jbrowse-plugin-graphgenomeviewer 6.25.0 → 6.26.1

package/dist/chunks/{AddTrackWorkflow-ZKAN5JYJ.js → AddTrackWorkflow-ELAP73WV.js}

@@ -1,2 +1,2 @@
-import{a as H,b as j,c as O,d as z,g as J}from"./chunk-2I4VPDLZ.js";import{d as w,e as R}from"./chunk-NDRLCGPC.js";import"./chunk-R3TRNF7N.js";import"./chunk-7WIBGKBU.js";import"./chunk-OGQ6OQDN.js";import{b as T,h as G,j as S,m as A}from"./chunk-TENPGIPX.js";import{g as r}from"./chunk-6OPB7FOJ.js";import{A as _,B as W,E as b,a as v,e as x,f as p,n as E,r as B,s as I,t as P,z as N}from"./chunk-ECD5B2ZM.js";import{b as t,c as g,d as M}from"./chunk-JMBDTNUR.js";var s=JBrowseExports["@jbrowse/core/util/tss-react"],$=o=>s!=null&&o in Object(s)?s[o]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+o+"' from '@jbrowse/core/util/tss-react' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:o});var D=$("makeStyles"),oe=s&&s.__esModule?s.default:s;var ee=D()(o=>({paper:{margin:o.spacing(),padding:o.spacing()},field:{marginTop:o.spacing(2)},submit:{marginTop:25,marginBottom:100,display:"block"}})),te=["RgfaTabixAdapter","GbzBaseSyntenyAdapter","MinigraphBubbleAdapter"],ae=M(function({model:a}){let{classes:l}=ee(),f=S(a),d=w(a),[n,V]=r("RgfaTabixAdapter"),[i,X]=r(),[y,q]=r(),[k,K]=r(),m=n==="GbzBaseSyntenyAdapter",[C,Q]=r(""),[h,U]=r("Pangenome graph"),[F,u]=r(),[Y,L]=r(!1);async function Z(){if(!i||!a.assembly)return;u(void 0),L(!0);let e=n==="RgfaTabixAdapter"?await H(i,G(a).pluginManager):void 0;if(L(!1),!(!R(a)||!a.assembly))try{let c=h.trim();T({model:a,session:f,conf:J({choice:n,loc:i,indexLoc:y,readsLoc:m?k:void 0,manifest:e,assembly:a.assembly,sample:C,trackId:A({name:c}),name:c})})}catch(c){u(c)}}return g(N,{className:l.paper,children:[F?t(x,{error:F}):null,g(B,{children:[t(P,{children:"File type"}),t(W,{value:n,onChange:e=>{V(e.target.value),u(void 0)},children:te.map(e=>t(I,{value:e,control:t(_,{}),label:j[e]},e))})]}),t(p,{location:i,name:O[n],rootModel:d,setLocation:X}),t(p,{location:y,name:z[n],rootModel:d,setLocation:q}),m?t(p,{location:k,name:"Path to reads aligned to the graph as GAF (optional; a .gz is read by the .tbi beside it)",rootModel:d,setLocation:K}):null,t(b,{className:l.field,value:C,onChange:e=>{Q(e.target.value)},label:"Sample name in the graph",slotProps:{htmlInput:{"data-testid":"graph-sample-input"}},helperText:m?"Optional. The graph's sample for this assembly, e.g. GRCh38 where the assembly is hg38; leave blank when they share a name or the graph has one reference sample":"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}),t(b,{className:l.field,value:h,helperText:"Track name",slotProps:{htmlInput:{"data-testid":"graph-track-name-input"}},onChange:e=>{U(e.target.value)}}),t(v,{session:f,helperText:"Select assembly to add track to",selected:a.assembly,onChange:e=>{a.setAssembly(e)},fullWidth:!0}),t(E,{variant:"contained",className:l.submit,disabled:!i||!h.trim()||!a.assembly||Y,onClick:()=>{Z()},children:"Submit"})]})}),ue=ae;export{ue as default};
-//# sourceMappingURL=AddTrackWorkflow-ZKAN5JYJ.js.map
+import{a as H,b as j,c as O,d as z,g as J}from"./chunk-2I4VPDLZ.js";import{d as w,e as R}from"./chunk-NDRLCGPC.js";import"./chunk-R3TRNF7N.js";import"./chunk-7WIBGKBU.js";import"./chunk-OGQ6OQDN.js";import{b as T,h as G,j as S,m as A}from"./chunk-TENPGIPX.js";import{g as r}from"./chunk-6OPB7FOJ.js";import{A as N,B as _,C as W,F as b,a as v,e as x,f as p,o as E,s as B,t as I,u as P}from"./chunk-E3WYW7Z6.js";import{b as t,c as g,d as M}from"./chunk-JMBDTNUR.js";var s=JBrowseExports["@jbrowse/core/util/tss-react"],$=o=>s!=null&&o in Object(s)?s[o]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+o+"' from '@jbrowse/core/util/tss-react' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:o});var D=$("makeStyles"),oe=s&&s.__esModule?s.default:s;var ee=D()(o=>({paper:{margin:o.spacing(),padding:o.spacing()},field:{marginTop:o.spacing(2)},submit:{marginTop:25,marginBottom:100,display:"block"}})),te=["RgfaTabixAdapter","GbzBaseSyntenyAdapter","MinigraphBubbleAdapter"],ae=M(function({model:a}){let{classes:l}=ee(),f=S(a),d=w(a),[n,V]=r("RgfaTabixAdapter"),[i,X]=r(),[y,q]=r(),[k,K]=r(),m=n==="GbzBaseSyntenyAdapter",[C,Q]=r(""),[h,U]=r("Pangenome graph"),[F,u]=r(),[Y,L]=r(!1);async function Z(){if(!i||!a.assembly)return;u(void 0),L(!0);let e=n==="RgfaTabixAdapter"?await H(i,G(a).pluginManager):void 0;if(L(!1),!(!R(a)||!a.assembly))try{let c=h.trim();T({model:a,session:f,conf:J({choice:n,loc:i,indexLoc:y,readsLoc:m?k:void 0,manifest:e,assembly:a.assembly,sample:C,trackId:A({name:c}),name:c})})}catch(c){u(c)}}return g(N,{className:l.paper,children:[F?t(x,{error:F}):null,g(B,{children:[t(P,{children:"File type"}),t(W,{value:n,onChange:e=>{V(e.target.value),u(void 0)},children:te.map(e=>t(I,{value:e,control:t(_,{}),label:j[e]},e))})]}),t(p,{location:i,name:O[n],rootModel:d,setLocation:X}),t(p,{location:y,name:z[n],rootModel:d,setLocation:q}),m?t(p,{location:k,name:"Path to reads aligned to the graph as GAF (optional; a .gz is read by the .tbi beside it)",rootModel:d,setLocation:K}):null,t(b,{className:l.field,value:C,onChange:e=>{Q(e.target.value)},label:"Sample name in the graph",slotProps:{htmlInput:{"data-testid":"graph-sample-input"}},helperText:m?"Optional. The graph's sample for this assembly, e.g. GRCh38 where the assembly is hg38; leave blank when they share a name or the graph has one reference sample":"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}),t(b,{className:l.field,value:h,helperText:"Track name",slotProps:{htmlInput:{"data-testid":"graph-track-name-input"}},onChange:e=>{U(e.target.value)}}),t(v,{session:f,helperText:"Select assembly to add track to",selected:a.assembly,onChange:e=>{a.setAssembly(e)},fullWidth:!0}),t(E,{variant:"contained",className:l.submit,disabled:!i||!h.trim()||!a.assembly||Y,onClick:()=>{Z()},children:"Submit"})]})}),ue=ae;export{ue as default};
+//# sourceMappingURL=AddTrackWorkflow-ELAP73WV.js.map

package/dist/chunks/{ChooseSamplesDialog-75F3KRRG.js → ChooseSamplesDialog-BNVYBGJQ.js}

@@ -1,2 +1,2 @@
-import{a as i}from"./chunk-5JXGPUTF.js";import"./chunk-6OPB7FOJ.js";import"./chunk-ECD5B2ZM.js";import{b as a,d as s}from"./chunk-JMBDTNUR.js";var t=s(function({model:o,onClose:p}){let{samples:l}=o.walkRowSampleChoices;return a(i,{title:"Choose samples",label:"Samples",testId:"graph-choose-samples",caption:`${l.length.toLocaleString()} samples in this cut. Their walks show in pairs, in the order picked.`,options:l,initial:o.walkRowSamples??[],confirmLabel:e=>e.length>0?"Show these samples":"Show every sample",onPick:e=>{o.setWalkRowSamples(e.length>0?e:void 0)},onClose:p})}),h=t;export{h as default};
-//# sourceMappingURL=ChooseSamplesDialog-75F3KRRG.js.map
