;c++){for(let S=0;S<16;S++)i[S]=n.getUint32(c*64+S*4);for(let S=16;S<64;S++){let g=i[S-15],x=i[S-2],y=ve(g,7)^ve(g,18)^g>>>3,E=ve(x,17)^ve(x,19)^x>>>10;i[S]=i[S-16]+y+i[S-7]+E}let l=s[0],h=s[1],d=s[2],p=s[3],m=s[4],u=s[5],w=s[6],b=s[7];for(let S=0;S<64;S++){let g=ve(m,6)^ve(m,11)^ve(m,25),x=m&u^~m&w,y=b+g+x+Ls[S]+i[S]|0,E=ve(l,2)^ve(l,13)^ve(l,22),A=l&h^l&d^h&d;b=w,w=u,u=m,m=p+y|0,p=d,d=h,h=l,l=y+E+A|0}[l,h,d,p,m,u,w,b].forEach((S,g)=>{s[g]=s[g]+S})}let a=new Uint8Array(32),f=new DataView(a.buffer);for(let c=0;c<8;c++)f.setUint32(c*4,s[c]);return a}function eo(r,e){let t=new Map;if(r!==void 0)for(let n of r.split(";")){let o=n.split(","),[s,i]=o;if(o.length!==2||!s||!i)throw new Error(`Invalid ${e} relationship: ${n}`);let a=t.get(s);a||(a=new Set,t.set(s,a)),a.add(i)}return t}function ro(r){return{name:r.get("pggname"),subgraph:eo(r.get("subgraph"),"subgraph"),translation:eo(r.get("translation"),"translation")}}function to(r,e){for(let[t,n]of e){let o=r.get(t);o||(o=new Set,r.set(t,o));for(let s of n)o.add(s)}}function oo(r,e){let t={name:r,subgraph:new Map,translation:new Map};return e.name!==void 0&&(t.subgraph.set(r,new Set([e.name])),to(t.subgraph,e.subgraph),to(t.translation,e.translation)),t}function no(r){return[...r.entries()].sort(([e],[t])=>e<t?-1:e>t?1:0).flatMap(([e,t])=>[...t].sort().map(n=>[e,n]))}function so(r){let e=[];r.name!==void 0&&e.push(`H	NM:Z:${r.name}`);for(let[t,n]of no(r.subgraph))e.push(`H	SG:Z:${t},${n}`);for(let[t,n]of no(r.translation))e.push(`H	TL:Z:${t},${n}`);return e}async function io(r){let e=r.reduce((i,a)=>i+a.length,0),t=new Uint8Array(e),n=0;for(let i of r)t.set(i,n),n+=i.length;let o=globalThis.crypto?.subtle;return[...o?new Uint8Array(await o.digest("SHA-256",t)):Jr(t)].map(i=>i.toString(16).padStart(2,"0")).join("")}var Fs="_gbwt_ref";function me(r){let e=`${r.sample}#${r.haplotype}#${r.contig}`;return r.end===void 0?e:`${e}[${r.fragment}-${r.end}]`}var $s=/^([^#]+)#(\d+)#([^#]+?)(?:\[\d+-\d+\])?$/,qs=/^([^#]+?)(?:\[\d+-\d+\])?$/;function Bs(r){let e=$s.exec(r);if(e)return{sample:e[1],haplotype:Number(e[2]),contig:e[3]};let t=qs.exec(r);if(t)return{contig:t[1]};throw new Error(`"${r}" is not a path name; expected "sample#haplotype#contig" or a bare contig`)}function We(r){return typeof r=="string"?Bs(r):r}function Ve(r,e){return{sample:r.sample??Fs,contig:r.contig,haplotype:r.haplotype??0,fragment:e}}var Hs=4096;function Fn(r){let e=[];for(let t of r){let n=e[e.length-1];n&&t-n[1]<=Hs?n[1]=t:e.push([t,t])}return e}var Ds=32768,ao={mostChosenPaths:32},Ln=class{byNode=new Map;get(e){return this.byNode.get(e.node)?.get(e.offset)}set(e,t){let n=this.byNode.get(e.node);n||(n=new Map,this.byNode.set(e.node,n)),n.set(e.offset,t)}},ie=class extends Error{};function Rt(r,e,t,n){return r==="forward"?e+t:e-n}function fo(r,e,t,n){return r==="forward"?e-n:e+t}function co(r){return Le(re(r.handles[r.handles.length-1]),re(r.handles[0]))}function at(r){return`${r.pathHandle}:${r.hapStart}:${r.hapEnd}`}async function lo(r){let{db:e,records:t,signal:n}=r,o=performance.now(),s=()=>{let v=performance.now(),R=v-o;return o=v,R},i={spacing:await e.haplotypeAnchorSpacing(),anchors:void 0,anchorsRead:0,chosenPaths:0,scans:[],scanRows:0,strays:void 0,pieces:0,sources:{reference:0,section:0,stray:0,chain:0,twin:0},walks:{},twins:{tried:0,found:0},graphFetches:0,fallback:void 0,ms:{scan:0,walks:0,check:0,twins:0}},a=(v,R)=>{let _=`${v}: ${R}`;i.walks[_]=(i.walks[_]??0)+1},f=await e.haplotypeSampleInterval()??4096,c=new Map,l=async v=>{let R=t.get(v)??c.get(v);if(R)return R;let _=await e.getRecord(v);if(i.graphFetches+=1,!_)throw new Error(`Node record ${v} is missing from the database`);return c.set(v,_),_},h=v=>t.get(v).sequenceLen,d=await e.pathsByHandle(),p=v=>{let R=d.get(v);return R!==void 0&&r.keep(R.name)},m=[],u=new Ln,w=new Map,b=new Set,S=new Set,g=async v=>{let R=(await l(v.node)).gbwt().lf(v.offset);return R===void 0||R.node===0?void 0:R},x=async(v,R)=>{let _=(await l(re(v.node))).gbwt().predecessorAt(v.offset);if(_===void 0||R!==void 0&&!R.has(_))return;let L=(await l(_)).gbwt().offsetTo(v);if(L===void 0)throw new Error(`No offset in ${_} leads to ${v.node}:${v.offset}`);return{node:_,offset:L}},y=(v,R,_,L)=>{let B=_.map(V=>V.pos.node),W=_.map(V=>V.pos.offset),J=0;for(let V of B)J+=h(V);let q=R==="forward"?_[0].left:_[_.length-1].left,$=m.length;m.push({pathHandle:v,orientation:R,handles:B,offsets:W,len:J,hapStart:q,hapEnd:q+J,canonical:Le(B[0],B[B.length-1]),source:L});for(let V of _)u.set(V.pos,$);let K=w.get(v);return K?K.push($):w.set(v,[$]),$},E=async(v,R,_,L)=>{let B=[],W=v;for(;;){n?.throwIfAborted();let q=await x(W.pos,t);if(!q)break;W={pos:q,left:fo(_,W.left,h(W.pos.node),h(q.node))},B.push(W)}B.reverse();let J=[v];for(W=v;;){n?.throwIfAborted();let q=await g(W.pos);if(!q||!t.has(q.node))break;W={pos:q,left:Rt(_,W.left,h(W.pos.node),h(q.node))},J.push(W)}return y(R,_,[...B,...J],L)},A=async(v,R,_,L)=>m[u.get(v.pos)??await E(v,R,_,L)],N=v=>{let R=v.handles[v.handles.length-1];return{pos:{node:R,offset:v.offsets[v.offsets.length-1]},left:v.orientation==="forward"?v.hapEnd-h(R):v.hapStart}},k=v=>{let R=v.handles[0];return{pos:{node:R,offset:v.offsets[0]},left:v.orientation==="forward"?v.hapStart:v.hapEnd-h(R)}},F=await E({pos:r.referencePos,left:r.referenceLeft},r.referenceHandle,"forward","reference"),M=m[F],T=()=>{if(i.fallback!==void 0)return{reference:M,pieces:[],stats:i};let v=new Map;m.forEach((_,L)=>{L!==F&&v.set(at(_),[...v.get(at(_))??[],_])});let R=[];for(let _ of v.values()){let L=new Set;for(let B of _)B.canonical&&!L.has(B.orientation)&&(L.add(B.orientation),R.push(B),i.sources[B.source]+=1)}return i.sources.reference=1,i.pieces=R.length+1,{reference:M,pieces:R,stats:i}},C=async(v,R)=>{let _=R?b:S,L=R?S:b,B=v;for(;;){if(_.has(B))return;_.add(B);let W=m[B],J=R?N(W):k(W),q=0,$;for(;$===void 0;){n?.throwIfAborted();let K=R?await g(J.pos):await x(J.pos);if(!K){$="endmarker";break}let V=(await l(J.pos.node)).sequenceLen,Ie=(await l(K.node)).sequenceLen,oe=R?Rt(W.orientation,J.left,V,Ie):fo(W.orientation,J.left,V,Ie);if(t.has(K.node)){let ee=u.get(K);ee===void 0?(B=await E({pos:K,left:oe},W.pathHandle,W.orientation,"chain"),L.add(B),$="landed"):(L.add(ee),$="merge")}else q>Ds?$="bound":(q+=Ie,J={pos:K,left:oe})}if(a("chain",$),$!=="landed")return}},D=async v=>{if(r.context>v.context)throw new ie(`the context of ${r.context} bp exceeds the ${v.context} bp the haplotype index's stray rows cover`);let R=i.spacing;if(R===void 0)throw new ie("the haplotype index has no anchors");let{bin:_,bound:L}=v,{fills:B,inserted:W}=r.snarls;if(r.snarls.mode==="overlapping"&&B.length>0)throw new ie("the haplotype index's stray rows cover contained snarls only");for(let I of B){if(I.inserted>0&&I.low===I.high)throw new ie(`the haplotype index's stray rows leave out the snarl bounded by node ${I.low} at both ends`);if(I.inserted>0&&(v.snarlNodes===void 0||I.nodes>v.snarlNodes))throw new ie(v.snarlNodes===void 0?"the haplotype index's stray rows leave snarls out":`a snarl of ${I.nodes} nodes exceeds the ${v.snarlNodes} the haplotype index's stray rows cover`)}let J=Math.floor(r.window.start/_),q=Math.floor((r.window.end-1)/_),$=J*_,K=(q+1)*_,V=new Map,Ie=async(I,P)=>{let U=await e.haplotypeAnchorsBetween(r.referenceHandle,I*R,P*R);for(let G of U)V.set(G.anchorOffset/R,G)},oe=Math.max(0,Math.floor(($-L)/R)-1),ee=Math.ceil((K+L)/R)+1,[{listed:xt,strays:ce}]=await Promise.all([e.haplotypeBinData(r.referenceHandle,J,q),Ie(oe,ee)]);for(let I of t.keys()){let P=O(I);if(!j(I)&&!xt(P)&&!W.has(P))throw new ie(`the haplotype index lists node ${P} of the subgraph in no bin that the window touches`)}i.scans=Fn([...t.keys()].sort((I,P)=>I-P));let de=Promise.all(i.scans.map(([I,P])=>e.haplotypeSamplesInRange(I,P)));for(de.catch(()=>{});oe>0&&(V.get(oe)?.pathOffset??Number.POSITIVE_INFINITY)>=$-L;)oe-=1,await Ie(oe,oe);for(;V.has(ee)&&V.get(ee).pathOffset<=K+L;)ee+=1,await Ie(ee,ee);let xe=[...V.keys()].sort((I,P)=>I-P),Pe=V.get(xe[0]??-1);if(!Pe)throw new ie("the haplotype index has no anchors on this path");let pe=I=>V.get(I).pathOffset,tt=new Map;for(let I of xe){let P=O(V.get(I).node);tt.set(P,[...tt.get(P)??[],I])}let vn=[...tt.keys()],Er=vn.map(I=>V.get(tt.get(I)[0]).visits);if(!Er[vn.indexOf(O(Pe.node))].some(I=>I.pathHandle===r.referenceHandle&&I.orientation==="forward"&&I.pathOffset===Pe.pathOffset))throw new Error(`The haplotype index has no anchor row for the reference path ${r.referenceHandle} at offset ${Pe.pathOffset} (node ${O(Pe.node)}); it does not match this graph`);let Ar=xe.filter(I=>pe(I)<=r.window.start),Rs=xe.filter(I=>pe(I)>=r.window.end);i.anchors=[pe(Ar[Ar.length-1]??xe[0]),pe(Rs[0]??xe[xe.length-1])],i.anchorsRead=xe.length;let En=new Map,Cr=new Set;if(vn.forEach((I,P)=>{let U=tt.get(I),G=U.length===1?U[0]:void 0;for(let z of Er[P])Cr.add(z.pathHandle),z.orientation==="forward"&&p(z.pathHandle)&&En.set(z.pathHandle,[...En.get(z.pathHandle)??[],{k:G,row:z}])}),i.chosenPaths=[...Cr].filter(p).length,i.chosenPaths>ao.mostChosenPaths)throw new ie(`${i.chosenPaths} chosen paths pass the anchors, more than ${ao.mostChosenPaths}`);let yt=[],Te=Number.POSITIVE_INFINITY,ke=0;for(let[I,P]of En){P.sort((U,G)=>U.row.pathOffset-G.row.pathOffset);for(let U=0;U+1<P.length;U++){let G=P[U],z=P[U+1];if(G.k===void 0||z.k===void 0||Math.abs(G.k-z.k)!==1)continue;let[Z,te]=pe(G.k)<=pe(z.k)?[G,z]:[z,G],ne=pe(Z.k),se=pe(te.k);ne<K&&se>=$?(yt.push({pathHandle:I,from:G.row,to:z.row}),Te=Math.min(Te,ne-L),ke=Math.max(ke,se+L)):ne>=K&&ne-K<=L?(yt.push({pathHandle:I,from:Z.row,to:void 0}),Te=Math.min(Te,ne-L),ke=Math.max(ke,ne+L)):se<$&&$-se<=L&&(yt.push({pathHandle:I,from:te.row,to:void 0}),Te=Math.min(Te,se-L),ke=Math.max(ke,se+L))}}let Ms=new Set(B.map(I=>`${I.low}:${I.high}`)),Ps=ce.filter(I=>p(I.pathHandle)&&(I.snarl===void 0||Ms.has(`${I.snarl[0]}:${I.snarl[1]}`))).sort((I,P)=>I.pathHandle-P.pathHandle||I.pathStart-P.pathStart);i.strays={bins:q-J+1,rows:ce.length,walked:0,outsideBp:0},ke>0&&await r.prefetchReferenceRange(r.referenceHandle,Math.max(0,Te),ke+1),i.ms.scan=s();let Rr=8*R+2*(r.window.end-r.window.start),Mr=i.strays,nt=0,Pr=I=>{if(Mr.outsideBp+=I,nt+=I,nt>Rr)throw new ie(`a walk of a chosen path near the window went past its cap of ${Rr} bp`)},An=new Map,kr=(I,P,U)=>(An.get(I)??[]).some(([G,z])=>G<=P&&U<z),_r=(I,P,U)=>{An.set(I,[...An.get(I)??[],[P,U]])},Or=async(I,P,U,G,z)=>{let Z=P,te=U,ne=te;for(;Z&&te<=G;){n?.throwIfAborted();let se;if(t.has(Z.node)){let rt=await A({pos:Z,left:te},I,"forward",z),Tr=N(rt);Z=Tr.pos,te=Tr.left,se=h(Z.node),ne=Math.max(ne,rt.hapEnd)}else se=(await l(Z.node)).sequenceLen,Pr(se),ne=Math.max(ne,te+se);Z=await g(Z),te+=se}return ne},ks=async(I,P,U,G)=>{let z={pos:P,left:U},Z=U;for(;z.left>G;){n?.throwIfAborted();let te=await x(z.pos);if(!te)break;let ne=(await l(te.node)).sequenceLen,se=z.left-ne;if(t.has(te.node)){let rt=await A({pos:te,left:se},I,"forward","section");z=k(rt),Z=Math.min(Z,rt.hapStart)}else Pr(ne),z={pos:te,left:se},Z=Math.min(Z,se)}return Z};for(let{pathHandle:I,from:P,to:U}of yt){let G=P.pathOffset,z=(U??P).pathOffset+L;if(kr(I,G-L,z))continue;let Z={node:P.node,offset:P.offset};nt=0;let te=await Or(I,Z,G,z,"section");nt=0;let ne=await ks(I,Z,G,G-L);_r(I,Math.min(ne,G-L),Math.max(te,z+1)),a(U?"section":"visit",U?"past the far anchor":"bound")}for(let I of Ps){if(kr(I.pathHandle,I.pathStart,I.pathEnd))continue;nt=0;let P=await Or(I.pathHandle,{node:I.node,offset:I.offset},I.pathStart,I.pathEnd,"stray");_r(I.pathHandle,I.pathStart,Math.max(P,I.pathEnd+1)),Mr.walked+=1}i.ms.walks=s();let Nr=[];for(let I of await de)for(let P of I)if(i.scanRows+=1,t.has(P.node)&&p(P.pathHandle)){if(!(w.get(P.pathHandle)??[]).some(U=>{let G=m[U];return G.hapStart<=P.pathOffset&&P.pathOffset<G.hapEnd}))throw new ie(`chosen path ${P.pathHandle} has a sample at ${P.pathOffset} on the window's nodes that no walk reached`);P.orientation==="reverse"&&Nr.push(P)}for(let I of Nr)await A({pos:{node:I.node,offset:I.offset},left:I.pathOffset},I.pathHandle,"reverse","twin");i.ms.check=s()},Y=async()=>{let v=new Map,R=q=>{let $=at(q),K=v.get($);K?K.add(q.orientation):v.set($,new Set([q.orientation]))},_=0,L=()=>{for(;_<m.length;_++)R(m[_])};L();let B=q=>(v.get(at(q))?.size??0)>1,W=2*f,J=(q,$)=>$===F?p(r.referenceHandle)&&co(q):!q.canonical||co(q);for(let q=0;q<m.length;q++){let $=m[q];if(B($)||!J($,q))continue;i.twins.tried+=1;let K=$.orientation==="forward"?"reverse":"forward",V=N($),Ie=0,oe;for(;!oe&&Ie<=W;){n?.throwIfAborted();let ce=await g(V.pos);if(!ce)break;let de=(await l(ce.node)).sequenceLen,xe=Rt($.orientation,V.left,(await l(V.pos.node)).sequenceLen,de),Pe=re(ce.node);oe=(await e.haplotypeSamplesInRange(Pe,Pe)).find(pe=>pe.pathHandle===$.pathHandle&&pe.orientation===K&&pe.pathOffset===xe),Ie+=de,V={pos:ce,left:xe}}let ee=oe&&{pos:{node:oe.node,offset:oe.offset},left:oe.pathOffset},xt=0;for(;ee&&!B($)&&xt<=W+$.len;){if(n?.throwIfAborted(),t.has(ee.pos.node)){let ce=await A(ee,$.pathHandle,K,"twin"),de=m.indexOf(ce);await C(de,!0),await C(de,!1),L(),ee=N(ce)}if(!B($)){let ce=(await l(ee.pos.node)).sequenceLen;xt+=ce;let de=await g(ee.pos);ee=de?{pos:de,left:Rt(K,ee.left,ce,(await l(de.node)).sequenceLen)}:void 0}}if(L(),!B($))throw new ie(`piece ${at($)} was found in one orientation where extractPaths keeps the other`);i.twins.found+=1}i.ms.twins=s()};try{let v=await e.haplotypeStrayOptions();if(v===void 0)throw new ie("the haplotype index has no stray rows; gbz-haplotype-index 0.2.0 writes them");await D(v),await Y()}catch(v){if(!(v instanceof ie))throw v;i.fallback=v.message}return T()}function ho(r,e){return r.handles[0]-e.handles[0]||r.offsets[0]-e.offsets[0]}function Mt(r,e){let t=0,n=r.length;for(;t<n;){let o=t+n>>1;r[o]<e?t=o+1:n=o}return t}var Pt=class{ending;tree;constructor(e){this.ending=new Float64Array(e),this.tree=new Int32Array(e+1).fill(-1)}bestBefore(e){let t=-1;for(let n=e;n>0;n-=n&-n){let o=this.tree[n];o!==-1&&(t===-1||this.ending[o]>this.ending[t])&&(t=o)}return t}raise(e,t){this.ending[e]=t;for(let n=e+1;n<this.tree.length;n+=n&-n){let o=this.tree[n];(o===-1||t>this.ending[o])&&(this.tree[n]=e)}}},$n=class{pairs=[];total=0;a;b;weight;occurrences=new Map;constructor(e,t,n){this.a=e,this.b=t,this.weight=n,t.forEach((o,s)=>{let i=this.occurrences.get(o);i?i.push(s):this.occurrences.set(o,[s])})}solve(e,t,n,o){let s=0;for(;e+s<t&&n+s<o&&this.a[e+s]===this.b[n+s];)this.match(e+s,n+s),s+=1;let i=0;for(;t-i>e+s&&o-i>n+s&&this.a[t-i-1]===this.b[o-i-1];)i+=1;this.solveMiddle(e+s,t-i,n+s,o-i);for(let a=i;a>0;a--)this.match(t-a,o-a)}match(e,t){this.pairs.push([e,t]),this.total+=this.weight(this.a[e])}solveMiddle(e,t,n,o){if(e===t||n===o)return;let s=this.matchCount(e,t,n,o);if(s===0)return;if(s<=t-e+(o-n)){this.chain(e,t,n,o,s);return}let i=e+t>>1,a=this.split(e,i,t,n,o);this.solve(e,i,n,a),this.solve(i,t,a,o)}matchCount(e,t,n,o){let s=0;for(let i=e;i<t;i++){let a=this.occurrences.get(this.a[i]);a&&(s+=Mt(a,o)-Mt(a,n))}return s}sweep(e,t,n,o,s,i,a){for(let f=e;f!