jbrowse-plugin-graphgenomeviewer 4.6.0 → 4.8.0

package/README.md

@@ -72,7 +72,9 @@ Needs JBrowse 5.0.0-beta.11 or later.
 ```
 
 - **File → Open track** opens an rGFA index (`.segs.bed.gz` from
-  `build_rgfa_tabix.sh`) or a gbz-base database (`.gbz.db`) as a `GraphTrack`
+  `build_rgfa_tabix.sh`) or a gbz-base database (`.gbz.db`) as a `GraphTrack`.
+  It finds the links and indexes beside the url, which a presigned url's
+  signature doesn't cover; spell out each location in a config instead
 - A hand-written track needs only the adapter:
 
 ```json

package/dist/chunks/ChooseWalksDialog-GVQLSGHX.js

@@ -0,0 +1,2 @@
+import{a as y}from"./chunk-J6KYLXRD.js";import{a as c,b as u,c as w,d as C}from"./chunk-TYJTJGPO.js";import{b as t}from"./chunk-FY3BTKY4.js";var k=t(y(),1),p=t(u(),1),e=t(C(),1),h=t(w(),1),a=t(c(),1),b=(0,h.observer)(function({model:l,onClose:i}){let{walkChoices:n}=l,d=new Set(n.map(o=>o.name)),[r,g]=(0,k.useState)(()=>l.walkLayers.map(o=>o.walk).filter(o=>d.has(o)));return(0,a.jsxs)(p.Dialog,{open:!0,onClose:i,title:"Choose walks",children:[(0,a.jsxs)(e.DialogContent,{children:[(0,a.jsx)(e.Autocomplete,{multiple:!0,disableCloseOnSelect:!0,"data-testid":"graph-choose-walks",options:n.map(o=>o.name),getOptionLabel:o=>l.walkLabel(o),value:r,onChange:(o,s)=>{g(s)},renderOption:({key:o,...s},m,{selected:f})=>(0,a.jsxs)("li",{...s,children:[(0,a.jsx)(e.Checkbox,{size:"small",checked:f}),l.walkLabel(m)]},o),renderInput:o=>(0,a.jsx)(e.TextField,{...o,autoFocus:!0,label:"Walks",placeholder:"type to search"})}),(0,a.jsxs)(e.Typography,{variant:"caption",color:"text.secondary",children:[n.length.toLocaleString()," walks in this cut. The ones picked are lifted out of the drawing in this order, and the rest fades."]})]}),(0,a.jsxs)(e.DialogActions,{children:[(0,a.jsx)(e.Button,{onClick:i,children:"Cancel"}),(0,a.jsx)(e.Button,{variant:"contained",onClick:()=>{l.liftWalks(r),i()},children:"Lift these walks"})]})]})}),L=b;export{L as default};
+//# sourceMappingURL=ChooseWalksDialog-GVQLSGHX.js.map

package/dist/chunks/ChooseWalksDialog-GVQLSGHX.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/GraphGenomeView/components/ChooseWalksDialog.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 WalkPicker = Pick<\n  GraphPaneModel,\n  'walkChoices' | 'walkLayers' | 'walkLabel' | 'liftWalks'\n>\n\n// Which walks to lift, searched by name, for a graph with more walks than a\n// menu can list\nconst ChooseWalksDialog = observer(function ChooseWalksDialog({\n  model,\n  onClose,\n}: {\n  model: WalkPicker\n  onClose: () => void\n}) {\n  const { walkChoices } = model\n  const names = new Set(walkChoices.map(c => c.name))\n  const [picked, setPicked] = useState(() =>\n    model.walkLayers.map(l => l.walk).filter(name => names.has(name)),\n  )\n  return (\n    <Dialog open onClose={onClose} title=\"Choose walks\">\n      <DialogContent>\n        <Autocomplete\n          multiple\n          disableCloseOnSelect\n          data-testid=\"graph-choose-walks\"\n          options={walkChoices.map(c => c.name)}\n          getOptionLabel={name => model.walkLabel(name)}\n          value={picked}\n          onChange={(_, value) => {\n            setPicked(value)\n          }}\n          renderOption={({ key, ...props }, name, { selected }) => (\n            <li key={key} {...props}>\n              <Checkbox size=\"small\" checked={selected} />\n              {model.walkLabel(name)}\n            </li>\n          )}\n          renderInput={params => (\n            <TextField\n              {...params}\n              autoFocus\n              label=\"Walks\"\n              placeholder=\"type to search\"\n            />\n          )}\n        />\n        <Typography variant=\"caption\" color=\"text.secondary\">\n          {walkChoices.length.toLocaleString()} walks in this cut. The ones\n          picked are lifted out of the drawing in this order, and the rest\n          fades.\n        </Typography>\n      </DialogContent>\n      <DialogActions>\n        <Button onClick={onClose}>Cancel</Button>\n        <Button\n          variant=\"contained\"\n          onClick={() => {\n            model.liftWalks(picked)\n            onClose()\n          }}\n        >\n          Lift these walks\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n})\n\nexport default ChooseWalksDialog\n"],
+  "mappings": "6IAAA,IAAAA,EAAyB,SAEzBC,EAAuB,SACvBC,EAQO,SACPC,EAAyB,SAqCbC,EAAA,SA1BNC,KAAoB,YAAS,SAA2B,CAC5D,MAAAC,EACA,QAAAC,CACF,EAGG,CACD,GAAM,CAAE,YAAAC,CAAY,EAAIF,EAClBG,EAAQ,IAAI,IAAID,EAAY,IAAIE,GAAKA,EAAE,IAAI,CAAC,EAC5C,CAACC,EAAQC,CAAS,KAAI,YAAS,IACnCN,EAAM,WAAW,IAAIO,GAAKA,EAAE,IAAI,EAAE,OAAOC,GAAQL,EAAM,IAAIK,CAAI,CAAC,CAClE,EACA,SACE,QAAC,UAAO,KAAI,GAAC,QAASP,EAAS,MAAM,eACnC,qBAAC,iBACC,oBAAC,gBACC,SAAQ,GACR,qBAAoB,GACpB,cAAY,qBACZ,QAASC,EAAY,IAAIE,GAAKA,EAAE,IAAI,EACpC,eAAgBI,GAAQR,EAAM,UAAUQ,CAAI,EAC5C,MAAOH,EACP,SAAU,CAACI,EAAGC,IAAU,CACtBJ,EAAUI,CAAK,CACjB,EACA,aAAc,CAAC,CAAE,IAAAC,EAAK,GAAGC,CAAM,EAAGJ,EAAM,CAAE,SAAAK,CAAS,OACjD,QAAC,MAAc,GAAGD,EAChB,oBAAC,YAAS,KAAK,QAAQ,QAASC,EAAU,EACzCb,EAAM,UAAUQ,CAAI,IAFdG,CAGT,EAEF,YAAaG,MACX,OAAC,aACE,GAAGA,EACJ,UAAS,GACT,MAAM,QACN,YAAY,iBACd,EAEJ,KACA,QAAC,cAAW,QAAQ,UAAU,MAAM,iBACjC,UAAAZ,EAAY,OAAO,eAAe,EAAE,wGAGvC,GACF,KACA,QAAC,iBACC,oBAAC,UAAO,QAASD,EAAS,kBAAM,KAChC,OAAC,UACC,QAAQ,YACR,QAAS,IAAM,CACbD,EAAM,UAAUK,CAAM,EACtBJ,EAAQ,CACV,EACD,4BAED,GACF,GACF,CAEJ,CAAC,EAEMc,EAAQhB",
+  "names": ["import_react", "import_ui", "import_material", "import_mobx_react", "import_jsx_runtime", "ChooseWalksDialog", "model", "onClose", "walkChoices", "names", "c", "picked", "setPicked", "l", "name", "_", "value", "key", "props", "selected", "params", "ChooseWalksDialog_default"]
+}

package/dist/chunks/{GbzBaseSyntenyAdapter-AZBYMDIW.js → GbzBaseSyntenyAdapter-VOGKGHQ6.js}

@@ -5,4 +5,4 @@ import{a as _n,b as Ps,c as kr,d as Lr}from"./chunk-S3X3QFQD.js";import{e as Ms,
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Set(e.map(o=>Math.floor((o-1)*this.pageSize/this.blockSize)))].filter(o=>!this.blocks.has(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;let i=[];for(let a=0;a<t;a++){let f=a*this.blockSize;i.push(e+a),this.blocks.set(e+a,s.then(c=>c.subarray(f,f+this.blockSize)))}this.forgetOnFailure(s,i),this.evict()}forgetOnFailure(e,t){e.catch(()=>{for(let r of t)this.blocks.delete(r)})}evict(){for(;this.blocks.size>this.maxBlocks;){let e=this.blocks.keys().next().value;if(e===void 0)break;this.blocks.delete(e)}}async page(e){let t=(e-1)*this.pageSize;if(e<1||t+this.pageSize>this.fileSize)throw new Error(`SQLite page ${e} is 