jbrowse-plugin-graphgenomeviewer 6.1.0 → 6.1.2

package/dist/chunks/{AddTrackWorkflow-U3UNCVXJ.js → AddTrackWorkflow-F5YBOJ3E.js}

@@ -1,2 +1,2 @@
-import{b as F,c as T,i as y}from"./chunk-4T7DPQTR.js";import{a as N}from"./chunk-J4OLMLS5.js";import{a as W}from"./chunk-FCWXYIFC.js";import{a as O}from"./chunk-J6KYLXRD.js";import{a as C,b as B,c as H,d as _}from"./chunk-TYJTJGPO.js";import{a as w,b as t}from"./chunk-FY3BTKY4.js";var S=w((q,L)=>{L.exports=JBrowseExports["@jbrowse/core/util/tss-react"]});var s=t(O(),1),i=t(B(),1),l=t(N(),1),A=t(S(),1),R=t(W(),1),e=t(_(),1),x=t(H(),1);var o=t(C(),1),j=(0,A.makeStyles)()(n=>({paper:{margin:n.spacing(),padding:n.spacing()},field:{marginTop:n.spacing(2)},submit:{marginTop:25,marginBottom:100,display:"block"}})),D=["RgfaTabixAdapter","MinigraphBubbleAdapter"],J=(0,x.observer)(function({model:r}){let{classes:c}=j(),h=(0,l.getSession)(r),b=(0,R.getRoot)(r),[m,G]=(0,s.useState)("RgfaTabixAdapter"),[p,v]=(0,s.useState)(),[g,P]=(0,s.useState)(),[u,I]=(0,s.useState)(""),[d,M]=(0,s.useState)("Pangenome graph"),[f,k]=(0,s.useState)();function E(){if(!(!p||!r.assembly))try{k(void 0);let a=d.trim();(0,l.addTrackFromWidget)({model:r,session:h,conf:y({choice:m,loc:p,indexLoc:g,assembly:r.assembly,sample:u,trackId:(0,l.makeTrackId)({name:a}),name:a})})}catch(a){k(a)}}return(0,o.jsxs)(e.Paper,{className:c.paper,children:[f?(0,o.jsx)(i.ErrorMessage,{error:f}):null,(0,o.jsxs)(e.FormControl,{children:[(0,o.jsx)(e.FormLabel,{children:"File type"}),(0,o.jsx)(e.RadioGroup,{value:m,onChange:a=>{G(a.target.value)},children:D.map(a=>(0,o.jsx)(e.FormControlLabel,{value:a,control:(0,o.jsx)(e.Radio,{}),label:F[a]},a))})]}),(0,o.jsx)(i.FileSelector,{location:p,name:T[m],rootModel:b,setLocation:v}),(0,o.jsx)(i.FileSelector,{location:g,name:"Path to tabix index (optional; the sibling .tbi is assumed, a .csi is recognised by name)",rootModel:b,setLocation:P}),(0,o.jsx)(e.TextField,{className:c.field,value:u,onChange:a=>{I(a.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,o.jsx)(e.TextField,{className:c.field,value:d,helperText:"Track name",slotProps:{htmlInput:{"data-testid":"graph-track-name-input"}},onChange:a=>{M(a.target.value)}}),(0,o.jsx)(i.AssemblySelector,{session:h,helperText:"Select assembly to add track to",selected:r.assembly,onChange:a=>{r.setAssembly(a)},fullWidth:!0}),(0,o.jsx)(e.Button,{variant:"contained",className:c.submit,disabled:!p||!d.trim()||!r.assembly,onClick:E,children:"Submit"})]})}),K=J;export{K as default};
-//# sourceMappingURL=AddTrackWorkflow-U3UNCVXJ.js.map
+import{a as W}from"./chunk-FCWXYIFC.js";import{b as F,c as T,i as y}from"./chunk-4T7DPQTR.js";import{a as N}from"./chunk-J4OLMLS5.js";import{a as O}from"./chunk-J6KYLXRD.js";import{a as C,b as B,c as H,d as _}from"./chunk-TYJTJGPO.js";import{a as w,b as t}from"./chunk-FY3BTKY4.js";var S=w((q,L)=>{L.exports=JBrowseExports["@jbrowse/core/util/tss-react"]});var s=t(O(),1),i=t(B(),1),l=t(N(),1),A=t(S(),1),R=t(W(),1),e=t(_(),1),x=t(H(),1);var o=t(C(),1),j=(0,A.makeStyles)()(n=>({paper:{margin:n.spacing(),padding:n.spacing()},field:{marginTop:n.spacing(2)},submit:{marginTop:25,marginBottom:100,display:"block"}})),D=["RgfaTabixAdapter","MinigraphBubbleAdapter"],J=(0,x.observer)(function({model:r}){let{classes:c}=j(),h=(0,l.getSession)(r),b=(0,R.getRoot)(r),[m,G]=(0,s.useState)("RgfaTabixAdapter"),[p,v]=(0,s.useState)(),[g,P]=(0,s.useState)(),[u,I]=(0,s.useState)(""),[d,M]=(0,s.useState)("Pangenome graph"),[f,k]=(0,s.useState)();function E(){if(!(!p||!r.assembly))try{k(void 0);let a=d.trim();(0,l.addTrackFromWidget)({model:r,session:h,conf:y({choice:m,loc:p,indexLoc:g,assembly:r.assembly,sample:u,trackId:(0,l.makeTrackId)({name:a}),name:a})})}catch(a){k(a)}}return(0,o.jsxs)(e.Paper,{className:c.paper,children:[f?(0,o.jsx)(i.ErrorMessage,{error:f}):null,(0,o.jsxs)(e.FormControl,{children:[(0,o.jsx)(e.FormLabel,{children:"File type"}),(0,o.jsx)(e.RadioGroup,{value:m,onChange:a=>{G(a.target.value)},children:D.map(a=>(0,o.jsx)(e.FormControlLabel,{value:a,control:(0,o.jsx)(e.Radio,{}),label:F[a]},a))})]}),(0,o.jsx)(i.FileSelector,{location:p,name:T[m],rootModel:b,setLocation:v}),(0,o.jsx)(i.FileSelector,{location:g,name:"Path to tabix index (optional; the sibling .tbi is assumed, a .csi is recognised by name)",rootModel:b,setLocation:P}),(0,o.jsx)(e.TextField,{className:c.field,value:u,onChange:a=>{I(a.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,o.jsx)(e.TextField,{className:c.field,value:d,helperText:"Track name",slotProps:{htmlInput:{"data-testid":"graph-track-name-input"}},onChange:a=>{M(a.target.value)}}),(0,o.jsx)(i.AssemblySelector,{session:h,helperText:"Select assembly to add track to",selected:r.assembly,onChange:a=>{r.setAssembly(a)},fullWidth:!0}),(0,o.jsx)(e.Button,{variant:"contained",className:c.submit,disabled:!p||!d.trim()||!r.assembly,onClick:E,children:"Submit"})]})}),K=J;export{K as default};
+//# sourceMappingURL=AddTrackWorkflow-F5YBOJ3E.js.map

package/dist/chunks/ChooseSamplesDialog-KVTDIA4A.js

@@ -0,0 +1,2 @@
+import{a as C}from"./chunk-J6KYLXRD.js";import{a as r,b as S,c as u,d as w}from"./chunk-TYJTJGPO.js";import{b as a}from"./chunk-FY3BTKY4.js";var c=a(C(),1),m=a(S(),1),e=a(w(),1),h=a(u(),1),o=a(r(),1),y=(0,h.observer)(function({model:t,onClose:i}){let{samples:s}=t.walkRowSampleChoices,[p,d]=(0,c.useState)(()=>(t.walkRowSamples??[]).filter(l=>s.includes(l)));return(0,o.jsxs)(m.Dialog,{open:!0,onClose:i,title:"Choose samples",children:[(0,o.jsxs)(e.DialogContent,{children:[(0,o.jsx)(e.Autocomplete,{multiple:!0,disableCloseOnSelect:!0,"data-testid":"graph-choose-samples",options:s,value:p,onChange:(l,n)=>{d(n)},renderOption:({key:l,...n},k,{selected:g})=>(0,o.jsxs)("li",{...n,children:[(0,o.jsx)(e.Checkbox,{size:"small",checked:g}),k]},l),renderInput:l=>(0,o.jsx)(e.TextField,{...l,autoFocus:!0,label:"Samples",placeholder:"type to search"})}),(0,o.jsxs)(e.Typography,{variant:"caption",color:"text.secondary",children:[s.length.toLocaleString()," samples in this cut. Their walks show in pairs, in the order picked."]})]}),(0,o.jsxs)(e.DialogActions,{children:[(0,o.jsx)(e.Button,{onClick:i,children:"Cancel"}),(0,o.jsx)(e.Button,{variant:"contained",disabled:p.length===0,onClick:()=>{t.setWalkRowSamples(p),i()},children:"Show these samples"})]})]})}),D=y;export{D as default};
+//# sourceMappingURL=ChooseSamplesDialog-KVTDIA4A.js.map

package/dist/chunks/ChooseSamplesDialog-KVTDIA4A.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/GraphGenomeView/components/ChooseSamplesDialog.tsx"],
+  "sourcesContent": ["import { useState } from 'react'\n\nimport { Dialog } from '@jbrowse/core/ui'\nimport {\n  Autocomplete,\n  Button,\n  Checkbox,\n  DialogActions,\n  DialogContent,\n  TextField,\n  Typography,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport type { GraphPaneModel } from '../model'\n\ntype SamplePicker = Pick<\n  GraphPaneModel,\n  'walkRowSampleChoices' | 'walkRowSamples' | 'setWalkRowSamples'\n>\n\n// Which samples' walks walk rows show, searched by name, in the order picked\nconst ChooseSamplesDialog = observer(function ChooseSamplesDialog({\n  model,\n  onClose,\n}: {\n  model: SamplePicker\n  onClose: () => void\n}) {\n  const { samples } = model.walkRowSampleChoices\n  const [picked, setPicked] = useState(() =>\n    (model.walkRowSamples ?? []).filter(s => samples.includes(s)),\n  )\n  return (\n    <Dialog open onClose={onClose} title=\"Choose samples\">\n      <DialogContent>\n        <Autocomplete\n          multiple\n          disableCloseOnSelect\n          data-testid=\"graph-choose-samples\"\n          options={samples}\n          value={picked}\n          onChange={(_, value) => {\n            setPicked(value)\n          }}\n          renderOption={({ key, ...props }, sample, { selected }) => (\n            <li key={key} {...props}>\n              <Checkbox size=\"small\" checked={selected} />\n              {sample}\n            </li>\n          )}\n          renderInput={params => (\n            <TextField\n              {...params}\n              autoFocus\n              label=\"Samples\"\n              placeholder=\"type to search\"\n            />\n          )}\n        />\n        <Typography variant=\"caption\" color=\"text.secondary\">\n          {samples.length.toLocaleString()} samples in this cut. Their walks\n          show in pairs, in the order picked.\n        </Typography>\n      </DialogContent>\n      <DialogActions>\n        <Button onClick={onClose}>Cancel</Button>\n        <Button\n          variant=\"contained\"\n          disabled={picked.length === 0}\n          onClick={() => {\n            model.setWalkRowSamples(picked)\n            onClose()\n          }}\n        >\n          Show these samples\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n})\n\nexport default ChooseSamplesDialog\n"],
+  "mappings": "6IAAA,IAAAA,EAAyB,SAEzBC,EAAuB,SACvBC,EAQO,SACPC,EAAyB,SAkCbC,EAAA,SAxBNC,KAAsB,YAAS,SAA6B,CAChE,MAAAC,EACA,QAAAC,CACF,EAGG,CACD,GAAM,CAAE,QAAAC,CAAQ,EAAIF,EAAM,qBACpB,CAACG,EAAQC,CAAS,KAAI,YAAS,KAClCJ,EAAM,gBAAkB,CAAC,GAAG,OAAOK,GAAKH,EAAQ,SAASG,CAAC,CAAC,CAC9D,EACA,SACE,QAAC,UAAO,KAAI,GAAC,QAASJ,EAAS,MAAM,iBACnC,qBAAC,iBACC,oBAAC,gBACC,SAAQ,GACR,qBAAoB,GACpB,cAAY,uBACZ,QAASC,EACT,MAAOC,EACP,SAAU,CAACG,EAAGC,IAAU,CACtBH,EAAUG,CAAK,CACjB,EACA,aAAc,CAAC,CAAE,IAAAC,EAAK,GAAGC,CAAM,EAAGC,EAAQ,CAAE,SAAAC,CAAS,OACnD,QAAC,MAAc,GAAGF,EAChB,oBAAC,YAAS,KAAK,QAAQ,QAASE,EAAU,EACzCD,IAFMF,CAGT,EAEF,YAAaI,MACX,OAAC,aACE,GAAGA,EACJ,UAAS,GACT,MAAM,UACN,YAAY,iBACd,EAEJ,KACA,QAAC,cAAW,QAAQ,UAAU,MAAM,iBACjC,UAAAV,EAAQ,OAAO,eAAe,EAAE,yEAEnC,GACF,KACA,QAAC,iBACC,oBAAC,UAAO,QAASD,EAAS,kBAAM,KAChC,OAAC,UACC,QAAQ,YACR,SAAUE,EAAO,SAAW,EAC5B,QAAS,IAAM,CACbH,EAAM,kBAAkBG,CAAM,EAC9BF,EAAQ,CACV,EACD,8BAED,GACF,GACF,CAEJ,CAAC,EAEMY,EAAQd",
+  "names": ["import_react", "import_ui", "import_material", "import_mobx_react", "import_jsx_runtime", "ChooseSamplesDialog", "model", "onClose", "samples", "picked", "setPicked", "s", "_", "value", "key", "props", "sample", "selected", "params", "ChooseSamplesDialog_default"]
+}

package/dist/chunks/{GbzBaseSyntenyAdapter-2BKLBC4F.js → GbzBaseSyntenyAdapter-Z4NDQGEZ.js}

@@ -1,8 +1,8 @@
-import{a as Ln,b as qs,c as Gr,d as zr}from"./chunk-DKNKJWYF.js";import{f as Hs,g as _n,h as Ce,i as kn,j as On,k as St,l as Nn,m as vt,o as Tn}from"./chunk-IKKD4EOI.js";import{a as Br}from"./chunk-KWAXLUPQ.js";import"./chunk-E7J6SB5P.js";import{a as Ds,d as Hr,e as qr,f as Dr}from"./chunk-4T7DPQTR.js";import{a as ot}from"./chunk-J4OLMLS5.js";import{a as Fn,b as $n}from"./chunk-S2YZT446.js";import"./chunk-CNQYRKZ3.js";import"./chunk-YBLNN5FU.js";import{e as bt,f as ze,g as Pn}from"./chunk-LRBVMAUV.js";import{a as Bs,b as ce}from"./chunk-FY3BTKY4.js";var Cs=Bs((rd,As)=>{As.exports=JBrowseExports["@jbrowse/core/util/installClearHoverOnSurfaceMove"]});function ye(n,e){return 2*n+(e==="reverse"?1:0)}function O(n){return Math.floor(n/2)}function je(n){return n%2===0?"forward":"reverse"}function z(n){return n%2===1}function re(n){return n%2===0?n+1:n-1}function jr(n){return n==="left"?"right":"left"}function It(n){return n==="forward"?"left":"right"}function Et(n){return n==="forward"?"right":"left"}function Ur(n){return n==="left"?"forward":"reverse"}function Wr(n){return n==="right"?"forward":"reverse"}function Ue(n,e){let t=O(n),r=O(e);return z(n)?r>t||r===t&&!z(e):r>=t}function st(n){return Fe(n[0],n[n.length-1])}function Fe(n,e){return n===void 0||e===void 0?!0:z(n)===z(e)?!z(n):Ue(n,e)}var it=class{offset=0;bytes;constructor(e){this.bytes=e}get done(){return this.offset>=this.bytes.length}byte(){let e=this.bytes[this.offset];if(e!==void 0)return this.offset+=1,e}int(){let e=1,t=0;for(;this.offset<this.bytes.length;){let r=this.bytes[this.offset];if(this.offset+=1,t+=(r&127)*e,e*=128,(r&128)===0)return t}}},Vr=255,Gs=256,At=class{source;sigma;threshold;constructor(e,t){this.source=new it(e),this.sigma=t===0?Number.MAX_SAFE_INTEGER:t,this.threshold=this.sigma<Vr?Math.floor(Gs/this.sigma):0}next(){if(this.sigma>=Vr){let o=this.source.int(),s=this.source.int();return o===void 0||s===void 0?void 0:{value:o,len:s+1}}let e=this.source.byte();if(e===void 0)return;let t=e%this.sigma,r=Math.floor(e/this.sigma)+1;if(r===this.threshold){let o=this.source.int();if(o===void 0)return;r+=o}return{value:t,len:r}}*[Symbol.iterator](){for(let e=this.next();e!==void 0;e=this.next())yield e}};function Qr(n){let e=new it(n),t=e.int();if(t===void 0||t===0)return[];let r=[],o=0;for(let s=0;s<t;s++){let i=e.int(),a=e.int();if(i===void 0||a===void 0)throw new Error("GBWT edge list ends early");o+=i,r.push({node:o,offset:a})}return r}var Ct=class{edges;bwt;constructor(e,t){this.edges=e,this.bwt=t}runs(){return new At(this.bwt,this.edges.length)}edge(e){let t=this.edges[e];if(t===void 0)throw new Error(`GBWT run refers to edge rank ${e} of ${this.edges.length}`);return t}lf(e){let t=this.edges.map(o=>o.offset),r=0;for(let o of this.runs()){let s=this.edge(o.value),i=t[o.value];if(r+o.len>e)return s.node===0?void 0:{node:s.node,offset:i+(e-r)};t[o.value]=i+o.len,r+=o.len}}edgeTo(e){let t=0,r=this.edges.length;for(;t<r;){let o=t+r>>1,s=this.edges[o];if(s.node===e)return o;s.node<e?t=o+1:r=o}}offsetTo(e){if(e.node===0)return;let t=this.edgeTo(e.node);if(t===void 0)return;let r=this.edges[t].offset;if(r>e.offset)return;let o=0;for(let s of this.runs())if(o+=s.len,s.value===t&&(r+=s.len,r>e.offset))return o-(r-e.offset)}predecessorAt(e){let t=this.edges.map(o=>({node:o.node===0?0:re(o.node),count:0}));for(let o of this.runs()){let s=t[o.value];s&&(s.count+=o.len)}for(let o=1;o<t.length;o++){let s=t[o-1],i=t[o];O(s.node)===O(i.node)&&(t[o-1]=i,t[o]=s)}let r=0;for(let o of t)if(r+=o.count,r>e)return o.node===0?void 0:o.node}decompressArrays(){let e=this.edges.map(i=>i.offset),t=0;for(let i of this.runs())t+=i.len;let r=new Int32Array(t),o=new Int32Array(t),s=0;for(let i of this.runs()){let a=this.edge(i.value),f=e[i.value];for(let c=0;c<i.len;c++)r[s]=a.node,o[s]=f,f+=1,s+=1;e[i.value]=f}return{nodes:r,offsets:o}}decompress(){let e=this.edges.map(r=>r.offset),t=[];for(let r of this.runs()){let o=this.edge(r.value);for(let s=0;s<r.len;s++)t.push({node:o.node,offset:e[r.value]}),e[r.value]=e[r.value]+1}return t}};var zs=["","A","C","G","T","N"];function Yr(n){let e=n[n.length-1];if(e===void 0)return 0;let t=e,r=0;for(let o=0;o<3&&t%6!==0;o++)t=Math.floor(t/6),r+=1;return 3*(n.length-1)+r}function Kr(n){let e="";for(let t of n){let r=t;for(let o=0;o<3;o++){let s=zs[r%6];if(s==="")return e;r=Math.floor(r/6),e+=s}}return e}var js={A:"T",C:"G",G:"C",T:"A",N:"N"};function Rt(n){let e="";for(let t=n.length-1;t>=0;t--)e+=js[n[t]]??"N";return e}var Us=Uint32Array.from([1116352408,1899447441,3049323471,3921009573,961987163,1508970993,2453635748,2870763221,3624381080,310598401,607225278,1426881987,1925078388,2162078206,2614888103,3248222580,3835390401,4022224774,264347078,604807628,770255983,1249150122,1555081692,1996064986,2554220882,2821834349,2952996808,3210313671,3336571891,3584528711,113926993,338241895,666307205,773529912,1294757372,1396182291,1695183700,1986661051,2177026350,2456956037,2730485921,2820302411,3259730800,3345764771,3516065817,3600352804,4094571909,275423344,430227734,506948616,659060556,883997877,958139571,1322822218,1537002063,1747873779,1955562222,2024104815,2227730452,2361852424,2428436474,2756734187,3204031479,3329325298]),Ie=(n,e)=>n>>>e|n<<32-e;function Xr(n){let e=Math.ceil((n.length+9)/64),t=new Uint8Array(e*64);t.set(n),t[n.length]=128;let r=new DataView(t.buffer),o=n.length*8;r.setUint32(t.length-8,Math.floor(o/2**32)),r.setUint32(t.length-4,o>>>0);let s=Uint32Array.from([1779033703,3144134277,1013904242,2773480762,1359893119,2600822924,528734635,1541459225]),i=new Uint32Array(64);for(let c=0;c<e;c++){for(let S=0;S<16;S++)i[S]=r.getUint32(c*64+S*4);for(let S=16;S<64;S++){let g=i[S-15],b=i[S-2],x=Ie(g,7)^Ie(g,18)^g>>>3,E=Ie(b,17)^Ie(b,19)^b>>>10;i[S]=i[S-16]+x+i[S-7]+E}let l=s[0],h=s[1],d=s[2],p=s[3],u=s[4],m=s[5],w=s[6],y=s[7];for(let S=0;S<64;S++){let g=Ie(u,6)^Ie(u,11)^Ie(u,25),b=u&m^~u&w,x=y+g+b+Us[S]+i[S]|0,E=Ie(l,2)^Ie(l,13)^Ie(l,22),A=l&h^l&d^h&d;y=w,w=m,m=u,u=p+x|0,p=d,d=h,h=l,l=x+E+A|0}[l,h,d,p,u,m,w,y].forEach((S,g)=>{s[g]=s[g]+S})}let a=new Uint8Array(32),f=new DataView(a.buffer);for(let c=0;c<8;c++)f.setUint32(c*4,s[c]);return a}function Zr(n,e){let t=new Map;if(n!==void 0)for(let r of n.split(";")){let o=r.split(","),[s,i]=o;if(o.length!==2||!s||!i)throw new Error(`Invalid ${e} relationship: ${r}`);let a=t.get(s);a||(a=new Set,t.set(s,a)),a.add(i)}return t}function to(n){return{name:n.get("pggname"),subgraph:Zr(n.get("subgraph"),"subgraph"),translation:Zr(n.get("translation"),"translation")}}function Jr(n,e){for(let[t,r]of e){let o=n.get(t);o||(o=new Set,n.set(t,o));for(let s of r)o.add(s)}}function no(n,e){let t={name:n,subgraph:new Map,translation:new Map};return e.name!==void 0&&(t.subgraph.set(n,new Set([e.name])),Jr(t.subgraph,e.subgraph),Jr(t.translation,e.translation)),t}function eo(n){return[...n.entries()].sort(([e],[t])=>e<t?-1:e>t?1:0).flatMap(([e,t])=>[...t].sort().map(r=>[e,r]))}function ro(n){let e=[];n.name!==void 0&&e.push(`H	NM:Z:${n.name}`);for(let[t,r]of eo(n.subgraph))e.push(`H	SG:Z:${t},${r}`);for(let[t,r]of eo(n.translation))e.push(`H	TL:Z:${t},${r}`);return e}async function oo(n){let e=n.reduce((i,a)=>i+a.length,0),t=new Uint8Array(e),r=0;for(let i of n)t.set(i,r),r+=i.length;let o=globalThis.crypto?.subtle;return[...o?new Uint8Array(await o.digest("SHA-256",t)):Xr(t)].map(i=>i.toString(16).padStart(2,"0")).join("")}var Ws="_gbwt_ref";function me(n){let e=`${n.sample}#${n.haplotype}#${n.contig}`;return n.end===void 0?e:`${e}[${n.fragment}-${n.end}]`}var Vs=/^([^#]+)#(\d+)#([^#]+?)(?:\[\d+-\d+\])?$/,Qs=/^([^#]+?)(?:\[\d+-\d+\])?$/;function Ys(n){let e=Vs.exec(n);if(e)return{sample:e[1],haplotype:Number(e[2]),contig:e[3]};let t=Qs.exec(n);if(t)return{contig:t[1]};throw new Error(`"${n}" is not a path name; expected "sample#haplotype#contig" or a bare contig`)}function We(n){return typeof n=="string"?Ys(n):n}function Ve(n,e){return{sample:n.sample??Ws,contig:n.contig,haplotype:n.haplotype??0,fragment:e}}var Ks=4096;function Hn(n){let e=[];for(let t of n){let r=e[e.length-1];r&&t-r[1]<=Ks?r[1]=t:e.push([t,t])}return e}var Xs=32768,so={mostChosenPaths:32},Bn=class{byNode=new Map;get(e){return this.byNode.get(e.node)?.get(e.offset)}set(e,t){let r=this.byNode.get(e.node);r||(r=new Map,this.byNode.set(e.node,r)),r.set(e.offset,t)}},ie=class extends Error{};function Mt(n,e,t,r){return n==="forward"?e+t:e-r}function io(n,e,t,r){return n==="forward"?e-r:e+t}function ao(n){return Fe(re(n.handles[n.handles.length-1]),re(n.handles[0]))}function at(n){return`${n.pathHandle}:${n.hapStart}:${n.hapEnd}`}async function fo(n){let{db:e,records:t,signal:r}=n,o=performance.now(),s=()=>{let I=performance.now(),R=I-o;return o=I,R},i={spacing:await e.haplotypeAnchorSpacing(),anchors:void 0,anchorsRead:0,chosenPaths:0,scans:[],scanRows:0,strays:void 0,pieces:0,sources:{reference:0,section:0,stray:0,chain:0,twin:0},walks:{},twins:{tried:0,found:0},graphFetches:0,fallback:void 0,ms:{scan:0,walks:0,check:0,twins:0}},a=(I,R)=>{let k=`${I}: ${R}`;i.walks[k]=(i.walks[k]??0)+1},f=await e.haplotypeSampleInterval()??4096,c=new Map,l=async I=>{let R=t.get(I)??c.get(I);if(R)return R;let k=await e.getRecord(I);if(i.graphFetches+=1,!k)throw new Error(`Node record ${I} is missing from the database`);return c.set(I,k),k},h=I=>t.get(I).sequenceLen,d=await e.pathsByHandle(),p=I=>{let R=d.get(I);return R!==void 0&&n.keep(R.name)},u=[],m=new Bn,w=new Map,y=new Set,S=new Set,g=async I=>{let R=(await l(I.node)).gbwt().lf(I.offset);return R===void 0||R.node===0?void 0:R},b=async(I,R)=>{let k=(await l(re(I.node))).gbwt().predecessorAt(I.offset);if(k===void 0||R!==void 0&&!R.has(k))return;let L=(await l(k)).gbwt().offsetTo(I);if(L===void 0)throw new Error(`No offset in ${k} leads to ${I.node}:${I.offset}`);return{node:k,offset:L}},x=(I,R,k,L)=>{let H=k.map(V=>V.pos.node),W=k.map(V=>V.pos.offset),J=0;for(let V of H)J+=h(V);let B=R==="forward"?k[0].left:k[k.length-1].left,F=u.length;u.push({pathHandle:I,orientation:R,handles:H,offsets:W,len:J,hapStart:B,hapEnd:B+J,canonical:Fe(H[0],H[H.length-1]),source:L});for(let V of k)m.set(V.pos,F);let K=w.get(I);return K?K.push(F):w.set(I,[F]),F},E=async(I,R,k,L)=>{let H=[],W=I;for(;;){r?.throwIfAborted();let B=await b(W.pos,t);if(!B)break;W={pos:B,left:io(k,W.left,h(W.pos.node),h(B.node))},H.push(W)}H.reverse();let J=[I];for(W=I;;){r?.throwIfAborted();let B=await g(W.pos);if(!B||!t.has(B.node))break;W={pos:B,left:Mt(k,W.left,h(W.pos.node),h(B.node))},J.push(W)}return x(R,k,[...H,...J],L)},A=async(I,R,k,L)=>u[m.get(I.pos)??await E(I,R,k,L)],_=I=>{let R=I.handles[I.handles.length-1];return{pos:{node:R,offset:I.offsets[I.offsets.length-1]},left:I.orientation==="forward"?I.hapEnd-h(R):I.hapStart}},T=I=>{let R=I.handles[0];return{pos:{node:R,offset:I.offsets[0]},left:I.orientation==="forward"?I.hapStart:I.hapEnd-h(R)}},$=await E({pos:n.referencePos,left:n.referenceLeft},n.referenceHandle,"forward","reference"),C=u[$],N=()=>{if(i.fallback!==void 0)return{reference:C,pieces:[],stats:i};let I=new Map;u.forEach((k,L)=>{L!==$&&I.set(at(k),[...I.get(at(k))??[],k])});let R=[];for(let k of I.values()){let L=new Set;for(let H of k)H.canonical&&!L.has(H.orientation)&&(L.add(H.orientation),R.push(H),i.sources[H.source]+=1)}return i.sources.reference=1,i.pieces=R.length+1,{reference:C,pieces:R,stats:i}},P=async(I,R)=>{let k=R?y:S,L=R?S:y,H=I;for(;;){if(k.has(H))return;k.add(H);let W=u[H],J=R?_(W):T(W),B=0,F;for(;F===void 0;){r?.throwIfAborted();let K=R?await g(J.pos):await b(J.pos);if(!K){F="endmarker";break}let V=(await l(J.pos.node)).sequenceLen,ve=(await l(K.node)).sequenceLen,oe=R?Mt(W.orientation,J.left,V,ve):io(W.orientation,J.left,V,ve);if(t.has(K.node)){let ee=m.get(K);ee===void 0?(H=await E({pos:K,left:oe},W.pathHandle,W.orientation,"chain"),L.add(H),F="landed"):(L.add(ee),F="merge")}else B>Xs?F="bound":(B+=ve,J={pos:K,left:oe})}if(a("chain",F),F!=="landed")return}},U=async I=>{if(n.context>I.context)throw new ie(`the context of ${n.context} bp exceeds the ${I.context} bp the haplotype index's stray rows cover`);let R=i.spacing;if(R===void 0)throw new ie("the haplotype index has no anchors");let{bin:k,bound:L}=I,{fills:H,inserted:W}=n.snarls;if(n.snarls.mode==="overlapping"&&H.length>0)throw new ie("the haplotype index's stray rows cover contained snarls only");for(let v of H){if(v.inserted>0&&v.low===v.high)throw new ie(`the haplotype index's stray rows leave out the snarl bounded by node ${v.low} at both ends`);if(v.inserted>0&&(I.snarlNodes===void 0||v.nodes>I.snarlNodes))throw new ie(I.snarlNodes===void 0?"the haplotype index's stray rows leave snarls out":`a snarl of ${v.nodes} nodes exceeds the ${I.snarlNodes} the haplotype index's stray rows cover`)}let J=Math.floor(n.window.start/k),B=Math.floor((n.window.end-1)/k),F=J*k,K=(B+1)*k,V=new Map,ve=async(v,M)=>{let j=await e.haplotypeAnchorsBetween(n.referenceHandle,v*R,M*R);for(let D of j)V.set(D.anchorOffset/R,D)},oe=Math.max(0,Math.floor((F-L)/R)-1),ee=Math.ceil((K+L)/R)+1,[{listed:xt,strays:fe}]=await Promise.all([e.haplotypeBinData(n.referenceHandle,J,B),ve(oe,ee)]);for(let v of t.keys()){let M=O(v);if(!z(v)&&!xt(M)&&!W.has(M))throw new ie(`the haplotype index lists node ${M} of the subgraph in no bin that the window touches`)}i.scans=Hn([...t.keys()].sort((v,M)=>v-M));let de=Promise.all(i.scans.map(([v,M])=>e.haplotypeSamplesInRange(v,M)));for(de.catch(()=>{});oe>0&&(V.get(oe)?.pathOffset??Number.POSITIVE_INFINITY)>=F-L;)oe-=1,await ve(oe,oe);for(;V.has(ee)&&V.get(ee).pathOffset<=K+L;)ee+=1,await ve(ee,ee);let xe=[...V.keys()].sort((v,M)=>v-M),_e=V.get(xe[0]??