jbrowse-plugin-graphgenomeviewer 8.4.0 → 8.6.0

package/dist/chunks/{AddTrackWorkflow-JAIB6H2T.js → AddTrackWorkflow-IOPTETLH.js}

@@ -1,2 +1,2 @@
-import{b as J,c as D,d as V,e as X,f as q,h as K}from"./chunk-ZEE3HTOT.js";import"./chunk-3VGXCEMQ.js";import"./chunk-6VNDP3UB.js";import"./chunk-OGQ6OQDN.js";import{d as M,e as P}from"./chunk-3WG3GF2A.js";import{b as w,h as v,j as A,m as x}from"./chunk-J5RMHLFJ.js";import{i as o}from"./chunk-NIEZKWQV.js";import{A as O,B as j,C as z,F as h,a as H,f as E,g as c,o as B,s as N,t as W,u as _}from"./chunk-5Z4VIKXZ.js";import{b as a,c as f,d as I}from"./chunk-JMBDTNUR.js";var n=JBrowseExports["@jbrowse/core/util/tss-react"],oe=s=>n!=null&&s in Object(n)?n[s]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+s+"' from '@jbrowse/core/util/tss-react' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:s});var Q=oe("makeStyles"),ie=n&&n.__esModule?n.default:n;var se=Q()(s=>({paper:{margin:s.spacing(),padding:s.spacing()},field:{marginTop:s.spacing(2)},submit:{marginTop:25,marginBottom:100,display:"block"}})),re=["RgfaTabixAdapter","RgfaTabixWalks","GbzBaseSyntenyAdapter","MinigraphBubbleAdapter"],ne=I(function({model:t}){let{classes:i}=se(),y=A(t),d=M(t),[r,U]=o("RgfaTabixAdapter"),[l,Y]=o(),[k,G]=o(),[T,Z]=o(),m=r==="GbzBaseSyntenyAdapter",u=r==="RgfaTabixWalks",[C,$]=o(""),[R,ee]=o(""),[b,ae]=o("Pangenome graph"),[S,g]=o(),[F,L]=o(!1);async function te(){if(!l||!t.assembly)return;g(void 0),L(!0);let e=r==="RgfaTabixAdapter"?await J(l,v(t).pluginManager):void 0;if(L(!1),!(!P(t)||!t.assembly))try{let p=b.trim();w({model:t,session:y,conf:K({choice:r,loc:l,indexLoc:k,readsLoc:m?T:void 0,manifest:e,assembly:t.assembly,sample:C,haplotypes:u?q(R):void 0,trackId:x({name:p}),name:p})})}catch(p){g(p)}}return f(O,{className:i.paper,children:[S?a(E,{error:S}):null,f(N,{children:[a(_,{children:"File type"}),a(z,{value:r,onChange:e=>{U(e.target.value),G(void 0),g(void 0)},children:re.map(e=>a(W,{value:e,control:a(j,{}),label:D[e]},e))})]}),a(c,{location:l,name:V[r],rootModel:d,setLocation:Y}),a(c,{location:k,name:X[r],rootModel:d,setLocation:G}),m?a(c,{location:T,name:"Path to reads aligned to the graph as GAF (optional; a .gz is read by the .tbi beside it)",rootModel:d,setLocation:Z}):null,a(h,{className:i.field,value:C,onChange:e=>{$(e.target.value)},label:"Sample name in the graph",slotProps:{htmlInput:{"data-testid":"graph-sample-input"}},helperText:m?"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":u?"Optional. The PanSN sample this assembly is in the graph; blank takes it from the file name, GRCh38 in chr22.GRCh38.walks.bed.gz":"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}),u?a(h,{className:i.field,value:R,onChange:e=>{ee(e.target.value)},label:"Haplotypes",slotProps:{htmlInput:{"data-testid":"graph-haplotypes-input"}},helperText:"Optional. The haplotypes the track cuts for until you pick others in its menu, as PanSN names separated by commas (HG002#1, or HG002 for both); blank is every haplotype in the file",placeholder:"HG002, HG00733",fullWidth:!0}):null,a(h,{className:i.field,value:b,label:"Track name",slotProps:{htmlInput:{"data-testid":"graph-track-name-input"}},onChange:e=>{ae(e.target.value)}}),a(H,{session:y,helperText:"Select assembly to add track to",selected:t.assembly,onChange:e=>{t.setAssembly(e)},fullWidth:!0}),a(B,{variant:"contained",className:i.submit,disabled:!l||!b.trim()||!t.assembly||F,onClick:()=>{te()},children:F?"Reading graph.json\u2026":"Submit"})]})}),ye=ne;export{ye as default};
-//# sourceMappingURL=AddTrackWorkflow-JAIB6H2T.js.map
+import{b as J,c as D,d as V,e as X,f as q,h as K}from"./chunk-CGPYVMGQ.js";import"./chunk-TMM73K4C.js";import"./chunk-6VNDP3UB.js";import"./chunk-D6TY2QEG.js";import{d as M,e as P}from"./chunk-FLKXKTS2.js";import{b as w,h as v,j as A,m as x}from"./chunk-TC265JAP.js";import{i as o}from"./chunk-J2PN6CG3.js";import{A as O,B as j,C as z,F as h,a as H,f as E,g as c,o as B,s as N,t as W,u as _}from"./chunk-WE7DQVXF.js";import{b as a,c as f,d as I}from"./chunk-DUU6T2I5.js";var n=JBrowseExports["@jbrowse/core/util/tss-react"],oe=s=>n!=null&&s in Object(n)?n[s]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+s+"' from '@jbrowse/core/util/tss-react' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:s});var Q=oe("makeStyles"),ie=n&&n.__esModule?n.default:n;var se=Q()(s=>({paper:{margin:s.spacing(),padding:s.spacing()},field:{marginTop:s.spacing(2)},submit:{marginTop:25,marginBottom:100,display:"block"}})),re=["RgfaTabixAdapter","RgfaTabixWalks","GbzBaseSyntenyAdapter","MinigraphBubbleAdapter"],ne=I(function({model:t}){let{classes:i}=se(),y=A(t),d=M(t),[r,U]=o("RgfaTabixAdapter"),[l,Y]=o(),[k,G]=o(),[T,Z]=o(),m=r==="GbzBaseSyntenyAdapter",u=r==="RgfaTabixWalks",[C,$]=o(""),[R,ee]=o(""),[b,ae]=o("Pangenome graph"),[S,g]=o(),[F,L]=o(!1);async function te(){if(!l||!t.assembly)return;g(void 0),L(!0);let e=r==="RgfaTabixAdapter"?await J(l,v(t).pluginManager):void 0;if(L(!1),!(!P(t)||!t.assembly))try{let p=b.trim();w({model:t,session:y,conf:K({choice:r,loc:l,indexLoc:k,readsLoc:m?T:void 0,manifest:e,assembly:t.assembly,sample:C,haplotypes:u?q(R):void 0,trackId:x({name:p}),name:p})})}catch(p){g(p)}}return f(O,{className:i.paper,children:[S?a(E,{error:S}):null,f(N,{children:[a(_,{children:"File type"}),a(z,{value:r,onChange:e=>{U(e.target.value),G(void 0),g(void 0)},children:re.map(e=>a(W,{value:e,control:a(j,{}),label:D[e]},e))})]}),a(c,{location:l,name:V[r],rootModel:d,setLocation:Y}),a(c,{location:k,name:X[r],rootModel:d,setLocation:G}),m?a(c,{location:T,name:"Path to reads aligned to the graph as GAF (optional; a .gz is read by the .tbi beside it)",rootModel:d,setLocation:Z}):null,a(h,{className:i.field,value:C,onChange:e=>{$(e.target.value)},label:"Sample name in the graph",slotProps:{htmlInput:{"data-testid":"graph-sample-input"}},helperText:m?"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":u?"Optional. The PanSN sample this assembly is in the graph; blank takes it from the file name, GRCh38 in chr22.GRCh38.walks.bed.gz":"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}),u?a(h,{className:i.field,value:R,onChange:e=>{ee(e.target.value)},label:"Haplotypes",slotProps:{htmlInput:{"data-testid":"graph-haplotypes-input"}},helperText:"Optional. The haplotypes the track cuts for until you pick others in its menu, as PanSN names separated by commas (HG002#1, or HG002 for both); blank is every haplotype in the file",placeholder:"HG002, HG00733",fullWidth:!0}):null,a(h,{className:i.field,value:b,label:"Track name",slotProps:{htmlInput:{"data-testid":"graph-track-name-input"}},onChange:e=>{ae(e.target.value)}}),a(H,{session:y,helperText:"Select assembly to add track to",selected:t.assembly,onChange:e=>{t.setAssembly(e)},fullWidth:!0}),a(B,{variant:"contained",className:i.submit,disabled:!l||!b.trim()||!t.assembly||F,onClick:()=>{te()},children:F?"Reading graph.json\u2026":"Submit"})]})}),ye=ne;export{ye as default};
+//# sourceMappingURL=AddTrackWorkflow-IOPTETLH.js.map

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

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["jbrowse-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(\"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        { 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 {\n  addTrackFromWidget,\n  getEnv,\n  getSession,\n  makeTrackId,\n} from '@jbrowse/core/util'\nimport { makeStyles } from '@jbrowse/core/util/tss-react'\nimport { getRoot, isAlive } 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  parseHaplotypes,\n} from './buildTrackConfig'\nimport { readGraphManifest } from './graphManifest'\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  'RgfaTabixWalks',\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 walks = choice === 'RgfaTabixWalks'\n  const [sample, setSample] = useState('')\n  const [haplotypes, setHaplotypes] = useState('')\n  const [trackName, setTrackName] = useState('Pangenome graph')\n  const [error, setError] = useState<unknown>()\n  const [submitting, setSubmitting] = useState(false)\n\n  async function handleSubmit() {\n    if (!loc || !model.assembly) {\n      return\n    }\n    setError(undefined)\n    setSubmitting(true)\n    const manifest =\n      choice === 'RgfaTabixAdapter'\n        ? await readGraphManifest(loc, getEnv(model).pluginManager)\n        : undefined\n    setSubmitting(false)\n    if (!isAlive(model) || !model.assembly) {\n      return\n    }\n    try {\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          manifest,\n          assembly: model.assembly,\n          sample,\n          haplotypes: walks ? parseHaplotypes(haplotypes) : undefined,\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            setIndexLoc(undefined)\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            : walks\n              ? 'Optional. The PanSN sample this assembly is in the graph; blank takes it from the file name, GRCh38 in chr22.GRCh38.walks.bed.gz'\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      {walks ? (\n        <TextField\n          className={classes.field}\n          value={haplotypes}\n          onChange={event => {\n            setHaplotypes(event.target.value)\n          }}\n          label=\"Haplotypes\"\n          slotProps={{ htmlInput: { 'data-testid': 'graph-haplotypes-input' } }}\n          helperText=\"Optional. The haplotypes the track cuts for until you pick others in its menu, as PanSN names separated by commas (HG002#1, or HG002 for both); blank is every haplotype in the file\"\n          placeholder=\"HG002, HG00733\"\n          fullWidth\n        />\n      ) : null}\n      <TextField\n        className={classes.field}\n        value={trackName}\n        label=\"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 || submitting}\n        onClick={() => {\n          void handleSubmit()\n        }}\n      >\n        {submitting ? 'Reading graph.json\u2026' : 'Submit'}\n      </Button>\n    </Paper>\n  )\n})\n\nexport default GraphAddTrackWidget\n"],
+  "mappings": "udAAA,IAAMA,EAAO,eAAe,8BAA8B,EACpDC,GAAOC,GACXF,GAAQ,MAAQE,KAAQ,OAAOF,CAAI,EAC/BA,EAAKE,CAAI,EACT,OAAO,OACL,UAAY,CACV,MAAM,IAAI,MAAM,kCAAoCA,EAAO,8IAA6J,CAC1N,EACA,CAAE,mBAAoBA,CAAK,CAC7B,EAGC,IAAMC,EAA6BC,GAAK,YAAY,EACpDC,GAAQC,GAAQA,EAAK,WAAaA,EAAK,QAAUA,EC0BxD,IAAMC,GAAYC,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,GAA6B,CACjC,mBACA,iBACA,wBACA,wBACF,EAEMC,GAAsBC,EAAS,SAA6B,CAChE,MAAAC,CACF,EAEG,CACD,GAAM,CAAE,QAAAC,CAAQ,EAAIP,GAAU,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,wBACjBU,EAAQV,IAAW,iBACnB,CAACW,EAAQC,CAAS,EAAIV,EAAS,EAAE,EACjC,CAACW,EAAYC,EAAa,EAAIZ,EAAS,EAAE,EACzC,CAACa,EAAWC,EAAY,EAAId,EAAS,iBAAiB,EACtD,CAACe,EAAOC,CAAQ,EAAIhB,EAAkB,EACtC,CAACiB,EAAYC,CAAa,EAAIlB,EAAS,EAAK,EAElD,eAAemB,IAAe,CAC5B,GAAI,CAAClB,GAAO,CAACT,EAAM,SACjB,OAEFwB,EAAS,MAAS,EAClBE,EAAc,EAAI,EAClB,IAAME,EACJtB,IAAW,mBACP,MAAMuB,EAAkBpB,EAAKqB,EAAO9B,CAAK,EAAE,aAAa,EACxD,OAEN,GADA0B,EAAc,EAAK,EACf,GAACK,EAAQ/B,CAAK,GAAK,CAACA,EAAM,UAG9B,GAAI,CACF,IAAMgC,EAAOX,EAAU,KAAK,EAC5BY,EAAmB,CACjB,MAAAjC,EACA,QAAAE,EACA,KAAMgC,EAAiB,CACrB,OAAA5B,EACA,IAAAG,EACA,SAAAE,EACA,SAAUI,EAAMF,EAAW,OAC3B,SAAAe,EACA,SAAU5B,EAAM,SAChB,OAAAiB,EACA,WAAYD,EAAQmB,EAAgBhB,CAAU,EAAI,OAClD,QAASiB,EAAY,CAAE,KAAAJ,CAAK,CAAC,EAC7B,KAAAA,CACF,CAAC,CACH,CAAC,CACH,OAASK,EAAG,CACVb,EAASa,CAAC,CACZ,CACF,CAEA,OACEC,EAACC,EAAA,CAAM,UAAWtC,EAAQ,MACvB,UAAAsB,EAAQiB,EAACC,EAAA,CAAa,MAAOlB,EAAO,EAAK,KAC1Ce,EAACI,EAAA,CACC,UAAAF,EAACG,EAAA,CAAU,qBAAS,EACpBH,EAACI,EAAA,CACC,MAAOtC,EACP,SAAUuC,GAAS,CACjBtC,EAAUsC,EAAM,OAAO,KAAwB,EAC/CjC,EAAY,MAAS,EACrBY,EAAS,MAAS,CACpB,EAEC,SAAA3B,GAAQ,IAAIiD,GACXN,EAACO,EAAA,CAEC,MAAOD,EACP,QAASN,EAACQ,EAAA,EAAM,EAChB,MAAOC,EAAkBH,CAAM,GAH1BA,CAIP,CACD,EACH,GACF,EACAN,EAACU,EAAA,CACC,SAAUzC,EACV,KAAM0C,EAAkB7C,CAAM,EAC9B,UAAWF,EACX,YAAaM,EACf,EACA8B,EAACU,EAAA,CACC,SAAUvC,EACV,KAAMyC,EAAmB9C,CAAM,EAC/B,UAAWF,EACX,YAAaQ,EACf,EACCG,EACCyB,EAACU,EAAA,CACC,SAAUrC,EACV,KAAK,4FACL,UAAWT,EACX,YAAaU,EACf,EACE,KACJ0B,EAACa,EAAA,CACC,UAAWpD,EAAQ,MACnB,MAAOgB,EACP,SAAU4B,GAAS,CACjB3B,EAAU2B,EAAM,OAAO,KAAK,CAC9B,EACA,MAAM,2BACN,UAAW,CAAE,UAAW,CAAE,cAAe,oBAAqB,CAAE,EAChE,WACE9B,EACI,mKACAC,EACE,mIACA,qJAER,YAAY,SACZ,UAAS,GACX,EACCA,EACCwB,EAACa,EAAA,CACC,UAAWpD,EAAQ,MACnB,MAAOkB,EACP,SAAU0B,GAAS,CACjBzB,GAAcyB,EAAM,OAAO,KAAK,CAClC,EACA,MAAM,aACN,UAAW,CAAE,UAAW,CAAE,cAAe,wBAAyB,CAAE,EACpE,WAAW,uLACX,YAAY,iBACZ,UAAS,GACX,EACE,KACJL,EAACa,EAAA,CACC,UAAWpD,EAAQ,MACnB,MAAOoB,EACP,MAAM,aACN,UAAW,CAAE,UAAW,CAAE,cAAe,wBAAyB,CAAE,EACpE,SAAUwB,GAAS,CACjBvB,GAAauB,EAAM,OAAO,KAAK,CACjC,EACF,EACAL,EAACc,EAAA,CACC,QAASpD,EACT,WAAW,kCACX,SAAUF,EAAM,SAChB,SAAUuD,GAAO,CACfvD,EAAM,YAAYuD,CAAG,CACvB,EACA,UAAS,GACX,EACAf,EAACgB,EAAA,CACC,QAAQ,YACR,UAAWvD,EAAQ,OACnB,SAAU,CAACQ,GAAO,CAACY,EAAU,KAAK,GAAK,CAACrB,EAAM,UAAYyB,EAC1D,QAAS,IAAM,CACRE,GAAa,CACpB,EAEC,SAAAF,EAAa,2BAAwB,SACxC,GACF,CAEJ,CAAC,EAEMgC,GAAQ3D",
+  "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", "walks", "sample", "setSample", "haplotypes", "setHaplotypes", "trackName", "setTrackName", "error", "setError", "submitting", "setSubmitting", "handleSubmit", "manifest", "readGraphManifest", "getEnv", "isAlive", "name", "addTrackFromWidget", "buildTrackConfig", "parseHaplotypes", "makeTrackId", "e", "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-LO7FKFSS.js → ChooseSamplesDialog-7RI573UO.js}

@@ -1,2 +1,2 @@
-import{a as i}from"./chunk-CBKSPAUI.js";import"./chunk-NIEZKWQV.js";import"./chunk-5Z4VIKXZ.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:`${l.length.toLocaleString()} samples in this cut. Their walks show in pairs, in the order picked.`,options:l,initial:o.walkRowSamples??[],confirmLabel:e=>e.length>0?"Show these samples":"Show every sample",onPick:e=>{o.setWalkRowSamples(e.length>0?e:void 0)},onClose:p})}),h=t;export{h as default};
-//# sourceMappingURL=ChooseSamplesDialog-LO7FKFSS.js.map
+import{a as i}from"./chunk-6OZGIMZC.js";import"./chunk-J2PN6CG3.js";import"./chunk-WE7DQVXF.js";import{b as a,d as s}from"./chunk-DUU6T2I5.js";var t=s(function({model:o,onClose:p}){let{samples:l}=o.walkRowSampleChoices;return a(i,{title:"Choose samples",label:"Samples",testId:"graph-choose-samples",caption:`${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-7RI573UO.js.map

package/dist/chunks/{ChooseSamplesDialog-LO7FKFSS.js.map → ChooseSamplesDialog-7RI573UO.js.map}

@@ -3,5 +3,5 @@
   "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": "+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"]
+  "names": ["ChooseSamplesDialog", "observer", "model", "onClose", "samples", "jsx", "PickNamesDialog_default", "picked", "ChooseSamplesDialog_default"]
 }

package/dist/chunks/{ChooseWalksDialog-JJSOVCEU.js → ChooseWalksDialog-4LDYDQH2.js}

@@ -1,2 +1,2 @@
-import{a as t}from"./chunk-CBKSPAUI.js";import"./chunk-NIEZKWQV.js";import"./chunk-5Z4VIKXZ.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:`${a.length.toLocaleString()} haplotypes in this cut. The ones picked are highlighted in this order, and the rest fades.`,options:a.map(e=>e.name),initial:o.walkLayers.map(e=>e.walk),optionLabel:e=>o.walkLabel(e),confirmLabel:e=>e.length>0?"Highlight these":"Clear highlights",onPick:e=>{o.liftAmongChoices(e)},onClose:s})}),k=h;export{k as default};
-//# sourceMappingURL=ChooseWalksDialog-JJSOVCEU.js.map
+import{a as t}from"./chunk-6OZGIMZC.js";import"./chunk-J2PN6CG3.js";import"./chunk-WE7DQVXF.js";import{b as l,d as i}from"./chunk-DUU6T2I5.js";var h=i(function({model:o,onClose:s}){let{walkChoices:a}=o;return l(t,{title:"Choose haplotypes",label:"Haplotypes",testId:"graph-choose-walks",caption:`${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.liftAmongChoices(e)},onClose:s})}),k=h;export{k as default};
+//# sourceMappingURL=ChooseWalksDialog-4LDYDQH2.js.map

package/dist/chunks/{ChooseWalksDialog-JJSOVCEU.js.map → ChooseWalksDialog-4LDYDQH2.js.map}

@@ -3,5 +3,5 @@
   "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' | 'liftAmongChoices'\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.liftAmongChoices(picked)\n      }}\n      onClose={onClose}\n    />\n  )\n})\n\nexport default ChooseWalksDialog\n"],
   "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,iBAAiBQ,CAAM,CAC/B,EACA,QAASP,EACX,CAEJ,CAAC,EAEMQ,EAAQX",
-  "names": ["ChooseWalksDialog", "observer", "model", "onClose", "walkChoices", "jsx", "PickNamesDialog", "c", "l", "name", "picked", "ChooseWalksDialog_default"]
+  "names": ["ChooseWalksDialog", "observer", "model", "onClose", "walkChoices", "jsx", "PickNamesDialog_default", "c", "l", "name", "picked", "ChooseWalksDialog_default"]
 }

package/dist/chunks/{GbzBaseSyntenyAdapter-CJQVZJPA.js → GbzBaseSyntenyAdapter-67NMRHWZ.js}