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 ft=class n{pager;btree;objects;constructor(e,t,r){this.pager=e,this.btree=t,this.objects=r}static async open(e,t={}){let r=await e.read(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 d=i.getUint32(28);if(d===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 h=d*f,u=new $t(e,f,h,t);u.seed(0,r),u.fetches+=1,u.bytesFetched+=r.length;let p=new Ht(u,c),m=new Map;for await(let{values:w}of p.tableScan(1)){let[x,S,g,I,y]=w;typeof x=="string"&&typeof S=="string"&&typeof g=="string"&&typeof I=="number"&&m.set(S,{type:x,name:S,tableName:g,rootPage:I,sql:typeof y=="string"?y:""})}return new n(u,p,m)}rootPage(e){let t=this.objects.get(e);if(!t)throw new Error(`SQLite database has no object named ${e}`);return t.rootPage}indexOn(e){let t=[...this.objects.values()].find(o=>o.type==="index"&&o.tableName===e);if(t)return t.rootPage;let r=this.objects.get(e);if(r?.type==="table"&&/without\s+rowid/i.test(r.sql))return r.rootPage;throw new Error(`SQLite table ${e} has no index`)}byRowid(e,t){return this.btree.tableRowid(this.rootPage(e),t)}prefetchRows(e,t,r){return this.btree.prefetchRowidRange(this.rootPage(e),t,r)}scan(e){return this.btree.tableScan(this.rootPage(e))}indexSeekLE(e,t){return this.btree.indexSeekLE(this.indexOn(e),t)}indexScanFrom(e,t){return this.btree.indexScanFrom(this.indexOn(e),t)}has(e){return this.objects.has(e)}};var Dn="GBZ-base version 4",Bt=class extends Error{name="UnknownPathError";path;constructor(e){super(`the graph has no path named ${ge(e)}`),this.path=e}},Gt=class extends Error{name="ForwardOnlyIndexError";constructor(){super("the haplotype index was written with --forward-only, which cannot name the walks stored against their reference (about half of them); rebuild it with gbz-haplotype-index without --forward-only")}},Dt=class extends Error{name="SchemaVersionError";found;constructor(e){super(e===void 0?"not a gbz-base database: its Tags table has no version":`unsupported database schema "${e}"; this reader understands "${Dn}"`),this.found=e}},Gn=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=Br(o)}get id(){return M(this.handle)}get orientation(){return je(this.handle)}get sequence(){return this.decoded??=Gr(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 ${this.handle} is empty`);return new It(this.edges,this.bwt)}};function q(n,e){if(typeof n!="number")throw new Error(`${e} is not a number in the database`);return n}function zt(n,e){if(typeof n!="string")throw new Error(`${e} is not text in the database`);return n}function qt(n,e){if(!(n instanceof Uint8Array))throw new Error(`${e} is not a blob in the database`);return n}function vo(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:zt(e[5],"Paths.sample"),contig:zt(e[6],"Paths.contig"),haplotype:q(e[7],"Paths.haplotype"),fragment:q(e[8],"Paths.fragment")},isIndexed:q(e[9],"Paths.is_indexed")!==0}}async function Eo(n){let e=new Map;for await(let{values:t}of n.scan("Tags"))e.set(zt(t[0],"Tags.key"),zt(t[1],"Tags.value"));return e}var ct=class n{tagCache;pathCache;pathMapCache;indexTags=new Map;sqlite;index;constructor(e,t){this.sqlite=e,this.index=t}static async open(e){let{source:t,haplotypeIndex:r}=e,o={blockSize:e.blockSize,maxBlocks:e.maxBlocks},s=await ft.open(t,o);for(let c of["Tags","Nodes","Paths","ReferenceIndex"])s.rootPage(c);let i=r?await ft.open(r,o):void 0,a=new n(s,i),f=await a.tag("version");if(f!