jbrowse-plugin-graphgenomeviewer 1.0.1 → 3.0.4

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-6UTRY4CV.js

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0:{...r,queryStart:r.queryStart+(t?d.I:p.I),queryEnd:r.queryEnd-(t?p.I:d.I),targetStart:r.targetStart+p.D,targetEnd:r.targetEnd-d.D,edits:n,sharedBases:r.sharedBases-a}}function Co(r,e,t,n){let o={query:new Uint8Array(e),target:new Uint8Array(t)},s=r.map(f=>{let l=[];Gt(f,(p,d,h,u)=>{if(p==="="||p==="X")for(let m=0;m<d;m++)l.push([f.strand==="-"?h-m:h+m,u+m])});for(let[p,d]of l)o.query[p]=Math.min(255,o.query[p]+1),o.target[d]=Math.min(255,o.target[d]+1);return l}),i={query:new Map,target:new Map};s.forEach((f,l)=>{for(let[p,d]of f)for(let[h,u]of[["query",p],["target",d]])if(o[h][u]>1){let m=i[h].get(u);m?m.at(-1)!==l&&m.push(l):i[h].set(u,[l])}});let a=new Map,c=(f,l,p)=>{let d=`${p}:${f}:${l}`,h=a.get(d);if(h===void 0){let[u,m]=Gn(r[f],p),[y,x]=Gn(r[l],p),S=Math.max(u,y),g=Math.min(m,x);h=Bn(r[f],p,S,g)<Bn(r[l],p,S,g),a.set(d,h)}return h};return r.flatMap((f,l)=>{let p=s[l],d=new 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u=L(p)!==L(e[h]),m=u?-1:1;if(!f.has(c(d-1,h-m,u))){let y=d,x=h;for(;y<r.length&&x>=0&&x<e.length&&f.has(c(y,x,u));)y+=1,x+=m;let S=x-m;l.push({qs:t[d],qe:t[y],ts:n[Math.min(h,S)],te:n[Math.max(h,S)+1],flipped:u})}}}),l}function Kn(r,e,t,n={}){let o=Dn(r,t),s=Dn(e,t),i=Ro(r,e,zn(r,t),zn(e,t)),a=n.minMatch??mo,c=[];for(let f of $t(i,n.maxGap??1/0,a,xo)){let l=[],p=f[0],d=f.at(-1),{flipped:h}=p.run;Qe(f,o,s,l,(u,m,y,x,S)=>{for(let g of Ao(u,m,y,a)){let b=S+m.length;c.push({...g,queryStart:x+g.queryStart,queryEnd:x+g.queryEnd,targetStart:h?b-g.targetEnd:S+g.targetStart,targetEnd:h?b-g.targetStart:S+g.targetEnd,strand:h?"+":"-",edits:h?g.edits.reverse():g.edits,shared:[]})}}),c.push({queryStart:p.run.qs+p.trim,queryEnd:d.run.qe,targetStart:h?d.run.ts:p.run.ts+p.trim,targetEnd:h?p.run.te-p.trim:d.run.te,strand:h?"-":"+",edits:h?l.reverse():l,sharedBases:f.reduce((u,{run:m,trim:y})=>u+m.qe-m.qs-y,0),shared:f.map(({run:u,trim:m})=>[u.qs+m,u.qe])})}return Co(c,o.length,s.length,a).map(({shared:f,...l})=>l).sort((f,l)=>f.queryStart-l.queryStart)}function Xn(r){return r.map(([e,t])=>`${t}${e}`).join("")}var X=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 ${t.windowBp} bp window`),this.limit=e,this.windowBp=t?.windowBp,this.walkedBp=t?.walkedBp}};function Dt(r,e){return r[0]<e[0]||r[0]===e[0]&&(r[1]<e[1]||r[1]===e[1]&&r[2]<e[2])}var _e=class{heap=[];push(e,t,n){let o=this.heap;o.push([e,t,n]);let s=o.length-1;for(;s>0;){let i=s-1>>1;if(Dt(o[s],o[i]))[o[s],o[i]]=[o[i],o[s]],s=i;else break}}pop(){let e=this.heap,t=e[0],n=e.pop();if(e.length>0&&n!==void 0){e[0]=n;let o=0;for(;;){let s=2*o+1,i=s+1,a=o;if(s<e.length&&Dt(e[s],e[a])&&(a=s),i<e.length&&Dt(e[i],e[a])&&(a=i),a===o)break;[e[o],e[a]]=[e[a],e[o]],o=a}}return t}get size(){return this.heap.length}};function _o(r){let e=new Int32Array(r.length),t=new Int32Array(r.length);return r.forEach(([n,o],s)=>{e[s]=n,t[s]=o}),{pathAt:e,refAt:t,count:r.length}}function Po(r,e){let t=0,n=r.length;for(;t<n;){let o=t+n>>1;r[o]>e?n=o:t=o+1}return r[t]}function fe(r){return`${r.node}:${r.offset}`}function ko(r,e){let t=e.identity.hapStart-r.identity.hapEnd,n=r.strand==="+"?e.refStart-r.refEnd:r.refStart-e.refEnd;return r.strand===e.strand&&t>=0&&n>=0?{insertion:t,deletion:n}:void 0}function Mo(r,e,t){let[n,o]=r.strand==="+"?[r,e]:[e,r],s=n.edits.map(([f,l])=>[f,l]);Jn(s,t.insertion,t.deletion);for(let[f,l]of o.edits)z(s,f,l);let i=r.identity.walkForward,[a,c]=i?[r,e]:[e,r];return{strand:r.strand,refStart:n.refStart,refEnd:o.refEnd,edits:s,weight:void 0,path:[...a.path,...c.path],start:a.start,identity:{pathHandle:r.identity.pathHandle,name:r.identity.name,hapStart:r.identity.hapStart,hapEnd:e.identity.hapEnd,walkForward:i}}}function Oo(r){if(r.some(o=>o.weight!==void 0))return r;let e=new Map;r.forEach((o,s)=>{if(o.identity){let i=e.get(o.identity.pathHandle);i?i.push(s):e.set(o.identity.pathHandle,[s])}});let t=new Map,n=new Set;for(let o of e.values()){o.sort((a,c)=>r[a].identity.hapStart-r[c].identity.hapStart);let s=o[0],i=r[s];for(let a of o.slice(1)){let c=r[a],f=ko(i,c);f?(i=Mo(i,c,f),n.add(a)):(t.set(s,i),s=a,i=c)}t.set(s,i)}return r.flatMap((o,s)=>n.has(s)?[]:[t.get(s)??o])}function Ye(r,e){return{node:r.path[e],offset:r.offsets[e]}}var Lo=4096;function Zn(r){let e=[];for(let t of r){let n=e[e.length-1];n&&t-n[1]<=Lo?n[1]=t:e.push([t,t])}return e}var To=32768,No=65536;function Fo(r){let e=[...r].sort((n,o)=>n-o),t=[];for(let n of e){let o=t[t.length-1];o&&n-o[1]<=To?o[1]=n:t.push([n,n])}return t}var Pe=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(V(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 X(this.limit);let t=await this.db.getRecord(V(e,"forward")),n=await this.db.getRecord(V(e,"reverse"));if(!t||!n)throw new Error(`Node ${e} does not exist in the graph`);this.records.set(t.handle,t),this.records.set(n.handle,n)}async ensureNode(e){this.hasNode(e)||await this.addNode(e)}clearPaths(){this.paths=[],this.twinStarts.clear(),this.