jbrowse-plugin-graphgenomeviewer 1.0.0 → 3.0.3

package/README.md

@@ -1,36 +1,214 @@
 # jbrowse-plugin-graphgenomeviewer
 
-WIP for displaying graph genome as a view in JBrowse 2
+A JBrowse 2 plugin that adds a **GraphGenomeView** for pangenome graphs (GFA /
+rGFA), plus a right-click launcher to open the local subgraph around a region
+from a linear genome view.
 
-## Screenshot
+## Screenshots
 
-![](img/1.png)
+The LPA KIV-2 window of the HPRC release 2 graph in the **force-directed
+layout**: the GRCh38 backbone runs left to right, coloured by position the way
+the rGFA segments track above it is, and the kringle repeat array is the knot of
+loops in the middle. Each bubble the graph holds is haloed along its own nodes
+and labelled by what it is; the label opens the bubble on its own.
 
-## Concept
+![KIV-2, force-directed, with its bubbles marked](img/force_kiv2.png)
 
-The code adds:
+Clicking the array's label opens its 29 segments in the same layout, with a
+button back to the window. A popped graph derives its own bubbles, so a
+superbubble opens level by level:
 
-- a simple file selector for the user to open .gfa files to display alognside
-  the genome browser (these are meant to be locus-specific smallish GFA, not
-  full assembly graphs)
-- alternatively, can configure a "GFA server" which will use the `vg chunk`
-  command to extract the region into a web based bandage-like graph genome
-  viewer https://github.com/cmdcolin/graphgenomeviewer
+![The KIV-2 array popped open](img/force_kiv2_popped.png)
 
-## Thanks
+Over a gbz-base database the cut carries the haplotypes' walks. A node draws
+thicker the more of them carry it, Bandage's depth as width, and every route
+through a bubble is labelled at the far point of its loop for the haplotypes
+that take it and how long it is, so the array reads as one copy count per
+haplotype:
 
-To the StableGenomics team for their PAG workshop helping explain some vg
-toolkit commands and concepts https://github.com/StableGenomics/PangPAG
+![KIV-2 over gbz-base, eight haplotypes, force-directed](img/force_kiv2_gbz.png)
 
-## TODOs
+Picking one walk lifts it out of the drawing. HG00133's route through the window
+keeps its ink and the other haplotypes fade; the readout says it carries 116 kb
+more than GRCh38 through the array:
 
-Shortlist of TODOs
+![HG00133's walk lifted out of the KIV-2 cut](img/force_kiv2_walk.png)
 
-- Easier navigation between the linear genome view and graph genome panel
-- Ability to launch a synteny-style view from the graph
-- Ability to use decompose graph into VCF track
-- Ability to show paths/walks
-- Debug issue where vg chunk GFA output not loadable in bandage
-- Improve scalability
-- Bi-directional mouseover from genome to graph and back
-- Less chunk-y-ness from the vg chunk graph (?)
+MHC class II, where one 254-segment superbubble covers the DRB haplotype block
+and a run of small indels follows it. The session's gene track is drawn onto the
+graph: exons as dark stretches along the backbone nodes that carry them, and
+each gene's name pinned under the backbone at its midpoint, so the superbubble
+reads as HLA-DRB5's and the indels as HLA-DRB6's and HLA-DRB1's:
+
+![MHC class II, force-directed, with genes on the backbone](img/force_mhc.png)
+
+The KIV-2 window as a **variant map**, the reference as one line with one typed
+glyph per bubble:
+
+![Variant map of KIV-2](img/variant_map_kiv2.png)
+
+It ships six layouts:
+
+- **Force-directed**: the graph's shape, computed by the OGDF FMMM engine from
+  [Bandage](https://github.com/rrwick/Bandage), seeded along the reference and
+  turned to read left to right. The engine lays out unbranching runs rather than
+  nodes, so a base-level cut of 15,000 nodes draws in a few seconds. The Walk
+  picker lifts one haplotype out: its route keeps its ink, the rest fades, and a
+  readout gives its length against the reference.
+- **Variant map** (rGFA or a reference path): the reference as a line, one typed
+  glyph per bubble, click to open a bubble's graph, and again for a bubble
+  inside it.
+- **Ordered** (rGFA or a reference path): x is reference order rather than bp,
+  so every node gets room and a bubble reads as a lens. Scrolls sideways.
+- **Anchored** (rGFA or a reference path): x is reference bp, one row per stable
+  rank, aligned under a linear view.
+- **Sample rows**: x is reference bp, one row per contributing assembly.
+- **Walk rows** (W or P lines): x is each walk's own bp, one bar per haplotype,
+  sequence the reference also carries in blue and sequence it does not in
+  purple, so a repeat expansion reads as bar length. The Repeat picker tiles the
+  bars by a repeat annotation's unit and marks the allele a genotyper called.
+
+The bubbles come from `gfatools bubble` output beside the rGFA index
+(`<prefix>.bubbles.bed.gz`), which HPRC's hosted graph has and
+`scripts/build_rgfa_tabix.sh` in jbrowse-components writes, or, for a graph with
+no index, a GBZ cut, a pggb file or a popped bubble, from the graph itself off
+the ordered layout's layering. Every node layout marks them as halos; the
+variant map draws them as glyphs.
+
+### Demonstration loci
+
+Six HPRC release 2 windows, the ones the
+[HPRC tutorials](https://jbrowse.org/jb2/docs/tutorials/pangenome_hprc/) walk
+through, are the standing test set for layout screenshots. Each cuts to under
+300 nodes and shows a different kind of variation:
+
+| Locus        | Window                         | What it shows                       |
+| ------------ | ------------------------------ | ----------------------------------- |
+| LPA KIV-2    | `chr6:160,525,000-160,655,000` | the kringle repeat, copy per loop   |
+| MHC class II | `chr6:32,510,000-32,600,000`   | DRB haplotypes, dozens of alleles   |
+| AMY1         | `chr1:103,690,000-103,780,000` | amylase copy number                 |
+| C4           | `chr6:31,980,000-32,050,000`   | one bubble over the C4 duplication  |
+| CFH          | `chr1:196,640,000-196,900,000` | an 84 kb deletion as a bare edge    |
+| KIR          | `chr19:54,750,000-54,840,000`  | the KIR cluster, densest of the six |
+
+[docs/layout-experiments.md](docs/layout-experiments.md) draws all six in every
+layout the plugin has and in the ones proposed to replace them, and
+`scripts/layout-lab/` reproduces the figures.
+
+## License (GPL-3.0)
+
+This plugin is **GPL-3.0-or-later**. The force-directed layout is computed by a
+WebAssembly build of Bandage's FMMM layout from [OGDF](https://ogdf.github.io/),
+and both Bandage and OGDF are GPL-licensed, so this plugin takes the same
+license rather than linking around it.
+
+JBrowse itself is unaffected and stays Apache-2.0: this is a separate plugin,
+loaded at runtime only by configs that ask for it. The anchored and sample-row
+layouts are pure TypeScript and need no external engine.
+
+## Developing
+
+Requires [pnpm](https://pnpm.io/installation). The plugin builds against the
+published `@jbrowse/*` packages at 5.0.0-beta.9 and needs a host of at least
+that version: it hands its RPC calls an AbortSignal, which an earlier JBrowse 5
+beta cannot post to its worker.
+
+```console
+pnpm install
+pnpm start        # esbuild watch, serves dist/out.js on :9000 with CORS
+```
+
+In another terminal, serve a JBrowse Web that points at `config.json` (its
+`plugins` entry already targets `http://localhost:9000/dist/out.js`).
+
+## Building
+
+```console
+pnpm build        # native ESM bundle via esbuild (code-split)
+pnpm typecheck    # tsc, separately — esbuild strips types without checking them
+```
+
+This writes the plugin to `dist/`, and the **whole directory must be served
+together** — the entry loads its sibling chunks relative to its own url:
+
+- `jbrowse-plugin-graphgenomeviewer.esm.js` — the plugin entry
+- `chunks/bandage-layout-<hash>.js` — the Bandage layout engine (~425kb),
+  imported on demand and named by content hash so a redeployed engine is never
+  served from cache
+- `chunks/*.js` — other lazily-loaded code split out of the entry
+
+Load the plugin from any JBrowse config, 5.0.0-beta.9 or later, with an
+`esmUrl`:
+
+```json
+{
+  "plugins": [
+    {
+      "name": "GraphGenomeView",
+      "esmUrl": "https://your-host/jbrowse-plugin-graphgenomeviewer.esm.js"
+    }
+  ]
+}
+```
+
+Note: ESM plugins are loaded via a dynamic `import()`, which cannot carry a
+subresource-integrity hash the way a UMD `<script integrity>` can — there is
+nowhere to put a digest. For a deployment that needs pinned, tamper-evident
+bytes, serve the plugin from an immutable, version-pinned url on a host you
+control. The engine chunk is already immutable by content hash.
+
+The engine is a lazy chunk: it is only fetched the first time someone selects
+the force-directed layout, so sessions that use the anchored or sample-row
+layouts never download it. Its url is not configured anywhere — `loadBandage` is
+a plain dynamic `import()`, so the browser resolves the chunk relative to the
+plugin module's own url (`import.meta.url`, defined on the main thread and in
+the RPC worker alike). That is why the whole `dist/` has to be served together,
+and it is also why there is nothing to point elsewhere: to host the engine on
+another origin, rebuild with the chunk emitted there.
+
+### Rebuilding the engine
+
+`src/bandage/bandage-layout.js` is a committed build artifact, so a normal
+`pnpm build` never needs Emscripten. Regenerate it only when the C++ layout
+sources change:
+
+```console
+pnpm build:wasm   # needs emsdk, nothing else
+```
+
+Emscripten is the only thing you have to install. OGDF is vendored at
+`vendor/ogdf` (a stock checkout of it does not build for wasm at all — see
+[`vendor/README.md`](vendor/README.md)), so this works offline from a fresh
+clone of this repo alone. Roughly four minutes the first time, seconds after
+that.
+
+It compiles with `-sSINGLE_FILE=1`, embedding the wasm as base64 so the result
+is one self-contained ES module that esbuild can copy rather than bundle.
+
+A rebuild has to be checked against the drawing rather than against the file,
+since the artifact's bytes move for reasons the layout does not — see
+[`src/bandage/README.md`](src/bandage/README.md) for
+`scripts/layout-digest.mjs`.
+
+## Testing
+
+```console
+pnpm test         # vitest unit tests
+pnpm test:watch
+pnpm test:wasm    # runs the committed Bandage engine, no deps needed
+pnpm test:e2e     # puppeteer, opt-in — see test/README.md
+pnpm host-compat  # boots dist/ on the hosted JBrowse releases and cuts a graph
+pnpm lint
+pnpm typecheck
+```
+
+`pnpm test:e2e` drives the force layout through a real JBrowse in a headless
+browser, behind `RUN_E2E=1` because it needs a jbrowse-web build to serve;
+[`test/README.md`](test/README.md) explains how to run it.
+
+`pnpm host-compat` is the check a publish has to pass, and `pnpm version` runs
+it. It serves the built `dist/` to a real shipped config on each hosted release
+and cuts a subgraph there, because the failures it catches pass tsc, eslint and
+the unit tests: an RPC argument a released core cannot post to its worker, or a
+re-export the host no longer serves, shows only when the bundle runs on the
+host.