@@ -1,2 +1,2 @@
-import{a as ne,b as ae,c as ue,d as re,e as oe,f as O,g as ie,h as se}from"./chunk-5Q56NPNH.js";import{a as te}from"./chunk-ZA5GPTUM.js";import{a as ee}from"./chunk-KOB7YIMR.js";import{a as Q,b as D,c as Z,d as u,e as k,f as M,g as j,h as $,i as W,k as U}from"./chunk-XLVKVQJB.js";import"./chunk-M2D7NUOY.js";import{h as z,i as E}from"./chunk-E23AOQPE.js";import"./chunk-YBLNN5FU.js";import"./chunk-U6SNNNFV.js";import"./chunk-ELC7POI6.js";import{E as V,a as K,c as L}from"./chunk-PX4IRCTO.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import{g as F,h as N,i as C}from"./chunk-CL4PYWKC.js";import"./chunk-OTBDKJEA.js";import"./chunk-3VGXCEMQ.js";import{e as G,h as X,i as Y,j as J}from"./chunk-6VNDP3UB.js";import{a as P}from"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{e as _,o as B}from"./chunk-J5RMHLFJ.js";function A(n){let i=/\.gbz\.db$/i;return i.test(n)?n.replace(i,".haplotype-index.db"):void 0}function ge(n){return Y(n)&&A(X(n))?J(n,i=>A(i)):void 0}function ye(n){return n instanceof Error&&(/\bHTTP 40[34]\b/.test(n.message)||n.code==="ENOENT")}async function ce(n,i){let e=ge(n);if(!e)return{};try{return await P(e,i).stat(),{location:e}}catch(t){return ye(t)?{}:{unreadable:String(t)}}}var be=5e3,we=50*2**20,H=class extends Error{constructor(e){super(`this GAF is ${(e/2**20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`);this.name="UnindexedGafTooLargeError"}};function xe(n,i){if(n.length<=i)return n;let e=n.length/i;return Array.from({length:i},(t,a)=>n[Math.floor(a*e)])}var pe=(n,i)=>n.path.some(e=>i.has(e.name)),v=class{constructor(i,e){this.file=i;this.tabix=e;this.whole=L({setup:async({signal:i})=>{let{size:e}=await this.file.stat();if(e>we)throw new H(e);let t=await this.file.readFile({signal:i}),a=new TextDecoder().decode(t[0]===31&&t[1]===139?await K(t):t);return E(a)}})}async readIndexed(i,e,t){let a=1/0,r=-1/0;for(let s of e){let c=Number(s);Number.isInteger(c)&&(a=Math.min(a,c),r=Math.max(r,c))}let o=[];return a<=r&&await i.getLines("{node}",a,r+1,{signal:t,lineCallback:s=>{let c=z(s);c&&pe(c,e)&&o.push(c)}}),o}async readsOver(i,{signal:e}={}){let t=this.tabix?await this.readIndexed(this.tabix,i,e):(await this.whole({signal:e})).filter(a=>pe(a,i));return{records:xe(t,be),total:t.length}}};var I=class extends Error{constructor(e){super(e===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${e}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`);this.name="NoHaplotypeIndexError"}},q=class extends Error{constructor(e,t){super(`the graph is cut on its reference, ${t}; a window on ${e} has no reference coordinates to cut at. Open the graph from a ${t} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function Se(n,i){return`${u(n)}#${n.contig}@${i.start.node}.${i.start.offset}`}function Ne({alignment:n,assemblyName:i,refName:e,lane:t}){let{refStart:a,refEnd:r,strand:o,cigar:s}=n;if(!(r<=a)){let{name:c,hapStart:p,hapEnd:l}=n,f=Se(c,n),g={uniqueId:f,assemblyName:i,refName:e,start:a,end:r,type:"match",strand:o==="-"?-1:1,CIGAR:s,syntenyId:f,mate:{refName:c.contig,start:p,end:l,assemblyName:t}};return new ne(g)}}function Pe({pair:n,lane:i,mateLane:e}){return se({target:{name:`${u(n.target)}#${n.target.contig}`,assemblyName:i,refName:n.target.contig,start:n.targetStart,end:n.targetEnd},query:{name:`${u(n.query)}#${n.query.contig}`,assemblyName:e,refName:n.query.contig,start:n.queryStart,end:n.queryEnd},strand:n.strand,cigar:n.cigar,matches:n.matches,columns:n.columns})}var Le=12e4;function Re(n,i){let e=new Map;for(let a of n)for(let{name:r,start:o,end:s}of a.walkSpans()){let c=u(r);if(i.has(c)){let p=`${c}#${r.contig}`,l=e.get(p);l?l.push([o,s]):e.set(p,[[o,s]])}}let t=0;for(let a of e.values()){a.sort((r,o)=>r[0]-o[0]);for(let r=1;r<a.length;r++){let o=a[r][0]-a[r-1][1];o>0&&o<=Le&&(t=Math.max(t,o))}}return t}function fe(n,i){return n instanceof Z&&(n.message=`Zoom in to about ${_(n.fitsBp)} to see ${i}`),n}var le=(n,i,e)=>ie(fe(W(n,i,e)??n,"lanes"),e),me=n=>({...n,start:Math.floor(n.start),end:Math.ceil(n.end)}),T=class extends ae{constructor(){super(...arguments);this.graph=L({label:"Opening pangenome database",setup:async()=>{let e=this.getConf("gbzDbLocation"),t=this.getConf("haplotypeIndexLocation"),a=G(t)?{location:t}:await ce(e,this.pluginManager),r=a.location,o=await D.open({source:P(e,this.pluginManager),haplotypeIndex:r?P(r,this.pluginManager):void 0}),s=this.getConf("assemblyNames")[0];if(s===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let c=await M(o),p=j({configured:this.getConf("referenceSample"),anchorPrefix:N(this,s),referenceSamples:c});return{db:o,anchor:s,referenceSample:p,referenceSamples:c,unreadableIndex:a.unreadable}}});this.gaf=L({label:"Opening reads",setup:async()=>{let e=this.getConf("readsLocation"),t=this.getConf(["readsIndex","location"]);return G(e)?new v(P(e,this.pluginManager),G(t)?V(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(e,t){let{db:a,referenceSample:r}=await this.graph(t);return $(a,r,e)}async getHaplotypes(e={}){let{db:t,referenceSamples:a}=await this.graph(e),r=new Map;for(let o of await t.paths()){let s=u(o.name),c=r.get(s);c?c.contigs.includes(o.name.contig)||c.contigs.push(o.name.contig):r.set(s,{prefix:s,sample:o.name.sample,haplotype:o.name.haplotype,contigs:[o.name.contig],isReference:a.includes(o.name.sample)})}return[...r.values()]}async getHeader(e={}){let{anchor:t,referenceSample:a}=await this.graph(e),r=C(this),o=[];for(let s of await this.getHaplotypes(e))s.sample!==a&&o.push({name:O(r,s.prefix),label:s.prefix,group:s.sample});return{hasCoarseTier:!1,anchorAssemblyName:t,lanes:o}}async getRefNames(e={}){let{db:t,anchor:a,referenceSample:r}=await this.graph(e),{assemblyName:o}=e,s=o===a?void 0:N(this,o),c=(await t.paths()).filter(p=>o===a?p.isIndexed&&p.name.sample===r:F(u(p.name),s)).map(p=>p.name.contig);return[...new Set(c)]}keepPredicate(e,t){let a=e===void 0||e.length===0?void 0:e.map(r=>N(this,r));return a===void 0&&t===void 0?void 0:r=>k(r,a)&&(t===void 0||F(u(r),t))}async getSubgraph(e,t={}){let{signal:a}=t,{db:r,anchor:o,referenceSample:s,unreadableIndex:c}=await this.graph({signal:a}),{assemblyName:p,refName:l,start:f,end:g}=me(e);if(p!==o)throw new q(p,o);let y=await this.referenceQuery(l,{signal:a});if(!y)throw new Error(`${s} has no indexed path ${l} in this graph`);let b=this.keepPredicate(t.haplotypes);if(b!==void 0&&!r.hasHaplotypeIndex)throw new I(c);let d=await U(r,y,f,g,{context:this.getConf("context"),snarls:t.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:t.signal,keep:b}).catch(w=>{throw fe(w,"the graph")});return typeof d=="string"?d:te(d,{start:f,end:g},t.walkRows)}async getReads(e,t={}){let a=await this.gaf(t);return a?a.readsOver(new Set(e),t):{records:[],total:0}}async laneHaplotypes(e,t){let a=N(this,e);return(await this.getHaplotypes(t)).filter(r=>F(r.prefix,a))}async anchorFeatures(e,t){let{db:a}=await this.graph(t),{assemblyName:r,refName:o,start:s,end:c}=e,p=N(this,t.targetAssemblyName),l=C(this),f=this.keepPredicate(t.haplotypes,p),g=await this.referenceQuery(o,t),y=this.getConf("nodeLimit");return(g?await B(`Reading graph ${o}:${s.toLocaleString()}-${c.toLocaleString()}`,t.statusCallback,()=>a.getAlignments({path:g,start:s,end:c,context:this.getConf("context"),haplotypes:"all",limit:y,signal:t.signal,keep:f}).catch(d=>{throw le(d,y,c-s)})):[]).flatMap(d=>{let w=d.resolved?Ne({alignment:d,assemblyName:r,refName:o,lane:O(l,u(d.name))}):void 0;return w===void 0?[]:[w]})}async pairFeatures(e,t,a){let{db:r}=await this.graph(a),{refName:o,start:s,end:c}=e,l=(await Promise.all(t.map(async m=>({pair:m,featureSide:await this.laneHaplotypes(m.queryAssemblyName,a),mateSide:await this.laneHaplotypes(m.targetAssemblyName,a)})))).filter(({featureSide:m,mateSide:h})=>m.length>0&&h.length>0),f=new Set(l.flatMap(({featureSide:m,mateSide:h})=>[...m,...h].map(u))),g=await this.referenceQuery(o,a),y=this.getConf("nodeLimit"),b=this.getConf("context"),d=(m,h)=>r.getSubgraphs({path:m,start:s,end:c,context:h,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:a.signal,keep:x=>f.has(u(x))}),w=async m=>{let h=await d(m,b).catch(S=>{throw le(S,y,c-s)}),x=Re(h,f),R=Math.ceil(x/2)+2e3;return x>0&&R>b?d(m,R).catch(S=>{if(S instanceof Q)return h;throw S}):h};return(g&&l.length>0?await B(oe(t),a.statusCallback,()=>w(g)):[]).flatMap(m=>l.flatMap(({pair:h,featureSide:x,mateSide:R})=>x.flatMap(S=>R.flatMap(de=>m.pairAlignments({target:S,query:de,bases:!1}).map(he=>Pe({pair:he,lane:h.queryAssemblyName,mateLane:h.targetAssemblyName}))))))}getFeatures(e,t={}){let a=me(e);return ee(async r=>{let{db:o,anchor:s,unreadableIndex:c}=await this.graph(t);if(!o.hasHaplotypeIndex)throw new I(c);if(a.assemblyName===s){let p=re(t),l=p.length>0?await this.pairFeatures(a,p,t):await this.anchorFeatures(a,t);for(let f of l)r.next(f)}r.complete()},t.signal)}};export{I as NoHaplotypeIndexError,ue as PairTargetError,T as default,Re as widestWalkGap};
-//# sourceMappingURL=GbzBaseSyntenyAdapter-CJQVZJPA.js.map
+import{a as ne,b as ae,c as ue,d as re,e as oe,f as O,g as ie,h as se}from"./chunk-SVDQVLEU.js";import{a as te}from"./chunk-ZA5GPTUM.js";import{a as ee}from"./chunk-V55TK2NP.js";import{a as Q,b as D,c as Z,d as u,e as k,f as M,g as j,h as $,i as W,k as U}from"./chunk-XLVKVQJB.js";import"./chunk-M2D7NUOY.js";import{h as z,i as E}from"./chunk-E23AOQPE.js";import"./chunk-YBLNN5FU.js";import"./chunk-U6SNNNFV.js";import"./chunk-ELC7POI6.js";import{E as V,a as K,c as L}from"./chunk-VNWCN47G.js";import"./chunk-YBLNN5FU.js";import"./chunk-QUDJ7AM3.js";import{g as F,h as N,i as C}from"./chunk-CL4PYWKC.js";import"./chunk-AGUEPVOR.js";import"./chunk-TMM73K4C.js";import{e as G,h as X,i as Y,j as J}from"./chunk-6VNDP3UB.js";import{a as P}from"./chunk-D6TY2QEG.js";import"./chunk-FLKXKTS2.js";import{e as _,o as B}from"./chunk-TC265JAP.js";function A(n){let i=/\.gbz\.db$/i;return i.test(n)?n.replace(i,".haplotype-index.db"):void 0}function ge(n){return Y(n)&&A(X(n))?J(n,i=>A(i)):void 0}function ye(n){return n instanceof Error&&(/\bHTTP 40[34]\b/.test(n.message)||n.code==="ENOENT")}async function ce(n,i){let e=ge(n);if(!e)return{};try{return await P(e,i).stat(),{location:e}}catch(t){return ye(t)?{}:{unreadable:String(t)}}}var be=5e3,we=50*2**20,H=class extends Error{constructor(e){super(`this GAF is ${(e/2**20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`);this.name="UnindexedGafTooLargeError"}};function xe(n,i){if(n.length<=i)return n;let e=n.length/i;return Array.from({length:i},(t,a)=>n[Math.floor(a*e)])}var pe=(n,i)=>n.path.some(e=>i.has(e.name)),v=class{constructor(i,e){this.file=i;this.tabix=e;this.whole=L({setup:async({signal:i})=>{let{size:e}=await this.file.stat();if(e>we)throw new H(e);let t=await this.file.readFile({signal:i}),a=new TextDecoder().decode(t[0]===31&&t[1]===139?await K(t):t);return E(a)}})}async readIndexed(i,e,t){let a=1/0,r=-1/0;for(let s of e){let c=Number(s);Number.isInteger(c)&&(a=Math.min(a,c),r=Math.max(r,c))}let o=[];return a<=r&&await i.getLines("{node}",a,r+1,{signal:t,lineCallback:s=>{let c=z(s);c&&pe(c,e)&&o.push(c)}}),o}async readsOver(i,{signal:e}={}){let t=this.tabix?await this.readIndexed(this.tabix,i,e):(await this.whole({signal:e})).filter(a=>pe(a,i));return{records:xe(t,be),total:t.length}}};var I=class extends Error{constructor(e){super(e===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${e}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`);this.name="NoHaplotypeIndexError"}},q=class extends Error{constructor(e,t){super(`the graph is cut on its reference, ${t}; a window on ${e} has no reference coordinates to cut at. Open the graph from a ${t} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function Se(n,i){return`${u(n)}#${n.contig}@${i.start.node}.${i.start.offset}`}function Ne({alignment:n,assemblyName:i,refName:e,lane:t}){let{refStart:a,refEnd:r,strand:o,cigar:s}=n;if(!(r<=a)){let{name:c,hapStart:p,hapEnd:l}=n,f=Se(c,n),g={uniqueId:f,assemblyName:i,refName:e,start:a,end:r,type:"match",strand:o==="-"?-1:1,CIGAR:s,syntenyId:f,mate:{refName:c.contig,start:p,end:l,assemblyName:t}};return new ne(g)}}function Pe({pair:n,lane:i,mateLane:e}){return se({target:{name:`${u(n.target)}#${n.target.contig}`,assemblyName:i,refName:n.target.contig,start:n.targetStart,end:n.targetEnd},query:{name:`${u(n.query)}#${n.query.contig}`,assemblyName:e,refName:n.query.contig,start:n.queryStart,end:n.queryEnd},strand:n.strand,cigar:n.cigar,matches:n.matches,columns:n.columns})}var Le=12e4;function Re(n,i){let e=new Map;for(let a of n)for(let{name:r,start:o,end:s}of a.walkSpans()){let c=u(r);if(i.has(c)){let p=`${c}#${r.contig}`,l=e.get(p);l?l.push([o,s]):e.set(p,[[o,s]])}}let t=0;for(let a of e.values()){a.sort((r,o)=>r[0]-o[0]);for(let r=1;r<a.length;r++){let o=a[r][0]-a[r-1][1];o>0&&o<=Le&&(t=Math.max(t,o))}}return t}function fe(n,i){return n instanceof Z&&(n.message=`Zoom in to about ${_(n.fitsBp)} to see ${i}`),n}var le=(n,i,e)=>ie(fe(W(n,i,e)??n,"lanes"),e),me=n=>({...n,start:Math.floor(n.start),end:Math.ceil(n.end)}),T=class extends ae{constructor(){super(...arguments);this.graph=L({label:"Opening pangenome database",setup:async()=>{let e=this.getConf("gbzDbLocation"),t=this.getConf("haplotypeIndexLocation"),a=G(t)?{location:t}:await ce(e,this.pluginManager),r=a.location,o=await D.open({source:P(e,this.pluginManager),haplotypeIndex:r?P(r,this.pluginManager):void 0}),s=this.getConf("assemblyNames")[0];if(s===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let c=await M(o),p=j({configured:this.getConf("referenceSample"),anchorPrefix:N(this,s),referenceSamples:c});return{db:o,anchor:s,referenceSample:p,referenceSamples:c,unreadableIndex:a.unreadable}}});this.gaf=L({label:"Opening reads",setup:async()=>{let e=this.getConf("readsLocation"),t=this.getConf(["readsIndex","location"]);return G(e)?new v(P(e,this.pluginManager),G(t)?V(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(e,t){let{db:a,referenceSample:r}=await this.graph(t);return $(a,r,e)}async getHaplotypes(e={}){let{db:t,referenceSamples:a}=await this.graph(e),r=new Map;for(let o of await t.paths()){let s=u(o.name),c=r.get(s);c?c.contigs.includes(o.name.contig)||c.contigs.push(o.name.contig):r.set(s,{prefix:s,sample:o.name.sample,haplotype:o.name.haplotype,contigs:[o.name.contig],isReference:a.includes(o.name.sample)})}return[...r.values()]}async getHeader(e={}){let{anchor:t,referenceSample:a}=await this.graph(e),r=C(this),o=[];for(let s of await this.getHaplotypes(e))s.sample!==a&&o.push({name:O(r,s.prefix),label:s.prefix,group:s.sample});return{hasCoarseTier:!1,anchorAssemblyName:t,lanes:o}}async getRefNames(e={}){let{db:t,anchor:a,referenceSample:r}=await this.graph(e),{assemblyName:o}=e,s=o===a?void 0:N(this,o),c=(await t.paths()).filter(p=>o===a?p.isIndexed&&p.name.sample===r:F(u(p.name),s)).map(p=>p.name.contig);return[...new Set(c)]}keepPredicate(e,t){let a=e===void 0||e.length===0?void 0:e.map(r=>N(this,r));return a===void 0&&t===void 0?void 0:r=>k(r,a)&&(t===void 0||F(u(r),t))}async getSubgraph(e,t={}){let{signal:a}=t,{db:r,anchor:o,referenceSample:s,unreadableIndex:c}=await this.graph({signal:a}),{assemblyName:p,refName:l,start:f,end:g}=me(e);if(p!==o)throw new q(p,o);let y=await this.referenceQuery(l,{signal:a});if(!y)throw new Error(`${s} has no indexed path ${l} in this graph`);let b=this.keepPredicate(t.haplotypes);if(b!==void 0&&!r.hasHaplotypeIndex)throw new I(c);let d=await U(r,y,f,g,{context:this.getConf("context"),snarls:t.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:t.signal,keep:b}).catch(w=>{throw fe(w,"the graph")});return typeof d=="string"?d:te(d,{start:f,end:g},t.walkRows)}async getReads(e,t={}){let a=await this.gaf(t);return a?a.readsOver(new Set(e),t):{records:[],total:0}}async laneHaplotypes(e,t){let a=N(this,e);return(await this.getHaplotypes(t)).filter(r=>F(r.prefix,a))}async anchorFeatures(e,t){let{db:a}=await this.graph(t),{assemblyName:r,refName:o,start:s,end:c}=e,p=N(this,t.targetAssemblyName),l=C(this),f=this.keepPredicate(t.haplotypes,p),g=await this.referenceQuery(o,t),y=this.getConf("nodeLimit");return(g?await B(`Reading graph ${o}:${s.toLocaleString()}-${c.toLocaleString()}`,t.statusCallback,()=>a.getAlignments({path:g,start:s,end:c,context:this.getConf("context"),haplotypes:"all",limit:y,signal:t.signal,keep:f}).catch(d=>{throw le(d,y,c-s)})):[]).flatMap(d=>{let w=d.resolved?Ne({alignment:d,assemblyName:r,refName:o,lane:O(l,u(d.name))}):void 0;return w===void 0?[]:[w]})}async pairFeatures(e,t,a){let{db:r}=await this.graph(a),{refName:o,start:s,end:c}=e,l=(await Promise.all(t.map(async m=>({pair:m,featureSide:await this.laneHaplotypes(m.queryAssemblyName,a),mateSide:await this.laneHaplotypes(m.targetAssemblyName,a)})))).filter(({featureSide:m,mateSide:h})=>m.length>0&&h.length>0),f=new Set(l.flatMap(({featureSide:m,mateSide:h})=>[...m,...h].map(u))),g=await this.referenceQuery(o,a),y=this.getConf("nodeLimit"),b=this.getConf("context"),d=(m,h)=>r.getSubgraphs({path:m,start:s,end:c,context:h,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:a.signal,keep:x=>f.has(u(x))}),w=async m=>{let h=await d(m,b).catch(S=>{throw le(S,y,c-s)}),x=Re(h,f),R=Math.ceil(x/2)+2e3;return x>0&&R>b?d(m,R).catch(S=>{if(S instanceof Q)return h;throw S}):h};return(g&&l.length>0?await B(oe(t),a.statusCallback,()=>w(g)):[]).flatMap(m=>l.flatMap(({pair:h,featureSide:x,mateSide:R})=>x.flatMap(S=>R.flatMap(de=>m.pairAlignments({target:S,query:de,bases:!1}).map(he=>Pe({pair:he,lane:h.queryAssemblyName,mateLane:h.targetAssemblyName}))))))}getFeatures(e,t={}){let a=me(e);return ee(async r=>{let{db:o,anchor:s,unreadableIndex:c}=await this.graph(t);if(!o.hasHaplotypeIndex)throw new I(c);if(a.assemblyName===s){let p=re(t),l=p.length>0?await this.pairFeatures(a,p,t):await this.anchorFeatures(a,t);for(let f of l)r.next(f)}r.complete()},t.signal)}};export{I as NoHaplotypeIndexError,ue as PairTargetError,T as default,Re as widestWalkGap};
+//# sourceMappingURL=GbzBaseSyntenyAdapter-67NMRHWZ.js.map

package/dist/chunks/{GraphGenomeView-EM7KNQHB.js → GraphGenomeView-RD2XGX6D.js}

@@ -1,4 +1,4 @@
-import{b as C}from"./chunk-FUPBKEC2.js";import"./chunk-DKYX6XBX.js";import"./chunk-3ROUAVMP.js";import"./chunk-TL2FTG3H.js";import{p as d}from"./chunk-UWBKGUBZ.js";import"./chunk-DMLYMYLG.js";import"./chunk-4DQWDJG7.js";import"./chunk-UC2NHZ7E.js";import"./chunk-OPWSPSAE.js";import"./chunk-W5HHWDGZ.js";import"./chunk-E23AOQPE.js";import"./chunk-YBLNN5FU.js";import"./chunk-U6SNNNFV.js";import"./chunk-ELC7POI6.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-CL4PYWKC.js";import"./chunk-3VGXCEMQ.js";import"./chunk-6VNDP3UB.js";import"./chunk-3WG3GF2A.js";import"./chunk-J5RMHLFJ.js";import{i as L}from"./chunk-NIEZKWQV.js";import{A as l,F as G,H as p,e as s,j as v,o as n,x as y}from"./chunk-5Z4VIKXZ.js";import{a as h,b as e,c as r,d as i}from"./chunk-JMBDTNUR.js";var N=d()({paper:{padding:16,margin:8,maxWidth:560,marginInline:"auto",display:"flex",flexDirection:"column",gap:12},row:{display:"flex",alignItems:"center",justifyContent:"space-between",gap:8}}),S=i(function({model:a}){let{classes:t}=N();return!a.error&&!a.loadCanceled?r(l,{className:t.paper,"data-testid":"graph-genome-loading",children:[r("div",{className:t.row,children:[e(v,{variant:"h6",message:a.statusMessage||void 0}),a.canCancelLoad?e(n,{size:"small","data-testid":"graph-genome-cancel",onClick:()=>{a.cancelLoad()},children:"Cancel"}):null]}),e(y,{variant:"indeterminate"})]}):a.error?e(l,{className:t.paper,children:e(s,{error:a.error,onReset:()=>{a.retryLoad()}})}):e(l,{className:t.paper,"data-testid":"graph-genome-load-canceled",children:r("div",{className:t.row,children:[e(p,{variant:"h6",children:"Loading canceled"}),e(n,{variant:"contained",size:"small","data-testid":"graph-genome-retry",onClick:()=>{a.retryLoad()},children:"Retry"})]})})}),f=S;var T=`H	VN:Z:1.0
+import{b as C}from"./chunk-Y7MQVQAS.js";import"./chunk-4XY7HUQR.js";import"./chunk-DIGIM3XY.js";import"./chunk-WE7XHNAH.js";import{p as d}from"./chunk-X2QGBINE.js";import"./chunk-WO644UAC.js";import"./chunk-4DQWDJG7.js";import"./chunk-UC2NHZ7E.js";import"./chunk-OPWSPSAE.js";import"./chunk-W5HHWDGZ.js";import"./chunk-E23AOQPE.js";import"./chunk-YBLNN5FU.js";import"./chunk-U6SNNNFV.js";import"./chunk-ELC7POI6.js";import"./chunk-YBLNN5FU.js";import"./chunk-QUDJ7AM3.js";import"./chunk-CL4PYWKC.js";import"./chunk-TMM73K4C.js";import"./chunk-6VNDP3UB.js";import"./chunk-FLKXKTS2.js";import"./chunk-TC265JAP.js";import{i as L}from"./chunk-J2PN6CG3.js";import{A as l,F as G,H as p,e as s,j as v,o as n,x as y}from"./chunk-WE7DQVXF.js";import{a as h,b as e,c as r,d as i}from"./chunk-DUU6T2I5.js";var N=d()({paper:{padding:16,margin:8,maxWidth:560,marginInline:"auto",display:"flex",flexDirection:"column",gap:12},row:{display:"flex",alignItems:"center",justifyContent:"space-between",gap:8}}),S=i(function({model:a}){let{classes:t}=N();return!a.error&&!a.loadCanceled?r(l,{className:t.paper,"data-testid":"graph-genome-loading",children:[r("div",{className:t.row,children:[e(v,{variant:"h6",message:a.statusMessage||void 0}),a.canCancelLoad?e(n,{size:"small","data-testid":"graph-genome-cancel",onClick:()=>{a.cancelLoad()},children:"Cancel"}):null]}),e(y,{variant:"indeterminate"})]}):a.error?e(l,{className:t.paper,children:e(s,{error:a.error,onReset:()=>{a.retryLoad()}})}):e(l,{className:t.paper,"data-testid":"graph-genome-load-canceled",children:r("div",{className:t.row,children:[e(p,{variant:"h6",children:"Loading canceled"}),e(n,{variant:"contained",size:"small","data-testid":"graph-genome-retry",onClick:()=>{a.retryLoad()},children:"Retry"})]})})}),f=S;var T=`H	VN:Z:1.0
 S	1	ACGT
 S	2	GGCC
 S	3	TTAA
@@ -7,4 +7,4 @@ L	1	+	2	+	0M
 L	1	+	3	+	0M
 L	2	+	4	+	0M
 L	3	+	4	+	0M`,E=d()({column:{display:"flex",flexDirection:"column",gap:8},rowEnd:{display:"flex",gap:8,alignItems:"flex-end"},rowCenter:{display:"flex",gap:8,alignItems:"center"},flex1:{flex:1},paper:{padding:16,margin:8,maxWidth:560,marginInline:"auto"},header:{marginBottom:12},footer:{marginTop:12,display:"flex",justifyContent:"flex-end"}}),F=i(function({model:a}){let{classes:t}=E(),[m,w]=L("");function u(){let o=m.trim();o&&a.openGfaLocation({uri:o,locationType:"UriLocation"})}function M(o){let c=o.target.files?.[0];o.target.value="",c&&a.loadGFAFile(c,c.name)}return r(l,{className:t.paper,children:[e("div",{className:t.header,children:e(p,{variant:"h6",children:"Load a GFA graph"})}),r("div",{className:t.column,children:[r("div",{className:t.rowCenter,children:[r(n,{variant:"outlined",component:"label",size:"small",children:["Choose file",e("input",{type:"file",accept:".gfa,.gfa1,.gfa2,.gz",hidden:!0,onChange:o=>{M(o)}})]}),e(p,{variant:"caption",color:"text.secondary",children:"Whole-file GFA; best for small/medium graphs."})]}),r("div",{className:t.rowEnd,children:[e(G,{size:"small",label:"URL",placeholder:"https://example.com/graph.gfa",value:m,onChange:o=>{w(o.target.value)},onKeyDown:o=>{o.key==="Enter"&&u()},className:t.flex1}),e(n,{variant:"contained",onClick:()=>{u()},disabled:!m.trim(),children:"Open"})]})]}),e("div",{className:t.footer,children:e(n,{size:"small",onClick:()=>{a.loadGFA(T,"Example graph")},children:"Load 4-node example"})}),a.error?e(s,{error:a.error}):null]})}),x=F;var B=i(function({model:a}){return a.hasGraph?e(C,{model:a}):a.canRetryLoad?e(f,{model:a}):r(h,{children:[a.isLoading?e(f,{model:a}):null,e("div",{hidden:a.isLoading,children:e(x,{model:a})})]})}),q=B;export{q as default};
-//# sourceMappingURL=GraphGenomeView-EM7KNQHB.js.map
+//# sourceMappingURL=GraphGenomeView-RD2XGX6D.js.map

package/dist/chunks/GraphTrackSettingsDialog-R3XOY32L.js

@@ -0,0 +1,4 @@
+import{a as G,b as L}from"./chunk-4XY7HUQR.js";import{b as v,c as x,p as f}from"./chunk-X2QGBINE.js";import"./chunk-UC2NHZ7E.js";import"./chunk-OPWSPSAE.js";import"./chunk-ELC7POI6.js";import"./chunk-QUDJ7AM3.js";import"./chunk-CL4PYWKC.js";import"./chunk-TMM73K4C.js";import"./chunk-6VNDP3UB.js";import{h as g,i as d}from"./chunk-J2PN6CG3.js";import{F as y,H as h,n as H}from"./chunk-WE7DQVXF.js";import{b as p,c as i,d as s}from"./chunk-DUU6T2I5.js";var k=f()({section:{marginBottom:24}}),w=[{value:"0",label:"None"},{value:"1",label:"1 hop"},{value:"2",label:"2 hops"}],F=s(function({model:t}){let{classes:o}=k(),e=t.sourceAdapter;return e?.type==="RgfaTabixAdapter"&&!v(e)?i("div",{className:o.section,children:[p(G,{label:"Graph context",sx:{minWidth:200},value:String(t.subgraphContext),options:w,testId:"graph-context-select",onChange:n=>{t.setSubgraphContext(Number(n)),t.recut()}}),p(h,{variant:"caption",component:"div",color:"text.secondary",children:"How far the cut follows links out of the region. At none, a detour that leaves the window draws as two stubs. No effect on gfa-to-tabix's default anchored index."})]}):null}),M=F;var I=f()({section:{marginBottom:24}});function A(a){return a.split(/[\s,]+/).filter(t=>t!=="")}var N=(a,t)=>a.join(`
+`)===t.join(`
+`);function P(a,t){let o=a.cutHaplotypes??[],[e,n]=d(o);return N(o,e)||(n(o),t()),r=>{N(r,o)||(n(r),a.setSubgraphHaplotypes(r),a.recut())}}var D=s(function({model:t}){let[o,e]=d(t.cutHaplotypes?.join(", ")??""),n=P(t,()=>{e(t.cutHaplotypes?.join(", ")??"")}),r=()=>{n(A(o))};return p(y,{fullWidth:!0,label:"Haplotypes",placeholder:"every haplotype",value:o,slotProps:{htmlInput:{"data-testid":"graph-haplotypes-field"}},onChange:c=>{e(c.target.value)},onBlur:()=>{r()},onKeyDown:c=>{c.key==="Enter"&&r()}})}),B=s(function({model:t,names:o}){let[e,n]=d(t.cutHaplotypes??[]),r=g(e),c=g(""),[b,S]=d(!1),C=P(t,()=>{r.current=t.cutHaplotypes??[],n(r.current)});return p(H,{multiple:!0,freeSolo:!0,disableCloseOnSelect:!0,options:o,value:e,open:b,onOpen:()=>{S(!0)},onInputChange:(u,l)=>{c.current=l},onClose:(u,l)=>{S(!1);let m=c.current.trim();l==="blur"&&m&&!r.current.includes(m)&&(r.current=[...r.current,m],n(r.current)),C(r.current)},onChange:(u,l)=>{r.current=l,n(l),b||C(l)},renderInput:u=>p(y,{...u,label:"Haplotypes",placeholder:e.length===0?"every haplotype":void 0,slotProps:{...u.slotProps,htmlInput:{...u.slotProps.htmlInput,"data-testid":"graph-haplotypes-field"}}})})}),O=s(function({model:t}){let{classes:o}=I(),e=t.haplotypeNames,n=t.sourceAdapter;return n&&x(n)?i("div",{className:o.section,children:[e?p(B,{model:t,names:e}):p(D,{model:t}),i(h,{variant:"caption",component:"div",color:"text.secondary",children:[e?`Which of the graph's ${e.length.toLocaleString()} haplotypes to cut, or a PanSN prefix (HG002 for both).`:"Which haplotypes to cut, as lane assembly names or PanSN prefixes (HG002#1, or HG002 for both) separated by commas."," ","Empty is every haplotype."]})]}):null}),T=O;var ot=s(function({model:t,onClose:o}){return i(L,{model:t,onClose:o,children:[p(M,{model:t}),p(T,{model:t})]})});export{ot as default};
+//# sourceMappingURL=GraphTrackSettingsDialog-R3XOY32L.js.map

package/dist/chunks/{GraphTrackSettingsDialog-GTQ6Z2HA.js.map → GraphTrackSettingsDialog-R3XOY32L.js.map}