-1);if(!_e)throw new ie("the haplotype index has no anchors on this path");let pe=v=>V.get(v).pathOffset,tt=new Map;for(let v of xe){let M=O(V.get(v).node);tt.set(M,[...tt.get(M)??[],v])}let Cn=[...tt.keys()],Rr=Cn.map(v=>V.get(tt.get(v)[0]).visits);if(!Rr[Cn.indexOf(O(_e.node))].some(v=>v.pathHandle===n.referenceHandle&&v.orientation==="forward"&&v.pathOffset===_e.pathOffset))throw new Error(`The haplotype index has no anchor row for the reference path ${n.referenceHandle} at offset ${_e.pathOffset} (node ${O(_e.node)}); it does not match this graph`);let Mr=xe.filter(v=>pe(v)<=n.window.start),Ts=xe.filter(v=>pe(v)>=n.window.end);i.anchors=[pe(Mr[Mr.length-1]??xe[0]),pe(Ts[0]??xe[xe.length-1])],i.anchorsRead=xe.length;let Rn=new Map,Pr=new Set;if(Cn.forEach((v,M)=>{let j=tt.get(v),D=j.length===1?j[0]:void 0;for(let G of Rr[M])Pr.add(G.pathHandle),G.orientation==="forward"&&p(G.pathHandle)&&Rn.set(G.pathHandle,[...Rn.get(G.pathHandle)??[],{k:D,row:G}])}),i.chosenPaths=[...Pr].filter(p).length,i.chosenPaths>so.mostChosenPaths)throw new ie(`${i.chosenPaths} chosen paths pass the anchors, more than ${so.mostChosenPaths}`);let yt=[],Le=Number.POSITIVE_INFINITY,ke=0;for(let[v,M]of Rn){M.sort((j,D)=>j.row.pathOffset-D.row.pathOffset);for(let j=0;j+1<M.length;j++){let D=M[j],G=M[j+1];if(D.k===void 0||G.k===void 0||Math.abs(D.k-G.k)!==1)continue;let[Z,te]=pe(D.k)<=pe(G.k)?[D,G]:[G,D],ne=pe(Z.k),se=pe(te.k);ne<K&&se>=F?(yt.push({pathHandle:v,from:D.row,to:G.row}),Le=Math.min(Le,ne-L),ke=Math.max(ke,se+L)):ne>=K&&ne-K<=L?(yt.push({pathHandle:v,from:Z.row,to:void 0}),Le=Math.min(Le,ne-L),ke=Math.max(ke,ne+L)):se<F&&F-se<=L&&(yt.push({pathHandle:v,from:te.row,to:void 0}),Le=Math.min(Le,se-L),ke=Math.max(ke,se+L))}}let Ls=new Set(H.map(v=>`${v.low}:${v.high}`)),Fs=fe.filter(v=>p(v.pathHandle)&&(v.snarl===void 0||Ls.has(`${v.snarl[0]}:${v.snarl[1]}`))).sort((v,M)=>v.pathHandle-M.pathHandle||v.pathStart-M.pathStart);i.strays={bins:B-J+1,rows:fe.length,walked:0,outsideBp:0},ke>0&&await n.prefetchReferenceRange(n.referenceHandle,Math.max(0,Le),ke+1),i.ms.scan=s();let _r=8*R+2*(n.window.end-n.window.start),kr=i.strays,nt=0,Or=v=>{if(kr.outsideBp+=v,nt+=v,nt>_r)throw new ie(`a walk of a chosen path near the window went past its cap of ${_r} bp`)},Mn=new Map,Nr=(v,M,j)=>(Mn.get(v)??[]).some(([D,G])=>D<=M&&j<G),Tr=(v,M,j)=>{Mn.set(v,[...Mn.get(v)??[],[M,j]])},Lr=async(v,M,j,D,G)=>{let Z=M,te=j,ne=te;for(;Z&&te<=D;){r?.throwIfAborted();let se;if(t.has(Z.node)){let rt=await A({pos:Z,left:te},v,"forward",G),$r=_(rt);Z=$r.pos,te=$r.left,se=h(Z.node),ne=Math.max(ne,rt.hapEnd)}else se=(await l(Z.node)).sequenceLen,Or(se),ne=Math.max(ne,te+se);Z=await g(Z),te+=se}return ne},$s=async(v,M,j,D)=>{let G={pos:M,left:j},Z=j;for(;G.left>D;){r?.throwIfAborted();let te=await b(G.pos);if(!te)break;let ne=(await l(te.node)).sequenceLen,se=G.left-ne;if(t.has(te.node)){let rt=await A({pos:te,left:se},v,"forward","section");G=T(rt),Z=Math.min(Z,rt.hapStart)}else Or(ne),G={pos:te,left:se},Z=Math.min(Z,se)}return Z};for(let{pathHandle:v,from:M,to:j}of yt){let D=M.pathOffset,G=(j??M).pathOffset+L;if(Nr(v,D-L,G))continue;let Z={node:M.node,offset:M.offset};nt=0;let te=await Lr(v,Z,D,G,"section");nt=0;let ne=await $s(v,Z,D,D-L);Tr(v,Math.min(ne,D-L),Math.max(te,G+1)),a(j?"section":"visit",j?"past the far anchor":"bound")}for(let v of Fs){if(Nr(v.pathHandle,v.pathStart,v.pathEnd))continue;nt=0;let M=await Lr(v.pathHandle,{node:v.node,offset:v.offset},v.pathStart,v.pathEnd,"stray");Tr(v.pathHandle,v.pathStart,Math.max(M,v.pathEnd+1)),kr.walked+=1}i.ms.walks=s();let Fr=[];for(let v of await de)for(let M of v)if(i.scanRows+=1,t.has(M.node)&&p(M.pathHandle)){if(!(w.get(M.pathHandle)??[]).some(j=>{let D=u[j];return D.hapStart<=M.pathOffset&&M.pathOffset<D.hapEnd}))throw new ie(`chosen path ${M.pathHandle} has a sample at ${M.pathOffset} on the window's nodes that no walk reached`);M.orientation==="reverse"&&Fr.push(M)}for(let v of Fr)await A({pos:{node:v.node,offset:v.offset},left:v.pathOffset},v.pathHandle,"reverse","twin");i.ms.check=s()},Y=async()=>{let I=new Map,R=B=>{let F=at(B),K=I.get(F);K?K.add(B.orientation):I.set(F,new Set([B.orientation]))},k=0,L=()=>{for(;k<u.length;k++)R(u[k])};L();let H=B=>(I.get(at(B))?.size??0)>1,W=2*f,J=(B,F)=>F===$?p(n.referenceHandle)&&ao(B):!B.canonical||ao(B);for(let B=0;B<u.length;B++){let F=u[B];if(H(F)||!J(F,B))continue;i.twins.tried+=1;let K=F.orientation==="forward"?"reverse":"forward",V=_(F),ve=0,oe;for(;!oe&&ve<=W;){r?.throwIfAborted();let fe=await g(V.pos);if(!fe)break;let de=(await l(fe.node)).sequenceLen,xe=Mt(F.orientation,V.left,(await l(V.pos.node)).sequenceLen,de),_e=re(fe.node);oe=(await e.haplotypeSamplesInRange(_e,_e)).find(pe=>pe.pathHandle===F.pathHandle&&pe.orientation===K&&pe.pathOffset===xe),ve+=de,V={pos:fe,left:xe}}let ee=oe&&{pos:{node:oe.node,offset:oe.offset},left:oe.pathOffset},xt=0;for(;ee&&!H(F)&&xt<=W+F.len;){if(r?.throwIfAborted(),t.has(ee.pos.node)){let fe=await A(ee,F.pathHandle,K,"twin"),de=u.indexOf(fe);await P(de,!0),await P(de,!1),L(),ee=_(fe)}if(!H(F)){let fe=(await l(ee.pos.node)).sequenceLen;xt+=fe;let de=await g(ee.pos);ee=de?{pos:de,left:Mt(K,ee.left,fe,(await l(de.node)).sequenceLen)}:void 0}}if(L(),!H(F))throw new ie(`piece ${at(F)} was found in one orientation where extractPaths keeps the other`);i.twins.found+=1}i.ms.twins=s()};try{let I=await e.haplotypeStrayOptions();if(I===void 0)throw new ie("the haplotype index has no stray rows; gbz-haplotype-index 0.2.0 writes them");await U(I),await Y()}catch(I){if(!(I instanceof ie))throw I;i.fallback=I.message}return N()}function co(n,e){return n.handles[0]-e.handles[0]||n.offsets[0]-e.offsets[0]}function Pt(n,e){let t=0,r=n.length;for(;t<r;){let o=t+r>>1;n[o]<e?t=o+1:r=o}return t}var _t=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 o=this.tree[r];o!==-1&&(t===-1||this.ending[o]>this.ending[t])&&(t=o)}return t}raise(e,t){this.ending[e]=t;for(let r=e+1;r<this.tree.length;r+=r&-r){let o=this.tree[r];(o===-1||t>this.ending[o])&&(this.tree[r]=e)}}},qn=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((o,s)=>{let i=this.occurrences.get(o);i?i.push(s):this.occurrences.set(o,[s])})}solve(e,t,r,o){let s=0;for(;e+s<t&&r+s<o&&this.a[e+s]===this.b[r+s];)this.match(e+s,r+s),s+=1;let i=0;for(;t-i>e+s&&o-i>r+s&&this.a[t-i-1]===this.b[o-i-1];)i+=1;this.solveMiddle(e+s,t-i,r+s,o-i);for(let a=i;a>0;a--)this.match(t-a,o-a)}match(e,t){this.pairs.push([e,t]),this.total+=this.weight(this.a[e])}solveMiddle(e,t,r,o){if(e===t||r===o)return;let s=this.matchCount(e,t,r,o);if(s===0)return;if(s<=t-e+(o-r)){this.chain(e,t,r,o,s);return}let i=e+t>>1,a=this.split(e,i,t,r,o);this.solve(e,i,r,a),this.solve(i,t,a,o)}matchCount(e,t,r,o){let s=0;for(let i=e;i<t;i++){let a=this.occurrences.get(this.a[i]);a&&(s+=Pt(a,o)-Pt(a,r))}return s}sweep(e,t,r,o,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]),h=Pt(c,o),d=Pt(c,s);for(let p=0;p<d-h;p++){let u=r===1?c[d-1-p]-o:s-1-c[h+p],m=i.bestBefore(u),w=(m===-1?0:i.ending[m])+l;if(w>i.ending[u]&&(i.raise(u,w),a)){let y=a.count++;a.row[y]=f,a.column[y]=u,a.previous[y]=m===-1?-1:a.endingMatch[m],a.endingMatch[u]=y}}}}chain(e,t,r,o,s){let i=new _t(o-r),a={row:new Int32Array(s),column:new Int32Array(s),previous:new Int32Array(s),endingMatch:new Int32Array(o-r),count:0};this.sweep(e,t,1,r,o,i,a);let f=i.bestBefore(o-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,o,s){let i=new _t(s-o);this.sweep(e,t,r,o,s,i);let a=new Float64Array(s-o+1);for(let f=0;f<s-o;f++)a[f+1]=Math.max(a[f],i.ending[f]);return a}split(e,t,r,o,s){let i=s-o,a=this.frontier(e,t,1,o,s),f=this.frontier(r-1,t-1,-1,o,s),c=0,l=-1;for(let h=0;h<=i;h++){let d=a[h]+f[i-h];d>l&&(l=d,c=h)}return o+c}};function lo(n,e,t){let r=new qn(n,e,t);return r.solve(0,n.length,0,e.length),[r.pairs,r.total]}var Zs=100,zn=4e6,Js=5e3,le=15,ei=64,ti=8,xo=1,jn=-4,ae=-6,Re=-1,Qe=-(2**30),Ot=0,Dn=1,yo=2;function $e(n,e,t){let r=n.at(-1);t>0&&(r?.[0]===e?r[1]+=t:n.push([e,t]))}function kt(n,e,t){return n>=t&&n>=e?Ot:t>=e?yo:Dn}function bo(n,e,t){let r=n.length,o=e.length,s=o+1,i=new Uint8Array((r+1)*s),a=new Int32Array(s).fill(Qe),f=new Int32Array(s).fill(Qe),c=new Int32Array(s).fill(Qe);a[0]=0;for(let u=1;u<=o;u++)c[u]=ae+(u-1)*Re,i[u]=(u===1?Ot:yo)<<4;for(let u=1;u<=r;u++){let m=new Int32Array(s).fill(Qe),w=new Int32Array(s).fill(Qe),y=new Int32Array(s).fill(Qe);w[0]=ae+(u-1)*Re,i[u*s]=(u===1?Ot:Dn)<<2;let S=n.charCodeAt(u-1);for(let g=1;g<=o;g++){let b=kt(a[g-1],f[g-1],c[g-1]);m[g]=Math.max(a[g-1],f[g-1],c[g-1])+(S===e.charCodeAt(g-1)?xo:jn);let x=kt(a[g]+ae,f[g]+Re,c[g]+ae);w[g]=Math.max(a[g]+ae,f[g]+Re,c[g]+ae);let E=kt(m[g-1]+ae,w[g-1]+ae,y[g-1]+Re);y[g]=Math.max(m[g-1]+ae,w[g-1]+ae,y[g-1]+Re),i[u*s+g]=b|x<<2|E<<4}a=m,f=w,c=y}let l=[],h=r,d=o,p=kt(a[o],f[o],c[o]);for(;h>0||d>0;){let u=i[h*s+d]>>2*p&3;p===Ot?(l.push(n[h-1]===e[d-1]?"=":"X"),h-=1,d-=1):p===Dn?(l.push("I"),h-=1):(l.push("D"),d-=1),p=u}for(let u of l.reverse())$e(t,u,1)}function ni(n,e){let t=Math.abs(n-e);return(t===0?0:Math.min(-ae-(t-1)*Re,-ae+10*Math.log2(t)))+(Math.min(n,e)>0?-jn:0)}function So(n,e){let t=Math.abs(n-e);return t===0?0:.01*le*t+.5*Math.log2(t)}function ho(n,e,t){return{qs:n.qs+e,qe:n.qs+t,ts:n.flipped?n.te-t:n.ts+e,te:n.flipped?n.te-e:n.ts+t,flipped:n.flipped}}function ri(n,e,t){let r=n.qe-n.qs,o=[];for(let[a,f]of e){let c=Math.max(0,a-n.qs),l=Math.min(r,f-n.qs);c<l&&o.push([c,l])}for(let[a,f]of t){let c=Math.max(0,n.flipped?n.te-f:a-n.ts),l=Math.min(r,n.flipped?n.te-a:f-n.ts);c<l&&o.push([c,l])}if(o.length===0)return[n];o.sort((a,f)=>a[0]-f[0]);let s=[],i=0;for(let[a,f]of o)a-i>=le&&s.push(ho(n,i,a)),i=Math.max(i,f);return r-i>=le&&s.push(ho(n,i,r)),s}function Un(n,e,t,r,o=1/0){let s=[],i={query:[],target:[]},a={forward:{query:[],target:[]},flipped:{query:[],target:[]}},f=[...n].sort((c,l)=>c.qs-l.qs||c.ts-l.ts);for(;f.length>0&&s.length<o;){let c=f.map(g=>g.qe-g.qs),l=new Int32Array(f.length).fill(-1),h=new Int32Array(f.length);for(let g=0;g<f.length;g++){let b=f[g],x=b.qe-b.qs;for(let E=g-1;E>=Math.max(0,g-Js);E--){if(c[E]+x<=c[g])continue;let A=f[E];if(A.flipped===b.flipped&&A.qs<b.qs&&(b.flipped?b.te<A.te:A.ts<b.ts)){let T=Math.max(0,A.qe-b.qs,b.flipped?b.te-A.ts:A.te-b.ts),$=b.qs+T-A.qe,C=b.flipped?A.ts-(b.te-T):b.ts+T-A.te;if(T<x&&$<=e&&C<=e){let N=c[E]+x-T-r($,C);N>c[g]&&(c[g]=N,l[g]=E,h[g]=T)}}}}let d=new Int32Array(f.length),p=-1;for(let g=0;g<f.length;g++){let b=f[g];d[g]=(d[l[g]]??0)+b.qe-b.qs-h[g],d[g]>=t&&(p<0||c[g]>c[p])&&(p=g)}if(p<0)break;let u=[];for(let g=p;g>=0;g=l[g])u.push({run:f[g],trim:h[g]});u.reverse(),s.push(u);let m=u[0],w=u.at(-1),{flipped:y}=m.run,S=y?a.flipped:a.forward;S.query.push([m.run.qs+m.trim,w.run.qe]),S.target.push(y?[w.run.ts,m.run.te-m.trim]:[m.run.ts+m.trim,w.run.te]);for(let{run:g,trim:b}of u)i.query.push([g.qs+b,g.qe]),i.target.push(g.flipped?[g.ts,g.te-b]:[g.ts+b,g.te]);f=f.flatMap(g=>{let b=g.flipped?a.flipped:a.forward;return ri(g,[...i.query,...b.query],[...i.target,...b.target])}).sort((g,b)=>g.qs-b.qs||g.ts-b.ts)}return s}function Gn(n,e){let t=new Map;for(let s=0;s+le<=e.length;s++){let i=e.slice(s,s+le),a=t.get(i);a?a.push(s):t.set(i,[s])}let r=[],o=new Map;for(let s=0;s+le<=n.length;s++){let i=t.get(n.slice(s,s+le));if(i&&i.length<=ei)for(let a of i){let f=a-s,c=o.get(f);if(c&&s<=c.qe)c.qe=s+le,c.te=a+le;else{let l={qs:s,qe:s+le,ts:a,te:a+le,flipped:!1};o.set(f,l),r.push(l)}}}return r}function oi(n,e){return[...Gn(n,e),...Gn(n,Rt(e)).map(t=>({...t,ts:e.length-t.te,te:e.length-t.ts,flipped:!0}))]}function Nt(n,e,t,r,o){let s;for(let{run:i,trim:a}of n){let f=i.qs+a;if(s){let c=i.flipped?i.te-a:s.te,l=i.flipped?s.ts:i.ts+a,h=t.slice(c,l);o(e.slice(s.qe,f),i.flipped?Rt(h):h,r,s.qe,c)}$e(r,"=",i.qe-f),s=i}}function Wn(n,e,t){$e(t,"I",n.length),$e(t,"D",e.length)}function vo(n,e,t){n.length*e.length<=zn?bo(n,e,t):Wn(n,e,t)}function Vn(n,e,t,r=0){let[o]=n.length*e.length>zn&&r<ti?Un(Gn(n,e),1/0,le,So,1):[];if(!o){vo(n,e,t);return}let s=(f,c,l)=>{Vn(f,c,l,r+1)},i=o[0].run,a=o.at(-1).run;s(n.slice(0,i.qs),e.slice(0,i.ts),t),Nt(o,n,e,t,s),s(n.slice(a.qe),e.slice(a.te),t)}function si(n,e,t){Vn(n,e,t)}function ii(n,e,t){let r=[];Nt(n,e,t,r,si);let o=n[0],s=n.at(-1),{flipped:i}=o.run;return{queryStart:o.run.qs+o.trim,queryEnd:s.run.qe,targetStart:i?s.run.ts:o.run.ts+o.trim,targetEnd:i?o.run.te-o.trim:s.run.te,strand:i?"-":"+",edits:i?r.reverse():r,sharedBases:0}}function ai(n,e,t,r){let o=[];if(n.length*e.length<=zn)bo(n,e,t);else{let s=Un(oi(n,e),1/0,Math.max(r,le),So),i=s.find(a=>!a[0].run.flipped);if(o=s.filter(a=>a[0].run.flipped).map(a=>ii(a,n,e)),i){let a=(l,h,d,p,u)=>{o.some(w=>p<w.queryEnd&&w.queryStart<p+l.length||u<w.targetEnd&&w.targetStart<u+h.length)?vo(l,h,d):Vn(l,h,d)},f=i[0].run,c=i.at(-1).run;a(n.slice(0,f.qs),e.slice(0,f.ts),t,0,0),Nt(i,n,e,t,a),a(n.slice(c.qe),e.slice(c.te),t,c.qe,c.te)}else Wn(n,e,t)}return o}function Qn(n,e){let t=n.strand==="-",r=0,o=0;for(let[s,i]of n.edits)e(s,i,t?n.queryEnd-1-r:n.queryStart+r,n.targetStart+o),s!=="D"&&(r+=i),s!=="I"&&(o+=i)}function po(n,e,t,r){let o=e==="query"&&n.strand==="-"?-1:1,s=0;return Qn(n,(i,a,f,c)=>{let l=e==="query"?f:c,h=d=>{let p=l+o*d;return p>=t&&p<r};if(i==="="||i==="X")for(let d=0;d<a;d++)h(d)&&(s+=i==="="?xo:jn);else if(i==="I"==(e==="query"))for(let d=0;d<a;d++)h(d)&&(s+=d===0?ae:Re);else h(0)&&(s+=ae+(a-1)*Re)}),s}function uo(n,e){return e==="query"?[n.queryStart,n.queryEnd]:[n.targetStart,n.targetEnd]}function fi(n,e){let t=n.strand==="-",r=[],o=0,s=0,i=0,a=0,f=new Uint8Array(n.queryEnd-n.queryStart);for(let[p,u]of n.shared)f.fill(1,p-n.queryStart,u-n.queryStart);let c=p=>f[p-n.queryStart]===1,l=()=>{$e(r,"I",o),$e(r,"D",s),o=0,s=0};Qn(n,(p,u,m)=>{if(p==="I")o+=u;else if(p==="D")s+=u;else{for(let w=0;w<u;w++)e[i+w]?(o+=1,s+=1,c(t?m-w:m+w)&&(a+=1)):((o>0||s>0)&&l(),$e(r,p,1));i+=u}}),l();let h={I:0,D:0};for(;r[0]?.[0]==="I"||r[0]?.[0]==="D";){let[p,u]=r.shift();h[p]+=u}let d={I:0,D:0};for(;r.at(-1)?.[0]==="I"||r.at(-1)?.[0]==="D";){let[p,u]=r.pop();d[p]+=u}return r.length===0?void 0:{...n,queryStart:n.queryStart+(t?d.I:h.I),queryEnd:n.queryEnd-(t?h.I:d.I),targetStart:n.targetStart+h.D,targetEnd:n.targetEnd-d.D,edits:r,sharedBases:n.sharedBases-a}}function ci(n,e,t,r){let o={query:new Uint8Array(e),target:new Uint8Array(t)},s=n.map(c=>{let l=[];Qn(c,(h,d,p,u)=>{if(h==="="||h==="X")for(let m=0;m<d;m++)l.push([c.strand==="-"?p-m:p+m,u+m])});for(let[h,d]of l)o.query[h]=Math.min(255,o.query[h]+1),o.target[d]=Math.min(255,o.target[d]+1);return l}),i={query:new Map,target:new Map};s.forEach((c,l)=>{for(let[h,d]of c)for(let[p,u]of[["query",h],["target",d]])if(o[p][u]>1){let m=i[p].get(u);m?m.at(-1)!==l&&m.push(l):i[p].set(u,[l])}});let a=new Map,f=(c,l,h)=>{let d=`${h}:${c}:${l}`,p=a.get(d);if(p===void 0){let[u,m]=uo(n[c],h),[w,y]=uo(n[l],h),S=Math.max(u,w),g=Math.min(m,y),[b,x]=[n[c],n[l]];p=[po(x,h,S,g)-po(b,h,S,g),x.sharedBases-b.sharedBases,c-l].find(A=>A!==0)>0,a.set(d,p)}return p};return n.flatMap((c,l)=>{let h=s[l],d=new Uint8Array(h.length);if(h.forEach(([m,w],y)=>{for(let[S,g]of[["query",m],["target",w]])!d[y]&&i[S].get(g)?.some(b=>b!==l&&f(l,b,S))&&(d[y]=1)}),!d.includes(1))return[c];let p=fi(c,d),u=p?.edits.reduce((m,[w,y])=>m+(w==="="?y:0),0)??0;return p&&u>=r?[p]:[]})}function mo(n,e){return n.map(t=>{let r=e(O(t));return z(t)?Rt(r):r}).join("")}function go(n,e){let t=[0];for(let r of n)t.push(t.at(-1)+e(O(r)).length);return t}function wo(n){let e=new Map,t=new Map;n.forEach((i,a)=>{let f=O(i);e.has(f)?t.set(f,a):e.set(f,a)});let r=new Int32Array(n.length+1);for(let[i,a]of t)r[e.get(i)]+=1,r[a+1]-=1;let o=new Uint8Array(n.length),s=0;for(let i=0;i<n.length;i++)s+=r[i],o[i]=s>0?1:0;return o}function li(n,e,t,r){let o=wo(n),s=wo(e),i=new Map;e.forEach((h,d)=>{s[d]||i.set(O(h),[d])});let a=2*e.length,f=(h,d,p)=>h*a+2*d+(p?1:0),c=new Set;n.forEach((h,d)=>{for(let p of o[d]?[]:i.get(O(h))??[])c.add(f(d,p,z(h)!==z(e[p])))});let l=[];return n.forEach((h,d)=>{for(let p of o[d]?[]:i.get(O(h))??[]){let u=z(h)!==z(e[p]),m=u?-1:1,w=p-m;if(!(d>0&&w>=0&&w<e.length&&c.has(f(d-1,w,u)))){let S=d,g=p;for(;S<n.length&&g>=0&&g<e.length&&c.has(f(S,g,u));)S+=1,g+=m;let b=g-m;l.push({qs:t[d],qe:t[S],ts:r[Math.min(p,b)],te:r[Math.max(p,b)+1],flipped:u})}}}),l}function Io(n){let{query:e,target:t,sequenceOf:r}=n,o=mo(e,r),s=mo(t,r),i=li(e,t,go(e,r),go(t,r)),a=n.minMatch??Zs,f=n.bases??!0,c=[];for(let l of Un(i,n.maxGap??1/0,a,ni)){let h=[],d=l[0],p=l.at(-1),{flipped:u}=d.run;Nt(l,o,s,h,f?(w,y,S,g,b)=>{for(let x of ai(w,y,S,a)){let E=b+y.length;c.push({...x,queryStart:g+x.queryStart,queryEnd:g+x.queryEnd,targetStart:u?E-x.targetEnd:b+x.targetStart,targetEnd:u?E-x.targetStart:b+x.targetEnd,strand:u?"+":"-",edits:u?x.edits.reverse():x.edits,shared:[]})}}:Wn),c.push({queryStart:d.run.qs+d.trim,queryEnd:p.run.qe,targetStart:u?p.run.ts:d.run.ts+d.trim,targetEnd:u?d.run.te-d.trim:p.run.te,strand:u?"-":"+",edits:u?h.reverse():h,sharedBases:l.reduce((w,{run:y,trim:S})=>w+y.qe-y.qs-S,0),shared:l.map(({run:w,trim:y})=>[w.qs+y,w.qe])})}return ci(c,o.length,s.length,a).map(({shared:l,...h})=>h).sort((l,h)=>l.queryStart-h.queryStart)}function Eo(n){return n.map(([e,t])=>`${t}${e}`).join("")}var be=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 ${t.windowBp} bp window`),this.limit=e,this.windowBp=t?.windowBp,this.walkedBp=t?.walkedBp}};function Yn(n,e){return n[0]<e[0]||n[0]===e[0]&&(n[1]<e[1]||n[1]===e[1]&&n[2]<e[2])}var ct=class{heap=[];push(e,t,r){let o=this.heap;o.push([e,t,r]);let s=o.length-1;for(;s>0;){let i=s-1>>1;if(Yn(o[s],o[i]))[o[s],o[i]]=[o[i],o[s]],s=i;else break}}pop(){let e=this.heap,t=e[0],r=e.pop();if(e.length>0&&r!==void 0){e[0]=r;let o=0;for(;;){let s=2*o+1,i=s+1,a=o;if(s<e.length&&Yn(e[s],e[a])&&(a=s),i<e.length&&Yn(e[i],e[a])&&(a=i),a===o)break;[e[o],e[a]]=[e[a],e[o]],o=a}}return t}get size(){return this.heap.length}};function hi(n){let e=new Int32Array(n.length),t=new Int32Array(n.length);return n.forEach(([r,o],s)=>{e[s]=r,t[s]=o}),{pathAt:e,refAt:t,count:n.length}}function di(n,e){let t=0,r=n.length;for(;t<r;){let o=t+r>>1;n[o]>e?r=o:t=o+1}return n[t]}function Be(n){return`${n.node}:${n.offset}`}function ft(n){return n.map(e=>re(e)).reverse()}function pi(n,e){let t=e.identity.hapStart-n.identity.hapEnd,r=n.strand==="+"?e.refStart-n.refEnd:n.refStart-e.refEnd;return n.strand===e.strand&&t>=0&&r>=0?{insertion:t,deletion:r}:void 0}function ui(n,e,t){let[r,o]=n.strand==="+"?[n,e]:[e,n],s=r.edits.map(([c,l])=>[c,l]);Co(s,t.insertion,t.deletion);for(let[c,l]of o.edits)X(s,c,l);let i=n.identity.walkForward,[a,f]=i?[n,e]:[e,n];return{strand:n.strand,refStart:r.refStart,refEnd:o.refEnd,edits:s,weight:void 0,path:[...a.path,...f.path],start:a.start,pieces:[...a.pieces,...f.pieces],soloAligned:[...a.soloAligned,...f.soloAligned],identity:{pathHandle:n.identity.pathHandle,name:n.identity.name,hapStart:n.identity.hapStart,hapEnd:e.identity.hapEnd,walkForward:i}}}function mi(n,e,t){if(n.some(i=>i.weight!==void 0))return n;let r=new Map;n.forEach((i,a)=>{if(i.identity){let f=r.get(i.identity.pathHandle);f?f.push(a):r.set(i.identity.pathHandle,[a])}});let o=new Map,s=new Set;for(let i of r.values()){i.sort((l,h)=>n[l].identity.hapStart-n[h].identity.hapStart);let a=i[0],f=n[a],c=[];for(let l of i.slice(1)){let h=n[l],d=c.length===0?pi(f,h):void 0;if(d){f=ui(f,h,d),s.add(l);continue}if(!e(h)){c.push(l);continue}let p=e(f)?t([f,...c.map(u=>n[u]),h]):void 0;if(p){f=p;for(let u of[...c,l])s.add(u)}else o.set(a,f),a=l,f=h;c=[]}o.set(a,f)}return n.flatMap((i,a)=>s.has(a)?[]:[o.get(a)??i])}function Tt(n,e){return{node:n.path[e],offset:n.offsets[e]}}var gi=32768;function wi(n){let e=[...n].sort((r,o)=>r-o),t=[];for(let r of e){let o=t[t.length-1];o&&r-o[1]<=gi?o[1]=r:t.push([r,r])}return t}var $t=class n{records=new Map;paths=[];twinStarts=new Set;twinDeferred=!1;unsettled;refId;refPath;refHandle;refInterval;refIndexCache;refPrefixCache;walkedBp;snarlMode="none";snarlFills=[];snarlNodes=new Set;stats={orderedAlignments:0,lcsAlignments:0,snarls:{fills:0,inserted:0},identificationSteps:0,identificationFetches:0,identification:{interval:0,scans:[],windowSamples:0,fragmentLengths:[],companionSeeks:0,companionMisses:0,graphLookups:0,graphFetches:0,chains:[]},keep:void 0};db;limit;signal;constructor(e,t){this.db=e,this.limit=t.limit,this.signal=t.signal}static create(e,t={}){return new n(e,t)}get nodeCount(){return this.records.size/2}get pathCount(){return this.settleDeferred(),this.paths.length}get referenceInterval(){return this.refInterval&&this.refPath?