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 ${q(e,e.fragment)}`);if(!t.isIndexed)throw new Error(`Path ${q(t.name,t.name.fragment)} has not been indexed for random access`);let n=e.fragment-t.name.fragment,o=await this.db.indexedPosition(t.handle,n);if(!o)throw new Error(`Path ${q(t.name,t.name.fragment)} has not been indexed for random access`);return this.findPathPosition(t,n,o.pathOffset,o.pos)}async findPathPosition(e,t,n,o){let s=n,i=o;for(;;){await this.ensureNode(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 c=a.gbwt().lf(i.offset);if(!c)throw new Error(`Path ${q(e.name,e.name.fragment)} does not contain offset ${t}`);i=c}}async aroundPosition(e,t,n){let o=A(e);await this.ensureNode(o);let s=this.record(e),i=me(e),a=new _e;return a.push(t,o,He(i)),a.push(s.sequenceLen-t-1,o,qe(i)),this.insertContext(a,n)}prefetchReferenceWalk(e,t){return this.prefetchReferenceRange(e.handle,e.position.seqOffset,e.position.seqOffset+t)}async prefetchReferenceRange(e,t,n){let[o,s]=await Promise.all([this.db.indexedPosition(e,t),this.db.indexedPosition(e,n)]);if(o&&s){let i=o.pos.node,a=s.pos.node;if(!await this.db.prefetchRecords(Math.min(i,a),Math.max(i,a)+1)){let f=await this.db.indexedPositionsBetween(e,t,n),l=Fo(f.map(p=>p.pos.node));await Promise.all(l.map(([p,d])=>this.db.prefetchRecords(p,d+2)))}}return o}async aroundInterval(e,t,n){if(t===0)throw new Error("Interval length must be greater than 0");this.walkedBp=0;try{return await this.walkInterval(e,t,n)}catch(o){throw o instanceof X&&o.windowBp===void 0?new X(o.limit,{windowBp:t,walkedBp:this.walkedBp}):o}}get referenceWalkedBp(){return this.walkedBp}async walkInterval(e,t,n){let o={node:e.handle,offset:e.gbwtOffset},s=e.nodeOffset,i=t,a=new _e;for(;;){let c=A(o.node),f=me(o.node);this.walkedBp=t-i,await this.ensureNode(c);let l=this.record(o.node);if(s>=l.sequenceLen)throw new Error(`Offset ${s} in node ${c} of length ${l.sequenceLen}`);a.push(s,c,He(f));let p=l.sequenceLen-s;if(i<=p){a.push(i===p?0:p-i-1,c,qe(f));break}a.push(0,c,qe(f));let d=l.gbwt().lf(o.offset);if(!d)throw new Error(`No successor for GBWT position (${o.node}, ${o.offset})`);o=d,s=0,i-=p}return this.walkedBp=t,this.insertContext(a,n)}async aroundNodes(e,t){let n=new _e;for(let o of e)await this.ensureNode(o),n.push(0,o,"left"),n.push(0,o,"right");return this.insertContext(n,t)}async insertContext(e,t){this.clearPaths();let n=new Set,o=new Set;for(let i of this.records.keys())o.add(A(i));let s=0;for(;e.size>0;){let[i,a,c]=e.pop(),f=`${a}:${c}`;if(n.has(f))continue;n.add(f),o.delete(a),this.hasNode(a)||(await this.addNode(a),s+=1);let l=vn(c);if(!n.has(`${a}:${l}`)){let h=this.record(V(a,In(c))),u=i+h.sequenceLen-1;u<=t&&e.push(u,a,l)}let p=this.record(V(a,An(c))),d=i+1;if(d<=t)for(let h of p.successors()){let u=A(h),m=He(me(h));n.has(`${u}:${m}`)||e.push(d,u,m)}}for(let i of o)this.records.delete(V(i,"forward")),this.records.delete(V(i,"reverse"));return{inserted:s,removed:o.size}}async betweenNodes(e,t){this.clearPaths();let n=[e,G(t)],o=new Set([A(e),A(t)]),s=0;for(;n.length>0;){let i=n.pop(),a=A(i);this.hasNode(a)||(await this.addNode(a),s+=1);for(let c of this.record(i).successors()){let f=A(c);o.has(f)||(n.push(c,G(c)),o.add(f))}}return s}async extractSnarls(e){let t=0;for(let[n,o]of await this.overlappingSnarls(e))t+=await this.betweenNodes(n,o);return t}async overlappingSnarls(e){let t=[];if(e!=="none"){let n=!1;for(let o of this.sortedHandles()){let s=this.record(o),i=s.next;i!==void 0&&(n=!0,this.hasHandle(i)?ge(o,i)&&t.push([o,i]):e==="overlapping"&&this.isSnarlEntryInSubgraph(s)&&t.push([o,i]))}if(!n&&e==="overlapping"&&await this.db.hasChainLinks()){let o=await this.findCoveringSnarl();o&&t.push(o)}}return t}isSnarlEntryInSubgraph(e){let t=e.successors(),n=t.find(o=>this.hasHandle(o));return n===void 0?!1:t.length>1||this.record(G(n)).successors().length>1}recordReader(e){let t=new Map;return async n=>{let o=this.records.get(n);if(o)return o;let s=t.get(n);if(!s){if(s=await this.db.getRecord(n),e?.(),!s)throw new Error(`Node record ${n} is missing from the database`);t.set(n,s)}return s}}async findCoveringSnarl(){let e=this.recordReader(),t=async c=>{let f=c.successors(),l=f[0];return l===void 0?!1:f.length>1||(await e(G(l))).successors().length>1},n=async c=>{let f=await e(G(c));return f.next!==void 0?await t(f)?{kind:"snarl-exit",snarl:[G(c),f.next]}:{kind:"chain"}:(await e(c)).next!==void 0?{kind:"chain"}:{kind:"regular"}},o=new Set,s=this.sortedHandles().flatMap(c=>this.record(c).successors()),i,a=!1;for(;!a&&s.length>0;){let c=s.shift(),f=A(c);if(!this.hasHandle(c)&&!o.has(f)){o.add(f);let l=await n(c);if(l.kind==="snarl-exit")i=l.snarl,a=!0;else if(l.kind==="chain")a=!0;else for(let p of["forward","reverse"])s.push(...