package/dist/chunks/AddTrackWorkflow-Y3OBHM33.js

@@ -0,0 +1,2 @@
+import{a as z}from"./chunk-FCWXYIFC.js";import{a as $}from"./chunk-D7XFR2IV.js";import{a as L,b as j,c as O,d as J,e as U}from"./chunk-XEJ47DLD.js";import{a as H}from"./chunk-J4OLMLS5.js";import{a as D,b as r}from"./chunk-FY3BTKY4.js";var C=D((Z,y)=>{y.exports=JBrowseExports["@jbrowse/core/util/tss-react"]});var c=r(U(),1),p=r(J(),1),m=r(H(),1),E=r(C(),1),B=r(z(),1),i=r(O(),1),P=r(j(),1);var b=r($(),1),S={RgfaTabixAdapter:"rGFA segments (tabix BED pair)",MinigraphBubbleAdapter:"Minigraph bubbles (tabix BED)"},R={RgfaTabixAdapter:"Path to segments BED (.segs.bed.gz from build_rgfa_tabix.sh; the .links.bed.gz and both .tbi are assumed beside it)",MinigraphBubbleAdapter:"Path to bubbles BED (.bed.gz from gfatools bubble; the .tbi is assumed beside it)"},u=".segs.bed.gz";function f(t){return"uri"in t?t.uri:"localPath"in t?t.localPath:""}function X(t){let e=f(t);if(!e.endsWith(u))throw new Error(`Expected a segments BED ending in ${u}, got ${e||"a blob"}`);let a=`${e.slice(0,-u.length)}.links.bed.gz`;return"uri"in t?{...t,uri:a}:"localPath"in t?{...t,localPath:a}:t}function A(t,e){return e?{location:e,indexType:(0,b.makeIndexType)(f(e),"CSI","TBI")}:{location:(0,b.makeIndex)(t,".tbi"),indexType:"TBI"}}function q(t,e){return e!==void 0&&f(e).endsWith(".csi")?{location:(0,b.makeIndex)(t,".csi"),indexType:"CSI"}:{location:(0,b.makeIndex)(t,".tbi"),indexType:"TBI"}}function I(t,e){let a=e.trim();return a?{assemblyNameToPanSN:{[t]:a}}:{}}function K({choice:t,loc:e,indexLoc:a,assembly:s,sample:l}){if(t==="MinigraphBubbleAdapter")return{type:"MinigraphBubbleAdapter",bubblesLocation:e,index:A(e,a),...I(s,l)};let d=X(e);return{type:"RgfaTabixAdapter",segmentsLocation:e,segmentsIndex:A(e,a),linksLocation:d,linksIndex:q(d,a),...I(s,l)}}function G(t){let{choice:e,assembly:a,trackId:s,name:l}=t;return{type:"FeatureTrack",trackId:s,name:l,assemblyNames:[a],adapter:K(t),...e==="RgfaTabixAdapter"?{displayDefaults:{showLabels:"none"}}:{}}}var n=r(L(),1),Q=(0,E.makeStyles)()(t=>({paper:{margin:t.spacing(),padding:t.spacing()},field:{marginTop:t.spacing(2)},submit:{marginTop:25,marginBottom:100,display:"block"}})),V=["RgfaTabixAdapter","MinigraphBubbleAdapter"],Y=(0,P.observer)(function({model:e}){let{classes:a}=Q(),s=(0,m.getSession)(e),l=(0,B.getRoot)(e),[d,M]=(0,c.useState)("RgfaTabixAdapter"),[g,N]=(0,c.useState)(),[F,v]=(0,c.useState)(),[k,w]=(0,c.useState)(""),[h,_]=(0,c.useState)("Pangenome graph"),[x,T]=(0,c.useState)();function W(){if(!(!g||!e.assembly))try{T(void 0);let o=h.trim();(0,m.addTrackFromWidget)({model:e,session:s,conf:G({choice:d,loc:g,indexLoc:F,assembly:e.assembly,sample:k,trackId:(0,m.makeTrackId)({name:o}),name:o})})}catch(o){T(o)}}return(0,n.jsxs)(i.Paper,{className:a.paper,children:[x?(0,n.jsx)(p.ErrorMessage,{error:x}):null,(0,n.jsxs)(i.FormControl,{children:[(0,n.jsx)(i.FormLabel,{children:"File type"}),(0,n.jsx)(i.RadioGroup,{value:d,onChange:o=>{M(o.target.value)},children:V.map(o=>(0,n.jsx)(i.FormControlLabel,{value:o,control:(0,n.jsx)(i.Radio,{}),label:S[o]},o))})]}),(0,n.jsx)(p.FileSelector,{location:g,name:R[d],rootModel:l,setLocation:N}),(0,n.jsx)(p.FileSelector,{location:F,name:"Path to tabix index (optional; the sibling .tbi is assumed, a .csi is recognised by name)",rootModel:l,setLocation:v}),(0,n.jsx)(i.TextField,{className:a.field,value:k,onChange:o=>{w(o.target.value)},label:"Sample name in the graph",slotProps:{htmlInput:{"data-testid":"graph-sample-input"}},helperText:"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}),(0,n.jsx)(i.TextField,{className:a.field,value:h,helperText:"Track name",slotProps:{htmlInput:{"data-testid":"graph-track-name-input"}},onChange:o=>{_(o.target.value)}}),(0,n.jsx)(p.AssemblySelector,{session:s,helperText:"Select assembly to add track to",selected:e.assembly,onChange:o=>{e.setAssembly(o)},fullWidth:!0}),(0,n.jsx)(i.Button,{variant:"contained",className:a.submit,disabled:!g||!h.trim()||!e.assembly,onClick:W,children:"Submit"})]})}),ae=Y;export{ae as default};
+//# sourceMappingURL=AddTrackWorkflow-Y3OBHM33.js.map

package/dist/chunks/AddTrackWorkflow-Y3OBHM33.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["global-externals:@jbrowse/core/util/tss-react", "../../src/GraphAddTrackWorkflow/AddTrackWorkflow.tsx", "../../src/GraphAddTrackWorkflow/buildTrackConfig.ts"],
+  "sourcesContent": ["module.exports = JBrowseExports[\"@jbrowse/core/util/tss-react\"];", "import { useState } from 'react'\n\nimport { AssemblySelector, ErrorMessage, FileSelector } from '@jbrowse/core/ui'\nimport { addTrackFromWidget, getSession, makeTrackId } from '@jbrowse/core/util'\nimport { makeStyles } from '@jbrowse/core/util/tss-react'\nimport { getRoot } from '@jbrowse/mobx-state-tree'\nimport {\n  Button,\n  FormControl,\n  FormControlLabel,\n  FormLabel,\n  Paper,\n  Radio,\n  RadioGroup,\n  TextField,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport {\n  GRAPH_FILE_FIELDS,\n  GRAPH_FILE_LABELS,\n  buildTrackConfig,\n} from './buildTrackConfig'\n\nimport type { GraphFileChoice } from './buildTrackConfig'\nimport type {\n  AbstractRootModel,\n  AddTrackWorkflowModel,\n  FileLocation,\n} from '@jbrowse/core/util'\n\nconst useStyles = makeStyles()(theme => ({\n  paper: {\n    margin: theme.spacing(),\n    padding: theme.spacing(),\n  },\n  field: {\n    marginTop: theme.spacing(2),\n  },\n  submit: {\n    marginTop: 25,\n    marginBottom: 100,\n    display: 'block',\n  },\n}))\n\nconst CHOICES: GraphFileChoice[] = [\n  'RgfaTabixAdapter',\n  '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 [sample, setSample] = useState('')\n  const [trackName, setTrackName] = useState('Pangenome graph')\n  const [error, setError] = useState<unknown>()\n\n  function handleSubmit() {\n    if (!loc || !model.assembly) {\n      return\n    }\n    try {\n      setError(undefined)\n      const name = trackName.trim()\n      addTrackFromWidget({\n        model,\n        session,\n        conf: buildTrackConfig({\n          choice,\n          loc,\n          indexLoc,\n          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          }}\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=\"Path to tabix index (optional; the sibling .tbi is assumed, a .csi is recognised by name)\"\n        rootModel={rootModel}\n        setLocation={setIndexLoc}\n      />\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=\"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        placeholder=\"GRCh38\"\n        fullWidth\n      />\n      <TextField\n        className={classes.field}\n        value={trackName}\n        helperText=\"Track name\"\n        slotProps={{ htmlInput: { 'data-testid': 'graph-track-name-input' } }}\n        onChange={event => {\n          setTrackName(event.target.value)\n        }}\n      />\n      <AssemblySelector\n        session={session}\n        helperText=\"Select assembly to add track to\"\n        selected={model.assembly}\n        onChange={arg => {\n          model.setAssembly(arg)\n        }}\n        fullWidth\n      />\n      <Button\n        variant=\"contained\"\n        className={classes.submit}\n        disabled={!loc || !trackName.trim() || !model.assembly}\n        onClick={handleSubmit}\n      >\n        Submit\n      </Button>\n    </Paper>\n  )\n})\n\nexport default GraphAddTrackWidget\n", "import { makeIndex, makeIndexType } from '@jbrowse/core/util/tracks'\n\nimport type { FileLocation } from '@jbrowse/core/util'\n\nexport type GraphFileChoice = 'RgfaTabixAdapter' | 'MinigraphBubbleAdapter'\n\nexport const GRAPH_FILE_LABELS: Record<GraphFileChoice, string> = {\n  RgfaTabixAdapter: 'rGFA segments (tabix BED pair)',\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 build_rgfa_tabix.sh; the .links.bed.gz and both .tbi are assumed beside it)',\n  MinigraphBubbleAdapter:\n    'Path to bubbles BED (.bed.gz from gfatools bubble; the .tbi is assumed beside it)',\n}\n\nconst SEGMENTS_SUFFIX = '.segs.bed.gz'\n\nfunction locationName(loc: FileLocation) {\n  return 'uri' in loc ? loc.uri : 'localPath' in loc ? loc.localPath : ''\n}\n\nfunction linksLocation(loc: FileLocation) {\n  const name = locationName(loc)\n  if (!name.endsWith(SEGMENTS_SUFFIX)) {\n    throw new Error(\n      `Expected a segments BED ending in ${SEGMENTS_SUFFIX}, got ${name || 'a blob'}`,\n    )\n  }\n  const links = `${name.slice(0, -SEGMENTS_SUFFIX.length)}.links.bed.gz`\n  return 'uri' in loc\n    ? { ...loc, uri: links }\n    : 'localPath' in loc\n      ? { ...loc, localPath: links }\n      : loc\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: makeIndex(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 = indexLoc !== undefined && locationName(indexLoc).endsWith('.csi')\n  return csi\n    ? { location: makeIndex(loc, '.csi'), indexType: 'CSI' }\n    : { location: makeIndex(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\nexport function buildAdapterConfig({\n  choice,\n  loc,\n  indexLoc,\n  assembly,\n  sample,\n}: {\n  choice: GraphFileChoice\n  loc: FileLocation\n  indexLoc: FileLocation | undefined\n  assembly: string\n  sample: string\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    ...panSN(assembly, sample),\n  }\n}\n\nexport function buildTrackConfig(args: {\n  choice: GraphFileChoice\n  loc: FileLocation\n  indexLoc: FileLocation | undefined\n  assembly: string\n  sample: string\n  trackId: string\n  name: string\n}) {\n  const { choice, assembly, trackId, name } = args\n  return {\n    type: 'FeatureTrack',\n    trackId,\n    name,\n    assemblyNames: [assembly],\n    adapter: buildAdapterConfig(args),\n    ...(choice === 'RgfaTabixAdapter'\n      ? { displayDefaults: { showLabels: 'none' } }\n      : {}),\n  }\n}\n"],
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+}