+import{a as i}from"./chunk-AHFQHYJI.js";import"./chunk-6OPB7FOJ.js";import"./chunk-E3WYW7Z6.js";import{b as a,d as s}from"./chunk-JMBDTNUR.js";var t=s(function({model:o,onClose:p}){let{samples:l}=o.walkRowSampleChoices;return a(i,{title:"Choose samples",label:"Samples",testId:"graph-choose-samples",caption:`${l.length.toLocaleString()} samples in this cut. Their walks show in pairs, in the order picked.`,options:l,initial:o.walkRowSamples??[],confirmLabel:e=>e.length>0?"Show these samples":"Show every sample",onPick:e=>{o.setWalkRowSamples(e.length>0?e:void 0)},onClose:p})}),h=t;export{h as default};
+//# sourceMappingURL=ChooseSamplesDialog-BNVYBGJQ.js.map

package/dist/chunks/{ChooseWalksDialog-L23LYMKI.js → ChooseWalksDialog-EN3C6AQA.js}

@@ -1,2 +1,2 @@
-import{a as t}from"./chunk-5JXGPUTF.js";import"./chunk-6OPB7FOJ.js";import"./chunk-ECD5B2ZM.js";import{b as l,d as i}from"./chunk-JMBDTNUR.js";var h=i(function({model:o,onClose:s}){let{walkChoices:a}=o;return l(t,{title:"Choose haplotypes",label:"Haplotypes",testId:"graph-choose-walks",caption:`${a.length.toLocaleString()} haplotypes in this cut. The ones picked are highlighted in this order, and the rest fades.`,options:a.map(e=>e.name),initial:o.walkLayers.map(e=>e.walk),optionLabel:e=>o.walkLabel(e),confirmLabel:e=>e.length>0?"Highlight these":"Clear highlights",onPick:e=>{o.liftWalks(e)},onClose:s})}),k=h;export{k as default};
-//# sourceMappingURL=ChooseWalksDialog-L23LYMKI.js.map
+import{a as t}from"./chunk-AHFQHYJI.js";import"./chunk-6OPB7FOJ.js";import"./chunk-E3WYW7Z6.js";import{b as l,d as i}from"./chunk-JMBDTNUR.js";var h=i(function({model:o,onClose:s}){let{walkChoices:a}=o;return l(t,{title:"Choose haplotypes",label:"Haplotypes",testId:"graph-choose-walks",caption:`${a.length.toLocaleString()} haplotypes in this cut. The ones picked are highlighted in this order, and the rest fades.`,options:a.map(e=>e.name),initial:o.walkLayers.map(e=>e.walk),optionLabel:e=>o.walkLabel(e),confirmLabel:e=>e.length>0?"Highlight these":"Clear highlights",onPick:e=>{o.liftWalks(e)},onClose:s})}),k=h;export{k as default};
+//# sourceMappingURL=ChooseWalksDialog-EN3C6AQA.js.map

package/dist/chunks/{GbzBaseSyntenyAdapter-RLEI3RDF.js → GbzBaseSyntenyAdapter-KTZMVVMW.js}

@@ -1,2 +1,2 @@
-import{a as H,b as ae,c as fe,d as re}from"./chunk-W7UGHWWS.js";import{b as G,c as V,d as te,e as ne}from"./chunk-AHE4Y2TX.js";import{a as E,b as O}from"./chunk-ANYQG5I7.js";import{h as W,i as Z,j as de,k as U,l as u,m as B,n as M,o as F,p as k,q as z,s as X,t as ee}from"./chunk-BPN3IL3K.js";import"./chunk-WAGGHKBL.js";import"./chunk-D257CI4F.js";import"./chunk-YBLNN5FU.js";import{e as R,f as P,g as C}from"./chunk-E2GK6JEL.js";import"./chunk-E7J6SB5P.js";import{b as Y,c as J,d as K}from"./chunk-R3TRNF7N.js";import"./chunk-7WIBGKBU.js";import{a as N}from"./chunk-OGQ6OQDN.js";import{e as j,o as $}from"./chunk-TENPGIPX.js";function A(t){let s=/\.gbz\.db$/i;return s.test(t)?t.replace(s,".haplotype-index.db"):void 0}function he(t){return J(t)&&A(Y(t))?K(t,s=>A(s)):void 0}function ue(t){return t instanceof Error&&(/\bHTTP 40[34]\b/.test(t.message)||t.code==="ENOENT")}async function oe(t,s){let n=he(t);if(!n)return{};try{return await N(n,s).stat(),{location:n}}catch(e){return ue(e)?{}:{unreadable:String(e)}}}var ge=5e3,ye=50*2**20,q=class extends Error{constructor(n){super(`this GAF is ${(n/2**20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`);this.name="UnindexedGafTooLargeError"}};function be(t,s){if(t.length<=s)return t;let n=t.length/s;return Array.from({length:s},(e,a)=>t[Math.floor(a*n)])}var se=(t,s)=>t.path.some(n=>s.has(n.name)),I=class{constructor(s,n){this.file=s;this.tabix=n;this.whole=G({setup:async({signal:s})=>{let{size:n}=await this.file.stat();if(n>ye)throw new q(n);let e=await this.file.readFile({signal:s}),a=new TextDecoder().decode(e[0]===31&&e[1]===139?await te(e):e);return O(a)}})}async readIndexed(s,n,e){let a=1/0,r=-1/0;for(let c of n){let i=Number(c);Number.isInteger(i)&&(a=Math.min(a,i),r=Math.max(r,i))}let o=[];return a<=r&&await s.getLines("{node}",a,r+1,{signal:e,lineCallback:c=>{let i=E(c);i&&se(i,n)&&o.push(i)}}),o}async readsOver(s,{signal:n}={}){let e=this.tabix?await this.readIndexed(this.tabix,s,n):(await this.whole({signal:n})).filter(a=>se(a,s));return{records:be(e,ge),total:e.length}}};var v=class extends Error{constructor(n){super(n===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${n}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`);this.name="NoHaplotypeIndexError"}},Q=class extends Error{constructor(n,e){super(`the graph is cut on its reference, ${e}; a window on ${n} has no reference coordinates to cut at. Open the graph from a ${e} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function ie(t,s){let n=u(s);return t[n]??t[s.sample]??n}function we(t,s){return`${u(t)}#${t.contig}@${s.start.node}.${s.start.offset}`}function xe({alignment:t,assemblyName:s,refName:n,lane:e}){let{refStart:a,refEnd:r,strand:o,cigar:c}=t;if(!(!t.resolved||r<=a)){let{name:i,hapStart:p,hapEnd:d}=t,f=we(i,t),g={uniqueId:f,assemblyName:s,refName:n,start:a,end:r,type:"match",strand:o==="-"?-1:1,CIGAR:c,syntenyId:f,mate:{refName:i.contig,start:p,end:d,assemblyName:e}};return new H(g)}}function Se({pair:t,lane:s,mateLane:n}){let e=`${u(t.target)}#${t.target.contig}:${t.targetStart}-${t.targetEnd}|${u(t.query)}#${t.query.contig}:${t.queryStart}-${t.queryEnd}`;return new H({uniqueId:e,assemblyName:s,refName:t.target.contig,start:t.targetStart,end:t.targetEnd,type:"match",strand:t.strand==="-"?-1:1,CIGAR:t.cigar,syntenyId:e,identity:t.matches/Math.max(t.columns,1),numMatches:t.matches,blockLen:t.columns,mate:{refName:t.query.contig,start:t.queryStart,end:t.queryEnd,assemblyName:n}})}var Pe=12e4;function Ne(t,s){let n=new Map;for(let a of t)for(let{name:r,start:o,end:c}of a.walkSpans()){let i=u(r);if(s.has(i)){let p=`${i}#${r.contig}`;n.set(p,[...n.get(p)??[],[o,c]])}}let e=0;for(let a of n.values()){a.sort((r,o)=>r[0]-o[0]);for(let r=1;r<a.length;r++){let o=a[r][0]-a[r-1][1];o>0&&o<=Pe&&(e=Math.max(e,o))}}return e}function T(t,s){return t instanceof U&&(t.message=`Zoom in to about ${j(t.fitsBp)} to see ${s}`),t}var ce=t=>({...t,start:Math.floor(t.start),end:Math.ceil(t.end)}),_=t=>!("uri"in t)||t.uri!=="",D=class extends ae{constructor(){super(...arguments);this.graph=G({label:"Opening pangenome database",setup:async()=>{let n=this.getConf("gbzDbLocation"),e=this.getConf("haplotypeIndexLocation"),a=_(e)?{location:e}:await oe(n,this.pluginManager),r=a.location,o=await Z.open({source:N(n,this.pluginManager),haplotypeIndex:r?N(r,this.pluginManager):void 0}),c=this.getConf("assemblyNames")[0];if(c===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let i=await M(o),p=F({configured:this.getConf("referenceSample"),anchorPrefix:P(this,c),referenceSamples:i});return{db:o,anchor:c,referenceSample:p,referenceSamples:i,unreadableIndex:a.unreadable}}});this.gaf=G({label:"Opening reads",setup:async()=>{let n=this.getConf("readsLocation"),e=this.getConf(["readsIndex","location"]);return _(n)?new I(N(n,this.pluginManager),_(e)?ne(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(n,e){let{db:a,referenceSample:r}=await this.graph(e);return k(a,r,n)}async getHaplotypes(n={}){let{db:e,referenceSamples:a}=await this.graph(n),r=new Map;for(let o of await e.paths()){let c=u(o.name),i=r.get(c);i?i.contigs.includes(o.name.contig)||i.contigs.push(o.name.contig):r.set(c,{prefix:c,sample:o.name.sample,haplotype:o.name.haplotype,contigs:[o.name.contig],isReference:a.includes(o.name.sample)})}return[...r.values()]}async getHeader(n={}){let{anchor:e,referenceSample:a,referenceSamples:r}=await this.graph(n),o=C(this),c=[];for(let i of await this.getHaplotypes(n))i.sample!