(await e(V(f,p))).successors())}}return i}extractPaths(e,t){if(this.clearPaths(),t==="none")return;let n=e?.position;this.refPath=e?.name,this.refHandle=e?.handle;let o=this.sortedHandles(),s=o.length,i=new Map;o.forEach((w,v)=>i.set(w,v));let a=new Int32Array(s+1),c=new Int32Array(s),f=[];for(let w=0;w<s;w++){let v=this.record(o[w]),I=v.gbwt().decompressArrays();c[w]=v.sequenceLen,f.push(I),a[w+1]=a[w]+I.nodes.length}let l=a[s],p=new Int32Array(l),d=new Int32Array(l),h=new Uint8Array(l);for(let w=0;w<s;w++){let v=f[w];p.set(v.nodes,a[w]),d.set(v.offsets,a[w])}f.length=0;for(let w=0;w<l;w++){let v=i.get(p[w]);v===void 0?p[w]=-1:(p[w]=v,h[a[v]+d[w]]=1)}let u=n===void 0?void 0:i.get(n.handle),m=n?.gbwtOffset,y,x=(w,v,I)=>{let R=[],C=0,_=0,E=-1,k=w,O=v;for(;;){k===u&&O===m&&(E=C),I&&(I.push(o[k]),R.push(O)),C+=1,_+=c[k];let N=a[k]+O,F=p[N];if(F<0)break;O=d[N],k=F}return{offsets:R,len:_,refAt:E,last:k}},S=(w,v,I,R)=>{R>=0&&(this.refId=this.paths.length,y=R),this.paths.push({path:w,offsets:v,len:I,weight:void 0,identity:void 0})},g=new Int32Array(s),b=u!==void 0&&L(o[u]);for(let w=0;w<s;w++){let v=o[w];if(!L(v)){let I=a[w],R=a[w+1]-I;for(let C=0;C<R;C++)if(h[I+C]===0){let _=[],{offsets:E,len:k,refAt:O,last:N}=x(w,C,_),F=o[N];if(O>=0||$e(v,F)){if(S(_,E,k,O),!L(F)){let H=i.get(G(F));g[H]=g[H]+1}}else this.twinStarts.add(fe({node:v,offset:C}))}}}for(let w=0;w<s;w++){let v=o[w];if(L(v)){let I=a[w],R=a[w+1]-I,C=0;for(let E=0;E<R;E++)h[I+E]===0&&(C+=1);let _=!b&&C===g[w];for(let E=0;E<R;E++)if(h[I+E]===0){let k=_?void 0:x(w,E,void 0);if(k&&(k.refAt>=0||$e(v,o[k.last]))){let O=[],{offsets:N,len:F,refAt:H}=x(w,E,O);S(O,N,F,H)}else this.twinStarts.add(fe({node:v,offset:E}))}}}if(n){if(y===void 0||this.refId===void 0)throw this.clearPaths(),new Error("Could not find the reference path");let w=this.paths[this.refId],v=n.nodeOffset;for(let R of w.path.slice(0,y))v+=this.record(R).sequenceLen;let I=n.seqOffset-v;this.refInterval=[I,I+w.len],w.identity={pathHandle:e.handle,name:e.name,orientation:"forward",hapStart:I,hapEnd:I+w.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((o,s)=>zt(o.path,s.path)||o.len-s.len);let t=[],n;for(let o of this.paths){let s=t[t.length-1];s&&zt(s.path,o.path)===0?s.weight=(s.weight??0)+1:(e&&zt(o.path,e)===0&&(n=t.length),t.push({...o,weight:1}))}this.paths=t,this.refId=n}keepHaplotypes(e){let t=this.refId===void 0?void 0:this.paths[this.refId],n=this.paths.filter((s,i)=>i===this.refId||s.identity!==void 0&&e(s.identity.name)),o=new Set;for(let s of n)for(let i of s.path)o.add(A(i));for(let s of[...this.records.keys()])o.has(A(s))||this.records.delete(s);this.paths=n,this.refId=t===void 0?void 0:n.indexOf(t)}async walkHaplotypesFromAnchor(e,t,n,o,s){let i=e.position.seqOffset,a=i+t,c=Math.floor(i/n)*n,f=Math.min(n,No),l=4*(n+t)+f,p={spacing:n,anchorOffset:c,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 d=performance.now(),h=()=>{let M=performance.now(),U=M-d;return d=M,U};this.clearPaths(),this.records.clear();let u=this.recordReader(()=>{p.graphFetches+=1}),m=await this.db.haplotypeAnchor(e.handle,c);if(m===void 0)throw new Error(`The haplotype index names no anchor for ${q(e.name,e.name.fragment)} at offset ${c}; it was not built with anchors at ${n} bp for this graph`);p.anchorNodeOffset=m.pathOffset;let y=await this.prefetchReferenceRange(e.handle,m.pathOffset,a+f);if(!y)throw new Error(`Path ${q(e.name,e.name.fragment)} has not been indexed for random access`);let x=await this.walkReference(u,y,m,i,a,a+f),{anchor:S,refOffsetOf:g,refHandles:b,windowSteps:w}=x;p.anchorHandle=S.pos.node,p.referenceSteps=x.steps,this.walkedBp=t;let v=[],I=[],R=0;for(let M of w)await this.ensureNode(A(M.pos.node)),v.push(M.pos.node),I.push(M.pos.offset),R+=this.record(M.pos.node).sequenceLen;let C=w[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+R],this.refId=0,this.paths.push({path:v,offsets:I,len:R,weight:void 0,identity:{pathHandle:e.handle,name:e.name,orientation:"forward",hapStart:C.refOffset,hapEnd:C.refOffset+R}}),p.ms.reference=h();let _=await this.db.haplotypeSamplesAtNode(S.pos.node);p.rows=_.length,p.ms.rows=h();let E=_.find(M=>M.offset===S.pos.offset&&M.pathHandle===e.handle&&M.pathOffset===S.offset);if(E===void 0)throw new Error(`The haplotype index has no anchor row for ${q(e.name,e.name.fragment)} at offset ${S.offset} (node ${A(S.pos.node)}); it was not built with anchors at ${n} bp for this graph`);let k=await this.db.pathsByHandle(),O=M=>{let U=k.get(M);if(!U)throw new Error(`Path ${M} is missing from the database`);return U.name},N=new Set([e.handle]),F=new Map;for(let M of _)if(M!==E&&o(O(M.pathHandle))){let U=F.get(M.pathHandle);U?U.push(M):F.set(M.pathHandle,[M])}let H;for(let[M,U]of F)if(H===void 0){let he=ae=>Math.abs(ae.offset-E.offset);U.sort((ae,to)=>he(ae)-he(to));let de;for(let ae of U)N.has(M)||(de=await this.walkAndKeep(u,ae,"anchor",O(M),g,a,l,s,N,p));N.has(M)||(H=de)}p.ms.walks=h();let Ie=H===void 0?await this.samplesOfUnwalkedContigs(v,g,b,o,N,O,p):new Map;if(p.ms.scan=h(),Ie.size>0){await this.mapReferenceBefore(u,e.handle,Math.max(0,m.pathOffset-2*n),m.pathOffset,g,b);for(let[M,U]of Ie)if(H===void 0){let he=O(M),de;for(let ae of U)de??=await this.entryBefore(u,ae,g,b,this.refInterval[0],l);H=de===void 0?