package/dist/chunks/GbzBaseSyntenyAdapter-EFIOI2SN.js

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0&&e.push(`H	NM:Z:${o.name}`);for(let[t,r]of hr(o.subgraph))e.push(`H	SG:Z:${t},${r}`);for(let[t,r]of hr(o.translation))e.push(`H	TL:Z:${t},${r}`);return e}async function gr(o){let e=o.reduce((s,i)=>s+i.length,0),t=new Uint8Array(e),r=0;for(let s of o)t.set(s,r),r+=s.length;let n=await globalThis.crypto.subtle.digest("SHA-256",t);return[...new Uint8Array(n)].map(s=>s.toString(16).padStart(2,"0")).join("")}var Tn="_gbwt_ref";function $(o,e){return`${o.sample}#${o.haplotype}#${o.contig}[${o.fragment}-${e}]`}var Mn=/^([^#]+)#(\d+)#([^#]+?)(?:\[\d+-\d+\])?$/,Nn=/^([^#]+?)(?:\[\d+-\d+\])?$/;function Fn(o){let e=Mn.exec(o);if(e)return{sample:e[1],haplotype:Number(e[2]),contig:e[3]};let t=Nn.exec(o);if(t)return{contig:t[1]};throw new Error(`"${o}" is not a path name; expected "sample#haplotype#contig" or a bare contig`)}function xr(o){return typeof o=="string"?Fn(o):o}function Se(o,e){return{sample:o.sample??Tn,contig:o.contig,haplotype:o.haplotype??0,fragment:e}}function He(o,e){let t=0,r=o.length;for(;t<r;){let n=t+r>>1;o[n]<e?t=n+1:r=n}return t}var $e=class{ending;tree;constructor(e){this.ending=new Float64Array(e),this.tree=new Int32Array(e+1).fill(-1)}bestBefore(e){let t=-1;for(let r=e;r>0;r-=r&-r){let n=this.tree[r];n!==-1&&(t===-1||this.ending[n]>this.ending[t])&&(t=n)}return t}raise(e,t){this.ending[e]=t;for(let r=e+1;r<this.tree.length;r+=r&-r){let n=this.tree[r];(n===-1||t>this.ending[n])&&(this.tree[r]=e)}}},At=class{pairs=[];total=0;a;b;weight;occurrences=new Map;constructor(e,t,r){this.a=e,this.b=t,this.weight=r,t.forEach((n,s)=>{let i=this.occurrences.get(n);i?i.push(s):this.occurrences.set(n,[s])})}solve(e,t,r,n){let s=0;for(;e+s<t&&r+s<n&&this.a[e+s]===this.b[r+s];)this.match(e+s,r+s),s+=1;let i=0;for(;t-i>e+s&&n-i>r+s&&this.a[t-i-1]===this.b[n-i-1];)i+=1;this.solveMiddle(e+s,t-i,r+s,n-i);for(let a=i;a>0;a--)this.match(t-a,n-a)}match(e,t){this.pairs.push([e,t]),this.total+=this.weight(this.a[e])}solveMiddle(e,t,r,n){if(e===t||r===n)return;let s=this.matchCount(e,t,r,n);if(s===0)return;if(s<=t-e+(n-r)){this.chain(e,t,r,n,s);return}let i=e+t>>1,a=this.split(e,i,t,r,n);this.solve(e,i,r,a),this.solve(i,t,a,n)}matchCount(e,t,r,n){let s=0;for(let i=e;i<t;i++){let a=this.occurrences.get(this.a[i]);a&&(s+=He(a,n)-He(a,r))}return s}sweep(e,t,r,n,s,i,a){for(let f=e;f!==t;f+=r){let c=this.occurrences.get(this.a[f]);if(!c)continue;let l=this.weight(this.a[f]),p=He(c,n),u=He(c,s);for(let h=0;h<u-p;h++){let d=r===1?c[u-1-h]-n:s-1-c[p+h],m=i.bestBefore(d),x=(m===-1?0:i.ending[m])+l;if(x>i.ending[d]&&(i.raise(d,x),a)){let w=a.count++;a.row[w]=f,a.column[w]=d,a.previous[w]=m===-1?-1:a.endingMatch[m],a.endingMatch[d]=w}}}}chain(e,t,r,n,s){let i=new $e(n-r),a={row:new Int32Array(s),column:new Int32Array(s),previous:new Int32Array(s),endingMatch:new Int32Array(n-r),count:0};this.sweep(e,t,1,r,n,i,a);let f=i.bestBefore(n-r);if(f===-1)return;this.total+=i.ending[f];let c=[];for(let l=a.endingMatch[f];l!==-1;l=a.previous[l])c.push([a.row[l],r+a.column[l]]);for(let l=c.length-1;l>=0;l--)this.pairs.push(c[l])}frontier(e,t,r,n,s){let i=new $e(s-n);this.sweep(e,t,r,n,s,i);let a=new Float64Array(s-n+1);for(let f=0;f<s-n;f++)a[f+1]=Math.max(a[f],i.ending[f]);return a}split(e,t,r,n,s){let i=s-n,a=this.frontier(e,t,1,n,s),f=this.frontier(r-1,t-1,-1,n,s),c=0,l=-1;for(let p=0;p<=i;p++){let u=a[p]+f[i-p];u>l&&(l=u,c=p)}return n+c}};function wr(o,e,t){let r=new At(o,e,t);return r.solve(0,o.length,0,e.length),[r.pairs,r.total]}var V=class extends Error{name="SubgraphLimitError";limit;windowBp;walkedBp;constructor(e,t){super(t===void 0?`Subgraph size limit of ${e} nodes exceeded`:`Subgraph size limit of ${e} nodes exceeded ${t.walkedBp} bp into a ${t.windowBp} bp window`),this.limit=e,this.windowBp=t?.windowBp,this.walkedBp=t?.walkedBp}};function Et(o,e){return o[0]<e[0]||o[0]===e[0]&&(o[1]<e[1]||o[1]===e[1]&&o[2]<e[2])}var ve=class{heap=[];push(e,t,r){let n=this.heap;n.push([e,t,r]);let s=n.length-1;for(;s>0;){let i=s-1>>1;if(Et(n[s],n[i]))[n[s],n[i]]=[n[i],n[s]],s=i;else break}}pop(){let e=this.heap,t=e[0],r=e.pop();if(e.length>0&&r!==void 0){e[0]=r;let n=0;for(;;){let s=2*n+1,i=s+1,a=n;if(s<e.length&&Et(e[s],e[a])&&(a=s),i<e.length&&Et(e[i],e[a])&&(a=i),a===n)break;[e[n],e[a]]=[e[a],e[n]],n=a}}return t}get size(){return this.heap.length}};function Hn(o){let e=new Int32Array(o.length),t=new Int32Array(o.length);return o.forEach(([r,n],s)=>{e[s]=r,t[s]=n}),{pathAt:e,refAt:t,count:o.length}}function $n(o,e){let t=0,r=o.length;for(;t<r;){let n=t+r>>1;o[n]>e?r=n:t=n+1}return o[t]}function re(o){return`${o.node}:${o.offset}`}function Bn(o,e){let t=e.identity.hapStart-o.identity.hapEnd,r=o.strand==="+"?e.refStart-o.refEnd:o.refStart-e.refEnd;return o.strand===e.strand&&t>=0&&r>=0?{insertion:t,deletion:r}:void 0}function Gn(o,e,t){let[r,n]=o.strand==="+"?[o,e]:[e,o],s=r.edits.map(([c,l])=>[c,l]);br(s,t.insertion,t.deletion);for(let[c,l]of n.edits)D(s,c,l);let i=o.identity.walkForward,[a,f]=i?[o,e]:[e,o];return{strand:o.strand,refStart:r.refStart,refEnd:n.refEnd,edits:s,weight:void 0,path:[...a.path,...f.path],start:a.start,identity:{pathHandle:o.identity.pathHandle,name:o.identity.name,hapStart:o.identity.hapStart,hapEnd:e.identity.hapEnd,walkForward:i}}}function Dn(o){if(o.some(n=>n.weight!==void 0))return o;let e=new Map;o.forEach((n,s)=>{if(n.identity){let i=e.get(n.identity.pathHandle);i?i.push(s):e.set(n.identity.pathHandle,[s])}});let t=new Map,r=new Set;for(let n of e.values()){n.sort((a,f)=>o[a].identity.hapStart-o[f].identity.hapStart);let s=n[0],i=o[s];for(let a of n.slice(1)){let f=o[a],c=Bn(i,f);c?(i=Gn(i,f,c),r.add(a)):(t.set(s,i),s=a,i=f)}t.set(s,i)}return o.flatMap((n,s)=>r.has(s)?[]:[t.get(s)??n])}function Be(o,e){return{node:o.path[e],offset:o.offsets[e]}}var zn=4096;function yr(o){let e=[];for(let t of o){let r=e[e.length-1];r&&t-r[1]<=zn?r[1]=t:e.push([t,t])}return e}var jn=32768,qn=65536;function Wn(o){let e=[...o].sort((r,n)=>r-n),t=[];for(let r of e){let n=t[t.length-1];n&&r-n[1]<=jn?n[1]=r:t.push([r,r])}return t}var Ie=class{records=new Map;paths=[];twinStarts=new Set;refId;refPath;refHandle;refInterval;refIndexCache;refPrefixCache;walkedBp;stats={orderedAlignments:0,lcsAlignments:0,identificationSteps:0,identificationFetches:0,identification:{interval:0,scans:[],windowSamples:0,fragmentLengths:[],companionSeeks:0,companionMisses:0,graphLookups:0,graphFetches:0,chains:[]},anchorWalk:void 0};db;limit;signal;constructor(e,t={}){this.db=e,this.limit=t.limit,this.signal=t.signal}get nodeCount(){return this.records.size/2}get pathCount(){return this.paths.length}get referenceInterval(){return this.refInterval&&this.refPath?{name:this.refPath,start:this.refPath.fragment+this.refInterval[0],end:this.refPath.fragment+this.refInterval[1]}:void 0}hasNode(e){return this.records.has(Y(e,"forward"))}hasHandle(e){return this.records.has(e)}record(e){let t=this.records.get(e);if(!t)throw new Error(`Subgraph has no record for handle ${e}`);return t}sortedHandles(){return[...this.records.keys()].sort((e,t)=>e-t)}async addNode(e){if(this.signal?.throwIfAborted(),this.limit!