{name:this.refPath,start:this.refPath.fragment+this.refInterval[0],end:this.refPath.fragment+this.refInterval[1]}:void 0}hasNode(e){return this.records.has(ye(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 be(this.limit);let t=await this.db.getRecord(ye(e,"forward")),r=await this.db.getRecord(ye(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.twinDeferred=!1,this.unsettled=void 0,this.refId=void 0,this.refPath=void 0,this.refHandle=void 0,this.refInterval=void 0,this.refIndexCache=void 0,this.refPrefixCache=void 0}async pathPosition(e){let t=await this.db.findPath(e);if(!t)throw new Error(`Cannot find a path covering offset ${e.fragment} of ${me(e)}`);if(!t.isIndexed)throw new Error(`The fragment of ${me(t.name)} at ${t.name.fragment} has not been indexed for random access`);let r=e.fragment-t.name.fragment,o=await this.db.indexedPosition(t.handle,r);if(!o)throw new Error(`The fragment of ${me(t.name)} at ${t.name.fragment} has not been indexed for random access`);return this.findPathPosition(t,r,o.pathOffset,o.pos)}async findPathPosition(e,t,r,o){let s=r,i=o;for(;;){await this.ensureNode(O(i.node));let a=this.record(i.node);if(s+a.sequenceLen>t)return{position:{seqOffset:t,handle:i.node,nodeOffset:t-s,gbwtOffset:i.offset},name:e.name,handle:e.handle};s+=a.sequenceLen;let f=a.gbwt().lf(i.offset);if(!f)throw new Error(`The fragment of ${me(e.name)} at ${e.name.fragment} does not contain offset ${t}`);i=f}}async aroundPosition(e,t,r){let o=O(e);await this.ensureNode(o);let s=this.record(e),i=je(e),a=new ct;return a.push(t,o,It(i)),a.push(s.sequenceLen-t-1,o,Et(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[o,s]=await Promise.all([this.db.indexedPosition(e,t),this.db.indexedPosition(e,r)]);if(o&&s){let i=o.pos.node,a=s.pos.node;if(!await this.db.prefetchRecords([[Math.min(i,a),Math.max(i,a)+1]])){let c=await this.db.indexedPositionsBetween(e,t,r);await this.db.prefetchRecords(wi(c.map(l=>l.pos.node)).map(([l,h])=>[l,h+2]),!0)}}return o}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(o){throw o instanceof be&&o.windowBp===void 0?new be(o.limit,{windowBp:t,walkedBp:this.walkedBp}):o}}get referenceWalkedBp(){return this.walkedBp}async walkInterval(e,t,r){let o={node:e.handle,offset:e.gbwtOffset},s=e.nodeOffset,i=t,a=new ct;for(;;){let f=O(o.node),c=je(o.node);this.walkedBp=t-i,await this.ensureNode(f);let l=this.record(o.node);if(s>=l.sequenceLen)throw new Error(`Offset ${s} in node ${f} of length ${l.sequenceLen}`);a.push(s,f,It(c));let h=l.sequenceLen-s;if(i<=h){a.push(i===h?0:h-i-1,f,Et(c));break}a.push(0,f,Et(c));let d=l.gbwt().lf(o.offset);if(!d)throw new Error(`No successor for GBWT position (${o.node}, ${o.offset})`);o=d,s=0,i-=h}return this.walkedBp=t,this.insertContext(a,r)}async aroundNodes(e,t){let r=new ct;for(let o of e)await this.ensureNode(o),r.push(0,o,"left"),r.push(0,o,"right");return this.insertContext(r,t)}async insertContext(e,t){this.clearPaths(),this.snarlMode="none",this.snarlFills=[],this.snarlNodes.clear(),this.stats.snarls={fills:0,inserted:0};let r=new Set,o=new Set;for(let i of this.records.keys())o.add(O(i));let s=0;for(;e.size>0;){let[i,a,f]=e.pop(),c=`${a}:${f}`;if(r.has(c))continue;r.add(c),o.delete(a),this.hasNode(a)||(await this.addNode(a),s+=1);let l=jr(f);if(!r.has(`${a}:${l}`)){let p=this.record(ye(a,Ur(f))),u=i+p.sequenceLen-1;u<=t&&e.push(u,a,l)}let h=this.record(ye(a,Wr(f))),d=i+1;if(d<=t)for(let p of h.successors()){let u=O(p),m=It(je(p));r.has(`${u}:${m}`)||e.push(d,u,m)}}for(let i of o)this.records.delete(ye(i,"forward")),this.records.delete(ye(i,"reverse"));return{inserted:s,removed:o.size}}async betweenNodes(e,t){return(await this.fillBetween(e,t)).inserted.length}async fillBetween(e,t){this.clearPaths();let r=[e,re(t)],o=new Set([O(e),O(t)]),s=[];for(;r.length>0;){let i=r.pop(),a=O(i);this.hasNode(a)||(await this.addNode(a),s.push(a));for(let f of this.record(i).successors()){let c=O(f);o.has(c)||(r.push(f,re(f)),o.add(c))}}return{inserted:s,nodes:o.size-2}}async extractSnarls(e){let t=0;this.snarlMode=e;for(let[r,o]of await this.overlappingSnarls(e)){let{inserted:s,nodes:i}=await this.fillBetween(r,o),a=O(r),f=O(o);this.snarlFills.push({low:Math.min(a,f),high:Math.max(a,f),nodes:i,inserted:s.length});for(let c of s)this.snarlNodes.add(c);t+=s.length}return this.stats.snarls={fills:this.snarlFills.length,inserted:this.snarlNodes.size},t}async overlappingSnarls(e){let t=[];if(e!=="none"){let r=!1;for(let o of this.sortedHandles()){let s=this.record(o),i=s.next;i!==void 0&&(r=!0,this.hasHandle(i)?Ue(o,i)&&t.push([o,i]):e==="overlapping"&&this.isSnarlEntryInSubgraph(s)&&t.push([o,i]))}if(!r&&e==="overlapping"&&await this.db.hasChainLinks()){let o=await this.findCoveringSnarl();o&&t.push(o)}}return t}isSnarlEntryInSubgraph(e){let t=e.successors(),r=t.find(o=>this.hasHandle(o));return r===void 0?!1:t.length>1||this.record(re(r)).successors().length>1}recordReader(e){let t=new Map;return async r=>{let o=this.records.get(r);if(o)return o;let s=t.get(r);if(!s){if(s=await this.db.getRecord(r),e?.(),!s)throw new Error(`Node record ${r} is missing from the database`);t.set(r,s)}return s}}async findCoveringSnarl(){let e=this.recordReader(),t=async f=>{let c=f.successors(),l=c[0];return l===void 0?!1:c.length>1||(await e(re(l))).successors().length>1},r=async f=>{let c=await e(re(f));return c.next!==void 0?await t(c)?{kind:"snarl-exit",snarl:[re(f),c.next]}:{kind:"chain"}:(await e(f)).next!==void 0?{kind:"chain"}:{kind:"regular"}},o=new Set,s=this.sortedHandles().flatMap(f=>this.record(f).successors()),i,a=!1;for(;!a&&s.length>0;){let f=s.shift(),c=O(f);if(!this.hasHandle(f)&&!o.has(c)){o.add(c);let l=await r(f);if(l.kind==="snarl-exit")i=l.snarl,a=!0;else if(l.kind==="chain")a=!0;else for(let h of["forward","reverse"])s.push(...(await e(ye(c,h))).successors())}}return i}extractPaths(e,t){if(this.clearPaths(),t==="none")return;let r=e?.position;this.refPath=e?.name,this.refHandle=e?.handle;let o=this.sortedHandles(),s=o.length,i=new Map;o.forEach((x,E)=>i.set(x,E));let a=new Int32Array(s+1),f=new Int32Array(s),c=[];for(let x=0;x<s;x++){let E=this.record(o[x]),A=E.gbwt().decompressArrays();f[x]=E.sequenceLen,c.push(A),a[x+1]=a[x]+A.nodes.length}let l=a[s],h=new Int32Array(l),d=new Int32Array(l),p=new Uint8Array(l);for(let x=0;x<s;x++){let E=c[x];h.set(E.nodes,a[x]),d.set(E.offsets,a[x])}c.length=0;for(let x=0;x<l;x++){let E=i.get(h[x]);E===void 0?h[x]=-1:(h[x]=E,p[a[E]+d[x]]=1)}let u=r===void 0?void 0:i.get(r.handle),m=r?.gbwtOffset,w,y=(x,E,A)=>{let _=[],T=0,$=0,C=-1,N=x,P=E;for(;;){N===u&&P===m&&(C=T),A&&(A.push(o[N]),_.push(P)),T+=1,$+=f[N];let U=a[N]+P,Y=h[U];if(Y<0)break;P=d[U],N=Y}return{offsets:_,len:$,refAt:C,last:N}},S=(x,E,A,_)=>{_>=0&&(this.refId=this.paths.length,w=_),this.paths.push({path:x,offsets:E,len:A,weight:void 0,identity:void 0})},g=new Int32Array(s);for(let x=0;x<s;x++){let E=o[x];if(!z(E)){let A=a[x],_=a[x+1]-A;for(let T=0;T<_;T++)if(p[A+T]===0){let $=[],{offsets:C,len:N,refAt:P,last:U}=y(x,T,$),Y=o[U];if(P>=0||Fe(E,Y)){if(S($,C,N,P),!z(Y)){let I=i.get(re(Y));g[I]=g[I]+1}}else this.twinStarts.add(Be({node:E,offset:T}))}}}for(let x=0;x<s;x++){let E=o[x];if(z(E)){let A=a[x],_=a[x+1]-A,T=0;for(let C=0;C<_;C++)p[A+C]===0&&(T+=1);let $=(u===void 0||w!==void 0)&&T===g[x];for(let C=0;C<_;C++)if(p[A+C]===0){let N=$?void 0:y(x,C,void 0);if(N&&(N.refAt>=0||Fe(E,o[N.last]))){let P=[],{offsets:U,len:Y,refAt:I}=y(x,C,P);S(P,U,Y,I)}else this.twinStarts.add(Be({node:E,offset:C}))}}}let b=this.refId===void 0?void 0:this.paths[this.refId];if(this.paths.sort((x,E)=>x.path[0]-E.path[0]||x.offsets[0]-E.offsets[0]),b&&(this.refId=this.paths.indexOf(b)),r){if(w===void 0||this.refId===void 0)throw this.clearPaths(),new Error("Could not find the reference path");let x=this.paths[this.refId],E=r.nodeOffset;for(let _ of x.path.slice(0,w))E+=this.record(_).sequenceLen;let A=r.seqOffset-E;this.refInterval=[A,A+x.len],x.identity={pathHandle:e.handle,name:e.name,orientation:"forward",hapStart:A,hapEnd:A+x.len}}if(t==="distinct")this.distinctPaths(!0);else if(t==="reference-only"){if(this.refId===void 0)throw new Error("Reference path is required for reference-only output");this.paths=[this.paths[this.refId]],this.refId=0}}distinctPaths(e){let t=this.refId===void 0?void 0:this.paths[this.refId],r=t?.path,o=r&&!st(r)?ft(r):void 0,s=c=>o!==void 0&&Kn(c,o)===0||st(ft(c)),i=e&&this.db.hasHaplotypeIndex;this.twinDeferred=!1,this.paths.sort((c,l)=>Kn(c.path,l.path)||c.len-l.len||(c===t?-1:l===t?1:0));let a=[],f;for(let c of this.paths){let l=a[a.length-1],h=i&&c!==t&&s(c.path);this.twinDeferred||=h,l&&Kn(l.path,c.path)===0&&!h?l.weight=(l.weight??1)+(c.weight??1):(c===t&&(f=a.length),a.push({...c,weight:c.weight??1}))}this.paths=a,this.refId=f}mergeDistinct(){this.twinDeferred?this.settleDeferred():this.distinctPaths(!1)}settleDeferred(){this.twinDeferred&&(this.unsettled={paths:[...this.paths],refId:this.refId},this.distinctPaths(!1))}dropTwins(){let e=this.refId===void 0?void 0:this.paths[this.refId],t=this.refInterval,r=i=>`${i.pathHandle}:${i.hapStart}-${i.hapEnd}`,o=new Set;e?.identity&&t&&o.add(r({...e.identity,hapStart:t[0],hapEnd:t[1]}));for(let i of this.paths)i!==e&&i.identity?.orientation==="forward"&&o.add(r(i.identity));let s=this.paths.filter(i=>i===e||i.identity?.orientation!=="reverse"||!o.has(r(i.identity)));s.length<this.paths.length&&(this.paths=s,this.refId=e===void 0?void 0:s.indexOf(e)),this.twinDeferred&&this.distinctPaths(!1)}keepHaplotypes(e){if(this.paths.some(i=>i.weight!==void 0))throw new Error("keepHaplotypes needs one walk per haplotype: extract with haplotypes 'all', then call mergeDistinct()");let t=this.paths.filter((i,a)=>a!==this.refId&&i.identity===void 0).length;if(t>0)throw new Error(`${t} of the window's ${this.paths.length} walks have no name, so the haplotypes to keep cannot be told from the rest; call identifyPaths() first, and check that the haplotype index was built for this graph`);let r=this.refId===void 0?void 0:this.paths[this.refId],o=this.paths.filter((i,a)=>a===this.refId||i.identity!==void 0&&e(i.identity.name)),s=new Set;for(let i of o)for(let a of i.path)s.add(O(a));for(let i of[...this.records.keys()])s.has(O(i))||this.records.delete(i);this.paths=o,this.refId=r===void 0?void 0:o.indexOf(r)}async extractChosenPaths(e,t,r,o){this.clearPaths();let s=e.position.seqOffset,i=await fo({db:this.db,records:this.records,referenceHandle:e.handle,referencePos:{node:e.position.handle,offset:e.position.gbwtOffset},referenceLeft:s-e.position.nodeOffset,window:{start:s,end:s+t},context:o,snarls:{mode:this.snarlMode,fills:this.snarlFills,inserted:this.snarlNodes},keep:r,signal:this.signal,prefetchReferenceRange:(l,h,d)=>this.prefetchReferenceRange(l,h,d)});if(this.stats.keep=i.stats,i.stats.fallback!==void 0)return!1;let a=await this.db.pathsByHandle(),f=l=>({path:l.handles,offsets:l.offsets,len:l.len,weight:void 0,identity:{pathHandle:l.pathHandle,name:l===i.reference?e.name:a.get(l.pathHandle).name,orientation:l.orientation,hapStart:l.hapStart,hapEnd:l.hapEnd}}),c=[i.reference,...i.pieces].sort(co);return this.paths=c.map(f),this.refId=c.indexOf(i.reference),this.refPath=e.name,this.refHandle=e.handle,this.refInterval=[i.reference.hapStart,i.reference.hapEnd],this.dropTwins(),!0}async identifyPaths(){if(!this.db.hasHaplotypeIndex)throw new Error("The database has no HaplotypeSamples table; run gbz-haplotype-index on it");this.unsettled&&({paths:this.paths,refId:this.refId}=this.unsettled,this.unsettled=void 0,this.twinDeferred=!0);let e=await this.db.haplotypeSampleGap()??4096,t=Hn(this.sortedHandles());if(t.length===0)return;let r=new Map,o=await Promise.all(t.map(([m,w])=>this.db.haplotypeSamplesInRange(m,w)));for(let m of o.flat())r.set(Be(m),m);let s=m=>{let w=0,y=t.length-1;for(;w<y;){let g=w+y+1>>1;t[g][0]<=m?w=g:y=g-1}let S=t[w];return S[0]<=m&&m<=S[1]},i=new Map;this.paths.forEach((m,w)=>{m.path.length>0&&w!==this.refId&&i.set(Be(Tt(m,0)),w)});let a=this.stats.identification;a.interval=e,a.scans=t,a.windowSamples=r.size,this.paths.forEach((m,w)=>{w!==this.refId&&a.fragmentLengths.push(m.len)});let f=this.recordReader(()=>{this.stats.identificationFetches+=1,a.graphFetches+=1}),c=m=>(a.graphLookups+=1,f(m)),l=async(m,w)=>{if(s(m.node))return r.get(Be(m));this.stats.identificationFetches+=1,a.companionSeeks+=1,w.seeks+=1;let y=await this.db.haplotypeSampleAt(m.node,m.offset);return y||(a.companionMisses+=1),y},h=new Map,d=async m=>{let w=h.get(m);if(!w){let y=await this.db.getPath(m);if(!y)throw new Error(`Path ${m} is missing from the database`);w=y.name,h.set(m,w)}return w},p=(m,w,y)=>m.orientation==="forward"?{pathHandle:m.pathHandle,orientation:"forward",base:m.pathOffset-w}:{pathHandle:m.pathHandle,orientation:"reverse",base:m.pathOffset+w+y},u=(m,w)=>m.orientation==="forward"?{pathHandle:m.pathHandle,orientation:"forward",base:m.hapStart-w}:{pathHandle:m.pathHandle,orientation:"reverse",base:m.hapEnd+w};for(let m=0;m<this.paths.length;m++){let w=this.paths[m];if(m===this.refId||w.identity)continue;let y=[],S=new Set,g={fragments:0,steps:0,seeks:0,reentries:0,twinLandings:0,end:"endmarker",pathHandle:void 0};a.chains.push(g);let b,x=0,E=m,A;for(;b===void 0;){if(this.signal?.throwIfAborted(),E!==void 0){if(S.has(E)){g.end="cycle";break}S.add(E);let N=this.paths[E];y.push({index:E,startBp:x}),g.fragments+=1;let P=x;for(let Y=0;Y<N.path.length;Y++){let I=Tt(N,Y),R=r.get(Be(I)),k=this.record(I.node).sequenceLen;if(R){b=p(R,P,k);break}P+=k}if(x+=N.len,b){g.end="in-fragment sample";break}let U=Tt(N,N.path.length-1);A=this.record(U.node).gbwt().lf(U.offset),E=void 0}if(A===void 0||A.node===0){g.end="endmarker";break}let _=Be(A),T=i.get(_);if(T!==void 0){let N=this.paths[T].identity;if(N){b=u(N,x),g.end="identified sibling";break}E=T;continue}this.records.has(A.node)&&(g.reentries+=1),this.twinStarts.has(_)&&(g.twinLandings+=1);let $=await l(A,g),C=await c(A.node);if($){b=p($,x,C.sequenceLen),g.end="out-of-window sample";break}if(this.stats.identificationSteps+=1,g.steps+=1,x-y[y.length-1].startBp>4*e+4*C.sequenceLen){g.end="bound";break}x+=C.sequenceLen,A=C.gbwt().lf(A.offset)}if(b){g.pathHandle=b.pathHandle;let _=await d(b.pathHandle);for(let{index:T,startBp:$}of y){let C=this.paths[T];C.identity=b.orientation==="forward"?{pathHandle:b.pathHandle,name:_,orientation:"forward",hapStart:b.base+$,hapEnd:b.base+$+C.len}:{pathHandle:b.pathHandle,name:_,orientation:"reverse",hapStart:b.base-$-C.len,hapEnd:b.base-$}}}}this.dropTwins()}refIndex(e){if(this.refIndexCache===void 0){let t=new Map;e.forEach((r,o)=>{let s=t.get(r);s?s.push(o):t.set(r,[o])}),this.refIndexCache=t}return this.refIndexCache}refPrefix(e){if(this.refPrefixCache===void 0){let t=[0];e.forEach((r,o)=>{t.push(t[o]+this.record(r).sequenceLen)}),this.refPrefixCache=t}return this.refPrefixCache}orderedMatches(e,t){let r=this.refIndex(t),o=new Int32Array(e.length),s=new Int32Array(e.length),i=0,a=-1;for(let f=0;f<e.length;f++){let c=r.get(e[f]);if(c){let l=di(c,a);if(l===void 0)return;o[i]=f,s[i]=l,i+=1,a=l}}return{pathAt:o,refAt:s,count:i}}pathLen(e){let t=0;for(let r of e)t+=this.record(r).sequenceLen;return t}prefixMatches(e,t){let r=0,o=0,s=0,i=0,a=0;for(;o<e.length&&s<t.length;){let f=this.record(e[o]).sequence,c=this.record(t[s]).sequence;for(;i<f.length&&a<c.length;){if(f[i]!==c[a])return r;i+=1,a+=1,r+=1}i===f.length&&(o+=1,i=0),a===c.length&&(s+=1,a=0)}return r}suffixMatches(e,t){let r=0,o=0,s=0,i=0,a=0;for(;o<e.length&&s<t.length;){let f=this.record(e[e.length-o-1]).sequence,c=this.record(t[t.length-s-1]).sequence;for(;i<f.length&&a<c.length;){if(f[f.length-i-1]!==c[c.length-a-1])return r;i+=1,a+=1,r+=1}i===f.length&&(o+=1,i=0),a===c.length&&(s+=1,a=0)}return r}align(e,t,r){let o=this.pathLen(e),s=this.pathLen(t),i=this.prefixMatches(e,t),a=this.suffixMatches(e,t);i+a>o&&(a=o-i),i+a>s&&(a=s-i),X(r,"M",i),Co(r,o-i-a,s-i-a),X(r,"M",a)}sharedWeight(e,t){let r=this.refIndex(t),o=0;for(let s of e)r.has(s)&&(o+=this.record(s).sequenceLen);return o}editsAgainst(e,t){let r=this.orderedMatches(e,t);r?this.stats.orderedAlignments+=1:this.stats.lcsAlignments+=1;let o=r??hi(lo(e,t,h=>this.record(h).sequenceLen)[0]),s=[],i=this.refPrefix(t),a=(h,d,p,u)=>{h===d?X(s,"D",i[u]-i[p]):p===u?X(s,"I",this.pathLen(e.slice(h,d))):this.align(e.slice(h,d),t.slice(p,u),s)},f=0,c=0,l=0;for(let h=0;h<o.count;h++){let d=o.pathAt[h],p=o.refAt[h];(c!==d||l!==p)&&a(c,d,l,p);let u=this.record(e[d]).sequenceLen;X(s,"M",u),f+=u,c=d+1,l=p+1}return a(c,e.length,l,t.length),{edits:s,matched:f,matches:o}}alignment(e){let t=this.paths[e];if(this.refId===void 0||e===this.refId||!t)return;let r=this.paths[this.refId].path,o;if(st(r)&&(t.identity===void 0||!st(ft(t.path))))o={...this.editsAgainst(t.path,r),flipped:!1};else{let s=ft(t.path),i=this.sharedWeight(t.path,r);if(this.sharedWeight(s,r)===0)o={...this.editsAgainst(t.path,r),flipped:!1};else if(i===0)o={...this.editsAgainst(s,r),flipped:!0};else{let f=this.editsAgainst(t.path,r),c=this.editsAgainst(s,r);o=c.matched>f.matched?{...c,flipped:!0}:{...f,flipped:!1}}}return o}alignToRef(e){return this.settleDeferred(),this.alignment(e)?.edits.map(([t,r])=>`${r}${t}`).join("")}alignments(){this.settleDeferred();let e=this.referenceInterval;if(this.refId===void 0||!e)throw new Error("Alignments need a reference path");let t=this.paths[this.refId].path,r=this.refPrefix(t)[t.length],o=(l,h,d,p)=>{let u=yi(l),m=this.paths[d[0]],w=this.paths[d[d.length-1]],y=m.identity,S=y?.orientation==="forward",[g,b]=S?[m,w]:[w,m];return{strand:h,refStart:e.start+u.leading,refEnd:e.start+r-u.trailing,edits:u.edits,weight:m.weight,path:d.flatMap(x=>this.paths[x].path),start:Tt(m,0),pieces:d,soloAligned:p,identity:y===void 0?void 0:{pathHandle:y.pathHandle,name:y.name,hapStart:y.name.fragment+g.identity.hapStart,hapEnd:y.name.fragment+b.identity.hapEnd,walkForward:S}}},s=l=>l.soloAligned.reduce((h,d)=>h+d,0),i=l=>l.pieces.reduce((h,d)=>h+this.paths[d].len,0),a=l=>2*s(l)>=i(l),f=l=>{let h=l[0],d=l[l.length-1],p=h.identity.walkForward;if(l.some((P,U)=>P.strand!==h.strand||P.identity.walkForward!==p||U>0&&P.identity.hapStart<l[U-1].identity.hapEnd))return;let u=p?l:[...l].reverse(),m=u.flatMap(P=>P.pieces),w=u.flatMap(P=>P.soloAligned),y=h.strand==="+"!==p,S=m.map(P=>this.paths[P]),g=S.slice(1).map((P,U)=>{let Y=S[U].identity;return p?P.identity.hapStart-Y.hapEnd:Y.hapStart-P.identity.hapEnd}),b=y?[...S].reverse():S,x=y?[...g].reverse():g,E=b.flatMap(P=>y?ft(P.path):P.path),{edits:A}=this.editsAgainst(E,t),_=Ao(A,b.map(P=>P.len)),T=new Map((y?[...m].reverse():m).map((P,U)=>[P,_[U]])),$=P=>2*P.pieces.reduce((U,Y)=>U+T.get(Y),0)>=s(P);if(!$(h)||!$(d))return;let C=[],N=0;return b.slice(0,-1).forEach((P,U)=>{N+=P.len,C.push([N,x[U]])}),o(bi(A,C),h.strand,m,w)},c=[];return this.paths.forEach((l,h)=>{if(h===this.refId)return;let{edits:d,flipped:p}=this.alignment(h),u=l.identity,m=u?u.orientation==="forward"!==p:!p;c.push(o(d,m?"+":"-",[h],Ao(d,[l.len])))}),mi(c,a,f).map(l=>{let{edits:h,identity:d,pieces:p,soloAligned:u,...m}=l,w={...m,cigar:Si(h)};return d?{...w,resolved:!0,name:d.name,label:me({...d.name,fragment:d.hapStart,end:d.hapEnd}),pathHandle:d.pathHandle,hapStart:d.hapStart,hapEnd:d.hapEnd}:{...w,resolved:!1}})}pairAlignments(e){let{target:t,query:r,...o}=e,s=this.paths.flatMap(l=>{let{identity:h}=l;return h?[{name:h.name,start:h.name.fragment+h.hapStart,steps:Ft(l,h)}]:[]}),i=l=>h=>h.sample===l.sample&&h.haplotype===l.haplotype,a=i(t),f=r?i(r):l=>!a(l),c=l=>this.record(ye(l,"forward")).sequence;return s.filter(l=>a(l.name)).flatMap(l=>s.filter(h=>f(h.name)).flatMap(h=>Io({...o,query:h.steps,target:l.steps,sequenceOf:c}).map(d=>({query:h.name,queryStart:h.start+d.queryStart,queryEnd:h.start+d.queryEnd,strand:d.strand,target:l.name,targetStart:l.start+d.targetStart,targetEnd:l.start+d.targetEnd,cigar:Eo(d.edits),matches:d.edits.reduce((p,[u,m])=>p+(u==="="?m:0),0),columns:d.edits.reduce((p,[,u])=>p+u,0),sharedBases:d.sharedBases}))))}canonicalEdges(e){let t=[];for(let r of["forward","reverse"]){let o=ye(e,r);for(let s of this.record(o).successors())this.hasHandle(s)&&Ue(o,s)&&t.push([r==="reverse"?1:0,O(s),z(s)?1:0])}return t.sort((r,o)=>r[0]-o[0]||r[1]-o[1]||r[2]-o[2]),t.filter((r,o)=>o===0||r[0]!==t[o-1][0]||r[1]!==t[o-1][1]||r[2]!==t[o-1][2])}async stableName(){let e=new TextEncoder,t=[];for(let r of this.sortedHandles())if(!z(r)){let o=O(r),s=`S	${o}	${this.record(r).sequence}
+import{a as Ln,b as qs,c as Gr,d as zr}from"./chunk-B2UJRFGO.js";import{f as Hs,g as _n,h as Ce,i as kn,j as On,k as St,l as Nn,m as vt,o as Tn}from"./chunk-WV6GUYH7.js";import{a as Fn,b as $n}from"./chunk-6UUUO22M.js";import"./chunk-YPZ64NPV.js";import{a as Br}from"./chunk-KWAXLUPQ.js";import"./chunk-YBLNN5FU.js";import{e as bt,f as ze,g as Pn}from"./chunk-QU4UAKXZ.js";import"./chunk-E7J6SB5P.js";import{a as Ds,d as Hr,e as qr,f as Dr}from"./chunk-4T7DPQTR.js";import{a as ot}from"./chunk-J4OLMLS5.js";import{a as Bs,b as ce}from"./chunk-FY3BTKY4.js";var Cs=Bs((rd,As)=>{As.exports=JBrowseExports["@jbrowse/core/util/installClearHoverOnSurfaceMove"]});function ye(n,e){return 2*n+(e==="reverse"?1:0)}function O(n){return Math.floor(n/2)}function je(n){return n%2===0?"forward":"reverse"}function z(n){return n%2===1}function re(n){return n%2===0?n+1:n-1}function jr(n){return n==="left"?"right":"left"}function It(n){return n==="forward"?"left":"right"}function Et(n){return n==="forward"?"right":"left"}function Ur(n){return n==="left"?"forward":"reverse"}function Wr(n){return n==="right"?"forward":"reverse"}function Ue(n,e){let t=O(n),r=O(e);return z(n)?r>t||r===t&&!z(e):r>=t}function st(n){return Fe(n[0],n[n.length-1])}function Fe(n,e){return n===void 0||e===void 0?!0:z(n)===z(e)?!z(n):Ue(n,e)}var it=class{offset=0;bytes;constructor(e){this.bytes=e}get done(){return this.offset>=this.bytes.length}byte(){let e=this.bytes[this.offset];if(e!==void 0)return this.offset+=1,e}int(){let e=1,t=0;for(;this.offset<this.bytes.length;){let r=this.bytes[this.offset];if(this.offset+=1,t+=(r&127)*e,e*=128,(r&128)===0)return t}}},Vr=255,Gs=256,At=class{source;sigma;threshold;constructor(e,t){this.source=new it(e),this.sigma=t===0?Number.MAX_SAFE_INTEGER:t,this.threshold=this.sigma<Vr?Math.floor(Gs/this.sigma):0}next(){if(this.sigma>=Vr){let o=this.source.int(),s=this.source.int();return o===void 0||s===void 0?void 0:{value:o,len:s+1}}let e=this.source.byte();if(e===void 0)return;let t=e%this.sigma,r=Math.floor(e/this.sigma)+1;if(r===this.threshold){let o=this.source.int();if(o===void 0)return;r+=o}return{value:t,len:r}}*[Symbol.iterator](){for(let e=this.next();e!==void 0;e=this.next())yield e}};function Qr(n){let e=new it(n),t=e.int();if(t===void 0||t===0)return[];let r=[],o=0;for(let s=0;s<t;s++){let i=e.int(),a=e.int();if(i===void 0||a===void 0)throw new Error("GBWT edge list ends early");o+=i,r.push({node:o,offset:a})}return r}var Ct=class{edges;bwt;constructor(e,t){this.edges=e,this.bwt=t}runs(){return new At(this.bwt,this.edges.length)}edge(e){let t=this.edges[e];if(t===void 0)throw new Error(`GBWT run refers to edge rank ${e} of ${this.edges.length}`);return t}lf(e){let t=this.edges.map(o=>o.offset),r=0;for(let o of this.runs()){let s=this.edge(o.value),i=t[o.value];if(r+o.len>e)return s.node===0?void 0:{node:s.node,offset:i+(e-r)};t[o.value]=i+o.len,r+=o.len}}edgeTo(e){let t=0,r=this.edges.length;for(;t<r;){let o=t+r>>1,s=this.edges[o];if(s.node===e)return o;s.node<e?t=o+1:r=o}}offsetTo(e){if(e.node===0)return;let t=this.edgeTo(e.node);if(t===void 0)return;let r=this.edges[t].offset;if(r>e.offset)return;let o=0;for(let s of this.runs())if(o+=s.len,s.value===t&&(r+=s.len,r>e.offset))return o-(r-e.offset)}predecessorAt(e){let t=this.edges.map(o=>({node:o.node===0?0:re(o.node),count:0}));for(let o of this.runs()){let s=t[o.value];s&&(s.count+=o.len)}for(let o=1;o<t.length;o++){let s=t[o-1],i=t[o];O(s.node)===O(i.node)&&(t[o-1]=i,t[o]=s)}let r=0;for(let o of t)if(r+=o.count,r>e)return o.node===0?void 0:o.node}decompressArrays(){let e=this.edges.map(i=>i.offset),t=0;for(let i of this.runs())t+=i.len;let r=new Int32Array(t),o=new Int32Array(t),s=0;for(let i of this.runs()){let a=this.edge(i.value),f=e[i.value];for(let c=0;c<i.len;c++)r[s]=a.node,o[s]=f,f+=1,s+=1;e[i.value]=f}return{nodes:r,offsets:o}}decompress(){let e=this.edges.map(r=>r.offset),t=[];for(let r of this.runs()){let o=this.edge(r.value);for(let s=0;s<r.len;s++)t.push({node:o.node,offset:e[r.value]}),e[r.value]=e[r.value]+1}return t}};var zs=["","A","C","G","T","N"];function Yr(n){let e=n[n.length-1];if(e===void 0)return 0;let t=e,r=0;for(let o=0;o<3&&t%6!