==Dn)throw new Dt(f);if(i){for(let u of["Tags","HaplotypeSamples","HaplotypeLengths"])i.rootPage(u);a.indexTags=await Eo(i);let c=a.indexTags.get("haplotype_index_paths"),l=await a.tag("paths");if(c!==l)throw new Error(`haplotype index was built for ${c??"an unknown number of"} paths but the graph has ${l}`);let d=a.indexTags.get("haplotype_index_nodes"),h=await a.tag("nodes");if(d!==void 0&&d!==h)throw new Error(`haplotype index was built for a graph with ${d} nodes but this one has ${h}`);if(a.indexTags.get("haplotype_index_orientations")==="forward")throw new Gt}return a}tags(){return this.tagCache??=Eo(this.sqlite),this.tagCache}async tag(e){return(await this.tags()).get(e)}prefetchRecords(e,t){return this.sqlite.prefetchRows("Nodes",e,t)}async getRecord(e){let t=await this.sqlite.byRowid("Nodes",e);if(!t)return;let r=t[4];return new Gn(e,qr(qt(t[1],"Nodes.edges")),qt(t[2],"Nodes.bwt"),qt(t[3],"Nodes.sequence"),typeof r=="number"?r:void 0)}paths(){return this.pathCache??=(async()=>{let e=[];for await(let{rowid:t,values:r}of this.sqlite.scan("Paths"))e.push(vo(t,r));return e})(),this.pathCache}async getPath(e){let t=await this.sqlite.byRowid("Paths",e);return t?vo(e,t):void 0}pathsByHandle(){return this.pathMapCache??=this.paths().then(e=>new Map(e.map(t=>[t.handle,t]))),this.pathMapCache}async findPath(e){return(await this.paths()).filter(r=>r.name.sample===e.sample&&r.name.contig===e.contig&&r.name.haplotype===e.haplotype&&r.name.fragment<=e.fragment).sort((r,o)=>o.name.fragment-r.name.fragment)[0]}async pathsNamed(e){let t=Qe(We(e),0);return(await this.paths()).filter(r=>r.name.sample===t.sample&&r.name.contig===t.contig&&r.name.haplotype===t.haplotype).sort((r,o)=>r.name.fragment-o.name.fragment)}async hasPath(e){return(await this.pathsNamed(e)).length>0}pathLengths=new Map;pathLength(e){let t=this.pathLengths.get(e);return t||(t=this.walkPathLength(e),this.pathLengths.set(e,t),t.catch(()=>this.pathLengths.delete(e))),t}async walkPathLength(e){let t=this.hasHaplotypeIndex?await this.haplotypeLength(e):void 0;if(t===void 0){let r=await this.indexedPosition(e,Number.MAX_SAFE_INTEGER);if(!r){let i=await this.getPath(e);throw new Error(`${i?`The fragment of ${ge(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,o=await this.pathsNamed(e.path);if(o.length===0)throw new Bt(Qe(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 Bn(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 Se&&f.walkedBp!==void 0?new Se(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 Bn(this,e)}subgraphAtOffset(e){return wo(this,e)}subgraphAroundNodes(e){return yo(this,e)}subgraphBetween(e){return xo(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=Ur(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("HaplotypeStrays")||!this.index.has("HaplotypeBinNodes")||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 haplotypeStraysInBins(e,t,r){let o=[];for await(let s of this.companion.indexScanFrom("HaplotypeStrays",[e,t])){let i=q(s[1],"HaplotypeStrays.bin");if(s[0]!==e||i>r)break;let a=q(s[4],"HaplotypeStrays.snarl_low"),f=q(s[5],"HaplotypeStrays.snarl_high");o.push({bin:i,pathHandle:q(s[2],"HaplotypeStrays.path_handle"),pathStart:q(s[3],"HaplotypeStrays.path_start"),snarl:f>0?