==void 0&&this.nodeCount>=this.limit)throw new V(this.limit);let t=await this.db.getRecord(Y(e,"forward")),r=await this.db.getRecord(Y(e,"reverse"));if(!t||!r)throw new Error(`Node ${e} does not exist in the graph`);this.records.set(t.handle,t),this.records.set(r.handle,r)}async ensureNode(e){this.hasNode(e)||await this.addNode(e)}clearPaths(){this.paths=[],this.twinStarts.clear(),this.refId=void 0,this.refPath=void 0,this.refHandle=void 0,this.refInterval=void 0,this.refIndexCache=void 0,this.refPrefixCache=void 0}async pathPosition(e){let t=await this.db.findPath(e);if(!t)throw new Error(`Cannot find a path covering ${$(e,e.fragment)}`);if(!t.isIndexed)throw new Error(`Path ${$(t.name,t.name.fragment)} has not been indexed for random access`);let r=e.fragment-t.name.fragment,n=await this.db.indexedPosition(t.handle,r);if(!n)throw new Error(`Path ${$(t.name,t.name.fragment)} has not been indexed for random access`);return this.findPathPosition(t,r,n.pathOffset,n.pos)}async findPathPosition(e,t,r,n){let s=r,i=n;for(;;){await this.ensureNode(A(i.node));let a=this.record(i.node);if(s+a.sequenceLen>t)return{position:{seqOffset:t,handle:i.node,nodeOffset:t-s,gbwtOffset:i.offset},name:e.name,handle:e.handle};s+=a.sequenceLen;let f=a.gbwt().lf(i.offset);if(!f)throw new Error(`Path ${$(e.name,e.name.fragment)} does not contain offset ${t}`);i=f}}async aroundPosition(e,t,r){let n=A(e);await this.ensureNode(n);let s=this.record(e),i=ce(e),a=new ve;return a.push(t,n,Le(i)),a.push(s.sequenceLen-t-1,n,Te(i)),this.insertContext(a,r)}prefetchReferenceWalk(e,t){return this.prefetchReferenceRange(e.handle,e.position.seqOffset,e.position.seqOffset+t)}async prefetchReferenceRange(e,t,r){let[n,s]=await Promise.all([this.db.indexedPosition(e,t),this.db.indexedPosition(e,r)]);if(n&&s){let i=n.pos.node,a=s.pos.node;if(!await this.db.prefetchRecords(Math.min(i,a),Math.max(i,a)+1)){let c=await this.db.indexedPositionsBetween(e,t,r),l=Wn(c.map(p=>p.pos.node));await Promise.all(l.map(([p,u])=>this.db.prefetchRecords(p,u+2)))}}return n}async aroundInterval(e,t,r){if(t===0)throw new Error("Interval length must be greater than 0");this.walkedBp=0;try{return await this.walkInterval(e,t,r)}catch(n){throw n instanceof V&&n.windowBp===void 0?new V(n.limit,{windowBp:t,walkedBp:this.walkedBp}):n}}get referenceWalkedBp(){return this.walkedBp}async walkInterval(e,t,r){let n={node:e.handle,offset:e.gbwtOffset},s=e.nodeOffset,i=t,a=new ve;for(;;){let f=A(n.node),c=ce(n.node);this.walkedBp=t-i,await this.ensureNode(f);let l=this.record(n.node);if(s>=l.sequenceLen)throw new Error(`Offset ${s} in node ${f} of length ${l.sequenceLen}`);a.push(s,f,Le(c));let p=l.sequenceLen-s;if(i<=p){a.push(i===p?0:p-i-1,f,Te(c));break}a.push(0,f,Te(c));let u=l.gbwt().lf(n.offset);if(!u)throw new Error(`No successor for GBWT position (${n.node}, ${n.offset})`);n=u,s=0,i-=p}return this.walkedBp=t,this.insertContext(a,r)}async aroundNodes(e,t){let r=new ve;for(let n of e)await this.ensureNode(n),r.push(0,n,"left"),r.push(0,n,"right");return this.insertContext(r,t)}async insertContext(e,t){this.clearPaths();let r=new Set,n=new Set;for(let i of this.records.keys())n.add(A(i));let s=0;for(;e.size>0;){let[i,a,f]=e.pop(),c=`${a}:${f}`;if(r.has(c))continue;r.add(c),n.delete(a),this.hasNode(a)||(await this.addNode(a),s+=1);let l=rr(f);if(!r.has(`${a}:${l}`)){let h=this.record(Y(a,nr(f))),d=i+h.sequenceLen-1;d<=t&&e.push(d,a,l)}let p=this.record(Y(a,or(f))),u=i+1;if(u<=t)for(let h of p.successors()){let d=A(h),m=Le(ce(h));r.has(`${d}:${m}`)||e.push(u,d,m)}}for(let i of n)this.records.delete(Y(i,"forward")),this.records.delete(Y(i,"reverse"));return{inserted:s,removed:n.size}}async betweenNodes(e,t){this.clearPaths();let r=[e,G(t)],n=new Set([A(e),A(t)]),s=0;for(;r.length>0;){let i=r.pop(),a=A(i);this.hasNode(a)||(await this.addNode(a),s+=1);for(let f of this.record(i).successors()){let c=A(f);n.has(c)||(r.push(f,G(f)),n.add(c))}}return s}async extractSnarls(e){let t=0;for(let[r,n]of await this.overlappingSnarls(e))t+=await this.betweenNodes(r,n);return t}async overlappingSnarls(e){let t=[];if(e!=="none"){let r=!1;for(let n of this.sortedHandles()){let s=this.record(n),i=s.next;i!==void 0&&(r=!0,this.hasHandle(i)?le(n,i)&&t.push([n,i]):e==="overlapping"&&this.isSnarlEntryInSubgraph(s)&&t.push([n,i]))}if(!r&&e==="overlapping"&&await this.db.hasChainLinks()){let n=await this.findCoveringSnarl();n&&t.push(n)}}return t}isSnarlEntryInSubgraph(e){let t=e.successors(),r=t.find(n=>this.hasHandle(n));return r===void 0?!1:t.length>1||this.record(G(r)).successors().length>1}recordReader(e){let t=new Map;return async r=>{let n=this.records.get(r);if(n)return n;let s=t.get(r);if(!s){if(s=await this.db.getRecord(r),e?.(),!s)throw new Error(`Node record ${r} is missing from the database`);t.set(r,s)}return s}}async findCoveringSnarl(){let e=this.recordReader(),t=async f=>{let c=f.successors(),l=c[0];return l===void 0?!1:c.length>1||(await e(G(l))).successors().length>1},r=async f=>{let c=await e(G(f));return c.next!==void 0?await t(c)?{kind:"snarl-exit",snarl:[G(f),c.next]}:{kind:"chain"}:(await e(f)).next!==void 0?{kind:"chain"}:{kind:"regular"}},n=new Set,s=this.sortedHandles().flatMap(f=>this.record(f).successors()),i,a=!1;for(;!a&&s.length>0;){let f=s.shift(),c=A(f);if(!this.hasHandle(f)&&!n.has(c)){n.add(c);let l=await r(f);if(l.kind==="snarl-exit")i=l.snarl,a=!0;else if(l.kind==="chain")a=!0;else for(let p of["forward","reverse"])s.push(...(await e(Y(c,p))).successors())}}return i}extractPaths(e,t){if(this.clearPaths(),t==="none")return;let r=e?.position;this.refPath=e?.name,this.refHandle=e?.handle;let n=this.sortedHandles(),s=n.length,i=new Map;n.forEach((g,b)=>i.set(g,b));let a=new Int32Array(s+1),f=new Int32Array(s),c=[];for(let g=0;g<s;g++){let b=this.record(n[g]),E=b.gbwt().decompressArrays();f[g]=b.sequenceLen,c.push(E),a[g+1]=a[g]+E.nodes.length}let l=a[s],p=new Int32Array(l),u=new Int32Array(l),h=new Uint8Array(l);for(let g=0;g<s;g++){let b=c[g];p.set(b.nodes,a[g]),u.set(b.offsets,a[g])}c.length=0;for(let g=0;g<l;g++){let b=i.get(p[g]);b===void 0?p[g]=-1:(p[g]=b,h[a[b]+u[g]]=1)}let d=r===void 0?void 0:i.get(r.handle),m=r?.gbwtOffset,x,w=(g,b,E)=>{let I=[],C=0,_=0,v=-1,O=g,L=b;for(;;){O===d&&L===m&&(v=C),E&&(E.push(n[O]),I.push(L)),C+=1,_+=f[O];let N=a[O]+L,F=p[N];if(F<0)break;L=u[N],O=F}return{offsets:I,len:_,refAt:v,last:O}},y=(g,b,E,I)=>{I>=0&&(this.refId=this.paths.length,x=I),this.paths.push({path:g,offsets:b,len:E,weight:void 0,identity:void 0})},S=new Int32Array(s),R=d!==void 0&&M(n[d]);for(let g=0;g<s;g++){let b=n[g];if(!M(b)){let E=a[g],I=a[g+1]-E;for(let C=0;C<I;C++)if(h[E+C]===0){let _=[],{offsets:v,len:O,refAt:L,last:N}=w(g,C,_),F=n[N];if(L>=0||Me(b,F)){if(y(_,v,O,L),!M(F)){let H=i.get(G(F));S[H]=S[H]+1}}else this.twinStarts.add(re({node:b,offset:C}))}}}for(let g=0;g<s;g++){let b=n[g];if(M(b)){let E=a[g],I=a[g+1]-E,C=0;for(let v=0;v<I;v++)h[E+v]===0&&(C+=1);let _=!R&&C===S[g];for(let v=0;v<I;v++)if(h[E+v]===0){let O=_?void 0:w(g,v,void 0);if(O&&(O.refAt>=0||Me(b,n[O.last]))){let L=[],{offsets:N,len:F,refAt:H}=w(g,v,L);y(L,N,F,H)}else this.twinStarts.add(re({node:b,offset:v}))}}}if(r){if(x===void 0||this.refId===void 0)throw this.clearPaths(),new Error("Could not find the reference path");let g=this.paths[this.refId],b=r.nodeOffset;for(let I of g.path.slice(0,x))b+=this.record(I).sequenceLen;let E=r.seqOffset-b;this.refInterval=[E,E+g.len],g.identity={pathHandle:e.handle,name:e.name,orientation:"forward",hapStart:E,hapEnd:E+g.len}}if(t==="distinct")this.distinctPaths();else if(t==="reference-only"){if(this.refId===void 0)throw new Error("Reference path is required for reference-only output");this.paths=[this.paths[this.refId]],this.refId=0}}distinctPaths(){let e=this.refId===void 0?void 0:this.paths[this.refId].path;this.paths.sort((n,s)=>Ct(n.path,s.path)||n.len-s.len);let t=[],r;for(let n of this.paths){let s=t[t.length-1];s&&Ct(s.path,n.path)===0?s.weight=(s.weight??0)+1:(e&&Ct(n.path,e)===0&&(r=t.length),t.push({...n,weight:1}))}this.paths=t,this.refId=r}keepHaplotypes(e){let t=this.refId===void 0?void 0:this.paths[this.refId],r=this.paths.filter((s,i)=>i===this.refId||s.identity!