==a&&c.push({name:ie(o,i),label:i.prefix,group:i.sample});return{hasCoarseTier:!1,anchorAssemblyName:e,referenceSample:a,referenceSamples:r,lanes:c}}async getRefNames(n={}){let{db:e,anchor:a,referenceSample:r}=await this.graph(n),{assemblyName:o}=n,c=o===a?void 0:P(this,o),i=(await e.paths()).filter(p=>o===a?p.isIndexed&&p.name.sample===r:R(u(p.name),c)).map(p=>p.name.contig);return[...new Set(i)]}keepPredicate(n,e){let a=n===void 0||n.length===0?void 0:n.map(r=>P(this,r));return a===void 0&&e===void 0?void 0:r=>B(r,a)&&(e===void 0||R(u(r),e))}async getSubgraph(n,e={}){let{signal:a}=e,{db:r,anchor:o,referenceSample:c,unreadableIndex:i}=await this.graph({signal:a}),{assemblyName:p,refName:d,start:f,end:g}=ce(n);if(p!==o)throw new Q(p,o);let y=await this.referenceQuery(d,{signal:a});if(!y)throw new Error(`${c} has no indexed path ${d} in this graph`);let x=this.keepPredicate(e.haplotypes);if(x!==void 0&&!r.hasHaplotypeIndex)throw new v(i);let l=await X(r,y,f,g,{context:this.getConf("context"),snarls:e.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:e.signal,keep:x}).catch(b=>{throw T(b,"the graph")});return typeof l=="string"?l:ee(l,{start:f,end:g},e.walkRows)}async getReads(n,e={}){let a=await this.gaf(e);return a?a.readsOver(new Set(n),e):{records:[],total:0}}async laneHaplotypes(n,e){let a=P(this,n);return(await this.getHaplotypes(e)).filter(r=>R(r.prefix,a))}async anchorFeatures(n,e){let{db:a}=await this.graph(e),{assemblyName:r,refName:o,start:c,end:i}=n,p=P(this,e.targetAssemblyName),d=C(this),f=this.keepPredicate(e.haplotypes,p),g=await this.referenceQuery(o,e),y=this.getConf("nodeLimit");return(g?await $(`Reading graph ${o}:${c.toLocaleString()}-${i.toLocaleString()}`,e.statusCallback,()=>a.getAlignments({path:g,start:c,end:i,context:this.getConf("context"),haplotypes:"all",limit:y,signal:e.signal,keep:f}).catch(l=>{throw T(z(l,y,i-c)??l,"lanes")})):[]).flatMap(l=>{let b=l.resolved?xe({alignment:l,assemblyName:r,refName:o,lane:ie(d,l.name)}):void 0;return b===void 0?[]:[b]})}async pairFeatures(n,e,a){let{db:r}=await this.graph(a),{refName:o,start:c,end:i}=n,d=(await Promise.all(e.map(async m=>({pair:m,featureSide:await this.laneHaplotypes(m.queryAssemblyName,a),mateSide:await this.laneHaplotypes(m.targetAssemblyName,a)})))).filter(({featureSide:m,mateSide:h})=>m.length>0&&h.length>0),f=new Set(d.flatMap(({featureSide:m,mateSide:h})=>[...m,...h].map(u))),g=await this.referenceQuery(o,a),y=this.getConf("nodeLimit"),x=this.getConf("context"),[l]=e,b=(m,h)=>r.getSubgraphs({path:m,start:c,end:i,context:h,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:a.signal,keep:S=>f.has(u(S))}),pe=async m=>{let h=await b(m,x).catch(w=>{throw T(z(w,y,i-c)??w,"lanes")}),S=Ne(h,f),L=Math.ceil(S/2)+2e3;return S>0&&L>x?b(m,L).catch(w=>{if(w instanceof W)return h;throw w}):h};return(g&&l&&d.length>0?await $(e.length===1?`Reading ${l.queryAssemblyName} against ${l.targetAssemblyName}`:`Reading ${e.length} lane pairs`,a.statusCallback,()=>pe(g)):[]).flatMap(m=>d.flatMap(({pair:h,featureSide:S,mateSide:L})=>S.flatMap(w=>L.flatMap(le=>m.pairAlignments({target:w,query:le,bases:!1}).map(me=>Se({pair:me,lane:h.queryAssemblyName,mateLane:h.targetAssemblyName}))))))}getFeatures(n,e={}){let a=ce(n);return V(async r=>{let{db:o,anchor:c,unreadableIndex:i}=await this.graph(e);if(!o.hasHaplotypeIndex)throw new v(i);if(a.assemblyName===c){let p=re(e),d=p.length>0?await this.pairFeatures(a,p,e):await this.anchorFeatures(a,e);for(let f of d)r.next(f)}r.complete()},e.signal)}};export{Q as HaplotypeWindowError,v as NoHaplotypeIndexError,de as NoReferenceSampleError,fe as PairTargetError,D as default,xe as fragmentFeature,ie as laneAssemblyName,Se as pairFeature,F as resolveReferenceSample,Ne as widestWalkGap};
-//# sourceMappingURL=GbzBaseSyntenyAdapter-RLEI3RDF.js.map
+import{a as H,b as ae,c as fe,d as re}from"./chunk-LCODIX3W.js";import{b as G,c as V,d as te,e as ne}from"./chunk-HHADQLAY.js";import{a as E,b as O}from"./chunk-C4ORW22P.js";import{c as W,d as Z,e as de,f as U,g as u,h as B,i as M,j as F,k,l as z,n as X}from"./chunk-3GI2K2L7.js";import{h as ee}from"./chunk-6NKKRJ2C.js";import"./chunk-VAATBXRG.js";import"./chunk-YBLNN5FU.js";import{e as R,f as P,g as C}from"./chunk-KFP5PZRE.js";import"./chunk-E7J6SB5P.js";import{b as Y,c as J,d as K}from"./chunk-R3TRNF7N.js";import"./chunk-7WIBGKBU.js";import{a as N}from"./chunk-OGQ6OQDN.js";import{e as j,o as $}from"./chunk-TENPGIPX.js";function A(t){let s=/\.gbz\.db$/i;return s.test(t)?t.replace(s,".haplotype-index.db"):void 0}function he(t){return J(t)&&A(Y(t))?K(t,s=>A(s)):void 0}function ue(t){return t instanceof Error&&(/\bHTTP 40[34]\b/.test(t.message)||t.code==="ENOENT")}async function oe(t,s){let n=he(t);if(!n)return{};try{return await N(n,s).stat(),{location:n}}catch(e){return ue(e)?{}:{unreadable:String(e)}}}var ge=5e3,ye=50*2**20,q=class extends Error{constructor(n){super(`this GAF is ${(n/2**20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`);this.name="UnindexedGafTooLargeError"}};function be(t,s){if(t.length<=s)return t;let n=t.length/s;return Array.from({length:s},(e,a)=>t[Math.floor(a*n)])}var se=(t,s)=>t.path.some(n=>s.has(n.name)),I=class{constructor(s,n){this.file=s;this.tabix=n;this.whole=G({setup:async({signal:s})=>{let{size:n}=await this.file.stat();if(n>ye)throw new q(n);let e=await this.file.readFile({signal:s}),a=new TextDecoder().decode(e[0]===31&&e[1]===139?await te(e):e);return O(a)}})}async readIndexed(s,n,e){let a=1/0,r=-1/0;for(let c of n){let i=Number(c);Number.isInteger(i)&&(a=Math.min(a,i),r=Math.max(r,i))}let o=[];return a<=r&&await s.getLines("{node}",a,r+1,{signal:e,lineCallback:c=>{let i=E(c);i&&se(i,n)&&o.push(i)}}),o}async readsOver(s,{signal:n}={}){let e=this.tabix?await this.readIndexed(this.tabix,s,n):(await this.whole({signal:n})).filter(a=>se(a,s));return{records:be(e,ge),total:e.length}}};var v=class extends Error{constructor(n){super(n===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${n}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`);this.name="NoHaplotypeIndexError"}},Q=class extends Error{constructor(n,e){super(`the graph is cut on its reference, ${e}; a window on ${n} has no reference coordinates to cut at. Open the graph from a ${e} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function ie(t,s){let n=u(s);return t[n]??t[s.sample]??n}function we(t,s){return`${u(t)}#${t.contig}@${s.start.node}.${s.start.offset}`}function xe({alignment:t,assemblyName:s,refName:n,lane:e}){let{refStart:a,refEnd:r,strand:o,cigar:c}=t;if(!