==t;f+=n){let c=this.occurrences.get(this.a[f]);if(!c)continue;let l=this.weight(this.a[f]),h=Mt(c,o),d=Mt(c,s);for(let p=0;p<d-h;p++){let m=n===1?c[d-1-p]-o:s-1-c[h+p],u=i.bestBefore(m),w=(u===-1?0:i.ending[u])+l;if(w>i.ending[m]&&(i.raise(m,w),a)){let b=a.count++;a.row[b]=f,a.column[b]=m,a.previous[b]=u===-1?-1:a.endingMatch[u],a.endingMatch[m]=b}}}}chain(e,t,n,o,s){let i=new Pt(o-n),a={row:new Int32Array(s),column:new Int32Array(s),previous:new Int32Array(s),endingMatch:new Int32Array(o-n),count:0};this.sweep(e,t,1,n,o,i,a);let f=i.bestBefore(o-n);if(f===-1)return;this.total+=i.ending[f];let c=[];for(let l=a.endingMatch[f];l!==-1;l=a.previous[l])c.push([a.row[l],n+a.column[l]]);for(let l=c.length-1;l>=0;l--)this.pairs.push(c[l])}frontier(e,t,n,o,s){let i=new Pt(s-o);this.sweep(e,t,n,o,s,i);let a=new Float64Array(s-o+1);for(let f=0;f<s-o;f++)a[f+1]=Math.max(a[f],i.ending[f]);return a}split(e,t,n,o,s){let i=s-o,a=this.frontier(e,t,1,o,s),f=this.frontier(n-1,t-1,-1,o,s),c=0,l=-1;for(let h=0;h<=i;h++){let d=a[h]+f[i-h];d>l&&(l=d,c=h)}return o+c}};function po(r,e,t){let n=new $n(r,e,t);return n.solve(0,r.length,0,e.length),[n.pairs,n.total]}var Gs=100,Hn=4e6,zs=5e3,le=15,js=64,Us=8,bo=1,Dn=-4,ae=-6,Ce=-1,Qe=-(2**30),_t=0,qn=1,So=2;function Fe(r,e,t){let n=r.at(-1);t>0&&(n?.[0]===e?n[1]+=t:r.push([e,t]))}function kt(r,e,t){return r>=t&&r>=e?_t:t>=e?So:qn}function Io(r,e,t){let n=r.length,o=e.length,s=o+1,i=new Uint8Array((n+1)*s),a=new Int32Array(s).fill(Qe),f=new Int32Array(s).fill(Qe),c=new Int32Array(s).fill(Qe);a[0]=0;for(let m=1;m<=o;m++)c[m]=ae+(m-1)*Ce,i[m]=(m===1?_t:So)<<4;for(let m=1;m<=n;m++){let u=new Int32Array(s).fill(Qe),w=new Int32Array(s).fill(Qe),b=new Int32Array(s).fill(Qe);w[0]=ae+(m-1)*Ce,i[m*s]=(m===1?_t:qn)<<2;let S=r.charCodeAt(m-1);for(let g=1;g<=o;g++){let x=kt(a[g-1],f[g-1],c[g-1]);u[g]=Math.max(a[g-1],f[g-1],c[g-1])+(S===e.charCodeAt(g-1)?bo:Dn);let y=kt(a[g]+ae,f[g]+Ce,c[g]+ae);w[g]=Math.max(a[g]+ae,f[g]+Ce,c[g]+ae);let E=kt(u[g-1]+ae,w[g-1]+ae,b[g-1]+Ce);b[g]=Math.max(u[g-1]+ae,w[g-1]+ae,b[g-1]+Ce),i[m*s+g]=x|y<<2|E<<4}a=u,f=w,c=b}let l=[],h=n,d=o,p=kt(a[o],f[o],c[o]);for(;h>0||d>0;){let m=i[h*s+d]>>2*p&3;p===_t?(l.push(r[h-1]===e[d-1]?"=":"X"),h-=1,d-=1):p===qn?(l.push("I"),h-=1):(l.push("D"),d-=1),p=m}for(let m of l.reverse())Fe(t,m,1)}function Ws(r,e){let t=Math.abs(r-e);return(t===0?0:Math.min(-ae-(t-1)*Ce,-ae+10*Math.log2(t)))+(Math.min(r,e)>0?-Dn:0)}function vo(r,e){let t=Math.abs(r-e);return t===0?0:.01*le*t+.5*Math.log2(t)}function uo(r,e,t){return{qs:r.qs+e,qe:r.qs+t,ts:r.flipped?r.te-t:r.ts+e,te:r.flipped?r.te-e:r.ts+t,flipped:r.flipped}}function Vs(r,e,t){let n=r.qe-r.qs,o=[];for(let[a,f]of e){let c=Math.max(0,a-r.qs),l=Math.min(n,f-r.qs);c<l&&o.push([c,l])}for(let[a,f]of t){let c=Math.max(0,r.flipped?r.te-f:a-r.ts),l=Math.min(n,r.flipped?r.te-a:f-r.ts);c<l&&o.push([c,l])}if(o.length===0)return[r];o.sort((a,f)=>a[0]-f[0]);let s=[],i=0;for(let[a,f]of o)a-i>=le&&s.push(uo(r,i,a)),i=Math.max(i,f);return n-i>=le&&s.push(uo(r,i,n)),s}function Gn(r,e,t,n,o=1/0){let s=[],i={query:[],target:[]},a={forward:{query:[],target:[]},flipped:{query:[],target:[]}},f=[...r].sort((c,l)=>c.qs-l.qs||c.ts-l.ts);for(;f.length>0&&s.length<o;){let c=f.map(g=>g.qe-g.qs),l=new Int32Array(f.length).fill(-1),h=new Int32Array(f.length);for(let g=0;g<f.length;g++){let x=f[g],y=x.qe-x.qs;for(let E=g-1;E>=Math.max(0,g-zs);E--){if(c[E]+y<=c[g])continue;let A=f[E];if(A.flipped===x.flipped&&A.qs<x.qs&&(x.flipped?x.te<A.te:A.ts<x.ts)){let k=Math.max(0,A.qe-x.qs,x.flipped?x.te-A.ts:A.te-x.ts),F=x.qs+k-A.qe,M=x.flipped?A.ts-(x.te-k):x.ts+k-A.te;if(k<y&&F<=e&&M<=e){let T=c[E]+y-k-n(F,M);T>c[g]&&(c[g]=T,l[g]=E,h[g]=k)}}}}let d=new Int32Array(f.length),p=-1;for(let g=0;g<f.length;g++){let x=f[g];d[g]=(d[l[g]]??0)+x.qe-x.qs-h[g],d[g]>=t&&(p<0||c[g]>c[p])&&(p=g)}if(p<0)break;let m=[];for(let g=p;g>=0;g=l[g])m.push({run:f[g],trim:h[g]});m.reverse(),s.push(m);let u=m[0],w=m.at(-1),{flipped:b}=u.run,S=b?a.flipped:a.forward;S.query.push([u.run.qs+u.trim,w.run.qe]),S.target.push(b?[w.run.ts,u.run.te-u.trim]:[u.run.ts+u.trim,w.run.te]);for(let{run:g,trim:x}of m)i.query.push([g.qs+x,g.qe]),i.target.push(g.flipped?[g.ts,g.te-x]:[g.ts+x,g.te]);f=f.flatMap(g=>{let x=g.flipped?a.flipped:a.forward;return Vs(g,[...i.query,...x.query],[...i.target,...x.target])}).sort((g,x)=>g.qs-x.qs||g.ts-x.ts)}return s}function Bn(r,e){let t=new Map;for(let s=0;s+le<=e.length;s++){let i=e.slice(s,s+le),a=t.get(i);a?a.push(s):t.set(i,[s])}let n=[],o=new Map;for(let s=0;s+le<=r.length;s++){let i=t.get(r.slice(s,s+le));if(i&&i.length<=js)for(let a of i){let f=a-s,c=o.get(f);if(c&&s<=c.qe)c.qe=s+le,c.te=a+le;else{let l={qs:s,qe:s+le,ts:a,te:a+le,flipped:!1};o.set(f,l),n.push(l)}}}return n}function Qs(r,e){return[...Bn(r,e),...Bn(r,Ct(e)).map(t=>({...t,ts:e.length-t.te,te:e.length-t.ts,flipped:!0}))]}function Ot(r,e,t,n,o){let s;for(let{run:i,trim:a}of r){let f=i.qs+a;if(s){let c=i.flipped?i.te-a:s.te,l=i.flipped?s.ts:i.ts+a,h=t.slice(c,l);o(e.slice(s.qe,f),i.flipped?Ct(h):h,n,s.qe,c)}Fe(n,"=",i.qe-f),s=i}}function zn(r,e,t){Fe(t,"I",r.length),Fe(t,"D",e.length)}function Eo(r,e,t){r.length*e.length<=Hn?Io(r,e,t):zn(r,e,t)}function jn(r,e,t,n=0){let[o]=r.length*e.length>Hn&&n<Us?Gn(Bn(r,e),1/0,le,vo,1):[];if(!o){Eo(r,e,t);return}let s=(f,c,l)=>{jn(f,c,l,n+1)},i=o[0].run,a=o.at(-1).run;s(r.slice(0,i.qs),e.slice(0,i.ts),t),Ot(o,r,e,t,s),s(r.slice(a.qe),e.slice(a.te),t)}function Ys(r,e,t){jn(r,e,t)}function Ks(r,e,t){let n=[];Ot(r,e,t,n,Ys);let o=r[0],s=r.at(-1),{flipped:i}=o.run;return{queryStart:o.run.qs+o.trim,queryEnd:s.run.qe,targetStart:i?s.run.ts:o.run.ts+o.trim,targetEnd:i?o.run.te-o.trim:s.run.te,strand:i?"-":"+",edits:i?n.reverse():n,sharedBases:0}}function Xs(r,e,t,n){let o=[];if(r.length*e.length<=Hn)Io(r,e,t);else{let s=Gn(Qs(r,e),1/0,Math.max(n,le),vo),i=s.find(a=>!a[0].run.flipped);if(o=s.filter(a=>a[0].run.flipped).map(a=>Ks(a,r,e)),i){let a=(l,h,d,p,m)=>{o.some(w=>p<w.queryEnd&&w.queryStart<p+l.length||m<w.targetEnd&&w.targetStart<m+h.length)?Eo(l,h,d):jn(l,h,d)},f=i[0].run,c=i.at(-1).run;a(r.slice(0,f.qs),e.slice(0,f.ts),t,0,0),Ot(i,r,e,t,a),a(r.slice(c.qe),e.slice(c.te),t,c.qe,c.te)}else zn(r,e,t)}return o}function Un(r,e){let t=r.strand==="-",n=0,o=0;for(let[s,i]of r.edits)e(s,i,t?r.queryEnd-1-n:r.queryStart+n,r.targetStart+o),s!=="D"&&(n+=i),s!=="I"&&(o+=i)}function mo(r,e,t,n){let o=e==="query"&&r.strand==="-"?-1:1,s=0;return Un(r,(i,a,f,c)=>{let l=e==="query"?f:c,h=d=>{let p=l+o*d;return p>=t&&p<n};if(i==="="||i==="X")for(let d=0;d<a;d++)h(d)&&(s+=i==="="?bo:Dn);else if(i==="I"==(e==="query"))for(let d=0;d<a;d++)h(d)&&(s+=d===0?ae:Ce);else h(0)&&(s+=ae+(a-1)*Ce)}),s}function go(r,e){return e==="query"?[r.queryStart,r.queryEnd]:[r.targetStart,r.targetEnd]}function Zs(r,e){let t=r.strand==="-",n=[],o=0,s=0,i=0,a=0,f=new Uint8Array(r.queryEnd-r.queryStart);for(let[p,m]of r.shared)f.fill(1,p-r.queryStart,m-r.queryStart);let c=p=>f[p-r.queryStart]===1,l=()=>{Fe(n,"I",o),Fe(n,"D",s),o=0,s=0};Un(r,(p,m,u)=>{if(p==="I")o+=m;else if(p==="D")s+=m;else{for(let w=0;w<m;w++)e[i+w]?(o+=1,s+=1,c(t?u-w:u+w)&&(a+=1)):((o>0||s>0)&&l(),Fe(n,p,1));i+=m}}),l();let h={I:0,D:0};for(;n[0]?.[0]==="I"||n[0]?.[0]==="D";){let[p,m]=n.shift();h[p]+=m}let d={I:0,D:0};for(;n.at(-1)?.[0]==="I"||n.at(-1)?.[0]==="D";){let[p,m]=n.pop();d[p]+=m}return n.length===0?void 0:{...r,queryStart:r.queryStart+(t?d.I:h.I),queryEnd:r.queryEnd-(t?h.I:d.I),targetStart:r.targetStart+h.D,targetEnd:r.targetEnd-d.D,edits:n,sharedBases:r.sharedBases-a}}function Js(r,e,t,n){let o={query:new Uint8Array(e),target:new Uint8Array(t)},s=r.map(c=>{let l=[];Un(c,(h,d,p,m)=>{if(h==="="||h==="X")for(let u=0;u<d;u++)l.push([c.strand==="-"?p-u:p+u,m+u])});for(let[h,d]of l)o.query[h]=Math.min(255,o.query[h]+1),o.target[d]=Math.min(255,o.target[d]+1);return l}),i={query:new Map,target:new Map};s.forEach((c,l)=>{for(let[h,d]of c)for(let[p,m]of[["query",h],["target",d]])if(o[p][m]>1){let u=i[p].get(m);u?u.at(-1)!==l&&u.push(l):i[p].set(m,[l])}});let a=new Map,f=(c,l,h)=>{let d=`${h}:${c}:${l}`,p=a.get(d);if(p===void 0){let[m,u]=go(r[c],h),[w,b]=go(r[l],h),S=Math.max(m,w),g=Math.min(u,b),[x,y]=[r[c],r[l]];p=[mo(y,h,S,g)-mo(x,h,S,g),y.sharedBases-x.sharedBases,c-l].find(A=>A!==0)>0,a.set(d,p)}return p};return r.flatMap((c,l)=>{let h=s[l],d=new Uint8Array(h.length);if(h.forEach(([u,w],b)=>{for(let[S,g]of[["query",u],["target",w]])!d[b]&&i[S].get(g)?.some(x=>x!==l&&f(l,x,S))&&(d[b]=1)}),!d.includes(1))return[c];let p=Zs(c,d),m=p?.edits.reduce((u,[w,b])=>u+(w==="="?b:0),0)??0;return p&&m>=n?[p]:[]})}function wo(r,e){return r.map(t=>{let n=e(O(t));return j(t)?Ct(n):n}).join("")}function xo(r,e){let t=[0];for(let n of r)t.push(t.at(-1)+e(O(n)).length);return t}function yo(r){let e=new Map,t=new Map;r.forEach((i,a)=>{let f=O(i);e.has(f)?t.set(f,a):e.set(f,a)});let n=new Int32Array(r.length+1);for(let[i,a]of t)n[e.get(i)]+=1,n[a+1]-=1;let o=new Uint8Array(r.length),s=0;for(let i=0;i<r.length;i++)s+=n[i],o[i]=s>0?1:0;return o}function ei(r,e,t,n){let o=yo(r),s=yo(e),i=new Map;e.forEach((h,d)=>{s[d]||i.set(O(h),[d])});let a=2*e.length,f=(h,d,p)=>h*a+2*d+(p?1:0),c=new Set;r.forEach((h,d)=>{for(let p of o[d]?[]:i.get(O(h))??[])c.add(f(d,p,j(h)!==j(e[p])))});let l=[];return r.forEach((h,d)=>{for(let p of o[d]?[]:i.get(O(h))??[]){let m=j(h)!==j(e[p]),u=m?-1:1,w=p-u;if(!(d>0&&w>=0&&w<e.length&&c.has(f(d-1,w,m)))){let S=d,g=p;for(;S<r.length&&g>=0&&g<e.length&&c.has(f(S,g,m));)S+=1,g+=u;let x=g-u;l.push({qs:t[d],qe:t[S],ts:n[Math.min(p,x)],te:n[Math.max(p,x)+1],flipped:m})}}}),l}function Ao(r){let{query:e,target:t,sequenceOf:n}=r,o=wo(e,n),s=wo(t,n),i=ei(e,t,xo(e,n),xo(t,n)),a=r.minMatch??Gs,f=r.bases??!0,c=[];for(let l of Gn(i,r.maxGap??1/0,a,Ws)){let h=[],d=l[0],p=l.at(-1),{flipped:m}=d.run;Ot(l,o,s,h,f?(w,b,S,g,x)=>{for(let y of Xs(w,b,S,a)){let E=x+b.length;c.push({...y,queryStart:g+y.queryStart,queryEnd:g+y.queryEnd,targetStart:m?E-y.targetEnd:x+y.targetStart,targetEnd:m?E-y.targetStart:x+y.targetEnd,strand:m?"+":"-",edits:m?y.edits.reverse():y.edits,shared:[]})}}:zn),c.push({queryStart:d.run.qs+d.trim,queryEnd:p.run.qe,targetStart:m?p.run.ts:d.run.ts+d.trim,targetEnd:m?d.run.te-d.trim:p.run.te,strand:m?"-":"+",edits:m?h.reverse():h,sharedBases:l.reduce((w,{run:b,trim:S})=>w+b.qe-b.qs-S,0),shared:l.map(({run:w,trim:b})=>[w.qs+b,w.qe])})}return Js(c,o.length,s.length,a).map(({shared:l,...h})=>h).sort((l,h)=>l.queryStart-h.queryStart)}function Co(r){return r.map(([e,t])=>`${t}${e}`).join("")}var fe=class extends Error{name="SubgraphLimitError";limit;windowBp;walkedBp;constructor(e,t){super(t===void 0?`Subgraph size limit of ${e} nodes exceeded`:`Subgraph size limit of ${e} nodes exceeded ${t.walkedBp} bp into a ${t.windowBp} bp window`),this.limit=e,this.windowBp=t?.windowBp,this.walkedBp=t?.walkedBp}};function Wn(r,e){return r[0]<e[0]||r[0]===e[0]&&(r[1]<e[1]||r[1]===e[1]&&r[2]<e[2])}var ct=class{heap=[];push(e,t,n){let o=this.heap;o.push([e,t,n]);let s=o.length-1;for(;s>0;){let i=s-1>>1;if(Wn(o[s],o[i]))[o[s],o[i]]=[o[i],o[s]],s=i;else break}}pop(){let e=this.heap,t=e[0],n=e.pop();if(e.length>0&&n!==void 0){e[0]=n;let o=0;for(;;){let s=2*o+1,i=s+1,a=o;if(s<e.length&&Wn(e[s],e[a])&&(a=s),i<e.length&&Wn(e[i],e[a])&&(a=i),a===o)break;[e[o],e[a]]=[e[a],e[o]],o=a}}return t}get size(){return this.heap.length}};function ti(r){let e=new Int32Array(r.length),t=new Int32Array(r.length);return r.forEach(([n,o],s)=>{e[s]=n,t[s]=o}),{pathAt:e,refAt:t,count:r.length}}function ni(r,e){let t=0,n=r.length;for(;t<n;){let o=t+n>>1;r[o]>e?n=o:t=o+1}return r[t]}function $e(r){return`${r.node}:${r.offset}`}function ft(r){return r.map(e=>re(e)).reverse()}function ri(r,e){let t=e.identity.hapStart-r.identity.hapEnd,n=r.strand==="+"?e.refStart-r.refEnd:r.refStart-e.refEnd;return r.strand===e.strand&&t>=0&&n>=0?{insertion:t,deletion:n}:void 0}function oi(r,e,t){let[n,o]=r.strand==="+"?[r,e]:[e,r],s=n.edits.map(([c,l])=>[c,l]);Mo(s,t.insertion,t.deletion);for(let[c,l]of o.edits)X(s,c,l);let i=r.identity.walkForward,[a,f]=i?[r,e]:[e,r];return{strand:r.strand,refStart:n.refStart,refEnd:o.refEnd,edits:s,weight:void 0,path:[...a.path,...f.path],start:a.start,pieces:[...a.pieces,...f.pieces],soloAligned:[...a.soloAligned,...f.soloAligned],identity:{pathHandle:r.identity.pathHandle,name:r.identity.name,hapStart:r.identity.hapStart,hapEnd:e.identity.hapEnd,walkForward:i}}}function si(r,e,t){if(r.some(i=>i.weight!==void 0))return r;let n=new Map;r.forEach((i,a)=>{if(i.identity){let f=n.get(i.identity.pathHandle);f?f.push(a):n.set(i.identity.pathHandle,[a])}});let o=new Map,s=new Set;for(let i of n.values()){i.sort((l,h)=>r[l].identity.hapStart-r[h].identity.hapStart);let a=i[0],f=r[a],c=[];for(let l of i.slice(1)){let h=r[l],d=c.length===0?ri(f,h):void 0;if(d){f=oi(f,h,d),s.add(l);continue}if(!e(h)){c.push(l);continue}let p=e(f)?t([f,...c.map(m=>r[m]),h]):void 0;if(p){f=p;for(let m of[...c,l])s.add(m)}else o.set(a,f),a=l,f=h;c=[]}o.set(a,f)}return r.flatMap((i,a)=>s.has(a)?[]:[o.get(a)??i])}function Nt(r,e){return{node:r.path[e],offset:r.offsets[e]}}var ii=32768;function ai(r){let e=[...r].sort((n,o)=>n-o),t=[];for(let n of e){let o=t[t.length-1];o&&n-o[1]<=ii?o[1]=n:t.push([n,n])}return t}var lt=class r{records=new Map;paths=[];twinStarts=new Set;twinDeferred=!1;unsettled;refId;refPath;refHandle;refInterval;refIndexCache;refPrefixCache;walkedBp;snarlMode="none";snarlFills=[];snarlNodes=new Set;stats={orderedAlignments:0,lcsAlignments:0,snarls:{fills:0,inserted:0},identificationSteps:0,identificationFetches:0,identification:{interval:0,scans:[],windowSamples:0,fragmentLengths:[],companionSeeks:0,companionMisses:0,graphLookups:0,graphFetches:0,chains:[]},keep:void 0};db;limit;signal;constructor(e,t){this.db=e,this.limit=t.limit,this.signal=t.signal}static create(e,t={}){return new r(e,t)}get nodeCount(){return this.records.size/2}get pathCount(){return this.settleDeferred(),this.paths.length}get referenceInterval(){return this.refInterval&&this.refPath?{name:this.refPath,start:this.refPath.fragment+this.refInterval[0],end:this.refPath.fragment+this.refInterval[1]}:void 0}hasNode(e){return this.records.has(be(e,"forward"))}hasHandle(e){return this.records.has(e)}record(e){let t=this.records.get(e);if(!t)throw new Error(`Subgraph has no record for handle ${e}`);return t}sortedHandles(){return[...this.records.keys()].sort((e,t)=>e-t)}async addNode(e){if(this.signal?.throwIfAborted(),this.limit!