==0;o++)t=Math.floor(t/6),r+=1;return 3*(n.length-1)+r}function Kr(n){let e="";for(let t of n){let r=t;for(let o=0;o<3;o++){let s=zs[r%6];if(s==="")return e;r=Math.floor(r/6),e+=s}}return e}var js={A:"T",C:"G",G:"C",T:"A",N:"N"};function Rt(n){let e="";for(let t=n.length-1;t>=0;t--)e+=js[n[t]]??"N";return e}var Us=Uint32Array.from([1116352408,1899447441,3049323471,3921009573,961987163,1508970993,2453635748,2870763221,3624381080,310598401,607225278,1426881987,1925078388,2162078206,2614888103,3248222580,3835390401,4022224774,264347078,604807628,770255983,1249150122,1555081692,1996064986,2554220882,2821834349,2952996808,3210313671,3336571891,3584528711,113926993,338241895,666307205,773529912,1294757372,1396182291,1695183700,1986661051,2177026350,2456956037,2730485921,2820302411,3259730800,3345764771,3516065817,3600352804,4094571909,275423344,430227734,506948616,659060556,883997877,958139571,1322822218,1537002063,1747873779,1955562222,2024104815,2227730452,2361852424,2428436474,2756734187,3204031479,3329325298]),Ie=(n,e)=>n>>>e|n<<32-e;function Xr(n){let e=Math.ceil((n.length+9)/64),t=new Uint8Array(e*64);t.set(n),t[n.length]=128;let r=new DataView(t.buffer),o=n.length*8;r.setUint32(t.length-8,Math.floor(o/2**32)),r.setUint32(t.length-4,o>>>0);let s=Uint32Array.from([1779033703,3144134277,1013904242,2773480762,1359893119,2600822924,528734635,1541459225]),i=new Uint32Array(64);for(let c=0;c<e;c++){for(let S=0;S<16;S++)i[S]=r.getUint32(c*64+S*4);for(let S=16;S<64;S++){let g=i[S-15],b=i[S-2],x=Ie(g,7)^Ie(g,18)^g>>>3,E=Ie(b,17)^Ie(b,19)^b>>>10;i[S]=i[S-16]+x+i[S-7]+E}let l=s[0],h=s[1],d=s[2],p=s[3],u=s[4],m=s[5],w=s[6],y=s[7];for(let S=0;S<64;S++){let g=Ie(u,6)^Ie(u,11)^Ie(u,25),b=u&m^~u&w,x=y+g+b+Us[S]+i[S]|0,E=Ie(l,2)^Ie(l,13)^Ie(l,22),A=l&h^l&d^h&d;y=w,w=m,m=u,u=p+x|0,p=d,d=h,h=l,l=x+E+A|0}[l,h,d,p,u,m,w,y].forEach((S,g)=>{s[g]=s[g]+S})}let a=new Uint8Array(32),f=new DataView(a.buffer);for(let c=0;c<8;c++)f.setUint32(c*4,s[c]);return a}function Zr(n,e){let t=new Map;if(n!==void 0)for(let r of n.split(";")){let o=r.split(","),[s,i]=o;if(o.length!==2||!s||!i)throw new Error(`Invalid ${e} relationship: ${r}`);let a=t.get(s);a||(a=new Set,t.set(s,a)),a.add(i)}return t}function to(n){return{name:n.get("pggname"),subgraph:Zr(n.get("subgraph"),"subgraph"),translation:Zr(n.get("translation"),"translation")}}function Jr(n,e){for(let[t,r]of e){let o=n.get(t);o||(o=new Set,n.set(t,o));for(let s of r)o.add(s)}}function no(n,e){let t={name:n,subgraph:new Map,translation:new Map};return e.name!==void 0&&(t.subgraph.set(n,new Set([e.name])),Jr(t.subgraph,e.subgraph),Jr(t.translation,e.translation)),t}function eo(n){return[...n.entries()].sort(([e],[t])=>e<t?-1:e>t?1:0).flatMap(([e,t])=>[...t].sort().map(r=>[e,r]))}function ro(n){let e=[];n.name!==void 0&&e.push(`H	NM:Z:${n.name}`);for(let[t,r]of eo(n.subgraph))e.push(`H	SG:Z:${t},${r}`);for(let[t,r]of eo(n.translation))e.push(`H	TL:Z:${t},${r}`);return e}async function oo(n){let e=n.reduce((i,a)=>i+a.length,0),t=new Uint8Array(e),r=0;for(let i of n)t.set(i,r),r+=i.length;let o=globalThis.crypto?.subtle;return[...o?new Uint8Array(await o.digest("SHA-256",t)):Xr(t)].map(i=>i.toString(16).padStart(2,"0")).join("")}var Ws="_gbwt_ref";function me(n){let e=`${n.sample}#${n.haplotype}#${n.contig}`;return n.end===void 0?e:`${e}[${n.fragment}-${n.end}]`}var Vs=/^([^#]+)#(\d+)#([^#]+?)(?:\[\d+-\d+\])?$/,Qs=/^([^#]+?)(?:\[\d+-\d+\])?$/;function Ys(n){let e=Vs.exec(n);if(e)return{sample:e[1],haplotype:Number(e[2]),contig:e[3]};let t=Qs.exec(n);if(t)return{contig:t[1]};throw new Error(`"${n}" is not a path name; expected "sample#haplotype#contig" or a bare contig`)}function We(n){return typeof n=="string"?Ys(n):n}function Ve(n,e){return{sample:n.sample??Ws,contig:n.contig,haplotype:n.haplotype??0,fragment:e}}var Ks=4096;function Hn(n){let e=[];for(let t of n){let r=e[e.length-1];r&&t-r[1]<=Ks?r[1]=t:e.push([t,t])}return e}var Xs=32768,so={mostChosenPaths:32},Bn=class{byNode=new Map;get(e){return this.byNode.get(e.node)?.get(e.offset)}set(e,t){let r=this.byNode.get(e.node);r||(r=new Map,this.byNode.set(e.node,r)),r.set(e.offset,t)}},ie=class extends Error{};function Mt(n,e,t,r){return n==="forward"?e+t:e-r}function io(n,e,t,r){return n==="forward"?e-r:e+t}function ao(n){return Fe(re(n.handles[n.handles.length-1]),re(n.handles[0]))}function at(n){return`${n.pathHandle}:${n.hapStart}:${n.hapEnd}`}async function fo(n){let{db:e,records:t,signal:r}=n,o=performance.now(),s=()=>{let I=performance.now(),R=I-o;return o=I,R},i={spacing:await e.haplotypeAnchorSpacing(),anchors:void 0,anchorsRead:0,chosenPaths:0,scans:[],scanRows:0,strays:void 0,pieces:0,sources:{reference:0,section:0,stray:0,chain:0,twin:0},walks:{},twins:{tried:0,found:0},graphFetches:0,fallback:void 0,ms:{scan:0,walks:0,check:0,twins:0}},a=(I,R)=>{let k=`${I}: ${R}`;i.walks[k]=(i.walks[k]??0)+1},f=await e.haplotypeSampleInterval()??4096,c=new Map,l=async I=>{let R=t.get(I)??c.get(I);if(R)return R;let k=await e.getRecord(I);if(i.graphFetches+=1,!k)throw new Error(`Node record ${I} is missing from the database`);return c.set(I,k),k},h=I=>t.get(I).sequenceLen,d=await e.pathsByHandle(),p=I=>{let R=d.get(I);return R!==void 0&&n.keep(R.name)},u=[],m=new Bn,w=new Map,y=new Set,S=new Set,g=async I=>{let R=(await l(I.node)).gbwt().lf(I.offset);return R===void 0||R.node===0?void 0:R},b=async(I,R)=>{let k=(await l(re(I.node))).gbwt().predecessorAt(I.offset);if(k===void 0||R!==void 0&&!R.has(k))return;let L=(await l(k)).gbwt().offsetTo(I);if(L===void 0)throw new Error(`No offset in ${k} leads to ${I.node}:${I.offset}`);return{node:k,offset:L}},x=(I,R,k,L)=>{let H=k.map(V=>V.pos.node),W=k.map(V=>V.pos.offset),J=0;for(let V of H)J+=h(V);let B=R==="forward"?k[0].left:k[k.length-1].left,F=u.length;u.push({pathHandle:I,orientation:R,handles:H,offsets:W,len:J,hapStart:B,hapEnd:B+J,canonical:Fe(H[0],H[H.length-1]),source:L});for(let V of k)m.set(V.pos,F);let K=w.get(I);return K?K.push(F):w.set(I,[F]),F},E=async(I,R,k,L)=>{let H=[],W=I;for(;;){r?.throwIfAborted();let B=await b(W.pos,t);if(!B)break;W={pos:B,left:io(k,W.left,h(W.pos.node),h(B.node))},H.push(W)}H.reverse();let J=[I];for(W=I;;){r?.throwIfAborted();let B=await g(W.pos);if(!B||!t.has(B.node))break;W={pos:B,left:Mt(k,W.left,h(W.pos.node),h(B.node))},J.push(W)}return x(R,k,[...H,...J],L)},A=async(I,R,k,L)=>u[m.get(I.pos)??await E(I,R,k,L)],_=I=>{let R=I.handles[I.handles.length-1];return{pos:{node:R,offset:I.offsets[I.offsets.length-1]},left:I.orientation==="forward"?I.hapEnd-h(R):I.hapStart}},T=I=>{let R=I.handles[0];return{pos:{node:R,offset:I.offsets[0]},left:I.orientation==="forward"?I.hapStart:I.hapEnd-h(R)}},$=await E({pos:n.referencePos,left:n.referenceLeft},n.referenceHandle,"forward","reference"),C=u[$],N=()=>{if(i.fallback!==void 0)return{reference:C,pieces:[],stats:i};let I=new Map;u.forEach((k,L)=>{L!==$&&I.set(at(k),[...I.get(at(k))??[],k])});let R=[];for(let k of I.values()){let L=new Set;for(let H of k)H.canonical&&!L.has(H.orientation)&&(L.add(H.orientation),R.push(H),i.sources[H.source]+=1)}return i.sources.reference=1,i.pieces=R.length+1,{reference:C,pieces:R,stats:i}},P=async(I,R)=>{let k=R?y:S,L=R?S:y,H=I;for(;;){if(k.has(H))return;k.add(H);let W=u[H],J=R?_(W):T(W),B=0,F;for(;F===void 0;){r?.throwIfAborted();let K=R?await g(J.pos):await b(J.pos);if(!K){F="endmarker";break}let V=(await l(J.pos.node)).sequenceLen,ve=(await l(K.node)).sequenceLen,oe=R?Mt(W.orientation,J.left,V,ve):io(W.orientation,J.left,V,ve);if(t.has(K.node)){let ee=m.get(K);ee===void 0?(H=await E({pos:K,left:oe},W.pathHandle,W.orientation,"chain"),L.add(H),F="landed"):(L.add(ee),F="merge")}else B>Xs?F="bound":(B+=ve,J={pos:K,left:oe})}if(a("chain",F),F!=="landed")return}},U=async I=>{if(n.context>I.context)throw new ie(`the context of ${n.context} bp exceeds the ${I.context} bp the haplotype index's stray rows cover`);let R=i.spacing;if(R===void 0)throw new ie("the haplotype index has no anchors");let{bin:k,bound:L}=I,{fills:H,inserted:W}=n.snarls;if(n.snarls.mode==="overlapping"&&H.length>0)throw new ie("the haplotype index's stray rows cover contained snarls only");for(let v of H){if(v.inserted>0&&v.low===v.high)throw new ie(`the haplotype index's stray rows leave out the snarl bounded by node ${v.low} at both ends`);if(v.inserted>0&&(I.snarlNodes===void 0||v.nodes>I.snarlNodes))throw new ie(I.snarlNodes===void 0?"the haplotype index's stray rows leave snarls out":`a snarl of ${v.nodes} nodes exceeds the ${I.snarlNodes} the haplotype index's stray rows cover`)}let J=Math.floor(n.window.start/k),B=Math.floor((n.window.end-1)/k),F=J*k,K=(B+1)*k,V=new Map,ve=async(v,M)=>{let j=await e.haplotypeAnchorsBetween(n.referenceHandle,v*R,M*R);for(let D of j)V.set(D.anchorOffset/R,D)},oe=Math.max(0,Math.floor((F-L)/R)-1),ee=Math.ceil((K+L)/R)+1,[{listed:xt,strays:fe}]=await Promise.all([e.haplotypeBinData(n.referenceHandle,J,B),ve(oe,ee)]);for(let v of t.keys()){let M=O(v);if(!z(v)&&!xt(M)&&!W.has(M))throw new ie(`the haplotype index lists node ${M} of the subgraph in no bin that the window touches`)}i.scans=Hn([...t.keys()].sort((v,M)=>v-M));let de=Promise.all(i.scans.map(([v,M])=>e.haplotypeSamplesInRange(v,M)));for(de.catch(()=>{});oe>0&&(V.get(oe)?.pathOffset??Number.POSITIVE_INFINITY)>=F-L;)oe-=1,await ve(oe,oe);for(;V.has(ee)&&V.get(ee).pathOffset<=K+L;)ee+=1,await ve(ee,ee);let xe=[...V.keys()].sort((v,M)=>v-M),_e=V.get(xe[0]??-1);if(!_e)throw new ie("the haplotype index has no anchors on this path");let pe=v=>V.get(v).pathOffset,tt=new Map;for(let v of xe){let M=O(V.get(v).node);tt.set(M,[...tt.get(M)??[],v])}let Cn=[...tt.keys()],Rr=Cn.map(v=>V.get(tt.get(v)[0]).visits);if(!Rr[Cn.indexOf(O(_e.node))].some(v=>v.pathHandle===n.referenceHandle&&v.orientation==="forward"&&v.pathOffset===_e.pathOffset))throw new Error(`The haplotype index has no anchor row for the reference path ${n.referenceHandle} at offset ${_e.pathOffset} (node ${O(_e.node)}); it does not match this graph`);let Mr=xe.filter(v=>pe(v)<=n.window.start),Ts=xe.filter(v=>pe(v)>=n.window.end);i.anchors=[pe(Mr[Mr.length-1]??xe[0]),pe(Ts[0]??xe[xe.length-1])],i.anchorsRead=xe.length;let Rn=new Map,Pr=new Set;if(Cn.forEach((v,M)=>{let j=tt.get(v),D=j.length===1?j[0]:void 0;for(let G of Rr[M])Pr.add(G.pathHandle),G.orientation==="forward"&&p(G.pathHandle)&&Rn.set(G.pathHandle,[...Rn.get(G.pathHandle)??[],{k:D,row:G}])}),i.chosenPaths=[...Pr].filter(p).length,i.chosenPaths>so.mostChosenPaths)throw new ie(`${i.chosenPaths} chosen paths pass the anchors, more than ${so.mostChosenPaths}`);let yt=[],Le=Number.POSITIVE_INFINITY,ke=0;for(let[v,M]of Rn){M.sort((j,D)=>j.row.pathOffset-D.row.pathOffset);for(let j=0;j+1<M.length;j++){let D=M[j],G=M[j+1];if(D.k===void 0||G.k===void 0||Math.abs(D.k-G.k)!==1)continue;let[Z,te]=pe(D.k)<=pe(G.k)?[D,G]:[G,D],ne=pe(Z.k),se=pe(te.k);ne<K&&se>=F?(yt.push({pathHandle:v,from:D.row,to:G.row}),Le=Math.min(Le,ne-L),ke=Math.max(ke,se+L)):ne>=K&&ne-K<=L?(yt.push({pathHandle:v,from:Z.row,to:void 0}),Le=Math.min(Le,ne-L),ke=Math.max(ke,ne+L)):se<F&&F-se<=L&&(yt.push({pathHandle:v,from:te.row,to:void 0}),Le=Math.min(Le,se-L),ke=Math.max(ke,se+L))}}let Ls=new Set(H.map(v=>`${v.low}:${v.high}`)),Fs=fe.filter(v=>p(v.pathHandle)&&(v.snarl===void 0||Ls.has(`${v.snarl[0]}:${v.snarl[1]}`))).sort((v,M)=>v.pathHandle-M.pathHandle||v.pathStart-M.pathStart);i.strays={bins:B-J+1,rows:fe.length,walked:0,outsideBp:0},ke>0&&await n.prefetchReferenceRange(n.referenceHandle,Math.max(0,Le),ke+1),i.ms.scan=s();let _r=8*R+2*(n.window.end-n.window.start),kr=i.strays,nt=0,Or=v=>{if(kr.outsideBp+=v,nt+=v,nt>_r)throw new ie(`a walk of a chosen path near the window went past its cap of ${_r} bp`)},Mn=new Map,Nr=(v,M,j)=>(Mn.get(v)??[]).some(([D,G])=>D<=M&&j<G),Tr=(v,M,j)=>{Mn.set(v,[...Mn.get(v)??[],[M,j]])},Lr=async(v,M,j,D,G)=>{let Z=M,te=j,ne=te;for(;Z&&te<=D;){r?.throwIfAborted();let se;if(t.has(Z.node)){let rt=await A({pos:Z,left:te},v,"forward",G),$r=_(rt);Z=$r.pos,te=$r.left,se=h(Z.node),ne=Math.max(ne,rt.hapEnd)}else se=(await l(Z.node)).sequenceLen,Or(se),ne=Math.max(ne,te+se);Z=await g(Z),te+=se}return ne},$s=async(v,M,j,D)=>{let G={pos:M,left:j},Z=j;for(;G.left>D;){r?.throwIfAborted();let te=await b(G.pos);if(!te)break;let ne=(await l(te.node)).sequenceLen,se=G.left-ne;if(t.has(te.node)){let rt=await A({pos:te,left:se},v,"forward","section");G=T(rt),Z=Math.min(Z,rt.hapStart)}else Or(ne),G={pos:te,left:se},Z=Math.min(Z,se)}return Z};for(let{pathHandle:v,from:M,to:j}of yt){let D=M.pathOffset,G=(j??M).pathOffset+L;if(Nr(v,D-L,G))continue;let Z={node:M.node,offset:M.offset};nt=0;let te=await Lr(v,Z,D,G,"section");nt=0;let ne=await $s(v,Z,D,D-L);Tr(v,Math.min(ne,D-L),Math.max(te,G+1)),a(j?"section":"visit",j?"past the far anchor":"bound")}for(let v of Fs){if(Nr(v.pathHandle,v.pathStart,v.pathEnd))continue;nt=0;let M=await Lr(v.pathHandle,{node:v.node,offset:v.offset},v.pathStart,v.pathEnd,"stray");Tr(v.pathHandle,v.pathStart,Math.max(M,v.pathEnd+1)),kr.walked+=1}i.ms.walks=s();let Fr=[];for(let v of await de)for(let M of v)if(i.scanRows+=1,t.has(M.node)&&p(M.pathHandle)){if(!(w.get(M.pathHandle)??[]).some(j=>{let D=u[j];return D.hapStart<=M.pathOffset&&M.pathOffset<D.hapEnd}))throw new ie(`chosen path ${M.pathHandle} has a sample at ${M.pathOffset} on the window's nodes that no walk reached`);M.orientation==="reverse"&&Fr.push(M)}for(let v of Fr)await A({pos:{node:v.node,offset:v.offset},left:v.pathOffset},v.pathHandle,"reverse","twin");i.ms.check=s()},Y=async()=>{let I=new Map,R=B=>{let F=at(B),K=I.get(F);K?K.add(B.orientation):I.set(F,new Set([B.orientation]))},k=0,L=()=>{for(;k<u.length;k++)R(u[k])};L();let H=B=>(I.get(at(B))?.size??0)>1,W=2*f,J=(B,F)=>F===$?p(n.referenceHandle)&&ao(B):!B.canonical||ao(B);for(let B=0;B<u.length;B++){let F=u[B];if(H(F)||!J(F,B))continue;i.twins.tried+=1;let K=F.orientation==="forward"?"reverse":"forward",V=_(F),ve=0,oe;for(;!oe&&ve<=W;){r?.throwIfAborted();let fe=await g(V.pos);if(!fe)break;let de=(await l(fe.node)).sequenceLen,xe=Mt(F.orientation,V.left,(await l(V.pos.node)).sequenceLen,de),_e=re(fe.node);oe=(await e.haplotypeSamplesInRange(_e,_e)).find(pe=>pe.pathHandle===F.pathHandle&&pe.orientation===K&&pe.pathOffset===xe),ve+=de,V={pos:fe,left:xe}}let ee=oe&&{pos:{node:oe.node,offset:oe.offset},left:oe.pathOffset},xt=0;for(;ee&&!H(F)&&xt<=W+F.len;){if(r?.throwIfAborted(),t.has(ee.pos.node)){let fe=await A(ee,F.pathHandle,K,"twin"),de=u.indexOf(fe);await P(de,!0),await P(de,!1),L(),ee=_(fe)}if(!H(F)){let fe=(await l(ee.pos.node)).sequenceLen;xt+=fe;let de=await g(ee.pos);ee=de?{pos:de,left:Mt(K,ee.left,fe,(await l(de.node)).sequenceLen)}:void 0}}if(L(),!H(F))throw new ie(`piece ${at(F)} was found in one orientation where extractPaths keeps the other`);i.twins.found+=1}i.ms.twins=s()};try{let I=await e.haplotypeStrayOptions();if(I===void 0)throw new ie("the haplotype index has no stray rows; gbz-haplotype-index 0.2.0 writes them");await U(I),await Y()}catch(I){if(!(I instanceof ie))throw I;i.fallback=I.message}return N()}function co(n,e){return n.handles[0]-e.handles[0]||n.offsets[0]-e.offsets[0]}function Pt(n,e){let t=0,r=n.length;for(;t<r;){let o=t+r>>1;n[o]<e?t=o+1:r=o}return t}var _t=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 o=this.tree[r];o!==-1&&(t===-1||this.ending[o]>this.ending[t])&&(t=o)}return t}raise(e,t){this.ending[e]=t;for(let r=e+1;r<this.tree.length;r+=r&-r){let o=this.tree[r];(o===-1||t>this.ending[o])&&(this.tree[r]=e)}}},qn=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((o,s)=>{let i=this.occurrences.get(o);i?i.push(s):this.occurrences.set(o,[s])})}solve(e,t,r,o){let s=0;for(;e+s<t&&r+s<o&&this.a[e+s]===this.b[r+s];)this.match(e+s,r+s),s+=1;let i=0;for(;t-i>e+s&&o-i>r+s&&this.a[t-i-1]===this.b[o-i-1];)i+=1;this.solveMiddle(e+s,t-i,r+s,o-i);for(let a=i;a>0;a--)this.match(t-a,o-a)}match(e,t){this.pairs.push([e,t]),this.total+=this.weight(this.a[e])}solveMiddle(e,t,r,o){if(e===t||r===o)return;let s=this.matchCount(e,t,r,o);if(s===0)return;if(s<=t-e+(o-r)){this.chain(e,t,r,o,s);return}let i=e+t>>1,a=this.split(e,i,t,r,o);this.solve(e,i,r,a),this.solve(i,t,a,o)}matchCount(e,t,r,o){let s=0;for(let i=e;i<t;i++){let a=this.occurrences.get(this.a[i]);a&&(s+=Pt(a,o)-Pt(a,r))}return s}sweep(e,t,r,o,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]),h=Pt(c,o),d=Pt(c,s);for(let p=0;p<d-h;p++){let u=r===1?c[d-1-p]-o:s-1-c[h+p],m=i.bestBefore(u),w=(m===-1?0:i.ending[m])+l;if(w>i.ending[u]&&(i.raise(u,w),a)){let y=a.count++;a.row[y]=f,a.column[y]=u,a.previous[y]=m===-1?-1:a.endingMatch[m],a.endingMatch[u]=y}}}}chain(e,t,r,o,s){let i=new _t(o-r),a={row:new Int32Array(s),column:new Int32Array(s),previous:new Int32Array(s),endingMatch:new Int32Array(o-r),count:0};this.sweep(e,t,1,r,o,i,a);let f=i.bestBefore(o-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,o,s){let i=new _t(s-o);this.sweep(e,t,r,o,s,i);let a=new Float64Array(s-o+1);for(let f=0;f<s-o;f++)a[f+1]=Math.max(a[f],i.ending[f]);return a}split(e,t,r,o,s){let i=s-o,a=this.frontier(e,t,1,o,s),f=this.frontier(r-1,t-1,-1,o,s),c=0,l=-1;for(let h=0;h<=i;h++){let d=a[h]+f[i-h];d>l&&(l=d,c=h)}return o+c}};function lo(n,e,t){let r=new qn(n,e,t);return r.solve(0,n.length,0,e.length),[r.pairs,r.total]}var Zs=100,zn=4e6,Js=5e3,le=15,ei=64,ti=8,xo=1,jn=-4,ae=-6,Re=-1,Qe=-(2**30),Ot=0,Dn=1,yo=2;function $e(n,e,t){let r=n.at(-1);t>0&&(r?.[0]===e?r[1]+=t:n.push([e,t]))}function kt(n,e,t){return n>=t&&n>=e?Ot:t>=e?yo:Dn}function bo(n,e,t){let r=n.length,o=e.length,s=o+1,i=new Uint8Array((r+1)*s),a=new Int32Array(s).fill(Qe),f=new Int32Array(s).fill(Qe),c=new Int32Array(s).fill(Qe);a[0]=0;for(let u=1;u<=o;u++)c[u]=ae+(u-1)*Re,i[u]=(u===1?Ot:yo)<<4;for(let u=1;u<=r;u++){let m=new Int32Array(s).fill(Qe),w=new Int32Array(s).fill(Qe),y=new Int32Array(s).fill(Qe);w[0]=ae+(u-1)*Re,i[u*s]=(u===1?Ot:Dn)<<2;let S=n.charCodeAt(u-1);for(let g=1;g<=o;g++){let b=kt(a[g-1],f[g-1],c[g-1]);m[g]=Math.max(a[g-1],f[g-1],c[g-1])+(S===e.charCodeAt(g-1)?xo:jn);let x=kt(a[g]+ae,f[g]+Re,c[g]+ae);w[g]=Math.max(a[g]+ae,f[g]+Re,c[g]+ae);let E=kt(m[g-1]+ae,w[g-1]+ae,y[g-1]+Re);y[g]=Math.max(m[g-1]+ae,w[g-1]+ae,y[g-1]+Re),i[u*s+g]=b|x<<2|E<<4}a=m,f=w,c=y}let l=[],h=r,d=o,p=kt(a[o],f[o],c[o]);for(;h>0||d>0;){let u=i[h*s+d]>>2*p&3;p===Ot?(l.push(n[h-1]===e[d-1]?"=":"X"),h-=1,d-=1):p===Dn?(l.push("I"),h-=1):(l.push("D"),d-=1),p=u}for(let u of l.reverse())$e(t,u,1)}function ni(n,e){let t=Math.abs(n-e);return(t===0?0:Math.min(-ae-(t-1)*Re,-ae+10*Math.log2(t)))+(Math.min(n,e)>0?-jn:0)}function So(n,e){let t=Math.abs(n-e);return t===0?0:.01*le*t+.5*Math.log2(t)}function ho(n,e,t){return{qs:n.qs+e,qe:n.qs+t,ts:n.flipped?n.te-t:n.ts+e,te:n.flipped?n.te-e:n.ts+t,flipped:n.flipped}}function ri(n,e,t){let r=n.qe-n.qs,o=[];for(let[a,f]of e){let c=Math.max(0,a-n.qs),l=Math.min(r,f-n.qs);c<l&&o.push([c,l])}for(let[a,f]of t){let c=Math.max(0,n.flipped?n.te-f:a-n.ts),l=Math.min(r,n.flipped?n.te-a:f-n.ts);c<l&&o.push([c,l])}if(o.length===0)return[n];o.sort((a,f)=>a[0]-f[0]);let s=[],i=0;for(let[a,f]of o)a-i>=le&&s.push(ho(n,i,a)),i=Math.max(i,f);return r-i>=le&&s.push(ho(n,i,r)),s}function Un(n,e,t,r,o=1/0){let s=[],i={query:[],target:[]},a={forward:{query:[],target:[]},flipped:{query:[],target:[]}},f=[...n].sort((c,l)=>c.qs-l.qs||c.ts-l.ts);for(;f.length>0&&s.length<o;){let c=f.map(g=>g.qe-g.qs),l=new Int32Array(f.length).fill(-1),h=new Int32Array(f.length);for(let g=0;g<f.length;g++){let b=f[g],x=b.qe-b.qs;for(let E=g-1;E>=Math.max(0,g-Js);E--){if(c[E]+x<=c[g])continue;let A=f[E];if(A.flipped===b.flipped&&A.qs<b.qs&&(b.flipped?b.te<A.te:A.ts<b.ts)){let T=Math.max(0,A.qe-b.qs,b.flipped?b.te-A.ts:A.te-b.ts),$=b.qs+T-A.qe,C=b.flipped?A.ts-(b.te-T):b.ts+T-A.te;if(T<x&&$<=e&&C<=e){let N=c[E]+x-T-r($,C);N>c[g]&&(c[g]=N,l[g]=E,h[g]=T)}}}}let d=new Int32Array(f.length),p=-1;for(let g=0;g<f.length;g++){let b=f[g];d[g]=(d[l[g]]??0)+b.qe-b.qs-h[g],d[g]>=t&&(p<0||c[g]>c[p])&&(p=g)}if(p<0)break;let u=[];for(let g=p;g>=0;g=l[g])u.push({run:f[g],trim:h[g]});u.reverse(),s.push(u);let m=u[0],w=u.at(-1),{flipped:y}=m.run,S=y?a.flipped:a.forward;S.query.push([m.run.qs+m.trim,w.run.qe]),S.target.push(y?[w.run.ts,m.run.te-m.trim]:[m.run.ts+m.trim,w.run.te]);for(let{run:g,trim:b}of u)i.query.push([g.qs+b,g.qe]),i.target.push(g.flipped?[g.ts,g.te-b]:[g.ts+b,g.te]);f=f.flatMap(g=>{let b=g.flipped?a.flipped:a.forward;return ri(g,[...i.query,...b.query],[...i.target,...b.target])}).sort((g,b)=>g.qs-b.qs||g.ts-b.ts)}return s}function Gn(n,e){let t=new Map;for(let s=0;s+le<=e.length;s++){let i=e.slice(s,s+le),a=t.get(i);a?a.push(s):t.set(i,[s])}let r=[],o=new Map;for(let s=0;s+le<=n.length;s++){let i=t.get(n.slice(s,s+le));if(i&&i.length<=ei)for(let a of i){let f=a-s,c=o.get(f);if(c&&s<=c.qe)c.qe=s+le,c.te=a+le;else{let l={qs:s,qe:s+le,ts:a,te:a+le,flipped:!1};o.set(f,l),r.push(l)}}}return r}function oi(n,e){return[...Gn(n,e),...Gn(n,Rt(e)).map(t=>({...t,ts:e.length-t.te,te:e.length-t.ts,flipped:!0}))]}function Nt(n,e,t,r,o){let s;for(let{run:i,trim:a}of n){let f=i.qs+a;if(s){let c=i.flipped?i.te-a:s.te,l=i.flipped?s.ts:i.ts+a,h=t.slice(c,l);o(e.slice(s.qe,f),i.flipped?Rt(h):h,r,s.qe,c)}$e(r,"=",i.qe-f),s=i}}function Wn(n,e,t){$e(t,"I",n.length),$e(t,"D",e.length)}function vo(n,e,t){n.length*e.length<=zn?bo(n,e,t):Wn(n,e,t)}function Vn(n,e,t,r=0){let[o]=n.length*e.length>zn&&r<ti?Un(Gn(n,e),1/0,le,So,1):[];if(!o){vo(n,e,t);return}let s=(f,c,l)=>{Vn(f,c,l,r+1)},i=o[0].run,a=o.at(-1).run;s(n.slice(0,i.qs),e.slice(0,i.ts),t),Nt(o,n,e,t,s),s(n.slice(a.qe),e.slice(a.te),t)}function si(n,e,t){Vn(n,e,t)}function ii(n,e,t){let r=[];Nt(n,e,t,r,si);let o=n[0],s=n.at(-1),{flipped:i}=o.run;return{queryStart:o.run.qs+o.trim,queryEnd:s.run.qe,targetStart:i?s.run.ts:o.run.ts+o.trim,targetEnd:i?o.run.te-o.trim:s.run.te,strand:i?"-":"+",edits:i?r.reverse():r,sharedBases:0}}function ai(n,e,t,r){let o=[];if(n.length*e.length<=zn)bo(n,e,t);else{let s=Un(oi(n,e),1/0,Math.max(r,le),So),i=s.find(a=>!a[0].run.flipped);if(o=s.filter(a=>a[0].run.flipped).map(a=>ii(a,n,e)),i){let a=(l,h,d,p,u)=>{o.some(w=>p<w.queryEnd&&w.queryStart<p+l.length||u<w.targetEnd&&w.targetStart<u+h.length)?vo(l,h,d):Vn(l,h,d)},f=i[0].run,c=i.at(-1).run;a(n.slice(0,f.qs),e.slice(0,f.ts),t,0,0),Nt(i,n,e,t,a),a(n.slice(c.qe),e.slice(c.te),t,c.qe,c.te)}else Wn(n,e,t)}return o}function Qn(n,e){let t=n.strand==="-",r=0,o=0;for(let[s,i]of n.edits)e(s,i,t?n.queryEnd-1-r:n.queryStart+r,n.targetStart+o),s!=="D"&&(r+=i),s!=="I"&&(o+=i)}function po(n,e,t,r){let o=e==="query"&&n.strand==="-"?-1:1,s=0;return Qn(n,(i,a,f,c)=>{let l=e==="query"?f:c,h=d=>{let p=l+o*d;return p>=t&&p<r};if(i==="="||i==="X")for(let d=0;d<a;d++)h(d)&&(s+=i==="="?xo:jn);else if(i==="I"==(e==="query"))for(let d=0;d<a;d++)h(d)&&(s+=d===0?ae:Re);else h(0)&&(s+=ae+(a-1)*Re)}),s}function uo(n,e){return e==="query"?[n.queryStart,n.queryEnd]:[n.targetStart,n.targetEnd]}function fi(n,e){let t=n.strand==="-",r=[],o=0,s=0,i=0,a=0,f=new Uint8Array(n.queryEnd-n.queryStart);for(let[p,u]of n.shared)f.fill(1,p-n.queryStart,u-n.queryStart);let c=p=>f[p-n.queryStart]===1,l=()=>{$e(r,"I",o),$e(r,"D",s),o=0,s=0};Qn(n,(p,u,m)=>{if(p==="I")o+=u;else if(p==="D")s+=u;else{for(let w=0;w<u;w++)e[i+w]?(o+=1,s+=1,c(t?m-w:m+w)&&(a+=1)):((o>0||s>0)&&l(),$e(r,p,1));i+=u}}),l();let h={I:0,D:0};for(;r[0]?.[0]==="I"||r[0]?.[0]==="D";){let[p,u]=r.shift();h[p]+=u}let d={I:0,D:0};for(;r.at(-1)?.[0]==="I"||r.at(-1)?.