(!t.resolved||r<=a)){let{name:i,hapStart:p,hapEnd:d}=t,f=we(i,t),g={uniqueId:f,assemblyName:s,refName:n,start:a,end:r,type:"match",strand:o==="-"?-1:1,CIGAR:c,syntenyId:f,mate:{refName:i.contig,start:p,end:d,assemblyName:e}};return new H(g)}}function Se({pair:t,lane:s,mateLane:n}){let e=`${u(t.target)}#${t.target.contig}:${t.targetStart}-${t.targetEnd}|${u(t.query)}#${t.query.contig}:${t.queryStart}-${t.queryEnd}`;return new H({uniqueId:e,assemblyName:s,refName:t.target.contig,start:t.targetStart,end:t.targetEnd,type:"match",strand:t.strand==="-"?-1:1,CIGAR:t.cigar,syntenyId:e,identity:t.matches/Math.max(t.columns,1),numMatches:t.matches,blockLen:t.columns,mate:{refName:t.query.contig,start:t.queryStart,end:t.queryEnd,assemblyName:n}})}var Pe=12e4;function Ne(t,s){let n=new Map;for(let a of t)for(let{name:r,start:o,end:c}of a.walkSpans()){let i=u(r);if(s.has(i)){let p=`${i}#${r.contig}`;n.set(p,[...n.get(p)??[],[o,c]])}}let e=0;for(let a of n.values()){a.sort((r,o)=>r[0]-o[0]);for(let r=1;r<a.length;r++){let o=a[r][0]-a[r-1][1];o>0&&o<=Pe&&(e=Math.max(e,o))}}return e}function T(t,s){return t instanceof U&&(t.message=`Zoom in to about ${j(t.fitsBp)} to see ${s}`),t}var ce=t=>({...t,start:Math.floor(t.start),end:Math.ceil(t.end)}),_=t=>!("uri"in t)||t.uri!=="",D=class extends ae{constructor(){super(...arguments);this.graph=G({label:"Opening pangenome database",setup:async()=>{let n=this.getConf("gbzDbLocation"),e=this.getConf("haplotypeIndexLocation"),a=_(e)?{location:e}:await oe(n,this.pluginManager),r=a.location,o=await Z.open({source:N(n,this.pluginManager),haplotypeIndex:r?N(r,this.pluginManager):void 0}),c=this.getConf("assemblyNames")[0];if(c===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let i=await M(o),p=F({configured:this.getConf("referenceSample"),anchorPrefix:P(this,c),referenceSamples:i});return{db:o,anchor:c,referenceSample:p,referenceSamples:i,unreadableIndex:a.unreadable}}});this.gaf=G({label:"Opening reads",setup:async()=>{let n=this.getConf("readsLocation"),e=this.getConf(["readsIndex","location"]);return _(n)?new I(N(n,this.pluginManager),_(e)?ne(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(n,e){let{db:a,referenceSample:r}=await this.graph(e);return k(a,r,n)}async getHaplotypes(n={}){let{db:e,referenceSamples:a}=await this.graph(n),r=new Map;for(let o of await e.paths()){let c=u(o.name),i=r.get(c);i?i.contigs.includes(o.name.contig)||i.contigs.push(o.name.contig):r.set(c,{prefix:c,sample:o.name.sample,haplotype:o.name.haplotype,contigs:[o.name.contig],isReference:a.includes(o.name.sample)})}return[...r.values()]}async getHeader(n={}){let{anchor:e,referenceSample:a,referenceSamples:r}=await this.graph(n),o=C(this),c=[];for(let i of await this.getHaplotypes(n))i.sample!==a&&c.push({name:ie(o,i),label:i.prefix,group:i.sample});return{hasCoarseTier:!1,anchorAssemblyName:e,referenceSample:a,referenceSamples:r,lanes:c}}async getRefNames(n={}){let{db:e,anchor:a,referenceSample:r}=await this.graph(n),{assemblyName:o}=n,c=o===a?void 0:P(this,o),i=(await e.paths()).filter(p=>o===a?p.isIndexed&&p.name.sample===r:R(u(p.name),c)).map(p=>p.name.contig);return[...new Set(i)]}keepPredicate(n,e){let a=n===void 0||n.length===0?void 0:n.map(r=>P(this,r));return a===void 0&&e===void 0?void 0:r=>B(r,a)&&(e===void 0||R(u(r),e))}async getSubgraph(n,e={}){let{signal:a}=e,{db:r,anchor:o,referenceSample:c,unreadableIndex:i}=await this.graph({signal:a}),{assemblyName:p,refName:d,start:f,end:g}=ce(n);if(p!==o)throw new Q(p,o);let y=await this.referenceQuery(d,{signal:a});if(!y)throw new Error(`${c} has no indexed path ${d} in this graph`);let x=this.keepPredicate(e.haplotypes);if(x!==void 0&&!r.hasHaplotypeIndex)throw new v(i);let l=await X(r,y,f,g,{context:this.getConf("context"),snarls:e.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:e.signal,keep:x}).catch(b=>{throw T(b,"the graph")});return typeof l=="string"?l:ee(l,{start:f,end:g},e.walkRows)}async getReads(n,e={}){let a=await this.gaf(e);return a?a.readsOver(new Set(n),e):{records:[],total:0}}async laneHaplotypes(n,e){let a=P(this,n);return(await this.getHaplotypes(e)).filter(r=>R(r.prefix,a))}async anchorFeatures(n,e){let{db:a}=await this.graph(e),{assemblyName:r,refName:o,start:c,end:i}=n,p=P(this,e.targetAssemblyName),d=C(this),f=this.keepPredicate(e.haplotypes,p),g=await this.referenceQuery(o,e),y=this.getConf("nodeLimit");return(g?await $(`Reading graph ${o}:${c.toLocaleString()}-${i.toLocaleString()}`,e.statusCallback,()=>a.getAlignments({path:g,start:c,end:i,context:this.getConf("context"),haplotypes:"all",limit:y,signal:e.signal,keep:f}).catch(l=>{throw T(z(l,y,i-c)??l,"lanes")})):[]).flatMap(l=>{let b=l.resolved?xe({alignment:l,assemblyName:r,refName:o,lane:ie(d,l.name)}):void 0;return b===void 0?[]:[b]})}async pairFeatures(n,e,a){let{db:r}=await this.graph(a),{refName:o,start:c,end:i}=n,d=(await Promise.all(e.map(async m=>({pair:m,featureSide:await this.laneHaplotypes(m.queryAssemblyName,a),mateSide:await this.laneHaplotypes(m.targetAssemblyName,a)})))).filter(({featureSide:m,mateSide:h})=>m.length>0&&h.length>0),f=new Set(d.flatMap(({featureSide:m,mateSide:h})=>[...m,...h].map(u))),g=await this.referenceQuery(o,a),y=this.getConf("nodeLimit"),x=this.getConf("context"),[l]=e,b=(m,h)=>r.getSubgraphs({path:m,start:c,end:i,context:h,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:a.signal,keep:S=>f.has(u(S))}),pe=async m=>{let h=await b(m,x).catch(w=>{throw T(z(w,y,i-c)??w,"lanes")}),S=Ne(h,f),L=Math.ceil(S/2)+2e3;return S>0&&L>x?b(m,L).catch(w=>{if(w instanceof W)return h;throw w}):h};return(g&&l&&d.length>0?await $(e.length===1?`Reading ${l.queryAssemblyName} against ${l.targetAssemblyName}`:`Reading ${e.length} lane pairs`,a.statusCallback,()=>pe(g)):[]).flatMap(m=>d.flatMap(({pair:h,featureSide:S,mateSide:L})=>S.flatMap(w=>L.flatMap(le=>m.pairAlignments({target:w,query:le,bases:!1}).map(me=>Se({pair:me,lane:h.queryAssemblyName,mateLane:h.targetAssemblyName}))))))}getFeatures(n,e={}){let a=ce(n);return V(async r=>{let{db:o,anchor:c,unreadableIndex:i}=await this.graph(e);if(!o.hasHaplotypeIndex)throw new v(i);if(a.assemblyName===c){let p=re(e),d=p.length>0?await this.pairFeatures(a,p,e):await this.anchorFeatures(a,e);for(let f of d)r.next(f)}r.complete()},e.signal)}};export{Q as HaplotypeWindowError,v as NoHaplotypeIndexError,de as NoReferenceSampleError,fe as PairTargetError,D as default,xe as fragmentFeature,ie as laneAssemblyName,Se as pairFeature,F as resolveReferenceSample,Ne as widestWalkGap};
+//# sourceMappingURL=GbzBaseSyntenyAdapter-KTZMVVMW.js.map

package/dist/chunks/{GbzBaseSyntenyAdapter-RLEI3RDF.js.map → GbzBaseSyntenyAdapter-KTZMVVMW.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@10.0.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-FLFBYSJO.js", "../../src/GbzBaseSyntenyAdapter/companion.ts", "../../src/gaf/gafFile.ts", "../../src/GbzBaseSyntenyAdapter/GbzBaseSyntenyAdapter.ts"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@10.2.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-FLFBYSJO.js", "../../src/GbzBaseSyntenyAdapter/companion.ts", "../../src/gaf/gafFile.ts", "../../src/GbzBaseSyntenyAdapter/GbzBaseSyntenyAdapter.ts"],