==void 0&&this.nodeCount>=this.limit)throw new fe(this.limit);let t=await this.db.getRecord(be(e,"forward")),n=await this.db.getRecord(be(e,"reverse"));if(!t||!n)throw new Error(`Node ${e} does not exist in the graph`);this.records.set(t.handle,t),this.records.set(n.handle,n)}async ensureNode(e){this.hasNode(e)||await this.addNode(e)}clearPaths(){this.paths=[],this.twinStarts.clear(),this.twinDeferred=!1,this.unsettled=void 0,this.refId=void 0,this.refPath=void 0,this.refHandle=void 0,this.refInterval=void 0,this.refIndexCache=void 0,this.refPrefixCache=void 0}async pathPosition(e){let t=await this.db.findPath(e);if(!t)throw new Error(`Cannot find a path covering offset ${e.fragment} of ${me(e)}`);if(!t.isIndexed)throw new Error(`The fragment of ${me(t.name)} at ${t.name.fragment} has not been indexed for random access`);let n=e.fragment-t.name.fragment,o=await this.db.indexedPosition(t.handle,n);if(!o)throw new Error(`The fragment of ${me(t.name)} at ${t.name.fragment} has not been indexed for random access`);return this.findPathPosition(t,n,o.pathOffset,o.pos)}async findPathPosition(e,t,n,o){let s=n,i=o;for(;;){await this.ensureNode(O(i.node));let a=this.record(i.node);if(s+a.sequenceLen>t)return{position:{seqOffset:t,handle:i.node,nodeOffset:t-s,gbwtOffset:i.offset},name:e.name,handle:e.handle};s+=a.sequenceLen;let f=a.gbwt().lf(i.offset);if(!f)throw new Error(`The fragment of ${me(e.name)} at ${e.name.fragment} does not contain offset ${t}`);i=f}}async aroundPosition(e,t,n){let o=O(e);await this.ensureNode(o);let s=this.record(e),i=je(e),a=new ct;return a.push(t,o,It(i)),a.push(s.sequenceLen-t-1,o,vt(i)),this.insertContext(a,n)}prefetchReferenceWalk(e,t){return this.prefetchReferenceRange(e.handle,e.position.seqOffset,e.position.seqOffset+t)}async prefetchReferenceRange(e,t,n){let[o,s]=await Promise.all([this.db.indexedPosition(e,t),this.db.indexedPosition(e,n)]);if(o&&s){let i=o.pos.node,a=s.pos.node;if(!await this.db.prefetchRecords([[Math.min(i,a),Math.max(i,a)+1]])){let c=await this.db.indexedPositionsBetween(e,t,n);await this.db.prefetchRecords(ai(c.map(l=>l.pos.node)).map(([l,h])=>[l,h+2]),!0)}}return o}async aroundInterval(e,t,n){if(!(t>0))throw new Error("Interval length must be greater than 0");this.walkedBp=0;try{return await this.walkInterval(e,t,n)}catch(o){throw o instanceof fe&&o.windowBp===void 0?new fe(o.limit,{windowBp:t,walkedBp:this.walkedBp}):o}}get referenceWalkedBp(){return this.walkedBp}async walkInterval(e,t,n){let o={node:e.handle,offset:e.gbwtOffset},s=e.nodeOffset,i=t,a=new ct;for(;;){let f=O(o.node),c=je(o.node);this.walkedBp=t-i,await this.ensureNode(f);let l=this.record(o.node);if(s>=l.sequenceLen)throw new Error(`Offset ${s} in node ${f} of length ${l.sequenceLen}`);a.push(s,f,It(c));let h=l.sequenceLen-s;if(i<=h){a.push(i===h?0:h-i-1,f,vt(c));break}a.push(0,f,vt(c));let d=l.gbwt().lf(o.offset);if(!d)throw new Error(`No successor for GBWT position (${o.node}, ${o.offset})`);o=d,s=0,i-=h}return this.walkedBp=t,this.insertContext(a,n)}async aroundNodes(e,t){let n=new ct;for(let o of e)await this.ensureNode(o),n.push(0,o,"left"),n.push(0,o,"right");return this.insertContext(n,t)}async insertContext(e,t){this.clearPaths(),this.snarlMode="none",this.snarlFills=[],this.snarlNodes.clear(),this.stats.snarls={fills:0,inserted:0};let n=new Set,o=new Set;for(let i of this.records.keys())o.add(O(i));let s=0;for(;e.size>0;){let[i,a,f]=e.pop(),c=`${a}:${f}`;if(n.has(c))continue;n.add(c),o.delete(a),this.hasNode(a)||(await this.addNode(a),s+=1);let l=Wr(f);if(!n.has(`${a}:${l}`)){let p=this.record(be(a,Vr(f))),m=i+p.sequenceLen-1;m<=t&&e.push(m,a,l)}let h=this.record(be(a,Qr(f))),d=i+1;if(d<=t)for(let p of h.successors()){let m=O(p),u=It(je(p));n.has(`${m}:${u}`)||e.push(d,m,u)}}for(let i of o)this.records.delete(be(i,"forward")),this.records.delete(be(i,"reverse"));return{inserted:s,removed:o.size}}async betweenNodes(e,t){return(await this.fillBetween(e,t)).inserted.length}async fillBetween(e,t){this.clearPaths();let n=[e,re(t)],o=new Set([O(e),O(t)]),s=[];for(;n.length>0;){let i=n.pop(),a=O(i);this.hasNode(a)||(await this.addNode(a),s.push(a));for(let f of this.record(i).successors()){let c=O(f);o.has(c)||(n.push(f,re(f)),o.add(c))}}return{inserted:s,nodes:o.size-2}}async extractSnarls(e){let t=0;this.snarlMode=e;for(let[n,o]of await this.overlappingSnarls(e)){let{inserted:s,nodes:i}=await this.fillBetween(n,o),a=O(n),f=O(o);this.snarlFills.push({low:Math.min(a,f),high:Math.max(a,f),nodes:i,inserted:s.length});for(let c of s)this.snarlNodes.add(c);t+=s.length}return this.stats.snarls={fills:this.snarlFills.length,inserted:this.snarlNodes.size},t}async overlappingSnarls(e){let t=[];if(e!=="none"){let n=!1;for(let o of this.sortedHandles()){let s=this.record(o),i=s.next;i!==void 0&&(n=!0,this.hasHandle(i)?Ue(o,i)&&t.push([o,i]):e==="overlapping"&&this.isSnarlEntryInSubgraph(s)&&t.push([o,i]))}if(!n&&e==="overlapping"&&await this.db.hasChainLinks()){let o=await this.findCoveringSnarl();o&&t.push(o)}}return t}isSnarlEntryInSubgraph(e){let t=e.successors(),n=t.find(o=>this.hasHandle(o));return n===void 0?!1:t.length>1||this.record(re(n)).successors().length>1}recordReader(e){let t=new Map;return async n=>{let o=this.records.get(n);if(o)return o;let s=t.get(n);if(!s){if(s=await this.db.getRecord(n),e?.(),!s)throw new Error(`Node record ${n} is missing from the database`);t.set(n,s)}return s}}async findCoveringSnarl(){let e=this.recordReader(),t=async f=>{let c=f.successors(),l=c[0];return l===void 0?!1:c.length>1||(await e(re(l))).successors().length>1},n=async f=>{let c=await e(re(f));return c.next!==void 0?await t(c)?{kind:"snarl-exit",snarl:[re(f),c.next]}:{kind:"chain"}:(await e(f)).next!==void 0?{kind:"chain"}:{kind:"regular"}},o=new Set,s=this.sortedHandles().flatMap(f=>this.record(f).successors()),i,a=!1;for(;!a&&s.length>0;){let f=s.shift(),c=O(f);if(!this.hasHandle(f)&&!o.has(c)){o.add(c);let l=await n(f);if(l.kind==="snarl-exit")i=l.snarl,a=!0;else if(l.kind==="chain")a=!0;else for(let h of["forward","reverse"])s.push(...(await e(be(c,h))).successors())}}return i}extractPaths(e,t){if(this.clearPaths(),t==="none")return;let n=e?.position;this.refPath=e?.name,this.refHandle=e?.handle;let o=this.sortedHandles(),s=o.length,i=new Map;o.forEach((y,E)=>i.set(y,E));let a=new Int32Array(s+1),f=new Int32Array(s),c=[];for(let y=0;y<s;y++){let E=this.record(o[y]),A=E.gbwt().decompressArrays();f[y]=E.sequenceLen,c.push(A),a[y+1]=a[y]+A.nodes.length}let l=a[s],h=new Int32Array(l),d=new Int32Array(l),p=new Uint8Array(l);for(let y=0;y<s;y++){let E=c[y];h.set(E.nodes,a[y]),d.set(E.offsets,a[y])}c.length=0;for(let y=0;y<l;y++){let E=i.get(h[y]);E===void 0?h[y]=-1:(h[y]=E,p[a[E]+d[y]]=1)}let m=n===void 0?void 0:i.get(n.handle),u=n?.gbwtOffset,w,b=(y,E,A)=>{let N=[],k=0,F=0,M=-1,T=y,C=E;for(;;){T===m&&C===u&&(M=k),A&&(A.push(o[T]),N.push(C)),k+=1,F+=f[T];let D=a[T]+C,Y=h[D];if(Y<0)break;C=d[D],T=Y}return{offsets:N,len:F,refAt:M,last:T}},S=(y,E,A,N)=>{N>=0&&(this.refId=this.paths.length,w=N),this.paths.push({path:y,offsets:E,len:A,weight:void 0,identity:void 0})},g=new Int32Array(s);for(let y=0;y<s;y++){let E=o[y];if(!j(E)){let A=a[y],N=a[y+1]-A;for(let k=0;k<N;k++)if(p[A+k]===0){let F=[],{offsets:M,len:T,refAt:C,last:D}=b(y,k,F),Y=o[D];if(C>=0||Le(E,Y)){if(S(F,M,T,C),!j(Y)){let v=i.get(re(Y));g[v]=g[v]+1}}else this.twinStarts.add($e({node:E,offset:k}))}}}for(let y=0;y<s;y++){let E=o[y];if(j(E)){let A=a[y],N=a[y+1]-A,k=0;for(let M=0;M<N;M++)p[A+M]===0&&(k+=1);let F=(m===void 0||w!==void 0)&&k===g[y];for(let M=0;M<N;M++)if(p[A+M]===0){let T=F?void 0:b(y,M,void 0);if(T&&(T.refAt>=0||Le(E,o[T.last]))){let C=[],{offsets:D,len:Y,refAt:v}=b(y,M,C);S(C,D,Y,v)}else this.twinStarts.add($e({node:E,offset:M}))}}}let x=this.refId===void 0?void 0:this.paths[this.refId];if(this.paths.sort((y,E)=>y.path[0]-E.path[0]||y.offsets[0]-E.offsets[0]),x&&(this.refId=this.paths.indexOf(x)),n){if(w===void 0||this.refId===void 0)throw this.clearPaths(),new Error("Could not find the reference path");let y=this.paths[this.refId],E=n.nodeOffset;for(let N of y.path.slice(0,w))E+=this.record(N).sequenceLen;let A=n.seqOffset-E;this.refInterval=[A,A+y.len],y.identity={pathHandle:e.handle,name:e.name,orientation:"forward",hapStart:A,hapEnd:A+y.len}}if(t==="distinct")this.distinctPaths(!0);else if(t==="reference-only"){if(this.refId===void 0)throw new Error("Reference path is required for reference-only output");this.paths=[this.paths[this.refId]],this.refId=0}}distinctPaths(e){let t=this.refId===void 0?void 0:this.paths[this.refId],n=t?.path,o=n&&!st(n)?ft(n):void 0,s=c=>o!==void 0&&Vn(c,o)===0||st(ft(c)),i=e&&this.db.hasHaplotypeIndex;this.twinDeferred=!1,this.paths.sort((c,l)=>Vn(c.path,l.path)||c.len-l.len||(c===t?-1:l===t?1:0));let a=[],f;for(let c of this.paths){let l=a[a.length-1],h=i&&c!==t&&s(c.path);this.twinDeferred||=h,l&&Vn(l.path,c.path)===0&&!h?l.weight=(l.weight??1)+(c.weight??1):(c===t&&(f=a.length),a.push({...c,weight:c.weight??1}))}this.paths=a,this.refId=f}mergeDistinct(){this.twinDeferred?this.settleDeferred():this.distinctPaths(!1)}settleDeferred(){this.twinDeferred&&(this.unsettled={paths:[...this.paths],refId:this.refId},this.distinctPaths(!1))}dropTwins(){let e=this.refId===void 0?void 0:this.paths[this.refId],t=this.refInterval,n=i=>`${i.pathHandle}:${i.hapStart}-${i.hapEnd}`,o=new Set;e?.identity&&t&&o.add(n({...e.identity,hapStart:t[0],hapEnd:t[1]}));for(let i of this.paths)i!==e&&i.identity?.orientation==="forward"&&o.add(n(i.identity));let s=this.paths.filter(i=>i===e||i.identity?.orientation!=="reverse"||!o.has(n(i.identity)));s.length<this.paths.length&&(this.paths=s,this.refId=e===void 0?void 0:s.indexOf(e)),this.twinDeferred&&this.distinctPaths(!1)}keepHaplotypes(e){if(this.paths.some(i=>i.weight!==void 0))throw new Error("keepHaplotypes needs one walk per haplotype: extract with haplotypes 'all', then call mergeDistinct()");let t=this.paths.filter((i,a)=>a!==this.refId&&i.identity===void 0).length;if(t>0)throw new Error(`${t} of the window's ${this.paths.length} walks have no name, so the haplotypes to keep cannot be told from the rest; call identifyPaths() first, and check that the haplotype index was built for this graph`);let n=this.refId===void 0?void 0:this.paths[this.refId],o=this.paths.filter((i,a)=>a===this.refId||i.identity!==void 0&&e(i.identity.name)),s=new Set;for(let i of o)for(let a of i.path)s.add(O(a));for(let i of[...this.records.keys()])s.has(O(i))||this.records.delete(i);this.paths=o,this.refId=n===void 0?void 0:o.indexOf(n)}async extractChosenPaths(e,t,n,o){this.clearPaths();let s=e.position.seqOffset,i=await lo({db:this.db,records:this.records,referenceHandle:e.handle,referencePos:{node:e.position.handle,offset:e.position.gbwtOffset},referenceLeft:s-e.position.nodeOffset,window:{start:s,end:s+t},context:o,snarls:{mode:this.snarlMode,fills:this.snarlFills,inserted:this.snarlNodes},keep:n,signal:this.signal,prefetchReferenceRange:(l,h,d)=>this.prefetchReferenceRange(l,h,d)});if(this.stats.keep=i.stats,i.stats.fallback!==void 0)return!1;let a=await this.db.pathsByHandle(),f=l=>({path:l.handles,offsets:l.offsets,len:l.len,weight:void 0,identity:{pathHandle:l.pathHandle,name:l===i.reference?e.name:a.get(l.pathHandle).name,orientation:l.orientation,hapStart:l.hapStart,hapEnd:l.hapEnd}}),c=[i.reference,...i.pieces].sort(ho);return this.paths=c.map(f),this.refId=c.indexOf(i.reference),this.refPath=e.name,this.refHandle=e.handle,this.refInterval=[i.reference.hapStart,i.reference.hapEnd],this.dropTwins(),!0}async identifyPaths(){if(!this.db.hasHaplotypeIndex)throw new Error("The database has no HaplotypeSamples table; run gbz-haplotype-index on it");this.unsettled&&({paths:this.paths,refId:this.refId}=this.unsettled,this.unsettled=void 0,this.twinDeferred=!0);let e=await this.db.haplotypeSampleGap()??4096,t=Fn(this.sortedHandles());if(t.length===0)return;let n=new Map,o=await Promise.all(t.map(([u,w])=>this.db.haplotypeSamplesInRange(u,w)));for(let u of o.flat())n.set($e(u),u);let s=u=>{let w=0,b=t.length-1;for(;w<b;){let g=w+b+1>>1;t[g][0]<=u?w=g:b=g-1}let S=t[w];return S[0]<=u&&u<=S[1]},i=new Map;this.paths.forEach((u,w)=>{u.path.length>0&&w!==this.refId&&i.set($e(Nt(u,0)),w)});let a=this.stats.identification;a.interval=e,a.scans=t,a.windowSamples=n.size,this.paths.forEach((u,w)=>{w!==this.refId&&a.fragmentLengths.push(u.len)});let f=this.recordReader(()=>{this.stats.identificationFetches+=1,a.graphFetches+=1}),c=u=>(a.graphLookups+=1,f(u)),l=async(u,w)=>{if(s(u.node))return n.get($e(u));this.stats.identificationFetches+=1,a.companionSeeks+=1,w.seeks+=1;let b=await this.db.haplotypeSampleAt(u.node,u.offset);return b||(a.companionMisses+=1),b},h=new Map,d=async u=>{let w=h.get(u);if(!w){let b=await this.db.getPath(u);if(!b)throw new Error(`Path ${u} is missing from the database`);w=b.name,h.set(u,w)}return w},p=(u,w,b)=>u.orientation==="forward"?{pathHandle:u.pathHandle,orientation:"forward",base:u.pathOffset-w}:{pathHandle:u.pathHandle,orientation:"reverse",base:u.pathOffset+w+b},m=(u,w)=>u.orientation==="forward"?{pathHandle:u.pathHandle,orientation:"forward",base:u.hapStart-w}:{pathHandle:u.pathHandle,orientation:"reverse",base:u.hapEnd+w};for(let u=0;u<this.paths.length;u++){let w=this.paths[u];if(u===this.refId||w.identity)continue;let b=[],S=new Set,g={fragments:0,steps:0,seeks:0,reentries:0,twinLandings:0,end:"endmarker",pathHandle:void 0};a.chains.push(g);let x,y=0,E=u,A;for(;x===void 0;){if(this.signal?.throwIfAborted(),E!==void 0){if(S.has(E)){g.end="cycle";break}S.add(E);let T=this.paths[E];b.push({index:E,startBp:y}),g.fragments+=1;let C=y;for(let Y=0;Y<T.path.length;Y++){let v=Nt(T,Y),R=n.get($e(v)),_=this.record(v.node).sequenceLen;if(R){x=p(R,C,_);break}C+=_}if(y+=T.len,x){g.end="in-fragment sample";break}let D=Nt(T,T.path.length-1);A=this.record(D.node).gbwt().lf(D.offset),E=void 0}if(A===void 0||A.node===0){g.end="endmarker";break}let N=$e(A),k=i.get(N);if(k!==void 0){let T=this.paths[k].identity;if(T){x=m(T,y),g.end="identified sibling";break}E=k;continue}this.records.has(A.node)&&(g.reentries+=1),this.twinStarts.has(N)&&(g.twinLandings+=1);let F=await l(A,g),M=await c(A.node);if(F){x=p(F,y,M.sequenceLen),g.end="out-of-window sample";break}if(this.stats.identificationSteps+=1,g.steps+=1,y-b[b.length-1].startBp>4*e+4*M.sequenceLen){g.end="bound";break}y+=M.sequenceLen,A=M.gbwt().lf(A.offset)}if(x){g.pathHandle=x.pathHandle;let N=await d(x.pathHandle);for(let{index:k,startBp:F}of b){let M=this.paths[k];M.identity=x.orientation==="forward"?