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/LinearGraphDisplay/components/SubgraphContextSelect.tsx", "../../src/LinearGraphDisplay/components/SubgraphHaplotypesField.tsx", "../../src/LinearGraphDisplay/components/GraphTrackSettingsDialog.tsx"],
-  "sourcesContent": ["import { Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport LabelledSelect from '../../GraphGenomeView/components/LabelledSelect'\nimport { walkIndexed } from '../../graphTrackConfig'\n\nimport type { LinearGraphCutModel } from '../model'\n\nconst useStyles = makeStyles()({\n  section: {\n    marginBottom: 24,\n  },\n})\n\n// Only an rGFA cut from segment rows reads hops: a GBZ cut widens by its\n// adapter's bp `context`, and a walk-indexed cut follows its walks.\n// Hops past the region's own segments, each costing a tabix query per\n// off-reference segment already reached. One is the default: at none a single\n// detour draws as two unrelated stubs, which is a wrong picture of the graph\n// rather than a cheaper one. Two exists for a graph whose alleles have alleles\n// (HPRC's amylase window keeps growing at 2, the E. coli paa locus does not), and\n// it stops there because a frontier is still not a bubble decomposition. Cut an\n// exact slice with gfatools when that is what is wanted.\nconst SUBGRAPH_CONTEXTS = [\n  { value: '0', label: 'None' },\n  { value: '1', label: '1 hop' },\n  { value: '2', label: '2 hops' },\n]\n\nconst SubgraphContextSelect = observer(function SubgraphContextSelect({\n  model,\n}: {\n  model: LinearGraphCutModel\n}) {\n  const { classes } = useStyles()\n  const adapter = model.sourceAdapter\n  return adapter?.type === 'RgfaTabixAdapter' && !walkIndexed(adapter) ? (\n    <div className={classes.section}>\n      <LabelledSelect\n        label=\"Graph context\"\n        sx={{ minWidth: 200 }}\n        value={String(model.subgraphContext)}\n        options={SUBGRAPH_CONTEXTS}\n        testId=\"graph-context-select\"\n        onChange={hops => {\n          model.setSubgraphContext(Number(hops))\n          model.recut()\n        }}\n      />\n      <Typography variant=\"caption\" component=\"div\" color=\"text.secondary\">\n        How far the cut follows links out of the region. At none, a detour that\n        leaves the window draws as two stubs. No effect on gfa-to-tabix&apos;s\n        default anchored index.\n      </Typography>\n    </div>\n  ) : null\n})\n\nexport default SubgraphContextSelect\n", "import { useRef, useState } from 'react'\n\nimport { Autocomplete, TextField, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport { cutsByHaplotype } from '../../graphTrackConfig'\n\nimport type { LinearGraphCutModel } from '../model'\n\nconst useStyles = makeStyles()({\n  section: {\n    marginBottom: 24,\n  },\n})\n\nfunction parseHaplotypeList(text: string) {\n  return text.split(/[\\s,]+/).filter(name => name !== '')\n}\n\nconst sameList = (a: readonly string[], b: readonly string[]) =>\n  a.join('\\n') === b.join('\\n')\n\n// The cut's set, and the last one this field saw: an outside change (a\n// restored session, a launch) resets the draft, while the field's own apply\n// records what it set first, so it keeps its focus and draft\nfunction useCutHaplotypes(model: LinearGraphCutModel, reset: () => void) {\n  const current = model.cutHaplotypes ?? []\n  const [seen, setSeen] = useState(current)\n  if (!sameList(current, seen)) {\n    setSeen(current)\n    reset()\n  }\n  return (haplotypes: string[]) => {\n    if (!sameList(haplotypes, current)) {\n      setSeen(haplotypes)\n      model.setSubgraphHaplotypes(haplotypes)\n      model.recut()\n    }\n  }\n}\n\nconst HaplotypeListField = observer(function HaplotypeListField({\n  model,\n}: {\n  model: LinearGraphCutModel\n}) {\n  const [draft, setDraft] = useState(model.cutHaplotypes?.join(', ') ?? '')\n  const setCut = useCutHaplotypes(model, () => {\n    setDraft(model.cutHaplotypes?.join(', ') ?? '')\n  })\n  const apply = () => {\n    setCut(parseHaplotypeList(draft))\n  }\n  return (\n    <TextField\n      fullWidth\n      label=\"Haplotypes\"\n      placeholder=\"every haplotype\"\n      value={draft}\n      slotProps={{ htmlInput: { 'data-testid': 'graph-haplotypes-field' } }}\n      onChange={e => {\n        setDraft(e.target.value)\n      }}\n      onBlur={() => {\n        apply()\n      }}\n      onKeyDown={e => {\n        if (e.key === 'Enter') {\n          apply()\n        }\n      }}\n    />\n  )\n})\n\n// The haplotypes a walk-indexed graph's header names, searched as typed. A\n// typed prefix the list lacks (HG002 for both haplotypes) is kept too, on\n// Enter or when the field loses focus. The set applies when the list closes\n// or, with the list closed, as it changes. Not MUI's `autoSelect`: in a\n// multiple select its blur toggles the highlighted option, so a pick made by\n// keyboard was dropped again on Tab.\nconst HaplotypePickField = observer(function HaplotypePickField({\n  model,\n  names,\n}: {\n  model: LinearGraphCutModel\n  names: string[]\n}) {\n  const [draft, setDraft] = useState(model.cutHaplotypes ?? [])\n  const draftRef = useRef(draft)\n  const typed = useRef('')\n  const [open, setOpen] = useState(false)\n  const apply = useCutHaplotypes(model, () => {\n    draftRef.current = model.cutHaplotypes ?? []\n    setDraft(draftRef.current)\n  })\n  return (\n    <Autocomplete\n      multiple\n      freeSolo\n      disableCloseOnSelect\n      options={names}\n      value={draft}\n      open={open}\n      onOpen={() => {\n        setOpen(true)\n      }}\n      onInputChange={(_, text) => {\n        typed.current = text\n      }}\n      onClose={(_, reason) => {\n        setOpen(false)\n        const text = typed.current.trim()\n        if (reason === 'blur' && text && !draftRef.current.includes(text)) {\n          draftRef.current = [...draftRef.current, text]\n          setDraft(draftRef.current)\n        }\n        apply(draftRef.current)\n      }}\n      onChange={(_, value) => {\n        draftRef.current = value\n        setDraft(value)\n        if (!open) {\n          apply(value)\n        }\n      }}\n      renderInput={params => (\n        <TextField\n          {...params}\n          label=\"Haplotypes\"\n          placeholder={draft.length === 0 ? 'every haplotype' : undefined}\n          slotProps={{\n            ...params.slotProps,\n            htmlInput: {\n              ...params.slotProps.htmlInput,\n              'data-testid': 'graph-haplotypes-field',\n            },\n          }}\n        />\n      )}\n    />\n  )\n})\n\n// Only a GBZ cut and a walk-indexed rGFA cut read the set\nconst SubgraphHaplotypesField = observer(function SubgraphHaplotypesField({\n  model,\n}: {\n  model: LinearGraphCutModel\n}) {\n  const { classes } = useStyles()\n  const names = model.haplotypeNames\n  const adapter = model.sourceAdapter\n  return adapter && cutsByHaplotype(adapter) ? (\n    <div className={classes.section}>\n      {names ? (\n        <HaplotypePickField model={model} names={names} />\n      ) : (\n        <HaplotypeListField model={model} />\n      )}\n      <Typography variant=\"caption\" component=\"div\" color=\"text.secondary\">\n        {names\n          ? `Which of the graph's ${names.length.toLocaleString()} haplotypes to cut, or a PanSN prefix (HG002 for both).`\n          : 'Which haplotypes to cut, as lane assembly names or PanSN prefixes (HG002#1, or HG002 for both) separated by commas.'}{' '}\n        Empty is every haplotype.\n      </Typography>\n    </div>\n  ) : null\n})\n\nexport default SubgraphHaplotypesField\n", "import SubgraphContextSelect from './SubgraphContextSelect'\nimport SubgraphHaplotypesField from './SubgraphHaplotypesField'\nimport GraphSettingsDialog from '../../GraphGenomeView/components/GraphSettingsDialog'\n\nimport type { LinearGraphCutModel } from '../model'\n\nexport default function GraphTrackSettingsDialog({\n  model,\n  onClose,\n}: {\n  model: LinearGraphCutModel\n  onClose: () => void\n}) {\n  return (\n    <GraphSettingsDialog model={model} onClose={onClose}>\n      <SubgraphContextSelect model={model} />\n      <SubgraphHaplotypesField model={model} />\n    </GraphSettingsDialog>\n  )\n}\n"],
-  "mappings": "ocASA,IAAMA,EAAYC,EAAW,EAAE,CAC7B,QAAS,CACP,aAAc,EAChB,CACF,CAAC,EAWKC,EAAoB,CACxB,CAAE,MAAO,IAAK,MAAO,MAAO,EAC5B,CAAE,MAAO,IAAK,MAAO,OAAQ,EAC7B,CAAE,MAAO,IAAK,MAAO,QAAS,CAChC,EAEMC,EAAwBC,EAAS,SAA+B,CACpE,MAAAC,CACF,EAEG,CACD,GAAM,CAAE,QAAAC,CAAQ,EAAIN,EAAU,EACxBO,EAAUF,EAAM,cACtB,OAAOE,GAAS,OAAS,oBAAsB,CAACC,EAAYD,CAAO,EACjEE,EAAC,OAAI,UAAWH,EAAQ,QACtB,UAAAI,EAACC,EAAA,CACC,MAAM,gBACN,GAAI,CAAE,SAAU,GAAI,EACpB,MAAO,OAAON,EAAM,eAAe,EACnC,QAASH,EACT,OAAO,uBACP,SAAUU,GAAQ,CAChBP,EAAM,mBAAmB,OAAOO,CAAI,CAAC,EACrCP,EAAM,MAAM,CACd,EACF,EACAK,EAACG,EAAA,CAAW,QAAQ,UAAU,UAAU,MAAM,MAAM,iBAAiB,6KAIrE,GACF,EACE,IACN,CAAC,EAEMC,EAAQX,ECjDf,IAAMY,EAAYC,EAAW,EAAE,CAC7B,QAAS,CACP,aAAc,EAChB,CACF,CAAC,EAED,SAASC,EAAmBC,EAAc,CACxC,OAAOA,EAAK,MAAM,QAAQ,EAAE,OAAOC,GAAQA,IAAS,EAAE,CACxD,CAEA,IAAMC,EAAW,CAACC,EAAsBC,IACtCD,EAAE,KAAK;AAAA,CAAI,IAAMC,EAAE,KAAK;AAAA,CAAI,EAK9B,SAASC,EAAiBC,EAA4BC,EAAmB,CACvE,IAAMC,EAAUF,EAAM,eAAiB,CAAC,EAClC,CAACG,EAAMC,CAAO,EAAIC,EAASH,CAAO,EACxC,OAAKN,EAASM,EAASC,CAAI,IACzBC,EAAQF,CAAO,EACfD,EAAM,GAEAK,GAAyB,CAC1BV,EAASU,EAAYJ,CAAO,IAC/BE,EAAQE,CAAU,EAClBN,EAAM,sBAAsBM,CAAU,EACtCN,EAAM,MAAM,EAEhB,CACF,CAEA,IAAMO,EAAqBC,EAAS,SAA4B,CAC9D,MAAAR,CACF,EAEG,CACD,GAAM,CAACS,EAAOC,CAAQ,EAAIL,EAASL,EAAM,eAAe,KAAK,IAAI,GAAK,EAAE,EAClEW,EAASZ,EAAiBC,EAAO,IAAM,CAC3CU,EAASV,EAAM,eAAe,KAAK,IAAI,GAAK,EAAE,CAChD,CAAC,EACKY,EAAQ,IAAM,CAClBD,EAAOlB,EAAmBgB,CAAK,CAAC,CAClC,EACA,OACEI,EAACC,EAAA,CACC,UAAS,GACT,MAAM,aACN,YAAY,kBACZ,MAAOL,EACP,UAAW,CAAE,UAAW,CAAE,cAAe,wBAAyB,CAAE,EACpE,SAAUM,GAAK,CACbL,EAASK,EAAE,OAAO,KAAK,CACzB,EACA,OAAQ,IAAM,CACZH,EAAM,CACR,EACA,UAAWG,GAAK,CACVA,EAAE,MAAQ,SACZH,EAAM,CAEV,EACF,CAEJ,CAAC,EAQKI,EAAqBR,EAAS,SAA4B,CAC9D,MAAAR,EACA,MAAAiB,CACF,EAGG,CACD,GAAM,CAACR,EAAOC,CAAQ,EAAIL,EAASL,EAAM,eAAiB,CAAC,CAAC,EACtDkB,EAAWC,EAAOV,CAAK,EACvBW,EAAQD,EAAO,EAAE,EACjB,CAACE,EAAMC,CAAO,EAAIjB,EAAS,EAAK,EAChCO,EAAQb,EAAiBC,EAAO,IAAM,CAC1CkB,EAAS,QAAUlB,EAAM,eAAiB,CAAC,EAC3CU,EAASQ,EAAS,OAAO,CAC3B,CAAC,EACD,OACEL,EAACU,EAAA,CACC,SAAQ,GACR,SAAQ,GACR,qBAAoB,GACpB,QAASN,EACT,MAAOR,EACP,KAAMY,EACN,OAAQ,IAAM,CACZC,EAAQ,EAAI,CACd,EACA,cAAe,CAACE,EAAG9B,IAAS,CAC1B0B,EAAM,QAAU1B,CAClB,EACA,QAAS,CAAC8B,EAAGC,IAAW,CACtBH,EAAQ,EAAK,EACb,IAAM5B,EAAO0B,EAAM,QAAQ,KAAK,EAC5BK,IAAW,QAAU/B,GAAQ,CAACwB,EAAS,QAAQ,SAASxB,CAAI,IAC9DwB,EAAS,QAAU,CAAC,GAAGA,EAAS,QAASxB,CAAI,EAC7CgB,EAASQ,EAAS,OAAO,GAE3BN,EAAMM,EAAS,OAAO,CACxB,EACA,SAAU,CAACM,EAAGE,IAAU,CACtBR,EAAS,QAAUQ,EACnBhB,EAASgB,CAAK,EACTL,GACHT,EAAMc,CAAK,CAEf,EACA,YAAaC,GACXd,EAACC,EAAA,CACE,GAAGa,EACJ,MAAM,aACN,YAAalB,EAAM,SAAW,EAAI,kBAAoB,OACtD,UAAW,CACT,GAAGkB,EAAO,UACV,UAAW,CACT,GAAGA,EAAO,UAAU,UACpB,cAAe,wBACjB,CACF,EACF,EAEJ,CAEJ,CAAC,EAGKC,EAA0BpB,EAAS,SAAiC,CACxE,MAAAR,CACF,EAEG,CACD,GAAM,CAAE,QAAA6B,CAAQ,EAAItC,EAAU,EACxB0B,EAAQjB,EAAM,eACd8B,EAAU9B,EAAM,cACtB,OAAO8B,GAAWC,EAAgBD,CAAO,EACvCE,EAAC,OAAI,UAAWH,EAAQ,QACrB,UAAAZ,EACCJ,EAACG,EAAA,CAAmB,MAAOhB,EAAO,MAAOiB,EAAO,EAEhDJ,EAACN,EAAA,CAAmB,MAAOP,EAAO,EAEpCgC,EAACC,EAAA,CAAW,QAAQ,UAAU,UAAU,MAAM,MAAM,iBACjD,UAAAhB,EACG,wBAAwBA,EAAM,OAAO,eAAe,CAAC,0DACrD,sHAAuH,IAAI,6BAEjI,GACF,EACE,IACN,CAAC,EAEMiB,EAAQN,ECrKA,SAARO,EAA0C,CAC/C,MAAAC,EACA,QAAAC,CACF,EAGG,CACD,OACEC,EAACC,EAAA,CAAoB,MAAOH,EAAO,QAASC,EAC1C,UAAAG,EAACC,EAAA,CAAsB,MAAOL,EAAO,EACrCI,EAACE,EAAA,CAAwB,MAAON,EAAO,GACzC,CAEJ",
-  "names": ["useStyles", "makeStyles", "SUBGRAPH_CONTEXTS", "SubgraphContextSelect", "observer", "model", "classes", "adapter", "walkIndexed", "jsxs", "jsx", "LabelledSelect", "hops", "Typography", "SubgraphContextSelect_default", "useStyles", "makeStyles", "parseHaplotypeList", "text", "name", "sameList", "a", "b", "useCutHaplotypes", "model", "reset", "current", "seen", "setSeen", "useState", "haplotypes", "HaplotypeListField", "observer", "draft", "setDraft", "setCut", "apply", "jsx", "TextField", "e", "HaplotypePickField", "names", "draftRef", "useRef", "typed", "open", "setOpen", "Autocomplete", "_", "reason", "value", "params", "SubgraphHaplotypesField", "classes", "adapter", "cutsByHaplotype", "jsxs", "Typography", "SubgraphHaplotypesField_default", "GraphTrackSettingsDialog", "model", "onClose", "jsxs", "GraphSettingsDialog_default", "jsx", "SubgraphContextSelect_default", "SubgraphHaplotypesField_default"]
+  "sourcesContent": ["import { Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport LabelledSelect from '../../GraphGenomeView/components/LabelledSelect'\nimport { walkIndexed } from '../../graphTrackConfig'\n\nimport type { LinearGraphCutModel } from '../model'\n\nconst useStyles = makeStyles()({\n  section: {\n    marginBottom: 24,\n  },\n})\n\n// Only an rGFA cut from segment rows reads hops: a GBZ cut widens by its\n// adapter's bp `context`, and a walk-indexed cut follows its walks.\n// Hops past the region's own segments, each costing a tabix query per\n// off-reference segment already reached. One is the default: at none a single\n// detour draws as two unrelated stubs, which is a wrong picture of the graph\n// rather than a cheaper one. Two exists for a graph whose alleles have alleles\n// (HPRC's amylase window keeps growing at 2, the E. coli paa locus does not), and\n// it stops there because a frontier is still not a bubble decomposition. Cut an\n// exact slice with gfatools when that is what is wanted.\nconst SUBGRAPH_CONTEXTS = [\n  { value: '0', label: 'None' },\n  { value: '1', label: '1 hop' },\n  { value: '2', label: '2 hops' },\n]\n\nconst SubgraphContextSelect = observer(function SubgraphContextSelect({\n  model,\n}: {\n  model: LinearGraphCutModel\n}) {\n  const { classes } = useStyles()\n  const adapter = model.sourceAdapter\n  return adapter?.type === 'RgfaTabixAdapter' && !walkIndexed(adapter) ? (\n    <div className={classes.section}>\n      <LabelledSelect\n        label=\"Graph context\"\n        sx={{ minWidth: 200 }}\n        value={String(model.subgraphContext)}\n        options={SUBGRAPH_CONTEXTS}\n        testId=\"graph-context-select\"\n        onChange={hops => {\n          model.setSubgraphContext(Number(hops))\n          model.recut()\n        }}\n      />\n      <Typography variant=\"caption\" component=\"div\" color=\"text.secondary\">\n        How far the cut follows links out of the region. At none, a detour that\n        leaves the window draws as two stubs. No effect on gfa-to-tabix&apos;s\n        default anchored index.\n      </Typography>\n    </div>\n  ) : null\n})\n\nexport default SubgraphContextSelect\n", "import { useRef, useState } from 'react'\n\nimport { Autocomplete, TextField, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport { cutsByHaplotype } from '../../graphTrackConfig'\n\nimport type { LinearGraphCutModel } from '../model'\n\nconst useStyles = makeStyles()({\n  section: {\n    marginBottom: 24,\n  },\n})\n\nfunction parseHaplotypeList(text: string) {\n  return text.split(/[\\s,]+/).filter(name => name !== '')\n}\n\nconst sameList = (a: readonly string[], b: readonly string[]) =>\n  a.join('\\n') === b.join('\\n')\n\n// The cut's set, and the last one this field saw: an outside change (a\n// restored session, a launch) resets the draft, while the field's own apply\n// records what it set first, so it keeps its focus and draft\nfunction useCutHaplotypes(model: LinearGraphCutModel, reset: () => void) {\n  const current = model.cutHaplotypes ?? []\n  const [seen, setSeen] = useState(current)\n  if (!sameList(current, seen)) {\n    setSeen(current)\n    reset()\n  }\n  return (haplotypes: string[]) => {\n    if (!sameList(haplotypes, current)) {\n      setSeen(haplotypes)\n      model.setSubgraphHaplotypes(haplotypes)\n      model.recut()\n    }\n  }\n}\n\nconst HaplotypeListField = observer(function HaplotypeListField({\n  model,\n}: {\n  model: LinearGraphCutModel\n}) {\n  const [draft, setDraft] = useState(model.cutHaplotypes?.join(', ') ?? '')\n  const setCut = useCutHaplotypes(model, () => {\n    setDraft(model.cutHaplotypes?.join(', ') ?? '')\n  })\n  const apply = () => {\n    setCut(parseHaplotypeList(draft))\n  }\n  return (\n    <TextField\n      fullWidth\n      label=\"Haplotypes\"\n      placeholder=\"every haplotype\"\n      value={draft}\n      slotProps={{ htmlInput: { 'data-testid': 'graph-haplotypes-field' } }}\n      onChange={e => {\n        setDraft(e.target.value)\n      }}\n      onBlur={() => {\n        apply()\n      }}\n      onKeyDown={e => {\n        if (e.key === 'Enter') {\n          apply()\n        }\n      }}\n    />\n  )\n})\n\n// The haplotypes a walk-indexed graph's header names, searched as typed. A\n// typed prefix the list lacks (HG002 for both haplotypes) is kept too, on\n// Enter or when the field loses focus. The set applies when the list closes\n// or, with the list closed, as it changes. Not MUI's `autoSelect`: in a\n// multiple select its blur toggles the highlighted option, so a pick made by\n// keyboard was dropped again on Tab.\nconst HaplotypePickField = observer(function HaplotypePickField({\n  model,\n  names,\n}: {\n  model: LinearGraphCutModel\n  names: string[]\n}) {\n  const [draft, setDraft] = useState(model.cutHaplotypes ?? [])\n  const draftRef = useRef(draft)\n  const typed = useRef('')\n  const [open, setOpen] = useState(false)\n  const apply = useCutHaplotypes(model, () => {\n    draftRef.current = model.cutHaplotypes ?? []\n    setDraft(draftRef.current)\n  })\n  return (\n    <Autocomplete\n      multiple\n      freeSolo\n      disableCloseOnSelect\n      options={names}\n      value={draft}\n      open={open}\n      onOpen={() => {\n        setOpen(true)\n      }}\n      onInputChange={(_, text) => {\n        typed.current = text\n      }}\n      onClose={(_, reason) => {\n        setOpen(false)\n        const text = typed.current.trim()\n        if (reason === 'blur' && text && !draftRef.current.includes(text)) {\n          draftRef.current = [...draftRef.current, text]\n          setDraft(draftRef.current)\n        }\n        apply(draftRef.current)\n      }}\n      onChange={(_, value) => {\n        draftRef.current = value\n        setDraft(value)\n        if (!open) {\n          apply(value)\n        }\n      }}\n      renderInput={params => (\n        <TextField\n          {...params}\n          label=\"Haplotypes\"\n          placeholder={draft.length === 0 ? 'every haplotype' : undefined}\n          slotProps={{\n            ...params.slotProps,\n            htmlInput: {\n              ...params.slotProps.htmlInput,\n              'data-testid': 'graph-haplotypes-field',\n            },\n          }}\n        />\n      )}\n    />\n  )\n})\n\n// Only a GBZ cut and a walk-indexed rGFA cut read the set\nconst SubgraphHaplotypesField = observer(function SubgraphHaplotypesField({\n  model,\n}: {\n  model: LinearGraphCutModel\n}) {\n  const { classes } = useStyles()\n  const names = model.haplotypeNames\n  const adapter = model.sourceAdapter\n  return adapter && cutsByHaplotype(adapter) ? (\n    <div className={classes.section}>\n      {names ? (\n        <HaplotypePickField model={model} names={names} />\n      ) : (\n        <HaplotypeListField model={model} />\n      )}\n      <Typography variant=\"caption\" component=\"div\" color=\"text.secondary\">\n        {names\n          ? `Which of the graph's ${names.length.toLocaleString()} haplotypes to cut, or a PanSN prefix (HG002 for both).`\n          : 'Which haplotypes to cut, as lane assembly names or PanSN prefixes (HG002#1, or HG002 for both) separated by commas.'}{' '}\n        Empty is every haplotype.\n      </Typography>\n    </div>\n  ) : null\n})\n\nexport default SubgraphHaplotypesField\n", "import { observer } from 'mobx-react'\n\nimport SubgraphContextSelect from './SubgraphContextSelect'\nimport SubgraphHaplotypesField from './SubgraphHaplotypesField'\nimport GraphSettingsDialog from '../../GraphGenomeView/components/GraphSettingsDialog'\n\nimport type { LinearGraphCutModel } from '../model'\n\nexport default observer(function GraphTrackSettingsDialog({\n  model,\n  onClose,\n}: {\n  model: LinearGraphCutModel\n  onClose: () => void\n}) {\n  return (\n    <GraphSettingsDialog model={model} onClose={onClose}>\n      <SubgraphContextSelect model={model} />\n      <SubgraphHaplotypesField model={model} />\n    </GraphSettingsDialog>\n  )\n})\n"],
+  "mappings": "ocASA,IAAMA,EAAYC,EAAW,EAAE,CAC7B,QAAS,CACP,aAAc,EAChB,CACF,CAAC,EAWKC,EAAoB,CACxB,CAAE,MAAO,IAAK,MAAO,MAAO,EAC5B,CAAE,MAAO,IAAK,MAAO,OAAQ,EAC7B,CAAE,MAAO,IAAK,MAAO,QAAS,CAChC,EAEMC,EAAwBC,EAAS,SAA+B,CACpE,MAAAC,CACF,EAEG,CACD,GAAM,CAAE,QAAAC,CAAQ,EAAIN,EAAU,EACxBO,EAAUF,EAAM,cACtB,OAAOE,GAAS,OAAS,oBAAsB,CAACC,EAAYD,CAAO,EACjEE,EAAC,OAAI,UAAWH,EAAQ,QACtB,UAAAI,EAACC,EAAA,CACC,MAAM,gBACN,GAAI,CAAE,SAAU,GAAI,EACpB,MAAO,OAAON,EAAM,eAAe,EACnC,QAASH,EACT,OAAO,uBACP,SAAUU,GAAQ,CAChBP,EAAM,mBAAmB,OAAOO,CAAI,CAAC,EACrCP,EAAM,MAAM,CACd,EACF,EACAK,EAACG,EAAA,CAAW,QAAQ,UAAU,UAAU,MAAM,MAAM,iBAAiB,6KAIrE,GACF,EACE,IACN,CAAC,EAEMC,EAAQX,ECjDf,IAAMY,EAAYC,EAAW,EAAE,CAC7B,QAAS,CACP,aAAc,EAChB,CACF,CAAC,EAED,SAASC,EAAmBC,EAAc,CACxC,OAAOA,EAAK,MAAM,QAAQ,EAAE,OAAOC,GAAQA,IAAS,EAAE,CACxD,CAEA,IAAMC,EAAW,CAAC,EAAsBC,IACtC,EAAE,KAAK;AAAA,CAAI,IAAMA,EAAE,KAAK;AAAA,CAAI,EAK9B,SAASC,EAAiBC,EAA4BC,EAAmB,CACvE,IAAMC,EAAUF,EAAM,eAAiB,CAAC,EAClC,CAACG,EAAMC,CAAO,EAAIC,EAASH,CAAO,EACxC,OAAKL,EAASK,EAASC,CAAI,IACzBC,EAAQF,CAAO,EACfD,EAAM,GAEAK,GAAyB,CAC1BT,EAASS,EAAYJ,CAAO,IAC/BE,EAAQE,CAAU,EAClBN,EAAM,sBAAsBM,CAAU,EACtCN,EAAM,MAAM,EAEhB,CACF,CAEA,IAAMO,EAAqBC,EAAS,SAA4B,CAC9D,MAAAR,CACF,EAEG,CACD,GAAM,CAACS,EAAOC,CAAQ,EAAIL,EAASL,EAAM,eAAe,KAAK,IAAI,GAAK,EAAE,EAClEW,EAASZ,EAAiBC,EAAO,IAAM,CAC3CU,EAASV,EAAM,eAAe,KAAK,IAAI,GAAK,EAAE,CAChD,CAAC,EACKY,EAAQ,IAAM,CAClBD,EAAOjB,EAAmBe,CAAK,CAAC,CAClC,EACA,OACEI,EAACC,EAAA,CACC,UAAS,GACT,MAAM,aACN,YAAY,kBACZ,MAAOL,EACP,UAAW,CAAE,UAAW,CAAE,cAAe,wBAAyB,CAAE,EACpE,SAAUM,GAAK,CACbL,EAASK,EAAE,OAAO,KAAK,CACzB,EACA,OAAQ,IAAM,CACZH,EAAM,CACR,EACA,UAAWG,GAAK,CACVA,EAAE,MAAQ,SACZH,EAAM,CAEV,EACF,CAEJ,CAAC,EAQKI,EAAqBR,EAAS,SAA4B,CAC9D,MAAAR,EACA,MAAAiB,CACF,EAGG,CACD,GAAM,CAACR,EAAOC,CAAQ,EAAIL,EAASL,EAAM,eAAiB,CAAC,CAAC,EACtDkB,EAAWC,EAAOV,CAAK,EACvBW,EAAQD,EAAO,EAAE,EACjB,CAACE,EAAMC,CAAO,EAAIjB,EAAS,EAAK,EAChCO,EAAQb,EAAiBC,EAAO,IAAM,CAC1CkB,EAAS,QAAUlB,EAAM,eAAiB,CAAC,EAC3CU,EAASQ,EAAS,OAAO,CAC3B,CAAC,EACD,OACEL,EAACU,EAAA,CACC,SAAQ,GACR,SAAQ,GACR,qBAAoB,GACpB,QAASN,EACT,MAAOR,EACP,KAAMY,EACN,OAAQ,IAAM,CACZC,EAAQ,EAAI,CACd,EACA,cAAe,CAACE,EAAG7B,IAAS,CAC1ByB,EAAM,QAAUzB,CAClB,EACA,QAAS,CAAC6B,EAAGC,IAAW,CACtBH,EAAQ,EAAK,EACb,IAAM3B,EAAOyB,EAAM,QAAQ,KAAK,EAC5BK,IAAW,QAAU9B,GAAQ,CAACuB,EAAS,QAAQ,SAASvB,CAAI,IAC9DuB,EAAS,QAAU,CAAC,GAAGA,EAAS,QAASvB,CAAI,EAC7Ce,EAASQ,EAAS,OAAO,GAE3BN,EAAMM,EAAS,OAAO,CACxB,EACA,SAAU,CAACM,EAAGE,IAAU,CACtBR,EAAS,QAAUQ,EACnBhB,EAASgB,CAAK,EACTL,GACHT,EAAMc,CAAK,CAEf,EACA,YAAaC,GACXd,EAACC,EAAA,CACE,GAAGa,EACJ,MAAM,aACN,YAAalB,EAAM,SAAW,EAAI,kBAAoB,OACtD,UAAW,CACT,GAAGkB,EAAO,UACV,UAAW,CACT,GAAGA,EAAO,UAAU,UACpB,cAAe,wBACjB,CACF,EACF,EAEJ,CAEJ,CAAC,EAGKC,EAA0BpB,EAAS,SAAiC,CACxE,MAAAR,CACF,EAEG,CACD,GAAM,CAAE,QAAA6B,CAAQ,EAAIrC,EAAU,EACxByB,EAAQjB,EAAM,eACd8B,EAAU9B,EAAM,cACtB,OAAO8B,GAAWC,EAAgBD,CAAO,EACvCE,EAAC,OAAI,UAAWH,EAAQ,QACrB,UAAAZ,EACCJ,EAACG,EAAA,CAAmB,MAAOhB,EAAO,MAAOiB,EAAO,EAEhDJ,EAACN,EAAA,CAAmB,MAAOP,EAAO,EAEpCgC,EAACC,EAAA,CAAW,QAAQ,UAAU,UAAU,MAAM,MAAM,iBACjD,UAAAhB,EACG,wBAAwBA,EAAM,OAAO,eAAe,CAAC,0DACrD,sHAAuH,IAAI,6BAEjI,GACF,EACE,IACN,CAAC,EAEMiB,EAAQN,ECnKf,IAAOO,GAAQC,EAAS,SAAkC,CACxD,MAAAC,EACA,QAAAC,CACF,EAGG,CACD,OACEC,EAACC,EAAA,CAAoB,MAAOH,EAAO,QAASC,EAC1C,UAAAG,EAACC,EAAA,CAAsB,MAAOL,EAAO,EACrCI,EAACE,EAAA,CAAwB,MAAON,EAAO,GACzC,CAEJ,CAAC",
+  "names": ["useStyles", "makeStyles", "SUBGRAPH_CONTEXTS", "SubgraphContextSelect", "observer", "model", "classes", "adapter", "walkIndexed", "jsxs", "jsx", "LabelledSelect_default", "hops", "Typography", "SubgraphContextSelect_default", "useStyles", "makeStyles", "parseHaplotypeList", "text", "name", "sameList", "b", "useCutHaplotypes", "model", "reset", "current", "seen", "setSeen", "useState", "haplotypes", "HaplotypeListField", "observer", "draft", "setDraft", "setCut", "apply", "jsx", "TextField", "e", "HaplotypePickField", "names", "draftRef", "useRef", "typed", "open", "setOpen", "Autocomplete", "_", "reason", "value", "params", "SubgraphHaplotypesField", "classes", "adapter", "cutsByHaplotype", "jsxs", "Typography", "SubgraphHaplotypesField_default", "GraphTrackSettingsDialog_default", "observer", "model", "onClose", "jsxs", "GraphSettingsDialog_default", "jsx", "SubgraphContextSelect_default", "SubgraphHaplotypesField_default"]
 }