   "sourcesContent": ["import {\n  GBZ_CUT_DEFAULTS,\n  cutWindowGFA,\n  haplotypeWanted,\n  referencePathQuery,\n  referenceSamplesOf,\n  resolveReferenceSample\n} from \"./chunk-Q7LYHGGQ.js\";\n\n// src/gbzCut.ts\nimport { GBZBase } from \"@gmod/gbz-base\";\nvar HPRC_GBZ = {\n  db: \"https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/release2/minigraph-cactus/v2.1/hprc-v2.1-mc-grch38/hprc-v2.1-mc-grch38.gbz.db\",\n  index: \"https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38.haplotype-index.f3.db\"\n};\nfunction haplotypeIndexBeside(db) {\n  const GBZ_DB = /\\.gbz\\.db$/i;\n  return GBZ_DB.test(db) ? db.replace(GBZ_DB, \".haplotype-index.db\") : void 0;\n}\nfunction parseRegion(text) {\n  const m = /^\\s*([^:\\s]+):([\\d,]+)-([\\d,]+)\\s*$/.exec(text);\n  if (!m) {\n    throw new Error(\n      `\"${text}\" is not a region like chr6:160,614,798-160,647,758`\n    );\n  }\n  const n = (s) => Number(s.replaceAll(\",\", \"\"));\n  return { refName: m[1], start: n(m[2]), end: n(m[3]) };\n}\nasync function openGbz(db, index) {\n  const base = await GBZBase.open({ source: db, haplotypeIndex: index });\n  return { base, referenceSamples: await referenceSamplesOf(base) };\n}\nfunction referenceSample(ref, samples) {\n  try {\n    return resolveReferenceSample({\n      configured: \"\",\n      anchorPrefix: ref ?? samples[0] ?? \"\",\n      referenceSamples: samples\n    });\n  } catch (e) {\n    if (ref) {\n      return ref;\n    }\n    throw e;\n  }\n}\nasync function cutGbzRegion({ base, referenceSamples }, src, signal) {\n  const region = parseRegion(src.region);\n  const sample = referenceSample(src.referenceSample, referenceSamples);\n  const query = await referencePathQuery(base, sample, region.refName);\n  if (!query) {\n    throw new Error(`${sample} has no indexed path named ${region.refName}`);\n  }\n  signal?.throwIfAborted();\n  const wanted = src.haplotypes?.length ? src.haplotypes : void 0;\n  const text = await cutWindowGFA(base, query, region.start, region.end, {\n    context: src.context ?? GBZ_CUT_DEFAULTS.context,\n    snarls: src.snarls ?? GBZ_CUT_DEFAULTS.snarls,\n    limit: GBZ_CUT_DEFAULTS.limit,\n    signal,\n    keep: wanted ? (name) => haplotypeWanted(name, wanted) : void 0\n  });\n  return { text, region, sample };\n}\n\nexport {\n  HPRC_GBZ,\n  haplotypeIndexBeside,\n  parseRegion,\n  openGbz,\n  cutGbzRegion\n};\n", "import { haplotypeIndexBeside } from '@jbrowse/bandage-core/gbzCut'\nimport { openLocation } from '@jbrowse/core/util/io'\n\nimport { locationName, readsSiblings, renamed } from '../locationName'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { FileLocation } from '@jbrowse/core/util/types'\n\nexport function siblingCompanion(gbzDb: FileLocation) {\n  return readsSiblings(gbzDb) && haplotypeIndexBeside(locationName(gbzDb))\n    ? renamed(gbzDb, name => haplotypeIndexBeside(name)!)\n    : undefined\n}\n\n// 404 is a missing file, and so is 403 from a bucket that does not let a\n// reader list it; anything else leaves the file's presence unknown\nfunction isMissing(error: unknown) {\n  return (\n    error instanceof Error &&\n    (/\\bHTTP 40[34]\\b/.test(error.message) ||\n      (error as { code?: unknown }).code === 'ENOENT')\n  )\n}\n\n// `unreadable` is why a companion that may be there could not be checked, such\n// as a network error, or a server that answers a missing file without CORS\nexport async function findCompanion(\n  gbzDb: FileLocation,\n  pluginManager?: PluginManager,\n): Promise<{ location?: FileLocation; unreadable?: string }> {\n  const candidate = siblingCompanion(gbzDb)\n  if (!candidate) {\n    return {}\n  }\n  try {\n    await openLocation(candidate, pluginManager).stat()\n    return { location: candidate }\n  } catch (error) {\n    return isMissing(error) ? {} : { unreadable: String(error) }\n  }\n}\n", "import { unzip } from '@gmod/bgzf-filehandle'\nimport { parseGaf, parseGafLine } from '@jbrowse/bandage-core/gaf/parseGaf'\nimport { cachedSetup } from '@jbrowse/core/data_adapters/BaseAdapter'\n\nimport type { TabixIndexedFile } from '@gmod/tabix'\nimport type { GafRecord } from '@jbrowse/bandage-core/gaf/parseGaf'\n\ninterface WholeFile {\n  stat(): Promise<{ size: number }>\n  readFile(opts?: { signal?: AbortSignal }): Promise<Uint8Array>\n}\n\nexport interface GafReads {\n  records: GafRecord[]\n  // reads over the nodes before sampling\n  total: number\n}\n\n// The tube map lays reads out on the main thread at about 40 ms per thousand\nexport const MAX_READS = 5000\n\n// An unindexed GAF is read whole, once, into the worker\nconst MAX_UNINDEXED_BYTES = 50 * 2 ** 20\n\nexport class UnindexedGafTooLargeError extends Error {\n  override name = 'UnindexedGafTooLargeError'\n\n  constructor(size: number) {\n    super(\n      `this GAF is ${(size / 2 ** 20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`,\n    )\n  }\n}\n\n// Evenly spaced, so a pileup thins out rather than losing its right half\nfunction sample(records: GafRecord[], max: number) {\n  if (records.length <= max) {\n    return records\n  }\n  const stride = records.length / max\n  return Array.from({ length: max }, (_, k) => records[Math.floor(k * stride)]!)\n}\n\nconst touches = (record: GafRecord, names: ReadonlySet<string>) =>\n  record.path.some(step => names.has(step.name))\n\n// A GAF over a graph's segments: bgzipped and indexed with `tabix -p gaf`,\n// which keys each line by its lowest and highest node id and so needs numeric\n// segment names, or plain or gzipped and read whole.\nexport class GafFile {\n  // Shared by every window, so the signal is cachedSetup's own, which aborts\n  // once no caller is left waiting\n  private whole = cachedSetup({\n    setup: async ({ signal }) => {\n      const { size } = await this.file.stat()\n      if (size > MAX_UNINDEXED_BYTES) {\n        throw new UnindexedGafTooLargeError(size)\n      }\n      const bytes = await this.file.readFile({ signal })\n      const text = new TextDecoder().decode(\n        bytes[0] === 0x1f && bytes[1] === 0x8b ? await unzip(bytes) : bytes,\n      )\n      return parseGaf(text)\n    },\n  })\n\n  constructor(\n    private file: WholeFile,\n    private tabix?: TabixIndexedFile,\n  ) {}\n\n  private async readIndexed(\n    tabix: TabixIndexedFile,\n    names: ReadonlySet<string>,\n    signal?: AbortSignal,\n  ) {\n    let lo = Infinity\n    let hi = -Infinity\n    for (const name of names) {\n      const id = Number(name)\n      if (Number.isInteger(id)) {\n        lo = Math.min(lo, id)\n        hi = Math.max(hi, id)\n      }\n    }\n    const records: GafRecord[] = []\n    if (lo <= hi) {\n      // a GAF index ignores the refName, and getLines keeps a read whose node\n      // ids span min..max when min < end && max >= start, hence