[0]==="D";){let[p,u]=r.pop();d[p]+=u}return r.length===0?void 0:{...n,queryStart:n.queryStart+(t?d.I:h.I),queryEnd:n.queryEnd-(t?h.I:d.I),targetStart:n.targetStart+h.D,targetEnd:n.targetEnd-d.D,edits:r,sharedBases:n.sharedBases-a}}function ci(n,e,t,r){let o={query:new Uint8Array(e),target:new Uint8Array(t)},s=n.map(c=>{let l=[];Qn(c,(h,d,p,u)=>{if(h==="="||h==="X")for(let m=0;m<d;m++)l.push([c.strand==="-"?p-m:p+m,u+m])});for(let[h,d]of l)o.query[h]=Math.min(255,o.query[h]+1),o.target[d]=Math.min(255,o.target[d]+1);return l}),i={query:new Map,target:new Map};s.forEach((c,l)=>{for(let[h,d]of c)for(let[p,u]of[["query",h],["target",d]])if(o[p][u]>1){let m=i[p].get(u);m?m.at(-1)!==l&&m.push(l):i[p].set(u,[l])}});let a=new Map,f=(c,l,h)=>{let d=`${h}:${c}:${l}`,p=a.get(d);if(p===void 0){let[u,m]=uo(n[c],h),[w,y]=uo(n[l],h),S=Math.max(u,w),g=Math.min(m,y),[b,x]=[n[c],n[l]];p=[po(x,h,S,g)-po(b,h,S,g),x.sharedBases-b.sharedBases,c-l].find(A=>A!==0)>0,a.set(d,p)}return p};return n.flatMap((c,l)=>{let h=s[l],d=new Uint8Array(h.length);if(h.forEach(([m,w],y)=>{for(let[S,g]of[["query",m],["target",w]])!d[y]&&i[S].get(g)?.some(b=>b!==l&&f(l,b,S))&&(d[y]=1)}),!d.includes(1))return[c];let p=fi(c,d),u=p?.edits.reduce((m,[w,y])=>m+(w==="="?y:0),0)??0;return p&&u>=r?[p]:[]})}function mo(n,e){return n.map(t=>{let r=e(O(t));return z(t)?Rt(r):r}).join("")}function go(n,e){let t=[0];for(let r of n)t.push(t.at(-1)+e(O(r)).length);return t}function wo(n){let e=new Map,t=new Map;n.forEach((i,a)=>{let f=O(i);e.has(f)?t.set(f,a):e.set(f,a)});let r=new Int32Array(n.length+1);for(let[i,a]of t)r[e.get(i)]+=1,r[a+1]-=1;let o=new Uint8Array(n.length),s=0;for(let i=0;i<n.length;i++)s+=r[i],o[i]=s>0?1:0;return o}function li(n,e,t,r){let o=wo(n),s=wo(e),i=new Map;e.forEach((h,d)=>{s[d]||i.set(O(h),[d])});let a=2*e.length,f=(h,d,p)=>h*a+2*d+(p?1:0),c=new Set;n.forEach((h,d)=>{for(let p of o[d]?[]:i.get(O(h))??[])c.add(f(d,p,z(h)!==z(e[p])))});let l=[];return n.forEach((h,d)=>{for(let p of o[d]?[]:i.get(O(h))??[]){let u=z(h)!==z(e[p]),m=u?-1:1,w=p-m;if(!(d>0&&w>=0&&w<e.length&&c.has(f(d-1,w,u)))){let S=d,g=p;for(;S<n.length&&g>=0&&g<e.length&&c.has(f(S,g,u));)S+=1,g+=m;let b=g-m;l.push({qs:t[d],qe:t[S],ts:r[Math.min(p,b)],te:r[Math.max(p,b)+1],flipped:u})}}}),l}function Io(n){let{query:e,target:t,sequenceOf:r}=n,o=mo(e,r),s=mo(t,r),i=li(e,t,go(e,r),go(t,r)),a=n.minMatch??Zs,f=n.bases??!0,c=[];for(let l of Un(i,n.maxGap??1/0,a,ni)){let h=[],d=l[0],p=l.at(-1),{flipped:u}=d.run;Nt(l,o,s,h,f?(w,y,S,g,b)=>{for(let x of ai(w,y,S,a)){let E=b+y.length;c.push({...x,queryStart:g+x.queryStart,queryEnd:g+x.queryEnd,targetStart:u?E-x.targetEnd:b+x.targetStart,targetEnd:u?E-x.targetStart:b+x.targetEnd,strand:u?"+":"-",edits:u?x.edits.reverse():x.edits,shared:[]})}}:Wn),c.push({queryStart:d.run.qs+d.trim,queryEnd:p.run.qe,targetStart:u?p.run.ts:d.run.ts+d.trim,targetEnd:u?d.run.te-d.trim:p.run.te,strand:u?"-":"+",edits:u?h.reverse():h,sharedBases:l.reduce((w,{run:y,trim:S})=>w+y.qe-y.qs-S,0),shared:l.map(({run:w,trim:y})=>[w.qs+y,w.qe])})}return ci(c,o.length,s.length,a).map(({shared:l,...h})=>h).sort((l,h)=>l.queryStart-h.queryStart)}function Eo(n){return n.map(([e,t])=>`${t}${e}`).join("")}var be=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 ${t.windowBp} bp window`),this.limit=e,this.windowBp=t?.windowBp,this.walkedBp=t?.walkedBp}};function Yn(n,e){return n[0]<e[0]||n[0]===e[0]&&(n[1]<e[1]||n[1]===e[1]&&n[2]<e[2])}var ct=class{heap=[];push(e,t,r){let o=this.heap;o.push([e,t,r]);let s=o.length-1;for(;s>0;){let i=s-1>>1;if(Yn(o[s],o[i]))[o[s],o[i]]=[o[i],o[s]],s=i;else break}}pop(){let e=this.heap,t=e[0],r=e.pop();if(e.length>0&&r!==void 0){e[0]=r;let o=0;for(;;){let s=2*o+1,i=s+1,a=o;if(s<e.length&&Yn(e[s],e[a])&&(a=s),i<e.length&&Yn(e[i],e[a])&&(a=i),a===o)break;[e[o],e[a]]=[e[a],e[o]],o=a}}return t}get size(){return this.heap.length}};function hi(n){let e=new Int32Array(n.length),t=new Int32Array(n.length);return n.forEach(([r,o],s)=>{e[s]=r,t[s]=o}),{pathAt:e,refAt:t,count:n.length}}function di(n,e){let t=0,r=n.length;for(;t<r;){let o=t+r>>1;n[o]>e?r=o:t=o+1}return n[t]}function Be(n){return`${n.node}:${n.offset}`}function ft(n){return n.map(e=>re(e)).reverse()}function pi(n,e){let t=e.identity.hapStart-n.identity.hapEnd,r=n.strand==="+"?e.refStart-n.refEnd:n.refStart-e.refEnd;return n.strand===e.strand&&t>=0&&r>=0?{insertion:t,deletion:r}:void 0}function ui(n,e,t){let[r,o]=n.strand==="+"?[n,e]:[e,n],s=r.edits.map(([c,l])=>[c,l]);Co(s,t.insertion,t.deletion);for(let[c,l]of o.edits)X(s,c,l);let i=n.identity.walkForward,[a,f]=i?[n,e]:[e,n];return{strand:n.strand,refStart:r.refStart,refEnd:o.refEnd,edits:s,weight:void 0,path:[...a.path,...f.path],start:a.start,pieces:[...a.pieces,...f.pieces],soloAligned:[...a.soloAligned,...f.soloAligned],identity:{pathHandle:n.identity.pathHandle,name:n.identity.name,hapStart:n.identity.hapStart,hapEnd:e.identity.hapEnd,walkForward:i}}}function mi(n,e,t){if(n.some(i=>i.weight!==void 0))return n;let r=new Map;n.forEach((i,a)=>{if(i.identity){let f=r.get(i.identity.pathHandle);f?f.push(a):r.set(i.identity.pathHandle,[a])}});let o=new Map,s=new Set;for(let i of r.values()){i.sort((l,h)=>n[l].identity.hapStart-n[h].identity.hapStart);let a=i[0],f=n[a],c=[];for(let l of i.slice(1)){let h=n[l],d=c.length===0?pi(f,h):void 0;if(d){f=ui(f,h,d),s.add(l);continue}if(!e(h)){c.push(l);continue}let p=e(f)?t([f,...c.map(u=>n[u]),h]):void 0;if(p){f=p;for(let u of[...c,l])s.add(u)}else o.set(a,f),a=l,f=h;c=[]}o.set(a,f)}return n.flatMap((i,a)=>s.has(a)?[]:[o.get(a)??i])}function Tt(n,e){return{node:n.path[e],offset:n.offsets[e]}}var gi=32768;function wi(n){let e=[...n].sort((r,o)=>r-o),t=[];for(let r of e){let o=t[t.length-1];o&&r-o[1]<=gi?o[1]=r:t.push([r,r])}return t}var $t=class n{records=new Map;paths=[];twinStarts=new Set;twinDeferred=!1;unsettled;refId;refPath;refHandle;refInterval;refIndexCache;refPrefixCache;walkedBp;snarlMode="none";snarlFills=[];snarlNodes=new Set;stats={orderedAlignments:0,lcsAlignments:0,snarls:{fills:0,inserted:0},identificationSteps:0,identificationFetches:0,identification:{interval:0,scans:[],windowSamples:0,fragmentLengths:[],companionSeeks:0,companionMisses:0,graphLookups:0,graphFetches:0,chains:[]},keep:void 0};db;limit;signal;constructor(e,t){this.db=e,this.limit=t.limit,this.signal=t.signal}static create(e,t={}){return new n(e,t)}get nodeCount(){return this.records.size/2}get pathCount(){return this.settleDeferred(),this.paths.length}get referenceInterval(){return this.refInterval&&this.refPath?{name:this.refPath,start:this.refPath.fragment+this.refInterval[0],end:this.refPath.fragment+this.refInterval[1]}:void 0}hasNode(e){return this.records.has(ye(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 be(this.limit);let t=await this.db.getRecord(ye(e,"forward")),r=await this.db.getRecord(ye(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.twinDeferred=!1,this.unsettled=void 0,this.refId=void 0,this.refPath=void 0,this.refHandle=void 0,this.refInterval=void 0,this.refIndexCache=void 0,this.refPrefixCache=void 0}async pathPosition(e){let t=await this.db.findPath(e);if(!t)throw new Error(`Cannot find a path covering offset ${e.fragment} of ${me(e)}`);if(!t.isIndexed)throw new Error(`The fragment of ${me(t.name)} at ${t.name.fragment} has not been indexed for random access`);let r=e.fragment-t.name.fragment,o=await this.db.indexedPosition(t.handle,r);if(!o)throw new Error(`The fragment of ${me(t.name)} at ${t.name.fragment} has not been indexed for random access`);return this.findPathPosition(t,r,o.pathOffset,o.pos)}async findPathPosition(e,t,r,o){let s=r,i=o;for(;;){await this.ensureNode(O(i.node));let a=this.record(i.node);if(s+a.sequenceLen>t)return{position:{seqOffset:t,handle:i.node,nodeOffset:t-s,gbwtOffset:i.offset},name:e.name,handle:e.handle};s+=a.sequenceLen;let f=a.gbwt().lf(i.offset);if(!f)throw new Error(`The fragment of ${me(e.name)} at ${e.name.fragment} does not contain offset ${t}`);i=f}}async aroundPosition(e,t,r){let o=O(e);await this.ensureNode(o);let s=this.record(e),i=je(e),a=new ct;return a.push(t,o,It(i)),a.push(s.sequenceLen-t-1,o,Et(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[o,s]=await Promise.all([this.db.indexedPosition(e,t),this.db.indexedPosition(e,r)]);if(o&&s){let i=o.pos.node,a=s.pos.node;if(!await this.db.prefetchRecords([[Math.min(i,a),Math.max(i,a)+1]])){let c=await this.db.indexedPositionsBetween(e,t,r);await this.db.prefetchRecords(wi(c.map(l=>l.pos.node)).map(([l,h])=>[l,h+2]),!0)}}return o}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(o){throw o instanceof be&&o.windowBp===void 0?new be(o.limit,{windowBp:t,walkedBp:this.walkedBp}):o}}get referenceWalkedBp(){return this.walkedBp}async walkInterval(e,t,r){let o={node:e.handle,offset:e.gbwtOffset},s=e.nodeOffset,i=t,a=new ct;for(;;){let f=O(o.node),c=je(o.node);this.walkedBp=t-i,await this.ensureNode(f);let l=this.record(o.node);if(s>=l.sequenceLen)throw new Error(`Offset ${s} in node ${f} of length ${l.sequenceLen}`);a.push(s,f,It(c));let h=l.sequenceLen-s;if(i<=h){a.push(i===h?0:h-i-1,f,Et(c));break}a.push(0,f,Et(c));let d=l.gbwt().lf(o.offset);if(!d)throw new Error(`No successor for GBWT position (${o.node}, ${o.offset})`);o=d,s=0,i-=h}return this.walkedBp=t,this.insertContext(a,r)}async aroundNodes(e,t){let r=new ct;for(let o of e)await this.ensureNode(o),r.push(0,o,"left"),r.push(0,o,"right");return this.insertContext(r,t)}async insertContext(e,t){this.clearPaths(),this.snarlMode="none",this.snarlFills=[],this.snarlNodes.clear(),this.stats.snarls={fills:0,inserted:0};let r=new Set,o=new Set;for(let i of this.records.keys())o.add(O(i));let s=0;for(;e.size>0;){let[i,a,f]=e.pop(),c=`${a}:${f}`;if(r.has(c))continue;r.add(c),o.delete(a),this.hasNode(a)||(await this.addNode(a),s+=1);let l=jr(f);if(!r.has(`${a}:${l}`)){let p=this.record(ye(a,Ur(f))),u=i+p.sequenceLen-1;u<=t&&e.push(u,a,l)}let h=this.record(ye(a,Wr(f))),d=i+1;if(d<=t)for(let p of h.successors()){let u=O(p),m=It(je(p));r.has(`${u}:${m}`)||e.push(d,u,m)}}for(let i of o)this.records.delete(ye(i,"forward")),this.records.delete(ye(i,"reverse"));return{inserted:s,removed:o.size}}async betweenNodes(e,t){return(await this.fillBetween(e,t)).inserted.length}async fillBetween(e,t){this.clearPaths();let r=[e,re(t)],o=new Set([O(e),O(t)]),s=[];for(;r.length>0;){let i=r.pop(),a=O(i);this.hasNode(a)||(await this.addNode(a),s.push(a));for(let f of this.record(i).successors()){let c=O(f);o.has(c)||(r.push(f,re(f)),o.add(c))}}return{inserted:s,nodes:o.size-2}}async extractSnarls(e){let t=0;this.snarlMode=e;for(let[r,o]of await this.overlappingSnarls(e)){let{inserted:s,nodes:i}=await this.fillBetween(r,o),a=O(r),f=O(o);this.snarlFills.push({low:Math.min(a,f),high:Math.max(a,f),nodes:i,inserted:s.length});for(let c of s)this.snarlNodes.add(c);t+=s.length}return this.stats.snarls={fills:this.snarlFills.length,inserted:this.snarlNodes.size},t}async overlappingSnarls(e){let t=[];if(e!=="none"){let r=!1;for(let o of this.sortedHandles()){let s=this.record(o),i=s.next;i!==void 0&&(r=!0,this.hasHandle(i)?Ue(o,i)&&t.push([o,i]):e==="overlapping"&&this.isSnarlEntryInSubgraph(s)&&t.push([o,i]))}if(!r&&e==="overlapping"&&await this.db.hasChainLinks()){let o=await this.findCoveringSnarl();o&&t.push(o)}}return t}isSnarlEntryInSubgraph(e){let t=e.successors(),r=t.find(o=>this.hasHandle(o));return r===void 0?!1:t.length>1||this.record(re(r)).successors().length>1}recordReader(e){let t=new Map;return async r=>{let o=this.records.get(r);if(o)return o;let s=t.get(r);if(!s){if(s=await this.db.getRecord(r),e?.(),!s)throw new Error(`Node record ${r} is missing from the database`);t.set(r,s)}return s}}async findCoveringSnarl(){let e=this.recordReader(),t=async f=>{let c=f.successors(),l=c[0];return l===void 0?!1:c.length>1||(await e(re(l))).successors().length>1},r=async f=>{let c=await e(re(f));return c.next!==void 0?await t(c)?{kind:"snarl-exit",snarl:[re(f),c.next]}:{kind:"chain"}:(await e(f)).next!==void 0?{kind:"chain"}:{kind:"regular"}},o=new Set,s=this.sortedHandles().flatMap(f=>this.record(f).successors()),i,a=!1;for(;!a&&s.length>0;){let f=s.shift(),c=O(f);if(!this.hasHandle(f)&&!o.has(c)){o.add(c);let l=await r(f);if(l.kind==="snarl-exit")i=l.snarl,a=!0;else if(l.kind==="chain")a=!0;else for(let h of["forward","reverse"])s.push(...(await e(ye(c,h))).successors())}}return i}extractPaths(e,t){if(this.clearPaths(),t==="none")return;let r=e?.position;this.refPath=e?.name,this.refHandle=e?.handle;let o=this.sortedHandles(),s=o.length,i=new Map;o.forEach((x,E)=>i.set(x,E));let a=new Int32Array(s+1),f=new Int32Array(s),c=[];for(let x=0;x<s;x++){let E=this.record(o[x]),A=E.gbwt().decompressArrays();f[x]=E.sequenceLen,c.push(A),a[x+1]=a[x]+A.nodes.length}let l=a[s],h=new Int32Array(l),d=new Int32Array(l),p=new Uint8Array(l);for(let x=0;x<s;x++){let E=c[x];h.set(E.nodes,a[x]),d.set(E.offsets,a[x])}c.length=0;for(let x=0;x<l;x++){let E=i.get(h[x]);E===void 0?h[x]=-1:(h[x]=E,p[a[E]+d[x]]=1)}let u=r===void 0?void 0:i.get(r.handle),m=r?.gbwtOffset,w,y=(x,E,A)=>{let _=[],T=0,$=0,C=-1,N=x,P=E;for(;;){N===u&&P===m&&(C=T),A&&(A.push(o[N]),_.push(P)),T+=1,$+=f[N];let U=a[N]+P,Y=h[U];if(Y<0)break;P=d[U],N=Y}return{offsets:_,len:$,refAt:C,last:N}},S=(x,E,A,_)=>{_>=0&&(this.refId=this.paths.length,w=_),this.paths.push({path:x,offsets:E,len:A,weight:void 0,identity:void 0})},g=new Int32Array(s);for(let x=0;x<s;x++){let E=o[x];if(!z(E)){let A=a[x],_=a[x+1]-A;for(let T=0;T<_;T++)if(p[A+T]===0){let $=[],{offsets:C,len:N,refAt:P,last:U}=y(x,T,$),Y=o[U];if(P>=0||Fe(E,Y)){if(S($,C,N,P),!z(Y)){let I=i.get(re(Y));g[I]=g[I]+1}}else this.twinStarts.add(Be({node:E,offset:T}))}}}for(let x=0;x<s;x++){let E=o[x];if(z(E)){let A=a[x],_=a[x+1]-A,T=0;for(let C=0;C<_;C++)p[A+C]===0&&(T+=1);let $=(u===void 0||w!==void 0)&&T===g[x];for(let C=0;C<_;C++)if(p[A+C]===0){let N=$?void 0:y(x,C,void 0);if(N&&(N.refAt>=0||Fe(E,o[N.last]))){let P=[],{offsets:U,len:Y,refAt:I}=y(x,C,P);S(P,U,Y,I)}else this.twinStarts.add(Be({node:E,offset:C}))}}}let b=this.refId===void 0?void 0:this.paths[this.refId];if(this.paths.sort((x,E)=>x.path[0]-E.path[0]||x.offsets[0]-E.offsets[0]),b&&(this.refId=this.paths.indexOf(b)),r){if(w===void 0||this.refId===void 0)throw this.clearPaths(),new Error("Could not find the reference path");let x=this.paths[this.refId],E=r.nodeOffset;for(let _ of x.path.slice(0,w))E+=this.record(_).sequenceLen;let A=r.seqOffset-E;this.refInterval=[A,A+x.len],x.identity={pathHandle:e.handle,name:e.name,orientation:"forward",hapStart:A,hapEnd:A+x.len}}if(t==="distinct")this.distinctPaths(!0);else if(t==="reference-only"){if(this.refId===void 0)throw new Error("Reference path is required for reference-only output");this.paths=[this.paths[this.refId]],this.refId=0}}distinctPaths(e){let t=this.refId===void 0?void 0:this.paths[this.refId],r=t?.path,o=r&&!st(r)?ft(r):void 0,s=c=>o!==void 0&&Kn(c,o)===0||st(ft(c)),i=e&&this.db.hasHaplotypeIndex;this.twinDeferred=!1,this.paths.sort((c,l)=>Kn(c.path,l.path)||c.len-l.len||(c===t?-1:l===t?1:0));let a=[],f;for(let c of this.paths){let l=a[a.length-1],h=i&&c!==t&&s(c.path);this.twinDeferred||=h,l&&Kn(l.path,c.path)===0&&!h?l.weight=(l.weight??1)+(c.weight??1):(c===t&&(f=a.length),a.push({...c,weight:c.weight??1}))}this.paths=a,this.refId=f}mergeDistinct(){this.twinDeferred?this.settleDeferred():this.distinctPaths(!1)}settleDeferred(){this.twinDeferred&&(this.unsettled={paths:[...this.paths],refId:this.refId},this.distinctPaths(!1))}dropTwins(){let e=this.refId===void 0?void 0:this.paths[this.refId],t=this.refInterval,r=i=>`${i.pathHandle}:${i.hapStart}-${i.hapEnd}`,o=new Set;e?.identity&&t&&o.add(r({...e.identity,hapStart:t[0],hapEnd:t[1]}));for(let i of this.paths)i!==e&&i.identity?.orientation==="forward"&&o.add(r(i.identity));let s=this.paths.filter(i=>i===e||i.identity?.orientation!=="reverse"||!o.has(r(i.identity)));s.length<this.paths.length&&(this.paths=s,this.refId=e===void 0?void 0:s.indexOf(e)),this.twinDeferred&&this.distinctPaths(!1)}keepHaplotypes(e){if(this.paths.some(i=>i.weight!==void 0))throw new Error("keepHaplotypes needs one walk per haplotype: extract with haplotypes 'all', then call mergeDistinct()");let t=this.paths.filter((i,a)=>a!==this.refId&&i.identity===void 0).length;if(t>0)throw new Error(`${t} of the window's ${this.paths.length} walks have no name, so the haplotypes to keep cannot be told from the rest; call identifyPaths() first, and check that the haplotype index was built for this graph`);let r=this.refId===void 0?void 0:this.paths[this.refId],o=this.paths.filter((i,a)=>a===this.refId||i.identity!==void 0&&e(i.identity.name)),s=new Set;for(let i of o)for(let a of i.path)s.add(O(a));for(let i of[...this.records.keys()])s.has(O(i))||this.records.delete(i);this.paths=o,this.refId=r===void 0?void 0:o.indexOf(r)}async extractChosenPaths(e,t,r,o){this.clearPaths();let s=e.position.seqOffset,i=await fo({db:this.db,records:this.records,referenceHandle:e.handle,referencePos:{node:e.position.handle,offset:e.position.gbwtOffset},referenceLeft:s-e.position.nodeOffset,window:{start:s,end:s+t},context:o,snarls:{mode:this.snarlMode,fills:this.snarlFills,inserted:this.snarlNodes},keep:r,signal:this.signal,prefetchReferenceRange:(l,h,d)=>this.prefetchReferenceRange(l,h,d)});if(this.stats.keep=i.stats,i.stats.fallback!==void 0)return!1;let a=await this.db.pathsByHandle(),f=l=>({path:l.handles,offsets:l.offsets,len:l.len,weight:void 0,identity:{pathHandle:l.pathHandle,name:l===i.reference?e.name:a.get(l.pathHandle).name,orientation:l.orientation,hapStart:l.hapStart,hapEnd:l.hapEnd}}),c=[i.reference,...i.pieces].sort(co);return this.paths=c.map(f),this.refId=c.indexOf(i.reference),this.refPath=e.name,this.refHandle=e.handle,this.refInterval=[i.reference.hapStart,i.reference.hapEnd],this.dropTwins(),!0}async identifyPaths(){if(!this.db.hasHaplotypeIndex)throw new Error("The database has no HaplotypeSamples table; run gbz-haplotype-index on it");this.unsettled&&({paths:this.paths,refId:this.refId}=this.unsettled,this.unsettled=void 0,this.twinDeferred=!0);let e=await this.db.haplotypeSampleGap()??4096,t=Hn(this.sortedHandles());if(t.length===0)return;let r=new Map,o=await Promise.all(t.map(([m,w])=>this.db.haplotypeSamplesInRange(m,w)));for(let m of o.flat())r.set(Be(m),m);let s=m=>{let w=0,y=t.length-1;for(;w<y;){let g=w+y+1>>1;t[g][0]<=m?w=g:y=g-1}let S=t[w];return S[0]<=m&&m<=S[1]},i=new Map;this.paths.forEach((m,w)=>{m.path.length>0&&w!==this.refId&&i.set(Be(Tt(m,0)),w)});let a=this.stats.identification;a.interval=e,a.scans=t,a.windowSamples=r.size,this.paths.forEach((m,w)=>{w!==this.refId&&a.fragmentLengths.push(m.len)});let f=this.recordReader(()=>{this.stats.identificationFetches+=1,a.graphFetches+=1}),c=m=>(a.graphLookups+=1,f(m)),l=async(m,w)=>{if(s(m.node))return r.get(Be(m));this.stats.identificationFetches+=1,a.companionSeeks+=1,w.seeks+=1;let y=await this.db.haplotypeSampleAt(m.node,m.offset);return y||(a.companionMisses+=1),y},h=new Map,d=async m=>{let w=h.get(m);if(!w){let y=await this.db.getPath(m);if(!y)throw new Error(`Path ${m} is missing from the database`);w=y.name,h.set(m,w)}return w},p=(m,w,y)=>m.orientation==="forward"?{pathHandle:m.pathHandle,orientation:"forward",base:m.pathOffset-w}:{pathHandle:m.pathHandle,orientation:"reverse",base:m.pathOffset+w+y},u=(m,w)=>m.orientation==="forward"?{pathHandle:m.pathHandle,orientation:"forward",base:m.hapStart-w}:{pathHandle:m.pathHandle,orientation:"reverse",base:m.hapEnd+w};for(let m=0;m<this.paths.length;m++){let w=this.paths[m];if(m===this.refId||w.identity)continue;let y=[],S=new Set,g={fragments:0,steps:0,seeks:0,reentries:0,twinLandings:0,end:"endmarker",pathHandle:void 0};a.chains.push(g);let b,x=0,E=m,A;for(;b===void 0;){if(this.signal?.throwIfAborted(),E!==void 0){if(S.has(E)){g.end="cycle";break}S.add(E);let N=this.paths[E];y.push({index:E,startBp:x}),g.fragments+=1;let P=x;for(let Y=0;Y<N.path.length;Y++){let I=Tt(N,Y),R=r.get(Be(I)),k=this.record(I.node).sequenceLen;if(R){b=p(R,P,k);break}P+=k}if(x+=N.len,b){g.end="in-fragment sample";break}let U=Tt(N,N.path.length-1);A=this.record(U.node).gbwt().lf(U.offset),E=void 0}if(A===void 0||A.node===0){g.end="endmarker";break}let _=Be(A),T=i.get(_);if(T!==void 0){let N=this.paths[T].identity;if(N){b=u(N,x),g.end="identified sibling";break}E=T;continue}this.records.has(A.node)&&(g.reentries+=1),this.twinStarts.has(_)&&(g.twinLandings+=1);let $=await l(A,g),C=await c(A.node);if($){b=p($,x,C.sequenceLen),g.end="out-of-window sample";break}if(this.stats.identificationSteps+=1,g.steps+=1,x-y[y.length-1].startBp>4*e+4*C.sequenceLen){g.end="bound";break}x+=C.sequenceLen,A=C.gbwt().lf(A.offset)}if(b){g.pathHandle=b.pathHandle;let _=await d(b.pathHandle);for(let{index:T,startBp:$}of y){let C=this.paths[T];C.identity=b.orientation==="forward"?{pathHandle:b.pathHandle,name:_,orientation:"forward",hapStart:b.base+$,hapEnd:b.base+$+C.len}:{pathHandle:b.pathHandle,name:_,orientation:"reverse",hapStart:b.base-$-C.len,hapEnd:b.base-$}}}}this.dropTwins()}refIndex(e){if(this.refIndexCache===void 0){let t=new Map;e.forEach((r,o)=>{let s=t.get(r);s?s.push(o):t.set(r,[o])}),this.refIndexCache=t}return this.refIndexCache}refPrefix(e){if(this.refPrefixCache===void 0){let t=[0];e.forEach((r,o)=>{t.push(t[o]+this.record(r).sequenceLen)}),this.refPrefixCache=t}return this.refPrefixCache}orderedMatches(e,t){let r=this.refIndex(t),o=new Int32Array(e.length),s=new Int32Array(e.length),i=0,a=-1;for(let f=0;f<e.length;f++){let c=r.get(e[f]);if(c){let l=di(c,a);if(l===void 0)return;o[i]=f,s[i]=l,i+=1,a=l}}return{pathAt:o,refAt:s,count:i}}pathLen(e){let t=0;for(let r of e)t+=this.record(r).sequenceLen;return t}prefixMatches(e,t){let r=0,o=0,s=0,i=0,a=0;for(;o<e.length&&s<t.length;){let f=this.record(e[o]).sequence,c=this.record(t[s]).sequence;for(;i<f.length&&a<c.length;){if(f[i]!==c[a])return r;i+=1,a+=1,r+=1}i===f.length&&(o+=1,i=0),a===c.length&&(s+=1,a=0)}return r}suffixMatches(e,t){let r=0,o=0,s=0,i=0,a=0;for(;o<e.length&&s<t.length;){let f=this.record(e[e.length-o-1]).sequence,c=this.record(t[t.length-s-1]).sequence;for(;i<f.length&&a<c.length;){if(f[f.length-i-1]!==c[c.length-a-1])return r;i+=1,a+=1,r+=1}i===f.length&&(o+=1,i=0),a===c.length&&(s+=1,a=0)}return r}align(e,t,r){let o=this.pathLen(e),s=this.pathLen(t),i=this.prefixMatches(e,t),a=this.suffixMatches(e,t);i+a>o&&(a=o-i),i+a>s&&(a=s-i),X(r,"M",i),Co(r,o-i-a,s-i-a),X(r,"M",a)}sharedWeight(e,t){let r=this.refIndex(t),o=0;for(let s of e)r.has(s)&&(o+=this.record(s).sequenceLen);return o}editsAgainst(e,t){let r=this.orderedMatches(e,t);r?this.stats.orderedAlignments+=1:this.stats.lcsAlignments+=1;let o=r??hi(lo(e,t,h=>this.record(h).sequenceLen)[0]),s=[],i=this.refPrefix(t),a=(h,d,p,u)=>{h===d?X(s,"D",i[u]-i[p]):p===u?X(s,"I",this.pathLen(e.slice(h,d))):this.align(e.slice(h,d),t.slice(p,u),s)},f=0,c=0,l=0;for(let h=0;h<o.count;h++){let d=o.pathAt[h],p=o.refAt[h];(c!==d||l!