`no sample of ${q(he,he.fragment)} on the window's nodes runs with the reference`:await this.walkAndKeep(u,de,"sample",he,g,a,l,s,N,p)}p.ms.sampled=h()}return p.fallback=H,H}async walkAndKeep(e,t,n,o,s,i,a,c,f,l){let p=await this.walkFromRow(e,t,o,s,this.refInterval[0],i,a,c);l.walks.push({pathHandle:t.pathHandle,from:n,steps:p.steps,pieces:p.infos.length,end:p.end});let d;return p.end==="bound"||p.infos.length===0?d=`${q(o,t.pathOffset)} walked ${p.steps} steps from its ${n} without writing a walk through the window (${p.end})`:(f.add(t.pathHandle),this.paths.push(...p.infos)),d}async mapReferenceBefore(e,t,n,o,s,i){let a=await this.prefetchReferenceRange(t,n,o),c=a?.pos,f=a?.pathOffset??o;for(;c!==void 0&&c.node!==0&&f<o;){this.signal?.throwIfAborted();let l=await e(c.node),p=A(c.node);s.has(p)||(s.set(p,f),i.add(c.node)),f+=l.sequenceLen,c=l.gbwt().lf(c.offset)}}async runsWithReference(e,t,n,o,s){let i={node:t.node,offset:t.offset},a=0,c;for(;c===void 0;)if(this.signal?.throwIfAborted(),i===void 0||i.node===0||a>s)c=!1;else if(n.has(A(i.node)))c=o.has(i.node);else{let f=await e(i.node);a+=f.sequenceLen,i=f.gbwt().lf(i.offset)}return c}async entryBefore(e,t,n,o,s,i){let a=(await e(t.node)).sequenceLen,c=async(h,u)=>{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-u:t.pathOffset+a+u-m}},f={node:t.node,offset:t.offset},l=0,p,d=!await this.runsWithReference(e,t,n,o,i);for(;!d;){this.signal?.throwIfAborted();let h=n.get(A(f.node));if(h!==void 0&&h<s)p=await c(f,l),d=!0;else if(l>i)p={...t},d=!0;else{let m=(await e(G(f.node))).gbwt().predecessorAt(f.offset);if(m===void 0)p=await c(f,l),d=!0;else{let y=await e(m),x=y.gbwt().offsetTo(f);if(x===void 0)throw new Error(`No offset in ${m} leads to ${f.node}:${f.offset}`);f={node:m,offset:x},l+=y.sequenceLen}}}return p}async walkReference(e,t,n,o,s,i){let a=new Map,c=new Set,f=[],l,p=t.pos,d=t.pathOffset,h=0;for(;p!==void 0&&p.node!==0&&d<i;){this.signal?.throwIfAborted();let u=await e(p.node),m=d+u.sequenceLen;if(l===void 0&&d===n.pathOffset){if(p.node!==n.node)throw new Error(`The reference walk reaches node ${A(p.node)} at offset ${d} where the haplotype index names node ${A(n.node)} as the anchor`);l={pos:p,offset:d}}if(l!==void 0){h+=1;let y=A(p.node);a.has(y)||(a.set(y,d),c.add(p.node)),d<s&&m>o&&f.push({pos:p,refOffset:d})}d=m,p=u.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 ${n.pathOffset}`);return{anchor:l,refOffsetOf:a,refHandles:c,windowSteps:f,steps:h}}async walkFromRow(e,t,n,o,s,i,a,c){let f=(await e(t.node)).sequenceLen,l=t.orientation==="forward"?t.pathOffset:t.pathOffset+f,p=[],d=[],h=[],u=0,m=0,y=0,x,S,g={node:t.node,offset:t.offset};for(;S===void 0;)if(this.signal?.throwIfAborted(),g===void 0||g.node===0)S=x===void 0?"before the window":"ended in the window";else if(m>a)S="bound";else{let w=o.get(A(g.node)),v=x!==void 0;if(w!==void 0&&w>=i)S=v?"through the window":"past the window";else{!v&&w!==void 0&&w>=s&&(x=m);let I=await e(g.node);if(x!==void 0){let R={pos:g,at:m,len:I.sequenceLen};w===void 0?(h.push(R),u+=R.len):(u>c&&w<s?(p.push(d),d=[]):d.push(...h),h=[],u=0,d.push(R))}y+=1,m+=I.sequenceLen,g=I.gbwt().lf(g.offset)}}p.push(d);let b=[];for(let w of p){let v=w[0],I=w[w.length-1];if(v!==void 0&&I!==void 0){let R=[],C=[],_=0;for(let O of w)await this.ensureNode(A(O.pos.node)),R.push(O.pos.node),C.push(O.pos.offset),_+=O.len;let E=v.at,k=I.at+I.len;b.push({path:R,offsets:C,len:_,weight:void 0,identity:t.orientation==="forward"?{pathHandle:t.pathHandle,name:n,orientation:"forward",hapStart:l+E,hapEnd:l+k}:{pathHandle:t.pathHandle,name:n,orientation:"reverse",hapStart:l-k,hapEnd:l-E}})}}return{steps:y,end:S,infos:b}}async samplesOfUnwalkedContigs(e,t,n,o,s,i,a){let c=Zn([...e].sort((l,p)=>l-p));a.scans=c;let f=new Map;for(let[l,p]of c){let d=await this.db.haplotypeSamplesInRange(l,p);a.scanRows+=d.length;for(let h of d){let u=t.has(A(h.node));if(!s.has(h.pathHandle)&&(!u||n.has(h.node))&&o(i(h.pathHandle))){let m=f.get(h.pathHandle)??[];u?m.unshift(h):m.push(h),f.set(h.pathHandle,m)}}}return f}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=Zn(this.sortedHandles());if(t.length===0)return;let n=new Map;for(let[u,m]of t)for(let y of await this.db.haplotypeSamplesInRange(u,m))n.set(fe(y),y);let o=u=>{let m=0,y=t.length-1;for(;m<y;){let S=m+y+1>>1;t[S][0]<=u?m=S:y=S-1}let x=t[m];return x[0]<=u&&u<=x[1]},s=new Map;this.paths.forEach((u,m)=>{u.path.length>0&&m!==this.refId&&s.set(fe(Ye(u,0)),m)});let i=this.stats.identification;i.interval=e,i.scans=t,i.windowSamples=n.size,this.paths.forEach((u,m)=>{m!==this.refId&&i.fragmentLengths.push(u.len)});let a=this.recordReader(()=>{this.stats.identificationFetches+=1,i.graphFetches+=1}),c=u=>(i.graphLookups+=1,a(u)),f=async(u,m)=>{if(o(u.node))return n.get(fe(u));this.stats.identificationFetches+=1,i.companionSeeks+=1,m.seeks+=1;let y=await this.db.haplotypeSampleAt(u.node,u.offset);return y||(i.companionMisses+=1),y},l=new Map,p=async u=>{let m=l.get(u);if(!m){let y=await this.db.getPath(u);if(!y)throw new Error(`Path ${u} is missing from the database`);m=y.name,l.set(u,m)}return m},d=(u,m,y)=>u.orientation==="forward"?