jbrowse-plugin-graphgenomeviewer 6.24.1 → 6.25.0

package/README.md

@@ -33,19 +33,18 @@ Build the graph with [minigraph](https://github.com/lh3/minigraph) (rGFA),
 [Minigraph-Cactus](https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md)
 (GFA and GBZ), then index what you have:
 
-- **rGFA** — run
-  [`build_pangenome_graph.sh`](https://github.com/GMOD/jbrowse-components/blob/main/scripts/build_pangenome_graph.sh).
-  It calls [gfa-to-tabix](https://github.com/GMOD/gfa-to-tabix) and
-  [gfatools](https://github.com/lh3/gfatools) and writes `.segs.bed.gz`,
-  `.links.bed.gz`, `.bubbles.bed.gz`, a coarse tier and a track config. Adapter:
-  `RgfaTabixAdapter`
-- **Plain GFA** (pggb, odgi, vg, base-level Minigraph-Cactus) — the same script,
-  with `--reference`, `--assembly` and `--snarls`, a VCF from `vg deconstruct`
-  or `pggb -V`
-- **Alleles, with a CIGAR each** — `gfa-to-tabix alleles <prefix>` (0.7.0+)
-  reads a `--layout contig` segment and link index (`build_pangenome_graph.sh`
-  writes one as `.contig.*`) and writes `.alleles.bed.gz`, which an alignments
-  track draws
+- **rGFA** — `gfa-to-tabix build graph.rgfa.gz -o out` (0.11.0+). It calls
+  [gfatools](https://github.com/lh3/gfatools) for the bubbles and writes
+  `.segs.bed.gz`, `.links.bed.gz`, `.bubbles.bed.gz`, `.alleles.bed.gz`, a
+  coarse tier, a `.graph.json` manifest and a track config. Opening
+  `out.segs.bed.gz` in **Add pangenome graph track** reads the manifest.
+  Adapter: `RgfaTabixAdapter`
+- **Plain GFA** (pggb, odgi, vg, base-level Minigraph-Cactus) — the same
+  command, with `--reference`, `--assembly` and `--snarls`, a VCF from
+  `vg deconstruct -a` or `pggb -V`
+- **Alleles, with a CIGAR each** — `build` writes `.alleles.bed.gz`, which an
+  alignments track draws; `gfa-to-tabix alleles <prefix>` makes one from a
+  `--layout contig` index
 - **Haplotype walks, as tabix files** — `vg convert -f graph.gbz`, then
   `gfa-to-tabix --walks`. Adapter: `WalkTabixSyntenyAdapter`, or
   `RgfaTabixAdapter` with `walksUri`
@@ -54,8 +53,8 @@ Build the graph with [minigraph](https://github.com/lh3/minigraph) (rGFA),
   `GbzBaseSyntenyAdapter`
 - **Reads** — `vg giraffe -o gaf`, `vg gamsort -G`, `bgzip`, `tabix` make a
   `.gaf.gz` for a gbz-base adapter's `reads`
-- **Minigraph paths per assembly** — `minigraph -cxasm --call`, which
-  `build_minigraph_paths.sh` runs per sample
+- **Minigraph paths per assembly** — `minigraph -cxasm --call` per sample, then
+  `gfa-to-tabix paths` (0.9.0+) writes one row per bubble and sample
 
 [vg](https://github.com/vgteam/vg) 1.69.0 or later covers the GBZ steps.
 
@@ -138,6 +137,10 @@ Needs JBrowse 5.0.0-beta.11 or later.
   (`.gbz.db`) as a `GraphTrack`. It finds the links and indexes beside the url,
   which a presigned url's signature doesn't cover; spell out each location in a
   config instead
+- Open track's **Add pangenome graph track** workflow also reads
+  `<prefix>.graph.json` beside a `<prefix>.segs.bed.gz` (written by
+  `gfa-to-tabix build`) for the coarse tier and the reference's PanSN sample;
+  without one, the track has no coarse tier
 - A hand-written track needs only the adapter:
 
 ```json
@@ -150,8 +153,8 @@ Needs JBrowse 5.0.0-beta.11 or later.
     "type": "RgfaTabixAdapter",
     "uri": "https://example.com/hprc",
     "coarse": {
-      "uri": "https://example.com/hprc.tier10000",
-      "aboveBpPerPx": 1000
+      "uri": "https://example.com/hprc.fold10000",
+      "foldBelowBp": 10000
     }
   }
 }
@@ -160,8 +163,8 @@ Needs JBrowse 5.0.0-beta.11 or later.
 - The track menu picks layout, colour and highlighted haplotypes, and switches
   to the segments lane or, for gbz-base and walk-indexed graphs, the haplotype
   lanes
-- Cuts the window plus a window each side, up to 5 Mb; past `aboveBpPerPx`, the
-  `coarse` tier (`build_fold_tier.sh` in jbrowse-components)
+- Cuts the window plus a window each side, up to 5 Mb; past `aboveBpPerPx`
+  (default `foldBelowBp / 10`), the `coarse` tier (`gfa-to-tabix fold`)
 - Past the cut (5 Mb, or a gbz-base adapter's `nodeLimit`) the track asks you to
   zoom in. For a population view of a wide window, add the graph's VCF as a
   variant track (`vg deconstruct` makes one from a GBZ)

package/dist/chunks/AddTrackWorkflow-ZKAN5JYJ.js

@@ -0,0 +1,2 @@
+import{a as H,b as j,c as O,d as z,g as J}from"./chunk-2I4VPDLZ.js";import{d as w,e as R}from"./chunk-NDRLCGPC.js";import"./chunk-R3TRNF7N.js";import"./chunk-7WIBGKBU.js";import"./chunk-OGQ6OQDN.js";import{b as T,h as G,j as S,m as A}from"./chunk-TENPGIPX.js";import{g as r}from"./chunk-6OPB7FOJ.js";import{A as _,B as W,E as b,a as v,e as x,f as p,n as E,r as B,s as I,t as P,z as N}from"./chunk-ECD5B2ZM.js";import{b as t,c as g,d as M}from"./chunk-JMBDTNUR.js";var s=JBrowseExports["@jbrowse/core/util/tss-react"],$=o=>s!=null&&o in Object(s)?s[o]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+o+"' from '@jbrowse/core/util/tss-react' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:o});var D=$("makeStyles"),oe=s&&s.__esModule?s.default:s;var ee=D()(o=>({paper:{margin:o.spacing(),padding:o.spacing()},field:{marginTop:o.spacing(2)},submit:{marginTop:25,marginBottom:100,display:"block"}})),te=["RgfaTabixAdapter","GbzBaseSyntenyAdapter","MinigraphBubbleAdapter"],ae=M(function({model:a}){let{classes:l}=ee(),f=S(a),d=w(a),[n,V]=r("RgfaTabixAdapter"),[i,X]=r(),[y,q]=r(),[k,K]=r(),m=n==="GbzBaseSyntenyAdapter",[C,Q]=r(""),[h,U]=r("Pangenome graph"),[F,u]=r(),[Y,L]=r(!1);async function Z(){if(!i||!a.assembly)return;u(void 0),L(!0);let e=n==="RgfaTabixAdapter"?await H(i,G(a).pluginManager):void 0;if(L(!1),!(!R(a)||!a.assembly))try{let c=h.trim();T({model:a,session:f,conf:J({choice:n,loc:i,indexLoc:y,readsLoc:m?k:void 0,manifest:e,assembly:a.assembly,sample:C,trackId:A({name:c}),name:c})})}catch(c){u(c)}}return g(N,{className:l.paper,children:[F?t(x,{error:F}):null,g(B,{children:[t(P,{children:"File type"}),t(W,{value:n,onChange:e=>{V(e.target.value),u(void 0)},children:te.map(e=>t(I,{value:e,control:t(_,{}),label:j[e]},e))})]}),t(p,{location:i,name:O[n],rootModel:d,setLocation:X}),t(p,{location:y,name:z[n],rootModel:d,setLocation:q}),m?t(p,{location:k,name:"Path to reads aligned to the graph as GAF (optional; a .gz is read by the .tbi beside it)",rootModel:d,setLocation:K}):null,t(b,{className:l.field,value:C,onChange:e=>{Q(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":"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}),t(b,{className:l.field,value:h,helperText:"Track name",slotProps:{htmlInput:{"data-testid":"graph-track-name-input"}},onChange:e=>{U(e.target.value)}}),t(v,{session:f,helperText:"Select assembly to add track to",selected:a.assembly,onChange:e=>{a.setAssembly(e)},fullWidth:!0}),t(E,{variant:"contained",className:l.submit,disabled:!i||!h.trim()||!a.assembly||Y,onClick:()=>{Z()},children:"Submit"})]})}),ue=ae;export{ue as default};
+//# sourceMappingURL=AddTrackWorkflow-ZKAN5JYJ.js.map

package/dist/chunks/AddTrackWorkflow-ZKAN5JYJ.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["host:@jbrowse/core/util/tss-react", "../../src/GraphAddTrackWorkflow/AddTrackWorkflow.tsx"],
+  "sourcesContent": ["const host = JBrowseExports[\"@jbrowse/core/util/tss-react\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\n            \"This JBrowse does not provide '\" + name + \"' from '\" + \"@jbrowse/core/util/tss-react\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const cx = /* @__PURE__ */ read(\"cx\")\nexport const keyframes = /* @__PURE__ */ read(\"keyframes\")\nexport const makeStyles = /* @__PURE__ */ read(\"makeStyles\")\nexport default host && host.__esModule ? host.default : host", "import { useState } from 'react'\n\nimport { AssemblySelector, ErrorMessage, FileSelector } from '@jbrowse/core/ui'\nimport {\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} 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  'GbzBaseSyntenyAdapter',\n  'MinigraphBubbleAdapter',\n]\n\nconst GraphAddTrackWidget = observer(function GraphAddTrackWidget({\n  model,\n}: {\n  model: AddTrackWorkflowModel\n}) {\n  const { classes } = useStyles()\n  const session = getSession(model)\n  const rootModel = getRoot<AbstractRootModel>(model)\n  const [choice, setChoice] = useState<GraphFileChoice>('RgfaTabixAdapter')\n  const [loc, setLoc] = useState<FileLocation>()\n  const [indexLoc, setIndexLoc] = useState<FileLocation>()\n  const [readsLoc, setReadsLoc] = useState<FileLocation>()\n  const gbz = choice === 'GbzBaseSyntenyAdapter'\n  const [sample, setSample] = useState('')\n  const [trackName, setTrackName] = useState('Pangenome graph')\n  const [error, setError] = useState<unknown>()\n  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          trackId: makeTrackId({ name }),\n          name,\n        }),\n      })\n    } catch (e) {\n      setError(e)\n    }\n  }\n\n  return (\n    <Paper className={classes.paper}>\n      {error ? <ErrorMessage error={error} /> : null}\n      <FormControl>\n        <FormLabel>File type</FormLabel>\n        <RadioGroup\n          value={choice}\n          onChange={event => {\n            setChoice(event.target.value as GraphFileChoice)\n            setError(undefined)\n          }}\n        >\n          {CHOICES.map(option => (\n            <FormControlLabel\n              key={option}\n              value={option}\n              control={<Radio />}\n              label={GRAPH_FILE_LABELS[option]}\n            />\n          ))}\n        </RadioGroup>\n      </FormControl>\n      <FileSelector\n        location={loc}\n        name={GRAPH_FILE_FIELDS[choice]}\n        rootModel={rootModel}\n        setLocation={setLoc}\n      />\n      <FileSelector\n        location={indexLoc}\n        name={GRAPH_INDEX_FIELDS[choice]}\n        rootModel={rootModel}\n        setLocation={setIndexLoc}\n      />\n      {gbz ? (\n        <FileSelector\n          location={readsLoc}\n          name=\"Path to reads aligned to the graph as GAF (optional; a .gz is read by the .tbi beside it)\"\n          rootModel={rootModel}\n          setLocation={setReadsLoc}\n        />\n      ) : null}\n      <TextField\n        className={classes.field}\n        value={sample}\n        onChange={event => {\n          setSample(event.target.value)\n        }}\n        label=\"Sample name in the graph\"\n        slotProps={{ htmlInput: { 'data-testid': 'graph-sample-input' } }}\n        helperText={\n          gbz\n            ? \"Optional. The graph's sample for this assembly, e.g. GRCh38 where the assembly is hg38; leave blank when they share a name or the graph has one reference sample\"\n            : \"Optional. The PanSN prefix the graph gives this assembly, e.g. GRCh38 for HPRC's GRCh38#0#chr1; leave blank when the graph's stable names are bare\"\n        }\n        placeholder=\"GRCh38\"\n        fullWidth\n      />\n      <TextField\n        className={classes.field}\n        value={trackName}\n        helperText=\"Track name\"\n        slotProps={{ htmlInput: { 'data-testid': 'graph-track-name-input' } }}\n        onChange={event => {\n          setTrackName(event.target.value)\n        }}\n      />\n      <AssemblySelector\n        session={session}\n        helperText=\"Select assembly to add track to\"\n        selected={model.assembly}\n        onChange={arg => {\n          model.setAssembly(arg)\n        }}\n        fullWidth\n      />\n      <Button\n        variant=\"contained\"\n        className={classes.submit}\n        disabled={!loc || !trackName.trim() || !model.assembly || submitting}\n        onClick={() => {\n          void handleSubmit()\n        }}\n      >\n        Submit\n      </Button>\n    </Paper>\n  )\n})\n\nexport default GraphAddTrackWidget\n"],
+  "mappings": "gdAAA,IAAMA,EAAO,eAAe,8BAA8B,EACpDC,EAAOC,GACXF,GAAQ,MAAQE,KAAQ,OAAOF,CAAI,EAC/BA,EAAKE,CAAI,EACT,OAAO,OACL,UAAY,CACV,MAAM,IAAI,MACR,kCAAoCA,EAAO,8IAC7C,CACF,EACA,CAAE,mBAAoBA,CAAK,CAC7B,EAGC,IAAMC,EAA6BC,EAAK,YAAY,EACpDC,GAAQC,GAAQA,EAAK,WAAaA,EAAK,QAAUA,ECuBxD,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,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,wBACjB,CAACU,EAAQC,CAAS,EAAIT,EAAS,EAAE,EACjC,CAACU,EAAWC,CAAY,EAAIX,EAAS,iBAAiB,EACtD,CAACY,EAAOC,CAAQ,EAAIb,EAAkB,EACtC,CAACc,EAAYC,CAAa,EAAIf,EAAS,EAAK,EAElD,eAAegB,GAAe,CAC5B,GAAI,CAACf,GAAO,CAACT,EAAM,SACjB,OAEFqB,EAAS,MAAS,EAClBE,EAAc,EAAI,EAClB,IAAME,EACJnB,IAAW,mBACP,MAAMoB,EAAkBjB,EAAKkB,EAAO3B,CAAK,EAAE,aAAa,EACxD,OAEN,GADAuB,EAAc,EAAK,EACf,GAACK,EAAQ5B,CAAK,GAAK,CAACA,EAAM,UAG9B,GAAI,CACF,IAAM6B,EAAOX,EAAU,KAAK,EAC5BY,EAAmB,CACjB,MAAA9B,EACA,QAAAE,EACA,KAAM6B,EAAiB,CACrB,OAAAzB,EACA,IAAAG,EACA,SAAAE,EACA,SAAUI,EAAMF,EAAW,OAC3B,SAAAY,EACA,SAAUzB,EAAM,SAChB,OAAAgB,EACA,QAASgB,EAAY,CAAE,KAAAH,CAAK,CAAC,EAC7B,KAAAA,CACF,CAAC,CACH,CAAC,CACH,OAASI,EAAG,CACVZ,EAASY,CAAC,CACZ,CACF,CAEA,OACEC,EAACC,EAAA,CAAM,UAAWlC,EAAQ,MACvB,UAAAmB,EAAQgB,EAACC,EAAA,CAAa,MAAOjB,EAAO,EAAK,KAC1Cc,EAACI,EAAA,CACC,UAAAF,EAACG,EAAA,CAAU,qBAAS,EACpBH,EAACI,EAAA,CACC,MAAOlC,EACP,SAAUmC,GAAS,CACjBlC,EAAUkC,EAAM,OAAO,KAAwB,EAC/CpB,EAAS,MAAS,CACpB,EAEC,SAAAxB,GAAQ,IAAI6C,GACXN,EAACO,EAAA,CAEC,MAAOD,EACP,QAASN,EAACQ,EAAA,EAAM,EAChB,MAAOC,EAAkBH,CAAM,GAH1BA,CAIP,CACD,EACH,GACF,EACAN,EAACU,EAAA,CACC,SAAUrC,EACV,KAAMsC,EAAkBzC,CAAM,EAC9B,UAAWF,EACX,YAAaM,EACf,EACA0B,EAACU,EAAA,CACC,SAAUnC,EACV,KAAMqC,EAAmB1C,CAAM,EAC/B,UAAWF,EACX,YAAaQ,EACf,EACCG,EACCqB,EAACU,EAAA,CACC,SAAUjC,EACV,KAAK,4FACL,UAAWT,EACX,YAAaU,EACf,EACE,KACJsB,EAACa,EAAA,CACC,UAAWhD,EAAQ,MACnB,MAAOe,EACP,SAAUyB,GAAS,CACjBxB,EAAUwB,EAAM,OAAO,KAAK,CAC9B,EACA,MAAM,2BACN,UAAW,CAAE,UAAW,CAAE,cAAe,oBAAqB,CAAE,EAChE,WACE1B,EACI,mKACA,qJAEN,YAAY,SACZ,UAAS,GACX,EACAqB,EAACa,EAAA,CACC,UAAWhD,EAAQ,MACnB,MAAOiB,EACP,WAAW,aACX,UAAW,CAAE,UAAW,CAAE,cAAe,wBAAyB,CAAE,EACpE,SAAUuB,GAAS,CACjBtB,EAAasB,EAAM,OAAO,KAAK,CACjC,EACF,EACAL,EAACc,EAAA,CACC,QAAShD,EACT,WAAW,kCACX,SAAUF,EAAM,SAChB,SAAUmD,GAAO,CACfnD,EAAM,YAAYmD,CAAG,CACvB,EACA,UAAS,GACX,EACAf,EAACgB,EAAA,CACC,QAAQ,YACR,UAAWnD,EAAQ,OACnB,SAAU,CAACQ,GAAO,CAACS,EAAU,KAAK,GAAK,CAAClB,EAAM,UAAYsB,EAC1D,QAAS,IAAM,CACRE,EAAa,CACpB,EACD,kBAED,GACF,CAEJ,CAAC,EAEM6B,GAAQvD",
+  "names": ["host", "read", "name", "makeStyles", "read", "tss_react_default", "host", "useStyles", "makeStyles", "theme", "CHOICES", "GraphAddTrackWidget", "observer", "model", "classes", "session", "getSession", "rootModel", "getRoot", "choice", "setChoice", "useState", "loc", "setLoc", "indexLoc", "setIndexLoc", "readsLoc", "setReadsLoc", "gbz", "sample", "setSample", "trackName", "setTrackName", "error", "setError", "submitting", "setSubmitting", "handleSubmit", "manifest", "readGraphManifest", "getEnv", "isAlive", "name", "addTrackFromWidget", "buildTrackConfig", "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/{GbzBaseSyntenyAdapter-KX7DZETX.js → GbzBaseSyntenyAdapter-RLEI3RDF.js}

@@ -1,2 +1,2 @@
-import{a as H,b as ae,c as fe,d as re}from"./chunk-KX6CASVE.js";import{b as G,c as V,d as te,e as ne}from"./chunk-ROD6PMOR.js";import{a as E,b as O}from"./chunk-ANYQG5I7.js";import{h as W,i as Z,j as de,k as U,l as u,m as B,n as M,o as F,p as k,q as z,s as X,t as ee}from"./chunk-BPN3IL3K.js";import"./chunk-WAGGHKBL.js";import"./chunk-D257CI4F.js";import{a as N}from"./chunk-OGQ6OQDN.js";import"./chunk-YBLNN5FU.js";import{e as R,f as P,g as C}from"./chunk-E2GK6JEL.js";import"./chunk-E7J6SB5P.js";import{b as Y,c as J,d as K}from"./chunk-R3TRNF7N.js";import"./chunk-7WIBGKBU.js";import{e as j,o as $}from"./chunk-TENPGIPX.js";function A(t){let s=/\.gbz\.db$/i;return s.test(t)?t.replace(s,".haplotype-index.db"):void 0}function he(t){return J(t)&&A(Y(t))?K(t,s=>A(s)):void 0}function ue(t){return t instanceof Error&&(/\bHTTP 40[34]\b/.test(t.message)||t.code==="ENOENT")}async function oe(t,s){let n=he(t);if(!n)return{};try{return await N(n,s).stat(),{location:n}}catch(e){return ue(e)?{}:{unreadable:String(e)}}}var ge=5e3,ye=50*2**20,q=class extends Error{constructor(n){super(`this GAF is ${(n/2**20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`);this.name="UnindexedGafTooLargeError"}};function be(t,s){if(t.length<=s)return t;let n=t.length/s;return Array.from({length:s},(e,a)=>t[Math.floor(a*n)])}var se=(t,s)=>t.path.some(n=>s.has(n.name)),I=class{constructor(s,n){this.file=s;this.tabix=n;this.whole=G({setup:async({signal:s})=>{let{size:n}=await this.file.stat();if(n>ye)throw new q(n);let e=await this.file.readFile({signal:s}),a=new TextDecoder().decode(e[0]===31&&e[1]===139?await te(e):e);return O(a)}})}async readIndexed(s,n,e){let a=1/0,r=-1/0;for(let c of n){let i=Number(c);Number.isInteger(i)&&(a=Math.min(a,i),r=Math.max(r,i))}let o=[];return a<=r&&await s.getLines("{node}",a,r+1,{signal:e,lineCallback:c=>{let i=E(c);i&&se(i,n)&&o.push(i)}}),o}async readsOver(s,{signal:n}={}){let e=this.tabix?await this.readIndexed(this.tabix,s,n):(await this.whole({signal:n})).filter(a=>se(a,s));return{records:be(e,ge),total:e.length}}};var v=class extends Error{constructor(n){super(n===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${n}), 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(n,e){super(`the graph is cut on its reference, ${e}; a window on ${n} has no reference coordinates to cut at. Open the graph from a ${e} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function ie(t,s){let n=u(s);return t[n]??t[s.sample]??n}function we(t,s){return`${u(t)}#${t.contig}@${s.start.node}.${s.start.offset}`}function xe({alignment:t,assemblyName:s,refName:n,lane:e}){let{refStart:a,refEnd:r,strand:o,cigar:c}=t;if(!(!t.resolved||r<=a)){let{name:i,hapStart:p,hapEnd:d}=t,f=we(i,t),g={uniqueId:f,assemblyName:s,refName:n,start:a,end:r,type:"match",strand:o==="-"?-1:1,CIGAR:c,syntenyId:f,mate:{refName:i.contig,start:p,end:d,assemblyName:e}};return new H(g)}}function Se({pair:t,lane:s,mateLane:n}){let e=`${u(t.target)}#${t.target.contig}:${t.targetStart}-${t.targetEnd}|${u(t.query)}#${t.query.contig}:${t.queryStart}-${t.queryEnd}`;return new H({uniqueId:e,assemblyName:s,refName:t.target.contig,start:t.targetStart,end:t.targetEnd,type:"match",strand:t.strand==="-"?-1:1,CIGAR:t.cigar,syntenyId:e,identity:t.matches/Math.max(t.columns,1),numMatches:t.matches,blockLen:t.columns,mate:{refName:t.query.contig,start:t.queryStart,end:t.queryEnd,assemblyName:n}})}var Pe=12e4;function Ne(t,s){let n=new Map;for(let a of t)for(let{name:r,start:o,end:c}of a.walkSpans()){let i=u(r);if(s.has(i)){let p=`${i}#${r.contig}`;n.set(p,[...n.get(p)??[],[o,c]])}}let e=0;for(let a of n.