==p)&&a(c,d,l,p);let u=this.record(e[d]).sequenceLen;X(s,"M",u),f+=u,c=d+1,l=p+1}return a(c,e.length,l,t.length),{edits:s,matched:f,matches:o}}alignment(e){let t=this.paths[e];if(this.refId===void 0||e===this.refId||!t)return;let r=this.paths[this.refId].path,o;if(st(r)&&(t.identity===void 0||!st(ft(t.path))))o={...this.editsAgainst(t.path,r),flipped:!1};else{let s=ft(t.path),i=this.sharedWeight(t.path,r);if(this.sharedWeight(s,r)===0)o={...this.editsAgainst(t.path,r),flipped:!1};else if(i===0)o={...this.editsAgainst(s,r),flipped:!0};else{let f=this.editsAgainst(t.path,r),c=this.editsAgainst(s,r);o=c.matched>f.matched?{...c,flipped:!0}:{...f,flipped:!1}}}return o}alignToRef(e){return this.settleDeferred(),this.alignment(e)?.edits.map(([t,r])=>`${r}${t}`).join("")}alignments(){this.settleDeferred();let e=this.referenceInterval;if(this.refId===void 0||!e)throw new Error("Alignments need a reference path");let t=this.paths[this.refId].path,r=this.refPrefix(t)[t.length],o=(l,h,d,p)=>{let u=yi(l),m=this.paths[d[0]],w=this.paths[d[d.length-1]],y=m.identity,S=y?.orientation==="forward",[g,b]=S?[m,w]:[w,m];return{strand:h,refStart:e.start+u.leading,refEnd:e.start+r-u.trailing,edits:u.edits,weight:m.weight,path:d.flatMap(x=>this.paths[x].path),start:Tt(m,0),pieces:d,soloAligned:p,identity:y===void 0?void 0:{pathHandle:y.pathHandle,name:y.name,hapStart:y.name.fragment+g.identity.hapStart,hapEnd:y.name.fragment+b.identity.hapEnd,walkForward:S}}},s=l=>l.soloAligned.reduce((h,d)=>h+d,0),i=l=>l.pieces.reduce((h,d)=>h+this.paths[d].len,0),a=l=>2*s(l)>=i(l),f=l=>{let h=l[0],d=l[l.length-1],p=h.identity.walkForward;if(l.some((P,U)=>P.strand!==h.strand||P.identity.walkForward!==p||U>0&&P.identity.hapStart<l[U-1].identity.hapEnd))return;let u=p?l:[...l].reverse(),m=u.flatMap(P=>P.pieces),w=u.flatMap(P=>P.soloAligned),y=h.strand==="+"!==p,S=m.map(P=>this.paths[P]),g=S.slice(1).map((P,U)=>{let Y=S[U].identity;return p?P.identity.hapStart-Y.hapEnd:Y.hapStart-P.identity.hapEnd}),b=y?[...S].reverse():S,x=y?[...g].reverse():g,E=b.flatMap(P=>y?ft(P.path):P.path),{edits:A}=this.editsAgainst(E,t),_=Ao(A,b.map(P=>P.len)),T=new Map((y?[...m].reverse():m).map((P,U)=>[P,_[U]])),$=P=>2*P.pieces.reduce((U,Y)=>U+T.get(Y),0)>=s(P);if(!$(h)||!$(d))return;let C=[],N=0;return b.slice(0,-1).forEach((P,U)=>{N+=P.len,C.push([N,x[U]])}),o(bi(A,C),h.strand,m,w)},c=[];return this.paths.forEach((l,h)=>{if(h===this.refId)return;let{edits:d,flipped:p}=this.alignment(h),u=l.identity,m=u?u.orientation==="forward"!==p:!p;c.push(o(d,m?"+":"-",[h],Ao(d,[l.len])))}),mi(c,a,f).map(l=>{let{edits:h,identity:d,pieces:p,soloAligned:u,...m}=l,w={...m,cigar:Si(h)};return d?{...w,resolved:!0,name:d.name,label:me({...d.name,fragment:d.hapStart,end:d.hapEnd}),pathHandle:d.pathHandle,hapStart:d.hapStart,hapEnd:d.hapEnd}:{...w,resolved:!1}})}pairAlignments(e){let{target:t,query:r,...o}=e,s=this.paths.flatMap(l=>{let{identity:h}=l;return h?[{name:h.name,start:h.name.fragment+h.hapStart,steps:Ft(l,h)}]:[]}),i=l=>h=>h.sample===l.sample&&h.haplotype===l.haplotype,a=i(t),f=r?i(r):l=>!a(l),c=l=>this.record(ye(l,"forward")).sequence;return s.filter(l=>a(l.name)).flatMap(l=>s.filter(h=>f(h.name)).flatMap(h=>Io({...o,query:h.steps,target:l.steps,sequenceOf:c}).map(d=>({query:h.name,queryStart:h.start+d.queryStart,queryEnd:h.start+d.queryEnd,strand:d.strand,target:l.name,targetStart:l.start+d.targetStart,targetEnd:l.start+d.targetEnd,cigar:Eo(d.edits),matches:d.edits.reduce((p,[u,m])=>p+(u==="="?m:0),0),columns:d.edits.reduce((p,[,u])=>p+u,0),sharedBases:d.sharedBases}))))}canonicalEdges(e){let t=[];for(let r of["forward","reverse"]){let o=ye(e,r);for(let s of this.record(o).successors())this.hasHandle(s)&&Ue(o,s)&&t.push([r==="reverse"?1:0,O(s),z(s)?1:0])}return t.sort((r,o)=>r[0]-o[0]||r[1]-o[1]||r[2]-o[2]),t.filter((r,o)=>o===0||r[0]!==t[o-1][0]||r[1]!==t[o-1][1]||r[2]!==t[o-1][2])}async stableName(){let e=new TextEncoder,t=[];for(let r of this.sortedHandles())if(!z(r)){let o=O(r),s=`S	${o}	${this.record(r).sequence}
 `;for(let[i,a,f]of this.canonicalEdges(o))s+=`L	${o}	${i?"-":"+"}	${a}	${f?"-":"+"}
 `;t.push(e.encode(s))}return oo(t)}async toGFA(e={}){this.settleDeferred();let t=e.cigar??!1,r=[this.refPath?`H	VN:Z:1.1	RS:Z:${this.refPath.sample}`:"H	VN:Z:1.1",...ro(no(await this.stableName(),await this.db.graphName()))],o=this.sortedHandles();for(let c of o)z(c)||r.push(`S	${O(c)}	${this.record(c).sequence}`);let s=c=>z(c)?"-":"+";for(let c of o)for(let l of this.record(c).successors())this.hasHandle(l)&&Ue(c,l)&&r.push(`L	${O(c)}	${s(c)}	${O(l)}	${s(l)}	0M`);let i=(c,l,h,d,p)=>{let u=Ft(c,l).map(y=>`${z(y)?"<":">"}${O(y)}`).join(""),m=c.weight===void 0?"":`	WT:i:${c.weight}`,w=p===void 0?"":`	CG:Z:${p}`;return`W	${h.sample}	${h.haplotype}	${h.contig}	${h.fragment}	${d}	${u}${m}${w}`},a=this.refPath?.contig??"unknown";this.refId!==void 0&&this.refPath&&this.refInterval&&r.push(i(this.paths[this.refId],void 0,{...this.refPath,fragment:this.refPath.fragment+this.refInterval[0]},this.refPath.fragment+this.refInterval[1],void 0));let f=1;return this.paths.forEach((c,l)=>{if(l!==this.refId){let h=e.names!=="anonymous"?c.identity:void 0,d=t?this.alignToRef(l):void 0;r.push(h?i(c,h,{...h.name,fragment:h.name.fragment+h.hapStart},h.name.fragment+h.hapEnd,d):i(c,void 0,{sample:"unknown",contig:a,haplotype:f,fragment:0},c.len,d)),f+=1}}),`${r.join(`
 `)}
 `}outputPaths(e){this.settleDeferred();let t=e.cigar??!1,r=[],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]};r.push({info:this.paths[this.refId],identity:void 0,name:me({...i,end:this.refPath.fragment+this.refInterval[1]}),cigar:void 0})}let s=1;return this.paths.forEach((i,a)=>{if(a===this.refId)return;let f=e.names!=="anonymous"?i.identity:void 0;r.push({info:i,identity:f,name:f?me({...f.name,fragment:f.name.fragment+f.hapStart,end:f.name.fragment+f.hapEnd}):me({sample:"unknown",contig:o,haplotype:s,fragment:0,end:i.len}),cigar:t?this.alignToRef(a):void 0}),s+=1}),r}*outputEdges(){for(let e of this.sortedHandles())for(let t of this.record(e).successors())this.hasHandle(t)&&Ue(e,t)&&(yield[e,t])}toSubgraphJson(e={}){let t=this.sortedHandles().filter(s=>!z(s)).map(s=>({id:String(O(s)),sequence:this.record(s).sequence})),r=[];for(let[s,i]of this.outputEdges())r.push({from:String(O(s)),from_is_reverse:z(s),to:String(O(i)),to_is_reverse:z(i)});let o=this.outputPaths(e).map(s=>xi(s.info,s.identity,s.name,s.cigar));return{nodes:t,edges:r,paths:o}}toCompactSubgraph(e={}){let t=this.sortedHandles().filter(i=>!z(i)),r=new Int32Array(t.length),o=[];t.forEach((i,a)=>{r[a]=O(i),o.push(this.record(i).sequence)});let s=[];for(let[i,a]of this.outputEdges())s.push(i,a);return{nodeIds:r,nodeSequences:o,edges:Int32Array.from(s),paths:this.outputPaths(e).map(i=>({name:i.name,weight:i.info.weight,cigar:i.cigar,steps:Int32Array.from(Ft(i.info,i.identity))}))}}};function Ft(n,e){return e?.orientation==="reverse"?n.path.map(t=>re(t)).reverse():n.path}function xi(n,e,t,r){return{name:t,...n.weight===void 0?{}:{weight:n.weight},...r===void 0?{}:{cigar:r},path:Ft(n,e).map(o=>({id:String(O(o)),is_reverse:z(o)}))}}function Kn(n,e){let t=Math.min(n.length,e.length);for(let r=0;r<t;r++){let o=n[r],s=e[r];if(o!==s)return o<s?-1:1}return n.length-e.length}function X(n,e,t){if(t===0)return;let r=n[n.length-1];r?.[0]===e?r[1]+=t:n.push([e,t])}function Lt(n){return n===0?0:6+(n-1)}function Co(n,e,t){if(e===0)X(n,"D",t);else if(t===0)X(n,"I",e);else{let r=Math.min(e,t),o=4*r+Lt(e-r)+Lt(t-r),s=Lt(e)+Lt(t);o<=s?(X(n,"M",r),X(n,"I",e-r),X(n,"D",t-r)):(X(n,"I",e),X(n,"D",t))}}function yi(n){let e=0;for(;e<n.length&&n[e][0]!=="M";)e+=1;if(e===n.length){let a=n.filter(([c])=>c==="I"),f=n.filter(([c])=>c==="D").reduce((c,[,l])=>c+l,0);return{edits:a.map(([c,l])=>[c,l]),leading:0,trailing:f}}let t=n.length;for(;n[t-1][0]!=="M";)t-=1;let r=a=>({inserted:a.reduce((f,[c,l])=>f+(c==="I"?l:0),0),deleted:a.reduce((f,[c,l])=>f+(c==="D"?l:0),0)}),o=r(n.slice(0,e)),s=r(n.slice(t)),i=[];X(i,"I",o.inserted);for(let[a,f]of n.slice(e,t))X(i,a,f);return X(i,"I",s.inserted),{edits:i,leading:o.deleted,trailing:s.deleted}}function Ao(n,e){let t=e.map(()=>0),r=e.length-1,o=0,s=e[0],i=0;for(let[a,f]of n){if(a==="D")continue;let c=f;for(;c>0;){for(;o<r&&i>=s;)o+=1,s+=e[o];let l=o<r?Math.min(c,s-i):c;a==="M"&&(t[o]+=l),i+=l,c-=l}}return t}function bi(n,e){let t=[],r=0,o=0;for(let[s,i]of n){if(s==="D"){X(t,s,i);continue}let a=r;for(;o<e.length&&e[o][0]<r+i;){let[f,c]=e[o];X(t,s,f-a),X(t,"I",c),a=f,o+=1}X(t,s,r+i-a),r+=i}for(;o<e.length;o++)X(t,"I",e[o][1]);return t}function Si(n){return n.map(([e,t])=>`${t}${e}`).join("")}function Oe(n,e,t=0){if(!Number.isSafeInteger(e)||e<t)throw new Error(`${n} must be a whole number${t>0?` of at least ${t}`:""}, not ${e}`);return e}function Bt(n){return Oe("context",n.context??100)}function Ht(n,e){return e.limit!==void 0&&Oe("limit",e.limit),$t.create(n,e)}async function Ro(n,e){let t=Bt(e),r=Ht(n,e),o=await r.pathPosition(Ve(We(e.path),Oe("offset",e.offset)));return await r.aroundPosition(o.position.handle,o.position.nodeOffset,t),await r.extractSnarls(e.snarls??"none"),r.extractPaths(o,e.haplotypes??"all"),r}async function vi(n,e){let t=Oe("start",e.start),r=Oe("end",e.end),o=Bt(e),s=Ht(n,e);try{let i=await s.pathPosition(Ve(We(e.path),t));return await s.prefetchReferenceWalk(i,r-t),await s.aroundInterval(i.position,r-t,o),await s.extractSnarls(e.snarls??"none"),{subgraph:s,reference:i}}catch(i){throw i instanceof be&&i.windowBp===void 0?new be(i.limit,{windowBp:r-t,walkedBp:s.referenceWalkedBp??0}):i}}async function Xn(n,e){let{keep:t}=e,r=e.haplotypes??"all",o=r==="all"||r==="distinct";if(t!==void 0&&o&&!n.hasHaplotypeIndex)throw new Error("keep needs the haplotype index: this database cannot name its walks");let{subgraph:s,reference:i}=await vi(n,e);return t===void 0||!o?(s.extractPaths(i,r),s):(await s.extractChosenPaths(i,e.end-e.start,t,Bt(e))||(s.extractPaths(i,"all"),await s.identifyPaths()),s.keepHaplotypes(t),r==="distinct"&&s.mergeDistinct(),s)}async function Mo(n,e){let t=e.haplotypes??"all",r=e.snarls??"none";if(t==="reference-only")throw new Error("Cannot output a reference path in a node-based query");if(r==="overlapping"&&new Set(e.nodeIds).size>1)throw new Error("Overlapping snarls cannot be extracted for a node-based query with multiple nodes");let o=Bt(e);for(let i of e.nodeIds)Oe("node id",i,1);let s=Ht(n,e);return await s.aroundNodes(e.nodeIds,o),await s.extractSnarls(r),s.extractPaths(void 0,t),s}async function Po(n,e){let t=e.haplotypes??"all";if(t==="reference-only")throw new Error("Cannot output a reference path in a node-based query");let r=Ht(n,e);return await r.betweenNodes(Oe("startHandle",e.startHandle,2),Oe("endHandle",e.endHandle,2)),r.extractPaths(void 0,t),r}function Ee(n,e){let t=0;for(let o=0;o<8;o++){let s=n[e+o];if(s===void 0)throw new Error("SQLite varint runs past the end of the buffer");if(t=t*128+(s&127),(s&128)===0){if(o===7&&!Number.isSafeInteger(t))throw new Error("SQLite varint exceeds the safe integer range");return[t,e+o+1]}}let r=n[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 Ii(n,e,t){switch(t){case 1:return n.getInt8(e);case 2:return n.getInt16(e);case 3:return n.getInt8(e)<<16|n.getUint16(e+1);case 4:return n.getInt32(e);case 6:return n.getInt16(e)*4294967296+n.getUint32(e+2);default:{let r=n.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 Ei=new TextDecoder;function qt(n){let[e,t]=Ee(n,0),r=[],o=t;for(;o<e;){let[a,f]=Ee(n,o);r.push(a),o=f}let s=new DataView(n.buffer,n.byteOffset,n.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=Ii(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=n.subarray(i,i+f);return i+=f,a%2===0?c:Ei.decode(c)}throw new Error(`SQLite serial type ${a} is reserved`)})}var Gt=2,zt=5,_o=10,Dt=13;function ko(n,e){return n[e]*256+n[e+1]}function Ne(n,e){return n[e]*16777216+n[e+1]*65536+n[e+2]*256+n[e+3]}function Ai(n,e){let t=n[e];if(t!==Gt&&t!==zt&&t!==_o&&t!==Dt)throw new Error(`SQLite page has unknown b-tree type ${t}`);let r=t===Gt||t===zt;return{type:t,cellCount:ko(n,e+3),rightChild:r?Ne(n,e+8):0,cellPointers:e+(r?12:8)}}function Me(n,e,t){return ko(n,e.cellPointers+2*t)}var Ci=4096,jt=class{usable;pager;decodedIndexPages=new Map;tableDepths=new Map;constructor(e,t){this.pager=e,this.usable=e.pageSize-t}localPayloadSize(e,t){let r=this.usable,o=t?Math.floor((r-12)*64/255)-23:r-35;if(e<=o)return e;let s=Math.floor((r-12)*32/255)-23,i=s+(e-s)%(r-4);return i<=o?i:s}async payload(e,t,r,o){let s=this.localPayloadSize(r,o);if(s===r)return e.subarray(t,t+r);let i=new Uint8Array(r);i.set(e.subarray(t,t+s),0);let a=s,f=Ne(e,t+s);for(;f!==0&&a<r;){let c=await this.pager.page(f),l=c.subarray(4,4+Math.min(this.usable-4,r-a));i.set(l,a),a+=l.length,f=Ne(c,0)}if(a!==r)throw new Error("SQLite overflow chain ended before the payload was complete");return i}async pageAt(e){let t=await this.pager.page(e);return{page:t,header:Ai(t,e===1?100:0)}}tableDepth(e,t){let r=this.tableDepths.get(e);return r||(r=(async()=>{let o=e;for(let s=0;;s++){let{page:i,header:a}=await this.pageAt(o);if(a.type===Dt)return s;if(a.type!==zt)throw new Error("SQLite table b-tree contains an index page");let f=this.childIndexFor(i,a,t);o=f===a.cellCount?a.rightChild:Ne(i,Me(i,a,f))}})(),this.tableDepths.set(e,r),r.catch(()=>this.tableDepths.delete(e))),r}childIndexFor(e,t,r){let o=0,s=t.cellCount;for(;o<s;){let i=o+s>>1,[a]=Ee(e,Me(e,t,i)+4);a<r?o=i+1:s=i}return o}async prefetchRowidRanges(e,t,r=!1){if(t.length===0)return!0;let o=await this.tableDepth(e,t[0][0]),s=t.map(()=>[e]);for(let i=0;i<o;i++){s=await Promise.all(s.map((f,c)=>this.childrenInRange(f,...t[c])));let a=s.flat();if(r)this.pager.prefetchLeading(a);else if(!this.pager.prefetch(a))return!1}return!0}async childrenInRange(e,t,r){let o=await Promise.all(e.map(i=>this.pageAt(i))),s=[];return o.forEach(({page:i,header:a},f)=>{let c=f===0?this.childIndexFor(i,a,t):0,l=f===o.length-1?this.childIndexFor(i,a,r):a.cellCount;for(let h=c;h<=l;h++)s.push(h===a.cellCount?a.rightChild:Ne(i,Me(i,a,h)))}),s}async tableRowid(e,t){let r=e;for(;;){let{page:o,header:s}=await this.pageAt(r);if(s.type===Dt){let f=0,c=s.cellCount;for(;f<c;){let l=f+c>>1,h=Me(o,s,l),[d,p]=Ee(o,h),[u,m]=Ee(o,p);if(u===t)return qt(await this.payload(o,m,d,!1));u<t?f=l+1:c=l}return}if(s.type!==zt)throw new Error("SQLite table b-tree contains an index page");let i=0,a=s.cellCount;for(;i<a;){let f=i+a>>1,c=Me(o,s,f),[l]=Ee(o,c+4);l<t?i=f+1:a=f}r=i===s.cellCount?s.rightChild:Ne(o,Me(o,s,i))}}async*tableScan(e){yield*this.scanPage(e,await this.tableDepth(e,0))}async*scanPage(e,t){let{page:r,header:o}=await this.pageAt(e);if(o.type===Dt)for(let s=0;s<o.cellCount;s++){let i=Me(r,o,s),[a,f]=Ee(r,i),[c,l]=Ee(r,f);yield{rowid:c,values:qt(await this.payload(r,l,a,!1))}}else{let s=[];for(let i=0;i<o.cellCount;i++)s.push(Ne(r,Me(r,o,i)));s.push(o.rightChild),t===1&&this.pager.prefetchLeading(s);for(let i of s)yield*this.scanPage(i,t-1)}}decodedCells(e,t){let r=this.decodedIndexPages.get(e);if(r)this.decodedIndexPages.delete(e);else if(r=new Array(t.cellCount),this.decodedIndexPages.size>=Ci){let o=this.decodedIndexPages.keys().next().value;o!==void 0&&this.decodedIndexPages.delete(o)}return this.decodedIndexPages.set(e,r),r}async indexCell(e,t,r,o){let s=this.decodedCells(e,r),i=s[o];if(!i){let a=Me(t,r,o),f=r.type===Gt,[c,l]=Ee(t,f?a+4:a);i={values:qt(await this.payload(t,l,c,!0)),leftChild:f?Ne(t,a):0},s[o]=i}return i}async lowerBound(e,t,r,o,s,i){let a=s,f=r.cellCount;for(;a<f;){let c=a+f>>1,l=await this.indexCell(e,t,r,c),h=Zn(l.values,o);h<0||i&&h===0?a=c+1:f=c}return a}async*indexScanFrom(e,t,r){let{page:o,header:s}=await this.pageAt(e),i=await this.lowerBound(e,o,s,t,0,!1),a=s.type===Gt;if(a&&r){let f=await this.lowerBound(e,o,s,r,i,!0),c=[];for(let l=i;l<=f;l++)c.push(l===s.cellCount?s.rightChild:(await this.indexCell(e,o,s,l)).leftChild);this.pager.prefetchLeading(c)}for(let f=i;f<s.cellCount;f++){let c=await this.indexCell(e,o,s,f);if(a&&(yield*this.indexScanFrom(c.leftChild,t,r)),r&&Zn(c.values,r)>0)return;yield c.values}a&&(yield*this.indexScanFrom(s.rightChild,t,r))}async indexSeekLE(e,t){let r,o=e;for(;;){let{page:s,header:i}=await this.pageAt(o),a=0,f=i.cellCount,c=0;for(;a<f;){let l=a+f>>1,h=await this.indexCell(o,s,i,l);Zn(h.values,t)<=0?(r=h.values,a=l+1):(c=h.leftChild,f=l)}if(i.type===_o)return r;o=a===i.cellCount?i.rightChild:c}}};function Zn(n,e){for(let t=0;t<e.length;t++){let r=n[t],o=e[t];if(typeof r!="number"||o===void 0)throw new Error("SQLite index key is not numeric");if(r!==o)return r<o?-1:1}return 0}function Oo({blockSize:n,maxBlocks:e}){if(n!==void 0&&!(Number.isSafeInteger(n)&&n>0))throw new Error(`blockSize must be a positive integer, not ${n}`);if(e!==void 0&&!(Number.isSafeInteger(e)&&e>0))throw new Error(`maxBlocks must be a positive integer, not ${e}`)}var Ut=class{blocks=new Map;blockSize;maxBlocks;plan;bytesFetched=0;fetches=0;source;pageSize;fileSize;constructor(e,t,r,o={}){this.source=e,this.pageSize=t,this.fileSize=r;let s=o.blockSize??65536;this.blockSize=Math.max(t,Math.ceil(s/t)*t),this.maxBlocks=o.maxBlocks??256}async read(e,t){let r=await this.readRetrying(e,t);if(this.bytesFetched+=r.length,r.length<e)throw new Error(`the file ends at byte ${t+r.length}, short of the ${this.fileSize} bytes its SQLite header gives`);return r}async readRetrying(e,t){let r=0;for(;;)try{return await this.source.read(e,t)}catch(o){if(r+=1,r>=3)throw o;await new Promise(s=>setTimeout(s,200*r))}}seed(e,t){t.length===Math.min(this.blockSize,this.fileSize-e*this.blockSize)&&this.blocks.set(e,Promise.resolve(t))}block(e){this.follow(e);let t=this.touch(e);if(t)return t;let r=e*this.blockSize,o=Math.min(this.blockSize,this.fileSize-r),s=this.read(o,r);return this.fetches+=1,this.store(e,s),this.evict(),s}touch(e){let t=this.blocks.get(e);return t&&(this.blocks.delete(e),this.blocks.set(e,t)),t}blockOf(e){return Math.floor((e-1)*this.pageSize/this.blockSize)}get prefetchBudget(){return Math.max(1,Math.floor(this.maxBlocks/2))}get chunk(){return Math.max(1,Math.floor(this.prefetchBudget/2))}prefetch(e){let t=new Set(e.map(r=>this.blockOf(r)));return t.size>this.prefetchBudget?!1:(this.fetchBlocks(t),!0)}prefetchLeading(e){let t=[],r=new Map;for(let o of e){let s=this.blockOf(o);r.has(s)||(r.set(s,t.length),t.push(s))}this.plan={blocks:t,position:r,next:0},this.advance(this.prefetchBudget)}advance(e){let t=this.plan;if(!t)return;let r=t.blocks.slice(t.next,t.next+e);t.next+=r.length,t.next>=t.blocks.length&&(this.plan=void 0),this.fetchBlocks(new Set(r))}follow(e){let t=this.plan,r=t?.position.get(e);t&&r!==void 0&&r>=t.next-Math.ceil(this.chunk/2)&&this.advance(this.chunk)}fetchBlocks(e){let t=[...e].filter(o=>!this.touch(o)).sort((o,s)=>o-s),r=0;for(;r<t.length;){let o=r+1;for(;o<t.length&&t[o]===t[o-1]+1;)o+=1;this.fetchRun(t[r],o-r),r=o}}fetchRun(e,t){let r=e*this.blockSize,o=Math.min(t*this.blockSize,this.fileSize-r),s=this.read(o,r);this.fetches+=1;for(let i=0;i<t;i++){let a=i*this.blockSize;this.store(e+i,s.then(f=>f.subarray(a,a+this.blockSize)))}this.evict()}store(e,t){this.blocks.set(e,t),t.catch(()=>{this.blocks.get(e)===t&&this.blocks.delete(e)})}evict(){for(;this.blocks.size>this.maxBlocks;){let e=this.blocks.keys().next().value;if(e===void 0)break;this.blocks.delete(e)}}async page(e){let t=(e-1)*this.pageSize;if(e<1||t+this.pageSize>this.fileSize)throw new Error(`SQLite page ${e} is outside the file`);let r=await this.block(Math.floor(t/this.blockSize)),o=t%this.blockSize;return r.subarray(o,o+this.pageSize)}};var lt=class n{pager;btree;objects;constructor(e,t,r){this.pager=e,this.btree=t,this.objects=r}static async open(e,t={}){Oo(t);let r=await e.read(Math.max(512,t.blockSize??65536),0),o=r.subarray(0,100);if(new TextDecoder().decode(o.subarray(0,15))!=="SQLite format 3"||o.length<100)throw new Error("Not a SQLite database");let i=new DataView(o.buffer,o.byteOffset,o.byteLength),a=i.getUint16(16),f=a===1?65536:a,c=o[20]??0,l=i.getUint32(56);if(l!==1)throw new Error(`SQLite text encoding ${l} is not UTF-8`);let h=i.getUint32(28);if(h===0||i.getUint32(24)!==i.getUint32(92))throw new Error("SQLite header has no valid database size; the file was written by SQLite older than 3.7.0");let d=h*f,p=new Ut(e,f,d,t);p.seed(0,r),p.fetches+=1,p.bytesFetched+=r.length;let u=new jt(p,c),m=new Map;for await(let{values:w}of u.tableScan(1)){let[y,S,g,b,x]=w;typeof y=="string"&&typeof S=="string"&&typeof g=="string"&&typeof b=="number"&&m.set(S,{type:y,name:S,tableName:g,rootPage:b,sql:typeof x=="string"?x:""})}return new n(p,u,m)}rootPage(e){let t=this.objects.get(e);if(!t)throw new Error(`SQLite database has no object named ${e}`);return t.rootPage}withoutRowid(e){let t=this.objects.get(e);return t?.type==="table"&&/without\s+rowid/i.test(t.sql)}indexOn(e){let t=[...this.objects.values()].find(r=>r.type==="index"&&r.tableName===e);if(t)return t.rootPage;if(this.withoutRowid(e))return this.rootPage(e);throw new Error(`SQLite table ${e} has no index`)}byRowid(e,t){return this.btree.tableRowid(this.rootPage(e),t)}prefetchRows(e,t,r=!1){return this.btree.prefetchRowidRanges(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,r){return this.btree.indexScanFrom(this.indexOn(e),t,r)}has(e){return this.objects.has(e)}};var nr="GBZ-base version 4",Wt=class extends Error{name="UnknownPathError";path;constructor(e){super(`the graph has no path named ${me(e)}`),this.path=e}},Vt=class extends Error{name="ForwardOnlyIndexError";constructor(){super("the haplotype index was written with --forward-only, which cannot name the walks stored against their reference (about half of them); rebuild it with gbz-haplotype-index without --forward-only")}},Qt=class extends Error{name="SchemaVersionError";found;constructor(e){super(e===void 0?"not a gbz-base database: it has no version tag":`unsupported database schema "${e}"; this reader understands "${nr}"`),this.found=e}};function Ri(n){if(n.length===1)return n[0];let e=new Uint8Array(n.reduce((r,o)=>r+o.length,0)),t=0;for(let r of n)e.set(r,t),t+=r.length;return e}var Jn=3,Ye=class{at=0;bytes;constructor(e){this.bytes=e}get done(){return this.at>=this.bytes.length}next(){let e=0,t=1;for(;;){let r=this.bytes[this.at++];if(r===void 0)throw new Error("a haplotype index blob ends inside a number");if(e+=(r&127)*t,t*=128,(r&128)===0)return e}}};function Mi(n,e){let t=new Ye(n),r=0;for(;!t.done;){let o=r+t.next();r=o+t.next(),e.push([o,r])}}function Pi(n){n.sort((r,o)=>r[0]-o[0]);let e=[],t=[];for(let[r,o]of n){let s=t.length-1;s>=0&&r<=t[s]+1?t[s]=Math.max(t[s],o):(e.push(r),t.push(o))}return r=>{let o=0,s=e.length;for(;o<s;){let i=o+s>>1;e[i]<=r?o=i+1:s=i}return o>0&&r<=t[o-1]}}function _i(n,e,t){let r=new Ye(e);for(;!r.done;){let o=r.next(),s=r.next(),i=r.next(),a=r.next(),f=r.next();t.push({bin:n,pathHandle:o,pathStart:s,pathEnd:i,snarl:f>0?[a,f]:void 0,node:r.next(),offset:r.next()})}}function ki(n,e,t){let r=O(n);for(let o of e){let s=new Ye(o);for(;!s.done;){let i=s.next(),a=i%2;t.push({node:2*r+a,offset:s.next(),pathHandle:(i-a)/2,orientation:"forward",pathOffset:s.next()})}}}var tr=class{sequenceLen;handle;edges;bwt;encodedSequence;next;decoded;constructor(e,t,r,o,s){this.handle=e,this.edges=t,this.bwt=r,this.encodedSequence=o,this.next=s,this.sequenceLen=Yr(o)}get id(){return O(this.handle)}get orientation(){return je(this.handle)}get sequence(){return this.decoded??