{pathHandle:u.pathHandle,orientation:"forward",base:u.pathOffset-m}:{pathHandle:u.pathHandle,orientation:"reverse",base:u.pathOffset+m+y},h=(u,m)=>u.orientation==="forward"?{pathHandle:u.pathHandle,orientation:"forward",base:u.hapStart-m}:{pathHandle:u.pathHandle,orientation:"reverse",base:u.hapEnd+m};for(let u=0;u<this.paths.length;u++){let m=this.paths[u];if(u===this.refId||m.identity)continue;let y=[],x=new Set,S={fragments:0,steps:0,seeks:0,reentries:0,twinLandings:0,end:"endmarker",pathHandle:void 0};i.chains.push(S);let g,b=0,w=u,v;for(;g===void 0;){if(this.signal?.throwIfAborted(),w!==void 0){if(x.has(w)){S.end="cycle";break}x.add(w);let E=this.paths[w];y.push({index:w,startBp:b}),S.fragments+=1;let k=b;for(let N=0;N<E.path.length;N++){let F=Ye(E,N),H=n.get(fe(F)),Ie=this.record(F.node).sequenceLen;if(H){g=d(H,k,Ie);break}k+=Ie}if(b+=E.len,g){S.end="in-fragment sample";break}let O=Ye(E,E.path.length-1);v=this.record(O.node).gbwt().lf(O.offset),w=void 0}if(v===void 0||v.node===0){S.end="endmarker";break}let I=fe(v),R=s.get(I);if(R!==void 0){let E=this.paths[R].identity;if(E){g=h(E,b),S.end="identified sibling";break}w=R;continue}this.records.has(v.node)&&(S.reentries+=1),this.twinStarts.has(I)&&(S.twinLandings+=1);let C=await f(v,S),_=await c(v.node);if(C){g=d(C,b,_.sequenceLen),S.end="out-of-window sample";break}if(this.stats.identificationSteps+=1,S.steps+=1,b-y[y.length-1].startBp>4*e+4*_.sequenceLen){S.end="bound";break}b+=_.sequenceLen,v=_.gbwt().lf(v.offset)}if(g){S.pathHandle=g.pathHandle;let I=await p(g.pathHandle);for(let{index:R,startBp:C}of y){let _=this.paths[R];_.identity=g.orientation==="forward"?{pathHandle:g.pathHandle,name:I,orientation:"forward",hapStart:g.base+C,hapEnd:g.base+C+_.len}:{pathHandle:g.pathHandle,name:I,orientation:"reverse",hapStart:g.base-C-_.len,hapEnd:g.base-C}}}}}refIndex(e){if(this.refIndexCache===void 0){let t=new Map;e.forEach((n,o)=>{let s=t.get(n);s?s.push(o):t.set(n,[o])}),this.refIndexCache=t}return this.refIndexCache}refPrefix(e){if(this.refPrefixCache===void 0){let t=[0];e.forEach((n,o)=>{t.push(t[o]+this.record(n).sequenceLen)}),this.refPrefixCache=t}return this.refPrefixCache}orderedMatches(e,t){let n=this.refIndex(t),o=new Int32Array(e.length),s=new Int32Array(e.length),i=0,a=-1;for(let c=0;c<e.length;c++){let f=n.get(e[c]);if(f){let l=Po(f,a);if(l===void 0)return;o[i]=c,s[i]=l,i+=1,a=l}}return{pathAt:o,refAt:s,count:i}}pathLen(e){let t=0;for(let n of e)t+=this.record(n).sequenceLen;return t}prefixMatches(e,t){let n=0,o=0,s=0,i=0,a=0;for(;o<e.length&&s<t.length;){let c=this.record(e[o]).sequence,f=this.record(t[s]).sequence;for(;i<c.length&&a<f.length;){if(c[i]!==f[a])return n;i+=1,a+=1,n+=1}i===c.length&&(o+=1,i=0),a===f.length&&(s+=1,a=0)}return n}suffixMatches(e,t){let n=0,o=0,s=0,i=0,a=0;for(;o<e.length&&s<t.length;){let c=this.record(e[e.length-o-1]).sequence,f=this.record(t[t.length-s-1]).sequence;for(;i<c.length&&a<f.length;){if(c[c.length-i-1]!==f[f.length-a-1])return n;i+=1,a+=1,n+=1}i===c.length&&(o+=1,i=0),a===f.length&&(s+=1,a=0)}return n}align(e,t,n){let o=this.pathLen(e),s=this.pathLen(t),i=this.prefixMatches(e,t),a=this.suffixMatches(e,t);i+a>o&&(a=o-i),i+a>s&&(a=s-i),z(n,"M",i),Jn(n,o-i-a,s-i-a),z(n,"M",a)}sharedWeight(e,t){let n=this.refIndex(t),o=0;for(let s of e)n.has(s)&&(o+=this.record(s).sequenceLen);return o}editsAgainst(e,t){let n=this.orderedMatches(e,t);n?this.stats.orderedAlignments+=1:this.stats.lcsAlignments+=1;let o=n??_o(qn(e,t,p=>this.record(p).sequenceLen)[0]),s=[],i=this.refPrefix(t),a=(p,d,h,u)=>{p===d?z(s,"D",i[u]-i[h]):h===u?z(s,"I",this.pathLen(e.slice(p,d))):this.align(e.slice(p,d),t.slice(h,u),s)},c=0,f=0,l=0;for(let p=0;p<o.count;p++){let d=o.pathAt[p],h=o.refAt[p];(f!==d||l!==h)&&a(f,d,l,h);let u=this.record(e[d]).sequenceLen;z(s,"M",u),c+=u,f=d+1,l=h+1}return a(f,e.length,l,t.length),{edits:s,matched:c}}alignment(e){let t=this.paths[e];if(this.refId===void 0||e===this.refId||!t)return;let n=this.paths[this.refId].path,o;if(En(n))o={edits:this.editsAgainst(t.path,n).edits,flipped:!1};else{let s=t.path.map(c=>G(c)).reverse(),i=this.sharedWeight(t.path,n);if(this.sharedWeight(s,n)===0)o={edits:this.editsAgainst(t.path,n).edits,flipped:!1};else if(i===0)o={edits:this.editsAgainst(s,n).edits,flipped:!0};else{let c=this.editsAgainst(t.path,n),f=this.editsAgainst(s,n);o=f.matched>c.matched?{edits:f.edits,flipped:!0}:{edits:c.edits,flipped:!1}}}return o}alignToRef(e){return this.alignment(e)?.edits.map(([t,n])=>`${n}${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,n=this.refPrefix(t)[t.length],o=[];return this.paths.forEach((s,i)=>{if(i===this.refId)return;let{edits:a,flipped:c}=this.alignment(i),f=0,l=0;for(;f<a.length&&a[f][0]==="D";)l+=a[f][1],f+=1;let p=a.length,d=0;for(;p>f&&a[p-1][0]==="D";)d+=a[p-1][1],p-=1;let h=s.identity,u=h?h.orientation==="forward"!==c:!c;o.push({strand:u?"+":"-",refStart:e.start+l,refEnd:e.start+n-d,edits:a.slice(f,p),weight:s.weight,path:s.path,start:Ye(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"}})}),Oo(o).map(s=>{let{edits:i,identity:a,...c}=s,f={...c,cigar:qo(i)};return a?