package/dist/chunks/HighlightColorDialog-AKPIC56I.js

@@ -0,0 +1,2 @@
+import{x as v,y as C}from"./chunk-4DQWDJG7.js";import"./chunk-OPWSPSAE.js";import"./chunk-ELC7POI6.js";import"./chunk-CL4PYWKC.js";import{F as h,H as r,d as m,o as y,q as c,r as d,z as g}from"./chunk-WE7DQVXF.js";import{a as u,b as l,c as p,d as s}from"./chunk-DUU6T2I5.js";var f=s(function({model:o,onClose:t}){return p(m,{open:!0,onClose:t,title:"Color highlighted haplotypes",children:[p(d,{sx:{display:"grid",gridTemplateColumns:"auto 1fr 1fr",alignItems:"center",gap:1.5},children:[l(r,{variant:"subtitle2",children:"Haplotype"}),l(r,{variant:"subtitle2",children:"Color by"}),l(r,{variant:"subtitle2",children:"Palette"}),o.drawnWalks.map(({name:a,encoding:n})=>l(S,{label:o.walkLabel(a),field:n.field,scheme:n.scheme,onField:i=>{o.setWalkColor(a,{field:i})},onScheme:i=>{o.setWalkColor(a,{scheme:i})}},a))]}),l(c,{children:l(y,{variant:"contained",onClick:t,children:"Done"})})]})}),S=s(function({label:o,field:t,scheme:a,onField:n,onScheme:i}){return p(u,{children:[l(r,{variant:"body2",children:o}),l(h,{select:!0,size:"small",value:t,slotProps:{select:{SelectDisplayProps:{"aria-label":`Color ${o} by`}}},onChange:e=>{n(e.target.value)},children:v.map(e=>l(g,{value:e.value,children:e.label},e.value))}),l(h,{select:!0,size:"small",value:a,slotProps:{select:{SelectDisplayProps:{"aria-label":`Palette for ${o}`}}},onChange:e=>{i(e.target.value)},children:C.filter(e=>e.value!=="rainbow"||t==="reference").map(e=>l(g,{value:e.value,children:e.label},e.value))})]})}),T=f;export{T as default};
+//# sourceMappingURL=HighlightColorDialog-AKPIC56I.js.map

package/dist/chunks/{HighlightColorDialog-KNJFIFLO.js.map → HighlightColorDialog-AKPIC56I.js.map}

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/GraphGenomeView/components/HighlightColorDialog.tsx"],
-  "sourcesContent": ["import { WALK_FIELDS, WALK_SCHEMES } from '@jbrowse/bandage-core/walkEncoding'\nimport { Dialog } from '@jbrowse/core/ui'\nimport {\n  Button,\n  DialogActions,\n  DialogContent,\n  MenuItem,\n  TextField,\n  Typography,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport type { GraphPaneModel } from '../model'\n\ntype HighlightColors = Pick<\n  GraphPaneModel,\n  'drawnWalks' | 'walkLabel' | 'setWalkColor'\n>\n\nconst HighlightColorDialog = observer(function HighlightColorDialog({\n  model,\n  onClose,\n}: {\n  model: HighlightColors\n  onClose: () => void\n}) {\n  return (\n    <Dialog open onClose={onClose} title=\"Color highlighted haplotypes\">\n      <DialogContent\n        sx={{\n          display: 'grid',\n          gridTemplateColumns: 'auto 1fr 1fr',\n          alignItems: 'center',\n          gap: 1.5,\n        }}\n      >\n        <Typography variant=\"subtitle2\">Haplotype</Typography>\n        <Typography variant=\"subtitle2\">Color by</Typography>\n        <Typography variant=\"subtitle2\">Palette</Typography>\n        {model.drawnWalks.map(({ name, encoding }) => (\n          <Row\n            key={name}\n            label={model.walkLabel(name)}\n            field={encoding.field}\n            scheme={encoding.scheme}\n            onField={field => {\n              model.setWalkColor(name, { field })\n            }}\n            onScheme={scheme => {\n              model.setWalkColor(name, { scheme })\n            }}\n          />\n        ))}\n      </DialogContent>\n      <DialogActions>\n        <Button variant=\"contained\" onClick={onClose}>\n          Done\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n})\n\ntype Field = (typeof WALK_FIELDS)[number]['value']\ntype Scheme = (typeof WALK_SCHEMES)[number]['value']\n\nfunction Row({\n  label,\n  field,\n  scheme,\n  onField,\n  onScheme,\n}: {\n  label: string\n  field: Field\n  scheme: Scheme\n  onField: (field: Field) => void\n  onScheme: (scheme: Scheme) => void\n}) {\n  return (\n    <>\n      <Typography variant=\"body2\">{label}</Typography>\n      <TextField\n        select\n        size=\"small\"\n        value={field}\n        slotProps={{\n          select: { SelectDisplayProps: { 'aria-label': `Color ${label} by` } },\n        }}\n        onChange={e => {\n          onField(e.target.value as Field)\n        }}\n      >\n        {WALK_FIELDS.map(f => (\n          <MenuItem key={f.value} value={f.value}>\n            {f.label}\n          </MenuItem>\n        ))}\n      </TextField>\n      <TextField\n        select\n        size=\"small\"\n        value={scheme}\n        slotProps={{\n          select: {\n            SelectDisplayProps: { 'aria-label': `Palette for ${label}` },\n          },\n        }}\n        onChange={e => {\n          onScheme(e.target.value as Scheme)\n        }}\n      >\n        {WALK_SCHEMES.filter(\n          s => s.value !== 'rainbow' || field === 'reference',\n        ).map(s => (\n          <MenuItem key={s.value} value={s.value}>\n            {s.label}\n          </MenuItem>\n        ))}\n      </TextField>\n    </>\n  )\n}\n\nexport default HighlightColorDialog\n"],
-  "mappings": "kRAmBA,IAAMA,EAAuBC,EAAS,SAA8B,CAClE,MAAAC,EACA,QAAAC,CACF,EAGG,CACD,OACEC,EAACC,EAAA,CAAO,KAAI,GAAC,QAASF,EAAS,MAAM,+BACnC,UAAAC,EAACE,EAAA,CACC,GAAI,CACF,QAAS,OACT,oBAAqB,eACrB,WAAY,SACZ,IAAK,GACP,EAEA,UAAAC,EAACC,EAAA,CAAW,QAAQ,YAAY,qBAAS,EACzCD,EAACC,EAAA,CAAW,QAAQ,YAAY,oBAAQ,EACxCD,EAACC,EAAA,CAAW,QAAQ,YAAY,mBAAO,EACtCN,EAAM,WAAW,IAAI,CAAC,CAAE,KAAAO,EAAM,SAAAC,CAAS,IACtCH,EAACI,EAAA,CAEC,MAAOT,EAAM,UAAUO,CAAI,EAC3B,MAAOC,EAAS,MAChB,OAAQA,EAAS,OACjB,QAASE,GAAS,CAChBV,EAAM,aAAaO,EAAM,CAAE,MAAAG,CAAM,CAAC,CACpC,EACA,SAAUC,GAAU,CAClBX,EAAM,aAAaO,EAAM,CAAE,OAAAI,CAAO,CAAC,CACrC,GATKJ,CAUP,CACD,GACH,EACAF,EAACO,EAAA,CACC,SAAAP,EAACQ,EAAA,CAAO,QAAQ,YAAY,QAASZ,EAAS,gBAE9C,EACF,GACF,CAEJ,CAAC,EAKD,SAASQ,EAAI,CACX,MAAAK,EACA,MAAAJ,EACA,OAAAC,EACA,QAAAI,EACA,SAAAC,CACF,EAMG,CACD,OACEd,EAAAe,EAAA,CACE,UAAAZ,EAACC,EAAA,CAAW,QAAQ,QAAS,SAAAQ,EAAM,EACnCT,EAACa,EAAA,CACC,OAAM,GACN,KAAK,QACL,MAAOR,EACP,UAAW,CACT,OAAQ,CAAE,mBAAoB,CAAE,aAAc,SAASI,CAAK,KAAM,CAAE,CACtE,EACA,SAAU,GAAK,CACbC,EAAQ,EAAE,OAAO,KAAc,CACjC,EAEC,SAAAI,EAAY,IAAIC,GACff,EAACgB,EAAA,CAAuB,MAAOD,EAAE,MAC9B,SAAAA,EAAE,OADUA,EAAE,KAEjB,CACD,EACH,EACAf,EAACa,EAAA,CACC,OAAM,GACN,KAAK,QACL,MAAOP,EACP,UAAW,CACT,OAAQ,CACN,mBAAoB,CAAE,aAAc,eAAeG,CAAK,EAAG,CAC7D,CACF,EACA,SAAU,GAAK,CACbE,EAAS,EAAE,OAAO,KAAe,CACnC,EAEC,SAAAM,EAAa,OACZC,GAAKA,EAAE,QAAU,WAAab,IAAU,WAC1C,EAAE,IAAIa,GACJlB,EAACgB,EAAA,CAAuB,MAAOE,EAAE,MAC9B,SAAAA,EAAE,OADUA,EAAE,KAEjB,CACD,EACH,GACF,CAEJ,CAEA,IAAOC,EAAQ1B",
+  "sourcesContent": ["import { WALK_FIELDS, WALK_SCHEMES } from '@jbrowse/bandage-core/walkEncoding'\nimport { Dialog } from '@jbrowse/core/ui'\nimport {\n  Button,\n  DialogActions,\n  DialogContent,\n  MenuItem,\n  TextField,\n  Typography,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport type { GraphPaneModel } from '../model'\n\ntype HighlightColors = Pick<\n  GraphPaneModel,\n  'drawnWalks' | 'walkLabel' | 'setWalkColor'\n>\n\nconst HighlightColorDialog = observer(function HighlightColorDialog({\n  model,\n  onClose,\n}: {\n  model: HighlightColors\n  onClose: () => void\n}) {\n  return (\n    <Dialog open onClose={onClose} title=\"Color highlighted haplotypes\">\n      <DialogContent\n        sx={{\n          display: 'grid',\n          gridTemplateColumns: 'auto 1fr 1fr',\n          alignItems: 'center',\n          gap: 1.5,\n        }}\n      >\n        <Typography variant=\"subtitle2\">Haplotype</Typography>\n        <Typography variant=\"subtitle2\">Color by</Typography>\n        <Typography variant=\"subtitle2\">Palette</Typography>\n        {model.drawnWalks.map(({ name, encoding }) => (\n          <Row\n            key={name}\n            label={model.walkLabel(name)}\n            field={encoding.field}\n            scheme={encoding.scheme}\n            onField={field => {\n              model.setWalkColor(name, { field })\n            }}\n            onScheme={scheme => {\n              model.setWalkColor(name, { scheme })\n            }}\n          />\n        ))}\n      </DialogContent>\n      <DialogActions>\n        <Button variant=\"contained\" onClick={onClose}>\n          Done\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n})\n\ntype Field = (typeof WALK_FIELDS)[number]['value']\ntype Scheme = (typeof WALK_SCHEMES)[number]['value']\n\nconst Row = observer(function Row({\n  label,\n  field,\n  scheme,\n  onField,\n  onScheme,\n}: {\n  label: string\n  field: Field\n  scheme: Scheme\n  onField: (field: Field) => void\n  onScheme: (scheme: Scheme) => void\n}) {\n  return (\n    <>\n      <Typography variant=\"body2\">{label}</Typography>\n      <TextField\n        select\n        size=\"small\"\n        value={field}\n        slotProps={{\n          select: { SelectDisplayProps: { 'aria-label': `Color ${label} by` } },\n        }}\n        onChange={e => {\n          onField(e.target.value as Field)\n        }}\n      >\n        {WALK_FIELDS.map(f => (\n          <MenuItem key={f.value} value={f.value}>\n            {f.label}\n          </MenuItem>\n        ))}\n      </TextField>\n      <TextField\n        select\n        size=\"small\"\n        value={scheme}\n        slotProps={{\n          select: {\n            SelectDisplayProps: { 'aria-label': `Palette for ${label}` },\n          },\n        }}\n        onChange={e => {\n          onScheme(e.target.value as Scheme)\n        }}\n      >\n        {WALK_SCHEMES.filter(\n          s => s.value !== 'rainbow' || field === 'reference',\n        ).map(s => (\n          <MenuItem key={s.value} value={s.value}>\n            {s.label}\n          </MenuItem>\n        ))}\n      </TextField>\n    </>\n  )\n})\n\nexport default HighlightColorDialog\n"],
+  "mappings": "kRAmBA,IAAMA,EAAuBC,EAAS,SAA8B,CAClE,MAAAC,EACA,QAAAC,CACF,EAGG,CACD,OACEC,EAACC,EAAA,CAAO,KAAI,GAAC,QAASF,EAAS,MAAM,+BACnC,UAAAC,EAACE,EAAA,CACC,GAAI,CACF,QAAS,OACT,oBAAqB,eACrB,WAAY,SACZ,IAAK,GACP,EAEA,UAAAC,EAACC,EAAA,CAAW,QAAQ,YAAY,qBAAS,EACzCD,EAACC,EAAA,CAAW,QAAQ,YAAY,oBAAQ,EACxCD,EAACC,EAAA,CAAW,QAAQ,YAAY,mBAAO,EACtCN,EAAM,WAAW,IAAI,CAAC,CAAE,KAAAO,EAAM,SAAAC,CAAS,IACtCH,EAACI,EAAA,CAEC,MAAOT,EAAM,UAAUO,CAAI,EAC3B,MAAOC,EAAS,MAChB,OAAQA,EAAS,OACjB,QAASE,GAAS,CAChBV,EAAM,aAAaO,EAAM,CAAE,MAAAG,CAAM,CAAC,CACpC,EACA,SAAUC,GAAU,CAClBX,EAAM,aAAaO,EAAM,CAAE,OAAAI,CAAO,CAAC,CACrC,GATKJ,CAUP,CACD,GACH,EACAF,EAACO,EAAA,CACC,SAAAP,EAACQ,EAAA,CAAO,QAAQ,YAAY,QAASZ,EAAS,gBAE9C,EACF,GACF,CAEJ,CAAC,EAKKQ,EAAMV,EAAS,SAAa,CAChC,MAAAe,EACA,MAAAJ,EACA,OAAAC,EACA,QAAAI,EACA,SAAAC,CACF,EAMG,CACD,OACEd,EAAAe,EAAA,CACE,UAAAZ,EAACC,EAAA,CAAW,QAAQ,QAAS,SAAAQ,EAAM,EACnCT,EAACa,EAAA,CACC,OAAM,GACN,KAAK,QACL,MAAOR,EACP,UAAW,CACT,OAAQ,CAAE,mBAAoB,CAAE,aAAc,SAASI,CAAK,KAAM,CAAE,CACtE,EACA,SAAU,GAAK,CACbC,EAAQ,EAAE,OAAO,KAAc,CACjC,EAEC,SAAAI,EAAY,IAAIC,GACff,EAACgB,EAAA,CAAuB,MAAOD,EAAE,MAC9B,SAAAA,EAAE,OADUA,EAAE,KAEjB,CACD,EACH,EACAf,EAACa,EAAA,CACC,OAAM,GACN,KAAK,QACL,MAAOP,EACP,UAAW,CACT,OAAQ,CACN,mBAAoB,CAAE,aAAc,eAAeG,CAAK,EAAG,CAC7D,CACF,EACA,SAAU,GAAK,CACbE,EAAS,EAAE,OAAO,KAAe,CACnC,EAEC,SAAAM,EAAa,OACZC,GAAKA,EAAE,QAAU,WAAab,IAAU,WAC1C,EAAE,IAAIa,GACJlB,EAACgB,EAAA,CAAuB,MAAOE,EAAE,MAC9B,SAAAA,EAAE,OADUA,EAAE,KAEjB,CACD,EACH,GACF,CAEJ,CAAC,EAEMC,EAAQ1B",
   "names": ["HighlightColorDialog", "observer", "model", "onClose", "jsxs", "Dialog", "DialogContent", "jsx", "Typography", "name", "encoding", "Row", "field", "scheme", "DialogActions", "Button", "label", "onField", "onScheme", "Fragment", "TextField", "WALK_FIELDS", "f", "MenuItem", "WALK_SCHEMES", "s", "HighlightColorDialog_default"]
 }

package/dist/chunks/{LinearGraphDisplay-APDIIF7F.js → LinearGraphDisplay-RRAXTQFC.js}

