jbrowse-plugin-graphgenomeviewer 4.7.0 → 5.0.0

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
@@ -96,6 +98,10 @@ Needs JBrowse 5.0.0-beta.11 or later.
   lane or, for gbz-base, the haplotype lanes
 - Cuts the window plus a window each side, up to 5 Mb; past `aboveBpPerPx`, the
   `coarse` tier (`build_bubble_tier.sh` in jbrowse-components)
+- gbz-base past the cut (5 Mb, or the adapter's `nodeLimit`) draws the haplotype
+  index's overview instead: a band of how many haplotypes diverge from the
+  reference by 50 bp or more, then a row per haplotype, the track's lanes first.
+  Needs an index from `gbz-haplotype-index` 0.3 or later
 - gbz-base swaps in `{ "type": "GbzBaseSyntenyAdapter", "uri": "….gbz.db" }`; an
   `hg38` or `hs1` track finds the graph's GRCh38 or CHM13 reference sample, and
   `assemblyNameToPanSN` covers other names

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-CKKVHC2R.js

@@ -0,0 +1,4 @@
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r!==void 0?et(r):t!==void 0?Ke(t):void 0}var to=A(q(),1),ro=A(dr(),1);var oo=A(q(),1);var no=A(Cr(),1);var hr=A(q(),1),L=class extends hr.SimpleFeature{get(r){return r==="mismatches"?Oe(this.walkableCigar):r==="clipLengthAtStartOfRead"?this.clipLengthAtStartOfRead:r==="name"?super.get("name")??this.mate?.refName:super.get(r)}get mate(){return super.get("mate")}get walkableCigar(){let r=super.get("CIGAR"),t=super.get("coarseCigar");return typeof r=="string"?r:typeof t=="string"?Qe(t):void 0}get clipLengthAtStartOfRead(){return this.mate?.start??0}forEachMismatch(r,t){let o=this.get("start"),n=t?.start===void 0?void 0:t.start-o,i=t?.end===void 0?void 0:t.end-o,a=this.get("cs");if(a)Xe(a,r,n,i);else{let s=n??Number.NEGATIVE_INFINITY,p=i??Number.POSITIVE_INFINITY;for(let f of Oe(this.walkableCigar))(f.type==="deletion"||f.type==="skip"?f.start<p&&f.start+f.length>s:f.start>=s&&f.start<=p)&&(f.type==="mismatch"?r(88,f.start,f.length,f.base,f.qual??-1,0,0):f.type==="insertion"?r(73,f.start,f.length,f.insertedBases??"",-1,0,f.insertlen):f.type==="deletion"?r(68,f.start,f.length,"",-1,0,0):f.type==="skip"&&r(78,f.start,f.length,"",-1,0,0))}}};var io=["CIGAR","cs","coarseCigar","cg","cr"];function ao(e){return typeof e=="object"&&e!==null&&"refName"in e&&"start"in e&&"end"in e&&typeof e.refName=="string"&&typeof e.start=="number"&&typeof e.end=="number"}function so(e){let r=e.get("mate");return ao(r)?r:void 0}function fo(e,r,t,o){let n=Math.max(e.start,o.start),i=Math.min(e.end,o.end),a=(r.end-r.start)/Math.max(e.end-e.start,1),s=c=>t===-1?r.end-(c-e.start)*a:r.start+(c-e.start)*a,p=Math.round(s(n)),f=Math.round(s(i));return i>n?{start:n,end:i,mateStart:Math.min(p,f),mateEnd:Math.max(p,f)}:void 0}function po(e,r,t,o,n){let i={start:e.get("start"),end:e.get("end")},a=e.get("strand")===-1?-1:1,s=i.start>=t.start&&i.end<=t.end,p=s&&o===void 0&&!n?void 0:ot(e);if(p===void 0){let f=s?{...i,mateStart:r.start,mateEnd:r.end}:fo(i,r,a,t);return f===void 0?[]:[f]}else return(o===void 0?[{...i,mateStart:r.start,mateEnd:r.end,cigar:p}]:rt(p,i.start,r.start,r.end,a,o)).flatMap(c=>{let l=tt(c.cigar,c.start,c.mateStart,c.mateEnd,a,t.start,t.end);return l===void 0?[]:[l]})}function co(e,r,t,o,n,i){let a=`:${o.start}-${o.end}${n}`,s=e.toJSON(),p={...s,uniqueId:`${e.id()}${a}`,start:t.start,end:t.end,mate:{...r,start:t.mateStart,end:t.mateEnd}};s.syntenyId!==void 0&&(p.syntenyId=`${String(s.syntenyId)}${a}`);for(let f of io)delete p[f];return i&&t.cigar&&(p.alignmentOps=t.cigar),new L(p)}function xr(e,r,t,o=!1){let n=so(e);if(n===void 0)return[e];{let i=po(e,n,r,t,o);return i.map((a,s)=>co(e,n,a,r,i.length>1?