{...f,resolved:!0,name:a.name,label:q({...a.name,fragment:a.hapStart},a.hapEnd),pathHandle:a.pathHandle,hapStart:a.hapStart,hapEnd:a.hapEnd}:{...f,resolved:!1}})}pairAlignments(e){let{target:t,query:n,maxGap:o}=e,s=this.paths.flatMap(l=>{let{identity:p}=l;return p?[{name:p.name,start:p.name.fragment+p.hapStart,steps:Ke(l,p)}]:[]}),i=l=>p=>p.sample===l.sample&&p.haplotype===l.haplotype,a=i(t),c=n?i(n):l=>!a(l),f=l=>this.record(V(l,"forward")).sequence;return s.filter(l=>a(l.name)).flatMap(l=>s.filter(p=>c(p.name)).flatMap(p=>Kn(p.steps,l.steps,f,o===void 0?{}:{maxGap:o}).map(d=>({query:p.name,queryStart:p.start+d.queryStart,queryEnd:p.start+d.queryEnd,strand:d.strand,target:l.name,targetStart:l.start+d.targetStart,targetEnd:l.start+d.targetEnd,cigar:Xn(d.edits),matches:d.edits.reduce((h,[u,m])=>h+(u==="="?m:0),0),columns:d.edits.reduce((h,[,u])=>h+u,0),sharedBases:d.sharedBases}))))}canonicalEdges(e){let t=[];for(let n of["forward","reverse"]){let o=V(e,n);for(let s of this.record(o).successors())this.hasHandle(s)&&ge(o,s)&&t.push([n==="reverse"?1:0,A(s),L(s)?1:0])}return t.sort((n,o)=>n[0]-o[0]||n[1]-o[1]||n[2]-o[2]),t.filter((n,o)=>o===0||n[0]!==t[o-1][0]||n[1]!==t[o-1][1]||n[2]!==t[o-1][2])}async stableName(){let e=new TextEncoder,t=[];for(let n of this.sortedHandles())if(!L(n)){let o=A(n),s=`S	${o}	${this.record(n).sequence}
+`;for(let[i,a,c]of this.canonicalEdges(o))s+=`L	${o}	${i?"-":"+"}	${a}	${c?"-":"+"}
+`;t.push(e.encode(s))}return Fn(t)}async toGFA(e={}){let t=e.cigar??!1,n=[this.refPath?`H	VN:Z:1.1	RS:Z:${this.refPath.sample}`:"H	VN:Z:1.1",...Nn(Tn(await this.stableName(),await this.db.graphName()))],o=this.sortedHandles();for(let f of o)L(f)||n.push(`S	${A(f)}	${this.record(f).sequence}`);let s=f=>L(f)?"-":"+";for(let f of o)for(let l of this.record(f).successors())this.hasHandle(l)&&ge(f,l)&&n.push(`L	${A(f)}	${s(f)}	${A(l)}	${s(l)}	0M`);let i=(f,l,p,d,h)=>{let u=Ke(f,l).map(x=>`${L(x)?"<":">"}${A(x)}`).join(""),m=f.weight===void 0?"":`	WT:i:${f.weight}`,y=h===void 0?"":`	CG:Z:${h}`;return`W	${p.sample}	${p.haplotype}	${p.contig}	${p.fragment}	${d}	${u}${m}${y}`},a=this.refPath?.contig??"unknown";this.refId!==void 0&&this.refPath&&this.refInterval&&n.push(i(this.paths[this.refId],void 0,{...this.refPath,fragment:this.refPath.fragment+this.refInterval[0]},this.refPath.fragment+this.refInterval[1],void 0));let c=1;return this.paths.forEach((f,l)=>{if(l!==this.refId){let p=e.names==="resolved"?f.identity:void 0,d=t?this.alignToRef(l):void 0;n.push(p?i(f,p,{...p.name,fragment:p.name.fragment+p.hapStart},p.name.fragment+p.hapEnd,d):i(f,void 0,{sample:"unknown",contig:a,haplotype:c,fragment:0},f.len,d)),c+=1}}),`${n.join(`
+`)}
+`}outputPaths(e){let t=e.cigar??!1,n=[],o=this.refPath?.contig??"unknown";if(this.refId!==void 0&&this.refPath&&this.refInterval){let i={...this.refPath,fragment:this.refPath.fragment+this.refInterval[0]};n.push({info:this.paths[this.refId],identity:void 0,name:q(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 c=e.names==="resolved"?i.identity:void 0;n.push({info:i,identity:c,name:c?q({...c.name,fragment:c.name.fragment+c.hapStart},c.name.fragment+c.hapEnd):q({sample:"unknown",contig:o,haplotype:s,fragment:0},i.len),cigar:t?this.alignToRef(a):void 0}),s+=1}),n}*outputEdges(){for(let e of this.sortedHandles())for(let t of this.record(e).successors())this.hasHandle(t)&&ge(e,t)&&(yield[e,t])}toSubgraphJson(e={}){let t=this.sortedHandles().filter(s=>!L(s)).map(s=>({id:String(A(s)),sequence:this.record(s).sequence})),n=[];for(let[s,i]of 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outside the file`);let n=await this.block(Math.floor(t/this.blockSize)),o=t%this.blockSize;return n.subarray(o,o+this.pageSize)}};var Me=class r{pager;btree;objects;constructor(e,t,n){this.pager=e,this.btree=t,this.objects=n}static async open(e,t={}){let{size:n}=await e.stat(),o=await e.read(Math.min(t.blockSize??65536,n),0),s=o.subarray(0,100);if(new TextDecoder().decode(s.subarray(0,15))!=="SQLite format 3")throw new Error("Not a SQLite database");let a=new DataView(s.buffer,s.byteOffset,s.byteLength),c=a.getUint16(16),f=c===1?65536:c,l=s[20]??0,p=a.getUint32(56);if(p!==1)throw new Error(`SQLite text encoding ${p} is not UTF-8`);let d=new nt(e,f,n,t);d.seed(0,o),d.fetches+=1,d.bytesFetched+=o.length;let h=new tt(d,l),u=new Map;for await(let{values:m}of h.tableScan(1)){let[y,x,S,g,b]=m;typeof y=="string"&&typeof x=="string"&&typeof S=="string"&&typeof g=="number"&&u.set(x,{type:y,name:x,tableName:S,rootPage:g,sql:typeof b=="string"?b:""})}return new r(d,h,u)}rootPage(e){let 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(n=>n.type==="index"&&n.tableName===e);if(!t)throw new Error(`SQLite table ${e} has no index`);return t.rootPage}byRowid(e,t){return this.btree.tableRowid(this.rootPage(e),t)}prefetchRows(e,t,n){return this.btree.prefetchRowidRange(this.rootPage(e),t,n)}scan(e){return this.btree.tableScan(this.rootPage(e))}indexSeekLE(e,t){return