==void 0&&e(s.identity.name)),n=new Set;for(let s of r)for(let i of s.path)n.add(A(i));for(let s of[...this.records.keys()])n.has(A(s))||this.records.delete(s);this.paths=r,this.refId=t===void 0?void 0:r.indexOf(t)}async walkHaplotypesFromAnchor(e,t,r,n,s){let i=e.position.seqOffset,a=i+t,f=Math.floor(i/r)*r,c=Math.min(r,qn),l=4*(r+t)+c,p={spacing:r,anchorOffset:f,anchorNodeOffset:-1,anchorHandle:-1,referenceSteps:0,rows:0,walks:[],graphFetches:0,scans:[],scanRows:0,fallback:void 0,ms:{reference:0,rows:0,walks:0,scan:0,sampled:0}};this.stats.anchorWalk=p;let u=performance.now(),h=()=>{let k=performance.now(),j=k-u;return u=k,j};this.clearPaths(),this.records.clear();let d=this.recordReader(()=>{p.graphFetches+=1}),m=await this.db.haplotypeAnchor(e.handle,f);if(m===void 0)throw new Error(`The haplotype index names no anchor for ${$(e.name,e.name.fragment)} at offset ${f}; it was not built with anchors at ${r} bp for this graph`);p.anchorNodeOffset=m.pathOffset;let x=await this.prefetchReferenceRange(e.handle,m.pathOffset,a+c);if(!x)throw new Error(`Path ${$(e.name,e.name.fragment)} has not been indexed for random access`);let w=await this.walkReference(d,x,m,i,a,a+c),{anchor:y,refOffsetOf:S,refHandles:R,windowSteps:g}=w;p.anchorHandle=y.pos.node,p.referenceSteps=w.steps,this.walkedBp=t;let b=[],E=[],I=0;for(let k of g)await this.ensureNode(A(k.pos.node)),b.push(k.pos.node),E.push(k.pos.offset),I+=this.record(k.pos.node).sequenceLen;let C=g[0];if(C===void 0)throw new Error("The reference walk has no node in the window");this.refPath=e.name,this.refHandle=e.handle,this.refInterval=[C.refOffset,C.refOffset+I],this.refId=0,this.paths.push({path:b,offsets:E,len:I,weight:void 0,identity:{pathHandle:e.handle,name:e.name,orientation:"forward",hapStart:C.refOffset,hapEnd:C.refOffset+I}}),p.ms.reference=h();let _=await this.db.haplotypeSamplesAtNode(y.pos.node);p.rows=_.length,p.ms.rows=h();let v=_.find(k=>k.offset===y.pos.offset&&k.pathHandle===e.handle&&k.pathOffset===y.offset);if(v===void 0)throw new Error(`The haplotype index has no anchor row for ${$(e.name,e.name.fragment)} at offset ${y.offset} (node ${A(y.pos.node)}); it was not built with anchors at ${r} bp for this graph`);let O=await this.db.pathsByHandle(),L=k=>{let j=O.get(k);if(!j)throw new Error(`Path ${k} is missing from the database`);return j.name},N=new Set([e.handle]),F=new Map;for(let k of _)if(k!==v&&n(L(k.pathHandle))){let j=F.get(k.pathHandle);j?j.push(k):F.set(k.pathHandle,[k])}let H;for(let[k,j]of F)if(H===void 0){let ae=te=>Math.abs(te.offset-v.offset);j.sort((te,En)=>ae(te)-ae(En));let fe;for(let te of j)N.has(k)||(fe=await this.walkAndKeep(d,te,"anchor",L(k),S,a,l,s,N,p));N.has(k)||(H=fe)}p.ms.walks=h();let xe=H===void 0?await this.samplesOfUnwalkedContigs(b,S,R,n,N,L,p):new Map;if(p.ms.scan=h(),xe.size>0){await this.mapReferenceBefore(d,e.handle,Math.max(0,m.pathOffset-2*r),m.pathOffset,S,R);for(let[k,j]of xe)if(H===void 0){let ae=L(k),fe;for(let te of j)fe??=await this.entryBefore(d,te,S,R,this.refInterval[0],l);H=fe===void 0?`no sample of ${$(ae,ae.fragment)} on the window's nodes runs with the reference`:await this.walkAndKeep(d,fe,"sample",ae,S,a,l,s,N,p)}p.ms.sampled=h()}return p.fallback=H,H}async walkAndKeep(e,t,r,n,s,i,a,f,c,l){let p=await this.walkFromRow(e,t,n,s,this.refInterval[0],i,a,f);l.walks.push({pathHandle:t.pathHandle,from:r,steps:p.steps,pieces:p.infos.length,end:p.end});let u;return p.end==="bound"?u=`${$(n,t.pathOffset)} walked ${p.steps} steps from its ${r} without reaching the window's end (${p.end})`:(c.add(t.pathHandle),this.paths.push(...p.infos)),u}async mapReferenceBefore(e,t,r,n,s,i){let a=await this.prefetchReferenceRange(t,r,n),f=a?.pos,c=a?.pathOffset??n;for(;f!==void 0&&f.node!==0&&c<n;){this.signal?.throwIfAborted();let l=await e(f.node),p=A(f.node);s.has(p)||(s.set(p,c),i.add(f.node)),c+=l.sequenceLen,f=l.gbwt().lf(f.offset)}}async runsWithReference(e,t,r,n,s){let i={node:t.node,offset:t.offset},a=0,f;for(;f===void 0;)if(this.signal?.throwIfAborted(),i===void 0||i.node===0||a>s)f=!1;else if(r.has(A(i.node)))f=n.has(i.node);else{let c=await e(i.node);a+=c.sequenceLen,i=c.gbwt().lf(i.offset)}return f}async entryBefore(e,t,r,n,s,i){let a=(await e(t.node)).sequenceLen,f=async(h,d)=>{let m=(await e(h.node)).sequenceLen;return{node:h.node,offset:h.offset,pathHandle:t.pathHandle,orientation:t.orientation,pathOffset:t.orientation==="forward"?t.pathOffset-d:t.pathOffset+a+d-m}},c={node:t.node,offset:t.offset},l=0,p,u=!await this.runsWithReference(e,t,r,n,i);for(;!u;){this.signal?.throwIfAborted();let h=r.get(A(c.node));if(h!==void 0&&h<s)p=await f(c,l),u=!0;else if(l>i)p={...t},u=!0;else{let m=(await e(G(c.node))).gbwt().predecessorAt(c.offset);if(m===void 0)p=await f(c,l),u=!0;else{let x=await e(m),w=x.gbwt().offsetTo(c);if(w===void 0)throw new Error(`No offset in ${m} leads to ${c.node}:${c.offset}`);c={node:m,offset:w},l+=x.sequenceLen}}}return p}async walkReference(e,t,r,n,s,i){let a=new Map,f=new Set,c=[],l,p=t.pos,u=t.pathOffset,h=0;for(;p!==void 0&&p.node!==0&&u<i;){this.signal?.throwIfAborted();let d=await e(p.node),m=u+d.sequenceLen;if(l===void 0&&u===r.pathOffset){if(p.node!==r.node)throw new Error(`The reference walk reaches node ${A(p.node)} at offset ${u} where the haplotype index names node ${A(r.node)} as the anchor`);l={pos:p,offset:u}}if(l!==void 0){h+=1;let x=A(p.node);a.has(x)||(a.set(x,u),f.add(p.node)),u<s&&m>n&&c.push({pos:p,refOffset:u})}u=m,p=d.gbwt().lf(p.offset)}if(l===void 0)throw new Error(`The reference walk from offset ${t.pathOffset} never starts a node at the anchor offset ${r.pathOffset}`);return{anchor:l,refOffsetOf:a,refHandles:f,windowSteps:c,steps:h}}async walkFromRow(e,t,r,n,s,i,a,f){let c=(await e(t.node)).sequenceLen,l=t.orientation==="forward"?t.pathOffset:t.pathOffset+c,p=[],u=[],h=[],d=0,m=0,x=0,w,y,S={node:t.node,offset:t.offset};for(;y===void 0;)if(this.signal?.throwIfAborted(),S===void 0||S.node===0)y=w===void 0?"before the window":"ended in the window";else if(m>a)y="bound";else{let g=n.get(A(S.node)),b=w!==void 0;if(g!==void 0&&g>=i)y=b?"through the window":"past the window";else{!b&&g!==void 0&&g>=s&&(w=m);let E=await e(S.node);if(w!==void 0){let I={pos:S,at:m,len:E.sequenceLen};g===void 0?(h.push(I),d+=I.len):(d>f&&g<s?(p.push(u),u=[]):u.push(...h),h=[],d=0,u.push(I))}x+=1,m+=E.sequenceLen,S=E.gbwt().lf(S.offset)}}p.push(u);let R=[];for(let g of p){let b=g[0],E=g[g.length-1];if(b!==void 0&&E!==void 0){let I=[],C=[],_=0;for(let L of g)await this.ensureNode(A(L.pos.node)),I.push(L.pos.node),C.push(L.pos.offset),_+=L.len;let v=b.at,O=E.at+E.len;R.push({path:I,offsets:C,len:_,weight:void 0,identity:t.orientation==="forward"?{pathHandle:t.pathHandle,name:r,orientation:"forward",hapStart:l+v,hapEnd:l+O}:{pathHandle:t.pathHandle,name:r,orientation:"reverse",hapStart:l-O,hapEnd:l-v}})}}return{steps:x,end:y,infos:R}}async samplesOfUnwalkedContigs(e,t,r,n,s,i,a){let f=yr([...e].sort((l,p)=>l-p));a.scans=f;let c=new Map;for(let[l,p]of f){let u=await this.db.haplotypeSamplesInRange(l,p);a.scanRows+=u.length;for(let h of u){let d=t.has(A(h.node));if(!s.has(h.pathHandle)&&(!d||r.has(h.node))&&n(i(h.pathHandle))){let m=c.get(h.pathHandle)??[];d?m.unshift(h):m.push(h),c.set(h.pathHandle,m)}}}return c}async identifyPaths(){if(!this.db.hasHaplotypeIndex)throw new Error("The database has no HaplotypeSamples table; run gbz-haplotype-index on it");let e=await this.db.haplotypeSampleInterval()??4096,t=yr(this.sortedHandles());if(t.length===0)return;let r=new Map;for(let[d,m]of t)for(let x of await this.db.haplotypeSamplesInRange(d,m))r.set(re(x),x);let n=d=>{let m=0,x=t.length-1;for(;m<x;){let y=m+x+1>>1;t[y][0]<=d?m=y:x=y-1}let w=t[m];return w[0]<=d&&d<=w[1]},s=new Map;this.paths.forEach((d,m)=>{d.path.length>0&&m!