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<=Pe&&(e=Math.max(e,o))}}return e}function T(t,s){return t instanceof U&&(t.message=`Zoom in to about ${j(t.fitsBp)} to see ${s}`),t}var ce=t=>({...t,start:Math.floor(t.start),end:Math.ceil(t.end)}),_=t=>!("uri"in t)||t.uri!=="",D=class extends ae{constructor(){super(...arguments);this.graph=G({label:"Opening pangenome database",setup:async()=>{let n=this.getConf("gbzDbLocation"),e=this.getConf("haplotypeIndexLocation"),a=_(e)?{location:e}:await oe(n,this.pluginManager),r=a.location,o=await Z.open({source:N(n,this.pluginManager),haplotypeIndex:r?N(r,this.pluginManager):void 0}),c=this.getConf("assemblyNames")[0];if(c===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let i=await M(o),p=F({configured:this.getConf("referenceSample"),anchorPrefix:P(this,c),referenceSamples:i});return{db:o,anchor:c,referenceSample:p,referenceSamples:i,unreadableIndex:a.unreadable}}});this.gaf=G({label:"Opening reads",setup:async()=>{let n=this.getConf("readsLocation"),e=this.getConf(["readsIndex","location"]);return _(n)?new I(N(n,this.pluginManager),_(e)?ne(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(n,e){let{db:a,referenceSample:r}=await this.graph(e);return k(a,r,n)}async getHaplotypes(n={}){let{db:e,referenceSamples:a}=await this.graph(n),r=new Map;for(let o of await e.paths()){let c=u(o.name),i=r.get(c);i?i.contigs.includes(o.name.contig)||i.contigs.push(o.name.contig):r.set(c,{prefix:c,sample:o.name.sample,haplotype:o.name.haplotype,contigs:[o.name.contig],isReference:a.includes(o.name.sample)})}return[...r.values()]}async getHeader(n={}){let{anchor:e,referenceSample:a,referenceSamples:r}=await this.graph(n),o=C(this),c=[];for(let i of await this.getHaplotypes(n))i.sample!==a&&c.push({name:ie(o,i),label:i.prefix,group:i.sample});return{hasCoarseTier:!1,anchorAssemblyName:e,referenceSample:a,referenceSamples:r,lanes:c}}async getRefNames(n={}){let{db:e,anchor:a,referenceSample:r}=await this.graph(n),{assemblyName:o}=n,c=o===a?void 0:P(this,o),i=(await e.paths()).filter(p=>o===a?p.isIndexed&&p.name.sample===r:R(u(p.name),c)).map(p=>p.name.contig);return[...new Set(i)]}keepPredicate(n,e){let a=n===void 0||n.length===0?void 0:n.map(r=>P(this,r));return a===void 0&&e===void 0?void 0:r=>B(r,a)&&(e===void 0||R(u(r),e))}async getSubgraph(n,e={}){let{signal:a}=e,{db:r,anchor:o,referenceSample:c,unreadableIndex:i}=await this.graph({signal:a}),{assemblyName:p,refName:d,start:f,end:g}=ce(n);if(p!==o)throw new Q(p,o);let y=await this.referenceQuery(d,{signal:a});if(!y)throw new Error(`${c} has no indexed path ${d} in this graph`);let x=this.keepPredicate(e.haplotypes);if(x!==void 0&&!r.hasHaplotypeIndex)throw new v(i);let l=await X(r,y,f,g,{context:this.getConf("context"),snarls:e.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:e.signal,keep:x}).catch(b=>{throw T(b,"the graph")});return typeof l=="string"?l:ee(l,{start:f,end:g},e.walkRows)}async getReads(n,e={}){let a=await this.gaf(e);return a?a.readsOver(new Set(n),e):{records:[],total:0}}async laneHaplotypes(n,e){let a=P(this,n);return(await this.getHaplotypes(e)).filter(r=>R(r.prefix,a))}async anchorFeatures(n,e){let{db:a}=await this.graph(e),{assemblyName:r,refName:o,start:c,end:i}=n,p=P(this,e.targetAssemblyName),d=C(this),f=this.keepPredicate(e.haplotypes,p),g=await this.referenceQuery(o,e),y=this.getConf("nodeLimit");return(g?await $(`Reading graph ${o}:${c.toLocaleString()}-${i.toLocaleString()}`,e.statusCallback,()=>a.getAlignments({path:g,start:c,end:i,context:this.getConf("context"),haplotypes:"all",limit:y,signal:e.signal,keep:f}).catch(l=>{throw T(z(l,y,i-c)??l,"lanes")})):[]).flatMap(l=>{let b=l.resolved?xe({alignment:l,assemblyName:r,refName:o,lane:ie(d,l.name)}):void 0;return b===void 0?[]:[b]})}async pairFeatures(n,e,a){let{db:r}=await this.graph(a),{refName:o,start:c,end:i}=n,d=(await Promise.all(e.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(d.flatMap(({featureSide:m,mateSide:h})=>[...m,...h].map(u))),g=await this.referenceQuery(o,a),y=this.getConf("nodeLimit"),x=this.getConf("context"),[l]=e,b=(m,h)=>r.getSubgraphs({path:m,start:c,end:i,context:h,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:a.signal,keep:S=>f.has(u(S))}),pe=async m=>{let h=await b(m,x).catch(w=>{throw T(z(w,y,i-c)??w,"lanes")}),S=Ne(h,f),L=Math.ceil(S/2)+2e3;return S>0&&L>x?b(m,L).catch(w=>{if(w instanceof W)return h;throw w}):h};return(g&&l&&d.length>0?await $(e.length===1?`Reading ${l.queryAssemblyName} against ${l.targetAssemblyName}`:`Reading ${e.length} lane pairs`,a.statusCallback,()=>pe(g)):[]).flatMap(m=>d.flatMap(({pair:h,featureSide:S,mateSide:L})=>S.flatMap(w=>L.flatMap(le=>m.pairAlignments({target:w,query:le,bases:!1}).map(me=>Se({pair:me,lane:h.queryAssemblyName,mateLane:h.targetAssemblyName}))))))}getFeatures(n,e={}){let a=ce(n);return V(async r=>{let{db:o,anchor:c,unreadableIndex:i}=await this.graph(e);if(!o.hasHaplotypeIndex)throw new v(i);if(a.assemblyName===c){let p=re(e),d=p.length>0?await this.pairFeatures(a,p,e):await this.anchorFeatures(a,e);for(let f of d)r.next(f)}r.complete()},e.signal)}};export{Q as HaplotypeWindowError,v as NoHaplotypeIndexError,de as NoReferenceSampleError,fe as PairTargetError,D as default,xe as fragmentFeature,ie as laneAssemblyName,Se as pairFeature,F as resolveReferenceSample,Ne as widestWalkGap};
-//# sourceMappingURL=GbzBaseSyntenyAdapter-KX7DZETX.js.map
+import{a as H,b as ae,c as fe,d as re}from"./chunk-W7UGHWWS.js";import{b as G,c as V,d as te,e as ne}from"./chunk-AHE4Y2TX.js";import{a as E,b as O}from"./chunk-ANYQG5I7.js";import{h as W,i as Z,j as de,k as U,l as u,m as B,n as M,o as F,p as k,q as z,s as X,t as ee}from"./chunk-BPN3IL3K.js";import"./chunk-WAGGHKBL.js";import"./chunk-D257CI4F.js";import"./chunk-YBLNN5FU.js";import{e as R,f as P,g as C}from"./chunk-E2GK6JEL.js";import"./chunk-E7J6SB5P.js";import{b as Y,c as J,d as K}from"./chunk-R3TRNF7N.js";import"./chunk-7WIBGKBU.js";import{a as N}from"./chunk-OGQ6OQDN.js";import{e as j,o as $}from"./chunk-TENPGIPX.js";function A(t){let s=/\.gbz\.db$/i;return s.test(t)?t.replace(s,".haplotype-index.db"):void 0}function he(t){return J(t)&&A(Y(t))?K(t,s=>A(s)):void 0}function ue(t){return t instanceof Error&&(/\bHTTP 40[34]\b/.test(t.message)||t.code==="ENOENT")}async function oe(t,s){let n=he(t);if(!n)return{};try{return await N(n,s).stat(),{location:n}}catch(e){return ue(e)?{}:{unreadable:String(e)}}}var ge=5e3,ye=50*2**20,q=class extends Error{constructor(n){super(`this GAF is ${(n/2**20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`);this.name="UnindexedGafTooLargeError"}};function be(t,s){if(t.length<=s)return t;let n=t.length/s;return Array.from({length:s},(e,a)=>t[Math.floor(a*n)])}var se=(t,s)=>t.path.some(n=>s.has(n.name)),I=class{constructor(s,n){this.file=s;this.tabix=n;this.whole=G({setup:async({signal:s})=>{let{size:n}=await this.file.stat();if(n>ye)throw new q(n);let e=await this.file.readFile({signal:s}),a=new TextDecoder().decode(e[0]===31&&e[1]===139?await te(e):e);return O(a)}})}async readIndexed(s,n,e){let a=1/0,r=-1/0;for(let c of n){let i=Number(c);Number.isInteger(i)&&(a=Math.min(a,i),r=Math.max(r,i))}let o=[];return a<=r&&await s.getLines("{node}",a,r+1,{signal:e,lineCallback:c=>{let i=E(c);i&&se(i,n)&&o.push(i)}}),o}async readsOver(s,{signal:n}={}){let e=this.tabix?await this.readIndexed(this.tabix,s,n):(await this.whole({signal:n})).filter(a=>se(a,s));return{records:be(e,ge),total:e.length}}};var v=class extends Error{constructor(n){super(n===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${n}), 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(n,e){super(`the graph is cut on its reference, ${e}; a window on ${n} has no reference coordinates to cut at. Open the graph from a ${e} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function ie(t,s){let n=u(s);return t[n]??t[s.sample]??n}function we(t,s){return`${u(t)}#${t.contig}@${s.start.node}.${s.start.offset}`}function xe({alignment:t,assemblyName:s,refName:n,lane:e}){let{refStart:a,refEnd:r,strand:o,cigar:c}=t;if(!(!t.resolved||r<=a)){let{name:i,hapStart:p,hapEnd:d}=t,f=we(i,t),g={uniqueId:f,assemblyName:s,refName:n,start:a,end:r,type:"match",strand:o==="-"?-1:1,CIGAR:c,syntenyId:f,mate:{refName:i.contig,start:p,end:d,assemblyName:e}};return new H(g)}}function Se({pair:t,lane:s,mateLane:n}){let e=`${u(t.target)}#${t.target.contig}:${t.targetStart}-${t.targetEnd}|${u(t.query)}#${t.query.contig}:${t.queryStart}-${t.queryEnd}`;return new H({uniqueId:e,assemblyName:s,refName:t.target.contig,start:t.targetStart,end:t.targetEnd,type:"match",strand:t.strand==="-"?-1:1,CIGAR:t.cigar,syntenyId:e,identity:t.matches/Math.max(t.columns,1),numMatches:t.matches,blockLen:t.columns,mate:{refName:t.query.contig,start:t.queryStart,end:t.queryEnd,assemblyName:n}})}var Pe=12e4;function Ne(t,s){let n=new Map;for(let a of t)for(let{name:r,start:o,end:c}of a.walkSpans()){let i=u(r);if(s.has(i)){let p=`${i}#${r.contig}`;n.set(p,[...n.get(p)??[],[o,c]])}}let e=0;for(let a of n.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<=Pe&&(e=Math.max(e,o))}}return e}function T(t,s){return t instanceof U&&(t.message=`Zoom in to about ${j(t.fitsBp)} to see ${s}`),t}var ce=t=>({...t,start:Math.floor(t.start),end:Math.ceil(t.end)}),_=t=>!("uri"in t)||t.uri!