hi + 1\n      await tabix.getLines('{node}', lo, hi + 1, {\n        signal,\n        lineCallback: line => {\n          const record = parseGafLine(line)\n          if (record && touches(record, names)) {\n            records.push(record)\n          }\n        },\n      })\n    }\n    return records\n  }\n\n  async readsOver(\n    names: ReadonlySet<string>,\n    { signal }: { signal?: AbortSignal } = {},\n  ): Promise<GafReads> {\n    const records = this.tabix\n      ? await this.readIndexed(this.tabix, names, signal)\n      : (await this.whole({ signal })).filter(r => touches(r, names))\n    return { records: sample(records, MAX_READS), total: records.length }\n  }\n}\n", "import { GBZBase, SubgraphLimitError } from '@gmod/gbz-base'\nimport {\n  NodeLimitError,\n  cutWindowTables,\n  haplotypePrefix,\n  haplotypeWanted,\n  nodeLimitError,\n  referencePathQuery,\n  referenceSamplesOf,\n  resolveReferenceSample,\n} from '@jbrowse/bandage-core/gbzWindow'\nimport {\n  assemblyByPanSNPrefix,\n  panSNMatchesPrefix,\n  resolvePanSNPrefix,\n} from '@jbrowse/bandage-core/pansn'\nimport { cachedSetup } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { getBpDisplayStr, updateStatus } from '@jbrowse/core/util'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\n\nimport { findCompanion } from './companion.ts'\nimport { walkCutFor } from '../RgfaTabixAdapter/walkRowRuns.ts'\nimport { GafFile } from '../gaf/gafFile.ts'\nimport { openTabixSlot } from '../panSNTabix.ts'\nimport { ComparativeAdapterBase } from '../synteny/ComparativeAdapterBase.ts'\nimport SyntenyFeature from '../synteny/SyntenyFeature.ts'\nimport { requestedPairs } from '../synteny/lanePairs.ts'\n\nimport type { GbzBaseSyntenyAdapterConfig } from './configSchema.ts'\nimport type { SubgraphAdapterOptions } from '../GetSubgraph.ts'\nimport type { GafReads } from '../gaf/gafFile.ts'\nimport type { LaneFeatureOptions, LanePair } from '../synteny/lanePairs.ts'\nimport type {\n  HaplotypeAlignment,\n  HaplotypeRef,\n  PairAlignment,\n  PathName,\n  PathQuery,\n  Subgraph,\n} from '@gmod/gbz-base'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util'\nimport type { FileLocation, Region } from '@jbrowse/core/util/types'\n\nexport {\n  NoReferenceSampleError,\n  resolveReferenceSample,\n} from '@jbrowse/bandage-core/gbzWindow'\n\nexport class NoHaplotypeIndexError extends Error {\n  override name = 'NoHaplotypeIndexError'\n\n  constructor(unreadable?: string) {\n    super(\n      unreadable === undefined\n        ? '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'\n        : `the haplotype index beside the graph database could not be checked (${unreadable}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`,\n    )\n  }\n}\n\nexport interface GbzHaplotype {\n  prefix: string\n  sample: string\n  haplotype: number\n  contigs: string[]\n  isReference: boolean\n}\n\n/**\n * One lane the header declares, in the shape MultiWaySyntenyDisplay's lane\n * picker reads: `name` is the lane's assembly name, the same string the\n * fetched features' mates carry, `label` its PanSN prefix and `group` its\n * sample, so a diploid sample's two lanes sit together\n */\nexport interface GbzHeaderLane {\n  name: string\n  label: string\n  group: string\n}\n\nexport { PairTargetError } from '../synteny/lanePairs.ts'\nexport type { LanePair } from '../synteny/lanePairs.ts'\nexport type GbzFeatureOptions = LaneFeatureOptions\n\nexport class HaplotypeWindowError extends Error {\n  override name = 'HaplotypeWindowError'\n\n  constructor(assemblyName: string, anchor: string) {\n    super(\n      `the graph is cut on its reference, ${anchor}; a window on ${assemblyName} has no reference coordinates to cut at. Open the graph from a ${anchor} view, and find this haplotype's lane there`,\n    )\n  }\n}\n\n/**\n * The lane a haplotype draws on: the JBrowse assembly the config maps to it at\n * haplotype or sample depth, else its own PanSN prefix. The fallback stays at\n * haplotype depth, unlike the multi-genome PAF adapters', because a diploid\n * sample's two walks are two lanes here.\n */\nexport function laneAssemblyName(\n  asmByPrefix: Record<string, string>,\n  name: Pick<PathName, 'sample' | 'haplotype'>,\n) {\n  const prefix = haplotypePrefix(name)\n  return asmByPrefix[prefix] ?? asmByPrefix[name.sample] ?? prefix\n}\n\n/**\n * The id of one haplotype fragment: the walk's GBWT position at its first node\n * in the window, which is a property of the graph, so the same fragment gets\n * the same id on a refetch of the same window and the display's hover and\n * selection survive it. `clipToRegion` suffixes the window.\n */\nfunction fragmentId(name: PathName, alignment: HaplotypeAlignment) {\n  return `${haplotypePrefix(name)}#${name.contig}@${alignment.start.node}.${alignment.start.offset}`\n}\n\nexport function fragmentFeature({\n  alignment,\n  assemblyName,\n  refName,\n  lane,\n}: {\n  alignment: HaplotypeAlignment\n  assemblyName: string\n  refName: string\n  lane: string\n}) {\n  const { refStart, refEnd, strand, cigar } = alignment\n  if (!alignment.resolved || refEnd <= refStart) {\n    return undefined\n  } else {\n    const { name, hapStart, hapEnd } = alignment\n    const id = fragmentId(name, alignment)\n    const data: SimpleFeatureSerialized = {\n      uniqueId: id,\n      assemblyName,\n      refName,\n      start: refStart,\n      end: refEnd,\n      type: 'match',\n      strand: strand === '-' ? -1 : 1,\n      CIGAR: cigar,\n      syntenyId: id,\n      mate: {\n        refName: name.contig,\n        start: hapStart,\n        end: hapEnd,\n        assemblyName: lane,\n      },\n    }\n    return new SyntenyFeature(data)\n  }\n}\n\n/**\n * One record of a lane pair, on the target walk's own contig with the query\n * walk as its mate. gbz-base writes the CIGAR along the target, a `D` being\n * target bases the query lacks, which is the side a JBrowse feature is, so it\n * passes through unchanged.\n */\nexport function pairFeature({\n  pair,\n  lane,\n  mateLane,\n}: {\n  pair: PairAlignment\n  lane: string\n  mateLane: string\n}) {\n  const id = `${haplotypePrefix(pair.target)}#${pair.target.contig}:${pair.targetStart}-${pair.targetEnd}|${haplotypePrefix(pair.query)}#${pair.query.contig}:${pair.queryStart}-${pair.queryEnd}`\n  return new SyntenyFeature({\n    uniqueId: id,\n    assemblyName: lane,\n    refName: pair.target.contig,\n    start: pair.targetStart,\n    end: pair.targetEnd,\n    type: 'match',\n    strand: pair.strand === '-' ? -1 : 1,\n    CIGAR: pair.cigar,\n    syntenyId: id,\n    identity: pair.matches / Math.max(pair.columns, 1),\n    numMatches: pair.matches,\n    blockLen: pair.columns,\n    mate: {\n      refName: pair.query.contig,\n      start: pair.queryStart,\n      end: pair.queryEnd,\n      assemblyName: mateLane,\n    },\n  })\n}\n\n// The longest detour a pair cut widens its context to take in\nconst BRIDGE_MAX_BP = 120_000\n\n/**\n * The widest gap, up to `BRIDGE_MAX_BP`, between two pieces of one kept walk:\n * a haplotype that left the cut's nodes for sequence the reference lacks and\n * came back. Two kept haplotypes that share that sequence only align across it\n * once its nodes are in the cut.