@@ -1,2 +1,2 @@
-import{a,b as i}from"./chunk-FUPBKEC2.js";import"./chunk-DKYX6XBX.js";import"./chunk-3ROUAVMP.js";import"./chunk-TL2FTG3H.js";import"./chunk-UWBKGUBZ.js";import"./chunk-DMLYMYLG.js";import"./chunk-4DQWDJG7.js";import"./chunk-UC2NHZ7E.js";import"./chunk-OPWSPSAE.js";import"./chunk-W5HHWDGZ.js";import"./chunk-E23AOQPE.js";import"./chunk-YBLNN5FU.js";import"./chunk-U6SNNNFV.js";import"./chunk-ELC7POI6.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-CL4PYWKC.js";import"./chunk-3VGXCEMQ.js";import"./chunk-6VNDP3UB.js";import"./chunk-3WG3GF2A.js";import"./chunk-J5RMHLFJ.js";import"./chunk-NIEZKWQV.js";import"./chunk-5Z4VIKXZ.js";import{b as o,d as t}from"./chunk-JMBDTNUR.js";var e=JBrowseExports["@jbrowse/display-kit/DisplayChrome"];var s=e&&e.__esModule?e.default:e;var p=t(function({model:r}){return o(s,{model:r,factory:a,testid:"linear-graph-display","data-layout":r.chosenLayoutMode,"data-cut-tier":r.cutTier,"data-recuts":r.recuts,"data-node-count":r.hasGraph?r.nodeCount:void 0,"data-loading":r.isLoading?"":void 0,style:{width:r.paneWidth,height:r.height,overflow:"hidden"},children:n=>o(i,{model:r,handle:n})})}),c=p;export{c as default};
-//# sourceMappingURL=LinearGraphDisplay-APDIIF7F.js.map
+import{a,b as i}from"./chunk-Y7MQVQAS.js";import"./chunk-4XY7HUQR.js";import"./chunk-DIGIM3XY.js";import"./chunk-WE7XHNAH.js";import"./chunk-X2QGBINE.js";import"./chunk-WO644UAC.js";import"./chunk-4DQWDJG7.js";import"./chunk-UC2NHZ7E.js";import"./chunk-OPWSPSAE.js";import"./chunk-W5HHWDGZ.js";import"./chunk-E23AOQPE.js";import"./chunk-YBLNN5FU.js";import"./chunk-U6SNNNFV.js";import"./chunk-ELC7POI6.js";import"./chunk-YBLNN5FU.js";import"./chunk-QUDJ7AM3.js";import"./chunk-CL4PYWKC.js";import"./chunk-TMM73K4C.js";import"./chunk-6VNDP3UB.js";import"./chunk-FLKXKTS2.js";import"./chunk-TC265JAP.js";import"./chunk-J2PN6CG3.js";import"./chunk-WE7DQVXF.js";import{b as o,d as t}from"./chunk-DUU6T2I5.js";var e=JBrowseExports["@jbrowse/display-kit/DisplayChrome"];var s=e&&e.__esModule?e.default:e;var p=t(function({model:r}){return o(s,{model:r,factory:a,testid:"linear-graph-display","data-layout":r.chosenLayoutMode,"data-cut-tier":r.cutTier,"data-recuts":r.recuts,"data-node-count":r.hasGraph?r.nodeCount:void 0,"data-loading":r.isLoading?"":void 0,style:{width:r.paneWidth,height:r.height,overflow:"hidden"},children:n=>o(i,{model:r,handle:n})})}),c=p;export{c as default};
+//# sourceMappingURL=LinearGraphDisplay-RRAXTQFC.js.map

package/dist/chunks/LinearGraphDisplay-RRAXTQFC.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["jbrowse-host:@jbrowse/display-kit/DisplayChrome", "../../src/LinearGraphDisplay/components/LinearGraphDisplay.tsx"],
+  "sourcesContent": ["const host = JBrowseExports[\"@jbrowse/display-kit/DisplayChrome\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\"This JBrowse does not provide '\" + name + \"' from '\" + \"@jbrowse/display-kit/DisplayChrome\" + \"' to plugins: \" + \"GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\")\n        },\n        { jbrowseHostMissing: name },\n      )\nexport default host && host.__esModule ? host.default : host", "import DisplayChrome from '@jbrowse/display-kit/DisplayChrome'\nimport { observer } from 'mobx-react'\n\nimport GraphCanvas from '../../GraphGenomeView/components/GraphCanvas'\nimport { createGraphRenderer } from '../../GraphGenomeView/renderer/GraphRenderer'\n\nimport type { LinearGraphDisplayModel } from '../model'\n\nconst LinearGraphDisplay = observer(function LinearGraphDisplay({\n  model,\n}: {\n  model: LinearGraphDisplayModel\n}) {\n  return (\n    <DisplayChrome\n      model={model}\n      factory={createGraphRenderer}\n      testid=\"linear-graph-display\"\n      data-layout={model.chosenLayoutMode}\n      data-cut-tier={model.cutTier}\n      data-recuts={model.recuts}\n      data-node-count={model.hasGraph ? model.nodeCount : undefined}\n      data-loading={model.isLoading ? '' : undefined}\n      style={{\n        width: model.paneWidth,\n        height: model.height,\n        overflow: 'hidden',\n      }}\n    >\n      {handle => <GraphCanvas model={model} handle={handle} />}\n    </DisplayChrome>\n  )\n})\n\nexport default LinearGraphDisplay\n"],
+  "mappings": "isBAAA,IAAMA,EAAO,eAAe,oCAAoC,EAUhE,IAAOC,EAAQC,GAAQA,EAAK,WAAaA,EAAK,QAAUA,ECFxD,IAAMC,EAAqBC,EAAS,SAA4B,CAC9D,MAAAC,CACF,EAEG,CACD,OACEC,EAACC,EAAA,CACC,MAAOF,EACP,QAASG,EACT,OAAO,uBACP,cAAaH,EAAM,iBACnB,gBAAeA,EAAM,QACrB,cAAaA,EAAM,OACnB,kBAAiBA,EAAM,SAAWA,EAAM,UAAY,OACpD,eAAcA,EAAM,UAAY,GAAK,OACrC,MAAO,CACL,MAAOA,EAAM,UACb,OAAQA,EAAM,OACd,SAAU,QACZ,EAEC,SAAAI,GAAUH,EAACI,EAAA,CAAY,MAAOL,EAAO,OAAQI,EAAQ,EACxD,CAEJ,CAAC,EAEME,EAAQR",
+  "names": ["host", "DisplayChrome_default", "host", "LinearGraphDisplay", "observer", "model", "jsx", "DisplayChrome_default", "createGraphRenderer", "handle", "GraphCanvas_default", "LinearGraphDisplay_default"]
+}

package/dist/chunks/{MinigraphBubbleAdapter-QEC37MYN.js → MinigraphBubbleAdapter-2YTXBZYS.js}

@@ -1,2 +1,2 @@
-import{a as f,d as c,f as d}from"./chunk-W5HHWDGZ.js";import{a as g}from"./chunk-KOB7YIMR.js";import{E as p,F as u,b,z as m}from"./chunk-PX4IRCTO.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-CL4PYWKC.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{a as i,o as l}from"./chunk-J5RMHLFJ.js";var a=class extends b{constructor(){super(...arguments);this.bubbles=p(this,["bubblesLocation"],["index"]);this.refNames=new u(this.bubbles,this)}static{this.capabilities=["getFeatures","getRefNames"]}async getRefNames(t={}){return this.refNames.assemblyRefNames(t)}async getRegionByteSize(t,s={}){return this.refNames.regionBytes(t,s)}async hasDataForRefName(){return!0}getFeatures(t,s={}){let{signal:n,statusCallback:h}=s;return g(async r=>{let o=await this.refNames.resolveMapped(t,s);o!==void 0&&await l("Downloading bubbles",h,()=>m(this.bubbles,o,t.start,t.end,{signal:n,lineCallback:(N,y)=>{let e=f(N);r.next(new i({uniqueId:`bubble-${y}`,refName:t.refName,start:e.start,end:e.end,name:c(e),description:d(e),type:"bubble",score:e.segmentCount,segmentCount:e.segmentCount,pathCount:e.pathCount,inversion:e.inversion,shortestAlleleLength:e.shortestAlleleLength,longestAlleleLength:e.longestAlleleLength,segments:e.segments,shortestAllele:e.shortestAllele,longestAllele:e.longestAllele}))}})),r.complete()},n)}};export{a as default};
-//# sourceMappingURL=MinigraphBubbleAdapter-QEC37MYN.js.map
+import{a as f,d as c,f as d}from"./chunk-W5HHWDGZ.js";import{a as g}from"./chunk-V55TK2NP.js";import{E as p,F as u,b,z as m}from"./chunk-VNWCN47G.js";import"./chunk-YBLNN5FU.js";import"./chunk-QUDJ7AM3.js";import"./chunk-CL4PYWKC.js";import"./chunk-D6TY2QEG.js";import"./chunk-FLKXKTS2.js";import{a as i,o as l}from"./chunk-TC265JAP.js";var a=class extends b{constructor(){super(...arguments);this.bubbles=p(this,["bubblesLocation"],["index"]);this.refNames=new u(this.bubbles,this)}static{this.capabilities=["getFeatures","getRefNames"]}async getRefNames(t={}){return this.refNames.assemblyRefNames(t)}async getRegionByteSize(t,s={}){return this.refNames.regionBytes(t,s)}async hasDataForRefName(){return!0}getFeatures(t,s={}){let{signal:n,statusCallback:h}=s;return g(async r=>{let o=await this.refNames.resolveMapped(t,s);o!==void 0&&await l("Downloading bubbles",h,()=>m(this.bubbles,o,t.start,t.end,{signal:n,lineCallback:(N,y)=>{let e=f(N);r.next(new i({uniqueId:`bubble-${y}`,refName:t.refName,start:e.start,end:e.end,name:c(e),description:d(e),type:"bubble",score:e.segmentCount,segmentCount:e.segmentCount,pathCount:e.pathCount,inversion:e.inversion,shortestAlleleLength:e.shortestAlleleLength,longestAlleleLength:e.longestAlleleLength,segments:e.segments,shortestAllele:e.shortestAllele,longestAllele:e.longestAllele}))}})),r.complete()},n)}};export{a as default};
+//# sourceMappingURL=MinigraphBubbleAdapter-2YTXBZYS.js.map

package/dist/chunks/{RgfaTabixAdapter-ZGXDNU43.js → RgfaTabixAdapter-RCGS6YVM.js}

@@ -1,2 +1,2 @@
-import{a as F}from"./chunk-PRGG24TK.js";import"./chunk-ZA5GPTUM.js";import{a as N}from"./chunk-KOB7YIMR.js";import"./chunk-YBLNN5FU.js";import"./chunk-U6SNNNFV.js";import"./chunk-ELC7POI6.js";import{E as p,F as d,b as h,u,v as w,w as k,x,y as b,z as g}from"./chunk-PX4IRCTO.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-CL4PYWKC.js";import{e as f}from"./chunk-6VNDP3UB.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{a as l,o as m}from"./chunk-J5RMHLFJ.js";var c=class extends h{constructor(){super(...arguments);this.fine=this.openIndex([])}static{this.capabilities=["getFeatures","getRefNames"]}openIndex(e){let t=this.getConf("walksLocation"),n=e.length===0&&f(t)?new F(p(this,["walksLocation"],["walksIndex"]),this):void 0,r=e.length===0?this.getConf("graphLocation"):this.getConf(["coarse","graphLocation"]);if(f(r)){let s=p(this,[...e,"graphLocation"],[...e,"graphIndex"]);return{graph:s,walks:n,refNames:new d(n?.file??s,this)}}let a=p(this,[...e,"segmentsLocation"],[...e,"segmentsIndex"]),i=p(this,[...e,"linksLocation"],[...e,"linksIndex"]);return{segments:a,links:i,walks:n,refNames:new d(n?.file??a,this)}}async getHaplotypeNames(e={}){return this.fine.walks?.haplotypeNames(e)}index(e="fine"){return e==="fine"?this.fine:(this.coarse??=this.openIndex(["coarse"]),this.coarse)}async getRefNames(e={}){return this.fine.refNames.assemblyRefNames(e)}async getRegionByteSize(e,t={}){let{walks:n,refNames:r}=this.fine;return r.regionBytes(e,t,n&&((a,{start:i,end:s})=>n.reader.queryStart(i,{...t,refName:a,end:s})))}async hasDataForRefName(){return!0}getFeatures(e,t={}){return N(async n=>{let r=await this.fine.refNames.resolveMapped(e,t);if(r!==void 0){let{walks:a}=this.fine,i=s=>{n.next(s)};await(a?this.walkFeatures(a,r,e,t,i):this.segmentFeatures(r,e,t,i))}n.complete()},t.signal)}async walkFeatures(e,t,n,r,a){let i=await m("Downloading walks",r.statusCallback,()=>e.referenceNodes(t,n,r));for(let s of i){let o=String(s.id);a(new l({uniqueId:o,refName:n.refName,start:s.start,end:s.end,name:o,type:"segment",rank:0,stableName:s.refName}))}}async segmentRows(e,t,n,r){let a=this.fine;if("graph"in a){let i=k(await a.graph.getHeaderLines({signal:n.signal}));return g(a.graph,e,t.start,t.end,{signal:n.signal,lineCallback:s=>{let o=x(s,i);o?.kind==="N"&&r(o.segment,i.anchored)}})}return g(a.segments,e,t.start,t.end,{signal:n.signal,lineCallback:i=>{let{segment:s,anchored:o}=u(i);r(s,o)}})}async segmentFeatures(e,t,n,r){await m("Downloading segments",n.statusCallback,()=>this.segmentRows(e,t,n,(a,i)=>{if(i&&a.refName!==e)return;let s=w(a);r(new l({uniqueId:a.id,refName:t.refName,start:a.start,end:a.end,name:a.id,type:"segment",rank:a.rank,stableName:a.refName,...s&&{samples:s,sampleCount:s.length}}))}))}async getSubgraph(e,t={}){let{hops:n,signal:r,tier:a}=t,i=this.index(a),s=await i.refNames.resolveForCut(e,{signal:r});return i.walks?i.walks.subgraph(s,e,t):b(i,{refName:s,start:e.start,end:e.end},{hops:n,signal:r})}};export{c as default};
-//# sourceMappingURL=RgfaTabixAdapter-ZGXDNU43.js.map
+import{a as F}from"./chunk-HRTRECXN.js";import"./chunk-ZA5GPTUM.js";import{a as N}from"./chunk-V55TK2NP.js";import"./chunk-YBLNN5FU.js";import"./chunk-U6SNNNFV.js";import"./chunk-ELC7POI6.js";import{E as p,F as d,b as h,u,v as w,w as k,x,y as b,z as g}from"./chunk-VNWCN47G.js";import"./chunk-YBLNN5FU.js";import"./chunk-QUDJ7AM3.js";import"./chunk-CL4PYWKC.js";import{e as f}from"./chunk-6VNDP3UB.js";import"./chunk-D6TY2QEG.js";import"./chunk-FLKXKTS2.js";import{a as l,o as m}from"./chunk-TC265JAP.js";var c=class extends h{constructor(){super(...arguments);this.fine=this.openIndex([])}static{this.capabilities=["getFeatures","getRefNames"]}openIndex(e){let t=this.getConf("walksLocation"),n=e.length===0&&f(t)?new F(p(this,["walksLocation"],["walksIndex"]),this):void 0,r=e.length===0?this.getConf("graphLocation"):this.getConf(["coarse","graphLocation"]);if(f(r)){let s=p(this,[...e,"graphLocation"],[...e,"graphIndex"]);return{graph:s,walks:n,refNames:new d(n?.file??s,this)}}let a=p(this,[...e,"segmentsLocation"],[...e,"segmentsIndex"]),i=p(this,[...e,"linksLocation"],[...e,"linksIndex"]);return{segments:a,links:i,walks:n,refNames:new d(n?.file??a,this)}}async getHaplotypeNames(e={}){return this.fine.walks?.haplotypeNames(e)}index(e="fine"){return e==="fine"?this.fine:(this.coarse??=this.openIndex(["coarse"]),this.coarse)}async getRefNames(e={}){return this.fine.refNames.assemblyRefNames(e)}async getRegionByteSize(e,t={}){let{walks:n,refNames:r}=this.fine;return r.regionBytes(e,t,n&&((a,{start:i,end:s})=>n.reader.queryStart(i,{...t,refName:a,end:s})))}async hasDataForRefName(){return!0}getFeatures(e,t={}){return N(async n=>{let r=await this.fine.refNames.resolveMapped(e,t);if(r!==void 0){let{walks:a}=this.fine,i=s=>{n.next(s)};await(a?this.walkFeatures(a,r,e,t,i):this.segmentFeatures(r,e,t,i))}n.complete()},t.signal)}async walkFeatures(e,t,n,r,a){let i=await m("Downloading walks",r.statusCallback,()=>e.referenceNodes(t,n,r));for(let s of i){let o=String(s.id);a(new l({uniqueId:o,refName:n.refName,start:s.start,end:s.end,name:o,type:"segment",rank:0,stableName:s.refName}))}}async segmentRows(e,t,n,r){let a=this.fine;if("graph"in a){let i=k(await a.graph.getHeaderLines({signal:n.signal}));return g(a.graph,e,t.start,t.end,{signal:n.signal,lineCallback:s=>{let o=x(s,i);o?.kind==="N"&&r(o.segment,i.anchored)}})}return g(a.segments,e,t.start,t.end,{signal:n.signal,lineCallback:i=>{let{segment:s,anchored:o}=u(i);r(s,o)}})}async segmentFeatures(e,t,n,r){await m("Downloading segments",n.statusCallback,()=>this.segmentRows(e,t,n,(a,i)=>{if(i&&a.refName!==e)return;let s=w(a);r(new l({uniqueId:a.id,refName:t.refName,start:a.start,end:a.end,name:a.id,type:"segment",rank:a.rank,stableName:a.refName,...s&&{samples:s,sampleCount:s.length}}))}))}async getSubgraph(e,t={}){let{hops:n,signal:r,tier:a}=t,i=this.index(a),s=await i.refNames.resolveForCut(e,{signal:r});return i.walks?i.walks.subgraph(s,e,t):b(i,{refName:s,start:e.start,end:e.end},{hops:n,signal:r})}};export{c as default};
+//# sourceMappingURL=RgfaTabixAdapter-RCGS6YVM.js.map

package/dist/chunks/{TrackWarningsDialog-4YDIV2FN.js → TrackWarningsDialog-23WL6FPV.js}

@@ -1,2 +1,2 @@
-import{H as i,h as o,m as a}from"./chunk-5Z4VIKXZ.js";import{c as r,d as e}from"./chunk-JMBDTNUR.js";var u=e(function({model:n,title:s,children:l,handleClose:m}){return r(o,{open:!0,title:s,onClose:()=>{m()},children:[l,n.trackWarnings.flatMap(({name:f,warnings:g},p)=>g.map((t,c)=>r(a,{severity:"warning",style:{marginBottom:8},children:[r(i,{variant:"subtitle2",children:[f,": ",t.message]}),t.effect]},`${p}_${c}`)))]})}),x=u;export{x as default};
-//# sourceMappingURL=TrackWarningsDialog-4YDIV2FN.js.map
+import{H as i,h as o,m as a}from"./chunk-WE7DQVXF.js";import{c as r,d as e}from"./chunk-DUU6T2I5.js";var u=e(function({model:n,title:s,children:l,handleClose:m}){return r(o,{open:!0,title:s,onClose:()=>{m()},children:[l,n.trackWarnings.flatMap(({name:f,warnings:g},p)=>g.map((t,c)=>r(a,{severity:"warning",style:{marginBottom:8},children:[r(i,{variant:"subtitle2",children:[f,": ",t.message]}),t.effect]},`${p}_${c}`)))]})}),x=u;export{x as default};
+//# sourceMappingURL=TrackWarningsDialog-23WL6FPV.js.map

package/dist/chunks/{TrackWarningsDialog-4YDIV2FN.js.map → TrackWarningsDialog-23WL6FPV.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+synteny-core@5.0.0-beta.18_@emotion+react@11.14.0_@types+react@19.3.0_react@19_0b9c1c4d2b16eef60d202e26c552208a/node_modules/@jbrowse/synteny-core/esm/TrackWarningsDialog.js"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+synteny-core@5.0.0-beta.19_@emotion+react@11.14.0_@types+react@19.3.0_react@19_eb34fd01d29d05a1c3ac8167d41484d7/node_modules/@jbrowse/synteny-core/esm/TrackWarningsDialog.js"],
   "sourcesContent": ["import { jsxs as _jsxs } from \"react/jsx-runtime\";\nimport { InfoDialog } from '@jbrowse/core/ui';\nimport { Alert, Typography } from '@mui/material';\nimport { observer } from 'mobx-react';\n/**\n * The render-warnings report both comparative views open, over the rows\n * `collectTrackWarnings` builds for them. Reads them off the view rather than\n * taking a copy, so a refetch that raises or clears a warning while the dialog\n * is open shows in it.\n *\n * Grouped by track, with the track name leading each row: a stacked view's\n * levels raise the same swapped-assemblies warning verbatim, and so does every\n * overlaid track that hits it, so an ungrouped list repeated one sentence N\n * times without ever naming the file to go fix.\n *\n * Keyed by position \u2014 the message is not an identity, and neither is the track\n * name once one track raises two warnings.\n */\nconst TrackWarningsDialog = observer(function TrackWarningsDialog({ model, title, children, handleClose, }) {\n    return (_jsxs(InfoDialog, { open: true, title: title, onClose: () => {\n            handleClose();\n        }, children: [children, model.trackWarnings.flatMap(({ name, warnings }, i) => warnings.map((w, j) => (_jsxs(Alert\n            // eslint-disable-next-line @eslint-react/no-array-index-key -- see above\n            , { severity: \"warning\", style: { marginBottom: 8 }, children: [_jsxs(Typography, { variant: \"subtitle2\", children: [name, \": \", w.message] }), w.effect] }, `${i}_${j}`))))] }));\n});\nexport default TrackWarningsDialog;\n"],
   "mappings": "qGAkBA,IAAMA,EAAsBC,EAAS,SAA6B,CAAE,MAAAC,EAAO,MAAAC,EAAO,SAAAC,EAAU,YAAAC,CAAa,EAAG,CACxG,OAAQC,EAAMC,EAAY,CAAE,KAAM,GAAM,MAAOJ,EAAO,QAAS,IAAM,CAC7DE,EAAY,CAChB,EAAG,SAAU,CAACD,EAAUF,EAAM,cAAc,QAAQ,CAAC,CAAE,KAAAM,EAAM,SAAAC,CAAS,EAAGC,IAAMD,EAAS,IAAI,CAACE,EAAGC,IAAON,EAAMO,EAEvG,CAAE,SAAU,UAAW,MAAO,CAAE,aAAc,CAAE,EAAG,SAAU,CAACP,EAAMQ,EAAY,CAAE,QAAS,YAAa,SAAU,CAACN,EAAM,KAAMG,EAAE,OAAO,CAAE,CAAC,EAAGA,EAAE,MAAM,CAAE,EAAG,GAAGD,CAAC,IAAIE,CAAC,EAAE,CAAE,CAAC,CAAC,CAAE,CAAC,CAC3L,CAAC,EACMG,EAAQf",
   "names": ["TrackWarningsDialog", "observer", "model", "title", "children", "handleClose", "jsxs", "InfoDialog", "name", "warnings", "i", "w", "j", "Alert", "Typography", "TrackWarningsDialog_default"]

package/dist/chunks/{WalkFormsAdapter-QYFYWQJD.js → WalkFormsAdapter-3M5A4JL3.js}