`/${s}`:"",o))}}var Re=class extends yr.BaseFeatureDataAdapter{constructor(){super(...arguments);this.recordsAreAlignments=!0}static{this.capabilities=["getFeatures","getRefNames"]}async hasDataForRefName(){return!0}getFeaturesInMultipleRegions(t,o={}){let{clipToRegion:n,splitAtGapBp:i,keepAlignment:a,...s}=o,p=n&&this.recordsAreAlignments,f=(0,gr.createStatusFanOut)(s.statusCallback);return Ye(t).pipe(W((c,l)=>this.getFeatures(c,{...s,statusCallback:f()}).pipe(W(u=>p?xr(u,u.get("assemblyName")===c.assemblyName?c:{start:u.get("start"),end:u.get("end")},i,a):[u]),Ae(),X(u=>({index:l,features:u})))),Ae(),W(c=>c.sort((l,u)=>l.index-u.index).flatMap(l=>l.features)))}};var Me=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"}},ft=class extends Error{constructor(t){super(`a pair query names both lanes: queryAssemblyName ${t} came without a targetAssemblyName`);this.name="PairTargetError"}},Fe=class extends Error{constructor(t,o){super(`the graph is cut on its reference, ${o}; a window on ${t} has no reference coordinates to cut at. Open the graph from a ${o} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function nt(e,r){let t=T(r);return e[t]??e[r.sample]??t}function lo(e,r){return`${T(e)}#${e.contig}@${r.start.node}.${r.start.offset}`}function uo({alignment:e,assemblyName:r,refName:t,lane:o}){let{refStart:n,refEnd:i,strand:a,cigar:s}=e;if(!(!e.resolved||i<=n)){let{name:p,hapStart:f,hapEnd:c}=e,l=lo(p,e),u={uniqueId:l,assemblyName:r,refName:t,start:n,end:i,type:"match",strand:a==="-"?-1:1,CIGAR:s,syntenyId:l,mate:{refName:p.contig,start:f,end:c,assemblyName:o}};return new L(u)}}function mo({pair:e,lane:r,mateLane:t}){let o=`${T(e.target)}#${e.target.contig}:${e.targetStart}-${e.targetEnd}|${T(e.query)}#${e.query.contig}:${e.queryStart}-${e.queryEnd}`;return new L({uniqueId:o,assemblyName:r,refName:e.target.contig,start:e.targetStart,end:e.targetEnd,type:"match",strand:e.strand==="-"?-1:1,CIGAR:e.cigar,syntenyId:o,identity:e.matches/Math.max(e.columns,1),numMatches:e.matches,blockLen:e.columns,mate:{refName:e.query.contig,start:e.queryStart,end:e.queryEnd,assemblyName:t}})}function ho(e,r,t){let o=re(e,r,t);return o&&(o.message+="; the track's Graph display draws every haplotype's overview at any size"),o}var it=e=>!("uri"in e)||e.uri!=="",pt=class extends Re{constructor(){super(...arguments);this.graph=(0,at.cachedSetup)({label:"Opening pangenome database",setup:async()=>{let t=this.getConf("gbzDbLocation"),o=this.getConf("haplotypeIndexLocation"),n=it(o)?{location:o}:await Ct(t,this.pluginManager),i=n.location,a=await dt.open({source:(0,Te.openLocation)(t,this.pluginManager),haplotypeIndex:i?(0,Te.openLocation)(i,this.pluginManager):void 0}),s=this.getConf("assemblyNames")[0];if(s===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let p=await Le(a),f=te({configured:this.getConf("referenceSample"),anchorPrefix:k(this,s),referenceSamples:p});return{db:a,anchor:s,referenceSample:f,referenceSamples:p,unreadableIndex:n.unreadable}}});this.gaf=(0,at.cachedSetup)({label:"Opening reads",setup:async()=>{let t=this.getConf("readsLocation"),o=this.getConf(["readsIndex","location"]);return it(t)?new oe((0,Te.openLocation)(t,this.pluginManager),it(o)?wt(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(t,o){let{db:n,referenceSample:i}=await this.graph(o);return Ne(n,i,t)}async getHaplotypes(t={}){let{db:o,referenceSamples:n}=await this.graph(t),i=new Map;for(let a of await o.paths()){let s=T(a.name),p=i.get(s);p?p.contigs.includes(a.name.contig)||p.contigs.push(a.name.contig):i.set(s,{prefix:s,sample:a.name.sample,haplotype:a.name.haplotype,contigs:[a.name.contig],isReference:n.includes(a.name.sample)})}return[...i.values()]}async getHeader(t={}){let{anchor:o,referenceSample:n,referenceSamples:i}=await this.graph(t),a=ee(this),s=[];for(let p of await this.getHaplotypes(t))p.sample!