=="",D=class extends ae{constructor(){super(...arguments);this.graph=G({label:"Opening pangenome database",setup:async()=>{let n=this.getConf("gbzDbLocation"),e=this.getConf("haplotypeIndexLocation"),a=_(e)?{location:e}:await oe(n,this.pluginManager),r=a.location,o=await Z.open({source:N(n,this.pluginManager),haplotypeIndex:r?N(r,this.pluginManager):void 0}),c=this.getConf("assemblyNames")[0];if(c===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let i=await M(o),p=F({configured:this.getConf("referenceSample"),anchorPrefix:P(this,c),referenceSamples:i});return{db:o,anchor:c,referenceSample:p,referenceSamples:i,unreadableIndex:a.unreadable}}});this.gaf=G({label:"Opening reads",setup:async()=>{let n=this.getConf("readsLocation"),e=this.getConf(["readsIndex","location"]);return _(n)?new I(N(n,this.pluginManager),_(e)?ne(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(n,e){let{db:a,referenceSample:r}=await this.graph(e);return k(a,r,n)}async getHaplotypes(n={}){let{db:e,referenceSamples:a}=await this.graph(n),r=new Map;for(let o of await e.paths()){let c=u(o.name),i=r.get(c);i?i.contigs.includes(o.name.contig)||i.contigs.push(o.name.contig):r.set(c,{prefix:c,sample:o.name.sample,haplotype:o.name.haplotype,contigs:[o.name.contig],isReference:a.includes(o.name.sample)})}return[...r.values()]}async getHeader(n={}){let{anchor:e,referenceSample:a,referenceSamples:r}=await this.graph(n),o=C(this),c=[];for(let i of await this.getHaplotypes(n))i.sample!==a&&c.push({name:ie(o,i),label:i.prefix,group:i.sample});return{hasCoarseTier:!1,anchorAssemblyName:e,referenceSample:a,referenceSamples:r,lanes:c}}async getRefNames(n={}){let{db:e,anchor:a,referenceSample:r}=await this.graph(n),{assemblyName:o}=n,c=o===a?void 0:P(this,o),i=(await e.paths()).filter(p=>o===a?p.isIndexed&&p.name.sample===r:R(u(p.name),c)).map(p=>p.name.contig);return[...new Set(i)]}keepPredicate(n,e){let a=n===void 0||n.length===0?void 0:n.map(r=>P(this,r));return a===void 0&&e===void 0?void 0:r=>B(r,a)&&(e===void 0||R(u(r),e))}async getSubgraph(n,e={}){let{signal:a}=e,{db:r,anchor:o,referenceSample:c,unreadableIndex:i}=await this.graph({signal:a}),{assemblyName:p,refName:d,start:f,end:g}=ce(n);if(p!==o)throw new Q(p,o);let y=await this.referenceQuery(d,{signal:a});if(!y)throw new Error(`${c} has no indexed path ${d} in this graph`);let x=this.keepPredicate(e.haplotypes);if(x!==void 0&&!r.hasHaplotypeIndex)throw new v(i);let l=await X(r,y,f,g,{context:this.getConf("context"),snarls:e.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:e.signal,keep:x}).catch(b=>{throw T(b,"the graph")});return typeof l=="string"?l:ee(l,{start:f,end:g},e.walkRows)}async getReads(n,e={}){let a=await this.gaf(e);return a?a.readsOver(new Set(n),e):{records:[],total:0}}async laneHaplotypes(n,e){let a=P(this,n);return(await this.getHaplotypes(e)).filter(r=>R(r.prefix,a))}async anchorFeatures(n,e){let{db:a}=await this.graph(e),{assemblyName:r,refName:o,start:c,end:i}=n,p=P(this,e.targetAssemblyName),d=C(this),f=this.keepPredicate(e.haplotypes,p),g=await this.referenceQuery(o,e),y=this.getConf("nodeLimit");return(g?await $(`Reading graph ${o}:${c.toLocaleString()}-${i.toLocaleString()}`,e.statusCallback,()=>a.getAlignments({path:g,start:c,end:i,context:this.getConf("context"),haplotypes:"all",limit:y,signal:e.signal,keep:f}).catch(l=>{throw T(z(l,y,i-c)??l,"lanes")})):[]).flatMap(l=>{let b=l.resolved?xe({alignment:l,assemblyName:r,refName:o,lane:ie(d,l.name)}):void 0;return b===void 0?[]:[b]})}async pairFeatures(n,e,a){let{db:r}=await this.graph(a),{refName:o,start:c,end:i}=n,d=(await Promise.all(e.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(d.flatMap(({featureSide:m,mateSide:h})=>[...m,...h].map(u))),g=await this.referenceQuery(o,a),y=this.getConf("nodeLimit"),x=this.getConf("context"),[l]=e,b=(m,h)=>r.getSubgraphs({path:m,start:c,end:i,context:h,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:a.signal,keep:S=>f.has(u(S))}),pe=async m=>{let h=await b(m,x).catch(w=>{throw T(z(w,y,i-c)??w,"lanes")}),S=Ne(h,f),L=Math.ceil(S/2)+2e3;return S>0&&L>x?b(m,L).catch(w=>{if(w instanceof W)return h;throw w}):h};return(g&&l&&d.length>0?await $(e.length===1?`Reading ${l.queryAssemblyName} against ${l.targetAssemblyName}`:`Reading ${e.length} lane pairs`,a.statusCallback,()=>pe(g)):[]).flatMap(m=>d.flatMap(({pair:h,featureSide:S,mateSide:L})=>S.flatMap(w=>L.flatMap(le=>m.pairAlignments({target:w,query:le,bases:!1}).map(me=>Se({pair:me,lane:h.queryAssemblyName,mateLane:h.targetAssemblyName}))))))}getFeatures(n,e={}){let a=ce(n);return V(async r=>{let{db:o,anchor:c,unreadableIndex:i}=await this.graph(e);if(!o.hasHaplotypeIndex)throw new v(i);if(a.assemblyName===c){let p=re(e),d=p.length>0?await this.pairFeatures(a,p,e):await this.anchorFeatures(a,e);for(let f of d)r.next(f)}r.complete()},e.signal)}};export{Q as HaplotypeWindowError,v as NoHaplotypeIndexError,de as NoReferenceSampleError,fe as PairTargetError,D as default,xe as fragmentFeature,ie as laneAssemblyName,Se as pairFeature,F as resolveReferenceSample,Ne as widestWalkGap};
+//# sourceMappingURL=GbzBaseSyntenyAdapter-RLEI3RDF.js.map

package/dist/chunks/{MinigraphBubbleAdapter-T7I4AEYT.js → MinigraphBubbleAdapter-OEOJKDBZ.js}

@@ -1,2 +1,2 @@
-import{a as g,d as f,f as c}from"./chunk-7ANVPYX5.js";import{a as b,c as p,e as u,f as m}from"./chunk-ROD6PMOR.js";import"./chunk-OGQ6OQDN.js";import"./chunk-YBLNN5FU.js";import"./chunk-E2GK6JEL.js";import{a as i,o as l}from"./chunk-TENPGIPX.js";var r=class extends b{static{this.capabilities=["getFeatures","getRefNames"]}constructor(t,a,s){super(t,a,s),this.bubbles=u(this,["bubblesLocation"],["index"]),this.refNames=new m(this.bubbles,this)}async getRefNames(t={}){return this.refNames.assemblyRefNames(t)}async hasDataForRefName(){return!0}getFeatures(t,a={}){let{signal:s,statusCallback:d}=a;return p(async n=>{let o=await this.refNames.resolve(t,a);o!==void 0&&await l("Downloading bubbles",d,()=>this.bubbles.getLines(o,t.start,t.end,{signal:s,lineCallback:(h,A)=>{let e=g(h);n.next(new i({uniqueId:`bubble-${A}`,refName:t.refName,start:e.start,end:e.end,name:f(e),description:c(e),type:"bubble",score:e.segmentCount,segmentCount:e.segmentCount,pathCount:e.pathCount,inversion:e.inversion,shortestAlleleLength:e.shortestAlleleLength,longestAlleleLength:e.longestAlleleLength,segments:e.segments,shortestAllele:e.shortestAllele,longestAllele:e.longestAllele}))}})),n.complete()},s)}};export{r as default};
-//# sourceMappingURL=MinigraphBubbleAdapter-T7I4AEYT.js.map
+import{a as g,d as f,f as c}from"./chunk-7ANVPYX5.js";import{a as b,c as p,e as u,f as m}from"./chunk-AHE4Y2TX.js";import"./chunk-YBLNN5FU.js";import"./chunk-E2GK6JEL.js";import"./chunk-OGQ6OQDN.js";import{a as i,o as l}from"./chunk-TENPGIPX.js";var r=class extends b{static{this.capabilities=["getFeatures","getRefNames"]}constructor(t,a,s){super(t,a,s),this.bubbles=u(this,["bubblesLocation"],["index"]),this.refNames=new m(this.bubbles,this)}async getRefNames(t={}){return this.refNames.assemblyRefNames(t)}async hasDataForRefName(){return!0}getFeatures(t,a={}){let{signal:s,statusCallback:d}=a;return p(async n=>{let o=await this.refNames.resolve(t,a);o!==void 0&&await l("Downloading bubbles",d,()=>this.bubbles.getLines(o,t.start,t.end,{signal:s,lineCallback:(h,A)=>{let e=g(h);n.next(new i({uniqueId:`bubble-${A}`,refName:t.refName,start:e.start,end:e.end,name:f(e),description:c(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}))}})),n.complete()},s)}};export{r as default};
+//# sourceMappingURL=MinigraphBubbleAdapter-OEOJKDBZ.js.map

package/dist/chunks/{RgfaTabixAdapter-QCQRXP4Z.js → RgfaTabixAdapter-Q2URYHKT.js}

@@ -1,3 +1,3 @@
-import{a as u,b as P,c as O}from"./chunk-PNHULAAZ.js";import{a as B,c as I,e as R,f as v}from"./chunk-ROD6PMOR.js";import{t as T}from"./chunk-BPN3IL3K.js";import"./chunk-WAGGHKBL.js";import"./chunk-D257CI4F.js";import"./chunk-OGQ6OQDN.js";import"./chunk-YBLNN5FU.js";import{c as F,f as M}from"./chunk-E2GK6JEL.js";import{a as $,o as A}from"./chunk-TENPGIPX.js";function y(i){let e=i.split("	"),a=e.length>=8,r=a?5:0;return{anchored:a,segment:{refName:e[r],start:+e[r+1],end:+e[r+2],id:e[3],rank:+e[4],tags:e[a?8:5]??""}}}function G(i){let e=i.tags.split(" ").find(r=>r.startsWith("SM:Z:"));if(e===void 0)return;let a=e.slice(5).split(",").map(r=>r.trim()).filter(Boolean);return a.length>0?a:void 0}function W(i){return{id:i.slice(0,-1),strand:i.slice(-1)}}function w(i){let e=i.split("	"),a=W(e[3]),r=W(e[4]);return{source:a.id,sourceStrand:a.strand,target:r.id,targetStrand:r.strand,sourceSegment:{id:a.id,refName:e[5],start:+e[6],end:+e[7],rank:+e[8],tags:e[13]??""},targetSegment:{id:r.id,refName:e[9],start:+e[10],end:+e[11],rank:+e[12],tags:e[14]??""}}}function S(i){return`${i.source}${i.sourceStrand}${i.target}${i.targetStrand}`}function Z(i,e,a){let r=n=>n.rank!==0||n.refName!==a.refName?0:n.end<=a.start?-1:n.start>=a.end?1:0,t=new Map(i),s=new Map;for(let n of e)if(i.has(n.source)||i.has(n.target)||r(n.sourceSegment)*r(n.targetSegment)===-1){s.set(S(n),n);for(let o of[n.sourceSegment,n.targetSegment])t.has(o.id)||t.set(o.id,o)}for(let n of e)t.has(n.source)&&t.has(n.target)&&s.set(S(n),n);return{segments:t,links:s}}function H(i,e,a){let r=t=>t.refName!==a.refName||t.end<=a.start||t.start>=a.end;return[...j(i.filter(t=>t.rank>0),e,a.end-a.start),...j(i.filter(t=>t.rank===0&&r(t)),new Set(i.map(t=>t.id)),0)]}function j(i,e,a){let r=[...i].sort((s,n)=>b(s.refName,n.refName)||s.start-n.start),t=[];for(let s of r){let n=t.at(-1);n?.refName===s.refName&&s.start-n.end<=a?(n.needed||=s.start>n.end||e.has(s.id),n.end=Math.max(n.end,s.end)):t.push({refName:s.refName,start:s.start,end:s.end,needed:e.has(s.id)})}return t.filter(s=>s.needed).map(({refName:s,start:n,end:o})=>({refName:s,start:n,end:o}))}function _(i,e,a){let r=t=>e.has(t.id)||a.some(s=>s.refName===t.refName&&t.start>=s.start&&t.end<=s.end);return i.filter(t=>r(t.sourceSegment)&&r(t.targetSegment))}var K=/^[A-Za-z][A-Za-z0-9]:[AifZJHB]:/;function z(i){let{id:e,refName:a,start:r,end:t,rank:s,tags:n}=i,o=n.split(" ").filter(f=>K.test(f)),c=o.length===0?"":`	${o.join("	")}`;return`S	${e}	*	LN:i:${t-r}	SN:Z:${a}	SO:i:${r}	SR:i:${s}${c}`}function J(i){let{source:e,sourceStrand:a,target:r,targetStrand:t}=i;return`L	${e}	${a}	${r}	${t}	0M`}function b(i,e){return i<e?-1:i>e?1:0}function L(i,e){let a=[...i.values()].sort((t,s)=>b(t.refName,s.refName)||t.start-s.start||b(t.id,s.id)),r=[...e.keys()].sort((t,s)=>b(t,s));return["H	VN:Z:1.0",...a.map(t=>z(t)),...r.map(t=>J(e.get(t)))].join(`