this.btree.indexSeekLE(this.indexOn(e),t)}indexScanFrom(e,t){return this.btree.indexScanFrom(this.indexOn(e),t)}has(e){return this.objects.has(e)}};var Ut="GBZ-base version 4",rt=class extends Error{name="ForwardOnlyIndexError";constructor(){super("the haplotype index was written with --forward-only, which cannot name the walks stored against their reference (about half of them); rebuild it with gbz-haplotype-index without --forward-only")}},ot=class extends Error{name="SchemaVersionError";found;constructor(e){super(e===void 0?"not a gbz-base database: its Tags table has no version":`unsupported database schema "${e}"; this reader understands "${Ut}"`),this.found=e}},st=class{sequenceLen;handle;edges;bwt;encodedSequence;next;decoded;constructor(e,t,n,o,s){this.handle=e,this.edges=t,this.bwt=n,this.encodedSequence=o,this.next=s,this.sequenceLen=_n(o)}get id(){return A(this.handle)}get orientation(){return me(this.handle)}get sequence(){return this.decoded??=Pn(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 ${this.handle} is empty`);return new Ge(this.edges,this.bwt)}};function T(r,e){if(typeof r!="number")throw new Error(`${e} is not a number in the database`);return r}function it(r,e){if(typeof r!="string")throw new Error(`${e} is not text in the database`);return r}function jt(r,e){if(!(r instanceof Uint8Array))throw new Error(`${e} is not a blob in the database`);return r}function or(r,e){return{handle:r,fwStart:{node:T(e[1],"Paths.fw_node"),offset:T(e[2],"Paths.fw_offset")},revStart:{node:T(e[3],"Paths.rev_node"),offset:T(e[4],"Paths.rev_offset")},name:{sample:it(e[5],"Paths.sample"),contig:it(e[6],"Paths.contig"),haplotype:T(e[7],"Paths.haplotype"),fragment:T(e[8],"Paths.fragment")},isIndexed:T(e[9],"Paths.is_indexed")!==0}}async function sr(r){let e=new Map;for await(let{values:t}of r.scan("Tags"))e.set(it(t[0],"Tags.key"),it(t[1],"Tags.value"));return e}var Oe=class r{tagCache;pathCache;pathMapCache;indexTags;sqlite;index;constructor(e,t){this.sqlite=e,this.index=t}static async open(e,t={}){let{haplotypeIndex:n,...o}=t,s=await Me.open(e,o);for(let f of["Tags","Nodes","Paths","ReferenceIndex"])s.rootPage(f);let i=n?await Me.open(n,o):s,a=new r(s,i),c=await a.tag("version");if(c!==Ut)throw new ot(c);if(n){for(let h of["Tags","HaplotypeSamples","HaplotypeLengths"])i.rootPage(h);a.indexTags=await sr(i);let f=a.indexTags.get("haplotype_index_paths"),l=await a.tag("paths");if(f!==l)throw new Error(`haplotype index was built for ${f??"an unknown number of"} paths but the graph has ${l}`);let p=a.indexTags.get("haplotype_index_nodes"),d=await a.tag("nodes");if(p!==void 0&&p!==d)throw new Error(`haplotype index was built for a graph with ${p} nodes but this one has ${d}`)}if(a.hasHaplotypeIndex&&await a.haplotypeIndexTag("haplotype_index_orientations")==="forward")throw new rt;return a}tags(){return this.tagCache??=sr(this.sqlite),this.tagCache}async tag(e){return(await this.tags()).get(e)}prefetchRecords(e,t){return this.sqlite.prefetchRows("Nodes",e,t)}async getRecord(e){let t=await this.sqlite.byRowid("Nodes",e);if(!t)return;let n=t[4];return new st(e,Rn(jt(t[1],"Nodes.edges")),jt(t[2],"Nodes.bwt"),jt(t[3],"Nodes.sequence"),typeof n=="number"?n:void 0)}paths(){return this.pathCache??=(async()=>{let e=[];for await(let{rowid:t,values:n}of this.sqlite.scan("Paths"))e.push(or(t,n));return e})(),this.pathCache}async getPath(e){let t=await this.sqlite.byRowid("Paths",e);return t?or(e,t):void 0}pathsByHandle(){return this.pathMapCache??=this.paths().then(e=>new Map(e.map(t=>[t.handle,t]))),this.pathMapCache}async findPath(e){return(await this.paths()).filter(n=>n.name.sample===e.sample&&n.name.contig===e.contig&&n.name.haplotype===e.haplotype&&n.name.fragment<=e.fragment).sort((n,o)=>o.name.fragment-n.name.fragment)[0]}async pathsForSample(e){return(await this.paths()).filter(t=>t.name.sample===e)}async pathsNamed(e){let t=Re(Hn(e),0);return(await this.paths()).filter(n=>n.name.sample===t.sample&&n.name.contig===t.contig&&n.name.haplotype===t.haplotype).sort((n,o)=>n.name.fragment-o.name.fragment)}async hasPath(e){return(await this.pathsNamed(e)).length>0}pathLengths=new Map;pathLength(e){let t=this.pathLengths.get(e);return 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_s({alignment:r,assemblyName:e,refName:t,lane:n}){let{refStart:o,refEnd:s,strand:i,cigar:a}=r;if(!(!r.resolved||s<=o)){let{name:c,hapStart:f,hapEnd:l}=r,p=Rs(c,r),d={uniqueId:p,assemblyName:e,refName:t,start:o,end:s,type:"match",strand:i==="-"?-1:1,CIGAR:a,syntenyId:p,mate:{refName:c.contig,start:f,end:l,assemblyName:n}};return new se(d)}}function Ps({pair:r,lane:e,mateLane:t}){let n=`${ie(r.target)}#${r.target.contig}:${r.targetStart}-${r.targetEnd}|${ie(r.query)}#${r.query.contig}:${r.queryStart}-${r.queryEnd}`;return new se({uniqueId:n,assemblyName:e,refName:r.target.contig,start:r.targetStart,end:r.targetEnd,type:"match",strand:r.strand==="-"?