==this.refId&&s.set(re(Be(d,0)),m)});let i=this.stats.identification;i.interval=e,i.scans=t,i.windowSamples=r.size,this.paths.forEach((d,m)=>{m!==this.refId&&i.fragmentLengths.push(d.len)});let a=this.recordReader(()=>{this.stats.identificationFetches+=1,i.graphFetches+=1}),f=d=>(i.graphLookups+=1,a(d)),c=async(d,m)=>{if(n(d.node))return r.get(re(d));this.stats.identificationFetches+=1,i.companionSeeks+=1,m.seeks+=1;let x=await this.db.haplotypeSampleAt(d.node,d.offset);return x||(i.companionMisses+=1),x},l=new Map,p=async d=>{let m=l.get(d);if(!m){let x=await this.db.getPath(d);if(!x)throw new Error(`Path ${d} is missing from the database`);m=x.name,l.set(d,m)}return m},u=(d,m,x)=>d.orientation==="forward"?{pathHandle:d.pathHandle,orientation:"forward",base:d.pathOffset-m}:{pathHandle:d.pathHandle,orientation:"reverse",base:d.pathOffset+m+x},h=(d,m)=>d.orientation==="forward"?{pathHandle:d.pathHandle,orientation:"forward",base:d.hapStart-m}:{pathHandle:d.pathHandle,orientation:"reverse",base:d.hapEnd+m};for(let d=0;d<this.paths.length;d++){let m=this.paths[d];if(d===this.refId||m.identity)continue;let x=[],w=new Set,y={fragments:0,steps:0,seeks:0,reentries:0,twinLandings:0,end:"endmarker",pathHandle:void 0};i.chains.push(y);let S,R=0,g=d,b;for(;S===void 0;){if(this.signal?.throwIfAborted(),g!==void 0){if(w.has(g)){y.end="cycle";break}w.add(g);let v=this.paths[g];x.push({index:g,startBp:R}),y.fragments+=1;let O=R;for(let N=0;N<v.path.length;N++){let F=Be(v,N),H=r.get(re(F)),xe=this.record(F.node).sequenceLen;if(H){S=u(H,O,xe);break}O+=xe}if(R+=v.len,S){y.end="in-fragment sample";break}let L=Be(v,v.path.length-1);b=this.record(L.node).gbwt().lf(L.offset),g=void 0}if(b===void 0||b.node===0){y.end="endmarker";break}let E=re(b),I=s.get(E);if(I!==void 0){let v=this.paths[I].identity;if(v){S=h(v,R),y.end="identified sibling";break}g=I;continue}this.records.has(b.node)&&(y.reentries+=1),this.twinStarts.has(E)&&(y.twinLandings+=1);let C=await c(b,y),_=await f(b.node);if(C){S=u(C,R,_.sequenceLen),y.end="out-of-window sample";break}if(this.stats.identificationSteps+=1,y.steps+=1,R-x[x.length-1].startBp>4*e+4*_.sequenceLen){y.end="bound";break}R+=_.sequenceLen,b=_.gbwt().lf(b.offset)}if(S){y.pathHandle=S.pathHandle;let E=await p(S.pathHandle);for(let{index:I,startBp:C}of x){let _=this.paths[I];_.identity=S.orientation==="forward"?{pathHandle:S.pathHandle,name:E,orientation:"forward",hapStart:S.base+C,hapEnd:S.base+C+_.len}:{pathHandle:S.pathHandle,name:E,orientation:"reverse",hapStart:S.base-C-_.len,hapEnd:S.base-C}}}}}refIndex(e){if(this.refIndexCache===void 0){let t=new Map;e.forEach((r,n)=>{let s=t.get(r);s?s.push(n):t.set(r,[n])}),this.refIndexCache=t}return this.refIndexCache}refPrefix(e){if(this.refPrefixCache===void 0){let t=[0];e.forEach((r,n)=>{t.push(t[n]+this.record(r).sequenceLen)}),this.refPrefixCache=t}return this.refPrefixCache}orderedMatches(e,t){let r=this.refIndex(t),n=new Int32Array(e.length),s=new Int32Array(e.length),i=0,a=-1;for(let f=0;f<e.length;f++){let c=r.get(e[f]);if(c){let l=$n(c,a);if(l===void 0)return;n[i]=f,s[i]=l,i+=1,a=l}}return{pathAt:n,refAt:s,count:i}}pathLen(e){let t=0;for(let r of e)t+=this.record(r).sequenceLen;return t}prefixMatches(e,t){let r=0,n=0,s=0,i=0,a=0;for(;n<e.length&&s<t.length;){let f=this.record(e[n]).sequence,c=this.record(t[s]).sequence;for(;i<f.length&&a<c.length;){if(f[i]!==c[a])return r;i+=1,a+=1,r+=1}i===f.length&&(n+=1,i=0),a===c.length&&(s+=1,a=0)}return r}suffixMatches(e,t){let r=0,n=0,s=0,i=0,a=0;for(;n<e.length&&s<t.length;){let f=this.record(e[e.length-n-1]).sequence,c=this.record(t[t.length-s-1]).sequence;for(;i<f.length&&a<c.length;){if(f[f.length-i-1]!==c[c.length-a-1])return r;i+=1,a+=1,r+=1}i===f.length&&(n+=1,i=0),a===c.length&&(s+=1,a=0)}return r}align(e,t,r){let n=this.pathLen(e),s=this.pathLen(t),i=this.prefixMatches(e,t),a=this.suffixMatches(e,t);i+a>n&&(a=n-i),i+a>s&&(a=s-i),D(r,"M",i),br(r,n-i-a,s-i-a),D(r,"M",a)}sharedWeight(e,t){let r=this.refIndex(t),n=0;for(let s of e)r.has(s)&&(n+=this.record(s).sequenceLen);return n}editsAgainst(e,t){let r=this.orderedMatches(e,t);r?this.stats.orderedAlignments+=1:this.stats.lcsAlignments+=1;let n=r??Hn(wr(e,t,p=>this.record(p).sequenceLen)[0]),s=[],i=this.refPrefix(t),a=(p,u,h,d)=>{p===u?D(s,"D",i[d]-i[h]):h===d?D(s,"I",this.pathLen(e.slice(p,u))):this.align(e.slice(p,u),t.slice(h,d),s)},f=0,c=0,l=0;for(let p=0;p<n.count;p++){let u=n.pathAt[p],h=n.refAt[p];(c!==u||l!==h)&&a(c,u,l,h);let d=this.record(e[u]).sequenceLen;D(s,"M",d),f+=d,c=u+1,l=h+1}return a(c,e.length,l,t.length),{edits:s,matched:f}}alignment(e){let t=this.paths[e];if(this.refId===void 0||e===this.refId||!t)return;let r=this.paths[this.refId].path,n;if(sr(r))n={edits:this.editsAgainst(t.path,r).edits,flipped:!1};else{let s=t.path.map(f=>G(f)).reverse(),i=this.sharedWeight(t.path,r);if(this.sharedWeight(s,r)===0)n={edits:this.editsAgainst(t.path,r).edits,flipped:!1};else if(i===0)n={edits:this.editsAgainst(s,r).edits,flipped:!0};else{let f=this.editsAgainst(t.path,r),c=this.editsAgainst(s,r);n=c.matched>f.matched?{edits:c.edits,flipped:!0}:{edits:f.edits,flipped:!1}}}return n}alignToRef(e){return this.alignment(e)?.edits.map(([t,r])=>`${r}${t}`).join("")}alignments(){let e=this.referenceInterval;if(this.refId===void 0||!e)throw new Error("Alignments need a reference path");let t=this.paths[this.refId].path,r=this.refPrefix(t)[t.length],n=[];return this.paths.forEach((s,i)=>{if(i===this.refId)return;let{edits:a,flipped:f}=this.alignment(i),c=0,l=0;for(;c<a.length&&a[c][0]==="D";)l+=a[c][1],c+=1;let p=a.length,u=0;for(;p>c&&a[p-1][0]==="D";)u+=a[p-1][1],p-=1;let h=s.identity,d=h?h.orientation==="forward"!==f:!f;n.push({strand:d?"+":"-",refStart:e.start+l,refEnd:e.start+r-u,edits:a.slice(c,p),weight:s.weight,path:s.path,start:Be(s,0),identity:h===void 0?void 0:{pathHandle:h.pathHandle,name:h.name,hapStart:h.name.fragment+h.hapStart,hapEnd:h.name.fragment+h.hapEnd,walkForward:h.orientation==="forward"}})}),Dn(n).map(s=>{let{edits:i,identity:a,...f}=s,c={...f,cigar:Qn(i)};return a?{...c,resolved:!0,name:a.name,label:$({...a.name,fragment:a.hapStart},a.hapEnd),pathHandle:a.pathHandle,hapStart:a.hapStart,hapEnd:a.hapEnd}:{...c,resolved:!1}})}canonicalEdges(e){let t=[];for(let r of["forward","reverse"]){let n=Y(e,r);for(let s of this.record(n).successors())this.hasHandle(s)&&le(n,s)&&t.push([r==="reverse"?1:0,A(s),M(s)?1:0])}return t.sort((r,n)=>r[0]-n[0]||r[1]-n[1]||r[2]-n[2]),t.filter((r,n)=>n===0||r[0]!==t[n-1][0]||r[1]!==t[n-1][1]||r[2]!==t[n-1][2])}async stableName(){let e=new TextEncoder,t=[];for(let r of this.sortedHandles())if(!M(r)){let n=A(r),s=`S	${n}	${this.record(r).sequence}
+`;for(let[i,a,f]of this.canonicalEdges(n))s+=`L	${n}	${i?"-":"+"}	${a}	${f?"-":"+"}
+`;t.push(e.encode(s))}return gr(t)}async toGFA(e={}){let t=e.cigar??!1,r=[this.refPath?`H	VN:Z:1.1	RS:Z:${this.refPath.sample}`:"H	VN:Z:1.1",...mr(ur(await this.stableName(),await this.db.graphName()))],n=this.sortedHandles();for(let c of n)M(c)||r.push(`S	${A(c)}	${this.record(c).sequence}`);let s=c=>M(c)?"-":"+";for(let c of n)for(let l of this.record(c).successors())this.hasHandle(l)&&le(c,l)&&r.push(`L	${A(c)}	${s(c)}	${A(l)}	${s(l)}	0M`);let i=(c,l,p,u,h)=>{let d=Rt(c,l).map(w=>`${M(w)?"<":">"}${A(w)}`).join(""),m=c.weight===void 0?"":`	WT:i:${c.weight}`,x=h===void 0?"":`	CG:Z:${h}`;return`W	${p.sample}	${p.haplotype}	${p.contig}	${p.fragment}	${u}	${d}${m}${x}`},a=this.refPath?.contig??"unknown";this.refId!==void 0&&this.refPath&&this.refInterval&&r.push(i(this.paths[this.refId],void 0,{...this.refPath,fragment:this.refPath.fragment+this.refInterval[0]},this.refPath.fragment+this.refInterval[1],void 0));let f=1;return this.paths.forEach((c,l)=>{if(l!==this.refId){let p=e.names==="resolved"?c.identity:void 0,u=t?this.alignToRef(l):void 0;r.push(p?i(c,p,{...p.name,fragment:p.name.fragment+p.hapStart},p.name.fragment+p.hapEnd,u):i(c,void 0,{sample:"unknown",contig:a,haplotype:f,fragment:0},c.len,u)),f+=1}}),`${r.join(`