{pathHandle:x.pathHandle,name:N,orientation:"forward",hapStart:x.base+F,hapEnd:x.base+F+M.len}:{pathHandle:x.pathHandle,name:N,orientation:"reverse",hapStart:x.base-F-M.len,hapEnd:x.base-F}}}}this.dropTwins()}refIndex(e){if(this.refIndexCache===void 0){let t=new Map;e.forEach((n,o)=>{let s=t.get(n);s?s.push(o):t.set(n,[o])}),this.refIndexCache=t}return this.refIndexCache}refPrefix(e){if(this.refPrefixCache===void 0){let t=[0];e.forEach((n,o)=>{t.push(t[o]+this.record(n).sequenceLen)}),this.refPrefixCache=t}return this.refPrefixCache}orderedMatches(e,t){let n=this.refIndex(t),o=new Int32Array(e.length),s=new Int32Array(e.length),i=0,a=-1;for(let f=0;f<e.length;f++){let c=n.get(e[f]);if(c){let l=ni(c,a);if(l===void 0)return;o[i]=f,s[i]=l,i+=1,a=l}}return{pathAt:o,refAt:s,count:i}}pathLen(e){let t=0;for(let n of e)t+=this.record(n).sequenceLen;return t}prefixMatches(e,t){let n=0,o=0,s=0,i=0,a=0;for(;o<e.length&&s<t.length;){let f=this.record(e[o]).sequence,c=this.record(t[s]).sequence;for(;i<f.length&&a<c.length;){if(f[i]!==c[a])return n;i+=1,a+=1,n+=1}i===f.length&&(o+=1,i=0),a===c.length&&(s+=1,a=0)}return n}suffixMatches(e,t){let n=0,o=0,s=0,i=0,a=0;for(;o<e.length&&s<t.length;){let f=this.record(e[e.length-o-1]).sequence,c=this.record(t[t.length-s-1]).sequence;for(;i<f.length&&a<c.length;){if(f[f.length-i-1]!==c[c.length-a-1])return n;i+=1,a+=1,n+=1}i===f.length&&(o+=1,i=0),a===c.length&&(s+=1,a=0)}return n}align(e,t,n){let o=this.pathLen(e),s=this.pathLen(t),i=this.prefixMatches(e,t),a=this.suffixMatches(e,t);i+a>o&&(a=o-i),i+a>s&&(a=s-i),X(n,"M",i),Mo(n,o-i-a,s-i-a),X(n,"M",a)}sharedWeight(e,t){let n=this.refIndex(t),o=0;for(let s of e)n.has(s)&&(o+=this.record(s).sequenceLen);return o}editsAgainst(e,t){let n=this.orderedMatches(e,t);n?this.stats.orderedAlignments+=1:this.stats.lcsAlignments+=1;let o=n??ti(po(e,t,h=>this.record(h).sequenceLen)[0]),s=[],i=this.refPrefix(t),a=(h,d,p,m)=>{h===d?X(s,"D",i[m]-i[p]):p===m?X(s,"I",this.pathLen(e.slice(h,d))):this.align(e.slice(h,d),t.slice(p,m),s)},f=0,c=0,l=0;for(let h=0;h<o.count;h++){let d=o.pathAt[h],p=o.refAt[h];(c!==d||l!==p)&&a(c,d,l,p);let m=this.record(e[d]).sequenceLen;X(s,"M",m),f+=m,c=d+1,l=p+1}return a(c,e.length,l,t.length),{edits:s,matched:f,matches:o}}alignment(e){let t=this.paths[e];if(this.refId===void 0||e===this.refId||!t)return;let n=this.paths[this.refId].path,o;if(st(n)&&(t.identity===void 0||!st(ft(t.path))))o={...this.editsAgainst(t.path,n),flipped:!1};else{let s=ft(t.path),i=this.sharedWeight(t.path,n);if(this.sharedWeight(s,n)===0)o={...this.editsAgainst(t.path,n),flipped:!1};else if(i===0)o={...this.editsAgainst(s,n),flipped:!0};else{let f=this.editsAgainst(t.path,n),c=this.editsAgainst(s,n);o=c.matched>f.matched?{...c,flipped:!0}:{...f,flipped:!1}}}return o}alignToRef(e){return this.settleDeferred(),this.alignment(e)?.edits.map(([t,n])=>`${n}${t}`).join("")}alignments(){this.settleDeferred();let e=this.referenceInterval;if(this.refId===void 0||!e)throw new Error("Alignments need a reference path");let t=this.paths[this.refId].path,n=this.refPrefix(t)[t.length],o=(l,h,d,p)=>{let m=ci(l),u=this.paths[d[0]],w=this.paths[d[d.length-1]],b=u.identity,S=b?.orientation==="forward",[g,x]=S?[u,w]:[w,u];return{strand:h,refStart:e.start+m.leading,refEnd:e.start+n-m.trailing,edits:m.edits,weight:u.weight,path:d.flatMap(y=>this.paths[y].path),start:Nt(u,0),pieces:d,soloAligned:p,identity:b===void 0?void 0:{pathHandle:b.pathHandle,name:b.name,hapStart:b.name.fragment+g.identity.hapStart,hapEnd:b.name.fragment+x.identity.hapEnd,walkForward:S}}},s=l=>l.soloAligned.reduce((h,d)=>h+d,0),i=l=>l.pieces.reduce((h,d)=>h+this.paths[d].len,0),a=l=>2*s(l)>=i(l),f=l=>{let h=l[0],d=l[l.length-1],p=h.identity.walkForward;if(l.some((C,D)=>C.strand!==h.strand||C.identity.walkForward!==p||D>0&&C.identity.hapStart<l[D-1].identity.hapEnd))return;let m=p?l:[...l].reverse(),u=m.flatMap(C=>C.pieces),w=m.flatMap(C=>C.soloAligned),b=h.strand==="+"!==p,S=u.map(C=>this.paths[C]),g=S.slice(1).map((C,D)=>{let Y=S[D].identity;return p?C.identity.hapStart-Y.hapEnd:Y.hapStart-C.identity.hapEnd}),x=b?[...S].reverse():S,y=b?[...g].reverse():g,E=x.flatMap(C=>b?ft(C.path):C.path),{edits:A}=this.editsAgainst(E,t),N=Ro(A,x.map(C=>C.len)),k=new Map((b?[...u].reverse():u).map((C,D)=>[C,N[D]])),F=C=>2*C.pieces.reduce((D,Y)=>D+k.get(Y),0)>=s(C);if(!F(h)||!F(d))return;let M=[],T=0;return x.slice(0,-1).forEach((C,D)=>{T+=C.len,M.push([T,y[D]])}),o(li(A,M),h.strand,u,w)},c=[];return this.paths.forEach((l,h)=>{if(h===this.refId)return;let{edits:d,flipped:p}=this.alignment(h),m=l.identity,u=m?m.orientation==="forward"!==p:!p;c.push(o(d,u?"+":"-",[h],Ro(d,[l.len])))}),si(c,a,f).map(l=>{let{edits:h,identity:d,pieces:p,soloAligned:m,...u}=l,w={...u,cigar:hi(h)};return d?{...w,resolved:!0,name:d.name,label:me({...d.name,fragment:d.hapStart,end:d.hapEnd}),pathHandle:d.pathHandle,hapStart:d.hapStart,hapEnd:d.hapEnd}:{...w,resolved:!1}})}pairAlignments(e){let{target:t,query:n,...o}=e,s=this.paths.flatMap(l=>{let{identity:h}=l;return h?[{name:h.name,start:h.name.fragment+h.hapStart,steps:Lt(l,h)}]:[]}),i=l=>h=>h.sample===l.sample&&h.haplotype===l.haplotype,a=i(t),f=n?i(n):l=>!a(l),c=l=>this.record(be(l,"forward")).sequence;return s.filter(l=>a(l.name)).flatMap(l=>s.filter(h=>f(h.name)).flatMap(h=>Ao({...o,query:h.steps,target:l.steps,sequenceOf:c}).map(d=>({query:h.name,queryStart:h.start+d.queryStart,queryEnd:h.start+d.queryEnd,strand:d.strand,target:l.name,targetStart:l.start+d.targetStart,targetEnd:l.start+d.targetEnd,cigar:Co(d.edits),matches:d.edits.reduce((p,[m,u])=>p+(m==="="?u:0),0),columns:d.edits.reduce((p,[,m])=>p+m,0),sharedBases:d.sharedBases}))))}canonicalEdges(e){let t=[];for(let n of["forward","reverse"]){let o=be(e,n);for(let s of this.record(o).successors())this.hasHandle(s)&&Ue(o,s)&&t.push([n==="reverse"?1:0,O(s),j(s)?1:0])}return t.sort((n,o)=>n[0]-o[0]||n[1]-o[1]||n[2]-o[2]),t.filter((n,o)=>o===0||n[0]!==t[o-1][0]||n[1]!==t[o-1][1]||n[2]!==t[o-1][2])}async stableName(){let e=new TextEncoder,t=[];for(let n of this.sortedHandles())if(!j(n)){let o=O(n),s=`S	${o}	${this.record(n).sequence}
+`;for(let[i,a,f]of this.canonicalEdges(o))s+=`L	${o}	${i?"-":"+"}	${a}	${f?"-":"+"}
+`;t.push(e.encode(s))}return io(t)}async toGFA(e={}){this.settleDeferred();let t=e.cigar??!1,n=[this.refPath?`H	VN:Z:1.1	RS:Z:${this.refPath.sample}`:"H	VN:Z:1.1",...so(oo(await this.stableName(),await this.db.graphName()))],o=this.sortedHandles();for(let c of o)j(c)||n.push(`S	${O(c)}	${this.record(c).sequence}`);let s=c=>j(c)?"-":"+";for(let c of o)for(let l of this.record(c).successors())this.hasHandle(l)&&Ue(c,l)&&n.push(`L	${O(c)}	${s(c)}	${O(l)}	${s(l)}	0M`);let i=(c,l,h,d,p)=>{let m=Lt(c,l).map(b=>`${j(b)?"<":">"}${O(b)}`).join(""),u=c.weight===void 0?"":`	WT:i:${c.weight}`,w=p===void 0?"":`	CG:Z:${p}`;return`W	${h.sample}	${h.haplotype}	${h.contig}	${h.fragment}	${d}	${m}${u}${w}`},a=this.refPath?.contig??"unknown";this.refId!==void 0&&this.refPath&&this.refInterval&&n.push(i(this.paths[this.refId],void 0,{...this.refPath,fragment:this.refPath.fragment+this.refInterval[0]},this.refPath.fragment+this.refInterval[1],void 0));let f=1;return this.paths.forEach((c,l)=>{if(l!==this.refId){let h=e.names!=="anonymous"?c.identity:void 0,d=t?this.alignToRef(l):void 0;n.push(h?i(c,h,{...h.name,fragment:h.name.fragment+h.hapStart},h.name.fragment+h.hapEnd,d):i(c,void 0,{sample:"unknown",contig:a,haplotype:f,fragment:0},c.len,d)),f+=1}}),`${n.join(`
+`)}
+`}outputPaths(e){this.settleDeferred();let t=e.cigar??!1,n=[],o=this.refPath?.contig??"unknown";if(this.refId!==void 0&&this.refPath&&this.refInterval){let i={...this.refPath,fragment:this.refPath.fragment+this.refInterval[0]};n.push({info:this.paths[this.refId],identity:void 0,name:me({...i,end:this.refPath.fragment+this.refInterval[1]}),cigar:void 0})}let s=1;return this.paths.forEach((i,a)=>{if(a===this.refId)return;let f=e.names!=="anonymous"?i.identity:void 0;n.push({info:i,identity:f,name:f?me({...f.name,fragment:f.name.fragment+f.hapStart,end:f.name.fragment+f.hapEnd}):me({sample:"unknown",contig:o,haplotype:s,fragment:0,end:i.len}),cigar:t?this.alignToRef(a):void 0}),s+=1}),n}*outputEdges(){for(let e of this.sortedHandles())for(let t of this.record(e).successors())this.hasHandle(t)&&Ue(e,t)&&(yield[e,t])}walkSpans(){return this.settleDeferred(),this.paths.flatMap((e,t)=>{let n=t===this.refId?void 0:e.identity;return n?[{name:n.name,start:n.name.fragment+n.hapStart,end:n.name.fragment+n.hapEnd}]:[]})}toSubgraphJson(e={}){let t=this.sortedHandles().filter(s=>!j(s)).map(s=>({id:String(O(s)),sequence:this.record(s).sequence})),n=[];for(let[s,i]of this.outputEdges())n.push({from:String(O(s)),from_is_reverse:j(s),to:String(O(i)),to_is_reverse:j(i)});let o=this.outputPaths(e).map(s=>fi(s.info,s.identity,s.name,s.cigar));return{nodes:t,edges:n,paths:o}}toCompactSubgraph(e={}){let t=this.sortedHandles().filter(i=>!j(i)),n=new Int32Array(t.length),o=[];t.forEach((i,a)=>{n[a]=O(i),o.push(this.record(i).sequence)});let s=[];for(let[i,a]of this.outputEdges())s.push(i,a);return{nodeIds:n,nodeSequences:o,edges:Int32Array.from(s),paths:this.outputPaths(e).map(i=>({name:i.name,weight:i.info.weight,cigar:i.cigar,steps:Int32Array.from(Lt(i.info,i.identity))}))}}};function Lt(r,e){return e?.orientation==="reverse"?r.path.map(t=>re(t)).reverse():r.path}function fi(r,e,t,n){return{name:t,...r.weight===void 0?{}:{weight:r.weight},...n===void 0?{}:{cigar:n},path:Lt(r,e).map(o=>({id:String(O(o)),is_reverse:j(o)}))}}function Vn(r,e){let t=Math.min(r.length,e.length);for(let n=0;n<t;n++){let o=r[n],s=e[n];if(o!==s)return o<s?-1:1}return r.length-e.length}function X(r,e,t){if(t===0)return;let n=r[r.length-1];n?.[0]===e?n[1]+=t:r.push([e,t])}function Tt(r){return r===0?0:6+(r-1)}function Mo(r,e,t){if(e===0)X(r,"D",t);else if(t===0)X(r,"I",e);else{let n=Math.min(e,t),o=4*n+Tt(e-n)+Tt(t-n),s=Tt(e)+Tt(t);o<=s?(X(r,"M",n),X(r,"I",e-n),X(r,"D",t-n)):(X(r,"I",e),X(r,"D",t))}}function ci(r){let e=0;for(;e<r.length&&r[e][0]!=="M";)e+=1;if(e===r.length){let a=r.filter(([c])=>c==="I"),f=r.filter(([c])=>c==="D").reduce((c,[,l])=>c+l,0);return{edits:a.map(([c,l])=>[c,l]),leading:0,trailing:f}}let t=r.length;for(;r[t-1][0]!=="M";)t-=1;let n=a=>({inserted:a.reduce((f,[c,l])=>f+(c==="I"?l:0),0),deleted:a.reduce((f,[c,l])=>f+(c==="D"?l:0),0)}),o=n(r.slice(0,e)),s=n(r.slice(t)),i=[];X(i,"I",o.inserted);for(let[a,f]of r.slice(e,t))X(i,a,f);return X(i,"I",s.inserted),{edits:i,leading:o.deleted,trailing:s.deleted}}function Ro(r,e){let t=e.map(()=>0),n=e.length-1,o=0,s=e[0],i=0;for(let[a,f]of r){if(a==="D")continue;let c=f;for(;c>0;){for(;o<n&&i>=s;)o+=1,s+=e[o];let l=o<n?Math.min(c,s-i):c;a==="M"&&(t[o]+=l),i+=l,c-=l}}return t}function li(r,e){let t=[],n=0,o=0;for(let[s,i]of r){if(s==="D"){X(t,s,i);continue}let a=n;for(;o<e.length&&e[o][0]<n+i;){let[f,c]=e[o];X(t,s,f-a),X(t,"I",c),a=f,o+=1}X(t,s,n+i-a),n+=i}for(;o<e.length;o++)X(t,"I",e[o][1]);return t}function hi(r){return r.map(([e,t])=>`${t}${e}`).join("")}function _e(r,e,t=0){if(!Number.isSafeInteger(e)||e<t)throw new Error(`${r} must be a whole number${t>0?` of at least ${t}`:""}, not ${e}`);return e}function Ft(r){return _e("context",r.context??100)}function $t(r,e){return e.limit!==void 0&&_e("limit",e.limit),lt.create(r,e)}async function Po(r,e){let t=Ft(e),n=$t(r,e),o=await n.pathPosition(Ve(We(e.path),_e("offset",e.offset)));return await n.aroundPosition(o.position.handle,o.position.nodeOffset,t),await n.extractSnarls(e.snarls??"none"),n.extractPaths(o,e.haplotypes??"all"),n}async function di(r,e){let t=_e("start",e.start),n=_e("end",e.end),o=Ft(e),s=$t(r,e);try{let i=await s.pathPosition(Ve(We(e.path),t));return await s.prefetchReferenceWalk(i,n-t),await s.aroundInterval(i.position,n-t,o),await s.extractSnarls(e.snarls??"none"),{subgraph:s,reference:i}}catch(i){throw i instanceof fe&&i.windowBp===void 0?new fe(i.limit,{windowBp:n-t,walkedBp:s.referenceWalkedBp??0}):i}}async function Qn(r,e){let{keep:t}=e,n=e.haplotypes??"all",o=n==="all"||n==="distinct";if(t!==void 0&&o&&!r.hasHaplotypeIndex)throw new Error("keep needs the haplotype index: this database cannot name its walks");let{subgraph:s,reference:i}=await di(r,e);return t===void 0||!o?(s.extractPaths(i,n),s):(await s.extractChosenPaths(i,e.end-e.start,t,Ft(e))||(s.extractPaths(i,"all"),await s.identifyPaths()),s.keepHaplotypes(t),n==="distinct"&&s.mergeDistinct(),s)}async function ko(r,e){let t=e.haplotypes??"all",n=e.snarls??"none";if(t==="reference-only")throw new Error("Cannot output a reference path in a node-based query");if(n==="overlapping"&&new Set(e.nodeIds).size>1)throw new Error("Overlapping snarls cannot be extracted for a node-based query with multiple nodes");let o=Ft(e);for(let i of e.nodeIds)_e("node id",i,1);let s=$t(r,e);return await s.aroundNodes(e.nodeIds,o),await s.extractSnarls(n),s.extractPaths(void 0,t),s}async function _o(r,e){let t=e.haplotypes??"all";if(t==="reference-only")throw new Error("Cannot output a reference path in a node-based query");let n=$t(r,e);return await n.betweenNodes(_e("startHandle",e.startHandle,2),_e("endHandle",e.endHandle,2)),n.extractPaths(void 0,t),n}function Ee(r,e){let t=0;for(let o=0;o<8;o++){let s=r[e+o];if(s===void 0)throw new Error("SQLite varint runs past the end of the buffer");if(t=t*128+(s&127),(s&128)===0){if(o===7&&!Number.isSafeInteger(t))throw new Error("SQLite varint exceeds the safe integer range");return[t,e+o+1]}}let n=r[e+8];if(n===void 0)throw new Error("SQLite varint runs past the end of the buffer");if(t=t*256+n,!Number.isSafeInteger(t))throw new Error("SQLite varint exceeds the safe integer range");return[t,e+9]}function pi(r,e,t){switch(t){case 1:return r.getInt8(e);case 2:return r.getInt16(e);case 3:return r.getInt8(e)<<16|r.getUint16(e+1);case 4:return r.getInt32(e);case 6:return r.getInt16(e)*4294967296+r.getUint32(e+2);default:{let n=r.getBigInt64(e);if(n>BigInt(Number.MAX_SAFE_INTEGER)||n<BigInt(Number.MIN_SAFE_INTEGER))throw new Error(`SQLite integer ${n} exceeds the safe integer range`);return Number(n)}}}var ui=new TextDecoder;function qt(r){let[e,t]=Ee(r,0),n=[],o=t;for(;o<e;){let[a,f]=Ee(r,o);n.push(a),o=f}let s=new DataView(r.buffer,r.byteOffset,r.byteLength),i=e;return n.map(a=>{if(a===0)return null;if(a>=1&&a<=6){let f=a<=4?a:a===5?6:8,c=pi(s,i,f);return i+=f,c}if(a===7){let f=s.getFloat64(i);return i+=8,f}if(a===8)return 0;if(a===9)return 1;if(a>=12){let f=a-12>>1,c=r.subarray(i,i+f);return i+=f,a%2===0?c:ui.decode(c)}throw new Error(`SQLite serial type ${a} is reserved`)})}var Ht=2,Dt=5,Oo=10,Bt=13;function No(r,e){return r[e]*256+r[e+1]}function Oe(r,e){return r[e]*16777216+r[e+1]*65536+r[e+2]*256+r[e+3]}function mi(r,e){let t=r[e];if(t!