+import{a as u,b as P,c as O}from"./chunk-O5GO45MS.js";import{a as B,c as I,e as R,f as v}from"./chunk-AHE4Y2TX.js";import{t as T}from"./chunk-BPN3IL3K.js";import"./chunk-WAGGHKBL.js";import"./chunk-D257CI4F.js";import"./chunk-YBLNN5FU.js";import{c as F,f as M}from"./chunk-E2GK6JEL.js";import"./chunk-OGQ6OQDN.js";import{a as $,o as A}from"./chunk-TENPGIPX.js";function y(i){let e=i.split("	"),a=e.length>=8,r=a?5:0;return{anchored:a,segment:{refName:e[r],start:+e[r+1],end:+e[r+2],id:e[3],rank:+e[4],tags:e[a?8:5]??""}}}function G(i){let e=i.tags.split(" ").find(r=>r.startsWith("SM:Z:"));if(e===void 0)return;let a=e.slice(5).split(",").map(r=>r.trim()).filter(Boolean);return a.length>0?a:void 0}function W(i){return{id:i.slice(0,-1),strand:i.slice(-1)}}function w(i){let e=i.split("	"),a=W(e[3]),r=W(e[4]);return{source:a.id,sourceStrand:a.strand,target:r.id,targetStrand:r.strand,sourceSegment:{id:a.id,refName:e[5],start:+e[6],end:+e[7],rank:+e[8],tags:e[13]??""},targetSegment:{id:r.id,refName:e[9],start:+e[10],end:+e[11],rank:+e[12],tags:e[14]??""}}}function S(i){return`${i.source}${i.sourceStrand}${i.target}${i.targetStrand}`}function Z(i,e,a){let r=n=>n.rank!==0||n.refName!==a.refName?0:n.end<=a.start?-1:n.start>=a.end?1:0,t=new Map(i),s=new Map;for(let n of e)if(i.has(n.source)||i.has(n.target)||r(n.sourceSegment)*r(n.targetSegment)===-1){s.set(S(n),n);for(let o of[n.sourceSegment,n.targetSegment])t.has(o.id)||t.set(o.id,o)}for(let n of e)t.has(n.source)&&t.has(n.target)&&s.set(S(n),n);return{segments:t,links:s}}function H(i,e,a){let r=t=>t.refName!==a.refName||t.end<=a.start||t.start>=a.end;return[...j(i.filter(t=>t.rank>0),e,a.end-a.start),...j(i.filter(t=>t.rank===0&&r(t)),new Set(i.map(t=>t.id)),0)]}function j(i,e,a){let r=[...i].sort((s,n)=>b(s.refName,n.refName)||s.start-n.start),t=[];for(let s of r){let n=t.at(-1);n?.refName===s.refName&&s.start-n.end<=a?(n.needed||=s.start>n.end||e.has(s.id),n.end=Math.max(n.end,s.end)):t.push({refName:s.refName,start:s.start,end:s.end,needed:e.has(s.id)})}return t.filter(s=>s.needed).map(({refName:s,start:n,end:o})=>({refName:s,start:n,end:o}))}function _(i,e,a){let r=t=>e.has(t.id)||a.some(s=>s.refName===t.refName&&t.start>=s.start&&t.end<=s.end);return i.filter(t=>r(t.sourceSegment)&&r(t.targetSegment))}var K=/^[A-Za-z][A-Za-z0-9]:[AifZJHB]:/;function z(i){let{id:e,refName:a,start:r,end:t,rank:s,tags:n}=i,o=n.split(" ").filter(f=>K.test(f)),c=o.length===0?"":`	${o.join("	")}`;return`S	${e}	*	LN:i:${t-r}	SN:Z:${a}	SO:i:${r}	SR:i:${s}${c}`}function J(i){let{source:e,sourceStrand:a,target:r,targetStrand:t}=i;return`L	${e}	${a}	${r}	${t}	0M`}function b(i,e){return i<e?-1:i>e?1:0}function L(i,e){let a=[...i.values()].sort((t,s)=>b(t.refName,s.refName)||t.start-s.start||b(t.id,s.id)),r=[...e.keys()].sort((t,s)=>b(t,s));return["H	VN:Z:1.0",...a.map(t=>z(t)),...r.map(t=>J(e.get(t)))].join(`
 `)}function D(i){return i.filter(e=>e.rank>0)}var V=1e3,C=class extends B{static{this.capabilities=["getFeatures","getRefNames"]}constructor(e,a,r){super(e,a,r),this.fine=this.openIndex([])}openIndex(e){let a=R(this,[...e,"segmentsLocation"],[...e,"segmentsIndex"]),r=this.getConf("walksLocation"),t=e.length===0&&(!("uri"in r)||r.uri!==""),s=R(this,[...e,"linksLocation"],[...e,"linksIndex"]);return{segments:a,links:s,walks:t?new O({walks:R(this,["walksLocation"],["walksIndex"]),nodes:a,links:s},this.getConf("walkChunk")):void 0,refNames:new v(a,this)}}async getHaplotypeNames(e={}){let a=await this.fine.walks?.header(e);return a?.haplotypes.length?a.haplotypes:void 0}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 hasDataForRefName(){return!0}getFeatures(e,a={}){let{signal:r,statusCallback:t}=a;return I(async s=>{let n=await this.fine.refNames.resolve(e,a);if(n!==void 0){let o=this.fine.walks?await this.fine.walks.queryStart(e.start,a):e.start;await A("Downloading segments",t,()=>u(this.fine.segments,n,o,e.end,{signal:r,lineCallback:c=>{let{segment:f,anchored:h}=y(c);if(h&&f.refName!==n)return;let l=G(f);s.next(new $({uniqueId:f.id,refName:e.refName,start:f.start,end:f.end,name:f.id,type:"segment",rank:f.rank,stableName:f.refName,...l&&{samples:l,sampleCount:l.length}}))}}))}s.complete()},r)}async getSubgraph(e,a={}){let{hops:r=0,signal:t,tier:s}=a,n=this.index(s),o=new Map,c=new Map,f=await n.refNames.resolve(e,{signal:t}),h=async(p,m,g)=>{let d=[];return await u(n.links,p,m,g,{signal:t,lineCallback:E=>{let k=w(E);c.set(S(k),k);for(let N of[k.sourceSegment,k.targetSegment])o.has(N.id)||(o.set(N.id,N),d.push(N))}}),d};if(f===void 0)throw new Error(`${e.assemblyName} ${e.refName} is not in this graph's index; a graph with PanSN names (GRCh38#0#chr1) needs ${e.assemblyName} mapped to its prefix in assemblyNameToPanSN`);if(n.walks)return this.walkSubgraph(n.walks,f,e,a);let l={anchored:!1};if(await u(n.segments,f,e.start,e.end,{signal:t,lineCallback:p=>{let m=y(p);l.anchored||=m.anchored,o.set(m.segment.id,m.segment)}}),l.anchored){let p=[];await u(n.links,f,e.start,e.end,{signal:t,lineCallback:g=>{p.push(w(g))}});let m=Z(o,p,{refName:f,start:e.start,end:e.end});return L(m.segments,m.links)}let x=D(await h(f,e.start,e.end));for(let p=0;p<r;p++){let m=await Promise.all(x.map(g=>h(g.refName,g.start,g.end)));x=D(m.flat())}if(r>0){let p=H([...o.values()],new Set(x.map(g=>g.id)),{refName:f,start:e.start,end:e.end}),m=[];await Promise.all(p.map(g=>u(n.links,g.refName,g.start,g.end,{signal:t,lineCallback:d=>{m.push(w(d))}})));for(let g of _(m,o,p)){c.set(S(g),g);for(let d of[g.sourceSegment,g.targetSegment])o.has(d.id)||o.set(d.id,d)}}return L(o,c)}async walkSubgraph(e,a,r,t){let{graph:s,kept:n,fragments:o}=await e.cut(a,r,{signal:t.signal,keep:P(t.haplotypes?.map(c=>M(this,c)),F(a)),stepBudget:t.walkRows?1/0:this.getConf("walkStepBudget"),byteBudget:this.getConf("walkByteBudget"),context:V});return T(s.tables(n,o),r,t.walkRows)}};export{C as default};
-//# sourceMappingURL=RgfaTabixAdapter-QCQRXP4Z.js.map
+//# sourceMappingURL=RgfaTabixAdapter-Q2URYHKT.js.map

package/dist/chunks/{WalkTabixSyntenyAdapter-H7MKUBJ6.js → WalkTabixSyntenyAdapter-RXTCCCDB.js}

@@ -1,2 +1,2 @@
-import{b as O,c as D}from"./chunk-PNHULAAZ.js";import{a as _,b as q,d as j}from"./chunk-KX6CASVE.js";import{c as v,e as x,f as T}from"./chunk-ROD6PMOR.js";import{f as C,g as L,k as $,t as I}from"./chunk-BPN3IL3K.js";import"./chunk-WAGGHKBL.js";import"./chunk-D257CI4F.js";import"./chunk-OGQ6OQDN.js";import"./chunk-YBLNN5FU.js";import{a as S,c as P,d as F,e as A,f as N,g as W}from"./chunk-E2GK6JEL.js";import"./chunk-E7J6SB5P.js";import"./chunk-7WIBGKBU.js";import{o as R}from"./chunk-TENPGIPX.js";var Y=50;function Z(i){let e=[];for(let t=0;t<i.length;t++){let[r,s]=i[t],[a,n]=i[t+1]??[];s===n&&s<=Y&&(r==="I"&&a==="D"||r==="D"&&a==="I")?(e.push(["X",s]),t++):e.push([r,s])}return e}function ee(i){return i.map(([e,t])=>`${t}${e}`).join("")}function H(i){let e=new Map,t=a=>{let n=i.get(a),o=n===void 0?0:n.end-n.start,p=e.get(o);return p===void 0&&(p="N".repeat(o),e.set(o,p)),p},r=new Map,s=a=>{let n=r.get(a);return n===void 0&&(n=Array.from(a.ids,(o,p)=>2*o+a.rev[p]),r.set(a,n)),n};return(a,n)=>L({query:s(a),target:s(n),sequenceOf:t,bases:!1})}var te=100;function E(i,e,t){let r=i.at(-1);t>0&&(r?.[0]===e?r[1]+=t:i.push([e,t]))}function X(i){let e=s=>{let a=i.get(s>>1);return a===void 0?0:a.end-a.start},t=s=>{let a=new Float64Array(s.length+1);return s.forEach((n,o)=>{a[o+1]=a[o]+e(n)}),a},r=s=>Array.from(s.ids,(a,n)=>2*a+s.rev[n]);return(s,a)=>{let n=r(a),o=r(s),[p,g]=C(o,n,e),[f,l]=C(o.map(b=>b^1).reverse(),n,e),u=l>g,c=u?f:p,d=Math.max(g,l);if(d<te)return[];let h=t(n),m=t(o),y=b=>u?o.length-1-c[b][0]:c[b][0],w=[];c.forEach(([,b],k)=>{if(k>0){let[U,J]=[y(k-1),y(k)].sort((Q,V)=>Q-V);E(w,"I",m[J]-m[U+1]),E(w,"D",h[b]-h[c[k-1][1]+1])}E(w,"=",e(n[b]))});let[z,K]=[y(0),y(c.length-1)].sort((b,k)=>b-k);return[{queryStart:m[z],queryEnd:m[K+1],targetStart:h[c[0][1]],targetEnd:h[c.at(-1)[1]+1],strand:u?"