-1:1,CIGAR:r.cigar,syntenyId:n,identity:r.matches/Math.max(r.columns,1),numMatches:r.matches,blockLen:r.columns,mate:{refName:r.query.contig,start:r.queryStart,end:r.queryEnd,assemblyName:t}})}var xn=class extends Ot{constructor(){super(...arguments);this.graph=(0,Jr.cachedSetup)({label:"Opening pangenome database",setup:async()=>{let t=this.getConf("haplotypeIndexLocation"),n=!("uri"in t)||t.uri!=="",o=await Oe.open((0,dn.openLocation)(this.getConf("gbzDbLocation"),this.pluginManager),n?{haplotypeIndex:(0,dn.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 o.tag("gbwt_reference_samples")??"").split(/\s+/).filter(c=>c!==""),a=Cs({configured:this.getConf("referenceSample"),anchorPrefix:ue(this,s),referenceSamples:i});return{db:o,anchor:s,referenceSample:a,referenceSamples:i}}})}async referenceQuery(t,n){let{db:o,referenceSample:s}=await this.graph(n),i=(await o.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:n,referenceSamples:o}=await this.graph(t),s=new Map;for(let i of await n.paths()){let a=ie(i.name),c=s.get(a);c?c.contigs.includes(i.name.contig)||c.contigs.push(i.name.contig):s.set(a,{prefix:a,sample:i.name.sample,haplotype:i.name.haplotype,contigs:[i.name.contig],isReference:o.includes(i.name.sample)})}return[...s.values()]}async getHeader(t={}){let{anchor:n,referenceSample:o,referenceSamples:s}=await this.graph(t),i=Lt(this),a=[];for(let c of await this.getHaplotypes(t))c.sample!==o&&a.push({name:Zr(i,c),label:c.prefix,group:c.sample});return{hasCoarseTier:!1,anchorAssemblyName:n,referenceSample:o,referenceSamples:s,lanes:a}}async getRefNames(t={}){let{db:n,anchor:o,referenceSample:s}=await this.graph(t),{assemblyName:i}=t,a=i===o?void 0:ue(this,i),c=(await n.paths()).filter(f=>i===o?f.isIndexed&&f.name.sample===s:Ee(ie(f.name),a)).map(f=>f.name.contig);return[...new Set(c)]}keepPredicate(t,n){let o=t===void 0||t.length===0?void 0:t.map(s=>ue(this,s));return o===void 0&&n===void 0?void 0:s=>Es(s,o)&&(n===void 0||Ee(ie(s),n))}async getSubgraph(t,n={}){let{db:o,anchor:s}=await this.graph(),{assemblyName:i,refName:a,start:c,end:f}=t;if(i!==s)throw new yn(i,s);let l=await this.referenceQuery(a,{}),p=this.getConf("nodeLimit"),d=this.keepPredicate(n.haplotypes),h=l?await o.getSubgraphForRange(l,c,f,{context:this.getConf("context"),snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:p,signal:n.signal,...d===void 0?{}:{keep:d}}).catch(u=>{throw pn(u,p,f-c)??u}):void 0;return h?h.toGFA({names:"resolved"}):""}async laneHaplotypes(t,n){let o=ue(this,t);return(await this.getHaplotypes(n)).filter(s=>Ee(s.prefix,o))}async referencePieces(t,n,o,s){let{db:i,referenceSample:a}=await this.graph(s),c=(await i.paths()).filter(l=>l.isIndexed&&l.name.sample===a&&l.name.contig===t&&l.name.fragment>n&&l.name.fragment<o).map(l=>l.name.fragment),f=[n,...[...new Set(c)].sort((l,p)=>l-p),o];return f.slice(1).map((l,p)=>({start:f[p],end:l}))}async anchorFeatures(t,n){let{db:o}=await this.graph(n),{assemblyName:s,refName:i,start:a,end:c}=t,f=ue(this,n.targetAssemblyName),l=Lt(this),p=this.keepPredicate(n.haplotypes,f),d=await this.referenceQuery(i,n),h=this.getConf("nodeLimit");return(d?await(0,hn.updateStatus)(`Reading graph ${i}:${a.toLocaleString()}-${c.toLocaleString()}`,n.statusCallback,()=>o.getAlignmentsForRange(d,a,c,{context:this.getConf("context"),haplotypes:"all",limit:h,signal:n.signal,...p===void 0?{}:{keep:p}}).catch(m=>{throw pn(m,h,c-a)??m})):[]).flatMap(m=>{let y=m.resolved?_s({alignment:m,assemblyName:s,refName:i,lane:Zr(l,m.name)}):void 0;return y===void 0?[]:[y]})}async pairFeatures(t,n,o){let{targetAssemblyName:s}=o;if(s===void 0)throw new gn(n);let{db:i}=await this.graph(o),{refName:a,start:c,end:f}=t,l=await this.laneHaplotypes(n,o),p=await this.laneHaplotypes(s,o),d=[...l,...p],h=await this.referenceQuery(a,o),u=this.getConf("nodeLimit"),m=await i.haplotypeAnchorSpacing()!==void 0,y=(g,b)=>i.getSubgraphForRange(g,b.start,b.end,{context:this.getConf("context"),haplotypes:"all",limit:u,signal:o.signal,keep:w=>d.some(v=>v.sample===w.sample&&v.haplotype===w.haplotype)}).catch(w=>{throw pn(w,u,f-c)??w}),x=h&&m&&l.length>0&&p.length>0?(await(0,hn.updateStatus)(`Aligning ${n} to ${s}`,o.statusCallback,async()=>Promise.all((await this.referencePieces(a,c,f,o)).map(g=>y(h,g))))).filter(g=>g!==void 0):[];return x.every(g=>{let b=g.stats.anchorWalk;return b!==void 0&&b.fallback===void 0})?x.flatMap(g=>l.flatMap(b=>p.flatMap(w=>g.pairAlignments({target:b,query:w}).map(v=>Ps({pair:v,lane:n,mateLane:s}))))):[]}getFeatures(t,n={}){return(0,eo.ObservableCreate)(async o=>{let{db:s,anchor:i}=await this.graph(n);if(!s.hasHaplotypeIndex)throw new un;if(t.assemblyName===i){let a=n.queryAssemblyName===void 0?await this.anchorFeatures(t,n):await this.pairFeatures(t,n.queryAssemblyName,n);for(let c of a)o.next(c)}o.complete()},n.signal)}};export{yn as HaplotypeWindowError,un as NoHaplotypeIndexError,mn as NoReferenceSampleError,wn as NodeLimitError,gn as PairTargetError,xn as default,_s as fragmentFeature,ie as haplotypePrefix,Zr as laneAssemblyName,pn as nodeLimitError,Ps as pairFeature,Cs as resolveReferenceSample};
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