@@ -1,2 +1,2 @@
-import{a as x,b,c as N,d as R,f as c,g as C,h as P,i as T}from"./chunk-4LAVXP7J.js";import{a as k}from"./chunk-KOB7YIMR.js";import{E as $,b as l,d as g,e as w,f as h,g as p,k as y,o as B,s as F,t as S}from"./chunk-PX4IRCTO.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-CL4PYWKC.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{a as m,o as u}from"./chunk-J5RMHLFJ.js";var v=r=>`${(r/1e6).toFixed(1)} MB`,O=r=>`${(r/1e6).toFixed(1)} M`;function E(r,f){if(!(r instanceof g))return r;let t=N(f);if(r instanceof F)return new Error(`The pinned window ${t} is too large to read every walk in full for structural forms: its walks take ${O(r.steps)} steps, over the ${O(r.limit)} step budget, and about ${p(r.fitsBp)} of it fits. Pin a narrower window`);let e=`walkByteBudget, ${v(r.limit)}`;return new Error(`The pinned window ${t} is too large to cut for structural forms: ${r.zoomHelps?`about ${p(r.fitsBp)} of it fits in ${e}. Pin a narrower window or raise walkByteBudget`:`its cut fetches ${v(r.bytes??0)}, over ${e}. Raise walkByteBudget`}`)}var L=8,i=new Map;function A(r,f){let t=i.get(r),e=t??f();if(i.delete(r),i.set(r,e),!t){e.catch(()=>{i.get(r)===e&&i.delete(r)});for(let s of i.keys()){if(i.size<=L)break;i.delete(s)}}return e}var d=class extends l{constructor(){super(...arguments);this.reader=new y($(this,["walksLocation"],["walksIndex"]))}static{this.capabilities=["getFeatures","getRefNames"]}async referenceSample(t){let{references:e}=await this.reader.header(t);return e[0]??""}async getRefNames(t={}){let e=await this.reader.referenceSequences(t),s=await this.referenceSample(t),a=e.filter(o=>h(o,s)).map(o=>w(o));return a.length>0?[...new Set(a)]:e}pinned(){let t=x(this.getConf("pinned"));if(!t)throw new Error("WalkFormsAdapter needs `pinned`, the window its forms come from: { refName, start, end }");return t}forms(t){if(!this.formsRead){let e=this.pinned(),s=`${JSON.stringify(this.getConf("walksLocation"))}	${e.refName}:${e.start}-${e.end}`,a=this.getConf("walkByteBudget"),o=A(`${s}	${a}`,()=>u("Cutting walks",t.statusCallback,()=>S(this.reader,e,{byteBudget:a,partial:!1}).catch(n=>{throw E(n,e)}))).then(n=>B(n,{window:e,floorBp:b(this.getConf("floorBp")),exclude:this.getConf("exclude")}));o.catch(()=>{this.formsRead===o&&(this.formsRead=void 0)}),this.formsRead=o}return this.formsRead}maxForms(){return this.getConf("maxForms")}async getSourcesAndWarnings(t={}){let e=await this.forms(t),s=R(this.pinned());return{sources:c(e,this.maxForms()),warnings:C(e,this.maxForms()).map(a=>s+a)}}async getSources(t,e={}){return c(await this.forms(e),this.maxForms())}async onPinnedSequence(t,e){let s=await this.referenceSample(e),[a,o]=await Promise.all([this.reader.sequenceFor(s,t,e),this.reader.sequenceFor(s,this.pinned().refName,e)]);return a!==void 0&&a===o}getFeatures(t,e={}){return k(async s=>{let a=await this.forms(e),o=await this.onPinnedSequence(t.refName,e)?T(a,this.maxForms()).filter(n=>n.start<t.end&&n.end>t.start):[];for(let n of o)s.next(new m({uniqueId:`forms-${a.floorBp}-${n.id}`,refName:t.refName,start:n.start,end:n.end,name:n.name,description:n.description,type:n.type,svType:n.svType,consequence:n.consequence,REF:"N",ALT:[n.alt],INFO:{SVTYPE:[n.svType],SVLEN:[n.mark.delta]},mark:n.mark,genotypes:n.genotypes}));if(o.length===0){let n=Math.floor(t.start);s.next(new m({uniqueId:`forms-reference-${t.refName}-${n}`,refName:t.refName,start:n,end:n+1,REF:"N",ALT:["."],genotypes:P(a,this.maxForms())}))}s.complete()},e.signal)}};export{d as default};
-//# sourceMappingURL=WalkFormsAdapter-QYFYWQJD.js.map
+import{a as x,b,c as N,d as R,f as c,g as C,h as P,i as T}from"./chunk-ULPW4VGT.js";import{a as k}from"./chunk-V55TK2NP.js";import{E as $,b as l,d as g,e as w,f as h,g as p,k as y,o as B,s as F,t as S}from"./chunk-VNWCN47G.js";import"./chunk-YBLNN5FU.js";import"./chunk-QUDJ7AM3.js";import"./chunk-CL4PYWKC.js";import"./chunk-D6TY2QEG.js";import"./chunk-FLKXKTS2.js";import{a as m,o as u}from"./chunk-TC265JAP.js";var v=r=>`${(r/1e6).toFixed(1)} MB`,O=r=>`${(r/1e6).toFixed(1)} M`;function E(r,f){if(!(r instanceof g))return r;let t=N(f);if(r instanceof F)return new Error(`The pinned window ${t} is too large to read every walk in full for structural forms: its walks take ${O(r.steps)} steps, over the ${O(r.limit)} step budget, and about ${p(r.fitsBp)} of it fits. Pin a narrower window`);let e=`walkByteBudget, ${v(r.limit)}`;return new Error(`The pinned window ${t} is too large to cut for structural forms: ${r.zoomHelps?`about ${p(r.fitsBp)} of it fits in ${e}. Pin a narrower window or raise walkByteBudget`:`its cut fetches ${v(r.bytes??0)}, over ${e}. Raise walkByteBudget`}`)}var L=8,i=new Map;function A(r,f){let t=i.get(r),e=t??f();if(i.delete(r),i.set(r,e),!t){e.catch(()=>{i.get(r)===e&&i.delete(r)});for(let s of i.keys()){if(i.size<=L)break;i.delete(s)}}return e}var d=class extends l{constructor(){super(...arguments);this.reader=new y($(this,["walksLocation"],["walksIndex"]))}static{this.capabilities=["getFeatures","getRefNames"]}async referenceSample(t){let{references:e}=await this.reader.header(t);return e[0]??""}async getRefNames(t={}){let e=await this.reader.referenceSequences(t),s=await this.referenceSample(t),a=e.filter(o=>h(o,s)).map(o=>w(o));return a.length>0?[...new Set(a)]:e}pinned(){let t=x(this.getConf("pinned"));if(!t)throw new Error("WalkFormsAdapter needs `pinned`, the window its forms come from: { refName, start, end }");return t}forms(t){if(!this.formsRead){let e=this.pinned(),s=`${JSON.stringify(this.getConf("walksLocation"))}	${e.refName}:${e.start}-${e.end}`,a=this.getConf("walkByteBudget"),o=A(`${s}	${a}`,()=>u("Cutting walks",t.statusCallback,()=>S(this.reader,e,{byteBudget:a,partial:!1}).catch(n=>{throw E(n,e)}))).then(n=>B(n,{window:e,floorBp:b(this.getConf("floorBp")),exclude:this.getConf("exclude")}));o.catch(()=>{this.formsRead===o&&(this.formsRead=void 0)}),this.formsRead=o}return this.formsRead}maxForms(){return this.getConf("maxForms")}async getSourcesAndWarnings(t={}){let e=await this.forms(t),s=R(this.pinned());return{sources:c(e,this.maxForms()),warnings:C(e,this.maxForms()).map(a=>s+a)}}async getSources(t,e={}){return c(await this.forms(e),this.maxForms())}async onPinnedSequence(t,e){let s=await this.referenceSample(e),[a,o]=await Promise.all([this.reader.sequenceFor(s,t,e),this.reader.sequenceFor(s,this.pinned().refName,e)]);return a!==void 0&&a===o}getFeatures(t,e={}){return k(async s=>{let a=await this.forms(e),o=await this.onPinnedSequence(t.refName,e)?T(a,this.maxForms()).filter(n=>n.start<t.end&&n.end>t.start):[];for(let n of o)s.next(new m({uniqueId:`forms-${a.floorBp}-${n.id}`,refName:t.refName,start:n.start,end:n.end,name:n.name,description:n.description,type:n.type,svType:n.svType,consequence:n.consequence,REF:"N",ALT:[n.alt],INFO:{SVTYPE:[n.svType],SVLEN:[n.mark.delta]},mark:n.mark,genotypes:n.genotypes}));if(o.length===0){let n=Math.floor(t.start);s.next(new m({uniqueId:`forms-reference-${t.refName}-${n}`,refName:t.refName,start:n,end:n+1,REF:"N",ALT:["."],genotypes:P(a,this.maxForms())}))}s.complete()},e.signal)}};export{d as default};
+//# sourceMappingURL=WalkFormsAdapter-3M5A4JL3.js.map

package/dist/chunks/WalkTabixSyntenyAdapter-576RE5OE.js

@@ -0,0 +1,2 @@
+import{a as ee}from"./chunk-HRTRECXN.js";import{a as V,b as Z,d as q,e as J,f as B,g as Q,h as Y}from"./chunk-SVDQVLEU.js";import"./chunk-ZA5GPTUM.js";import{a as K}from"./chunk-V55TK2NP.js";import{p as L,q as H,r as U}from"./chunk-M2D7NUOY.js";import"./chunk-YBLNN5FU.js";import"./chunk-U6SNNNFV.js";import"./chunk-ELC7POI6.js";import{E as z,F as G,i as X}from"./chunk-VNWCN47G.js";import"./chunk-YBLNN5FU.js";import"./chunk-QUDJ7AM3.js";import{a as E,c as T,d as F,g as x,h as A,i as O}from"./chunk-CL4PYWKC.js";import"./chunk-AGUEPVOR.js";import"./chunk-TMM73K4C.js";import"./chunk-D6TY2QEG.js";import"./chunk-FLKXKTS2.js";import{o as M}from"./chunk-TC265JAP.js";var ce=50;function fe(r){let o=[];for(let e=0;e<r.length;e++){let[t,a]=r[e],[s,n]=r[e+1]??[];a===n&&a<=ce&&(t==="I"&&s==="D"||t==="D"&&s==="I")?(o.push(["X",a]),e++):o.push([t,a])}return o}function R(r){return Array.from(r.ids,(o,e)=>2*o+r.rev[e])}function P(r,o){let e=r.get(o);return e===void 0?0:e.end-e.start}function te(r){let o=new Map,e=s=>{let n=P(r,s),i=o.get(n);return i===void 0&&(i="N".repeat(n),o.set(n,i)),i},t=new Map,a=s=>{let n=t.get(s);return n===void 0&&(n=R(s),t.set(s,n)),n};return(s,n)=>H({query:a(s),target:a(n),sequenceOf:e,bases:!1})}var _=100;function I(r,o,e){let t=r.at(-1);e>0&&(t?.[0]===o?t[1]+=e:r.push([o,e]))}function ae(r){let o=t=>P(r,t>>1),e=t=>{let a=new Float64Array(t.length+1);return t.forEach((s,n)=>{a[n+1]=a[n]+o(s)}),a};return(t,a)=>{let s=R(a),n=R(t),[i,c]=L(n,s,o),[g,d]=L(n.map(y=>y^1).reverse(),s,o),l=d>c,f=l?g:i,b=Math.max(c,d);if(b<_)return[];let p=e(s),h=e(n),u=y=>l?n.length-1-f[y][0]:f[y][0],k=[];f.forEach(([,y],w)=>{if(w>0){let[v,m]=[u(w-1),u(w)].sort((W,C)=>W-C);I(k,"I",h[m]-h[v+1]),I(k,"D",p[y]-p[f[w-1][1]+1])}I(k,"=",o(s[y]))});let[N,S]=[u(0),u(f.length-1)].sort((y,w)=>y-w);return[{queryStart:h[N],queryEnd:h[S+1],targetStart:p[f[0][1]],targetEnd:p[f.at(-1)[1]+1],strand:l?"-":"+",edits:k,sharedBases:b}]}}function pe(r){let o=new Map,e=new Set;r.ids.forEach((t,a)=>{o.has(t)?e.add(t):o.set(t,r.rev[a])});for(let t of e)o.delete(t);return o}function ne(r){let o=new Map,e=t=>{let a=o.get(t);return a===void 0&&(a=pe(t),o.set(t,a)),a};return(t,a)=>{let s=e(a),n=0,i=0;for(let[c,g]of e(t)){let d=s.get(c);d===g?n+=P(r,c):d!==void 0&&(i+=P(r,c))}return{same:n,opposite:i}}}function se(r){let o=ae(r),e=te(r),t=ne(r);return(a,s)=>{let{same:n,opposite:i}=t(a,s);return n>=_&&i>=_?e(a,s):o(a,s)}}var ue=1e4;function re(r){let o=ae(r),e=te(r),t=ne(r);return(a,s)=>{let n=o(a,s),i=n[0]?.strand,{same:c,opposite:g}=t(a,s);return i===void 0||Math.min(c,g)<ue?n:[...n,...e(a,s).filter(d=>d.strand!==i)]}}function $({chain:r,target:o,query:e,assemblyName:t,refName:a,mateAssemblyName:s}){let n=fe(r.edits);return Y({target:{name:o.name,assemblyName:t,refName:a,start:o.hapStart+r.targetStart,end:o.hapStart+r.targetEnd},query:{name:e.name,assemblyName:s,refName:F(e.name),start:e.hapStart+r.queryStart,end:e.hapStart+r.queryEnd},strand:r.strand,cigar:U(n),matches:n.reduce((i,[c,g])=>i+(c==="="?g:0),0),columns:n.reduce((i,[,c])=>i+c,0)})}function ie(r,o,e,t,a){let s=a==="leave",n=i=>i.kind==="elsewhere"&&(s?i.chunk.start>=r.refStart:i.chunk.start<r.refStart);for(let i of e){let{name:c,fragStart:g,hapStart:d,ids:l,rev:f,before:b,after:p}=i;if(c===r.name&&g===r.fragStart){let h=d;for(let u=0;u<l.length;u++){let k=t.get(l[u]),N=k===void 0?0:k.end-k.start;if(k?.rank===0&&k.refName===o&&(s?k.end===r.refStart:k.start===r.refEnd)){let S=n(p)!==n(b)?n(p):u>0!=u<l.length-1?u>0:s!==(f[u]===1);return{skip:r,at:S?h+N:h,strand:S===s?"+":"-"}}h+=N}}}}function oe({crossing:r,refName:o,assemblyName:e,mateAssemblyName:t}){let{skip:a,at:s,strand:n}=r;return le({id:`${a.name}:${a.fragStart}:${a.piece}:skip`,assemblyName:e,refName:o,start:a.refStart,end:a.refEnd,reverse:n==="-",mate:{refName:F(a.name),start:s,end:s,assemblyName:t}})}function me({fragment:r,crossing:o,refName:e,assemblyName:t,mateAssemblyName:a}){let{name:s,fragStart:n,hapStart:i,hapEnd:c}=r;return le({id:`${s}:${n}:${i}:crossing`,assemblyName:t,refName:e,start:o.refStart,end:o.refEnd,reverse:o.reverse,mate:{refName:F(s),start:i,end:c,assemblyName:a}})}function le({id:r,assemblyName:o,refName:e,start:t,end:a,reverse:s,mate:n}){return new V({uniqueId:r,assemblyName:o,refName:e,start:t,end:a,type:"deletion",strand:s?-1:1,syntenyId:r,spansWindow:!0,mate:n})}var j=({name:r})=>T(r)??r,D=class extends Z{constructor(){super(...arguments);this.walks=new ee(z(this,["walksLocation"],["walksIndex"]),this);this.refNames=new G(this.walks.file,this)}get anchor(){let e=this.getConf("assemblyNames")[0];if(e===void 0)throw new Error("WalkTabixSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");return e}async getHaplotypeNames(e={}){return this.walks.haplotypeNames(e)}async getHeader(e={}){let{haplotypes:t}=await this.walks.reader.header(e),{anchor:a}=this,s=A(this,a),n=O(this);return{hasCoarseTier:!1,anchorAssemblyName:a,lanes:t.filter(i=>i!==s&&E(i)!==s).map(i=>({name:B(n,i),label:i,group:E(i)}))}}async getRefNames(e={}){let{assemblyName:t}=e;return t===void 0||t===this.anchor?this.refNames.assemblyRefNames({...e,assemblyName:this.anchor}):[]}async getSubgraph(e,t={}){let a=await this.refNames.resolveForCut(e,{signal:t.signal});return this.walks.subgraph(a,e,t)}async laneWalks(e,t,a,s,n){let i=X(a,e);return M(n,s.statusCallback,()=>this.walks.reader.cut(e,t,{...this.walks.budgets(),signal:s.signal,keep:i,expand:i,links:!1}).catch(c=>{throw Q(c,t.end-t.start)}))}async skipCrossings(e,t,a){let s=[],n=t;for(let i of["leave","rejoin"]){let c=await this.sideCrossings(e,n,i,a);for(let d of c)s.push(d);let g=new Set(c.map(d=>d.skip));n=n.filter(d=>!g.has(d))}return s}async sideCrossings(e,t,a,s){let{signal:n}=s,{chunk:i}=await this.walks.reader.header({signal:n}),c=l=>a==="leave"?l.refStart-1:l.refEnd,g=new Map;for(let l of t){let f=c(l),b=Math.floor(f/i),p=g.get(b);p?(p.group.push(l),p.start=Math.min(p.start,f),p.end=Math.max(p.end,f+1)):g.set(b,{group:[l],start:f,end:f+1})}return(await Promise.all([...g.values()].map(async({group:l,start:f,end:b})=>{let p=new Set(l.map(u=>u.name)),h=u=>p.has(u);try{let{graph:u,fragments:k}=await this.walks.reader.cut(e,{start:f,end:b},{...this.walks.budgets(),signal:n,keep:h,expand:h,context:0,contained:!0,links:!1});return l.map(N=>ie(N,e,k,u.nodes,a))}catch(u){if(n?.aborted)throw u;return[]}}))).flat().filter(l=>l!==void 0)}async anchorFeatures(e,t,a){let s=a.haplotypes?.length?a.haplotypes.map(m=>A(this,m)):void 0,n=A(this,a.targetAssemblyName),i=n===void 0?s:s===void 0||s.some(m=>x(n,m)||x(m,n))?[n]:[];if(i?.length===0)return[];let{start:c,end:g}=t,d=`Reading walks ${t.refName}:${c.toLocaleString()}-${g.toLocaleString()}`,{graph:l,fragments:f,skips:b}=await this.laneWalks(e,t,i,a,d),p=({name:m})=>i===void 0?0:i.findIndex(W=>x(m,W)),h=new Set(f.map(j)),u=await M(d,a.statusCallback,()=>this.skipCrossings(e,b.filter(m=>p(m)>=0&&!h.has(j(m))&&m.refStart<=c&&m.refEnd>=g),a)),k=re(l.nodes),N=O(this),S=m=>B(N,j(m)),y=f.filter(m=>m.name===e),w=f.filter(m=>m.name!==e&&p(m)>=0).map(m=>({rank:p(m),features:m.crossing?[me({fragment:m,crossing:m.crossing,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:S(m)})]:y.flatMap(W=>k(m,W).map(C=>$({chain:C,target:W,query:m,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:S(m)})))})),v=u.map(m=>({rank:p(m.skip),features:[oe({crossing:m,refName:t.refName,assemblyName:t.assemblyName,mateAssemblyName:S(m.skip)})]}));return[...w,...v].sort((m,W)=>m.rank-W.rank).flatMap(m=>m.features)}async pairFeatures(e,t,a,s){let n=a.map(l=>({pair:l,featurePrefix:A(this,l.queryAssemblyName),matePrefix:A(this,l.targetAssemblyName)})),{graph:i,fragments:c}=await this.laneWalks(e,t,n.flatMap(l=>[l.featurePrefix,l.matePrefix]),s,J(a)),g=se(i.nodes),d=l=>c.filter(f=>x(f.name,l));return n.flatMap(({pair:l,featurePrefix:f,matePrefix:b})=>d(f).flatMap(p=>d(b).flatMap(h=>g(h,p).map(u=>$({chain:u,target:p,query:h,assemblyName:l.queryAssemblyName,refName:F(p.name),mateAssemblyName:l.targetAssemblyName})))))}getFeatures(e,t={}){return K(async a=>{let s=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(s!==void 0){let n=q(t),i=n.length>0?await this.pairFeatures(s,e,n,t):await this.anchorFeatures(s,e,t);for(let c of i)a.next(c)}a.complete()},t.signal)}};export{D as default};
+//# sourceMappingURL=WalkTabixSyntenyAdapter-576RE5OE.js.map