\n */\nexport function widestWalkGap(subgraphs: Subgraph[], kept: Set<string>) {\n  const byPath = new Map<string, [number, number][]>()\n  for (const subgraph of subgraphs) {\n    for (const { name, start, end } of subgraph.walkSpans()) {\n      const prefix = haplotypePrefix(name)\n      if (kept.has(prefix)) {\n        const key = `${prefix}#${name.contig}`\n        byPath.set(key, [...(byPath.get(key) ?? []), [start, end]])\n      }\n    }\n  }\n  let widest = 0\n  for (const spans of byPath.values()) {\n    spans.sort((a, b) => a[0] - b[0])\n    for (let i = 1; i < spans.length; i++) {\n      const gap = spans[i]![0] - spans[i - 1]![1]\n      if (gap > 0 && gap <= BRIDGE_MAX_BP) {\n        widest = Math.max(widest, gap)\n      }\n    }\n  }\n  return widest\n}\n\n// A window past the node limit fails as a zoom-in notice naming a span that\n// fits\nfunction zoomInNotice(error: unknown, what: string) {\n  if (error instanceof NodeLimitError) {\n    error.message = `Zoom in to about ${getBpDisplayStr(error.fitsBp)} to see ${what}`\n  }\n  return error\n}\n\n// gbz-base reads whole bp; a view asks at fractional ones\nconst wholeBp = (region: Region) => ({\n  ...region,\n  start: Math.floor(region.start),\n  end: Math.ceil(region.end),\n})\n\nconst isSet = (location: FileLocation) =>\n  !('uri' in location) || location.uri !== ''\n\nexport default class GbzBaseSyntenyAdapter extends ComparativeAdapterBase<GbzBaseSyntenyAdapterConfig> {\n  private graph = cachedSetup({\n    label: 'Opening pangenome database',\n    setup: async () => {\n      const gbzDb: FileLocation = this.getConf('gbzDbLocation')\n      const configured: FileLocation = this.getConf('haplotypeIndexLocation')\n      const companion = isSet(configured)\n        ? { location: configured }\n        : await findCompanion(gbzDb, this.pluginManager)\n      const indexLocation = companion.location\n      const db = await GBZBase.open({\n        source: openLocation(gbzDb, this.pluginManager),\n        haplotypeIndex: indexLocation\n          ? openLocation(indexLocation, this.pluginManager)\n          : undefined,\n      })\n      const anchor = this.getConf('assemblyNames')[0]\n      if (anchor === undefined) {\n        throw new Error(\n          'GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as',\n        )\n      }\n      const referenceSamples = await referenceSamplesOf(db)\n      const referenceSample = resolveReferenceSample({\n        configured: this.getConf('referenceSample'),\n        anchorPrefix: resolvePanSNPrefix(this, anchor),\n        referenceSamples,\n      })\n      return {\n        db,\n        anchor,\n        referenceSample,\n        referenceSamples,\n        unreadableIndex: companion.unreadable,\n      }\n    },\n  })\n\n  /**\n   * The indexed reference path a window on `refName` resolves against, or\n   * undefined when the reference sample has no indexed path by that contig.\n   */\n  private async referenceQuery(\n    refName: string,\n    opts: BaseOptions,\n  ): Promise<PathQuery | undefined> {\n    const { db, referenceSample } = await this.graph(opts)\n    return referencePathQuery(db, referenceSample, refName)\n  }\n\n  /**\n   * Every haplotype the graph carries a walk for, `sample#haplotype` with its\n   * contigs, from the Paths scan the adapter already makes; the lane picker's\n   * source list. Reference samples are included and flagged.\n   */\n  async getHaplotypes(opts: BaseOptions = {}): Promise<GbzHaplotype[]> {\n    const { db, referenceSamples } = await this.graph(opts)\n    const byPrefix = new Map<string, GbzHaplotype>()\n    for (const path of await db.paths()) {\n      const prefix = haplotypePrefix(path.name)\n      const entry = byPrefix.get(prefix)\n      if (entry) {\n        if (!entry.contigs.includes(path.name.contig)) {\n          entry.contigs.push(path.name.contig)\n        }\n      } else {\n        byPrefix.set(prefix, {\n          prefix,\n          sample: path.name.sample,\n          haplotype: path.name.haplotype,\n          contigs: [path.name.contig],\n          isReference: referenceSamples.includes(path.name.sample),\n        })\n      }\n    }\n    return [...byPrefix.values()]\n  }\n\n  /**\n   * `lanes` is every haplotype but the reference sample's own, which is the\n   * anchor rather than a lane, declared up front so the display can offer the\n   * whole graph's haplotypes before a fetch has placed any of them.\n   */\n  async getHeader(opts: BaseOptions = {}) {\n    const { anchor, referenceSample, referenceSamples } = await this.graph(opts)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    const lanes: GbzHeaderLane[] = []\n    for (const haplotype of await this.getHaplotypes(opts)) {\n      if (haplotype.sample !== referenceSample) {\n        lanes.push({\n          name: laneAssemblyName(asmByPrefix, haplotype),\n          label: haplotype.prefix,\n          group: haplotype.sample,\n        })\n      }\n    }\n    return {\n      hasCoarseTier: false,\n      anchorAssemblyName: anchor,\n      referenceSample,\n      referenceSamples,\n      lanes,\n    }\n  }\n\n  async getRefNames(opts: BaseOptions = {}) {\n    const { db, anchor, referenceSample } = await this.graph(opts)\n    const { assemblyName } = opts\n    const prefix =\n      assemblyName === anchor\n        ? undefined\n        : resolvePanSNPrefix(this, assemblyName)\n    const contigs = (await db.paths())\n      .filter(path =>\n        assemblyName === anchor\n          ? path.isIndexed && path.name.sample === referenceSample\n          : panSNMatchesPrefix(haplotypePrefix(path.name), prefix),\n      )\n      .map(path => path.name.contig)\n    return [...new Set(contigs)]\n  }\n\n  /**\n   * The predicate gbz-base builds a window for, from the lanes a fetch asks\n   * for. With a companion whose stray rows cover the window gbz-base walks\n   * only the wanted haplotypes; otherwise it names every walk and keeps the\n   * ones the predicate accepts, and throws rather than guess when a walk has\n   * no name. Either way a cut holds those walks, the reference, and the nodes\n   * they visit. Undefined when every haplotype is wanted.\n   */\n  //\n  // `targetPrefix` is a pairwise view's one lane, and it belongs in here: left\n  // to filter what came back, it handed gbz-base no predicate, and every\n  // haplotype in the graph was walked for one to be kept.