+`)}
+`}outputPaths(e){let t=e.cigar??!1,r=[],n=this.refPath?.contig??"unknown";if(this.refId!==void 0&&this.refPath&&this.refInterval){let i={...this.refPath,fragment:this.refPath.fragment+this.refInterval[0]};r.push({info:this.paths[this.refId],identity:void 0,name:$(i,this.refPath.fragment+this.refInterval[1]),cigar:void 0})}let s=1;return this.paths.forEach((i,a)=>{if(a===this.refId)return;let f=e.names==="resolved"?i.identity:void 0;r.push({info:i,identity:f,name:f?$({...f.name,fragment:f.name.fragment+f.hapStart},f.name.fragment+f.hapEnd):$({sample:"unknown",contig:n,haplotype:s,fragment:0},i.len),cigar:t?this.alignToRef(a):void 0}),s+=1}),r}*outputEdges(){for(let e of this.sortedHandles())for(let t of this.record(e).successors())this.hasHandle(t)&&le(e,t)&&(yield[e,t])}toSubgraphJson(e={}){let t=this.sortedHandles().filter(s=>!M(s)).map(s=>({id:String(A(s)),sequence:this.record(s).sequence})),r=[];for(let[s,i]of this.outputEdges())r.push({from:String(A(s)),from_is_reverse:M(s),to:String(A(i)),to_is_reverse:M(i)});let n=this.outputPaths(e).map(s=>Un(s.info,s.identity,s.name,s.cigar));return{nodes:t,edges:r,paths:n}}toCompactSubgraph(e={}){let t=this.sortedHandles().filter(i=>!M(i)),r=new Int32Array(t.length),n=[];t.forEach((i,a)=>{r[a]=A(i),n.push(this.record(i).sequence)});let s=[];for(let[i,a]of this.outputEdges())s.push(i,a);return{nodeIds:r,nodeSequences:n,edges:Int32Array.from(s),paths:this.outputPaths(e).map(i=>({name:i.name,weight:i.info.weight,cigar:i.cigar,steps:Int32Array.from(Rt(i.info,i.identity))}))}}};function Rt(o,e){return e?.orientation==="reverse"?o.path.map(t=>G(t)).reverse():o.path}function Un(o,e,t,r){return{name:t,...o.weight===void 0?{}:{weight:o.weight},...r===void 0?{}:{cigar:r},path:Rt(o,e).map(n=>({id:String(A(n)),is_reverse:M(n)}))}}function Ct(o,e){let t=Math.min(o.length,e.length);for(let r=0;r<t;r++){let n=o[r],s=e[r];if(n!==s)return n<s?-1:1}return o.length-e.length}function D(o,e,t){if(t===0)return;let r=o[o.length-1];r?.[0]===e?r[1]+=t:o.push([e,t])}function Ge(o){return o===0?0:6+(o-1)}function br(o,e,t){if(e===0)D(o,"D",t);else if(t===0)D(o,"I",e);else{let r=Math.min(e,t),n=4*r+Ge(e-r)+Ge(t-r),s=Ge(e)+Ge(t);n<=s?(D(o,"M",r),D(o,"I",e-r),D(o,"D",t-r)):(D(o,"I",e),D(o,"D",t))}}function Qn(o){return o.map(([e,t])=>`${t}${e}`).join("")}async function De(o,e,t,r,n={}){let s=new Ie(o,n);try{let i=await s.pathPosition(Se(e,t));await s.prefetchReferenceWalk(i,r-t),await s.aroundInterval(i.position,r-t,n.context??100),await s.extractSnarls(n.snarls??"none"),s.extractPaths(i,n.haplotypes??"all")}catch(i){throw i instanceof V&&i.windowBp===void 0?new V(i.limit,{windowBp:r-t,walkedBp:s.referenceWalkedBp??0}):i}return s}async function Sr(o,e,t,r,n){if(!o.hasHaplotypeIndex)throw new Error("keep needs the haplotype index: this database cannot name its walks");let s=await o.haplotypeAnchorSpacing(),i,a;if(s!==void 0&&(n.haplotypes??"all")==="all"){let f=new Ie(o,n);try{let c=await f.pathPosition(Se(e,t));a=await f.walkHaplotypesFromAnchor(c,r-t,s,n.keep,n.context??100)}catch(c){throw c instanceof V&&c.windowBp===void 0?new V(c.limit,{windowBp:r-t,walkedBp:f.referenceWalkedBp??0}):c}if(a===void 0)i=f;else{a=`${a}; identified from the per-path samples instead`;let c=await De(o,e,t,r,n);await c.identifyPaths(),c.keepHaplotypes(n.keep),c.stats.anchorWalk=f.stats.anchorWalk,c.stats.anchorWalk&&(c.stats.anchorWalk.fallback=a),i=c}}else i=await De(o,e,t,r,n),await i.identifyPaths(),i.keepHaplotypes(n.keep);return i}function K(o,e){let t=0;for(let n=0;n<8;n++){let s=o[e+n];if(s===void 0)throw new Error("SQLite varint runs past the end of the buffer");if(t=t*128+(s&127),(s&128)===0)return[t,e+n+1]}let r=o[e+8];if(r===void 0)throw new Error("SQLite varint runs past the end of the buffer");if(t=t*256+r,!Number.isSafeInteger(t))throw new Error("SQLite varint exceeds the safe integer range");return[t,e+9]}function Yn(o,e,t){switch(t){case 1:return o.getInt8(e);case 2:return o.getInt16(e);case 3:return o.getInt8(e)<<16|o.getUint16(e+1);case 4:return o.getInt32(e);case 6:return o.getInt16(e)*4294967296+o.getUint32(e+2);default:{let r=o.getBigInt64(e);if(r>BigInt(Number.MAX_SAFE_INTEGER)||r<BigInt(Number.MIN_SAFE_INTEGER))throw new Error(`SQLite integer ${r} exceeds the safe integer range`);return Number(r)}}}var Vn=new TextDecoder;function ze(o){let[e,t]=K(o,0),r=[],n=t;for(;n<e;){let[a,f]=K(o,n);r.push(a),n=f}let s=new DataView(o.buffer,o.byteOffset,o.byteLength),i=e;return r.map(a=>{if(a===0)return null;if(a>=1&&a<=6){let f=a<=4?a:a===5?6:8,c=Yn(s,i,f);return i+=f,c}if(a===7){let f=s.getFloat64(i);return i+=8,f}if(a===8)return 0;if(a===9)return 1;if(a>=12){let f=a-12>>1,c=o.subarray(i,i+f);return i+=f,a%2===0?c:Vn.decode(c)}throw new Error(`SQLite serial type ${a} is reserved`)})}var Ae=2,qe=5,Ir=10,je=13;function Ar(o,e){return o[e]*256+o[e+1]}function 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r=this.decodedIndexPages.get(e);if(r)this.decodedIndexPages.delete(e);else if(r=new Array(t.cellCount),this.decodedIndexPages.size>=Xn){let n=this.decodedIndexPages.keys().next().value;n!==void 0&&this.decodedIndexPages.delete(n)}return this.decodedIndexPages.set(e,r),r}async indexCell(e,t,r,n){let s=this.decodedCells(e,r),i=s[n];if(!i){let a=Z(t,r,n),f=r.type===Ae,[c,l]=K(t,f?a+4:a);i={values:ze(await this.payload(t,l,c,!0)),leftChild:f?ee(t,a):0},s[n]=i}return i}async*indexScanFrom(e,t){let{page:r,header:n}=await this.pageAt(e),s=0,i=n.cellCount;for(;s<i;){let a=s+i>>1,f=await this.indexCell(e,r,n,a);vr(f.values,t)<0?s=a+1:i=a}for(let a=s;a<n.cellCount;a++){let f=await this.indexCell(e,r,n,a);n.type===Ae&&(yield*this.indexScanFrom(f.leftChild,t)),yield f.values}n.type===Ae&&(yield*this.indexScanFrom(n.rightChild,t))}async indexSeekLE(e,t){let r,n=e;for(;;){let{page:s,header:i}=await this.pageAt(n),a=0,f=i.cellCount,c=0;for(;a<f;){let l=a+f>>1,p=await 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r=e*this.blockSize,n=Math.min(this.blockSize,this.fileSize-r),s=this.read(n,r);return this.fetches+=1,this.blocks.set(e,s),this.forgetOnFailure(s,[e]),this.evict(),s}prefetch(e){let t=[...new Set(e.map(n=>Math.floor((n-1)*this.pageSize/this.blockSize)))].filter(n=>!this.blocks.has(n)).sort((n,s)=>n-s),r=0;for(;r<t.length;){let n=r+1;for(;n<t.length&&t[n]===t[n-1]+1;)n+=1;this.fetchRun(t[r],n-r),r=n}}fetchRun(e,t){let r=e*this.blockSize,n=Math.min(t*this.blockSize,this.fileSize-r),s=this.read(n,r);this.fetches+=1;let i=[];for(let a=0;a<t;a++){let f=a*this.blockSize;i.push(e+a),this.blocks.set(e+a,s.then(c=>c.subarray(f,f+this.blockSize)))}this.forgetOnFailure(s,i),this.evict()}forgetOnFailure(e,t){e.catch(()=>{for(let r of t)this.blocks.delete(r)})}evict(){for(;this.blocks.size>this.maxBlocks;){let e=this.blocks.keys().next().value;if(e===void 0)break;this.blocks.delete(e)}}async page(e){let t=(e-1)*this.pageSize;if(e<1||t+this.pageSize>this.fileSize)throw new Error(`SQLite page ${e} is 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t=this.objects.get(e);if(!t)throw new Error(`SQLite database has no object named ${e}`);return t.rootPage}indexOn(e){let t=[...this.objects.values()].find(r=>r.type==="index"&&r.tableName===e);if(!t)throw new Error(`SQLite table ${e} has no index`);return t.rootPage}byRowid(e,t){return this.btree.tableRowid(this.rootPage(e),t)}prefetchRows(e,t,r){return this.btree.prefetchRowidRange(this.rootPage(e),t,r)}scan(e){return this.btree.tableScan(this.rootPage(e))}indexSeekLE(e,t){return this.btree.indexSeekLE(this.indexOn(e),t)}indexScanFrom(e,t){return this.btree.indexScanFrom(this.indexOn(e),t)}has(e){return this.objects.has(e)}};var Pt="GBZ-base version 4",Qe=class extends Error{name="ForwardOnlyIndexError";constructor(){super("the haplotype index was written with --forward-only, which cannot name the walks stored against their reference (about half of them); rebuild it with gbz-haplotype-index without --forward-only")}},Ye=class extends Error{name="SchemaVersionError";found;constructor(e){super(e===void 0?"not a gbz-base database: its Tags table has no version":`unsupported database schema "${e}"; this reader understands "${Pt}"`),this.found=e}},Ve=class{sequenceLen;handle;edges;bwt;encodedSequence;next;decoded;constructor(e,t,r,n,s){this.handle=e,this.edges=t,this.bwt=r,this.encodedSequence=n,this.next=s,this.sequenceLen=fr(n)}get id(){return A(this.handle)}get orientation(){return ce(this.handle)}get sequence(){return this.decoded??