-":"+",edits:w,sharedBases:d}]}}function M({chain:i,target:e,query:t,assemblyName:r,refName:s,mateAssemblyName:a}){let n=e.hapStart+i.targetStart,o=e.hapStart+i.targetEnd,p=t.hapStart+i.queryStart,g=t.hapStart+i.queryEnd,f=Z(i.edits),l=f.reduce((d,[h,m])=>d+(h==="="?m:0),0),u=f.reduce((d,[,h])=>d+h,0),c=`${e.name}:${n}-${o}|${t.name}:${p}-${g}`;return new _({uniqueId:c,assemblyName:r,refName:s,start:n,end:o,type:"match",strand:i.strand==="-"?-1:1,CIGAR:ee(f),syntenyId:c,identity:l/Math.max(u,1),numMatches:l,blockLen:u,mate:{refName:F(t.name),start:p,end:g,assemblyName:a}})}var ae=1e3;function G(i,e){return i[e]??i[S(e)]??e}var ne=i=>P(i.name)??i.name,B=class extends q{constructor(e,t,r){super(e,t,r);let s=x(this,["nodesLocation"],["nodesIndex"]);this.reader=new D({walks:x(this,["walksLocation"],["walksIndex"]),nodes:s,links:x(this,["linksLocation"],["linksIndex"])},this.getConf("walkChunk")),this.refNames=new T(s,this)}get anchor(){let e=this.getConf("assemblyNames")[0];if(e===void 0)throw new Error("WalkTabixSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");return e}async getHaplotypeNames(e={}){let{haplotypes:t}=await this.reader.header(e);return t.length>0?t:void 0}async getHeader(e={}){let{haplotypes:t,references:r}=await this.reader.header(e),{anchor:s}=this,a=N(this,s),n=W(this);return{hasCoarseTier:!1,anchorAssemblyName:s,referenceSamples:r,lanes:t.filter(o=>o!==a&&S(o)!==a).map(o=>({name:G(n,o),label:o,group:S(o)}))}}async getRefNames(e={}){let{assemblyName:t}=e;return t===void 0||t===this.anchor?this.refNames.assemblyRefNames({...e,assemblyName:this.anchor}):[]}budgets(e){return{stepBudget:e?1/0:this.getConf("walkStepBudget"),byteBudget:this.getConf("walkByteBudget"),context:ae}}async getSubgraph(e,t={}){let{signal:r,haplotypes:s,walkRows:a}=t,n=await this.refNames.resolve(e,{signal:r});if(n===void 0)throw new Error(`${e.assemblyName} ${e.refName} is not in this graph's index; the graph is cut on ${this.anchor}, mapped to its PanSN prefix in assemblyNameToPanSN`);let{graph:o,kept:p,fragments:g}=await this.reader.cut(n,e,{...this.budgets(a),signal:r,keep:O(s?.map(f=>N(this,f)),P(n))});return I(o.tables(p,g),e,a)}async laneWalks(e,t,r,s,a){return R(a,s.statusCallback,()=>this.reader.cut(e,t,{...this.budgets(),signal:s.signal,keep:O(r,P(e)),links:!1}).catch(n=>{throw n instanceof $&&(n.message=n.message.replace("to see the graph","to see lanes")),n}))}async anchorFeatures(e,t,r){let s=r.haplotypes?.length?r.haplotypes.map(m=>N(this,m)):void 0,a=N(this,r.targetAssemblyName),n=a===void 0?s:s===void 0||s.some(m=>A(a,m)||A(m,a))?[a]:[];if(n?.length===0)return[];let{start:o,end:p}=t,{graph:g,fragments:f}=await this.laneWalks(e,t,n,r,`Reading walks ${t.refName}:${o.toLocaleString()}-${p.toLocaleString()}`),l=X(g.nodes),u=W(this),c=f.filter(m=>m.name===e),d=m=>n===void 0?0:n.findIndex(y=>A(m.name,y));return f.filter(m=>m.name!==e&&d(m)>=0).sort((m,y)=>d(m)-d(y)).flatMap(m=>c.flatMap(y=>l(m,y).map(w=>M({chain:w,target:y,query:m,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:G(u,ne(m))}))))}async pairFeatures(e,t,r,s){let[a]=r,n=r.map(l=>({pair:l,featurePrefix:N(this,l.queryAssemblyName),matePrefix:N(this,l.targetAssemblyName)})),{graph:o,fragments:p}=await this.laneWalks(e,t,n.flatMap(l=>[l.featurePrefix,l.matePrefix]),s,r.length===1&&a?`Reading ${a.queryAssemblyName} against ${a.targetAssemblyName}`:`Reading ${r.length} lane pairs`),g=H(o.nodes),f=l=>p.filter(u=>A(u.name,l));return n.flatMap(({pair:l,featurePrefix:u,matePrefix:c})=>f(u).flatMap(d=>f(c).flatMap(h=>g(h,d).map(m=>M({chain:m,target:d,query:h,assemblyName:l.queryAssemblyName,refName:F(d.name),mateAssemblyName:l.targetAssemblyName})))))}getFeatures(e,t={}){return v(async r=>{let s=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(s!==void 0){let a=j(t),n=a.length>0?await this.pairFeatures(s,e,a,t):await this.anchorFeatures(s,e,t);for(let o of n)r.next(o)}r.complete()},t.signal)}};export{B as default,G as laneOf};
-//# sourceMappingURL=WalkTabixSyntenyAdapter-H7MKUBJ6.js.map
+import{b as O,c as D}from"./chunk-O5GO45MS.js";import{a as _,b as q,d as j}from"./chunk-W7UGHWWS.js";import{c as v,e as x,f as T}from"./chunk-AHE4Y2TX.js";import{f as C,g as L,k as $,t as I}from"./chunk-BPN3IL3K.js";import"./chunk-WAGGHKBL.js";import"./chunk-D257CI4F.js";import"./chunk-YBLNN5FU.js";import{a as S,c as P,d as F,e as A,f as N,g as W}from"./chunk-E2GK6JEL.js";import"./chunk-E7J6SB5P.js";import"./chunk-7WIBGKBU.js";import"./chunk-OGQ6OQDN.js";import{o as R}from"./chunk-TENPGIPX.js";var Y=50;function Z(i){let e=[];for(let t=0;t<i.length;t++){let[r,s]=i[t],[a,n]=i[t+1]??[];s===n&&s<=Y&&(r==="I"&&a==="D"||r==="D"&&a==="I")?(e.push(["X",s]),t++):e.push([r,s])}return e}function ee(i){return i.map(([e,t])=>`${t}${e}`).join("")}function H(i){let e=new Map,t=a=>{let n=i.get(a),o=n===void 0?0:n.end-n.start,p=e.get(o);return p===void 0&&(p="N".repeat(o),e.set(o,p)),p},r=new Map,s=a=>{let n=r.get(a);return n===void 0&&(n=Array.from(a.ids,(o,p)=>2*o+a.rev[p]),r.set(a,n)),n};return(a,n)=>L({query:s(a),target:s(n),sequenceOf:t,bases:!1})}var te=100;function E(i,e,t){let r=i.at(-1);t>0&&(r?.[0]===e?r[1]+=t:i.push([e,t]))}function X(i){let e=s=>{let a=i.get(s>>1);return a===void 0?0:a.end-a.start},t=s=>{let a=new Float64Array(s.length+1);return s.forEach((n,o)=>{a[o+1]=a[o]+e(n)}),a},r=s=>Array.from(s.ids,(a,n)=>2*a+s.rev[n]);return(s,a)=>{let n=r(a),o=r(s),[p,g]=C(o,n,e),[f,l]=C(o.map(b=>b^1).reverse(),n,e),u=l>g,c=u?f:p,d=Math.max(g,l);if(d<te)return[];let h=t(n),m=t(o),y=b=>u?o.length-1-c[b][0]:c[b][0],w=[];c.forEach(([,b],k)=>{if(k>0){let[U,J]=[y(k-1),y(k)].sort((Q,V)=>Q-V);E(w,"I",m[J]-m[U+1]),E(w,"D",h[b]-h[c[k-1][1]+1])}E(w,"=",e(n[b]))});let[z,K]=[y(0),y(c.length-1)].sort((b,k)=>b-k);return[{queryStart:m[z],queryEnd:m[K+1],targetStart:h[c[0][1]],targetEnd:h[c.at(-1)[1]+1],strand:u?"-":"+",edits:w,sharedBases:d}]}}function M({chain:i,target:e,query:t,assemblyName:r,refName:s,mateAssemblyName:a}){let n=e.hapStart+i.targetStart,o=e.hapStart+i.targetEnd,p=t.hapStart+i.queryStart,g=t.hapStart+i.queryEnd,f=Z(i.edits),l=f.reduce((d,[h,m])=>d+(h==="="?m:0),0),u=f.reduce((d,[,h])=>d+h,0),c=`${e.name}:${n}-${o}|${t.name}:${p}-${g}`;return new _({uniqueId:c,assemblyName:r,refName:s,start:n,end:o,type:"match",strand:i.strand==="-"?-1:1,CIGAR:ee(f),syntenyId:c,identity:l/Math.max(u,1),numMatches:l,blockLen:u,mate:{refName:F(t.name),start:p,end:g,assemblyName:a}})}var ae=1e3;function G(i,e){return i[e]??i[S(e)]??e}var ne=i=>P(i.name)??i.name,B=class extends q{constructor(e,t,r){super(e,t,r);let s=x(this,["nodesLocation"],["nodesIndex"]);this.reader=new D({walks:x(this,["walksLocation"],["walksIndex"]),nodes:s,links:x(this,["linksLocation"],["linksIndex"])},this.getConf("walkChunk")),this.refNames=new T(s,this)}get anchor(){let e=this.getConf("assemblyNames")[0];if(e===void 0)throw new Error("WalkTabixSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");return e}async getHaplotypeNames(e={}){let{haplotypes:t}=await this.reader.header(e);return t.length>0?t:void 0}async getHeader(e={}){let{haplotypes:t,references:r}=await this.reader.header(e),{anchor:s}=this,a=N(this,s),n=W(this);return{hasCoarseTier:!1,anchorAssemblyName:s,referenceSamples:r,lanes:t.filter(o=>o!==a&&S(o)!==a).map(o=>({name:G(n,o),label:o,group:S(o)}))}}async getRefNames(e={}){let{assemblyName:t}=e;return t===void 0||t===this.anchor?this.refNames.assemblyRefNames({...e,assemblyName:this.anchor}):[]}budgets(e){return{stepBudget:e?1/0:this.getConf("walkStepBudget"),byteBudget:this.getConf("walkByteBudget"),context:ae}}async getSubgraph(e,t={}){let{signal:r,haplotypes:s,walkRows:a}=t,n=await this.refNames.resolve(e,{signal:r});if(n===void 0)throw new Error(`${e.assemblyName} ${e.refName} is not in this graph's index; the graph is cut on ${this.anchor}, mapped to its PanSN prefix in assemblyNameToPanSN`);let{graph:o,kept:p,fragments:g}=await this.reader.cut(n,e,{...this.budgets(a),signal:r,keep:O(s?.map(f=>N(this,f)),P(n))});return I(o.tables(p,g),e,a)}async laneWalks(e,t,r,s,a){return R(a,s.statusCallback,()=>this.reader.cut(e,t,{...this.budgets(),signal:s.signal,keep:O(r,P(e)),links:!1}).catch(n=>{throw n instanceof $&&(n.message=n.message.replace("to see the graph","to see lanes")),n}))}async anchorFeatures(e,t,r){let s=r.haplotypes?.length?r.haplotypes.map(m=>N(this,m)):void 0,a=N(this,r.targetAssemblyName),n=a===void 0?s:s===void 0||s.some(m=>A(a,m)||A(m,a))?[a]:[];if(n?.length===0)return[];let{start:o,end:p}=t,{graph:g,fragments:f}=await this.laneWalks(e,t,n,r,`Reading walks ${t.refName}:${o.toLocaleString()}-${p.toLocaleString()}`),l=X(g.nodes),u=W(this),c=f.filter(m=>m.name===e),d=m=>n===void 0?0:n.findIndex(y=>A(m.name,y));return f.filter(m=>m.name!==e&&d(m)>=0).sort((m,y)=>d(m)-d(y)).flatMap(m=>c.flatMap(y=>l(m,y).map(w=>M({chain:w,target:y,query:m,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:G(u,ne(m))}))))}async pairFeatures(e,t,r,s){let[a]=r,n=r.map(l=>({pair:l,featurePrefix:N(this,l.queryAssemblyName),matePrefix:N(this,l.targetAssemblyName)})),{graph:o,fragments:p}=await this.laneWalks(e,t,n.flatMap(l=>[l.featurePrefix,l.matePrefix]),s,r.length===1&&a?`Reading ${a.queryAssemblyName} against ${a.targetAssemblyName}`:`Reading ${r.length} lane pairs`),g=H(o.nodes),f=l=>p.filter(u=>A(u.name,l));return n.flatMap(({pair:l,featurePrefix:u,matePrefix:c})=>f(u).flatMap(d=>f(c).flatMap(h=>g(h,d).map(m=>M({chain:m,target:d,query:h,assemblyName:l.queryAssemblyName,refName:F(d.name),mateAssemblyName:l.targetAssemblyName})))))}getFeatures(e,t={}){return v(async r=>{let s=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(s!==void 0){let a=j(t),n=a.length>0?await this.pairFeatures(s,e,a,t):await this.anchorFeatures(s,e,t);for(let o of n)r.next(o)}r.complete()},t.signal)}};export{B as default,G as laneOf};