[a,f]:void 0,pathEnd:q(s[6],"HaplotypeStrays.path_end"),node:q(s[7],"HaplotypeStrays.node_handle"),offset:q(s[8],"HaplotypeStrays.node_offset")})}return o}async haplotypeBinNodes(e,t,r){let o=[];for await(let a of this.companion.indexScanFrom("HaplotypeBinNodes",[e,t])){if(a[0]!==e||q(a[1],"HaplotypeBinNodes.bin")>r)break;let f=qt(a[3],"HaplotypeBinNodes.nodes"),c=0,l=0,d=()=>{let h=0,u=1;for(;;){let p=f[l++];if(p===void 0)throw new Error("HaplotypeBinNodes.nodes ends inside a number");if(h+=(p&127)*u,u*=128,(p&128)===0)return h}};for(;l<f.length;){let h=c+d();c=h+d(),o.push([h,c])}}o.sort((a,f)=>a[0]-f[0]);let s=[],i=[];for(let[a,f]of o){let c=i.length-1;c>=0&&a<=i[c]+1?i[c]=Math.max(i[c],f):(s.push(a),i.push(f))}return a=>{let f=0,c=s.length;for(;f<c;){let l=f+c>>1;s[l]<=a?f=l+1:c=l}return f>0&&a<=i[f-1]}}async haplotypeAnchor(e,t){let r=await this.companion.indexSeekLE("HaplotypeAnchors",[e,t]),o=r?.[0]===e&&r[1]===t?await this.companion.byRowid("HaplotypeAnchors",q(r[2],"HaplotypeAnchors rowid")):void 0;return o?{node:q(o[2],"HaplotypeAnchors.node_handle"),pathOffset:q(o[3],"HaplotypeAnchors.path_offset")}:void 0}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])){if(q(o[0],"HaplotypeSamples.node_handle")>t)break;let i=await this.companion.byRowid("HaplotypeSamples",q(o[2],"HaplotypeSamples rowid"));i&&r.push(this.sampleFromRow(i))}return r}async haplotypeSampleAt(e,t){let r=await this.companion.indexSeekLE("HaplotypeSamples",[e,t]);if(r?.[0]!==e||r[1]!==t)return;let o=await this.companion.byRowid("HaplotypeSamples",q(r[2],"HaplotypeSamples rowid"));return o?this.sampleFromRow(o):void 0}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 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xs.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,bs.createStatusFanOut)(a.statusCallback);return Xn(t).pipe(Je((l,d)=>this.getFeatures(l,{...a,statusCallback:c()}).pipe(Je(h=>f?ys(h,h.get("assemblyName")===l.assemblyName?l:{start:h.get("start"),end:h.get("end")},s,i):[h]),dn(),ht(h=>({index:d,features:h})))),dn(),Je(l=>l.sort((d,h)=>d.index-h.index).flatMap(d=>d.features)))}};var xn=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"}},hr=class extends Error{constructor(t){super(`a pair query names both lanes: queryAssemblyName ${t} came without a targetAssemblyName`);this.name="PairTargetError"}},pr=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 ${r} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function Ss(n,e){let t=Ae(e);return n[t]??n[e.sample]??t}function ra(n,e){return`${Ae(n)}#${n.contig}@${e.start.node}.${e.start.offset}`}function oa({alignment:n,assemblyName:e,refName:t,lane:r}){let{refStart:o,refEnd:s,strand:i,cigar:a}=n;if(!(!n.resolved||s<=o)){let{name:f,hapStart:c,hapEnd:l}=n,d=ra(f,n),h={uniqueId:d,assemblyName:e,refName:t,start:o,end:s,type:"match",strand:i==="-"?-1:1,CIGAR:a,syntenyId:d,mate:{refName:f.contig,start:c,end:l,assemblyName:r}};return new Oe(h)}}function sa({pair:n,lane:e,mateLane:t}){let r=`${Ae(n.target)}#${n.target.contig}:${n.targetStart}-${n.targetEnd}|${Ae(n.query)}#${n.query.contig}:${n.queryStart}-${n.queryEnd}`;return new Oe({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}})}var cr=n=>!("uri"in n)||n.uri!