package/dist/chunks/WalkTabixSyntenyAdapter-576RE5OE.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/WalkTabixSyntenyAdapter/walkLanes.ts", "../../src/WalkTabixSyntenyAdapter/WalkTabixSyntenyAdapter.ts"],
+  "sourcesContent": ["import { weightedLcs } from '@gmod/gbz-base/lcs'\nimport { pairAlignments, pairCigar } from '@gmod/gbz-base/pairAlignment'\nimport { panSNContig } from '@jbrowse/bandage-core/pansn'\n\nimport SyntenyFeature from '../synteny/SyntenyFeature.ts'\nimport { matchFeature } from '../synteny/matchFeature.ts'\n\nimport type { PairChain, PairEdit } from '@gmod/gbz-base/pairAlignment'\nimport type {\n  WalkCrossing,\n  WalkFragment,\n  WalkNode,\n  WalkSkip,\n  WalkStop,\n} from '@jbrowse/graph-walks'\n\n// The longest bubble with equal bases on both sides that is written as\n// mismatches; a longer one stays an insertion and a deletion\nconst BALANCED_BUBBLE_MAX_BP = 50\n\n/**\n * A chain's edits with each short balanced bubble as `X`. The walks carry no\n * bases, so two walks differ wherever they leave a shared node, and a SNP is\n * one base inserted and one deleted until it is read as the mismatch it is.\n */\nexport function bubblesAsMismatches(edits: PairEdit[]) {\n  const out: PairEdit[] = []\n  for (let i = 0; i < edits.length; i++) {\n    const [op, len] = edits[i]!\n    const [nextOp, nextLen] = edits[i + 1] ?? []\n    if (\n      len === nextLen &&\n      len <= BALANCED_BUBBLE_MAX_BP &&\n      ((op === 'I' && nextOp === 'D') || (op === 'D' && nextOp === 'I'))\n    ) {\n      out.push(['X', len])\n      i++\n    } else {\n      out.push([op, len])\n    }\n  }\n  return out\n}\n\n// A walk's steps as the handles gbz-base reads, 2 * id + reversed\nfunction handlesOf(fragment: WalkFragment) {\n  return Array.from(fragment.ids, (id, i) => 2 * id + fragment.rev[i]!)\n}\n\nfunction nodeLength(nodes: Map<number, WalkNode>, id: number) {\n  const node = nodes.get(id)\n  return node === undefined ? 0 : node.end - node.start\n}\n\n/**\n * Aligns one walk fragment to another on the nodes both visit, from node\n * lengths alone: the fragments' steps as the handles gbz-base's chainer reads,\n * and a stand-in sequence of each node's length.\n */\nexport function walkAligner(nodes: Map<number, WalkNode>) {\n  const standIn = new Map<number, string>()\n  const sequenceOf = (id: number) => {\n    const length = nodeLength(nodes, id)\n    let sequence = standIn.get(length)\n    if (sequence === undefined) {\n      sequence = 'N'.repeat(length)\n      standIn.set(length, sequence)\n    }\n    return sequence\n  }\n  const handles = new Map<WalkFragment, number[]>()\n  const cachedHandles = (fragment: WalkFragment) => {\n    let steps = handles.get(fragment)\n    if (steps === undefined) {\n      steps = handlesOf(fragment)\n      handles.set(fragment, steps)\n    }\n    return steps\n  }\n  return (query: WalkFragment, target: WalkFragment) =>\n    pairAlignments({\n      query: cachedHandles(query),\n      target: cachedHandles(target),\n      sequenceOf,\n      bases: false,\n    })\n}\n\n// The fewest bases on shared nodes a record against the reference keeps,\n// gbz-base's floor for a pair record\nconst MIN_MATCH_BP = 100\n\nfunction appendEdit(edits: PairEdit[], op: PairEdit[0], len: number) {\n  const last = edits.at(-1)\n  if (len > 0) {\n    if (last?.[0] === op) {\n      last[1] += len\n    } else {\n      edits.push([op, len])\n    }\n  }\n}\n\n/**\n * Aligns a haplotype's walk fragment to the reference's as gbz-base aligns a\n * walk to its reference path: the heaviest common subsequence of their steps,\n * each node weighing its length, read in whichever direction shares more. A\n * pair chain leaves out every node either walk passes twice, which is the\n * whole of a collapsed copy-number array (amylase, KIV-2); the subsequence\n * matches one pass over it, and the other copies are insertions.\n */\nexport function referenceAligner(nodes: Map<number, WalkNode>) {\n  const lengthOf = (handle: number) => nodeLength(nodes, handle >> 1)\n  const offsets = (handles: number[]) => {\n    const out = new Float64Array(handles.length + 1)\n    handles.forEach((handle, i) => {\n      out[i + 1] = out[i]! + lengthOf(handle)\n    })\n    return out\n  }\n\n  return (query: WalkFragment, target: WalkFragment): PairChain[] => {\n    const ref = handlesOf(target)\n    const hap = handlesOf(query)\n    const [same, sameWeight] = weightedLcs(hap, ref, lengthOf)\n    const [turned, turnedWeight] = weightedLcs(\n      hap.map(handle => handle ^ 1).reverse(),\n      ref,\n      lengthOf,\n    )\n    const reverse = turnedWeight > sameWeight\n    const pairs = reverse ? turned : same\n    const sharedBases = Math.max(sameWeight, turnedWeight)\n    if (sharedBases < MIN_MATCH_BP) {\n      return []\n    }\n    const refAt = offsets(ref)\n    const hapAt = offsets(hap)\n    // a pair's haplotype step, counted along the haplotype\n    const stepOf = (k: number) =>\n      reverse ? hap.length - 1 - pairs[k]![0] : pairs[k]![0]\n    const edits: PairEdit[] = []\n    pairs.forEach(([, r], k) => {\n      if (k > 0) {\n        const [lo, hi] = [stepOf(k - 1), stepOf(k)].sort((x, y) => x - y)\n        appendEdit(edits, 'I', hapAt[hi!]! - hapAt[lo! + 1]!)\n        appendEdit(edits, 'D', refAt[r]! - refAt[pairs[k - 1]![1] + 1]!)\n      }\n      appendEdit(edits, '=', lengthOf(ref[r]!))\n    })\n    const [lo, hi] = [stepOf(0), stepOf(pairs.length - 1)].sort((x, y) => x - y)\n    return [\n      {\n        queryStart: hapAt[lo!]!,\n        queryEnd: hapAt[hi! + 1]!,\n        targetStart: refAt[pairs[0]![1]]!,\n        targetEnd: refAt[pairs.at(-1)![1] + 1]!,\n        strand: reverse ? '-' : '+',\n        edits,\n        sharedBases,\n      },\n    ]\n  }\n}\n\n// Each node a walk visits once, with the direction it passes it\nfunction singleVisits(fragment: WalkFragment) {\n  const rev = new Map<number, number>()\n  const twice = new Set<number>()\n  fragment.ids.forEach((id, i) => {\n    if (rev.has(id)) {\n      twice.add(id)\n    } else {\n      rev.set(id, fragment.rev[i]!)\n    }\n  })\n  for (const id of twice) {\n    rev.delete(id)\n  }\n  return rev\n}\n\n// The bases on singly visited nodes two walks pass the same way and the\n// opposite way\nfunction directionShares(nodes: Map<number, WalkNode>) {\n  const visits = new Map<WalkFragment, Map<number, number>>()\n  const visitsOf = (fragment: WalkFragment) => {\n    let found = visits.get(fragment)\n    if (found === undefined) {\n      found = singleVisits(fragment)\n      visits.set(fragment, found)\n    }\n    return found\n  }\n  return (query: WalkFragment, target: WalkFragment) => {\n    const theirs = visitsOf(target)\n    let same = 0\n    let opposite = 0\n    for (const [id, rev] of visitsOf(query)) {\n      const other = theirs.get(id)\n      if (other === rev) {\n        same += nodeLength(nodes, id)\n      } else if (other !== undefined) {\n        opposite += nodeLength(nodes, id)\n      }\n    }\n    return { same, opposite }\n  }\n}\n\n/**\n * Aligns one lane's walk fragment to another's. The weighted subsequence\n * (`referenceAligner`) is the fast route and matches through copy-number\n * arrays, but it reads one direction per pair, so an inversion between the\n * lanes comes out as an insertion beside a deletion. A pair sharing 100 bp\n * (MIN_MATCH_BP) or more of singly visited nodes in each direction goes to\n * pair chaining (`walkAligner`) instead, which answers the inverted stretch as\n * a reverse-strand record of its own. Chaining leaves out every node a walk\n * passes twice, so counting singly visited nodes misses no inversion it could\n * draw.\n */\nexport function lanePairAligner(nodes: Map<number, WalkNode>) {\n  const subsequence = referenceAligner(nodes)\n  const chained = walkAligner(nodes)\n  const shares = directionShares(nodes)\n  return (query: WalkFragment, target: WalkFragment) => {\n    const { same, opposite } = shares(query, target)\n    return same >= MIN_MATCH_BP && opposite >= MIN_MATCH_BP\n      ? chained(query, target)\n      : subsequence(query, target)\n  }\n}\n\n// The multi-way display's SPLIT_AT_GAP_BP, under which a turned stretch names\n// no inversion there\nconst TURNED_MIN_BP = 10_000\n\n/**\n * Aligns a haplotype's walk fragment to the reference's as `referenceAligner`\n * does, then adds the stretches it reads the other way. A walk sharing\n * TURNED_MIN_BP or more of singly visited nodes in each direction is chained\n * too, and the chained records on the strand the subsequence did not take are\n * its turned stretches. The subsequence record stays, so a copy-number array,\n * which chaining leaves out, still matches one pass alike in every lane.\n */\nexport function anchorAligner(nodes: Map<number, WalkNode>) {\n  const subsequence = referenceAligner(nodes)\n  const chained = walkAligner(nodes)\n  const shares = directionShares(nodes)\n  return (query: WalkFragment, target: WalkFragment) => {\n    const records = subsequence(query, target)\n    const taken = records[0]?.strand\n    const { same, opposite } = shares(query, target)\n    return taken === undefined || Math.min(same, opposite) < TURNED_MIN_BP\n      ? records\n      : [\n          ...records,\n          ...chained(query, target).filter(chain => chain.strand !== taken),\n        ]\n  }\n}\n\n/**\n * One record of a walk aligned to another, with its short balanced bubbles as\n * mismatches\n */\nexport function chainFeature({\n  chain,\n  target,\n  query,\n  assemblyName,\n  refName,\n  mateAssemblyName,\n}: {\n  chain: PairChain\n  target: WalkFragment\n  query: WalkFragment\n  assemblyName: string\n  refName: string\n  mateAssemblyName: string\n}) {\n  const edits = bubblesAsMismatches(chain.edits)\n  return matchFeature({\n    target: {\n      name: target.name,\n      assemblyName,\n      refName,\n      start: target.hapStart + chain.targetStart,\n      end: target.hapStart + chain.targetEnd,\n    },\n    query: {\n      name: query.name,\n      assemblyName: mateAssemblyName,\n      refName: panSNContig(query.name),\n      start: query.hapStart + chain.queryStart,\n      end: query.hapStart + chain.queryEnd,\n    },\n    strand: chain.strand,\n    cigar: pairCigar(edits),\n    matches: edits.reduce((sum, [op, n]) => sum + (op === '=' ? n : 0), 0),\n    columns: edits.reduce((sum, [, n]) => sum + n, 0),\n  })\n}\n\n/** The point on a haplotype's contig where it crosses a skipped stretch */\nexport interface SkipCrossing {\n  skip: WalkSkip\n  at: number\n  strand: '+' | '-'\n}\n\n/**\n * The reference node either side of a skipped stretch: the one a haplotype\n * leaves, ending at `refStart`, or the one it rejoins, starting at `refEnd`\n */\nexport type SkipSide = 'leave' | 'rejoin'\n\n/**\n * Where a haplotype that skips the window crosses its deletion, from a cut\n * over the reference node on one `side` of it. The jump lies on whichever end\n * of the walk's fragment goes on to a chunk across the stretch; with neither\n * or both, on the end the fragment's other steps leave free, and failing that\n * on the end the node's own direction points to. A walk that passes the node\n * inverted between two forward steps still crosses after it.\n */\nexport function skipCrossing(\n  skip: WalkSkip,\n  refName: string,\n  fragments: WalkFragment[],\n  nodes: Map<number, WalkNode>,\n  side: SkipSide,\n): SkipCrossing | undefined {\n  const leaving = side === 'leave'\n  const across = (stop: WalkStop) =>\n    stop.kind === 'elsewhere' &&\n    (leaving\n      ? stop.chunk.start >= skip.refStart\n      : stop.chunk.start < skip.refStart)\n  for (const fragment of fragments) {\n    const { name, fragStart, hapStart, ids, rev, before, after } = fragment\n    if (name === skip.name && fragStart === skip.fragStart) {\n      let at = hapStart\n      for (let i = 0; i < ids.length; i++) {\n        const node = nodes.get(ids[i]!)\n        const length = node === undefined ? 0 : node.end - node.start\n        if (\n          node?.rank === 0 &&\n          node.refName === refName &&\n          (leaving ? node.end === skip.refStart : node.start === skip.refEnd)\n        ) {\n          const jumpsAfter =\n            across(after) !== across(before)\n              ? across(after)\n              : i > 0 !== i < ids.length - 1\n                ? i > 0\n                : leaving !== (rev[i] === 1)\n          return {\n            skip,\n            at: jumpsAfter ? at + length : at,\n            strand: jumpsAfter === leaving ? '+' : '-',\n          }\n        }\n        at += length\n      }\n    }\n  }\n  return undefined\n}\n\n/**\n * A haplotype whose deletion spans the whole window, as the record a\n * multi-way display lifts out as a deletion: `spansWindow`, the skipped\n * stretch whole so its length heads the lane, and the crossing as its mate.\n * The record carries no CIGAR and no identity, so no ramp or identity filter\n * reads it as an alignment.\n */\nexport function skipFeature({\n  crossing,\n  refName,\n  assemblyName,\n  mateAssemblyName,\n}: {\n  crossing: SkipCrossing\n  refName: string\n  assemblyName: string\n  mateAssemblyName: string\n}) {\n  const { skip, at, strand } = crossing\n  return windowDeletion({\n    id: `${skip.name}:${skip.fragStart}:${skip.piece}:skip`,\n    assemblyName,\n    refName,\n    start: skip.refStart,\n    end: skip.refEnd,\n    reverse: strand === '-',\n    mate: {\n      refName: panSNContig(skip.name),\n      start: at,\n      end: at,\n      assemblyName: mateAssemblyName,\n    },\n  })\n}\n\n/**\n * A haplotype that leaves the reference before the window and rejoins after\n * it, through steps of its own, as the same record as a skip's, its mate the\n * haplotype's bp between the two reference steps\n */\nexport function crossingFeature({\n  fragment,\n  crossing,\n  refName,\n  assemblyName,\n  mateAssemblyName,\n}: {\n  fragment: WalkFragment\n  crossing: WalkCrossing\n  refName: string\n  assemblyName: string\n  mateAssemblyName: string\n}) {\n  const { name, fragStart, hapStart, hapEnd } = fragment\n  return windowDeletion({\n    id: `${name}:${fragStart}:${hapStart}:crossing`,\n    assemblyName,\n    refName,\n    start: crossing.refStart,\n    end: crossing.refEnd,\n    reverse: crossing.reverse,\n    mate: {\n      refName: panSNContig(name),\n      start: hapStart,\n      end: hapEnd,\n      assemblyName: mateAssemblyName,\n    },\n  })\n}\n\nfunction windowDeletion({\n  id,\n  assemblyName,\n  refName,\n  start,\n  end,\n  reverse,\n  mate,\n}: {\n  id: string\n  assemblyName: string\n  refName: string\n  start: number\n  end: number\n  reverse: boolean\n  mate: { refName: string; start: number; end: number; assemblyName: string }\n}) {\n  return new SyntenyFeature({\n    uniqueId: id,\n    assemblyName,\n    refName,\n    start,\n    end,\n    type: 'deletion',\n    strand: reverse ? -1 : 1,\n    syntenyId: id,\n    spansWindow: true,\n    mate,\n  })\n}\n", "import {\n  assemblyByPanSNPrefix,\n  panSNContig,\n  panSNHaplotype,\n  panSNMatchesPrefix,\n  panSNSample,\n  resolvePanSNPrefix,\n} from '@jbrowse/bandage-core/pansn'\nimport { updateStatus } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { walksKept } from '@jbrowse/graph-walks'\n\nimport {\n  anchorAligner,\n  chainFeature,\n  crossingFeature,\n  lanePairAligner,\n  skipCrossing,\n  skipFeature,\n} from './walkLanes.ts'\nimport { WalkIndex } from '../RgfaTabixAdapter/walkReader.ts'\nimport { PanSNRefNames, openTabixSlot } from '../panSNTabix.ts'\nimport { ComparativeAdapterBase } from '../synteny/ComparativeAdapterBase.ts'\nimport {\n  laneAssemblyName,\n  lanePairsStatus,\n  requestedPairs,\n} from '../synteny/lanePairs.ts'\nimport { laneZoomNotice } from '../synteny/laneZoomNotice.ts'\n\nimport type { WalkTabixSyntenyAdapterConfig } from './configSchema.ts'\nimport type { SkipCrossing, SkipSide } from './walkLanes.ts'\nimport type { SubgraphAdapterOptions } from '../GetSubgraph.ts'\nimport type { LaneFeatureOptions, LanePair } from '../synteny/lanePairs.ts'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { Region } from '@jbrowse/core/util/types'\nimport type { WalkSkip } from '@jbrowse/graph-walks'\n\nconst haplotypeOf = ({ name }: { name: string }) => panSNHaplotype(name) ?? name\n\nexport default class WalkTabixSyntenyAdapter extends ComparativeAdapterBase<WalkTabixSyntenyAdapterConfig> {\n  private readonly walks: WalkIndex = new WalkIndex(\n    openTabixSlot(this, ['walksLocation'], ['walksIndex']),\n    this,\n  )\n  private readonly refNames: PanSNRefNames = new PanSNRefNames(\n    this.walks.file,\n    this,\n  )\n\n  private get anchor() {\n    const anchor = this.getConf('assemblyNames')[0]\n    if (anchor === undefined) {\n      throw new Error(\n        'WalkTabixSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as',\n      )\n    }\n    return anchor\n  }\n\n  /**\n   * The haplotypes the walk file's header names, `sample#haplotype` in byte\n   * order, or undefined when it names none\n   */\n  async getHaplotypeNames(opts: BaseOptions = {}) {\n    return this.walks.haplotypeNames(opts)\n  }\n\n  /**\n   * `lanes` is every haplotype the header names but the anchor's own,\n   * declared up front so the display can offer the whole graph's haplotypes\n   * before a fetch has placed any of them\n   */\n  async getHeader(opts: BaseOptions = {}) {\n    const { haplotypes } = await this.walks.reader.header(opts)\n    const { anchor } = this\n    const anchorPrefix = resolvePanSNPrefix(this, anchor)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    return {\n      hasCoarseTier: false,\n      anchorAssemblyName: anchor,\n      lanes: haplotypes\n        .filter(\n          prefix =>\n            prefix !== anchorPrefix && panSNSample(prefix) !== anchorPrefix,\n        )\n        .map(prefix => ({\n          name: laneAssemblyName(asmByPrefix, prefix),\n          label: prefix,\n          group: panSNSample(prefix),\n        })),\n    }\n  }\n\n  // A lane's contigs are named only in its walk rows, so only the anchor's\n  // are listed\n  async getRefNames(opts: BaseOptions = {}) {\n    const { assemblyName } = opts\n    return assemblyName === undefined || assemblyName === this.anchor\n      ? this.refNames.assemblyRefNames({ ...opts, assemblyName: this.anchor })\n      : []\n  }\n\n  /**\n   * The graph display's cut of the window, as RgfaTabixAdapter cuts a\n   * walk-indexed graph: the reference walk first, then the walks `haplotypes`\n   * asks for, and the nodes and links they visit\n   */\n  async getSubgraph(region: Region, opts: SubgraphAdapterOptions = {}) {\n    const refName = await this.refNames.resolveForCut(region, {\n      signal: opts.signal,\n    })\n    return this.walks.subgraph(refName, region, opts)\n  }\n\n  // The window's walks for the haplotypes named and the reference, with no\n  // link read; a window past a budget fails as a zoom-in notice for lanes.\n  // Named lanes come back in full where format 5 abridged them: an abridged\n  // walk is two reference steps, which drew 15 of the HPRC MHC launch's 32\n  // lanes empty.\n  private async laneWalks(\n    refName: string,\n    region: Region,\n    prefixes: string[] | undefined,\n    opts: LaneFeatureOptions,\n    status: string,\n  ) {\n    const keep = walksKept(prefixes, refName)\n    return updateStatus(status, opts.statusCallback, () =>\n      this.walks.reader\n        .cut(refName, region, {\n          ...this.walks.budgets(),\n          signal: opts.signal,\n          keep,\n          expand: keep,\n          links: false,\n        })\n        .catch((error: unknown) => {\n          throw laneZoomNotice(error, region.end - region.start)\n        }),\n    )\n  }\n\n  /**\n   * Where each skipping haplotype crosses its deletion, read from contained\n   * cuts over the reference node it leaves, one cut per chunk those nodes\n   * fall in, and for any that cut misses, over the node it rejoins. A cut\n   * that fails drops only its own haplotypes' crossings.\n   */\n  private async skipCrossings(\n    refName: string,\n    skips: WalkSkip[],\n    opts: LaneFeatureOptions,\n  ) {\n    const found: SkipCrossing[] = []\n    let missed = skips\n    for (const side of ['leave', 'rejoin'] as const) {\n      const crossings = await this.sideCrossings(refName, missed, side, opts)\n      for (const crossing of crossings) {\n        found.push(crossing)\n      }\n      const placed = new Set(crossings.map(crossing => crossing.skip))\n      missed = missed.filter(skip => !placed.has(skip))\n    }\n    return found\n  }\n\n  private async sideCrossings(\n    refName: string,\n    skips: WalkSkip[],\n    side: SkipSide,\n    opts: LaneFeatureOptions,\n  ) {\n    const { signal } = opts\n    const { chunk } = await this.walks.reader.header({ signal })\n    const boundary = (skip: WalkSkip) =>\n      side === 'leave' ? skip.refStart - 1 : skip.refEnd\n    const byChunk = new Map<\n      number,\n      { group: WalkSkip[]; start: number; end: number }\n    >()\n    for (const skip of skips) {\n      const at = boundary(skip)\n      const cs = Math.floor(at / chunk)\n      const held = byChunk.get(cs)\n      if (held) {\n        held.group.push(skip)\n        held.start = Math.min(held.start, at)\n        held.end = Math.max(held.end, at + 1)\n      } else {\n        byChunk.set(cs, { group: [skip], start: at, end: at + 1 })\n      }\n    }\n    const found = await Promise.all(\n      [...byChunk.values()].map(async ({ group, start, end }) => {\n        const names = new Set(group.map(skip => skip.name))\n        const keep = (name: string) => names.has(name)\n        try {\n          const { graph, fragments } = await this.walks.reader.cut(\n            refName,\n            { start, end },\n            {\n              ...this.walks.budgets(),\n              signal,\n              keep,\n              expand: keep,\n              context: 0,\n              contained: true,\n              links: false,\n            },\n          )\n          return group.map(skip =>\n            skipCrossing(skip, refName, fragments, graph.nodes, side),\n          )\n        } catch (error) {\n          if (signal?.aborted) {\n            throw error\n          }\n          return []\n        }\n      }),\n    )\n    return found.flat().filter(crossing => crossing !