=Kr(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 ${this.handle} is empty`);return new Ct(this.edges,this.bwt)}};function Q(n,e){if(typeof n!="number")throw new Error(`${e} is not a number in the database`);return n}function ht(n,e){if(typeof n!="string")throw new Error(`${e} is not text in the database`);return n}function He(n,e){if(!(n instanceof Uint8Array))throw new Error(`${e} is not a blob in the database`);return n}function No(n,e){return{handle:n,fwStart:{node:Q(e[1],"Paths.fw_node"),offset:Q(e[2],"Paths.fw_offset")},revStart:{node:Q(e[3],"Paths.rev_node"),offset:Q(e[4],"Paths.rev_offset")},name:{sample:ht(e[5],"Paths.sample"),contig:ht(e[6],"Paths.contig"),haplotype:Q(e[7],"Paths.haplotype"),fragment:Q(e[8],"Paths.fragment")},isIndexed:Q(e[9],"Paths.is_indexed")!==0}}function er(n,e){return n.catch(e),n}async function To(n){let e=new Map;for await(let{values:t}of n.scan("Tags"))e.set(ht(t[0],"Tags.key"),ht(t[1],"Tags.value"));return e}var dt=class n{pathCache;pathMapCache;indexTags=new Map;overviewRowsCache;sqlite;index;tagMap;constructor(e,t,r){this.sqlite=e,this.index=t,this.tagMap=r}static async open(e){let{source:t,haplotypeIndex:r}=e,o={blockSize:e.blockSize,maxBlocks:e.maxBlocks},s=await lt.open(t,o),i=s.objects.has("Tags")?await To(s):new Map,a=i.get("version");if(a!==nr)throw new Qt(a);for(let l of["Nodes","Paths","ReferenceIndex"])s.rootPage(l);let f=r?await lt.open(r,o):void 0,c=new n(s,f,i);if(f){for(let m of["Tags","HaplotypeSamples","HaplotypeLengths"])if(!f.objects.has(m))throw new Error(`haplotypeIndex is not a gbz-base haplotype index: it has no ${m} table`);c.indexTags=await To(f);let l=c.indexTags.get("haplotype_index_paths"),h=await c.tag("paths");if(l!==h)throw new Error(`haplotype index was built for ${l??"an unknown number of"} paths but the graph has ${h}`);let d=c.indexTags.get("haplotype_index_nodes"),p=await c.tag("nodes");if(d!==void 0&&d!==p)throw new Error(`haplotype index was built for a graph with ${d} nodes but this one has ${p}`);if(c.indexTags.get("haplotype_index_orientations")==="forward")throw new Vt;let u=c.indexTags.get("haplotype_index_format");if(Number(u)!==Jn)throw new Error(u===void 0?`the haplotype index predates format ${Jn}; rebuild it with gbz-haplotype-index 0.3`:`the haplotype index has format ${u}; this version of @gmod/gbz-base reads format ${Jn}`)}return c}async tags(){return this.tagMap}async tag(e){return this.tagMap.get(e)}prefetchRecords(e,t=!1){return this.sqlite.prefetchRows("Nodes",e,t)}async getRecord(e){let t=await this.sqlite.byRowid("Nodes",e);if(!t)return;let r=t[4];return new tr(e,Qr(He(t[1],"Nodes.edges")),He(t[2],"Nodes.bwt"),He(t[3],"Nodes.sequence"),typeof r=="number"?r:void 0)}paths(){return this.pathCache??=er(this.scanPaths(),()=>{this.pathCache=void 0}),this.pathCache}async scanPaths(){let e=[];for await(let{rowid:t,values:r}of this.sqlite.scan("Paths"))e.push(No(t,r));return e}async getPath(e){let t=await this.sqlite.byRowid("Paths",e);return t?No(e,t):void 0}pathsByHandle(){return this.pathMapCache??=er(this.paths().then(e=>new Map(e.map(t=>[t.handle,t]))),()=>{this.pathMapCache=void 0}),this.pathMapCache}async findPath(e){return(await this.paths()).filter(r=>r.name.sample===e.sample&&r.name.contig===e.contig&&r.name.haplotype===e.haplotype&&r.name.fragment<=e.fragment).sort((r,o)=>o.name.fragment-r.name.fragment)[0]}async pathsNamed(e){let t=Ve(We(e),0);return(await this.paths()).filter(r=>r.name.sample===t.sample&&r.name.contig===t.contig&&r.name.haplotype===t.haplotype).sort((r,o)=>r.name.fragment-o.name.fragment)}async hasPath(e){return(await this.pathsNamed(e)).length>0}pathLengths=new Map;pathLength(e){let t=this.pathLengths.get(e);return t||(t=this.walkPathLength(e),this.pathLengths.set(e,t),t.catch(()=>this.pathLengths.delete(e))),t}async walkPathLength(e){let t=this.hasHaplotypeIndex?await this.haplotypeLength(e):void 0;if(t===void 0){let r=await this.indexedPosition(e,Number.MAX_SAFE_INTEGER);if(!r){let i=await this.getPath(e);throw new Error(`${i?`The fragment of ${me(i.name)} at ${i.name.fragment}`:`Path ${e}`} has not been indexed for random access`)}let o=r.pathOffset,s=r.pos;for(;;){let i=await this.getRecord(s.node);if(!i)throw new Error(`Node ${s.node} does not exist in the graph`);o+=i.sequenceLen;let a=i.gbwt().lf(s.offset);if(!a||a.node===0)return o;s=a}}return t}async getPathFragments(e){let{start:t,end:r}=e;if(Number.isNaN(t)||Number.isNaN(r))throw new Error(`The window ${t}..${r} is not a number range`);let o=await this.pathsNamed(e.path);if(o.length===0)throw new Wt(Ve(We(e.path),0));if(r<=t)return[];let s=o.filter(f=>f.name.fragment<=t).slice(-1),i=o.filter(f=>f.name.fragment>t&&f.name.fragment<r);return(await Promise.all([...s,...i].map(async f=>({path:f,start:f.name.fragment,end:f.name.fragment+await this.pathLength(f.handle)})))).filter(f=>t<f.end)}async subgraphForFragment(e,t){let{sample:r,contig:o,haplotype:s}=e.path.name,i=Math.max(t.start,e.start),a=t.haplotypes??"all";try{let f=await Xn(this,{...t,path:{sample:r,contig:o,haplotype:s},start:i,end:Math.min(t.end,e.end)});return t.keep===void 0&&this.hasHaplotypeIndex&&(a==="all"||a==="distinct")&&await f.identifyPaths(),f}catch(f){throw f instanceof be&&f.walkedBp!==void 0?new be(f.limit,{windowBp:t.end-t.start,walkedBp:i-t.start+f.walkedBp}):f}}async getSubgraphs(e){let t=await this.getPathFragments(e);return(await Promise.allSettled(t.map(o=>this.subgraphForFragment(o,e)))).map(o=>{if(o.status==="rejected")throw o.reason;return o.value})}async getAlignments(e){return(await this.getSubgraphs(e)).flatMap(t=>t.alignments())}subgraphInInterval(e){return Xn(this,e)}subgraphAtOffset(e){return Ro(this,e)}subgraphAroundNodes(e){return Mo(this,e)}subgraphBetween(e){return Po(this,e)}fetchStats(){let e=({pager:t})=>({fetches:t.fetches,bytesFetched:t.bytesFetched});return{graph:e(this.sqlite),haplotypeIndex:this.index?e(this.index):void 0}}async graphName(){let e=new Map;for(let[r,o]of await this.tags())r.startsWith("gbz_")&&e.set(r.slice(4),o);let t={name:void 0,subgraph:new Map,translation:new Map};try{t=to(e)}catch{}return t}async hasChainLinks(){let e=await this.tag("chain_links");return e!==void 0&&Number(e)>0}get hasHaplotypeIndex(){return this.index!==void 0}get companion(){if(!this.index)throw new Error("no haplotype index was opened with this database");return this.index}async haplotypeSampleInterval(){let e=this.indexTags.get("haplotype_index_interval");return e===void 0?void 0:Number(e)}async haplotypeSampleGap(){let e=await this.haplotypeSampleInterval(),t=this.indexTags.get("haplotype_index_reference_interval");return e===void 0?void 0:Math.max(e,t===void 0?0:Number(t))}async haplotypeAnchorSpacing(){let e=this.index?.has("HaplotypeAnchors")?this.indexTags.get("haplotype_index_anchor_spacing"):void 0;return e===void 0?void 0:Number(e)}async haplotypeStrayOptions(){let e=r=>this.indexTags.get(`haplotype_index_stray_${r}`);if(!this.index?.has("HaplotypeBins")||e("format")!=="2")return;let t=e("snarls")==="modeled"&&e("chain_links")===(await this.tag("chain_links")??"0");return{context:Number(e("context")),bin:Number(e("bin")),bound:Number(e("bound")),snarlNodes:t?Number(e("snarl_nodes")):void 0}}async blobRows(e,t,r){let o=[],s=[];for await(let i of this.companion.indexScanFrom(e,t,r))s.push(Q(i[i.length-1],`${e} rowid`));s.length>1&&await this.companion.prefetchRows(e,[[Math.min(...s),Math.max(...s)+1]],!0);for(let i of s){let a=await this.companion.byRowid(e,i);a&&o.push(a)}return o}async haplotypeBinData(e,t,r){let o=[],s=[];for(let i of await this.blobRows("HaplotypeBins",[e,t],[e,r])){let a=Q(i[1],"HaplotypeBins.bin");Mi(He(i[3],"HaplotypeBins.nodes"),o),_i(a,He(i[4],"HaplotypeBins.strays"),s)}return{listed:Pi(o),strays:s}}async haplotypeAnchorsBetween(e,t,r){let o=[],s=[],i=()=>{let a=o[o.length-1];a&&ki(a.node,s,a.visits),s=[]};for(let a of await this.blobRows("HaplotypeAnchors",[e,t],[e,r])){let f=Q(a[1],"HaplotypeAnchors.anchor_offset");o[o.length-1]?.anchorOffset!==f&&(i(),o.push({anchorOffset:f,node:Q(a[3],"HaplotypeAnchors.node_handle"),pathOffset:Q(a[4],"HaplotypeAnchors.path_offset"),visits:[]})),s.push(He(a[5],"HaplotypeAnchors.visits"))}return i(),o}async haplotypeAnchor(e,t){let[r]=await this.haplotypeAnchorsBetween(e,t,t);return r&&{node:r.node,pathOffset:r.pathOffset}}haplotypeSamplesAtNode(e){return this.haplotypeSamplesInRange(e,e)}sampleFromRow(e){return{node:Q(e[0],"HaplotypeSamples.node_handle"),offset:Q(e[1],"HaplotypeSamples.node_offset"),pathHandle:Q(e[2],"HaplotypeSamples.path_handle"),orientation:Q(e[3],"HaplotypeSamples.orientation")===0?"forward":"reverse",pathOffset:Q(e[4],"HaplotypeSamples.path_offset")}}async haplotypeSamplesInRange(e,t){let r=[];for await(let o of this.companion.indexScanFrom("HaplotypeSamples",[e,0],[t,Number.MAX_SAFE_INTEGER]))r.push(this.sampleFromRow(o));return r}async haplotypeSampleAt(e,t){let r=await this.companion.indexSeekLE("HaplotypeSamples",[e,t]);return r?.[0]===e&&r[1]===t?this.sampleFromRow(r):void 0}overviewRows(){return this.overviewRowsCache??=er((async()=>{let e=[];for await(let{rowid:t,values:r}of this.companion.scan("HaplotypeOverviewRows"))e[t]={sample:ht(r[1],"HaplotypeOverviewRows.sample"),haplotype:Q(r[2],"HaplotypeOverviewRows.haplotype")};return e})(),()=>{this.overviewRowsCache=void 0}),this.overviewRowsCache}async overviewChunks(e,t,r,o,s){let i=new Map;for(let a of await this.blobRows(e,[t,r,o],[t,r,s])){let f=Q(a[2],`${e}.chunk`),c=i.get(f)??[];c.push(He(a[4],`${e} blob`)),i.set(f,c)}return new Map([...i].map(([a,f])=>[a,Ri(f)]))}async haplotypeOverview(e){let t=u=>this.indexTags.get(`haplotype_index_overview_${u}`);if(!this.index?.has("HaplotypeOverviewClasses")||t("format")!=="1")return;let r=Number(t("bin")),o=Number(t("chunk")),s=Number(t("levels")),i=Math.max(0,Math.min(Math.floor(e.level??0)||0,s-1));if(e.level===void 0&&e.bpPerPixel!==void 0)for(;i+1<s&&r*4**(i+1)<=e.bpPerPixel;)i+=1;let a=r*4**i,[f,c]=await Promise.all([this.getPathFragments(e),this.overviewRows()]),l=Math.ceil(c.length/2),h=[],d=[];for(let u of f){let m=u.end-u.start,w=Math.max(e.start,u.start)-u.start,y=Math.min(e.end,u.end)-u.start,S=Math.floor(w/a),g=Math.floor((y-1)/a),b=Math.floor(S/o),x=Math.floor(g/o),[E,A]=await Promise.all([this.overviewChunks("HaplotypeOverviewBins",u.path.handle,i,b,x),this.overviewChunks("HaplotypeOverviewClasses",u.path.handle,i,b,x)]);for(let _=b;_<=x;_++){let T=new Ye(E.get(_)??new Uint8Array),$=A.get(_)??new Uint8Array;for(let C=_*o;!T.done;C++){let N=Array.from({length:7},()=>T.next());if(C<S||C>g)continue;h.push({start:u.start+C*a,end:u.start+Math.min((C+1)*a,m),classes:[N[0],N[1],N[2],N[3]],excursions:N[4],variants:N[5],longestExcursion:N[6]});let P=(C-_*o)*l;d.push($.subarray(P,P+l))}}}if(h.length===0)return;let p=new Uint8Array(h.length*c.length);return d.forEach((u,m)=>{for(let w=0;w<c.length;w++)p[m*c.length+w]=(u[w>>1]??0)>>4*(w%2)&15}),{level:i,bin:a,haplotypes:c,bins:h,cells:p}}async haplotypeLength(e){let t=await this.companion.byRowid("HaplotypeLengths",e);return t?Q(t[1],"HaplotypeLengths.length"):void 0}async indexedRow(e){let t=await this.sqlite.byRowid("ReferenceIndex",e);if(!t)throw new Error("ReferenceIndex row referenced by its index is missing");return{pathOffset:Q(t[1],"ReferenceIndex.path_offset"),pos:{node:Q(t[2],"ReferenceIndex.node_handle"),offset:Q(t[3],"ReferenceIndex.node_offset")}}}async indexedRowid(e,t){let r=await this.sqlite.indexSeekLE("ReferenceIndex",[e,t]);return r?.[0]===e?Q(r[2],"ReferenceIndex rowid"):void 0}async indexedPosition(e,t){let r=await this.indexedRowid(e,t);return r===void 0?void 0:this.indexedRow(r)}async indexedPositionsBetween(e,t,r){let[o,s]=await Promise.all([this.indexedRowid(e,t),this.indexedRowid(e,r)]),i=[];if(o!==void 0&&s!==void 0){await this.sqlite.prefetchRows("ReferenceIndex",[[o,s+1]]);for(let a=o;a<=s;a++)i.push(await this.indexedRow(a))}return i}};var Ir=ce(Ln(),1),wt=ce(ot(),1),En=ce(Br(),1),Ns=ce(qs(),1);function Yt(n){let e=/\.gbz\.db$/i;return e.test(n)?n.replace(e,".haplotype-index.db"):void 0}var Lo=ce(Br(),1);function Oi(n){return qr(n)&&Yt(Hr(n))?Dr(n,e=>Yt(e)):void 0}function Ni(n){return n instanceof Error&&(/\bHTTP 40[34]\b/.test(n.message)||n.code==="ENOENT")}async function Fo(n,e){let t=Oi(n);if(!t)return{};try{return await(0,Lo.openLocation)(t,e).stat(),{location:t}}catch(r){return Ni(r)?{}:{unreadable:String(r)}}}var Bo=ce(Ln(),1),Ti=5e3,Li=50*2**20,rr=class extends Error{constructor(t){super(`this GAF is ${(t/2**20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`);this.name="UnindexedGafTooLargeError"}};function Fi(n,e){if(n.length<=e)return n;let t=n.length/e;return Array.from({length:e},(r,o)=>n[Math.floor(o*t)])}var $o=(n,e)=>n.path.some(t=>e.has(t.name)),Kt=class{constructor(e,t){this.file=e;this.tabix=t;this.whole=(0,Bo.cachedSetup)({setup:async()=>{let{size:e}=await this.file.stat();if(e>Li)throw new rr(e);let t=await this.file.readFile(),r=new TextDecoder().decode(t[0]===31&&t[1]===139?await Gr(t):t);return $n(r)}})}async readIndexed(e,t,r){let o=1/0,s=-1/0;for(let a of t){let f=Number(a);Number.isInteger(f)&&(o=Math.min(o,f),s=Math.max(s,f))}let i=[];return o<=s&&await e.getLines("{node}",o,s+1,{signal:r,lineCallback:a=>{let f=Fn(a);f&&$o(f,t)&&i.push(f)}}),i}async readsOver(e,{signal:t}={}){let r=this.tabix?await this.readIndexed(this.tabix,e,t):(await this.whole({signal:t})).filter(o=>$o(o,e));return{records:Fi(r,Ti),total:r.length}}};var Ps=ce(Ln(),1),_s=ce(ot(),1);var or=function(n,e){return or=Object.setPrototypeOf||{__proto__:[]}instanceof Array&&function(t,r){t.__proto__=r}||function(t,r){for(var o in r)Object.prototype.hasOwnProperty.call(r,o)&&(t[o]=r[o])},or(n,e)};function pt(n,e){if(typeof e!="function"&&e!==null)throw new TypeError("Class extends value "+String(e)+" is not a constructor or null");or(n,e);function t(){this.constructor=n}n.prototype=e===null?Object.create(e):(t.prototype=e.prototype,new t)}function Ho(n,e,t,r){function o(s){return s instanceof t?s:new t(function(i){i(s)})}return new(t||(t=Promise))(function(s,i){function a(l){try{c(r.next(l))}catch(h){i(h)}}function f(l){try{c(r.throw(l))}catch(h){i(h)}}function c(l){l.done?s(l.value):o(l.value).then(a,f)}c((r=r.apply(n,e||[])).next())})}function Xt(n,e){var t={label:0,sent:function(){if(s[0]&1)throw s[1];return s[1]},trys:[],ops:[]},r,o,s,i=Object.create((typeof Iterator=="function"?Iterator:Object).prototype);return i.next=a(0),i.throw=a(1),i.return=a(2),typeof Symbol=="function"&&(i[Symbol.iterator]=function(){return this}),i;function a(c){return function(l){return f([c,l])}}function f(c){if(r)throw new TypeError("Generator is already executing.");for(;i&&(i=0,c[0]&&(t=0)),t;)try{if(r=1,o&&(s=c[0]&2?o.return:c[0]?o.throw||((s=o.return)&&s.call(o),0):o.next)&&!(s=s.call(o,c[1])).done)return s;switch(o=0,s&&(c=[c[0]&2,s.value]),c[0]){case 0:case 1:s=c;break;case 4:return t.label++,{value:c[1],done:!1};case 5:t.label++,o=c[1],c=[0];continue;case 7:c=t.ops.pop(),t.trys.pop();continue;default:if(s=t.trys,!(s=s.length>0&&s[s.length-1])&&(c[0]===6||c[0]===2)){t=0;continue}if(c[0]===3&&(!s||c[1]>s[0]&&c[1]<s[3])){t.label=c[1];break}if(c[0]===6&&t.label<s[1]){t.label=s[1],s=c;break}if(s&&t.label<s[2]){t.label=s[2],t.ops.push(c);break}s[2]&&t.ops.pop(),t.trys.pop();continue}c=e.call(n,t)}catch(l){c=[6,l],o=0}finally{r=s=0}if(c[0]&5)throw c[1];return{value:c[0]?c[1]:void 0,done:!0}}}function qe(n){var e=typeof Symbol=="function"&&Symbol.iterator,t=e&&n[e],r=0;if(t)return t.call(n);if(n&&typeof n.length=="number")return{next:function(){return n&&r>=n.length&&(n=void 0),{value:n&&n[r++],done:!n}}};throw new TypeError(e?"Object is not iterable.":"Symbol.iterator is not defined.")}function Ke(n,e){var t=typeof Symbol=="function"&&n[Symbol.iterator];if(!t)return n;var r=t.call(n),o,s=[],i;try{for(;(e===void 0||e-- >0)&&!(o=r.next()).done;)s.push(o.value)}catch(a){i={error:a}}finally{try{o&&!o.done&&(t=r.return)&&t.call(r)}finally{if(i)throw i.error}}return s}function Xe(n,e,t){if(t||arguments.length===2)for(var r=0,o=e.length,s;r<o;r++)(s||!(r in e))&&(s||(s=Array.prototype.slice.call(e,0,r)),s[r]=e[r]);return n.concat(s||Array.prototype.slice.call(e))}function De(n){return this instanceof De?(this.v=n,this):new De(n)}function qo(n,e,t){if(!Symbol.asyncIterator)throw new TypeError("Symbol.asyncIterator is not defined.");var r=t.apply(n,e||[]),o,s=[];return o=Object.create((typeof AsyncIterator=="function"?AsyncIterator:Object).prototype),a("next"),a("throw"),a("return",i),o[Symbol.asyncIterator]=function(){return this},o;function i(p){return function(u){return Promise.resolve(u).then(p,h)}}function a(p,u){r[p]&&(o[p]=function(m){return new Promise(function(w,y){s.push([p,m,w,y])>1||f(p,m)})},u&&(o[p]=u(o[p])))}function f(p,u){try{c(r[p](u))}catch(m){d(s[0][3],m)}}function c(p){p.value instanceof De?Promise.resolve(p.value.v).then(l,h):d(s[0][2],p)}function l(p){f("next",p)}function h(p){f("throw",p)}function d(p,u){p(u),s.shift(),s.length&&f(s[0][0],s[0][1])}}function Do(n){if(!Symbol.asyncIterator)throw new TypeError("Symbol.asyncIterator is not defined.");var e=n[Symbol.asyncIterator],t;return e?e.call(n):(n=typeof qe=="function"?qe(n):n[Symbol.iterator](),t={},r("next"),r("throw"),r("return"),t[Symbol.asyncIterator]=function(){return this},t);function r(s){t[s]=n[s]&&function(i){return new Promise(function(a,f){i=n[s](i),o(a,f,i.done,i.value)})}}function o(s,i,a,f){Promise.resolve(f).then(function(c){s({value:c,done:a})},i)}}function q(n){return typeof n=="function"}function Go(n){var e=function(r){Error.call(r),r.stack=new Error().stack},t=n(e);return t.prototype=Object.create(Error.prototype),t.prototype.constructor=t,t}var Zt=Go(function(n){return function(t){n(this),this.message=t?t.length+` errors occurred during unsubscription:
 `+t.map(function(r,o){return o+1+") "+r.toString()}).join(`
   `):"",this.name="UnsubscriptionError",this.errors=t}});function sr(n,e){if(n){var t=n.indexOf(e);0<=t&&n.splice(t,1)}}var Jt=(function(){function n(e){this.initialTeardown=e,this.closed=!1,this._parentage=null,this._finalizers=null}return n.prototype.unsubscribe=function(){var e,t,r,o,s;if(!this.closed){this.closed=!0;var i=this._parentage;if(i)if(this._parentage=null,Array.isArray(i))try{for(var a=qe(i),f=a.next();!f.done;f=a.next()){var c=f.value;c.remove(this)}}catch(m){e={error:m}}finally{try{f&&!f.done&&(t=a.return)&&t.call(a)}finally{if(e)throw e.error}}else i.remove(this);var l=this.initialTeardown;if(q(l))try{l()}catch(m){s=m instanceof Zt?m.errors:[m]}var h=this._finalizers;if(h){this._finalizers=null;try{for(var d=qe(h),p=d.next();!p.done;p=d.next()){var u=p.value;try{zo(u)}catch(m){s=s??[],m instanceof Zt?s=Xe(Xe([],Ke(s)),Ke(m.errors)):s.push(m)}}}catch(m){r={error:m}}finally{try{p&&!p.done&&(o=d.return)&&o.call(d)}finally{if(r)throw r.error}}}if(s)throw new Zt(s)}},n.prototype.add=function(e){var t;if(e&&e!==this)if(this.closed)zo(e);else{if(e instanceof n){if(e.closed||e._hasParent(this))return;e._addParent(this)}(this._finalizers=(t=this._finalizers)!==null&&t!==void 0?t:[]).push(e)}},n.prototype._hasParent=function(e){var t=this._parentage;return t===e||Array.isArray(t)&&t.includes(e)},n.prototype._addParent=function(e){var t=this._parentage;this._parentage=Array.isArray(t)?(t.push(e),t):t?[t,e]:e},n.prototype._removeParent=function(e){var t=this._parentage;t===e?this._parentage=null:Array.isArray(t)&&sr(t,e)},n.prototype.remove=function(e){var t=this._finalizers;t&&sr(t,e),e instanceof n&&e._removeParent(this)},n.EMPTY=(function(){var e=new n;return e.closed=!0,e})(),n})();var Kf=Jt.EMPTY;function en(n){return n instanceof Jt||n&&"closed"in n&&q(n.remove)&&q(n.add)&&q(n.unsubscribe)}function zo(n){q(n)?n():n.unsubscribe()}var Se={onUnhandledError:null,onStoppedNotification:null,Promise:void 0,useDeprecatedSynchronousErrorHandling:!1,useDeprecatedNextContext:!1};var Ze={setTimeout:function(n,e){for(var t=[],r=2;r<arguments.length;r++)t[r-2]=arguments[r];var o=Ze.delegate;return o?.setTimeout?o.setTimeout.apply(o,Xe([n,e],Ke(t))):setTimeout.apply(void 0,Xe([n,e],Ke(t)))},clearTimeout:function(n){var e=Ze.delegate;return(e?.clearTimeout||clearTimeout)(n)},delegate:void 0};function tn(n){Ze.setTimeout(function(){var e=Se.onUnhandledError;if(e)e(n);else throw n})}function ir(){}var jo=(function(){return ar("C",void 0,void 0)})();function Uo(n){return ar("E",void 0,n)}function Wo(n){return ar("N",n,void 0)}function ar(n,e,t){return{kind:n,value:e,error:t}}var Ge=null;function Vo(n){if(Se.useDeprecatedSynchronousErrorHandling){var e=!Ge;if(e&&(Ge={errorThrown:!1,error:null}),n(),e){var t=Ge,r=t.errorThrown,o=t.error;if(Ge=null,r)throw o}}else n()}function Qo(n){Se.useDeprecatedSynchronousErrorHandling&&Ge&&(Ge.errorThrown=!0,Ge.error=n)}var ut=(function(n){pt(e,n);function e(t){var r=n.call(this)||this;return r.isStopped=!1,t?(r.destination=t,en(t)&&t.add(r)):r.destination=qi,r}return e.create=function(t,r,o){return new rn(t,r,o)},e.prototype.next=function(t){this.isStopped?cr(Wo(t),this):this._next(t)},e.prototype.error=function(t){this.isStopped?cr(Uo(t),this):(this.isStopped=!0,this._error(t))},e.prototype.complete=function(){this.isStopped?cr(jo,this):(this.isStopped=!0,this._complete())},e.prototype.unsubscribe=function(){this.closed||(this.isStopped=!0,n.prototype.unsubscribe.call(this),this.destination=null)},e.prototype._next=function(t){this.destination.next(t)},e.prototype._error=function(t){try{this.destination.error(t)}finally{this.unsubscribe()}},e.prototype._complete=function(){try{this.destination.complete()}finally{this.unsubscribe()}},e})(Jt);var $i=Function.prototype.bind;function fr(n,e){return $i.call(n,e)}var Bi=(function(){function n(e){this.partialObserver=e}return n.prototype.next=function(e){var t=this.partialObserver;if(t.next)try{t.next(e)}catch(r){nn(r)}},n.prototype.error=function(e){var t=this.partialObserver;if(t.error)try{t.error(e)}catch(r){nn(r)}else nn(e)},n.prototype.complete=function(){var e=this.partialObserver;if(e.complete)try{e.complete()}catch(t){nn(t)}},n})(),rn=(function(n){pt(e,n);function e(t,r,o){var s=n.call(this)||this,i;if(q(t)||!t)i={next:t??void 0,error:r??void 0,complete:o??void 0};else{var a;s&&Se.useDeprecatedNextContext?