+//# sourceMappingURL=WalkTabixSyntenyAdapter-RXTCCCDB.js.map

package/dist/chunks/chunk-2I4VPDLZ.js

@@ -0,0 +1,2 @@
+import{b as o,c as p,d as s}from"./chunk-R3TRNF7N.js";import{b as u}from"./chunk-7WIBGKBU.js";import{a as x}from"./chunk-OGQ6OQDN.js";var B=".segs.bed.gz",G=5e3;function L(e){return typeof e=="string"&&/^[\w+-][\w.+-]*$/.test(e)}function b(e){return e==null}function S(e){return typeof e=="object"&&e!==null&&!Array.isArray(e)}function F(e){return S(e)&&L(e.prefix)&&typeof e.foldBelowBp=="number"&&Number.isFinite(e.foldBelowBp)&&e.foldBelowBp>0}function T(e){let n;try{n=JSON.parse(e)}catch{return}if(!S(n)||n.schema!==1)return;let{reference:i,tier:t,index:r,contig:a,bubbles:d,alleles:l}=n;if((b(i)||typeof i=="string"&&i.trim()!=="")&&(b(t)||F(t))&&[r,a,d,l].every(y=>b(y)||L(y)))return{...typeof i=="string"?{reference:i.trim()}:{},...F(t)?{tier:{prefix:t.prefix,foldBelowBp:t.foldBelowBp}}:{}}}function g(e,n){return s(e,i=>i.replace(/[^/\\]*$/,n))}function M(e){let n=o(e);return p(e)&&n.endsWith(B)?s(e,i=>`${i.slice(0,-B.length)}.graph.json`):void 0}async function D(e,n){let i=M(e);if(i)try{let t=await x(i,n).readFile({encoding:"utf8",signal:AbortSignal.timeout(G)});return T(t)}catch{return}}var H={RgfaTabixAdapter:"rGFA segments (tabix BED pair)",GbzBaseSyntenyAdapter:"GBZ database (.gbz.db)",MinigraphBubbleAdapter:"Minigraph bubbles (tabix BED)"},W={RgfaTabixAdapter:"Path to segments BED (.segs.bed.gz from gfa-to-tabix; the .links.bed.gz, its index and any .graph.json are read beside it)",GbzBaseSyntenyAdapter:"Path to the .gbz.db written by gbz-base construct",MinigraphBubbleAdapter:"Path to bubbles BED (.bed.gz from gfatools bubble)"},A="Path to tabix index (optional; the sibling .tbi is assumed, a .csi is recognised by name)",U={RgfaTabixAdapter:A,GbzBaseSyntenyAdapter:"Path to the haplotype index (optional; graph.haplotype-index.db beside the database is assumed)",MinigraphBubbleAdapter:A},c=".segs.bed.gz";function f(e,n){return s(e,i=>i+n)}function O(e){return p(e)&&o(e).endsWith(c)}function w(e){if(!o(e).endsWith(c))throw new Error(`Expected a segments BED ending in ${c}, got ${o(e)}`);return s(e,n=>`${n.slice(0,-c.length)}.links.bed.gz`)}function I(e,n){return n?{location:n,indexType:u(o(n),"CSI","TBI")}:{location:f(e,".tbi"),indexType:"TBI"}}function m(e,n){return n!==void 0&&u(o(n),"CSI","TBI")==="CSI"?{location:f(e,".csi"),indexType:"CSI"}:{location:f(e,".tbi"),indexType:"TBI"}}function h(e,n){let i=n.trim();return i?{assemblyNameToPanSN:{[e]:i}}:{}}function k(e,n,i){if(!i)return{};let t=g(e,`${i.prefix}${c}`),r=g(e,`${i.prefix}.links.bed.gz`);return{coarse:{foldBelowBp:i.foldBelowBp,segmentsLocation:t,segmentsIndex:m(t,n),linksLocation:r,linksIndex:m(r,n)}}}function E(e,n,i){let t=i===e?void 0:i;return h(e,n.trim()||t||"")}function z(e){return e?{readsLocation:e,...o(e).endsWith(".gz")&&p(e)?{readsIndex:{location:f(e,".tbi")}}:{}}:{}}function N({choice:e,loc:n,indexLoc:i,readsLoc:t,manifest:r,assembly:a,sample:d}){if(e==="GbzBaseSyntenyAdapter")return{type:"GbzBaseSyntenyAdapter",gbzDbLocation:n,...i?{haplotypeIndexLocation:i}:{},assemblyNames:[a],...z(t),...h(a,d)};if(e==="MinigraphBubbleAdapter")return{type:"MinigraphBubbleAdapter",bubblesLocation:n,index:I(n,i),...h(a,d)};let l=w(n);return{type:"RgfaTabixAdapter",segmentsLocation:n,segmentsIndex:I(n,i),linksLocation:l,linksIndex:m(l,i),...E(a,d,r?.reference),...k(n,i,r?.tier)}}function v(e){let{choice:n,assembly:i,trackId:t,name:r}=e;return{type:n==="MinigraphBubbleAdapter"?"FeatureTrack":"GraphTrack",trackId:t,name:r,assemblyNames:[i],adapter:N(e),...n==="RgfaTabixAdapter"?{displayDefaults:{showLabels:"none"}}:{}}}export{D as a,H as b,W as c,U as d,O as e,N as f,v as g};
+//# sourceMappingURL=chunk-2I4VPDLZ.js.map

package/dist/chunks/chunk-2I4VPDLZ.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/GraphAddTrackWorkflow/graphManifest.ts", "../../src/GraphAddTrackWorkflow/buildTrackConfig.ts"],
+  "sourcesContent": ["import { openLocation } from '@jbrowse/core/util/io'\n\nimport { locationName, readsSiblings, renamed } from '../locationName'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { FileLocation } from '@jbrowse/core/util'\n\n// The part of `<prefix>.graph.json`, written by `gfa-to-tabix build`, that\n// Open track reads\nexport interface GraphManifest {\n  reference?: string\n  tier?: { prefix: string; foldBelowBp: number }\n}\n\nconst SEGMENTS_SUFFIX = '.segs.bed.gz'\nconst FETCH_TIMEOUT_MS = 5000\n\n// A bare file name beside the manifest: no directory, scheme or leading dot\nfunction isSiblingName(name: unknown): name is string {\n  return typeof name === 'string' && /^[\\w+-][\\w.+-]*$/.test(name)\n}\n\nfunction isAbsent(value: unknown) {\n  return value === undefined || value === null\n}\n\nfunction isRecord(value: unknown): value is Record<string, unknown> {\n  return typeof value === 'object' && value !== null && !Array.isArray(value)\n}\n\nfunction isTier(tier: unknown): tier is NonNullable<GraphManifest['tier']> {\n  return (\n    isRecord(tier) &&\n    isSiblingName(tier.prefix) &&\n    typeof tier.foldBelowBp === 'number' &&\n    Number.isFinite(tier.foldBelowBp) &&\n    tier.foldBelowBp > 0\n  )\n}\n\nexport function parseGraphManifest(text: string): GraphManifest | undefined {\n  let json: unknown\n  try {\n    json = JSON.parse(text)\n  } catch {\n    return undefined\n  }\n  if (!isRecord(json) || json.schema !== 1) {\n    return undefined\n  }\n  const { reference, tier, index, contig, bubbles, alleles } = json\n  const valid =\n    (isAbsent(reference) ||\n      (typeof reference === 'string' && reference.trim() !== '')) &&\n    (isAbsent(tier) || isTier(tier)) &&\n    [index, contig, bubbles, alleles].every(\n      f => isAbsent(f) || isSiblingName(f),\n    )\n  if (!valid) {\n    return undefined\n  }\n  return {\n    ...(typeof reference === 'string' ? { reference: reference.trim() } : {}),\n    ...(isTier(tier)\n      ? { tier: { prefix: tier.prefix, foldBelowBp: tier.foldBelowBp } }\n      : {}),\n  }\n}\n\n// A file the manifest names, in the directory of the segments file opened\nexport function besideSegments(segs: FileLocation, fileName: string) {\n  return renamed(segs, name => name.replace(/[^/\\\\]*$/, fileName))\n}\n\nexport function manifestLocation(segs: FileLocation) {\n  const name = locationName(segs)\n  return readsSiblings(segs) && name.endsWith(SEGMENTS_SUFFIX)\n    ? renamed(segs, n => `${n.slice(0, -SEGMENTS_SUFFIX.length)}.graph.json`)\n    : undefined\n}\n\n// Undefined for a manifest that is missing, unreadable or not schema 1, so\n// Open track falls back to the files beside the segments alone\nexport async function readGraphManifest(\n  segs: FileLocation,\n  pluginManager?: PluginManager,\n) {\n  const loc = manifestLocation(segs)\n  if (!loc) {\n    return undefined\n  }\n  try {\n    const text = await openLocation(loc, pluginManager).readFile({\n      encoding: 'utf8',\n      signal: AbortSignal.timeout(FETCH_TIMEOUT_MS),\n    })\n    return parseGraphManifest(text)\n  } catch {\n    return undefined\n  }\n}\n", "import { makeIndexType } from '@jbrowse/core/util/tracks'\n\nimport { besideSegments } from './graphManifest'\nimport { locationName, readsSiblings, renamed } from '../locationName'\n\nimport type { GraphManifest } from './graphManifest'\nimport type { FileLocation } from '@jbrowse/core/util'\n\nexport type GraphFileChoice =\n  'RgfaTabixAdapter' | 'GbzBaseSyntenyAdapter' | 'MinigraphBubbleAdapter'\n\nexport const GRAPH_FILE_LABELS: Record<GraphFileChoice, string> = {\n  RgfaTabixAdapter: 'rGFA segments (tabix BED pair)',\n  GbzBaseSyntenyAdapter: 'GBZ database (.gbz.db)',\n  MinigraphBubbleAdapter: 'Minigraph bubbles (tabix BED)',\n}\n\nexport const GRAPH_FILE_FIELDS: Record<GraphFileChoice, string> = {\n  RgfaTabixAdapter:\n    'Path to segments BED (.segs.bed.gz from gfa-to-tabix; the .links.bed.gz, its index and any .graph.json are read beside it)',\n  GbzBaseSyntenyAdapter: 'Path to the .gbz.db written by gbz-base construct',\n  MinigraphBubbleAdapter: 'Path to bubbles BED (.bed.gz from gfatools bubble)',\n}\n\nconst TABIX_INDEX_FIELD =\n  'Path to tabix index (optional; the sibling .tbi is assumed, a .csi is recognised by name)'\n\nexport const GRAPH_INDEX_FIELDS: Record<GraphFileChoice, string> = {\n  RgfaTabixAdapter: TABIX_INDEX_FIELD,\n  GbzBaseSyntenyAdapter:\n    'Path to the haplotype index (optional; graph.haplotype-index.db beside the database is assumed)',\n  MinigraphBubbleAdapter: TABIX_INDEX_FIELD,\n}\n\nconst SEGMENTS_SUFFIX = '.segs.bed.gz'\n\nfunction sibling(loc: FileLocation, suffix: string) {\n  return renamed(loc, name => name + suffix)\n}\n\n// A segments BED the links BED can be found beside\nexport function isSegmentsLocation(loc: FileLocation) {\n  return readsSiblings(loc) && locationName(loc).endsWith(SEGMENTS_SUFFIX)\n}\n\nfunction linksLocation(loc: FileLocation) {\n  if (!locationName(loc).endsWith(SEGMENTS_SUFFIX)) {\n    throw new Error(\n      `Expected a segments BED ending in ${SEGMENTS_SUFFIX}, got ${locationName(loc)}`,\n    )\n  }\n  return renamed(\n    loc,\n    name => `${name.slice(0, -SEGMENTS_SUFFIX.length)}.links.bed.gz`,\n  )\n}\n\nfunction tabixIndex(loc: FileLocation, indexLoc: FileLocation | undefined) {\n  return indexLoc\n    ? {\n        location: indexLoc,\n        indexType: makeIndexType(locationName(indexLoc), 'CSI', 'TBI'),\n      }\n    : { location: sibling(loc, '.tbi'), indexType: 'TBI' }\n}\n\n// The links file's index is assumed beside it, of the kind the segments' is.