=cr(this.encodedSequence),this.decoded}successors(){return this.edges.filter(e=>e.node!==0).map(e=>e.node)}gbwt(){if(this.edges.length===0)throw new Error(`GBWT record for handle ${this.handle} is empty`);return new Fe(this.edges,this.bwt)}};function T(o,e){if(typeof o!="number")throw new Error(`${e} is not a number in the database`);return o}function Ke(o,e){if(typeof o!="string")throw new Error(`${e} is not text in the database`);return o}function _t(o,e){if(!(o instanceof 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wn.BaseFeatureDataAdapter{constructor(){super(...arguments);this.recordsAreAlignments=!0}static{this.capabilities=["getFeatures","getRefNames"]}async hasDataForRefName(){return!0}getFeaturesInMultipleRegions(t,r={}){let{clipToRegion:n,splitAtGapBp:s,...i}=r,a=n&&this.recordsAreAlignments,f=(0,yn.createStatusFanOut)(i.statusCallback);return Ft(t).pipe(me((c,l)=>this.getFeatures(c,{...i,statusCallback:f()}).pipe(me(p=>a?xn(p,c,s):[p]),gt(),Pe(p=>({index:l,features:p})))),gt(),me(c=>c.sort((l,p)=>l.index-p.index).flatMap(l=>l.features)))}};var Vt=class extends Error{constructor(){super("this .gbz.db has no HaplotypeSamples/HaplotypeLengths tables, so its walks cannot be named; run gbz-haplotype-index (from @gmod/gbz-base) over it first");this.name="NoHaplotypeIndexError"}},Kt=class extends Error{constructor(t,r){super(r.length===0?`the graph names no reference sample (gbwt_reference_samples) and the anchor "${t}" maps to none; set referenceSample`:`the anchor "${t}" is none of the graph's reference samples (${r.join(", ")}); set referenceSample or map it through assemblyNameToPanSN`);this.name="NoReferenceSampleError"}};function ge(o){return`${o.sample}#${o.haplotype}`}function No(o,e){let t=ge(o);return e===void 0||e.some(r=>Oe(t,r))}var Xt=class extends Error{constructor(t,r){super(`the graph is cut on its reference, ${r}; a window on ${t} has no reference coordinates to cut at. Open the graph from a ${r} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}},Zt=class extends Error{constructor(t,r,n){super(`this ${r.toLocaleString()} bp window reads more than nodeLimit (${t.toLocaleString()}) graph nodes; zoom in to about ${n.toLocaleString()} bp or raise nodeLimit`);this.name="NodeLimitError"}};function bn(o,e,t){if(o instanceof Error&&(o.name==="SubgraphLimitError"||/^Subgraph size limit of \d+ nodes exceeded/.test(o.message))){let n=o.walkedBp,s=typeof n=="number"&&n>0?Math.floor(n*.8):Math.floor(t/2);return new Zt(e,t,Math.max(s,1))}else return}function Sn(o,e){let t=ge(e);return o[t]??o[e.sample]??t}function Fo({configured:o,anchorPrefix:e,referenceSamples:t}){let r=tr(e);if(o!=="")return o;if(t.includes(r))return r;if(t.length===1)return t[0];throw new Kt(e,t)}function Ho(o,e){return`${ge(o)}#${o.contig}@${e.start.node}.${e.start.offset}`}function $o({alignment:o,assemblyName:e,refName:t,lane:r}){let{refStart:n,refEnd:s,strand:i,cigar:a}=o;if(!(!o.resolved||s<=n)){let{name:f,hapStart:c,hapEnd:l}=o,p=Ho(f,o),u={uniqueId:p,assemblyName:e,refName:t,start:n,end:s,type:"match",strand:i==="-"?-1:1,CIGAR:a,syntenyId:p,mate:{refName:f.contig,start:c,end:l,assemblyName:r}};return new ie(u)}}var Jt=class extends vt{constructor(){super(...arguments);this.graph=(0,vn.cachedSetup)({label:"Opening pangenome database",setup:async()=>{let t=this.getConf("haplotypeIndexLocation"),r=!("uri"in t)||t.uri!=="",n=await Ce.open((0,Yt.openLocation)(this.getConf("gbzDbLocation"),this.pluginManager),r?{haplotypeIndex:(0,Yt.openLocation)(t,this.pluginManager)}:{}),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 i=(await n.tag("gbwt_reference_samples")??"").split(/\s+/).filter(f=>f!==""),a=Fo({configured:this.getConf("referenceSample"),anchorPrefix:ye(this,s),referenceSamples:i});return{db:n,anchor:s,referenceSample:a,referenceSamples:i}}})}async referenceQuery(t,r){let{db:n,referenceSample:s}=await this.graph(r),i=(await n.paths()).find(a=>a.isIndexed&&a.name.sample===s&&a.name.contig===t);return i?{sample:i.name.sample,contig:t,haplotype:i.name.haplotype}:void 0}async getHaplotypes(t={}){let{db:r,referenceSamples:n}=await this.graph(t),s=new Map;for(let i of await r.paths()){let a=ge(i.name),f=s.get(a);f?f.contigs.includes(i.name.contig)||f.contigs.push(i.name.contig):s.set(a,{prefix:a,sample:i.name.sample,haplotype:i.name.haplotype,contigs:[i.name.contig],isReference:n.includes(i.name.sample)})}return[...s.values()]}async getHeader(t={}){let{anchor:r,referenceSample:n,referenceSamples:s}=await this.graph(t),i=It(this),a=[];for(let f of await this.getHaplotypes(t))f.sample!==n&&a.push({name:Sn(i,f),label:f.prefix,group:f.sample});return{hasCoarseTier:!1,anchorAssemblyName:r,referenceSample:n,referenceSamples:s,lanes:a}}async getRefNames(t={}){let{db:r,anchor:n,referenceSample:s}=await this.graph(t),{assemblyName:i}=t,a=i===n?void 0:ye(this,i),f=(await r.paths()).filter(c=>i===n?c.isIndexed&&c.name.sample===s:Oe(ge(c.name),a)).map(c=>c.name.contig);return[...new Set(f)]}keepPredicate(t,r){let n=t===void 0||t.length===0?void 0:t.map(s=>ye(this,s));return n===void 0&&r===void 0?void 0:s=>No(s,n)&&(r===void 0||Oe(ge(s),r))}async getSubgraph(t,r={}){let{db:n,anchor:s}=await this.graph(),{assemblyName:i,refName:a,start:f,end:c}=t;if(i!==s)throw new Xt(i,s);let l=await this.referenceQuery(a,{}),p=this.getConf("nodeLimit"),u=this.keepPredicate(r.haplotypes),h=l?await n.getSubgraphForRange(l,f,c,{context:this.getConf("context"),snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:p,signal:r.signal,...u===void 0?{}:{keep:u}}).catch(d=>{throw bn(d,p,c-f)??d}):void 0;return h?h.toGFA({names:"resolved"}):""}getFeatures(t,r={}){return(0,An.ObservableCreate)(async n=>{let{db:s,anchor:i}=await this.graph(r);if(!s.hasHaplotypeIndex)throw new Vt;let{assemblyName:a,refName:f,start:c,end:l}=t;if(a===i){let p=ye(this,r.targetAssemblyName),u=It(this),h=this.keepPredicate(r.haplotypes,p),d=await this.referenceQuery(f,r),m=this.getConf("nodeLimit"),x=d?await(0,In.updateStatus)(`Reading graph ${f}:${c.toLocaleString()}-${l.toLocaleString()}`,r.statusCallback,()=>s.getAlignmentsForRange(d,c,l,{context:this.getConf("context"),haplotypes:"all",limit:m,signal:r.signal,...h===void 0?{}:{keep:h}}).catch(w=>{throw bn(w,m,l-c)??w})):[];for(let w of x)if(w.resolved){let y=$o({alignment:w,assemblyName:a,refName:f,lane:Sn(u,w.name)});y!==void 0&&n.next(y)}}n.complete()},r.signal)}};export{Xt as HaplotypeWindowError,Vt as NoHaplotypeIndexError,Kt as NoReferenceSampleError,Zt as NodeLimitError,Jt as default,$o as fragmentFeature,ge as haplotypePrefix,Sn as laneAssemblyName,bn as nodeLimitError,Fo as resolveReferenceSample};
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