(a=Object.create(t),a.unsubscribe=function(){return s.unsubscribe()},i={next:t.next&&fr(t.next,a),error:t.error&&fr(t.error,a),complete:t.complete&&fr(t.complete,a)}):i=t}return s.destination=new Bi(i),s}return e})(ut);function nn(n){Se.useDeprecatedSynchronousErrorHandling?Qo(n):tn(n)}function Hi(n){throw n}function cr(n,e){var t=Se.onStoppedNotification;t&&Ze.setTimeout(function(){return t(n,e)})}var qi={closed:!0,next:ir,error:Hi,complete:ir};var Je=(function(){return typeof Symbol=="function"&&Symbol.observable||"@@observable"})();function Yo(n){return n}function Ko(n){return n.length===0?Yo:n.length===1?n[0]:function(t){return n.reduce(function(r,o){return o(r)},t)}}var he=(function(){function n(e){e&&(this._subscribe=e)}return n.prototype.lift=function(e){var t=new n;return t.source=this,t.operator=e,t},n.prototype.subscribe=function(e,t,r){var o=this,s=Gi(e)?e:new rn(e,t,r);return Vo(function(){var i=o,a=i.operator,f=i.source;s.add(a?a.call(s,f):f?o._subscribe(s):o._trySubscribe(s))}),s},n.prototype._trySubscribe=function(e){try{return this._subscribe(e)}catch(t){e.error(t)}},n.prototype.forEach=function(e,t){var r=this;return t=Xo(t),new t(function(o,s){var i=new rn({next:function(a){try{e(a)}catch(f){s(f),i.unsubscribe()}},error:s,complete:o});r.subscribe(i)})},n.prototype._subscribe=function(e){var t;return(t=this.source)===null||t===void 0?void 0:t.subscribe(e)},n.prototype[Je]=function(){return this},n.prototype.pipe=function(){for(var e=[],t=0;t<arguments.length;t++)e[t]=arguments[t];return Ko(e)(this)},n.prototype.toPromise=function(e){var t=this;return e=Xo(e),new e(function(r,o){var s;t.subscribe(function(i){return s=i},function(i){return o(i)},function(){return r(s)})})},n.create=function(e){return new n(e)},n})();function Xo(n){var e;return(e=n??Se.Promise)!==null&&e!==void 0?e:Promise}function Di(n){return n&&q(n.next)&&q(n.error)&&q(n.complete)}function Gi(n){return n&&n instanceof ut||Di(n)&&en(n)}function zi(n){return q(n?.lift)}function ge(n){return function(e){if(zi(e))return e.lift(function(t){try{return n(t,this)}catch(r){this.error(r)}});throw new TypeError("Unable to lift unknown Observable type")}}function Pe(n,e,t,r,o){return new ji(n,e,t,r,o)}var ji=(function(n){pt(e,n);function e(t,r,o,s,i,a){var f=n.call(this,t)||this;return f.onFinalize=i,f.shouldUnsubscribe=a,f._next=r?function(c){try{r(c)}catch(l){t.error(l)}}:n.prototype._next,f._error=s?function(c){try{s(c)}catch(l){t.error(l)}finally{this.unsubscribe()}}:n.prototype._error,f._complete=o?function(){try{o()}catch(c){t.error(c)}finally{this.unsubscribe()}}:n.prototype._complete,f}return e.prototype.unsubscribe=function(){var t;if(!this.shouldUnsubscribe||this.shouldUnsubscribe()){var r=this.closed;n.prototype.unsubscribe.call(this),!r&&((t=this.onFinalize)===null||t===void 0||t.call(this))}},e})(ut);var on=(function(n){return n&&typeof n.length=="number"&&typeof n!="function"});function sn(n){return q(n?.then)}function an(n){return q(n[Je])}function fn(n){return Symbol.asyncIterator&&q(n?.[Symbol.asyncIterator])}function cn(n){return new TypeError("You provided "+(n!==null&&typeof n=="object"?"an invalid object":"'"+n+"'")+" where a stream was expected. You can provide an Observable, Promise, ReadableStream, Array, AsyncIterable, or Iterable.")}function Ui(){return typeof Symbol!="function"||!Symbol.iterator?"@@iterator":Symbol.iterator}var ln=Ui();function hn(n){return q(n?.[ln])}function dn(n){return qo(this,arguments,function(){var t,r,o,s;return Xt(this,function(i){switch(i.label){case 0:t=n.getReader(),i.label=1;case 1:i.trys.push([1,,9,10]),i.label=2;case 2:return[4,De(t.read())];case 3:return r=i.sent(),o=r.value,s=r.done,s?[4,De(void 0)]:[3,5];case 4:return[2,i.sent()];case 5:return[4,De(o)];case 6:return[4,i.sent()];case 7:return i.sent(),[3,2];case 8:return[3,10];case 9:return t.releaseLock(),[7];case 10:return[2]}})})}function pn(n){return q(n?.getReader)}function Ae(n){if(n instanceof he)return n;if(n!=null){if(an(n))return Wi(n);if(on(n))return Vi(n);if(sn(n))return Qi(n);if(fn(n))return Zo(n);if(hn(n))return Yi(n);if(pn(n))return Ki(n)}throw cn(n)}function Wi(n){return new he(function(e){var t=n[Je]();if(q(t.subscribe))return t.subscribe(e);throw new TypeError("Provided object does not correctly implement Symbol.observable")})}function Vi(n){return new he(function(e){for(var t=0;t<n.length&&!e.closed;t++)e.next(n[t]);e.complete()})}function Qi(n){return new he(function(e){n.then(function(t){e.closed||(e.next(t),e.complete())},function(t){return e.error(t)}).then(null,tn)})}function Yi(n){return new he(function(e){var t,r;try{for(var o=qe(n),s=o.next();!s.done;s=o.next()){var i=s.value;if(e.next(i),e.closed)return}}catch(a){t={error:a}}finally{try{s&&!s.done&&(r=o.return)&&r.call(o)}finally{if(t)throw t.error}}e.complete()})}function Zo(n){return new he(function(e){Xi(n,e).catch(function(t){return e.error(t)})})}function Ki(n){return Zo(dn(n))}function Xi(n,e){var t,r,o,s;return Ho(this,void 0,void 0,function(){var i,a;return Xt(this,function(f){switch(f.label){case 0:f.trys.push([0,5,6,11]),t=Do(n),f.label=1;case 1:return[4,t.next()];case 2:if(r=f.sent(),!!r.done)return[3,4];if(i=r.value,e.next(i),e.closed)return[2];f.label=3;case 3:return[3,1];case 4:return[3,11];case 5:return a=f.sent(),o={error:a},[3,11];case 6:return f.trys.push([6,,9,10]),r&&!r.done&&(s=t.return)?[4,s.call(t)]:[3,8];case 7:f.sent(),f.label=8;case 8:return[3,10];case 9:if(o)throw o.error;return[7];case 10:return[7];case 11:return e.complete(),[2]}})})}function we(n,e,t,r,o){r===void 0&&(r=0),o===void 0&&(o=!1);var s=e.schedule(function(){t(),o?n.add(this.schedule(null,r)):this.unsubscribe()},r);if(n.add(s),!o)return s}function un(n,e){return e===void 0&&(e=0),ge(function(t,r){t.subscribe(Pe(r,function(o){return we(r,n,function(){return r.next(o)},e)},function(){return we(r,n,function(){return r.complete()},e)},function(o){return we(r,n,function(){return r.error(o)},e)}))})}function mn(n,e){return e===void 0&&(e=0),ge(function(t,r){r.add(n.schedule(function(){return t.subscribe(r)},e))})}function Jo(n,e){return Ae(n).pipe(mn(e),un(e))}function es(n,e){return Ae(n).pipe(mn(e),un(e))}function ts(n,e){return new he(function(t){var r=0;return e.schedule(function(){r===n.length?t.complete():(t.next(n[r++]),t.closed||this.schedule())})})}function ns(n,e){return new he(function(t){var r;return we(t,e,function(){r=n[ln](),we(t,e,function(){var o,s,i;try{o=r.next(),s=o.value,i=o.done}catch(a){t.error(a);return}i?t.complete():t.next(s)},0,!0)}),function(){return q(r?.return)&&r.return()}})}function gn(n,e){if(!n)throw new Error("Iterable cannot be null");return new he(function(t){we(t,e,function(){var r=n[Symbol.asyncIterator]();we(t,e,function(){r.next().then(function(o){o.done?t.complete():t.next(o.value)})},0,!0)})})}function rs(n,e){return gn(dn(n),e)}function os(n,e){if(n!=null){if(an(n))return Jo(n,e);if(on(n))return ts(n,e);if(sn(n))return es(n,e);if(fn(n))return gn(n,e);if(hn(n))return ns(n,e);if(pn(n))return rs(n,e)}throw cn(n)}function lr(n,e){return e?os(n,e):Ae(n)}function mt(n,e){return ge(function(t,r){var o=0;t.subscribe(Pe(r,function(s){r.next(n.call(e,s,o++))}))})}function ss(n,e,t,r,o,s,i,a){var f=[],c=0,l=0,h=!1,d=function(){h&&!f.length&&!c&&e.complete()},p=function(m){return c<r?u(m):f.push(m)},u=function(m){s&&e.next(m),c++;var w=!1;Ae(t(m,l++)).subscribe(Pe(e,function(y){o?.(y),s?p(y):e.next(y)},function(){w=!0},void 0,function(){if(w)try{c--;for(var y=function(){var S=f.shift();i?we(e,i,function(){return u(S)}):u(S)};f.length&&c<r;)y();d()}catch(S){e.error(S)}}))};return n.subscribe(Pe(e,p,function(){h=!0,d()})),function(){a?.()}}function et(n,e,t){return t===void 0&&(t=1/0),q(e)?et(function(r,o){return mt(function(s,i){return e(r,s,o,i)})(Ae(n(r,o)))},t):(typeof e=="number"&&(t=e),ge(function(r,o){return ss(r,o,n,t)}))}function is(n,e,t,r,o){return function(s,i){var a=t,f=e,c=0;s.subscribe(Pe(i,function(l){var h=c++;f=a?n(f,l,h):(a=!0,l),r&&i.next(f)},o&&(function(){a&&i.next(f),i.complete()})))}}function as(n,e){return ge(is(n,e,arguments.length>=2,!1,!0))}var Zi=function(n,e){return n.push(e),n};function wn(){return ge(function(n,e){as(Zi,[])(n).subscribe(e)})}function fs(n){let e=[],t=0,r;for(let o=0,s=n.length;o<s;o++){let i=n.charCodeAt(o);if(i>=48&&i<=57)t=t*10+i-48;else if(i===58)r=t,t=0;else{let a=n[o];a==="M"||a==="="||a==="X"?e.push({own:r===void 0?t:r,mate:t,op:"M"}):a==="I"?e.push({own:0,mate:t,op:a}):(a==="D"||a==="N")&&e.push({own:t,mate:0,op:a}),r=void 0,t=0}}return e}function pr(n){let e="";for(let{own:t,mate:r,op:o}of fs(n))e+=o==="M"?t===0?`${r}I`:r===0?`${t}D`:`${t}M`:`${o==="I"?r:t}${o}`;return e}var hr=2**28-1;function dr(n,e,t){for(let r=e;r>0;r-=hr)n.push((Math.min(r,hr)<<4|t)>>>0)}function Ji(n,e,t){if(e===t)dr(n,e,0);else{let r=Math.ceil(Math.max(e,t)/hr);for(let o=0;o<r;o++){let s=Math.floor(e*(o+1)/r)-Math.floor(e*o/r),i=Math.floor(t*(o+1)/r)-Math.floor(t*o/r);n.push((s<<4|9)>>>0,(i<<4|9)>>>0)}}}function ur(n){let e=[];for(let{own:t,mate:r,op:o}of fs(n))o==="M"?Ji(e,t,r):o==="I"?dr(e,r,1):dr(e,t,o==="N"?3:2);return Uint32Array.from(e)}function ea(n){return n>=48&&n<=57}function ta(n){return n!==void 0&&/[A-Za-z]/.test(n)}function cs(n,e){let t=e;for(;t<n.length&&ta(n[t]);)t++;return t}function ls(n,e){let t=e,r=0;for(;t<n.length&&ea(n.charCodeAt(t));)r=r*10+(n.charCodeAt(t)-48),t++;return{value:r,next:t}}function ms(n,e){let t=0;for(;t<n.length;){let r=n[t];if(r===":"){let{value:o,next:s}=ls(n,t+1);e(":",o,o,t+1,s),t=s}else if(r==="="){let o=cs(n,t+1),s=o-t-1;e("=",s,s,t+1,o),t=o}else if(r==="*")e("*",1,1,t+1,Math.min(t+3,n.length)),t+=3;else if(r==="+"||r==="-"){let o=cs(n,t+1),s=o-t-1;e(r,r==="-"?s:0,r==="+"?s:0,t+1,o),t=o}else if(r==="~"){let{value:o,next:s}=ls(n,t+3),i=Math.min(s+2,n.length);e("~",o,0,t+1,i),t=i}else t++}}function mr(n,e,t,r){let o=t??Number.NEGATIVE_INFINITY,s=r??Number.POSITIVE_INFINITY,i=0;ms(n,(a,f,c,l,h)=>{if(a==="*")i>=o&&i<s&&e(88,i,1,n[l+1]??"",-1,0,0);else if(a==="+"){if(i>=o&&i<=s){let d=n.slice(l,h);e(73,i,c,d,-1,0,c)}}else(a==="-"||a==="~")&&i<s&&i+f>o&&e(a==="-"?68:78,i,f,"",-1,0,0);i+=f})}function gs(n,e,t,r){let o=0,s=0,i=[],a=t&&e;for(let f=0,c=n.length;f<c;f++){let l=n[f],h=l>>>4,d=l&15;if(d===0||d===7){if(a)for(let p=0;p<h;p++)(e.charCodeAt(s+p)|32)!==(t.charCodeAt(o+p)|32)&&i.push({start:o+p,type:"mismatch",base:e[s+p],altbase:t[o+p],length:1});s+=h,o+=h}else if(d===1)i.push({start:o,type:"insertion",insertlen:h,insertedBases:e?.slice(s,s+h),length:0}),s+=h;else if(d===2)i.push({start:o,type:"deletion",length:h}),o+=h;else if(d===3)i.push({start:o,type:"skip",length:h}),o+=h;else if(d===8){for(let p=0;p<h;p++)i.push({start:o+p,type:"mismatch",base:e?.[s+p]||"X",qual:r?.[s+p],length:1});s+=h,o+=h}else d===5?i.push({start:o,type:"hardclip",cliplen:h,length:1}):d===4&&(i.push({start:o,type:"softclip",cliplen:h,length:1}),s+=h)}return i}function ws(n,e,t,r,o){if(!e)return[];let s=[],i=e.length,a=r.length,f=o!==void 0,c=t.length,l=!1;for(let S=0;S<c;S++)if(t[S].type==="skip"){l=!0;break}let h=0,d=0,p=0,u=0,m=0,w=0,y=n.length;for(;w<y;){let S=n.charCodeAt(w);if(S>=48&&S<=57){let g=0;for(;w<y;){let b=n.charCodeAt(w);if(b>=48&&b<=57)g=g*10+(b-48),w++;else break}h+=g}else if(S===94)for(w++;w<y&&n.charCodeAt(w)>=65;)w++,h++;else if(S>=65){let g=n[w];if(w++,l&&c>0)for(let _=m;_<c;_++){let T=t[_];T.type==="skip"&&h>=T.start&&(h+=T.length,m=_+1)}let b=p,x=u;for(let _=d;_<i&&x<=h;_++,d=_){let T=e[_],$=T>>>4,C=T&15;C===4||C===1?b+=$:C===2||C===6||C===3?x+=$:C!==5&&(b+=$,x+=$)}p=b,u=x;let E=b-(x-h),A=E<a?r[E]:"X";s.push({start:h,base:A,qual:f?o[E]:void 0,altbase:g,length:1,type:"mismatch"}),h++}else w++}return s}var xs={77:0,73:1,68:2,78:3,83:4,72:5,80:6,61:7,88:8};function ys(n=""){let e=0,t=[];for(let r=0,o=n.length;r<o;r++){let s=n.charCodeAt(r);if(s>=48&&s<=57)e=e*10+(s-48);else{let i=xs[s];t.push(e<<4|i),e=0}}return t}function xr(n=""){let e=0;for(let s=0,i=n.length;s<i;s++){let a=n.charCodeAt(s);(a<48||a>57)&&e++}let t=new Uint32Array(e),r=0,o=0;for(let s=0,i=n.length;s<i;s++){let a=n.charCodeAt(s);a>=48&&a<=57?r=r*10+(a-48):(t[o++]=r<<4|xs[a],r=0)}return t}function vn(n,e,t,r,o){let s=ys(n),i=n?gs(s,t,r,o):[];return e&&t?i.concat(ws(e,s,i,t,o)):i}var oa=397,sa=387,ia=385;function bs(n){return(1<<n&oa)!==0}function Ss(n){return(1<<n&sa)!==0}function vs(n){return(1<<n&ia)!==0}function yr(n,e,t,r,o,s,i){let a=o===-1?-1:1,f=e,c=o===-1?r:t,l=[],h=1/0,d=-1/0,p=1/0,u=-1/0,m=(w,y)=>{p=Math.min(p,w,y),u=Math.max(u,w,y)};for(let w=0;w<n.length;w++){let y=n[w],S=y>>>4,g=y&15,b=g===9,x=b||bs(g)?S:0,E=b?n[++w]>>>4:Ss(g)?S:0,A=f+x,_=c+E*a,T=f,$=A;if($>=s&&T<=i)if(x>0){let C=Math.max(T,s),N=Math.min($,i);if(N>C)if(h=Math.min(h,C),d=Math.max(d,N),b){let P=E/S,U=N-C,Y=Math.round(U*P),I=Math.round(c+(C-f)*P*a);l.push(U<<4|9,Y<<4|9),m(I,I+Y*a)}else l.push(N-C<<4|g),vs(g)?m(c+(C-f)*a,c+(N-f)*a):m(c,c)}else E>0&&(b?l.push(y,n[w]):l.push(y),h=Math.min(h,f),d=Math.max(d,f),m(c,_));if(f=A,c=_,f>i)break}if(l.length!==0)return{start:h,end:d,mateStart:p,mateEnd:u,cigar:Uint32Array.from(l)}}function aa(n){return n===1||n===2||n===3}function br(n,e,t,r,o,s){let i=o===-1?-1:1,a=[],f=e,c=o===-1?r:t,l,h=!1,d=()=>{l!==void 0&&h&&l.qHi>l.qLo&&a.push({start:l.qLo,end:l.qHi,mateStart:l.tLo,mateEnd:l.tHi,cigar:Uint32Array.from(l.ops)}),l=void 0,h=!1};for(let p=0;p<n.length;p++){let u=n[p],m=u>>>4,w=u&15,y=w===9,S=y?n[++p]:void 0,g=y||bs(w)?m:0,b=S!==void 0?S>>>4:Ss(w)?m:0,x=c+b*i;aa(w)&&m>=s?d():(g>0||b>0)&&(l===void 0&&(l={qLo:f,qHi:f,tLo:c,tHi:c,ops:[]}),l.qHi=f+g,l.tLo=Math.min(l.tLo,c,x),l.tHi=Math.max(l.tHi,c,x),l.ops.push(u),S!==void 0&&l.ops.push(S),h=h||y||vs(w)),f+=g,c=x}return d(),a}function Is(n){let e=n.get("CIGAR");return typeof e=="string"?e:void 0}function Es(n){let e=n.get("coarseCigar");return typeof e=="string"?e:void 0}function Sr(n){let e=Is(n),t=e===void 0?Es(n):void 0;return e!==void 0?xr(e):t!==void 0?ur(t):void 0}var fa=ce(ot(),1),ca=ce(Cs(),1);var la=ce(ot(),1);var ha=ce(Ds(),1);var Rs=ce(ot(),1),Te=class extends Rs.SimpleFeature{get(e){return e==="mismatches"?vn(this.walkableCigar):e==="clipLengthAtStartOfRead"?this.clipLengthAtStartOfRead:e==="name"?super.get("name")??this.mate?.refName:super.get(e)}get mate(){return super.get("mate")}get walkableCigar(){let e=super.get("CIGAR"),t=super.get("coarseCigar");return typeof e=="string"?e:typeof t=="string"?pr(t):void 0}get clipLengthAtStartOfRead(){return this.mate?.start??0}forEachMismatch(e,t){let r=this.get("start"),o=t?.start===void 0?void 0:t.start-r,s=t?.end===void 0?void 0:t.end-r,i=this.get("cs");if(i)mr(i,e,o,s);else{let a=o??Number.NEGATIVE_INFINITY,f=s??Number.POSITIVE_INFINITY;for(let c of vn(this.walkableCigar))(c.type==="deletion"||c.type==="skip"?c.start<f&&c.start+c.length>a:c.start>=a&&c.start<=f)&&(c.type==="mismatch"?e(88,c.start,c.length,c.base,c.qual??-1,0,0):c.type==="insertion"?e(73,c.start,c.length,c.insertedBases??"",-1,0,c.insertlen):c.type==="deletion"?e(68,c.start,c.length,"",-1,0,0):c.type==="skip"&&e(78,c.start,c.length,"",-1,0,0))}}};var da=["CIGAR","cs","coarseCigar","cg","cr"];function pa(n){return typeof n=="object"&&n!==null&&"refName"in n&&"start"in n&&"end"in n&&typeof n.refName=="string"&&typeof n.start=="number"&&typeof n.end=="number"}function ua(n){let e=n.get("mate");return pa(e)?e:void 0}function ma(n,e,t,r){let o=Math.max(n.start,r.start),s=Math.min(n.end,r.end),i=(e.end-e.start)/Math.max(n.end-n.start,1),a=l=>t===-1?e.end-(l-n.start)*i:e.start+(l-n.start)*i,f=Math.round(a(o)),c=Math.round(a(s));return s>o?{start:o,end:s,mateStart:Math.min(f,c),mateEnd:Math.max(f,c)}:void 0}function ga(n,e,t,r,o){let s={start:n.get("start"),end:n.get("end")},i=n.get("strand")===-1?-1:1,a=s.start>=t.start&&s.end<=t.end,f=a&&r===void 0&&!o?void 0:Sr(n);if(f===void 0){let c=a?{...s,mateStart:e.start,mateEnd:e.end}:ma(s,e,i,t);return c===void 0?[]:[c]}else return(r===void 0?[{...s,mateStart:e.start,mateEnd:e.end,cigar:f}]:br(f,s.start,e.start,e.end,i,r)).flatMap(l=>{let h=yr(l.cigar,l.start,l.mateStart,l.mateEnd,i,t.start,t.end);return h===void 0?[]:[h]})}function wa(n,e,t,r,o,s){let i=`:${r.start}-${r.end}${o}`,a=n.toJSON(),f={...a,uniqueId:`${n.id()}${i}`,start:t.start,end:t.end,mate:{...e,start:t.mateStart,end:t.mateEnd}};a.syntenyId!==void 0&&(f.syntenyId=`${String(a.syntenyId)}${i}`);for(let c of da)delete f[c];return s&&t.cigar&&(f.alignmentOps=t.cigar),new Te(f)}function Ms(n,e,t,r=!1){let o=ua(n);if(o===void 0)return[n];{let s=ga(n,o,e,t,r);return s.map((i,a)=>wa(n,o,i,e,s.length>1?`/${a}`:"",r))}}var In=class extends Ps.BaseFeatureDataAdapter{constructor(){super(...arguments);this.recordsAreAlignments=!0}static{this.capabilities=["getFeatures","getRefNames"]}async hasDataForRefName(){return!0}getFeaturesInMultipleRegions(t,r={}){let{clipToRegion:o,splitAtGapBp:s,keepAlignment:i,...a}=r,f=o&&this.recordsAreAlignments,c=(0,_s.createStatusFanOut)(a.statusCallback);return lr(t).pipe(et((l,h)=>this.getFeatures(l,{...a,statusCallback:c()}).pipe(et(d=>f?Ms(d,d.get("assemblyName")===l.assemblyName?l:{start:d.get("start"),end:d.get("end")},s,i):[d]),wn(),mt(d=>({index:h,features:d})))),wn(),et(l=>l.sort((h,d)=>h.index-d.index).flatMap(h=>h.features)))}};var An=class extends Error{constructor(t){super(t===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${t}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`);this.name="NoHaplotypeIndexError"}},Er=class extends Error{constructor(t){super(`a pair query names both lanes: queryAssemblyName ${t} came without a targetAssemblyName`);this.name="PairTargetError"}},Ar=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 ${r} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function ks(n,e){let t=Ce(e);return n[t]??n[e.sample]??t}function xa(n,e){return`${Ce(n)}#${n.contig}@${e.start.node}.${e.start.offset}`}function ya({alignment:n,assemblyName:e,refName:t,lane:r}){let{refStart:o,refEnd:s,strand:i,cigar:a}=n;if(!(!n.resolved||s<=o)){let{name:f,hapStart:c,hapEnd:l}=n,h=xa(f,n),d={uniqueId:h,assemblyName:e,refName:t,start:o,end:s,type:"match",strand:i==="-"?-1:1,CIGAR:a,syntenyId:h,mate:{refName:f.contig,start:c,end:l,assemblyName:r}};return new Te(d)}}function ba({pair:n,lane:e,mateLane:t}){let r=`${Ce(n.target)}#${n.target.contig}:${n.targetStart}-${n.targetEnd}|${Ce(n.query)}#${n.query.contig}:${n.queryStart}-${n.queryEnd}`;return new Te({uniqueId:r,assemblyName:e,refName:n.target.contig,start:n.targetStart,end:n.targetEnd,type:"match",strand:n.strand==="-"?-1:1,CIGAR:n.cigar,syntenyId:r,identity:n.matches/Math.max(n.columns,1),numMatches:n.matches,blockLen:n.columns,mate:{refName:n.query.contig,start:n.queryStart,end:n.queryEnd,assemblyName:t}})}function Os(n,e){return n instanceof _n&&(n.message=`Zoom in to about ${(0,wt.getBpDisplayStr)(n.fitsBp)} to see ${e}`),n}var vr=n=>!("uri"in n)||n.uri!=="",Cr=class extends In{constructor(){super(...arguments);this.graph=(0,Ir.cachedSetup)({label:"Opening pangenome database",setup:async()=>{let t=this.getConf("gbzDbLocation"),r=this.getConf("haplotypeIndexLocation"),o=vr(r)?{location:r}:await Fo(t,this.pluginManager),s=o.location,i=await dt.open({source:(0,En.openLocation)(t,this.pluginManager),haplotypeIndex:s?(0,En.openLocation)(s,this.pluginManager):void 0}),a=this.getConf("assemblyNames")[0];if(a===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let f=await On(i),c=St({configured:this.getConf("referenceSample"),anchorPrefix:ze(this,a),referenceSamples:f});return{db:i,anchor:a,referenceSample:c,referenceSamples:f,unreadableIndex:o.unreadable}}});this.gaf=(0,Ir.cachedSetup)({label:"Opening reads",setup:async()=>{let t=this.getConf("readsLocation"),r=this.getConf(["readsIndex","location"]);return vr(t)?new Kt((0,En.openLocation)(t,this.pluginManager),vr(r)?zr(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(t,r){let{db:o,referenceSample:s}=await this.graph(r);return Nn(o,s,t)}async getHaplotypes(t={}){let{db:r,referenceSamples:o}=await this.graph(t),s=new Map;for(let i of await r.paths()){let a=Ce(i.name),f=s.get(a);f?f.contigs.includes(i.name.contig)||f.contigs.push(i.name.contig):s.set(a,{prefix:a,sample:i.name.sample,haplotype:i.name.haplotype,contigs:[i.name.contig],isReference:o.includes(i.name.sample)})}return[...s.values()]}async getHeader(t={}){let{anchor:r,referenceSample:o,referenceSamples:s}=await this.graph(t),i=Pn(this),a=[];for(let f of await this.getHaplotypes(t))f.sample!==o&&a.push({name:ks(i,f),label:f.prefix,group:f.sample});return{hasCoarseTier:!1,anchorAssemblyName:r,referenceSample:o,referenceSamples:s,lanes:a}}async getRefNames(t={}){let{db:r,anchor:o,referenceSample:s}=await this.graph(t),{assemblyName:i}=t,a=i===o?void 0:ze(this,i),f=(await r.paths()).filter(c=>i===o?c.isIndexed&&c.name.sample===s:bt(Ce(c.name),a)).map(c=>c.name.contig);return[...new Set(f)]}keepPredicate(t,r){let o=t===void 0||t.length===0?void 0:t.map(s=>ze(this,s));return o===void 0&&r===void 0?void 0:s=>kn(s,o)&&(r===void 0||bt(Ce(s),r))}async getSubgraph(t,r={}){let{db:o,anchor:s,unreadableIndex:i}=await this.graph(),{assemblyName:a,refName:f,start:c,end:l}=t;if(a!==s)throw new Ar(a,s);let h=await this.referenceQuery(f,{}),d=this.keepPredicate(r.haplotypes);if(d!==void 0&&!o.hasHaplotypeIndex)throw new An(i);return Tn(o,h,c,l,{context:this.getConf("context"),snarls:r.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:r.signal,keep:d}).catch(p=>{throw Os(p,"the graph")})}async getReads(t,r={}){let o=await this.gaf(r);return o?o.readsOver(new Set(t),r):{records:[],total:0}}async laneHaplotypes(t,r){let o=ze(this,t);return(await this.getHaplotypes(r)).filter(s=>bt(s.prefix,o))}async anchorFeatures(t,r){let{db:o}=await this.graph(r),{assemblyName:s,refName:i,start:a,end:f}=t,c=ze(this,r.targetAssemblyName),l=Pn(this),h=this.keepPredicate(r.haplotypes,c),d=await this.referenceQuery(i,r),p=this.getConf("nodeLimit");return(d?await(0,wt.updateStatus)(`Reading graph ${i}:${a.toLocaleString()}-${f.toLocaleString()}`,r.statusCallback,()=>o.getAlignments({path:d,start:a,end:f,context:this.getConf("context"),haplotypes:"all",limit:p,signal:r.signal,keep:h}).catch(m=>{throw Os(vt(m,p,f-a)??m,"lanes")})):[]).flatMap(m=>{let w=m.resolved?ya({alignment:m,assemblyName:s,refName:i,lane:ks(l,m.name)}):void 0;return w===void 0?[]:[w]})}async pairFeatures(t,r,o){let{targetAssemblyName:s}=o;if(s===void 0)throw new Er(r);let{db:i}=await this.graph(o),{refName:a,start:f,end:c}=t,l=await this.laneHaplotypes(r,o),h=await this.laneHaplotypes(s,o),d=[...l,...h],p=await this.referenceQuery(a,o),u=this.getConf("nodeLimit"),m=y=>i.getSubgraphs({path:y,start:f,end:c,context:this.getConf("context"),snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:u,signal:o.signal,keep:S=>d.some(g=>g.sample===S.sample&&g.haplotype===S.haplotype)}).catch(S=>{throw vt(S,u,c-f)??S});return(p&&l.length>0&&h.length>0?await(0,wt.updateStatus)(`Reading ${r} against ${s}`,o.statusCallback,()=>m(p)):[]).flatMap(y=>l.flatMap(S=>h.flatMap(g=>y.pairAlignments({target:S,query:g,bases:!1}).map(b=>ba({pair:b,lane:r,mateLane:s})))))}getFeatures(t,r={}){return(0,Ns.ObservableCreate)(async o=>{let{db:s,anchor:i,unreadableIndex:a}=await this.graph(r);if(!s.hasHaplotypeIndex)throw new An(a);if(t.assemblyName===i){let f=r.queryAssemblyName===void 0?await this.anchorFeatures(t,r):await this.pairFeatures(t,r.queryAssemblyName,r);for(let c of f)o.next(c)}o.complete()},r.signal)}};export{Ar as HaplotypeWindowError,An as NoHaplotypeIndexError,Hs as NoReferenceSampleError,_n as NodeLimitError,Er as PairTargetError,Cr as default,ya as fragmentFeature,Ce as haplotypePrefix,ks as laneAssemblyName,vt as nodeLimitError,ba as pairFeature,St as resolveReferenceSample};
-//# sourceMappingURL=GbzBaseSyntenyAdapter-2BKLBC4F.js.map
+//# sourceMappingURL=GbzBaseSyntenyAdapter-Z4NDQGEZ.js.map