==Ht&&t!==Dt&&t!==Oo&&t!==Bt)throw new Error(`SQLite page has unknown b-tree type ${t}`);let n=t===Ht||t===Dt;return{type:t,cellCount:No(r,e+3),rightChild:n?Oe(r,e+8):0,cellPointers:e+(n?12:8)}}function Re(r,e,t){return No(r,e.cellPointers+2*t)}var gi=4096,Gt=class{usable;pager;decodedIndexPages=new Map;tableDepths=new Map;constructor(e,t){this.pager=e,this.usable=e.pageSize-t}localPayloadSize(e,t){let n=this.usable,o=t?Math.floor((n-12)*64/255)-23:n-35;if(e<=o)return e;let s=Math.floor((n-12)*32/255)-23,i=s+(e-s)%(n-4);return i<=o?i:s}async payload(e,t,n,o){let s=this.localPayloadSize(n,o);if(s===n)return e.subarray(t,t+n);let i=new Uint8Array(n);i.set(e.subarray(t,t+s),0);let a=s,f=Oe(e,t+s);for(;f!==0&&a<n;){let c=await this.pager.page(f),l=c.subarray(4,4+Math.min(this.usable-4,n-a));i.set(l,a),a+=l.length,f=Oe(c,0)}if(a!==n)throw new Error("SQLite overflow chain ended before the payload was complete");return i}async pageAt(e){let t=await this.pager.page(e);return{page:t,header:mi(t,e===1?100:0)}}tableDepth(e,t){let n=this.tableDepths.get(e);return n||(n=(async()=>{let o=e;for(let s=0;;s++){let{page:i,header:a}=await this.pageAt(o);if(a.type===Bt)return s;if(a.type!==Dt)throw new Error("SQLite table b-tree contains an index page");let f=this.childIndexFor(i,a,t);o=f===a.cellCount?a.rightChild:Oe(i,Re(i,a,f))}})(),this.tableDepths.set(e,n),n.catch(()=>this.tableDepths.delete(e))),n}childIndexFor(e,t,n){let o=0,s=t.cellCount;for(;o<s;){let i=o+s>>1,[a]=Ee(e,Re(e,t,i)+4);a<n?o=i+1:s=i}return o}async prefetchRowidRanges(e,t,n=!1){if(t.length===0)return!0;let o=await this.tableDepth(e,t[0][0]),s=t.map(()=>[e]);for(let i=0;i<o;i++){s=await Promise.all(s.map((f,c)=>this.childrenInRange(f,...t[c])));let a=s.flat();if(n)this.pager.prefetchLeading(a);else if(!this.pager.prefetch(a))return!1}return!0}async childrenInRange(e,t,n){let o=await Promise.all(e.map(i=>this.pageAt(i))),s=[];return o.forEach(({page:i,header:a},f)=>{let c=f===0?this.childIndexFor(i,a,t):0,l=f===o.length-1?this.childIndexFor(i,a,n):a.cellCount;for(let h=c;h<=l;h++)s.push(h===a.cellCount?a.rightChild:Oe(i,Re(i,a,h)))}),s}async tableRowid(e,t){let n=e;for(;;){let{page:o,header:s}=await this.pageAt(n);if(s.type===Bt){let f=0,c=s.cellCount;for(;f<c;){let l=f+c>>1,h=Re(o,s,l),[d,p]=Ee(o,h),[m,u]=Ee(o,p);if(m===t)return qt(await this.payload(o,u,d,!1));m<t?f=l+1:c=l}return}if(s.type!==Dt)throw new Error("SQLite table b-tree contains an index page");let i=0,a=s.cellCount;for(;i<a;){let f=i+a>>1,c=Re(o,s,f),[l]=Ee(o,c+4);l<t?i=f+1:a=f}n=i===s.cellCount?s.rightChild:Oe(o,Re(o,s,i))}}async*tableScan(e){yield*this.scanPage(e,await this.tableDepth(e,0))}async*scanPage(e,t){let{page:n,header:o}=await this.pageAt(e);if(o.type===Bt)for(let s=0;s<o.cellCount;s++){let i=Re(n,o,s),[a,f]=Ee(n,i),[c,l]=Ee(n,f);yield{rowid:c,values:qt(await this.payload(n,l,a,!1))}}else{let s=[];for(let i=0;i<o.cellCount;i++)s.push(Oe(n,Re(n,o,i)));s.push(o.rightChild),t===1&&this.pager.prefetchLeading(s);for(let i of s)yield*this.scanPage(i,t-1)}}decodedCells(e,t){let n=this.decodedIndexPages.get(e);if(n)this.decodedIndexPages.delete(e);else if(n=new Array(t.cellCount),this.decodedIndexPages.size>=gi){let o=this.decodedIndexPages.keys().next().value;o!==void 0&&this.decodedIndexPages.delete(o)}return this.decodedIndexPages.set(e,n),n}async indexCell(e,t,n,o){let s=this.decodedCells(e,n),i=s[o];if(!i){let a=Re(t,n,o),f=n.type===Ht,[c,l]=Ee(t,f?a+4:a);i={values:qt(await this.payload(t,l,c,!0)),leftChild:f?Oe(t,a):0},s[o]=i}return i}async lowerBound(e,t,n,o,s,i){let a=s,f=n.cellCount;for(;a<f;){let c=a+f>>1,l=await this.indexCell(e,t,n,c),h=Yn(l.values,o);h<0||i&&h===0?a=c+1:f=c}return a}async*indexScanFrom(e,t,n){let{page:o,header:s}=await this.pageAt(e),i=await this.lowerBound(e,o,s,t,0,!1),a=s.type===Ht;if(a&&n){let f=await this.lowerBound(e,o,s,n,i,!0),c=[];for(let l=i;l<=f;l++)c.push(l===s.cellCount?s.rightChild:(await this.indexCell(e,o,s,l)).leftChild);this.pager.prefetchLeading(c)}for(let f=i;f<s.cellCount;f++){let c=await this.indexCell(e,o,s,f);if(a&&(yield*this.indexScanFrom(c.leftChild,t,n)),n&&Yn(c.values,n)>0)return;yield c.values}a&&(yield*this.indexScanFrom(s.rightChild,t,n))}async indexSeekLE(e,t){let n,o=e;for(;;){let{page:s,header:i}=await this.pageAt(o),a=0,f=i.cellCount,c=0;for(;a<f;){let l=a+f>>1,h=await this.indexCell(o,s,i,l);Yn(h.values,t)<=0?(n=h.values,a=l+1):(c=h.leftChild,f=l)}if(i.type===Oo)return n;o=a===i.cellCount?i.rightChild:c}}};function Yn(r,e){for(let t=0;t<e.length;t++){let n=r[t],o=e[t];if(typeof n!="number"||o===void 0)throw new Error("SQLite index key is not numeric");if(n!==o)return n<o?-1:1}return 0}function To({blockSize:r,maxBlocks:e}){if(r!==void 0&&!(Number.isSafeInteger(r)&&r>0))throw new Error(`blockSize must be a positive integer, not ${r}`);if(e!==void 0&&!(Number.isSafeInteger(e)&&e>0))throw new Error(`maxBlocks must be a positive integer, not ${e}`)}var zt=class{blocks=new Map;blockSize;maxBlocks;plan;bytesFetched=0;fetches=0;source;pageSize;fileSize;constructor(e,t,n,o={}){this.source=e,this.pageSize=t,this.fileSize=n;let s=o.blockSize??65536;this.blockSize=Math.max(t,Math.ceil(s/t)*t),this.maxBlocks=o.maxBlocks??256}async read(e,t){let n=await this.readRetrying(e,t);if(this.bytesFetched+=n.length,n.length<e)throw new Error(`the file ends at byte ${t+n.length}, short of the ${this.fileSize} bytes its SQLite header gives`);return n}async readRetrying(e,t){let n=0;for(;;)try{return await this.source.read(e,t)}catch(o){if(n+=1,n>=3)throw o;await new Promise(s=>setTimeout(s,200*n))}}seed(e,t){t.length===Math.min(this.blockSize,this.fileSize-e*this.blockSize)&&this.blocks.set(e,Promise.resolve(t))}block(e){this.follow(e);let t=this.touch(e);if(t)return t;let n=e*this.blockSize,o=Math.min(this.blockSize,this.fileSize-n),s=this.read(o,n);return this.fetches+=1,this.store(e,s),this.evict(),s}touch(e){let t=this.blocks.get(e);return t&&(this.blocks.delete(e),this.blocks.set(e,t)),t}blockOf(e){return Math.floor((e-1)*this.pageSize/this.blockSize)}get prefetchBudget(){return Math.max(1,Math.floor(this.maxBlocks/2))}get chunk(){return Math.max(1,Math.floor(this.prefetchBudget/2))}prefetch(e){let t=new Set(e.map(n=>this.blockOf(n)));return t.size>this.prefetchBudget?!1:(this.fetchBlocks(t),!0)}prefetchLeading(e){let t=[],n=new Map;for(let o of e){let s=this.blockOf(o);n.has(s)||(n.set(s,t.length),t.push(s))}this.plan={blocks:t,position:n,next:0},this.advance(this.prefetchBudget)}advance(e){let t=this.plan;if(!t)return;let n=t.blocks.slice(t.next,t.next+e);t.next+=n.length,t.next>=t.blocks.length&&(this.plan=void 0),this.fetchBlocks(new Set(n))}follow(e){let t=this.plan,n=t?.position.get(e);t&&n!==void 0&&n>=t.next-Math.ceil(this.chunk/2)&&this.advance(this.chunk)}fetchBlocks(e){let t=[...e].filter(o=>!this.touch(o)).sort((o,s)=>o-s),n=0;for(;n<t.length;){let o=n+1;for(;o<t.length&&t[o]===t[o-1]+1;)o+=1;this.fetchRun(t[n],o-n),n=o}}fetchRun(e,t){let n=e*this.blockSize,o=Math.min(t*this.blockSize,this.fileSize-n),s=this.read(o,n);this.fetches+=1;for(let i=0;i<t;i++){let a=i*this.blockSize;this.store(e+i,s.then(f=>f.subarray(a,a+this.blockSize)))}this.evict()}store(e,t){this.blocks.set(e,t),t.catch(()=>{this.blocks.get(e)===t&&this.blocks.delete(e)})}evict(){for(;this.blocks.size>this.maxBlocks;){let e=this.blocks.keys().next().value;if(e===void 0)break;this.blocks.delete(e)}}async page(e){let t=(e-1)*this.pageSize;if(e<1||t+this.pageSize>this.fileSize)throw new Error(`SQLite page ${e} is outside the file`);let n=await this.block(Math.floor(t/this.blockSize)),o=t%this.blockSize;return n.subarray(o,o+this.pageSize)}};var ht=class r{pager;btree;objects;constructor(e,t,n){this.pager=e,this.btree=t,this.objects=n}static async open(e,t={}){To(t);let n=await e.read(Math.max(512,t.blockSize??65536),0),o=n.subarray(0,100);if(new TextDecoder().decode(o.subarray(0,15))!=="SQLite format 3"||o.length<100)throw new Error("Not a SQLite database");let i=new DataView(o.buffer,o.byteOffset,o.byteLength),a=i.getUint16(16),f=a===1?65536:a,c=o[20]??0,l=i.getUint32(56);if(l!==1)throw new Error(`SQLite text encoding ${l} is not UTF-8`);let h=i.getUint32(28);if(h===0||i.getUint32(24)!==i.getUint32(92))throw new Error("SQLite header has no valid database size; the file was written by SQLite older than 3.7.0");let d=h*f,p=new zt(e,f,d,t);p.seed(0,n),p.fetches+=1,p.bytesFetched+=n.length;let m=new Gt(p,c),u=new Map;for await(let{values:w}of m.tableScan(1)){let[b,S,g,x,y]=w;typeof b=="string"&&typeof S=="string"&&typeof g=="string"&&typeof x=="number"&&u.set(S,{type:b,name:S,tableName:g,rootPage:x,sql:typeof y=="string"?y:""})}return new r(p,m,u)}rootPage(e){let t=this.objects.get(e);if(!t)throw new Error(`SQLite database has no object named ${e}`);return t.rootPage}withoutRowid(e){let t=this.objects.get(e);return t?.type==="table"&&/without\s+rowid/i.test(t.sql)}indexOn(e){let t=[...this.objects.values()].find(n=>n.type==="index"&&n.tableName===e);if(t)return t.rootPage;if(this.withoutRowid(e))return this.rootPage(e);throw new Error(`SQLite table ${e} has no index`)}byRowid(e,t){return this.btree.tableRowid(this.rootPage(e),t)}prefetchRows(e,t,n=!1){return this.btree.prefetchRowidRanges(this.rootPage(e),t,n)}scan(e){return this.btree.tableScan(this.rootPage(e))}indexSeekLE(e,t){return this.btree.indexSeekLE(this.indexOn(e),t)}indexScanFrom(e,t,n){return this.btree.indexScanFrom(this.indexOn(e),t,n)}has(e){return this.objects.has(e)}};var Jn="GBZ-base version 4",jt=class extends Error{name="UnknownPathError";path;constructor(e){super(`the graph has no path named ${me(e)}`),this.path=e}},Ut=class extends Error{name="ForwardOnlyIndexError";constructor(){super("the haplotype index was written with --forward-only, which cannot name the walks stored against their reference (about half of them); rebuild it with gbz-haplotype-index without --forward-only")}},Wt=class extends Error{name="SchemaVersionError";found;constructor(e){super(e===void 0?"not a gbz-base database: it has no version tag":`unsupported database schema "${e}"; this reader understands "${Jn}"`),this.found=e}};function wi(r){if(r.length===1)return r[0];let e=new Uint8Array(r.reduce((n,o)=>n+o.length,0)),t=0;for(let n of r)e.set(n,t),t+=n.length;return e}var Kn=3,Ye=class{at=0;bytes;constructor(e){this.bytes=e}get done(){return this.at>=this.bytes.length}next(){let e=0,t=1;for(;;){let n=this.bytes[this.at++];if(n===void 0)throw new Error("a haplotype index blob ends inside a number");if(e+=(n&127)*t,t*=128,(n&128)===0)return e}}};function xi(r,e){let t=new Ye(r),n=0;for(;!t.done;){let o=n+t.next();n=o+t.next(),e.push([o,n])}}function yi(r){r.sort((n,o)=>n[0]-o[0]);let e=[],t=[];for(let[n,o]of r){let s=t.length-1;s>=0&&n<=t[s]+1?t[s]=Math.max(t[s],o):(e.push(n),t.push(o))}return n=>{let o=0,s=e.length;for(;o<s;){let i=o+s>>1;e[i]<=n?o=i+1:s=i}return o>0&&n<=t[o-1]}}function bi(r,e,t){let n=new Ye(e);for(;!n.done;){let o=n.next(),s=n.next(),i=n.next(),a=n.next(),f=n.next();t.push({bin:r,pathHandle:o,pathStart:s,pathEnd:i,snarl:f>0?[a,f]:void 0,node:n.next(),offset:n.next()})}}function Si(r,e,t){let n=O(r);for(let o of e){let s=new Ye(o);for(;!s.done;){let i=s.next(),a=i%2;t.push({node:2*n+a,offset:s.next(),pathHandle:(i-a)/2,orientation:"forward",pathOffset:s.next()})}}}var Zn=class{sequenceLen;handle;edges;bwt;encodedSequence;next;decoded;constructor(e,t,n,o,s){this.handle=e,this.edges=t,this.bwt=n,this.encodedSequence=o,this.next=s,this.sequenceLen=Xr(o)}get id(){return O(this.handle)}get orientation(){return je(this.handle)}get sequence(){return this.decoded??=Zr(this.encodedSequence),this.decoded}successors(){return this.edges.filter(e=>e.node!==0).map(e=>e.node)}gbwt(){if(this.edges.length===0)throw new Error(`GBWT record for handle ${this.handle} is empty`);return new At(this.edges,this.bwt)}};function Q(r,e){if(typeof r!="number")throw new Error(`${e} is not a number in the database`);return r}function dt(r,e){if(typeof r!="string")throw new Error(`${e} is not text in the database`);return r}function qe(r,e){if(!(r instanceof Uint8Array))throw new Error(`${e} is not a blob in the database`);return r}function Lo(r,e){return{handle:r,fwStart:{node:Q(e[1],"Paths.fw_node"),offset:Q(e[2],"Paths.fw_offset")},revStart:{node:Q(e[3],"Paths.rev_node"),offset:Q(e[4],"Paths.rev_offset")},name:{sample:dt(e[5],"Paths.sample"),contig:dt(e[6],"Paths.contig"),haplotype:Q(e[7],"Paths.haplotype"),fragment:Q(e[8],"Paths.fragment")},isIndexed:Q(e[9],"Paths.is_indexed")!==0}}function Xn(r,e){return r.catch(e),r}async function Fo(r){let e=new Map;for await(let{values:t}of r.scan("Tags"))e.set(dt(t[0],"Tags.key"),dt(t[1],"Tags.value"));return e}var pt=class r{pathCache;pathMapCache;indexTags=new Map;overviewRowsCache;sqlite;index;tagMap;constructor(e,t,n){this.sqlite=e,this.index=t,this.tagMap=n}static async open(e){let{source:t,haplotypeIndex:n}=e,o={blockSize:e.blockSize,maxBlocks:e.maxBlocks},s=await ht.open(t,o),i=s.objects.has("Tags")?await Fo(s):new Map,a=i.get("version");if(a!==Jn)throw new Wt(a);for(let l of["Nodes","Paths","ReferenceIndex"])s.rootPage(l);let f=n?await ht.open(n,o):void 0,c=new r(s,f,i);if(f){for(let u of["Tags","HaplotypeSamples","HaplotypeLengths"])if(!f.objects.has(u))throw new Error(`haplotypeIndex is not a gbz-base haplotype index: it has no ${u} table`);c.indexTags=await Fo(f);let l=c.indexTags.get("haplotype_index_paths"),h=await c.tag("paths");if(l!==h)throw new Error(`haplotype index was built for ${l??"an unknown number of"} paths but the graph has ${h}`);let d=c.indexTags.get("haplotype_index_nodes"),p=await c.tag("nodes");if(d!==void 0&&d!==p)throw new Error(`haplotype index was built for a graph with ${d} nodes but this one has ${p}`);if(c.indexTags.get("haplotype_index_orientations")==="forward")throw new Ut;let m=c.indexTags.get("haplotype_index_format");if(Number(m)!==Kn)throw new Error(m===void 0?`the haplotype index predates format ${Kn}; rebuild it with gbz-haplotype-index 0.3`:`the haplotype index has format ${m}; this version of @gmod/gbz-base reads format ${Kn}`)}return c}async tags(){return this.tagMap}async tag(e){return this.tagMap.get(e)}prefetchRecords(e,t=!1){return this.sqlite.prefetchRows("Nodes",e,t)}async getRecord(e){let t=await this.sqlite.byRowid("Nodes",e);if(!t)return;let n=t[4];return new Zn(e,Kr(qe(t[1],"Nodes.edges")),qe(t[2],"Nodes.bwt"),qe(t[3],"Nodes.sequence"),typeof n=="number"?n:void 0)}paths(){return this.pathCache??