=="",ur=class extends wn{constructor(){super(...arguments);this.graph=(0,lr.cachedSetup)({label:"Opening pangenome database",setup:async()=>{let t=this.getConf("gbzDbLocation"),r=this.getConf("haplotypeIndexLocation"),o=cr(r)?{location:r}:await Co(t,this.pluginManager),s=o.location,i=await ct.open({source:(0,yn.openLocation)(t,this.pluginManager),haplotypeIndex:s?(0,yn.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 En(i),c=gt({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,lr.cachedSetup)({label:"Opening reads",setup:async()=>{let t=this.getConf("readsLocation"),r=this.getConf(["readsIndex","location"]);return cr(t)?new jt((0,yn.openLocation)(t,this.pluginManager),cr(r)?Lr(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(t,r){let{db:o,referenceSample:s}=await this.graph(r);return An(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=Ae(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=In(this),a=[];for(let f of await this.getHaplotypes(t))f.sample!==o&&a.push({name:Ss(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:mt(Ae(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=>vn(s,o)&&(r===void 0||mt(Ae(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 pr(a,s);let d=await this.referenceQuery(f,{}),h=this.keepPredicate(r.haplotypes);if(h!==void 0&&!o.hasHaplotypeIndex)throw new xn(i);return Cn(o,d,c,l,{context:this.getConf("context"),snarls:r.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:r.signal,keep:h})}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=>mt(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=In(this),d=this.keepPredicate(r.haplotypes,c),h=await this.referenceQuery(i,r),u=this.getConf("nodeLimit");return(h?await(0,dr.updateStatus)(`Reading graph ${i}:${a.toLocaleString()}-${f.toLocaleString()}`,r.statusCallback,()=>o.getAlignments({path:h,start:a,end:f,context:this.getConf("context"),haplotypes:"all",limit:u,signal:r.signal,keep:d}).catch(m=>{throw wt(m,u,f-a)??m})):[]).flatMap(m=>{let w=m.resolved?oa({alignment:m,assemblyName:s,refName:i,lane:Ss(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 hr(r);let{db:i}=await this.graph(o),{refName:a,start:f,end:c}=t,l=await this.laneHaplotypes(r,o),d=await this.laneHaplotypes(s,o),h=[...l,...d],u=await this.referenceQuery(a,o),p=this.getConf("nodeLimit"),m=x=>i.getSubgraphs({path:x,start:f,end:c,context:this.getConf("context"),snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:p,signal:o.signal,keep:S=>h.some(g=>g.sample===S.sample&&g.haplotype===S.haplotype)}).catch(S=>{throw wt(S,p,c-f)??S});return(u&&l.length>0&&d.length>0?await(0,dr.updateStatus)(`Reading ${r} against ${s}`,o.statusCallback,()=>m(u)):[]).flatMap(x=>l.flatMap(S=>d.flatMap(g=>x.pairAlignments({target:S,query:g,bases:!1}).map(I=>sa({pair:I,lane:r,mateLane:s})))))}getFeatures(t,r={}){return(0,Is.ObservableCreate)(async o=>{let{db:s,anchor:i,unreadableIndex:a}=await this.graph(r);if(!s.hasHaplotypeIndex)throw new xn(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{pr as HaplotypeWindowError,xn as NoHaplotypeIndexError,Ms as NoReferenceSampleError,Rs as NodeLimitError,hr as PairTargetError,ur as default,oa as fragmentFeature,Ae as haplotypePrefix,Ss as laneAssemblyName,wt as nodeLimitError,sa as pairFeature,gt as resolveReferenceSample};
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