==n&&s.push({name:nt(a,p),label:p.prefix,group:p.sample});return{hasCoarseTier:!1,anchorAssemblyName:o,referenceSample:n,referenceSamples:i,lanes:s}}async getRefNames(t={}){let{db:o,anchor:n,referenceSample:i}=await this.graph(t),{assemblyName:a}=t,s=a===n?void 0:k(this,a),p=(await o.paths()).filter(f=>a===n?f.isIndexed&&f.name.sample===i:V(T(f.name),s)).map(f=>f.name.contig);return[...new Set(p)]}keepPredicate(t,o){let n=t===void 0||t.length===0?void 0:t.map(i=>k(this,i));return n===void 0&&o===void 0?void 0:i=>Pe(i,n)&&(o===void 0||V(T(i),o))}async getSubgraph(t,o={}){let{db:n,anchor:i,unreadableIndex:a}=await this.graph(),{assemblyName:s,refName:p,start:f,end:c}=t;if(s!==i)throw new Fe(s,i);let l=await this.referenceQuery(p,{}),u=this.keepPredicate(o.haplotypes);if(u!==void 0&&!n.hasHaplotypeIndex)throw new Me(a);return Ge(n,l,f,c,{context:this.getConf("context"),snarls:o.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:o.signal,keep:u})}async getOverview(t,o){let{db:n,anchor:i,referenceSample:a}=await this.graph(),{assemblyName:s,refName:p,start:f,end:c}=t;if(s!==i)throw new Fe(s,i);let l=await this.referenceQuery(p,{}),u=l?await n.haplotypeOverview({path:l,start:f,end:c,bpPerPixel:o.bpPerPx}):void 0;if(!u)return;let m=ee(this),y=u.haplotypes.map(h=>T(h)),d=new Set;for(let h of o.haplotypes??[]){let g=k(this,h);y.forEach((x,S)=>{V(x,g)&&d.add(S)})}return{level:u.level,bin:u.bin,rows:u.haplotypes.map(h=>nt(m,h)),pinned:[...d],reference:u.haplotypes.flatMap((h,g)=>h.sample===a?[g]:[]),bins:u.bins,cells:u.cells}}async getReads(t,o={}){let n=await this.gaf(o);return n?n.readsOver(new Set(t),o):{records:[],total:0}}async laneHaplotypes(t,o){let n=k(this,t);return(await this.getHaplotypes(o)).filter(i=>V(i.prefix,n))}async anchorFeatures(t,o){let{db:n}=await this.graph(o),{assemblyName:i,refName:a,start:s,end:p}=t,f=k(this,o.targetAssemblyName),c=ee(this),l=this.keepPredicate(o.haplotypes,f),u=await this.referenceQuery(a,o),m=this.getConf("nodeLimit");return(u?await(0,st.updateStatus)(`Reading graph ${a}:${s.toLocaleString()}-${p.toLocaleString()}`,o.statusCallback,()=>n.getAlignments({path:u,start:s,end:p,context:this.getConf("context"),haplotypes:"all",limit:m,signal:o.signal,keep:l}).catch(d=>{throw ho(d,m,p-s)??d})):[]).flatMap(d=>{let h=d.resolved?uo({alignment:d,assemblyName:i,refName:a,lane:nt(c,d.name)}):void 0;return h===void 0?[]:[h]})}async pairFeatures(t,o,n){let{targetAssemblyName:i}=n;if(i===void 0)throw new ft(o);let{db:a}=await this.graph(n),{refName:s,start:p,end:f}=t,c=await this.laneHaplotypes(o,n),l=await this.laneHaplotypes(i,n),u=[...c,...l],m=await this.referenceQuery(s,n),y=this.getConf("nodeLimit"),d=g=>a.getSubgraphs({path:g,start:p,end:f,context:this.getConf("context"),snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:n.signal,keep:x=>u.some(S=>S.sample===x.sample&&S.haplotype===x.haplotype)}).catch(x=>{throw re(x,y,f-p)??x});return(m&&c.length>0&&l.length>0?await(0,st.updateStatus)(`Reading ${o} against ${i}`,n.statusCallback,()=>d(m)):[]).flatMap(g=>c.flatMap(x=>l.flatMap(S=>g.pairAlignments({target:x,query:S,bases:!1}).map(v=>mo({pair:v,lane:o,mateLane:i})))))}getFeatures(t,o={}){return(0,br.ObservableCreate)(async n=>{let{db:i,anchor:a,unreadableIndex:s}=await this.graph(o);if(!i.hasHaplotypeIndex)throw new Me(s);if(t.assemblyName===a){let p=o.queryAssemblyName===void 0?await this.anchorFeatures(t,o):await this.pairFeatures(t,o.queryAssemblyName,o);for(let f of p)n.next(f)}n.complete()},o.signal)}};export{Fe as HaplotypeWindowError,Me as NoHaplotypeIndexError,vr as NoReferenceSampleError,wr as NodeLimitError,ft as PairTargetError,pt as default,uo as fragmentFeature,T as haplotypePrefix,nt as laneAssemblyName,re as nodeLimitError,mo as pairFeature,te as resolveReferenceSample};
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