=Xn(this.scanPaths(),()=>{this.pathCache=void 0}),this.pathCache}async scanPaths(){let e=[];for await(let{rowid:t,values:n}of this.sqlite.scan("Paths"))e.push(Lo(t,n));return e}async getPath(e){let t=await this.sqlite.byRowid("Paths",e);return t?Lo(e,t):void 0}pathsByHandle(){return this.pathMapCache??=Xn(this.paths().then(e=>new Map(e.map(t=>[t.handle,t]))),()=>{this.pathMapCache=void 0}),this.pathMapCache}async findPath(e){return(await this.paths()).filter(n=>n.name.sample===e.sample&&n.name.contig===e.contig&&n.name.haplotype===e.haplotype&&n.name.fragment<=e.fragment).sort((n,o)=>o.name.fragment-n.name.fragment)[0]}async pathsNamed(e){let t=Ve(We(e),0);return(await this.paths()).filter(n=>n.name.sample===t.sample&&n.name.contig===t.contig&&n.name.haplotype===t.haplotype).sort((n,o)=>n.name.fragment-o.name.fragment)}async hasPath(e){return(await this.pathsNamed(e)).length>0}pathLengths=new Map;pathLength(e){let t=this.pathLengths.get(e);return t||(t=this.walkPathLength(e),this.pathLengths.set(e,t),t.catch(()=>this.pathLengths.delete(e))),t}async walkPathLength(e){let t=this.hasHaplotypeIndex?await this.haplotypeLength(e):void 0;if(t===void 0){let n=await this.indexedPosition(e,Number.MAX_SAFE_INTEGER);if(!n){let i=await this.getPath(e);throw new Error(`${i?`The fragment of ${me(i.name)} at ${i.name.fragment}`:`Path ${e}`} has not been indexed for random access`)}let o=n.pathOffset,s=n.pos;for(;;){let i=await this.getRecord(s.node);if(!i)throw new Error(`Node ${s.node} does not exist in the graph`);o+=i.sequenceLen;let a=i.gbwt().lf(s.offset);if(!a||a.node===0)return o;s=a}}return t}async getPathFragments(e){let{start:t,end:n}=e;if(Number.isNaN(t)||Number.isNaN(n))throw new Error(`The window ${t}..${n} is not a number range`);let o=await this.pathsNamed(e.path);if(o.length===0)throw new jt(Ve(We(e.path),0));if(n<=t)return[];let s=o.filter(f=>f.name.fragment<=t).slice(-1),i=o.filter(f=>f.name.fragment>t&&f.name.fragment<n);return(await Promise.all([...s,...i].map(async f=>({path:f,start:f.name.fragment,end:f.name.fragment+await this.pathLength(f.handle)})))).filter(f=>t<f.end)}async subgraphForFragment(e,t){let{sample:n,contig:o,haplotype:s}=e.path.name,i=Math.max(t.start,e.start),a=t.haplotypes??"all";try{let f=await Qn(this,{...t,path:{sample:n,contig:o,haplotype:s},start:i,end:Math.min(t.end,e.end)});return t.keep===void 0&&this.hasHaplotypeIndex&&(a==="all"||a==="distinct")&&await f.identifyPaths(),f}catch(f){throw f instanceof fe&&f.walkedBp!==void 0?new fe(f.limit,{windowBp:t.end-t.start,walkedBp:i-t.start+f.walkedBp}):f}}async getSubgraphs(e){let t=await this.getPathFragments(e);return(await Promise.allSettled(t.map(o=>this.subgraphForFragment(o,e)))).map(o=>{if(o.status==="rejected")throw o.reason;return o.value})}async getAlignments(e){return(await this.getSubgraphs(e)).flatMap(t=>t.alignments())}subgraphInInterval(e){return Qn(this,e)}subgraphAtOffset(e){return Po(this,e)}subgraphAroundNodes(e){return ko(this,e)}subgraphBetween(e){return _o(this,e)}fetchStats(){let e=({pager:t})=>({fetches:t.fetches,bytesFetched:t.bytesFetched});return{graph:e(this.sqlite),haplotypeIndex:this.index?e(this.index):void 0}}async graphName(){let e=new Map;for(let[n,o]of await this.tags())n.startsWith("gbz_")&&e.set(n.slice(4),o);let t={name:void 0,subgraph:new Map,translation:new Map};try{t=ro(e)}catch{}return t}async hasChainLinks(){let e=await this.tag("chain_links");return e!==void 0&&Number(e)>0}get hasHaplotypeIndex(){return this.index!==void 0}get companion(){if(!this.index)throw new Error("no haplotype index was opened with this database");return this.index}async haplotypeSampleInterval(){let e=this.indexTags.get("haplotype_index_interval");return e===void 0?void 0:Number(e)}async haplotypeSampleGap(){let e=await this.haplotypeSampleInterval(),t=this.indexTags.get("haplotype_index_reference_interval");return e===void 0?void 0:Math.max(e,t===void 0?0:Number(t))}async haplotypeAnchorSpacing(){let e=this.index?.has("HaplotypeAnchors")?this.indexTags.get("haplotype_index_anchor_spacing"):void 0;return e===void 0?void 0:Number(e)}async haplotypeStrayOptions(){let e=n=>this.indexTags.get(`haplotype_index_stray_${n}`);if(!this.index?.has("HaplotypeBins")||e("format")!=="2")return;let t=e("snarls")==="modeled"&&e("chain_links")===(await this.tag("chain_links")??"0");return{context:Number(e("context")),bin:Number(e("bin")),bound:Number(e("bound")),snarlNodes:t?Number(e("snarl_nodes")):void 0}}async blobRows(e,t,n){let o=[],s=[];for await(let i of this.companion.indexScanFrom(e,t,n))s.push(Q(i[i.length-1],`${e} rowid`));s.length>1&&await this.companion.prefetchRows(e,[[Math.min(...s),Math.max(...s)+1]],!0);for(let i of s){let a=await this.companion.byRowid(e,i);a&&o.push(a)}return o}async haplotypeBinData(e,t,n){let o=[],s=[];for(let i of await this.blobRows("HaplotypeBins",[e,t],[e,n])){let a=Q(i[1],"HaplotypeBins.bin");xi(qe(i[3],"HaplotypeBins.nodes"),o),bi(a,qe(i[4],"HaplotypeBins.strays"),s)}return{listed:yi(o),strays:s}}async haplotypeAnchorsBetween(e,t,n){let o=[],s=[],i=()=>{let a=o[o.length-1];a&&Si(a.node,s,a.visits),s=[]};for(let a of await this.blobRows("HaplotypeAnchors",[e,t],[e,n])){let f=Q(a[1],"HaplotypeAnchors.anchor_offset");o[o.length-1]?.anchorOffset!==f&&(i(),o.push({anchorOffset:f,node:Q(a[3],"HaplotypeAnchors.node_handle"),pathOffset:Q(a[4],"HaplotypeAnchors.path_offset"),visits:[]})),s.push(qe(a[5],"HaplotypeAnchors.visits"))}return i(),o}async haplotypeAnchor(e,t){let[n]=await this.haplotypeAnchorsBetween(e,t,t);return n&&{node:n.node,pathOffset:n.pathOffset}}haplotypeSamplesAtNode(e){return this.haplotypeSamplesInRange(e,e)}sampleFromRow(e){return{node:Q(e[0],"HaplotypeSamples.node_handle"),offset:Q(e[1],"HaplotypeSamples.node_offset"),pathHandle:Q(e[2],"HaplotypeSamples.path_handle"),orientation:Q(e[3],"HaplotypeSamples.orientation")===0?"forward":"reverse",pathOffset:Q(e[4],"HaplotypeSamples.path_offset")}}async haplotypeSamplesInRange(e,t){let n=[];for await(let o of this.companion.indexScanFrom("HaplotypeSamples",[e,0],[t,Number.MAX_SAFE_INTEGER]))n.push(this.sampleFromRow(o));return n}async haplotypeSampleAt(e,t){let n=await this.companion.indexSeekLE("HaplotypeSamples",[e,t]);return n?.[0]===e&&n[1]===t?this.sampleFromRow(n):void 0}overviewRows(){return this.overviewRowsCache??=Xn((async()=>{let e=[];for await(let{rowid:t,values:n}of this.companion.scan("HaplotypeOverviewRows"))e[t]={sample:dt(n[1],"HaplotypeOverviewRows.sample"),haplotype:Q(n[2],"HaplotypeOverviewRows.haplotype")};return e})(),()=>{this.overviewRowsCache=void 0}),this.overviewRowsCache}async overviewChunks(e,t,n,o,s){let i=new Map;for(let a of await this.blobRows(e,[t,n,o],[t,n,s])){let f=Q(a[2],`${e}.chunk`),c=i.get(f)??[];c.push(qe(a[4],`${e} blob`)),i.set(f,c)}return new Map([...i].map(([a,f])=>[a,wi(f)]))}async haplotypeOverview(e){let{signal:t}=e;t?.throwIfAborted();let n=u=>this.indexTags.get(`haplotype_index_overview_${u}`);if(!this.index?.has("HaplotypeOverviewClasses")||n("format")!=="1")return;let o=Number(n("bin")),s=Number(n("chunk")),i=Number(n("levels")),a=Math.max(0,Math.min(Math.floor(e.level??0)||0,i-1));if(e.level===void 0&&e.bpPerPixel!==void 0)for(;a+1<i&&o*4**(a+1)<=e.bpPerPixel;)a+=1;let f=o*4**a,[c,l]=await Promise.all([this.getPathFragments(e),this.overviewRows()]);t?.throwIfAborted();let h=Math.ceil(l.length/2),d=[],p=[];for(let u of c){let w=u.end-u.start,b=Math.max(e.start,u.start)-u.start,S=Math.min(e.end,u.end)-u.start,g=Math.floor(b/f),x=Math.floor((S-1)/f),y=Math.floor(g/s),E=Math.floor(x/s),[A,N]=await Promise.all([this.overviewChunks("HaplotypeOverviewBins",u.path.handle,a,y,E),this.overviewChunks("HaplotypeOverviewClasses",u.path.handle,a,y,E)]);t?.throwIfAborted();for(let k=y;k<=E;k++){let F=new Ye(A.get(k)??new Uint8Array),M=N.get(k)??new Uint8Array;for(let T=k*s;!F.done;T++){let C=Array.from({length:7},()=>F.next());if(T<g||T>x)continue;d.push({start:u.start+T*f,end:u.start+Math.min((T+1)*f,w),classes:[C[0],C[1],C[2],C[3]],excursions:C[4],variants:C[5],longestExcursion:C[6]});let D=(T-k*s)*h;p.push(M.subarray(D,D+h))}}}if(d.length===0)return;let m=new Uint8Array(d.length*l.length);return p.forEach((u,w)=>{for(let b=0;b<l.length;b++)m[w*l.length+b]=(u[b>>1]??0)>>4*(b%2)&15}),{level:a,bin:f,haplotypes:l,bins:d,cells:m}}async haplotypeLength(e){let t=await this.companion.byRowid("HaplotypeLengths",e);return t?Q(t[1],"HaplotypeLengths.length"):void 0}async indexedRow(e){let t=await this.sqlite.byRowid("ReferenceIndex",e);if(!t)throw new Error("ReferenceIndex row referenced by its index is missing");return{pathOffset:Q(t[1],"ReferenceIndex.path_offset"),pos:{node:Q(t[2],"ReferenceIndex.node_handle"),offset:Q(t[3],"ReferenceIndex.node_offset")}}}async indexedRowid(e,t){let n=await this.sqlite.indexSeekLE("ReferenceIndex",[e,t]);return n?.[0]===e?Q(n[2],"ReferenceIndex rowid"):void 0}async indexedPosition(e,t){let n=await this.indexedRowid(e,t);return n===void 0?void 0:this.indexedRow(n)}async indexedPositionsBetween(e,t,n){let[o,s]=await Promise.all([this.indexedRowid(e,t),this.indexedRowid(e,n)]),i=[];if(o!==void 0&&s!==void 0){await this.sqlite.prefetchRows("ReferenceIndex",[[o,s+1]]);for(let a=o;a<=s;a++)i.push(await this.indexedRow(a))}return i}};function Vt(r){let e=/\.gbz\.db$/i;return e.test(r)?r.replace(e,".haplotype-index.db"):void 0}function Ii(r){return Hr(r)&&Vt(Br(r))?Dr(r,e=>Vt(e)):void 0}function vi(r){return r instanceof Error&&(/\bHTTP 40[34]\b/.test(r.message)||r.code==="ENOENT")}async function $o(r,e){let t=Ii(r);if(!t)return{};try{return await ze(t,e).stat(),{location:t}}catch(n){return vi(n)?{}:{unreadable:String(n)}}}var Ei=5e3,Ai=50*2**20,er=class extends Error{constructor(t){super(`this GAF is ${(t/2**20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`);this.name="UnindexedGafTooLargeError"}};function Ci(r,e){if(r.length<=e)return r;let t=r.length/e;return Array.from({length:e},(n,o)=>r[Math.floor(o*t)])}var qo=(r,e)=>r.path.some(t=>e.has(t.name)),Qt=class{constructor(e,t){this.file=e;this.tabix=t;this.whole=ot({setup:async({signal:e})=>{let{size:t}=await this.file.stat();if(t>Ai)throw new er(t);let n=await this.file.readFile({signal:e}),o=new TextDecoder().decode(n[0]===31&&n[1]===139?await jr(n):n);return Tn(o)}})}async readIndexed(e,t,n){let o=1/0,s=-1/0;for(let a of t){let f=Number(a);Number.isInteger(f)&&(o=Math.min(o,f),s=Math.max(s,f))}let i=[];return o<=s&&await e.getLines("{node}",o,s+1,{signal:n,lineCallback:a=>{let f=Nn(a);f&&qo(f,t)&&i.push(f)}}),i}async readsOver(e,{signal:t}={}){let n=this.tabix?await this.readIndexed(this.tabix,e,t):(await this.whole({signal:t})).filter(o=>qo(o,e));return{records:Ci(n,Ei),total:n.length}}};var tr=function(r,e){return tr=Object.setPrototypeOf||{__proto__:[]}instanceof Array&&function(t,n){t.__proto__=n}||function(t,n){for(var o in n)Object.prototype.hasOwnProperty.call(n,o)&&(t[o]=n[o])},tr(r,e)};function ut(r,e){if(typeof e!="function"&&e!==null)throw new TypeError("Class extends value "+String(e)+" is not a constructor or null");tr(r,e);function t(){this.constructor=r}r.prototype=e===null?Object.create(e):(t.prototype=e.prototype,new t)}function Bo(r,e,t,n){function o(s){return s instanceof t?s:new t(function(i){i(s)})}return new(t||(t=Promise))(function(s,i){function a(l){try{c(n.next(l))}catch(h){i(h)}}function f(l){try{c(n.throw(l))}catch(h){i(h)}}function c(l){l.done?s(l.value):o(l.value).then(a,f)}c((n=n.apply(r,e||[])).next())})}function Yt(r,e){var t={label:0,sent:function(){if(s[0]&1)throw s[1];return s[1]},trys:[],ops:[]},n,o,s,i=Object.create((typeof Iterator=="function"?Iterator:Object).prototype);return i.next=a(0),i.throw=a(1),i.return=a(2),typeof Symbol=="function"&&(i[Symbol.iterator]=function(){return this}),i;function a(c){return function(l){return f([c,l])}}function f(c){if(n)throw new TypeError("Generator is already executing.");for(;i&&(i=0,c[0]&&(t=0)),t;)try{if(n=1,o&&(s=c[0]&2?o.return:c[0]?o.throw||((s=o.return)&&s.call(o),0):o.next)&&!(s=s.call(o,c[1])).done)return s;switch(o=0,s&&(c=[c[0]&2,s.value]),c[0]){case 0:case 1:s=c;break;case 4:return t.label++,{value:c[1],done:!1};case 5:t.label++,o=c[1],c=[0];continue;case 7:c=t.ops.pop(),t.trys.pop();continue;default:if(s=t.trys,!(s=s.length>0&&s[s.length-1])&&(c[0]===6||c[0]===2)){t=0;continue}if(c[0]===3&&(!s||c[1]>s[0]&&c[1]<s[3])){t.label=c[1];break}if(c[0]===6&&t.label<s[1]){t.label=s[1],s=c;break}if(s&&t.label<s[2]){t.label=s[2],t.ops.push(c);break}s[2]&&t.ops.pop(),t.trys.pop();continue}c=e.call(r,t)}catch(l){c=[6,l],o=0}finally{n=s=0}if(c[0]&5)throw c[1];return{value:c[0]?c[1]:void 0,done:!0}}}function Be(r){var e=typeof Symbol=="function"&&Symbol.iterator,t=e&&r[e],n=0;if(t)return t.call(r);if(r&&typeof r.length=="number")return{next:function(){return r&&n>=r.length&&(r=void 0),{value:r&&r[n++],done:!r}}};throw new TypeError(e?"Object is not iterable.":"Symbol.iterator is not defined.")}function Ke(r,e){var t=typeof Symbol=="function"&&r[Symbol.iterator];if(!t)return r;var n=t.call(r),o,s=[],i;try{for(;(e===void 0||e-- >0)&&!(o=n.next()).done;)s.push(o.value)}catch(a){i={error:a}}finally{try{o&&!o.done&&(t=n.return)&&t.call(n)}finally{if(i)throw i.error}}return s}function Xe(r,e,t){if(t||arguments.length===2)for(var n=0,o=e.length,s;n<o;n++)(s||!(n in e))&&(s||(s=Array.prototype.slice.call(e,0,n)),s[n]=e[n]);return r.concat(s||Array.prototype.slice.call(e))}function He(r){return this instanceof He?(this.v=r,this):new He(r)}function Ho(r,e,t){if(!Symbol.asyncIterator)throw new TypeError("Symbol.asyncIterator is not defined.");var n=t.apply(r,e||[]),o,s=[];return o=Object.create((typeof AsyncIterator=="function"?AsyncIterator:Object).prototype),a("next"),a("throw"),a("return",i),o[Symbol.asyncIterator]=function(){return this},o;function i(p){return function(m){return Promise.resolve(m).then(p,h)}}function a(p,m){n[p]&&(o[p]=function(u){return new Promise(function(w,b){s.push([p,u,w,b])>1||f(p,u)})},m&&(o[p]=m(o[p])))}function f(p,m){try{c(n[p](m))}catch(u){d(s[0][3],u)}}function c(p){p.value instanceof He?Promise.resolve(p.value.v).then(l,h):d(s[0][2],p)}function l(p){f("next",p)}function h(p){f("throw",p)}function d(p,m){p(m),s.shift(),s.length&&f(s[0][0],s[0][1])}}function Do(r){if(!Symbol.asyncIterator)throw new TypeError("Symbol.asyncIterator is not defined.");var e=r[Symbol.asyncIterator],t;return e?e.call(r):(r=typeof Be=="function"?Be(r):r[Symbol.iterator](),t={},n("next"),n("throw"),n("return"),t[Symbol.asyncIterator]=function(){return this},t);function n(s){t[s]=r[s]&&function(i){return new Promise(function(a,f){i=r[s](i),o(a,f,i.done,i.value)})}}function o(s,i,a,f){Promise.resolve(f).then(function(c){s({value:c,done:a})},i)}}function H(r){return typeof r=="function"}function Go(r){var e=function(n){Error.call(n),n.stack=new Error().stack},t=r(e);return t.prototype=Object.create(Error.prototype),t.prototype.constructor=t,t}var Kt=Go(function(r){return function(t){r(this),this.message=t?t.length+` errors occurred during unsubscription:
+`+t.map(function(n,o){return o+1+") "+n.toString()}).join(`
+  `):"",this.name="UnsubscriptionError",this.errors=t}});function nr(r,e){if(r){var t=r.indexOf(e);0<=t&&r.splice(t,1)}}var Xt=(function(){function r(e){this.initialTeardown=e,this.closed=!1,this._parentage=null,this._finalizers=null}return r.prototype.unsubscribe=function(){var e,t,n,o,s;if(!this.closed){this.closed=!0;var i=this._parentage;if(i)if(this._parentage=null,Array.isArray(i))try{for(var a=Be(i),f=a.next();!f.done;f=a.next()){var c=f.value;c.remove(this)}}catch(u){e={error:u}}finally{try{f&&!f.done&&(t=a.return)&&t.call(a)}finally{if(e)throw e.error}}else i.remove(this);var l=this.initialTeardown;if(H(l))try{l()}catch(u){s=u instanceof Kt?u.errors:[u]}var h=this._finalizers;if(h){this._finalizers=null;try{for(var d=Be(h),p=d.next();!p.done;p=d.next()){var m=p.value;try{zo(m)}catch(u){s=s??[],u instanceof Kt?s=Xe(Xe([],Ke(s)),Ke(u.errors)):s.push(u)}}}catch(u){n={error:u}}finally{try{p&&!p.done&&(o=d.return)&&o.call(d)}finally{if(n)throw n.error}}}if(s)throw new Kt(s)}},r.prototype.add=function(e){var t;if(e&&e!==this)if(this.closed)zo(e);else{if(e instanceof r){if(e.closed||e._hasParent(this))return;e._addParent(this)}(this._finalizers=(t=this._finalizers)!==null&&t!==void 0?t:[]).push(e)}},r.prototype._hasParent=function(e){var t=this._parentage;return t===e||Array.isArray(t)&&t.includes(e)},r.prototype._addParent=function(e){var t=this._parentage;this._parentage=Array.isArray(t)?(t.push(e),t):t?[t,e]:e},r.prototype._removeParent=function(e){var t=this._parentage;t===e?this._parentage=null:Array.isArray(t)&&nr(t,e)},r.prototype.remove=function(e){var t=this._finalizers;t&&nr(t,e),e instanceof r&&e._removeParent(this)},r.EMPTY=(function(){var e=new r;return e.closed=!0,e})(),r})();var zf=Xt.EMPTY;function Zt(r){return r instanceof Xt||r&&"closed"in r&&H(r.remove)&&H(r.add)&&H(r.unsubscribe)}function zo(r){H(r)?r():r.unsubscribe()}var Se={onUnhandledError:null,onStoppedNotification:null,Promise:void 0,useDeprecatedSynchronousErrorHandling:!1,useDeprecatedNextContext:!1};var Ze={setTimeout:function(r,e){for(var t=[],n=2;n<arguments.length;n++)t[n-2]=arguments[n];var o=Ze.delegate;return o?.setTimeout?o.setTimeout.apply(o,Xe([r,e],Ke(t))):setTimeout.apply(void 0,Xe([r,e],Ke(t)))},clearTimeout:function(r){var e=Ze.delegate;return(e?.clearTimeout||clearTimeout)(r)},delegate:void 0};function Jt(r){Ze.setTimeout(function(){var e=Se.onUnhandledError;if(e)e(r);else throw r})}function rr(){}var jo=(function(){return or("C",void 0,void 0)})();function Uo(r){return or("E",void 0,r)}function Wo(r){return or("N",r,void 0)}function or(r,e,t){return{kind:r,value:e,error:t}}var De=null;function Vo(r){if(Se.useDeprecatedSynchronousErrorHandling){var e=!De;if(e&&(De={errorThrown:!1,error:null}),r(),e){var t=De,n=t.errorThrown,o=t.error;if(De=null,n)throw o}}else r()}function Qo(r){Se.useDeprecatedSynchronousErrorHandling&&De&&(De.errorThrown=!0,De.error=r)}var mt=(function(r){ut(e,r);function e(t){var n=r.call(this)||this;return n.isStopped=!1,t?(n.destination=t,Zt(t)&&t.add(n)):n.destination=ki,n}return e.create=function(t,n,o){return new tn(t,n,o)},e.prototype.next=function(t){this.isStopped?ir(Wo(t),this):this._next(t)},e.prototype.error=function(t){this.isStopped?ir(Uo(t),this):(this.isStopped=!0,this._error(t))},e.prototype.complete=function(){this.isStopped?ir(jo,this):(this.isStopped=!0,this._complete())},e.prototype.unsubscribe=function(){this.closed||(this.isStopped=!0,r.prototype.unsubscribe.call(this),this.destination=null)},e.prototype._next=function(t){this.destination.next(t)},e.prototype._error=function(t){try{this.destination.error(t)}finally{this.unsubscribe()}},e.prototype._complete=function(){try{this.destination.complete()}finally{this.unsubscribe()}},e})(Xt);var Ri=Function.prototype.bind;function sr(r,e){return Ri.call(r,e)}var Mi=(function(){function r(e){this.partialObserver=e}return r.prototype.next=function(e){var t=this.partialObserver;if(t.next)try{t.next(e)}catch(n){en(n)}},r.prototype.error=function(e){var t=this.partialObserver;if(t.error)try{t.error(e)}catch(n){en(n)}else en(e)},r.prototype.complete=function(){var e=this.partialObserver;if(e.complete)try{e.complete()}catch(t){en(t)}},r})(),tn=(function(r){ut(e,r);function e(t,n,o){var s=r.call(this)||this,i;if(H(t)||!t)i={next:t??void 0,error:n??void 0,complete:o??void 0};else{var a;s&&Se.useDeprecatedNextContext?(a=Object.create(t),a.unsubscribe=function(){return s.unsubscribe()},i={next:t.next&&sr(t.next,a),error:t.error&&sr(t.error,a),complete:t.complete&&sr(t.complete,a)}):i=t}return s.destination=new Mi(i),s}return e})(mt);function en(r){Se.useDeprecatedSynchronousErrorHandling?Qo(r):Jt(r)}function Pi(r){throw r}function ir(r,e){var t=Se.onStoppedNotification;t&&Ze.setTimeout(function(){return t(r,e)})}var ki={closed:!0,next:rr,error:Pi,complete:rr};var Je=(function(){return typeof Symbol=="function"&&Symbol.observable||"@@observable"})();function Yo(r){return r}function Ko(r){return r.length===0?Yo:r.length===1?r[0]:function(t){return r.reduce(function(n,o){return o(n)},t)}}var he=(function(){function r(e){e&&(this._subscribe=e)}return r.prototype.lift=function(e){var t=new r;return t.source=this,t.operator=e,t},r.prototype.subscribe=function(e,t,n){var o=this,s=Oi(e)?e:new tn(e,t,n);return Vo(function(){var i=o,a=i.operator,f=i.source;s.add(a?a.call(s,f):f?o._subscribe(s):o._trySubscribe(s))}),s},r.prototype._trySubscribe=function(e){try{return this._subscribe(e)}catch(t){e.error(t)}},r.prototype.forEach=function(e,t){var n=this;return t=Xo(t),new t(function(o,s){var i=new tn({next:function(a){try{e(a)}catch(f){s(f),i.unsubscribe()}},error:s,complete:o});n.subscribe(i)})},r.prototype._subscribe=function(e){var t;return(t=this.source)===null||t===void 0?void 0:t.subscribe(e)},r.prototype[Je]=function(){return this},r.prototype.pipe=function(){for(var e=[],t=0;t<arguments.length;t++)e[t]=arguments[t];return Ko(e)(this)},r.prototype.toPromise=function(e){var t=this;return e=Xo(e),new e(function(n,o){var s;t.subscribe(function(i){return s=i},function(i){return o(i)},function(){return n(s)})})},r.create=function(e){return new r(e)},r})();function Xo(r){var e;return(e=r??Se.Promise)!==null&&e!==void 0?e:Promise}function _i(r){return r&&H(r.next)&&H(r.error)&&H(r.complete)}function Oi(r){return r&&r instanceof mt||_i(r)&&Zt(r)}function Ni(r){return H(r?.lift)}function ge(r){return function(e){if(Ni(e))return e.lift(function(t){try{return r(t,this)}catch(n){this.error(n)}});throw new TypeError("Unable to lift unknown Observable type")}}function Me(r,e,t,n,o){return new Ti(r,e,t,n,o)}var Ti=(function(r){ut(e,r);function e(t,n,o,s,i,a){var f=r.call(this,t)||this;return f.onFinalize=i,f.shouldUnsubscribe=a,f._next=n?function(c){try{n(c)}catch(l){t.error(l)}}:r.prototype._next,f._error=s?function(c){try{s(c)}catch(l){t.error(l)}finally{this.unsubscribe()}}:r.prototype._error,f._complete=o?function(){try{o()}catch(c){t.error(c)}finally{this.unsubscribe()}}:r.prototype._complete,f}return e.prototype.unsubscribe=function(){var t;if(!this.shouldUnsubscribe||this.shouldUnsubscribe()){var n=this.closed;r.prototype.unsubscribe.call(this),!n&&((t=this.onFinalize)===null||t===void 0||t.call(this))}},e})(mt);var nn=(function(r){return r&&typeof r.length=="number"&&typeof r!="function"});function rn(r){return H(r?.then)}function on(r){return H(r[Je])}function sn(r){return Symbol.asyncIterator&&H(r?.[Symbol.asyncIterator])}function an(r){return new TypeError("You provided "+(r!==null&&typeof r=="object"?"an invalid object":"'"+r+"'")+" where a stream was expected. You can provide an Observable, Promise, ReadableStream, Array, AsyncIterable, or Iterable.")}function Li(){return typeof Symbol!="function"||!Symbol.iterator?"@@iterator":Symbol.iterator}var fn=Li();function cn(r){return H(r?.[fn])}function ln(r){return Ho(this,arguments,function(){var t,n,o,s;return Yt(this,function(i){switch(i.label){case 0:t=r.getReader(),i.label=1;case 1:i.trys.push([1,,9,10]),i.label=2;case 2:return[4,He(t.read())];case 3:return n=i.sent(),o=n.value,s=n.done,s?[4,He(void 0)]:[3,5];case 4:return[2,i.sent()];case 5:return[4,He(o)];case 6:return[4,i.sent()];case 7:return i.sent(),[3,2];case 8:return[3,10];case 9:return t.releaseLock(),[7];case 10:return[2]}})})}function hn(r){return H(r?.getReader)}function Ae(r){if(r instanceof he)return r;if(r!=null){if(on(r))return Fi(r);if(nn(r))return $i(r);if(rn(r))return qi(r);if(sn(r))return Zo(r);if(cn(r))return Bi(r);if(hn(r))return Hi(r)}throw an(r)}function Fi(r){return new he(function(e){var t=r[Je]();if(H(t.subscribe))return t.subscribe(e);throw new TypeError("Provided object does not correctly implement Symbol.observable")})}function $i(r){return new he(function(e){for(var t=0;t<r.length&&!e.closed;t++)e.next(r[t]);e.complete()})}function qi(r){return new he(function(e){r.then(function(t){e.closed||(e.next(t),e.complete())},function(t){return e.error(t)}).then(null,Jt)})}function Bi(r){return new he(function(e){var t,n;try{for(var o=Be(r),s=o.next();!s.done;s=o.next()){var i=s.value;if(e.next(i),e.closed)return}}catch(a){t={error:a}}finally{try{s&&!s.done&&(n=o.return)&&n.call(o)}finally{if(t)throw t.error}}e.complete()})}function Zo(r){return new he(function(e){Di(r,e).catch(function(t){return e.error(t)})})}function Hi(r){return Zo(ln(r))}function Di(r,e){var t,n,o,s;return Bo(this,void 0,void 0,function(){var i,a;return Yt(this,function(f){switch(f.label){case 0:f.trys.push([0,5,6,11]),t=Do(r),f.label=1;case 1:return[4,t.next()];case 2:if(n=f.sent(),!!n.done)return[3,4];if(i=n.value,e.next(i),e.closed)return[2];f.label=3;case 3:return[3,1];case 4:return[3,11];case 5:return a=f.sent(),o={error:a},[3,11];case 6:return f.trys.push([6,,9,10]),n&&!n.done&&(s=t.return)?[4,s.call(t)]:[3,8];case 7:f.sent(),f.label=8;case 8:return[3,10];case 9:if(o)throw o.error;return[7];case 10:return[7];case 11:return e.complete(),[2]}})})}function we(r,e,t,n,o){n===void 0&&(n=0),o===void 0&&(o=!1);var s=e.schedule(function(){t(),o?r.add(this.schedule(null,n)):this.unsubscribe()},n);if(r.add(s),!o)return s}function dn(r,e){return e===void 0&&(e=0),ge(function(t,n){t.subscribe(Me(n,function(o){return we(n,r,function(){return n.next(o)},e)},function(){return we(n,r,function(){return n.complete()},e)},function(o){return we(n,r,function(){return n.error(o)},e)}))})}function pn(r,e){return e===void 0&&(e=0),ge(function(t,n){n.add(r.schedule(function(){return t.subscribe(n)},e))})}function Jo(r,e){return Ae(r).pipe(pn(e),dn(e))}function es(r,e){return Ae(r).pipe(pn(e),dn(e))}function ts(r,e){return new he(function(t){var n=0;return e.schedule(function(){n===r.length?t.complete():(t.next(r[n++]),t.closed||this.schedule())})})}function ns(r,e){return new he(function(t){var n;return we(t,e,function(){n=r[fn](),we(t,e,function(){var o,s,i;try{o=n.next(),s=o.value,i=o.done}catch(a){t.error(a);return}i?t.complete():t.next(s)},0,!0)}),function(){return H(n?.return)&&n.return()}})}function un(r,e){if(!r)throw new Error("Iterable cannot be null");return new he(function(t){we(t,e,function(){var n=r[Symbol.asyncIterator]();we(t,e,function(){n.next().then(function(o){o.done?t.complete():t.next(o.value)})},0,!0)})})}function rs(r,e){return un(ln(r),e)}function os(r,e){if(r!=null){if(on(r))return Jo(r,e);if(nn(r))return ts(r,e);if(rn(r))return es(r,e);if(sn(r))return un(r,e);if(cn(r))return ns(r,e);if(hn(r))return rs(r,e)}throw an(r)}function ar(r,e){return e?os(r,e):Ae(r)}function gt(r,e){return ge(function(t,n){var o=0;t.subscribe(Me(n,function(s){n.next(r.call(e,s,o++))}))})}function ss(r,e,t,n,o,s,i,a){var f=[],c=0,l=0,h=!1,d=function(){h&&!f.length&&!c&&e.complete()},p=function(u){return c<n?m(u):f.push(u)},m=function(u){s&&e.next(u),c++;var w=!1;Ae(t(u,l++)).subscribe(Me(e,function(b){o?.(b),s?p(b):e.next(b)},function(){w=!0},void 0,function(){if(w)try{c--;for(var b=function(){var S=f.shift();i?we(e,i,function(){return m(S)}):m(S)};f.length&&c<n;)b();d()}catch(S){e.error(S)}}))};return r.subscribe(Me(e,p,function(){h=!0,d()})),function(){a?.()}}function et(r,e,t){return t===void 0&&(t=1/0),H(e)?et(function(n,o){return gt(function(s,i){return e(n,s,o,i)})(Ae(r(n,o)))},t):(typeof e=="number"&&(t=e),ge(function(n,o){return ss(n,o,r,t)}))}function is(r,e,t,n,o){return function(s,i){var a=t,f=e,c=0;s.subscribe(Me(i,function(l){var h=c++;f=a?r(f,l,h):(a=!0,l),n&&i.next(f)},o&&(function(){a&&i.next(f),i.complete()})))}}function as(r,e){return ge(is(r,e,arguments.length>=2,!1,!0))}var Gi=function(r,e){return r.push(e),r};function mn(){return ge(function(r,e){as(Gi,[])(r).subscribe(e)})}function fs(r){let e=[],t=0,n;for(let o=0,s=r.length;o<s;o++){let i=r.charCodeAt(o);if(i>=48&&i<=57)t=t*10+i-48;else if(i===58)n=t,t=0;else{let a=r[o];a==="M"||a==="="||a==="X"?e.push({own:n===void 0?t:n,mate:t,op:"M"}):a==="I"?e.push({own:0,mate:t,op:a}):(a==="D"||a==="N")&&e.push({own:t,mate:0,op:a}),n=void 0,t=0}}return e}function lr(r){let e="";for(let{own:t,mate:n,op:o}of fs(r))e+=o==="M"?t===0?`${n}I`:n===0?`${t}D`:`${t}M`:`${o==="I"?n:t}${o}`;return e}var fr=2**28-1;function cr(r,e,t){for(let n=e;n>0;n-=fr)r.push((Math.min(n,fr)<<4|t)>>>0)}function zi(r,e,t){if(e===t)cr(r,e,0);else{let n=Math.ceil(Math.max(e,t)/fr);for(let o=0;o<n;o++){let s=Math.floor(e*(o+1)/n)-Math.floor(e*o/n),i=Math.floor(t*(o+1)/n)-Math.floor(t*o/n);r.push((s<<4|9)>>>0,(i<<4|9)>>>0)}}}function hr(r){let e=[];for(let{own:t,mate:n,op:o}of fs(r))o==="M"?zi(e,t,n):o==="I"?cr(e,n,1):cr(e,t,o==="N"?3:2);return Uint32Array.from(e)}function ji(r){return r>=48&&r<=57}function Ui(r){return r!==void 0&&/[A-Za-z]/.test(r)}function cs(r,e){let t=e;for(;t<r.length&&Ui(r[t]);)t++;return t}function ls(r,e){let t=e,n=0;for(;t<r.length&&ji(r.charCodeAt(t));)n=n*10+(r.charCodeAt(t)-48),t++;return{value:n,next:t}}function ms(r,e){let t=0;for(;t<r.length;){let n=r[t];if(n===":"){let{value:o,next:s}=ls(r,t+1);e(":",o,o,t+1,s),t=s}else if(n==="="){let o=cs(r,t+1),s=o-t-1;e("=",s,s,t+1,o),t=o}else if(n==="*")e("*",1,1,t+1,Math.min(t+3,r.length)),t+=3;else if(n==="+"||n==="-"){let o=cs(r,t+1),s=o-t-1;e(n,n==="-"?s:0,n==="+"?s:0,t+1,o),t=o}else if(n==="~"){let{value:o,next:s}=ls(r,t+3),i=Math.min(s+2,r.length);e("~",o,0,t+1,i),t=i}else t++}}function dr(r,e,t,n){let o=t??Number.NEGATIVE_INFINITY,s=n??Number.POSITIVE_INFINITY,i=0;ms(r,(a,f,c,l,h)=>{if(a==="*")i>=o&&i<s&&e(88,i,1,r[l+1]??"",-1,0,0);else if(a==="+"){if(i>=o&&i<=s){let d=r.slice(l,h);e(73,i,c,d,-1,0,c)}}else(a==="-"||a==="~")&&i<s&&i+f>o&&e(a==="-"?68:78,i,f,"",-1,0,0);i+=f})}function gs(r,e,t,n){let o=0,s=0,i=[],a=t&&e;for(let f=0,c=r.length;f<c;f++){let l=r[f],h=l>>>4,d=l&15;if(d===0||d===7){if(a)for(let p=0;p<h;p++)(e.charCodeAt(s+p)|32)!