== undefined)\n  }\n\n  /**\n   * One record per stretch a haplotype's walk shares with the reference's,\n   * on the reference with the haplotype as its mate. A haplotype whose\n   * deletion spans the window, with no walk there on any contig, is one\n   * `spansWindow` record of the skipped stretch, as is one that crosses the\n   * window through steps of its own, its mate those steps' bp.\n   */\n  private async anchorFeatures(\n    refName: string,\n    region: Region,\n    opts: LaneFeatureOptions,\n  ) {\n    const wanted = opts.haplotypes?.length\n      ? opts.haplotypes.map(lane => resolvePanSNPrefix(this, lane))\n      : undefined\n    const target = resolvePanSNPrefix(this, opts.targetAssemblyName)\n    const prefixes =\n      target === undefined\n        ? wanted\n        : wanted === undefined ||\n            wanted.some(\n              prefix =>\n                panSNMatchesPrefix(target, prefix) ||\n                panSNMatchesPrefix(prefix, target),\n            )\n          ? [target]\n          : []\n    if (prefixes?.length === 0) {\n      return []\n    }\n    const { start, end } = region\n    const status = `Reading walks ${region.refName}:${start.toLocaleString()}-${end.toLocaleString()}`\n    const { graph, fragments, skips } = await this.laneWalks(\n      refName,\n      region,\n      prefixes,\n      opts,\n      status,\n    )\n    // lanes come back in the order the fetch names them, which is the order\n    // the display stacks lanes of equal weight in\n    const rank = ({ name }: { name: string }) =>\n      prefixes === undefined\n        ? 0\n        : prefixes.findIndex(prefix => panSNMatchesPrefix(name, prefix))\n    // NA19036#1 skips the IGL locus on one contig and walks it on another\n    const walking = new Set(fragments.map(haplotypeOf))\n    const crossings = await updateStatus(status, opts.statusCallback, () =>\n      this.skipCrossings(\n        refName,\n        skips.filter(\n          skip =>\n            rank(skip) >= 0 &&\n            !walking.has(haplotypeOf(skip)) &&\n            skip.refStart <= start &&\n            skip.refEnd >= end,\n        ),\n        opts,\n      ),\n    )\n    const align = anchorAligner(graph.nodes)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    const laneOf = (walk: { name: string }) =>\n      laneAssemblyName(asmByPrefix, haplotypeOf(walk))\n    const references = fragments.filter(f => f.name === refName)\n    const walked = fragments\n      .filter(fragment => fragment.name !== refName && rank(fragment) >= 0)\n      .map(query => ({\n        rank: rank(query),\n        features: query.crossing\n          ? [\n              crossingFeature({\n                fragment: query,\n                crossing: query.crossing,\n                assemblyName: region.assemblyName,\n                refName: region.refName,\n                mateAssemblyName: laneOf(query),\n              }),\n            ]\n          : references.flatMap(reference =>\n              align(query, reference).map(chain =>\n                chainFeature({\n                  chain,\n                  target: reference,\n                  query,\n                  assemblyName: region.assemblyName,\n                  refName: region.refName,\n                  mateAssemblyName: laneOf(query),\n                }),\n              ),\n            ),\n      }))\n    const skipped = crossings.map(crossing => ({\n      rank: rank(crossing.skip),\n      features: [\n        skipFeature({\n          crossing,\n          refName: region.refName,\n          assemblyName: region.assemblyName,\n          mateAssemblyName: laneOf(crossing.skip),\n        }),\n      ],\n    }))\n    return [...walked, ...skipped]\n      .sort((a, b) => a.rank - b.rank)\n      .flatMap(lane => lane.features)\n  }\n\n  /**\n   * Each pair's two lanes read out of the anchor window, all pairs in one\n   * read, and each walk of a pair's query lane aligned to each walk of its\n   * target lane. A pair's records sit on its query lane's contigs, the lane\n   * the display draws on top.\n   */\n  private async pairFeatures(\n    refName: string,\n    region: Region,\n    pairs: LanePair[],\n    opts: LaneFeatureOptions,\n  ) {\n    const sides = pairs.map(pair => ({\n      pair,\n      featurePrefix: resolvePanSNPrefix(this, pair.queryAssemblyName),\n      matePrefix: resolvePanSNPrefix(this, pair.targetAssemblyName),\n    }))\n    const { graph, fragments } = await this.laneWalks(\n      refName,\n      region,\n      sides.flatMap(side => [side.featurePrefix, side.matePrefix]),\n      opts,\n      lanePairsStatus(pairs),\n    )\n    const align = lanePairAligner(graph.nodes)\n    const walksOf = (prefix: string) =>\n      fragments.filter(f => panSNMatchesPrefix(f.name, prefix))\n    return sides.flatMap(({ pair, featurePrefix, matePrefix }) =>\n      walksOf(featurePrefix).flatMap(target =>\n        walksOf(matePrefix).flatMap(query =>\n          align(query, target).map(chain =>\n            chainFeature({\n              chain,\n              target,\n              query,\n              assemblyName: pair.queryAssemblyName,\n              refName: panSNContig(target.name),\n              mateAssemblyName: pair.targetAssemblyName,\n            }),\n          ),\n        ),\n      ),\n    )\n  }\n\n  // The files are filed under the reference alone, so a window on a\n  // haplotype lane has no answer: a lane pair is read inside the anchor's\n  getFeatures(region: Region, opts: LaneFeatureOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      const refName =\n        region.assemblyName === this.anchor\n          ? await this.refNames.resolve(region, opts)\n          : undefined\n      if (refName !== undefined) {\n        const pairs = requestedPairs(opts)\n        const features =\n          pairs.length > 0\n            ? await this.pairFeatures(refName, region, pairs, opts)\n            : await this.anchorFeatures(refName, region, opts)\n        for (const feature of features) {\n          observer.next(feature)\n        }\n      }\n      observer.complete()\n    }, opts.signal)\n  }\n}\n"],
+  "mappings": "0pBAkBA,IAAMA,GAAyB,GAOxB,SAASC,GAAoBC,EAAmB,CACrD,IAAMC,EAAkB,CAAC,EACzB,QAASC,EAAI,EAAGA,EAAIF,EAAM,OAAQE,IAAK,CACrC,GAAM,CAACC,EAAIC,CAAG,EAAIJ,EAAME,CAAC,EACnB,CAACG,EAAQC,CAAO,EAAIN,EAAME,EAAI,CAAC,GAAK,CAAC,EAEzCE,IAAQE,GACRF,GAAON,KACLK,IAAO,KAAOE,IAAW,KAASF,IAAO,KAAOE,IAAW,MAE7DJ,EAAI,KAAK,CAAC,IAAKG,CAAG,CAAC,EACnBF,KAEAD,EAAI,KAAK,CAACE,EAAIC,CAAG,CAAC,CAEtB,CACA,OAAOH,CACT,CAGA,SAASM,EAAUC,EAAwB,CACzC,OAAO,MAAM,KAAKA,EAAS,IAAK,CAACC,EAAIP,IAAM,EAAIO,EAAKD,EAAS,IAAIN,CAAC,CAAE,CACtE,CAEA,SAASQ,EAAWC,EAA8BF,EAAY,CAC5D,IAAMG,EAAOD,EAAM,IAAIF,CAAE,EACzB,OAAOG,IAAS,OAAY,EAAIA,EAAK,IAAMA,EAAK,KAClD,CAOO,SAASC,GAAYF,EAA8B,CACxD,IAAMG,EAAU,IAAI,IACdC,EAAcN,GAAe,CACjC,IAAMO,EAASN,EAAWC,EAAOF,CAAE,EAC/BQ,EAAWH,EAAQ,IAAIE,CAAM,EACjC,OAAIC,IAAa,SACfA,EAAW,IAAI,OAAOD,CAAM,EAC5BF,EAAQ,IAAIE,EAAQC,CAAQ,GAEvBA,CACT,EACMC,EAAU,IAAI,IACdC,EAAiBX,GAA2B,CAChD,IAAIY,EAAQF,EAAQ,IAAIV,CAAQ,EAChC,OAAIY,IAAU,SACZA,EAAQb,EAAUC,CAAQ,EAC1BU,EAAQ,IAAIV,EAAUY,CAAK,GAEtBA,CACT,EACA,MAAO,CAACC,EAAqBC,IAC3BC,EAAe,CACb,MAAOJ,EAAcE,CAAK,EAC1B,OAAQF,EAAcG,CAAM,EAC5B,WAAAP,EACA,MAAO,EACT,CAAC,CACL,CAIA,IAAMS,EAAe,IAErB,SAASC,EAAWzB,EAAmBG,EAAiBC,EAAa,CACnE,IAAMsB,EAAO1B,EAAM,GAAG,EAAE,EACpBI,EAAM,IACJsB,IAAO,CAAC,IAAMvB,EAChBuB,EAAK,CAAC,GAAKtB,EAEXJ,EAAM,KAAK,CAACG,EAAIC,CAAG,CAAC,EAG1B,CAUO,SAASuB,GAAiBhB,EAA8B,CAC7D,IAAMiB,EAAYC,GAAmBnB,EAAWC,EAAOkB,GAAU,CAAC,EAC5DC,EAAWZ,GAAsB,CACrC,IAAMjB,EAAM,IAAI,aAAaiB,EAAQ,OAAS,CAAC,EAC/C,OAAAA,EAAQ,QAAQ,CAACW,EAAQ3B,IAAM,CAC7BD,EAAIC,EAAI,CAAC,EAAID,EAAIC,CAAC,EAAK0B,EAASC,CAAM,CACxC,CAAC,EACM5B,CACT,EAEA,MAAO,CAACoB,EAAqBC,IAAsC,CACjE,IAAMS,EAAMxB,EAAUe,CAAM,EACtBU,EAAMzB,EAAUc,CAAK,EACrB,CAACY,EAAMC,CAAU,EAAIC,EAAYH,EAAKD,EAAKH,CAAQ,EACnD,CAACQ,EAAQC,CAAY,EAAIF,EAC7BH,EAAI,IAAIH,GAAUA,EAAS,CAAC,EAAE,QAAQ,EACtCE,EACAH,CACF,EACMU,EAAUD,EAAeH,EACzBK,EAAQD,EAAUF,EAASH,EAC3BO,EAAc,KAAK,IAAIN,EAAYG,CAAY,EACrD,GAAIG,EAAchB,EAChB,MAAO,CAAC,EAEV,IAAMiB,EAAQX,EAAQC,CAAG,EACnBW,EAAQZ,EAAQE,CAAG,EAEnBW,EAAUC,GACdN,EAAUN,EAAI,OAAS,EAAIO,EAAMK,CAAC,EAAG,CAAC,EAAIL,EAAMK,CAAC,EAAG,CAAC,EACjD5C,EAAoB,CAAC,EAC3BuC,EAAM,QAAQ,CAAC,CAAC,CAAEM,CAAC,EAAGD,IAAM,CAC1B,GAAIA,EAAI,EAAG,CACT,GAAM,CAACE,EAAIC,CAAE,EAAI,CAACJ,EAAOC,EAAI,CAAC,EAAGD,EAAOC,CAAC,CAAC,EAAE,KAAK,CAACI,EAAGC,IAAMD,EAAIC,CAAC,EAChExB,EAAWzB,EAAO,IAAK0C,EAAMK,CAAG,EAAKL,EAAMI,EAAM,CAAC,CAAE,EACpDrB,EAAWzB,EAAO,IAAKyC,EAAMI,CAAC,EAAKJ,EAAMF,EAAMK,EAAI,CAAC,EAAG,CAAC,EAAI,CAAC,CAAE,CACjE,CACAnB,EAAWzB,EAAO,IAAK4B,EAASG,EAAIc,CAAC,CAAE,CAAC,CAC1C,CAAC,EACD,GAAM,CAACC,EAAIC,CAAE,EAAI,CAACJ,EAAO,CAAC,EAAGA,EAAOJ,EAAM,OAAS,CAAC,CAAC,EAAE,KAAK,CAACS,EAAGC,IAAMD,EAAIC,CAAC,EAC3E,MAAO,CACL,CACE,WAAYP,EAAMI,CAAG,EACrB,SAAUJ,EAAMK,EAAM,CAAC,EACvB,YAAaN,EAAMF,EAAM,CAAC,EAAG,CAAC,CAAC,EAC/B,UAAWE,EAAMF,EAAM,GAAG,EAAE,EAAG,CAAC,EAAI,CAAC,EACrC,OAAQD,EAAU,IAAM,IACxB,MAAAtC,EACA,YAAAwC,CACF,CACF,CACF,CACF,CAGA,SAASU,GAAa1C,EAAwB,CAC5C,IAAM2C,EAAM,IAAI,IACVC,EAAQ,IAAI,IAClB5C,EAAS,IAAI,QAAQ,CAACC,EAAIP,IAAM,CAC1BiD,EAAI,IAAI1C,CAAE,EACZ2C,EAAM,IAAI3C,CAAE,EAEZ0C,EAAI,IAAI1C,EAAID,EAAS,IAAIN,CAAC,CAAE,CAEhC,CAAC,EACD,QAAWO,KAAM2C,EACfD,EAAI,OAAO1C,CAAE,EAEf,OAAO0C,CACT,CAIA,SAASE,GAAgB1C,EAA8B,CACrD,IAAM2C,EAAS,IAAI,IACbC,EAAY/C,GAA2B,CAC3C,IAAIgD,EAAQF,EAAO,IAAI9C,CAAQ,EAC/B,OAAIgD,IAAU,SACZA,EAAQN,GAAa1C,CAAQ,EAC7B8C,EAAO,IAAI9C,EAAUgD,CAAK,GAErBA,CACT,EACA,MAAO,CAACnC,EAAqBC,IAAyB,CACpD,IAAMmC,EAASF,EAASjC,CAAM,EAC1BW,EAAO,EACPyB,EAAW,EACf,OAAW,CAACjD,EAAI0C,CAAG,IAAKI,EAASlC,CAAK,EAAG,CACvC,IAAMsC,EAAQF,EAAO,IAAIhD,CAAE,EACvBkD,IAAUR,EACZlB,GAAQvB,EAAWC,EAAOF,CAAE,EACnBkD,IAAU,SACnBD,GAAYhD,EAAWC,EAAOF,CAAE,EAEpC,CACA,MAAO,CAAE,KAAAwB,EAAM,SAAAyB,CAAS,CAC1B,CACF,CAaO,SAASE,GAAgBjD,EAA8B,CAC5D,IAAMkD,EAAclC,GAAiBhB,CAAK,EACpCmD,EAAUjD,GAAYF,CAAK,EAC3BoD,EAASV,GAAgB1C,CAAK,EACpC,MAAO,CAACU,EAAqBC,IAAyB,CACpD,GAAM,CAAE,KAAAW,EAAM,SAAAyB,CAAS,EAAIK,EAAO1C,EAAOC,CAAM,EAC/C,OAAOW,GAAQT,GAAgBkC,GAAYlC,EACvCsC,EAAQzC,EAAOC,CAAM,EACrBuC,EAAYxC,EAAOC,CAAM,CAC/B,CACF,CAIA,IAAM0C,GAAgB,IAUf,SAASC,GAActD,EAA8B,CAC1D,IAAMkD,EAAclC,GAAiBhB,CAAK,EACpCmD,EAAUjD,GAAYF,CAAK,EAC3BoD,EAASV,GAAgB1C,CAAK,EACpC,MAAO,CAACU,EAAqBC,IAAyB,CACpD,IAAM4C,EAAUL,EAAYxC,EAAOC,CAAM,EACnC6C,EAAQD,EAAQ,CAAC,GAAG,OACpB,CAAE,KAAAjC,EAAM,SAAAyB,CAAS,EAAIK,EAAO1C,EAAOC,CAAM,EAC/C,OAAO6C,IAAU,QAAa,KAAK,IAAIlC,EAAMyB,CAAQ,EAAIM,GACrDE,EACA,CACE,GAAGA,EACH,GAAGJ,EAAQzC,EAAOC,CAAM,EAAE,OAAO8C,GAASA,EAAM,SAAWD,CAAK,CAClE,CACN,CACF,CAMO,SAASE,EAAa,CAC3B,MAAAD,EACA,OAAA9C,EACA,MAAAD,EACA,aAAAiD,EACA,QAAAC,EACA,iBAAAC,CACF,EAOG,CACD,IAAMxE,EAAQD,GAAoBqE,EAAM,KAAK,EAC7C,OAAOK,EAAa,CAClB,OAAQ,CACN,KAAMnD,EAAO,KACb,aAAAgD,EACA,QAAAC,EACA,MAAOjD,EAAO,SAAW8C,EAAM,YAC/B,IAAK9C,EAAO,SAAW8C,EAAM,SAC/B,EACA,MAAO,CACL,KAAM/C,EAAM,KACZ,aAAcmD,EACd,QAASE,EAAYrD,EAAM,IAAI,EAC/B,MAAOA,EAAM,SAAW+C,EAAM,WAC9B,IAAK/C,EAAM,SAAW+C,EAAM,QAC9B,EACA,OAAQA,EAAM,OACd,MAAOO,EAAU3E,CAAK,EACtB,QAASA,EAAM,OAAO,CAAC4E,EAAK,CAACzE,EAAI0E,CAAC,IAAMD,GAAOzE,IAAO,IAAM0E,EAAI,GAAI,CAAC,EACrE,QAAS7E,EAAM,OAAO,CAAC4E,EAAK,CAAC,CAAEC,CAAC,IAAMD,EAAMC,EAAG,CAAC,CAClD,CAAC,CACH,CAuBO,SAASC,GACdC,EACAR,EACAS,EACArE,EACAsE,EAC0B,CAC1B,IAAMC,EAAUD,IAAS,QACnBE,EAAUC,GACdA,EAAK,OAAS,cACbF,EACGE,EAAK,MAAM,OAASL,EAAK,SACzBK,EAAK,MAAM,MAAQL,EAAK,UAC9B,QAAWvE,KAAYwE,EAAW,CAChC,GAAM,CAAE,KAAAK,EAAM,UAAAC,EAAW,SAAAC,EAAU,IAAAC,EAAK,IAAArC,EAAK,OAAAsC,EAAQ,MAAAC,CAAM,EAAIlF,EAC/D,GAAI6E,IAASN,EAAK,MAAQO,IAAcP,EAAK,UAAW,CACtD,IAAIY,EAAKJ,EACT,QAASrF,EAAI,EAAGA,EAAIsF,EAAI,OAAQtF,IAAK,CACnC,IAAMU,EAAOD,EAAM,IAAI6E,EAAItF,CAAC,CAAE,EACxBc,EAASJ,IAAS,OAAY,EAAIA,EAAK,IAAMA,EAAK,MACxD,GACEA,GAAM,OAAS,GACfA,EAAK,UAAY2D,IAChBW,EAAUtE,EAAK,MAAQmE,EAAK,SAAWnE,EAAK,QAAUmE,EAAK,QAC5D,CACA,IAAMa,EACJT,EAAOO,CAAK,IAAMP,EAAOM,CAAM,EAC3BN,EAAOO,CAAK,EACZxF,EAAI,GAAMA,EAAIsF,EAAI,OAAS,EACzBtF,EAAI,EACJgF,KAAa/B,EAAIjD,CAAC,IAAM,GAChC,MAAO,CACL,KAAA6E,EACA,GAAIa,EAAaD,EAAK3E,EAAS2E,EAC/B,OAAQC,IAAeV,EAAU,IAAM,GACzC,CACF,CACAS,GAAM3E,CACR,CACF,CACF,CAEF,CASO,SAAS6E,GAAY,CAC1B,SAAAC,EACA,QAAAvB,EACA,aAAAD,EACA,iBAAAE,CACF,EAKG,CACD,GAAM,CAAE,KAAAO,EAAM,GAAAY,EAAI,OAAAI,CAAO,EAAID,EAC7B,OAAOE,GAAe,CACpB,GAAI,GAAGjB,EAAK,IAAI,IAAIA,EAAK,SAAS,IAAIA,EAAK,KAAK,QAChD,aAAAT,EACA,QAAAC,EACA,MAAOQ,EAAK,SACZ,IAAKA,EAAK,OACV,QAASgB,IAAW,IACpB,KAAM,CACJ,QAASrB,EAAYK,EAAK,IAAI,EAC9B,MAAOY,EACP,IAAKA,EACL,aAAcnB,CAChB,CACF,CAAC,CACH,CAOO,SAASyB,GAAgB,CAC9B,SAAAzF,EACA,SAAAsF,EACA,QAAAvB,EACA,aAAAD,EACA,iBAAAE,CACF,EAMG,CACD,GAAM,CAAE,KAAAa,EAAM,UAAAC,EAAW,SAAAC,EAAU,OAAAW,CAAO,EAAI1F,EAC9C,OAAOwF,GAAe,CACpB,GAAI,GAAGX,CAAI,IAAIC,CAAS,IAAIC,CAAQ,YACpC,aAAAjB,EACA,QAAAC,EACA,MAAOuB,EAAS,SAChB,IAAKA,EAAS,OACd,QAASA,EAAS,QAClB,KAAM,CACJ,QAASpB,EAAYW,CAAI,EACzB,MAAOE,EACP,IAAKW,EACL,aAAc1B,CAChB,CACF,CAAC,CACH,CAEA,SAASwB,GAAe,CACtB,GAAAvF,EACA,aAAA6D,EACA,QAAAC,EACA,MAAA4B,EACA,IAAAC,EACA,QAAA9D,EACA,KAAA+D,CACF,EAQG,CACD,OAAO,IAAIC,EAAe,CACxB,SAAU7F,EACV,aAAA6D,EACA,QAAAC,EACA,MAAA4B,EACA,IAAAC,EACA,KAAM,WACN,OAAQ9D,EAAU,GAAK,EACvB,UAAW7B,EACX,YAAa,GACb,KAAA4F,CACF,CAAC,CACH,CC7aA,IAAME,EAAc,CAAC,CAAE,KAAAC,CAAK,IAAwBC,EAAeD,CAAI,GAAKA,EAEvDE,EAArB,cAAqDC,CAAsD,CAA3G,kCACE,KAAiB,MAAmB,IAAIC,GACtCC,EAAc,KAAM,CAAC,eAAe,EAAG,CAAC,YAAY,CAAC,EACrD,IACF,EACA,KAAiB,SAA0B,IAAIC,EAC7C,KAAK,MAAM,KACX,IACF,EAEA,IAAY,QAAS,CACnB,IAAMC,EAAS,KAAK,QAAQ,eAAe,EAAE,CAAC,EAC9C,GAAIA,IAAW,OACb,MAAM,IAAI,MACR,gHACF,EAEF,OAAOA,CACT,CAMA,MAAM,kBAAkBC,EAAoB,CAAC,EAAG,CAC9C,OAAO,KAAK,MAAM,eAAeA,CAAI,CACvC,CAOA,MAAM,UAAUA,EAAoB,CAAC,EAAG,CACtC,GAAM,CAAE,WAAAC,CAAW,EAAI,MAAM,KAAK,MAAM,OAAO,OAAOD,CAAI,EACpD,CAAE,OAAAD,CAAO,EAAI,KACbG,EAAeC,EAAmB,KAAMJ,CAAM,EAC9CK,EAAcC,EAAsB,IAAI,EAC9C,MAAO,CACL,cAAe,GACf,mBAAoBN,EACpB,MAAOE,EACJ,OACCK,GACEA,IAAWJ,GAAgBK,EAAYD,CAAM,IAAMJ,CACvD,EACC,IAAII,IAAW,CACd,KAAME,EAAiBJ,EAAaE,CAAM,EAC1C,MAAOA,EACP,MAAOC,EAAYD,CAAM,CAC3B,EAAE,CACN,CACF,CAIA,MAAM,YAAYN,EAAoB,CAAC,EAAG,CACxC,GAAM,CAAE,aAAAS,CAAa,EAAIT,EACzB,OAAOS,IAAiB,QAAaA,IAAiB,KAAK,OACvD,KAAK,SAAS,iBAAiB,CAAE,GAAGT,EAAM,aAAc,KAAK,MAAO,CAAC,EACrE,CAAC,CACP,CAOA,MAAM,YAAYU,EAAgBV,EAA+B,CAAC,EAAG,CACnE,IAAMW,EAAU,MAAM,KAAK,SAAS,cAAcD,EAAQ,CACxD,OAAQV,EAAK,MACf,CAAC,EACD,OAAO,KAAK,MAAM,SAASW,EAASD,EAAQV,CAAI,CAClD,CAOA,MAAc,UACZW,EACAD,EACAE,EACAZ,EACAa,EACA,CACA,IAAMC,EAAOC,EAAUH,EAAUD,CAAO,EACxC,OAAOK,EAAaH,EAAQb,EAAK,eAAgB,IAC/C,KAAK,MAAM,OACR,IAAIW,EAASD,EAAQ,CACpB,GAAG,KAAK,MAAM,QAAQ,EACtB,OAAQV,EAAK,OACb,KAAAc,EACA,OAAQA,EACR,MAAO,EACT,CAAC,EACA,MAAOG,GAAmB,CACzB,MAAMC,EAAeD,EAAOP,EAAO,IAAMA,EAAO,KAAK,CACvD,CAAC,CACL,CACF,CAQA,MAAc,cACZC,EACAQ,EACAnB,EACA,CACA,IAAMoB,EAAwB,CAAC,EAC3BC,EAASF,EACb,QAAWG,IAAQ,CAAC,QAAS,QAAQ,EAAY,CAC/C,IAAMC,EAAY,MAAM,KAAK,cAAcZ,EAASU,EAAQC,EAAMtB,CAAI,EACtE,QAAWwB,KAAYD,EACrBH,EAAM,KAAKI,CAAQ,EAErB,IAAMC,EAAS,IAAI,IAAIF,EAAU,IAAIC,GAAYA,EAAS,IAAI,CAAC,EAC/DH,EAASA,EAAO,OAAOK,GAAQ,CAACD,EAAO,IAAIC,CAAI,CAAC,CAClD,CACA,OAAON,CACT,CAEA,MAAc,cACZT,EACAQ,EACAG,EACAtB,EACA,CACA,GAAM,CAAE,OAAA2B,CAAO,EAAI3B,EACb,CAAE,MAAA4B,CAAM,EAAI,MAAM,KAAK,MAAM,OAAO,OAAO,CAAE,OAAAD,CAAO,CAAC,EACrDE,EAAYH,GAChBJ,IAAS,QAAUI,EAAK,SAAW,EAAIA,EAAK,OACxCI,EAAU,IAAI,IAIpB,QAAWJ,KAAQP,EAAO,CACxB,IAAMY,EAAKF,EAASH,CAAI,EAClBM,EAAK,KAAK,MAAMD,EAAKH,CAAK,EAC1BK,EAAOH,EAAQ,IAAIE,CAAE,EACvBC,GACFA,EAAK,MAAM,KAAKP,CAAI,EACpBO,EAAK,MAAQ,KAAK,IAAIA,EAAK,MAAOF,CAAE,EACpCE,EAAK,IAAM,KAAK,IAAIA,EAAK,IAAKF,EAAK,CAAC,GAEpCD,EAAQ,IAAIE,EAAI,CAAE,MAAO,CAACN,CAAI,EAAG,MAAOK,EAAI,IAAKA,EAAK,CAAE,CAAC,CAE7D,CA8BA,OA7Bc,MAAM,QAAQ,IAC1B,CAAC,GAAGD,EAAQ,OAAO,CAAC,EAAE,IAAI,MAAO,CAAE,MAAAI,EAAO,MAAAC,EAAO,IAAAC,CAAI,IAAM,CACzD,IAAMC,EAAQ,IAAI,IAAIH,EAAM,IAAIR,GAAQA,EAAK,IAAI,CAAC,EAC5CZ,EAAQtB,GAAiB6C,EAAM,IAAI7C,CAAI,EAC7C,GAAI,CACF,GAAM,CAAE,MAAA8C,EAAO,UAAAC,CAAU,EAAI,MAAM,KAAK,MAAM,OAAO,IACnD5B,EACA,CAAE,MAAAwB,EAAO,IAAAC,CAAI,EACb,CACE,GAAG,KAAK,MAAM,QAAQ,EACtB,OAAAT,EACA,KAAAb,EACA,OAAQA,EACR,QAAS,EACT,UAAW,GACX,MAAO,EACT,CACF,EACA,OAAOoB,EAAM,IAAIR,GACfc,GAAad,EAAMf,EAAS4B,EAAWD,EAAM,MAAOhB,CAAI,CAC1D,CACF,OAASL,EAAO,CACd,GAAIU,GAAQ,QACV,MAAMV,EAER,MAAO,CAAC,CACV,CACF,CAAC,CACH,GACa,KAAK,EAAE,OAAOO,GAAYA,IAAa,MAAS,CAC/D,CASA,MAAc,eACZb,EACAD,EACAV,EACA,CACA,IAAMyC,EAASzC,EAAK,YAAY,OAC5BA,EAAK,WAAW,IAAI0C,GAAQvC,EAAmB,KAAMuC,CAAI,CAAC,EAC1D,OACEC,EAASxC,EAAmB,KAAMH,EAAK,kBAAkB,EACzDY,EACJ+B,IAAW,OACPF,EACAA,IAAW,QACTA,EAAO,KACLnC,GACEsC,EAAmBD,EAAQrC,CAAM,GACjCsC,EAAmBtC,EAAQqC,CAAM,CACrC,EACA,CAACA,CAAM,EACP,CAAC,EACT,GAAI/B,GAAU,SAAW,EACvB,MAAO,CAAC,EAEV,GAAM,CAAE,MAAAuB,EAAO,IAAAC,CAAI,EAAI1B,EACjBG,EAAS,iBAAiBH,EAAO,OAAO,IAAIyB,EAAM,eAAe,CAAC,IAAIC,EAAI,eAAe,CAAC,GAC1F,CAAE,MAAAE,EAAO,UAAAC,EAAW,MAAApB,CAAM,EAAI,MAAM,KAAK,UAC7CR,EACAD,EACAE,EACAZ,EACAa,CACF,EAGMgC,EAAO,CAAC,CAAE,KAAArD,CAAK,IACnBoB,IAAa,OACT,EACAA,EAAS,UAAUN,GAAUsC,EAAmBpD,EAAMc,CAAM,CAAC,EAE7DwC,EAAU,IAAI,IAAIP,EAAU,IAAIhD,CAAW,CAAC,EAC5CgC,EAAY,MAAMP,EAAaH,EAAQb,EAAK,eAAgB,IAChE,KAAK,cACHW,EACAQ,EAAM,OACJO,GACEmB,EAAKnB,CAAI,GAAK,GACd,CAACoB,EAAQ,IAAIvD,EAAYmC,CAAI,CAAC,GAC9BA,EAAK,UAAYS,GACjBT,EAAK,QAAUU,CACnB,EACApC,CACF,CACF,EACM+C,EAAQC,GAAcV,EAAM,KAAK,EACjClC,EAAcC,EAAsB,IAAI,EACxC4C,EAAUC,GACd1C,EAAiBJ,EAAab,EAAY2D,CAAI,CAAC,EAC3CC,EAAaZ,EAAU,OAAOa,GAAKA,EAAE,OAASzC,CAAO,EACrD0C,EAASd,EACZ,OAAOe,GAAYA,EAAS,OAAS3C,GAAWkC,EAAKS,CAAQ,GAAK,CAAC,EACnE,IAAIC,IAAU,CACb,KAAMV,EAAKU,CAAK,EAChB,SAAUA,EAAM,SACZ,CACEC,GAAgB,CACd,SAAUD,EACV,SAAUA,EAAM,SAChB,aAAc7C,EAAO,aACrB,QAASA,EAAO,QAChB,iBAAkBuC,EAAOM,CAAK,CAChC,CAAC,CACH,EACAJ,EAAW,QAAQM,GACjBV,EAAMQ,EAAOE,CAAS,EAAE,IAAIC,GAC1BC,EAAa,CACX,MAAAD,EACA,OAAQD,EACR,MAAAF,EACA,aAAc7C,EAAO,aACrB,QAASA,EAAO,QAChB,iBAAkBuC,EAAOM,CAAK,CAChC,CAAC,CACH,CACF,CACN,EAAE,EACEK,EAAUrC,EAAU,IAAIC,IAAa,CACzC,KAAMqB,EAAKrB,EAAS,IAAI,EACxB,SAAU,CACRqC,GAAY,CACV,SAAArC,EACA,QAASd,EAAO,QAChB,aAAcA,EAAO,aACrB,iBAAkBuC,EAAOzB,EAAS,IAAI,CACxC,CAAC,CACH,CACF,EAAE,EACF,MAAO,CAAC,GAAG6B,EAAQ,GAAGO,CAAO,EAC1B,KAAK,CAACE,EAAGC,IAAMD,EAAE,KAAOC,EAAE,IAAI,EAC9B,QAAQrB,GAAQA,EAAK,QAAQ,CAClC,CAQA,MAAc,aACZ/B,EACAD,EACAsD,EACAhE,EACA,CACA,IAAMiE,EAAQD,EAAM,IAAIE,IAAS,CAC/B,KAAAA,EACA,cAAe/D,EAAmB,KAAM+D,EAAK,iBAAiB,EAC9D,WAAY/D,EAAmB,KAAM+D,EAAK,kBAAkB,CAC9D,EAAE,EACI,CAAE,MAAA5B,EAAO,UAAAC,CAAU,EAAI,MAAM,KAAK,UACtC5B,EACAD,EACAuD,EAAM,QAAQ3C,GAAQ,CAACA,EAAK,cAAeA,EAAK,UAAU,CAAC,EAC3DtB,EACAmE,EAAgBH,CAAK,CACvB,EACMjB,EAAQqB,GAAgB9B,EAAM,KAAK,EACnC+B,EAAW/D,GACfiC,EAAU,OAAO,GAAKK,EAAmB,EAAE,KAAMtC,CAAM,CAAC,EAC1D,OAAO2D,EAAM,QAAQ,CAAC,CAAE,KAAAC,EAAM,cAAAI,EAAe,WAAAC,CAAW,IACtDF,EAAQC,CAAa,EAAE,QAAQ3B,GAC7B0B,EAAQE,CAAU,EAAE,QAAQhB,GAC1BR,EAAMQ,EAAOZ,CAAM,EAAE,IAAIe,GACvBC,EAAa,CACX,MAAAD,EACA,OAAAf,EACA,MAAAY,EACA,aAAcW,EAAK,kBACnB,QAASM,EAAY7B,EAAO,IAAI,EAChC,iBAAkBuB,EAAK,kBACzB,CAAC,CACH,CACF,CACF,CACF,CACF,CAIA,YAAYxD,EAAgBV,EAA2B,CAAC,EAAG,CACzD,OAAOyE,EAA0B,MAAMC,GAAY,CACjD,IAAM/D,EACJD,EAAO,eAAiB,KAAK,OACzB,MAAM,KAAK,SAAS,QAAQA,EAAQV,CAAI,EACxC,OACN,GAAIW,IAAY,OAAW,CACzB,IAAMqD,EAAQW,EAAe3E,CAAI,EAC3B4E,EACJZ,EAAM,OAAS,EACX,MAAM,KAAK,aAAarD,EAASD,EAAQsD,EAAOhE,CAAI,EACpD,MAAM,KAAK,eAAeW,EAASD,EAAQV,CAAI,EACrD,QAAW6E,KAAWD,EACpBF,EAAS,KAAKG,CAAO,CAEzB,CACAH,EAAS,SAAS,CACpB,EAAG1E,EAAK,MAAM,CAChB,CACF",
+  "names": ["BALANCED_BUBBLE_MAX_BP", "bubblesAsMismatches", "edits", "out", "i", "op", "len", "nextOp", "nextLen", "handlesOf", "fragment", "id", "nodeLength", "nodes", "node", "walkAligner", "standIn", "sequenceOf", "length", "sequence", "handles", "cachedHandles", "steps", "query", "target", "pairAlignments", "MIN_MATCH_BP", "appendEdit", "last", "referenceAligner", "lengthOf", "handle", "offsets", "ref", "hap", "same", "sameWeight", "weightedLcs", "turned", "turnedWeight", "reverse", "pairs", "sharedBases", "refAt", "hapAt", "stepOf", "k", "r", "lo", "hi", "x", "y", "singleVisits", "rev", "twice", "directionShares", "visits", "visitsOf", "found", "theirs", "opposite", "other", "lanePairAligner", "subsequence", "chained", "shares", "TURNED_MIN_BP", "anchorAligner", "records", "taken", "chain", "chainFeature", "assemblyName", "refName", "mateAssemblyName", "matchFeature", "panSNContig", "pairCigar", "sum", "n", "skipCrossing", "skip", "fragments", "side", "leaving", "across", "stop", "name", "fragStart", "hapStart", "ids", "before", "after", "at", "jumpsAfter", "skipFeature", "crossing", "strand", "windowDeletion", "crossingFeature", "hapEnd", "start", "end", "mate", "SyntenyFeature", "haplotypeOf", "name", "panSNHaplotype", "WalkTabixSyntenyAdapter", "ComparativeAdapterBase", "WalkIndex", "openTabixSlot", "PanSNRefNames", "anchor", "opts", "haplotypes", "anchorPrefix", "resolvePanSNPrefix", "asmByPrefix", "assemblyByPanSNPrefix", "prefix", "panSNSample", "laneAssemblyName", "assemblyName", "region", "refName", "prefixes", "status", "keep", "walksKept", "updateStatus", "error", "laneZoomNotice", "skips", "found", "missed", "side", "crossings", "crossing", "placed", "skip", "signal", "chunk", "boundary", "byChunk", "at", "cs", "held", "group", "start", "end", "names", "graph", "fragments", "skipCrossing", "wanted", "lane", "target", "panSNMatchesPrefix", "rank", "walking", "align", "anchorAligner", "laneOf", "walk", "references", "f", "walked", "fragment", "query", "crossingFeature", "reference", "chain", "chainFeature", "skipped", "skipFeature", "a", "b", "pairs", "sides", "pair", "lanePairsStatus", "lanePairAligner", "walksOf", "featurePrefix", "matePrefix", "panSNContig", "ObservableCreate", "observer", "requestedPairs", "features", "feature"]
+}