\nfunction siblingIndex(loc: FileLocation, indexLoc: FileLocation | undefined) {\n  const csi =\n    indexLoc !== undefined &&\n    makeIndexType(locationName(indexLoc), 'CSI', 'TBI') === 'CSI'\n  return csi\n    ? { location: sibling(loc, '.csi'), indexType: 'CSI' }\n    : { location: sibling(loc, '.tbi'), indexType: 'TBI' }\n}\n\nfunction panSN(assembly: string, sample: string) {\n  const name = sample.trim()\n  return name ? { assemblyNameToPanSN: { [assembly]: name } } : {}\n}\n\nfunction coarseTier(\n  loc: FileLocation,\n  indexLoc: FileLocation | undefined,\n  tier: GraphManifest['tier'],\n) {\n  if (!tier) {\n    return {}\n  }\n  const segs = besideSegments(loc, `${tier.prefix}${SEGMENTS_SUFFIX}`)\n  const links = besideSegments(loc, `${tier.prefix}.links.bed.gz`)\n  return {\n    coarse: {\n      foldBelowBp: tier.foldBelowBp,\n      segmentsLocation: segs,\n      segmentsIndex: siblingIndex(segs, indexLoc),\n      linksLocation: links,\n      linksIndex: siblingIndex(links, indexLoc),\n    },\n  }\n}\n\n// The user's sample wins; the manifest's reference stands in when blank\nfunction manifestPanSN(\n  assembly: string,\n  sample: string,\n  reference: string | undefined,\n) {\n  const fromManifest = reference === assembly ? undefined : reference\n  return panSN(assembly, sample.trim() || fromManifest || '')\n}\n\n// a bgzipped GAF is read by its tabix index, a plain one whole\nfunction readsConfig(readsLoc: FileLocation | undefined) {\n  return readsLoc\n    ? {\n        readsLocation: readsLoc,\n        ...(locationName(readsLoc).endsWith('.gz') && readsSiblings(readsLoc)\n          ? { readsIndex: { location: sibling(readsLoc, '.tbi') } }\n          : {}),\n      }\n    : {}\n}\n\nexport function buildAdapterConfig({\n  choice,\n  loc,\n  indexLoc,\n  readsLoc,\n  manifest,\n  assembly,\n  sample,\n}: {\n  choice: GraphFileChoice\n  loc: FileLocation\n  indexLoc: FileLocation | undefined\n  // a GBZ track's GAF reads, which no other choice takes\n  readsLoc?: FileLocation\n  // the `.graph.json` beside an rGFA segments file\n  manifest?: GraphManifest\n  assembly: string\n  sample: string\n}) {\n  if (choice === 'GbzBaseSyntenyAdapter') {\n    return {\n      type: 'GbzBaseSyntenyAdapter',\n      gbzDbLocation: loc,\n      ...(indexLoc ? { haplotypeIndexLocation: indexLoc } : {}),\n      assemblyNames: [assembly],\n      ...readsConfig(readsLoc),\n      ...panSN(assembly, sample),\n    }\n  }\n  if (choice === 'MinigraphBubbleAdapter') {\n    return {\n      type: 'MinigraphBubbleAdapter',\n      bubblesLocation: loc,\n      index: tabixIndex(loc, indexLoc),\n      ...panSN(assembly, sample),\n    }\n  }\n  const links = linksLocation(loc)\n  return {\n    type: 'RgfaTabixAdapter',\n    segmentsLocation: loc,\n    segmentsIndex: tabixIndex(loc, indexLoc),\n    linksLocation: links,\n    linksIndex: siblingIndex(links, indexLoc),\n    ...manifestPanSN(assembly, sample, manifest?.reference),\n    ...coarseTier(loc, indexLoc, manifest?.tier),\n  }\n}\n\nexport function buildTrackConfig(args: {\n  choice: GraphFileChoice\n  loc: FileLocation\n  indexLoc: FileLocation | undefined\n  readsLoc?: FileLocation\n  manifest?: GraphManifest\n  assembly: string\n  sample: string\n  trackId: string\n  name: string\n}) {\n  const { choice, assembly, trackId, name } = args\n  return {\n    type: choice === 'MinigraphBubbleAdapter' ? 'FeatureTrack' : 'GraphTrack',\n    trackId,\n    name,\n    assemblyNames: [assembly],\n    adapter: buildAdapterConfig(args),\n    ...(choice === 'RgfaTabixAdapter'\n      ? { displayDefaults: { showLabels: 'none' } }\n      : {}),\n  }\n}\n"],
+  "mappings": "sIAcA,IAAMA,EAAkB,eAClBC,EAAmB,IAGzB,SAASC,EAAcC,EAA+B,CACpD,OAAO,OAAOA,GAAS,UAAY,mBAAmB,KAAKA,CAAI,CACjE,CAEA,SAASC,EAASC,EAAgB,CAChC,OAA8BA,GAAU,IAC1C,CAEA,SAASC,EAASD,EAAkD,CAClE,OAAO,OAAOA,GAAU,UAAYA,IAAU,MAAQ,CAAC,MAAM,QAAQA,CAAK,CAC5E,CAEA,SAASE,EAAOC,EAA2D,CACzE,OACEF,EAASE,CAAI,GACbN,EAAcM,EAAK,MAAM,GACzB,OAAOA,EAAK,aAAgB,UAC5B,OAAO,SAASA,EAAK,WAAW,GAChCA,EAAK,YAAc,CAEvB,CAEO,SAASC,EAAmBC,EAAyC,CAC1E,IAAIC,EACJ,GAAI,CACFA,EAAO,KAAK,MAAMD,CAAI,CACxB,MAAQ,CACN,MACF,CACA,GAAI,CAACJ,EAASK,CAAI,GAAKA,EAAK,SAAW,EACrC,OAEF,GAAM,CAAE,UAAAC,EAAW,KAAAJ,EAAM,MAAAK,EAAO,OAAAC,EAAQ,QAAAC,EAAS,QAAAC,CAAQ,EAAIL,EAQ7D,IANGP,EAASQ,CAAS,GAChB,OAAOA,GAAc,UAAYA,EAAU,KAAK,IAAM,MACxDR,EAASI,CAAI,GAAKD,EAAOC,CAAI,IAC9B,CAACK,EAAOC,EAAQC,EAASC,CAAO,EAAE,MAChCC,GAAKb,EAASa,CAAC,GAAKf,EAAce,CAAC,CACrC,EAIF,MAAO,CACL,GAAI,OAAOL,GAAc,SAAW,CAAE,UAAWA,EAAU,KAAK,CAAE,EAAI,CAAC,EACvE,GAAIL,EAAOC,CAAI,EACX,CAAE,KAAM,CAAE,OAAQA,EAAK,OAAQ,YAAaA,EAAK,WAAY,CAAE,EAC/D,CAAC,CACP,CACF,CAGO,SAASU,EAAeC,EAAoBC,EAAkB,CACnE,OAAOC,EAAQF,EAAMhB,GAAQA,EAAK,QAAQ,WAAYiB,CAAQ,CAAC,CACjE,CAEO,SAASE,EAAiBH,EAAoB,CACnD,IAAMhB,EAAOoB,EAAaJ,CAAI,EAC9B,OAAOK,EAAcL,CAAI,GAAKhB,EAAK,SAASH,CAAe,EACvDqB,EAAQF,EAAMM,GAAK,GAAGA,EAAE,MAAM,EAAG,CAACzB,EAAgB,MAAM,CAAC,aAAa,EACtE,MACN,CAIA,eAAsB0B,EACpBP,EACAQ,EACA,CACA,IAAMC,EAAMN,EAAiBH,CAAI,EACjC,GAAKS,EAGL,GAAI,CACF,IAAMlB,EAAO,MAAMmB,EAAaD,EAAKD,CAAa,EAAE,SAAS,CAC3D,SAAU,OACV,OAAQ,YAAY,QAAQ1B,CAAgB,CAC9C,CAAC,EACD,OAAOQ,EAAmBC,CAAI,CAChC,MAAQ,CACN,MACF,CACF,CCzFO,IAAMoB,EAAqD,CAChE,iBAAkB,iCAClB,sBAAuB,yBACvB,uBAAwB,+BAC1B,EAEaC,EAAqD,CAChE,iBACE,6HACF,sBAAuB,oDACvB,uBAAwB,oDAC1B,EAEMC,EACJ,4FAEWC,EAAsD,CACjE,iBAAkBD,EAClB,sBACE,kGACF,uBAAwBA,CAC1B,EAEME,EAAkB,eAExB,SAASC,EAAQC,EAAmBC,EAAgB,CAClD,OAAOC,EAAQF,EAAKG,GAAQA,EAAOF,CAAM,CAC3C,CAGO,SAASG,EAAmBJ,EAAmB,CACpD,OAAOK,EAAcL,CAAG,GAAKM,EAAaN,CAAG,EAAE,SAASF,CAAe,CACzE,CAEA,SAASS,EAAcP,EAAmB,CACxC,GAAI,CAACM,EAAaN,CAAG,EAAE,SAASF,CAAe,EAC7C,MAAM,IAAI,MACR,qCAAqCA,CAAe,SAASQ,EAAaN,CAAG,CAAC,EAChF,EAEF,OAAOE,EACLF,EACAG,GAAQ,GAAGA,EAAK,MAAM,EAAG,CAACL,EAAgB,MAAM,CAAC,eACnD,CACF,CAEA,SAASU,EAAWR,EAAmBS,EAAoC,CACzE,OAAOA,EACH,CACE,SAAUA,EACV,UAAWC,EAAcJ,EAAaG,CAAQ,EAAG,MAAO,KAAK,CAC/D,EACA,CAAE,SAAUV,EAAQC,EAAK,MAAM,EAAG,UAAW,KAAM,CACzD,CAGA,SAASW,EAAaX,EAAmBS,EAAoC,CAI3E,OAFEA,IAAa,QACbC,EAAcJ,EAAaG,CAAQ,EAAG,MAAO,KAAK,IAAM,MAEtD,CAAE,SAAUV,EAAQC,EAAK,MAAM,EAAG,UAAW,KAAM,EACnD,CAAE,SAAUD,EAAQC,EAAK,MAAM,EAAG,UAAW,KAAM,CACzD,CAEA,SAASY,EAAMC,EAAkBC,EAAgB,CAC/C,IAAMX,EAAOW,EAAO,KAAK,EACzB,OAAOX,EAAO,CAAE,oBAAqB,CAAE,CAACU,CAAQ,EAAGV,CAAK,CAAE,EAAI,CAAC,CACjE,CAEA,SAASY,EACPf,EACAS,EACAO,EACA,CACA,GAAI,CAACA,EACH,MAAO,CAAC,EAEV,IAAMC,EAAOC,EAAelB,EAAK,GAAGgB,EAAK,MAAM,GAAGlB,CAAe,EAAE,EAC7DqB,EAAQD,EAAelB,EAAK,GAAGgB,EAAK,MAAM,eAAe,EAC/D,MAAO,CACL,OAAQ,CACN,YAAaA,EAAK,YAClB,iBAAkBC,EAClB,cAAeN,EAAaM,EAAMR,CAAQ,EAC1C,cAAeU,EACf,WAAYR,EAAaQ,EAAOV,CAAQ,CAC1C,CACF,CACF,CAGA,SAASW,EACPP,EACAC,EACAO,EACA,CACA,IAAMC,EAAeD,IAAcR,EAAW,OAAYQ,EAC1D,OAAOT,EAAMC,EAAUC,EAAO,KAAK,GAAKQ,GAAgB,EAAE,CAC5D,CAGA,SAASC,EAAYC,EAAoC,CACvD,OAAOA,EACH,CACE,cAAeA,EACf,GAAIlB,EAAakB,CAAQ,EAAE,SAAS,KAAK,GAAKnB,EAAcmB,CAAQ,EAChE,CAAE,WAAY,CAAE,SAAUzB,EAAQyB,EAAU,MAAM,CAAE,CAAE,EACtD,CAAC,CACP,EACA,CAAC,CACP,CAEO,SAASC,EAAmB,CACjC,OAAAC,EACA,IAAA1B,EACA,SAAAS,EACA,SAAAe,EACA,SAAAG,EACA,SAAAd,EACA,OAAAC,CACF,EAUG,CACD,GAAIY,IAAW,wBACb,MAAO,CACL,KAAM,wBACN,cAAe1B,EACf,GAAIS,EAAW,CAAE,uBAAwBA,CAAS,EAAI,CAAC,EACvD,cAAe,CAACI,CAAQ,EACxB,GAAGU,EAAYC,CAAQ,EACvB,GAAGZ,EAAMC,EAAUC,CAAM,CAC3B,EAEF,GAAIY,IAAW,yBACb,MAAO,CACL,KAAM,yBACN,gBAAiB1B,EACjB,MAAOQ,EAAWR,EAAKS,CAAQ,EAC/B,GAAGG,EAAMC,EAAUC,CAAM,CAC3B,EAEF,IAAMK,EAAQZ,EAAcP,CAAG,EAC/B,MAAO,CACL,KAAM,mBACN,iBAAkBA,EAClB,cAAeQ,EAAWR,EAAKS,CAAQ,EACvC,cAAeU,EACf,WAAYR,EAAaQ,EAAOV,CAAQ,EACxC,GAAGW,EAAcP,EAAUC,EAAQa,GAAU,SAAS,EACtD,GAAGZ,EAAWf,EAAKS,EAAUkB,GAAU,IAAI,CAC7C,CACF,CAEO,SAASC,EAAiBC,EAU9B,CACD,GAAM,CAAE,OAAAH,EAAQ,SAAAb,EAAU,QAAAiB,EAAS,KAAA3B,CAAK,EAAI0B,EAC5C,MAAO,CACL,KAAMH,IAAW,yBAA2B,eAAiB,aAC7D,QAAAI,EACA,KAAA3B,EACA,cAAe,CAACU,CAAQ,EACxB,QAASY,EAAmBI,CAAI,EAChC,GAAIH,IAAW,mBACX,CAAE,gBAAiB,CAAE,WAAY,MAAO,CAAE,EAC1C,CAAC,CACP,CACF",
+  "names": ["SEGMENTS_SUFFIX", "FETCH_TIMEOUT_MS", "isSiblingName", "name", "isAbsent", "value", "isRecord", "isTier", "tier", "parseGraphManifest", "text", "json", "reference", "index", "contig", "bubbles", "alleles", "f", "besideSegments", "segs", "fileName", "renamed", "manifestLocation", "locationName", "readsSiblings", "n", "readGraphManifest", "pluginManager", "loc", "openLocation", "GRAPH_FILE_LABELS", "GRAPH_FILE_FIELDS", "TABIX_INDEX_FIELD", "GRAPH_INDEX_FIELDS", "SEGMENTS_SUFFIX", "sibling", "loc", "suffix", "renamed", "name", "isSegmentsLocation", "readsSiblings", "locationName", "linksLocation", "tabixIndex", "indexLoc", "makeIndexType", "siblingIndex", "panSN", "assembly", "sample", "coarseTier", "tier", "segs", "besideSegments", "links", "manifestPanSN", "reference", "fromManifest", "readsConfig", "readsLoc", "buildAdapterConfig", "choice", "manifest", "buildTrackConfig", "args", "trackId"]
+}