==(t.charCodeAt(o+p)|32)&&i.push({start:o+p,type:"mismatch",base:e[s+p],altbase:t[o+p],length:1});s+=h,o+=h}else if(d===1)i.push({start:o,type:"insertion",insertlen:h,insertedBases:e?.slice(s,s+h),length:0}),s+=h;else if(d===2)i.push({start:o,type:"deletion",length:h}),o+=h;else if(d===3)i.push({start:o,type:"skip",length:h}),o+=h;else if(d===8){for(let p=0;p<h;p++)i.push({start:o+p,type:"mismatch",base:e?.[s+p]||"X",qual:n?.[s+p],length:1});s+=h,o+=h}else d===5?i.push({start:o,type:"hardclip",cliplen:h,length:1}):d===4&&(i.push({start:o,type:"softclip",cliplen:h,length:1}),s+=h)}return i}function ws(r,e,t,n,o){if(!e)return[];let s=[],i=e.length,a=n.length,f=o!==void 0,c=t.length,l=!1;for(let S=0;S<c;S++)if(t[S].type==="skip"){l=!0;break}let h=0,d=0,p=0,m=0,u=0,w=0,b=r.length;for(;w<b;){let S=r.charCodeAt(w);if(S>=48&&S<=57){let g=0;for(;w<b;){let x=r.charCodeAt(w);if(x>=48&&x<=57)g=g*10+(x-48),w++;else break}h+=g}else if(S===94)for(w++;w<b&&r.charCodeAt(w)>=65;)w++,h++;else if(S>=65){let g=r[w];if(w++,l&&c>0)for(let N=u;N<c;N++){let k=t[N];k.type==="skip"&&h>=k.start&&(h+=k.length,u=N+1)}let x=p,y=m;for(let N=d;N<i&&y<=h;N++,d=N){let k=e[N],F=k>>>4,M=k&15;M===4||M===1?x+=F:M===2||M===6||M===3?y+=F:M!==5&&(x+=F,y+=F)}p=x,m=y;let E=x-(y-h),A=E<a?n[E]:"X";s.push({start:h,base:A,qual:f?o[E]:void 0,altbase:g,length:1,type:"mismatch"}),h++}else w++}return s}var xs={77:0,73:1,68:2,78:3,83:4,72:5,80:6,61:7,88:8};function ys(r=""){let e=0,t=[];for(let n=0,o=r.length;n<o;n++){let s=r.charCodeAt(n);if(s>=48&&s<=57)e=e*10+(s-48);else{let i=xs[s];t.push(e<<4|i),e=0}}return t}function mr(r=""){let e=0;for(let s=0,i=r.length;s<i;s++){let a=r.charCodeAt(s);(a<48||a>57)&&e++}let t=new Uint32Array(e),n=0,o=0;for(let s=0,i=r.length;s<i;s++){let a=r.charCodeAt(s);a>=48&&a<=57?n=n*10+(a-48):(t[o++]=n<<4|xs[a],n=0)}return t}function bn(r,e,t,n,o){let s=ys(r),i=r?gs(s,t,n,o):[];return e&&t?i.concat(ws(e,s,i,t,o)):i}var Qi=397,Yi=387,Ki=385;function bs(r){return(1<<r&Qi)!==0}function Ss(r){return(1<<r&Yi)!==0}function Is(r){return(1<<r&Ki)!==0}function gr(r,e,t,n,o,s,i){let a=o===-1?-1:1,f=e,c=o===-1?n:t,l=[],h=1/0,d=-1/0,p=1/0,m=-1/0,u=(w,b)=>{p=Math.min(p,w,b),m=Math.max(m,w,b)};for(let w=0;w<r.length;w++){let b=r[w],S=b>>>4,g=b&15,x=g===9,y=x||bs(g)?S:0,E=x?r[++w]>>>4:Ss(g)?S:0,A=f+y,N=c+E*a,k=f,F=A;if(F>=s&&k<=i)if(y>0){let M=Math.max(k,s),T=Math.min(F,i);if(T>M)if(h=Math.min(h,M),d=Math.max(d,T),x){let C=E/S,D=T-M,Y=Math.round(D*C),v=Math.round(c+(M-f)*C*a);l.push(D<<4|9,Y<<4|9),u(v,v+Y*a)}else l.push(T-M<<4|g),Is(g)?u(c+(M-f)*a,c+(T-f)*a):u(c,c)}else E>0&&(x?l.push(b,r[w]):l.push(b),h=Math.min(h,f),d=Math.max(d,f),u(c,N));if(f=A,c=N,f>i)break}if(l.length!==0)return{start:h,end:d,mateStart:p,mateEnd:m,cigar:Uint32Array.from(l)}}function Xi(r){return r===1||r===2||r===3}function wr(r,e,t,n,o,s){let i=o===-1?-1:1,a=[],f=e,c=o===-1?n:t,l,h=!1,d=()=>{l!==void 0&&h&&l.qHi>l.qLo&&a.push({start:l.qLo,end:l.qHi,mateStart:l.tLo,mateEnd:l.tHi,cigar:Uint32Array.from(l.ops)}),l=void 0,h=!1};for(let p=0;p<r.length;p++){let m=r[p],u=m>>>4,w=m&15,b=w===9,S=b?r[++p]:void 0,g=b||bs(w)?u:0,x=S!==void 0?S>>>4:Ss(w)?u:0,y=c+x*i;Xi(w)&&u>=s?d():(g>0||x>0)&&(l===void 0&&(l={qLo:f,qHi:f,tLo:c,tHi:c,ops:[]}),l.qHi=f+g,l.tLo=Math.min(l.tLo,c,y),l.tHi=Math.max(l.tHi,c,y),l.ops.push(m),S!==void 0&&l.ops.push(S),h=h||b||Is(w)),f+=g,c=y}return d(),a}function vs(r){let e=r.get("CIGAR");return typeof e=="string"?e:void 0}function Es(r){let e=r.get("coarseCigar");return typeof e=="string"?e:void 0}function xr(r){let e=vs(r),t=e===void 0?Es(r):void 0;return e!==void 0?mr(e):t!==void 0?hr(t):void 0}var Ne=class extends Lr{get(e){return e==="mismatches"?bn(this.walkableCigar):e==="clipLengthAtStartOfRead"?this.clipLengthAtStartOfRead:e==="name"?super.get("name")??this.mate?.refName:super.get(e)}get mate(){return super.get("mate")}get walkableCigar(){let e=super.get("CIGAR"),t=super.get("coarseCigar");return typeof e=="string"?e:typeof t=="string"?lr(t):void 0}get clipLengthAtStartOfRead(){return this.mate?.start??0}forEachMismatch(e,t){let n=this.get("start"),o=t?.start===void 0?void 0:t.start-n,s=t?.end===void 0?void 0:t.end-n,i=this.get("cs");if(i)dr(i,e,o,s);else{let a=o??Number.NEGATIVE_INFINITY,f=s??Number.POSITIVE_INFINITY;for(let c of bn(this.walkableCigar))(c.type==="deletion"||c.type==="skip"?c.start<f&&c.start+c.length>a:c.start>=a&&c.start<=f)&&(c.type==="mismatch"?e(88,c.start,c.length,c.base,c.qual??-1,0,0):c.type==="insertion"?e(73,c.start,c.length,c.insertedBases??"",-1,0,c.insertlen):c.type==="deletion"?e(68,c.start,c.length,"",-1,0,0):c.type==="skip"&&e(78,c.start,c.length,"",-1,0,0))}}};var Zi=["CIGAR","cs","coarseCigar","cg","cr"];function Ji(r){return typeof r=="object"&&r!==null&&"refName"in r&&"start"in r&&"end"in r&&typeof r.refName=="string"&&typeof r.start=="number"&&typeof r.end=="number"}function ea(r){let e=r.get("mate");return Ji(e)?e:void 0}function ta(r,e,t,n){let o=Math.max(r.start,n.start),s=Math.min(r.end,n.end),i=(e.end-e.start)/Math.max(r.end-r.start,1),a=l=>t===-1?e.end-(l-r.start)*i:e.start+(l-r.start)*i,f=Math.round(a(o)),c=Math.round(a(s));return s>o?{start:o,end:s,mateStart:Math.min(f,c),mateEnd:Math.max(f,c)}:void 0}function na(r,e,t,n,o){let s={start:r.get("start"),end:r.get("end")},i=r.get("strand")===-1?-1:1,a=s.start>=t.start&&s.end<=t.end,f=a&&n===void 0&&!o?void 0:xr(r);if(f===void 0){let c=a?{...s,mateStart:e.start,mateEnd:e.end}:ta(s,e,i,t);return c===void 0?[]:[c]}else return(n===void 0?[{...s,mateStart:e.start,mateEnd:e.end,cigar:f}]:wr(f,s.start,e.start,e.end,i,n)).flatMap(l=>{let h=gr(l.cigar,l.start,l.mateStart,l.mateEnd,i,t.start,t.end);return h===void 0?[]:[h]})}function ra(r,e,t,n,o,s){let i=`:${n.start}-${n.end}${o}`,a=r.toJSON(),f={...a,uniqueId:`${r.id()}${i}`,start:t.start,end:t.end,mate:{...e,start:t.mateStart,end:t.mateEnd}};a.syntenyId!==void 0&&(f.syntenyId=`${String(a.syntenyId)}${i}`);for(let c of Zi)delete f[c];return s&&t.cigar&&(f.alignmentOps=t.cigar),new Ne(f)}function As(r,e,t,n=!1){let o=ea(r);if(o===void 0)return[r];{let s=na(r,o,e,t,n);return s.map((i,a)=>ra(r,o,i,e,s.length>1?`/${a}`:"",n))}}var Sn=class extends Gr{constructor(){super(...arguments);this.recordsAreAlignments=!0}static{this.capabilities=["getFeatures","getRefNames"]}async hasDataForRefName(){return!0}getFeaturesInMultipleRegions(t,n={}){let{clipToRegion:o,splitAtGapBp:s,keepAlignment:i,...a}=n,f=o&&this.recordsAreAlignments,c=Fr(a.statusCallback);return ar(t).pipe(et((l,h)=>this.getFeatures(l,{...a,statusCallback:c()}).pipe(et(d=>f?As(d,d.get("assemblyName")===l.assemblyName?l:{start:d.get("start"),end:d.get("end")},s,i):[d]),mn(),gt(d=>({index:h,features:d})))),mn(),et(l=>l.sort((h,d)=>h.index-d.index).flatMap(h=>h.features)))}};var In=class extends Error{constructor(t){super(t===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${t}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`);this.name="NoHaplotypeIndexError"}},Sr=class extends Error{constructor(t){super(`a pair query names both lanes: queryAssemblyName ${t} came without a targetAssemblyName`);this.name="PairTargetError"}};function oa(r,e){if(e===void 0)throw new Sr(r);return{queryAssemblyName:r,targetAssemblyName:e}}var Ir=class extends Error{constructor(t,n){super(`the graph is cut on its reference, ${n}; a window on ${t} has no reference coordinates to cut at. Open the graph from a ${n} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function Cs(r,e){let t=ye(e);return r[t]??r[e.sample]??t}function sa(r,e){return`${ye(r)}#${r.contig}@${e.start.node}.${e.start.offset}`}function ia({alignment:r,assemblyName:e,refName:t,lane:n}){let{refStart:o,refEnd:s,strand:i,cigar:a}=r;if(!(!r.resolved||s<=o)){let{name:f,hapStart:c,hapEnd:l}=r,h=sa(f,r),d={uniqueId:h,assemblyName:e,refName:t,start:o,end:s,type:"match",strand:i==="-"?-1:1,CIGAR:a,syntenyId:h,mate:{refName:f.contig,start:c,end:l,assemblyName:n}};return new Ne(d)}}function aa({pair:r,lane:e,mateLane:t}){let n=`${ye(r.target)}#${r.target.contig}:${r.targetStart}-${r.targetEnd}|${ye(r.query)}#${r.query.contig}:${r.queryStart}-${r.queryEnd}`;return new Ne({uniqueId:n,assemblyName:e,refName:r.target.contig,start:r.targetStart,end:r.targetEnd,type:"match",strand:r.strand==="-"?-1:1,CIGAR:r.cigar,syntenyId:n,identity:r.matches/Math.max(r.columns,1),numMatches:r.matches,blockLen:r.columns,mate:{refName:r.query.contig,start:r.queryStart,end:r.queryEnd,assemblyName:t}})}var fa=12e4;function ca(r,e){let t=new Map;for(let o of r)for(let{name:s,start:i,end:a}of o.walkSpans()){let f=ye(s);if(e.has(f)){let c=`${f}#${s.contig}`;t.set(c,[...t.get(c)??[],[i,a]])}}let n=0;for(let o of t.values()){o.sort((s,i)=>s[0]-i[0]);for(let s=1;s<o.length;s++){let i=o[s][0]-o[s-1][1];i>0&&i<=fa&&(n=Math.max(n,i))}}return n}function yr(r,e){return r instanceof qr&&(r.message=`Zoom in to about ${$r(r.fitsBp)} to see ${e}`),r}var br=r=>!("uri"in r)||r.uri!=="",vr=class extends Sn{constructor(){super(...arguments);this.graph=ot({label:"Opening pangenome database",setup:async()=>{let t=this.getConf("gbzDbLocation"),n=this.getConf("haplotypeIndexLocation"),o=br(n)?{location:n}:await $o(t,this.pluginManager),s=o.location,i=await pt.open({source:ze(t,this.pluginManager),haplotypeIndex:s?ze(s,this.pluginManager):void 0}),a=this.getConf("assemblyNames")[0];if(a===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let f=await Pn(i),c=St({configured:this.getConf("referenceSample"),anchorPrefix:Ge(this,a),referenceSamples:f});return{db:i,anchor:a,referenceSample:c,referenceSamples:f,unreadableIndex:o.unreadable}}});this.gaf=ot({label:"Opening reads",setup:async()=>{let t=this.getConf("readsLocation"),n=this.getConf(["readsIndex","location"]);return br(t)?new Qt(ze(t,this.pluginManager),br(n)?Ur(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(t,n){let{db:o,referenceSample:s}=await this.graph(n);return kn(o,s,t)}async getHaplotypes(t={}){let{db:n,referenceSamples:o}=await this.graph(t),s=new Map;for(let i of await n.paths()){let a=ye(i.name),f=s.get(a);f?f.contigs.includes(i.name.contig)||f.contigs.push(i.name.contig):s.set(a,{prefix:a,sample:i.name.sample,haplotype:i.name.haplotype,contigs:[i.name.contig],isReference:o.includes(i.name.sample)})}return[...s.values()]}async getHeader(t={}){let{anchor:n,referenceSample:o,referenceSamples:s}=await this.graph(t),i=Rn(this),a=[];for(let f of await this.getHaplotypes(t))f.sample!==o&&a.push({name:Cs(i,f),label:f.prefix,group:f.sample});return{hasCoarseTier:!1,anchorAssemblyName:n,referenceSample:o,referenceSamples:s,lanes:a}}async getRefNames(t={}){let{db:n,anchor:o,referenceSample:s}=await this.graph(t),{assemblyName:i}=t,a=i===o?void 0:Ge(this,i),f=(await n.paths()).filter(c=>i===o?c.isIndexed&&c.name.sample===s:bt(ye(c.name),a)).map(c=>c.name.contig);return[...new Set(f)]}keepPredicate(t,n){let o=t===void 0||t.length===0?void 0:t.map(s=>Ge(this,s));return o===void 0&&n===void 0?void 0:s=>Mn(s,o)&&(n===void 0||bt(ye(s),n))}async getSubgraph(t,n={}){let{signal:o}=n,{db:s,anchor:i,referenceSample:a,unreadableIndex:f}=await this.graph({signal:o}),{assemblyName:c,refName:l,start:h,end:d}=t;if(c!==i)throw new Ir(c,i);let p=await this.referenceQuery(l,{signal:o});if(!p)throw new Error(`${a} has no indexed path ${l} in this graph`);let m=this.keepPredicate(n.haplotypes);if(m!==void 0&&!s.hasHaplotypeIndex)throw new In(f);return On(s,p,h,d,{context:this.getConf("context"),snarls:n.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:n.signal,keep:m}).catch(u=>{throw yr(u,"the graph")})}async getReads(t,n={}){let o=await this.gaf(n);return o?o.readsOver(new Set(t),n):{records:[],total:0}}async laneHaplotypes(t,n){let o=Ge(this,t);return(await this.getHaplotypes(n)).filter(s=>bt(s.prefix,o))}async anchorFeatures(t,n){let{db:o}=await this.graph(n),{assemblyName:s,refName:i,start:a,end:f}=t,c=Ge(this,n.targetAssemblyName),l=Rn(this),h=this.keepPredicate(n.haplotypes,c),d=await this.referenceQuery(i,n),p=this.getConf("nodeLimit");return(d?await Cn(`Reading graph ${i}:${a.toLocaleString()}-${f.toLocaleString()}`,n.statusCallback,()=>o.getAlignments({path:d,start:a,end:f,context:this.getConf("context"),haplotypes:"all",limit:p,signal:n.signal,keep:h}).catch(u=>{throw yr(_n(u,p,f-a)??u,"lanes")})):[]).flatMap(u=>{let w=u.resolved?ia({alignment:u,assemblyName:s,refName:i,lane:Cs(l,u.name)}):void 0;return w===void 0?[]:[w]})}async pairFeatures(t,n,o){let{db:s}=await this.graph(o),{refName:i,start:a,end:f}=t,l=(await Promise.all(n.map(async g=>({pair:g,featureSide:await this.laneHaplotypes(g.queryAssemblyName,o),mateSide:await this.laneHaplotypes(g.targetAssemblyName,o)})))).filter(({featureSide:g,mateSide:x})=>g.length>0&&x.length>0),h=new Set(l.flatMap(({featureSide:g,mateSide:x})=>[...g,...x].map(ye))),d=await this.referenceQuery(i,o),p=this.getConf("nodeLimit"),m=this.getConf("context"),[u]=n,w=(g,x)=>s.getSubgraphs({path:g,start:a,end:f,context:x,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:p,signal:o.signal,keep:y=>h.has(ye(y))}),b=async g=>{let x=await w(g,m).catch(A=>{throw yr(_n(A,p,f-a)??A,"lanes")}),y=ca(x,h),E=Math.ceil(y/2)+2e3;return y>0&&E>m?w(g,E).catch(A=>{if(A instanceof fe)return x;throw A}):x};return(d&&u&&l.length>0?await Cn(n.length===1?`Reading ${u.queryAssemblyName} against ${u.targetAssemblyName}`:`Reading ${n.length} lane pairs`,o.statusCallback,()=>b(d)):[]).flatMap(g=>l.flatMap(({pair:x,featureSide:y,mateSide:E})=>y.flatMap(A=>E.flatMap(N=>g.pairAlignments({target:A,query:N,bases:!1}).map(k=>aa({pair:k,lane:x.queryAssemblyName,mateLane:x.targetAssemblyName}))))))}getFeatures(t,n={}){return zr(async o=>{let{db:s,anchor:i,unreadableIndex:a}=await this.graph(n);if(!s.hasHaplotypeIndex)throw new In(a);if(t.assemblyName===i){let f=n.lanePairs?.length?await this.pairFeatures(t,n.lanePairs,n):n.queryAssemblyName===void 0?await this.anchorFeatures(t,n):await this.pairFeatures(t,[oa(n.queryAssemblyName,n.targetAssemblyName)],n);for(let c of f)o.next(c)}o.complete()},n.signal)}};export{Ir as HaplotypeWindowError,In as NoHaplotypeIndexError,_s as NoReferenceSampleError,Sr as PairTargetError,vr as default,ia as fragmentFeature,Cs as laneAssemblyName,aa as pairFeature,St as resolveReferenceSample,ca as widestWalkGap};
+//# sourceMappingURL=GbzBaseSyntenyAdapter-WPRJGI7E.js.map