\n  private keepPredicate(\n    haplotypes: string[] | undefined,\n    targetPrefix?: string,\n  ) {\n    const wantedPrefixes =\n      haplotypes === undefined || haplotypes.length === 0\n        ? undefined\n        : haplotypes.map(lane => resolvePanSNPrefix(this, lane))\n    return wantedPrefixes === undefined && targetPrefix === undefined\n      ? undefined\n      : (name: PathName) =>\n          haplotypeWanted(name, wantedPrefixes) &&\n          (targetPrefix === undefined ||\n            panSNMatchesPrefix(haplotypePrefix(name), targetPrefix))\n  }\n\n  /**\n   * The graph view's cut of the window, as tables: the reference walk, every\n   * top-level snarl contained in it, and one walk per haplotype, PanSN-named\n   * when the database (or its companion) carries the haplotype index and\n   * `unknown#N` otherwise. The reference walk is the first, which is the one\n   * the view anchors on by default. With `haplotypes` the walks are that\n   * set's and the nodes those walks visit, the reference walk kept. With\n   * `walkRows` the rows' runs come along, as on a walk-file cut.\n   *\n   * Only a window on the anchor can be cut: a haplotype lane's coordinates\n   * are its own contig's, and the graph is indexed for random access on the\n   * reference sample's paths alone.\n   */\n  async getSubgraph(region: Region, opts: SubgraphAdapterOptions = {}) {\n    const { signal } = opts\n    const { db, anchor, referenceSample, unreadableIndex } = await this.graph({\n      signal,\n    })\n    const { assemblyName, refName, start, end } = wholeBp(region)\n    if (assemblyName !== anchor) {\n      throw new HaplotypeWindowError(assemblyName, anchor)\n    }\n    const query = await this.referenceQuery(refName, { signal })\n    if (!query) {\n      throw new Error(\n        `${referenceSample} has no indexed path ${refName} in this graph`,\n      )\n    }\n    const keep = this.keepPredicate(opts.haplotypes)\n    if (keep !== undefined && !db.hasHaplotypeIndex) {\n      throw new NoHaplotypeIndexError(unreadableIndex)\n    }\n    const cut = await cutWindowTables(db, query, start, end, {\n      context: this.getConf('context'),\n      snarls: opts.snarls ?? this.getConf('subgraphSnarls'),\n      limit: this.getConf('nodeLimit'),\n      signal: opts.signal,\n      keep,\n    }).catch((error: unknown) => {\n      throw zoomInNotice(error, 'the graph')\n    })\n    return typeof cut === 'string'\n      ? cut\n      : walkCutFor(cut, { start, end }, opts.walkRows)\n  }\n\n  private gaf = cachedSetup({\n    label: 'Opening reads',\n    setup: async () => {\n      const location: FileLocation = this.getConf('readsLocation')\n      const index: FileLocation = this.getConf(['readsIndex', 'location'])\n      return isSet(location)\n        ? new GafFile(\n            openLocation(location, this.pluginManager),\n            isSet(index)\n              ? openTabixSlot(this, ['readsLocation'], ['readsIndex'])\n              : undefined,\n          )\n        : undefined\n    },\n  })\n\n  /**\n   * The reads over a cut's segments, from `readsLocation`, sampled down to\n   * what the tube map lays out at interactive speed\n   */\n  async getReads(\n    nodeNames: string[],\n    opts: BaseOptions = {},\n  ): Promise<GafReads> {\n    const gaf = await this.gaf(opts)\n    return gaf\n      ? gaf.readsOver(new Set(nodeNames), opts)\n      : { records: [], total: 0 }\n  }\n\n  private async laneHaplotypes(\n    assemblyName: string,\n    opts: BaseOptions,\n  ): Promise<HaplotypeRef[]> {\n    const prefix = resolvePanSNPrefix(this, assemblyName)\n    return (await this.getHaplotypes(opts)).filter(haplotype =>\n      panSNMatchesPrefix(haplotype.prefix, prefix),\n    )\n  }\n\n  private async anchorFeatures(region: Region, opts: GbzFeatureOptions) {\n    const { db } = await this.graph(opts)\n    const { assemblyName, refName, start, end } = region\n    const targetPrefix = resolvePanSNPrefix(this, opts.targetAssemblyName)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    const keep = this.keepPredicate(opts.haplotypes, targetPrefix)\n    const query = await this.referenceQuery(refName, opts)\n    const nodeLimit: number = this.getConf('nodeLimit')\n    const alignments = query\n      ? await updateStatus(\n          `Reading graph ${refName}:${start.toLocaleString()}-${end.toLocaleString()}`,\n          opts.statusCallback,\n          () =>\n            db\n              .getAlignments({\n                path: query,\n                start,\n                end,\n                context: this.getConf('context'),\n                haplotypes: 'all',\n                limit: nodeLimit,\n                signal: opts.signal,\n                keep,\n              })\n              .catch((error: unknown) => {\n                throw zoomInNotice(\n                  nodeLimitError(error, nodeLimit, end - start) ?? error,\n                  'lanes',\n                )\n              }),\n        )\n      : []\n    return alignments.flatMap(alignment => {\n      const feature = alignment.resolved\n        ? fragmentFeature({\n            alignment,\n            assemblyName,\n            refName,\n            lane: laneAssemblyName(asmByPrefix, alignment.name),\n          })\n        : undefined\n      return feature === undefined ? [] : [feature]\n    })\n  }\n\n  /**\n   * Each pair's two lanes cut out of the anchor window alone, all pairs in one\n   * cut, and each walk of a pair's query lane aligned to each walk of its\n   * target lane on the nodes both visit, with no base compared. A pair's\n   * records sit on its query lane's contigs, the lane the display draws on top.\n   *\n   * Whether the index has anchor rows changes only how fast gbz-base finds\n   * the walks: both routes cut the same pieces.\n   */\n  private async pairFeatures(\n    region: Region,\n    pairs: LanePair[],\n    opts: GbzFeatureOptions,\n  ) {\n    const { db } = await this.graph(opts)\n    const { refName, start, end } = region\n    const sides = await Promise.all(\n      pairs.map(async pair => ({\n        pair,\n        featureSide: await this.laneHaplotypes(pair.queryAssemblyName, opts),\n        mateSide: await this.laneHaplotypes(pair.targetAssemblyName, opts),\n      })),\n    )\n    const answerable = sides.filter(\n      ({ featureSide, mateSide }) =>\n        featureSide.length > 0 && mateSide.length > 0,\n    )\n    const kept = new Set(\n      answerable.flatMap(({ featureSide, mateSide }) =>\n        [...featureSide, ...mateSide].map(haplotypePrefix),\n      ),\n    )\n    const query = await this.referenceQuery(refName, opts)\n    const nodeLimit: number = this.getConf('nodeLimit')\n    const baseContext: number = this.getConf('context')\n    const [first] = pairs\n    const cut = (path: PathQuery, context: number) =>\n      db.getSubgraphs({\n        path,\n        start,\n        end,\n        context,\n        snarls: this.getConf('subgraphSnarls'),\n        haplotypes: 'all',\n        limit: nodeLimit,\n        signal: opts.signal,\n        keep: name => kept.has(haplotypePrefix(name)),\n      })\n    // a cut past the node limit for the wider context keeps the first one\n    const bridged = async (path: PathQuery) => {\n      const subgraphs = await cut(path, baseContext).catch((error: unknown) => {\n        throw zoomInNotice(\n          nodeLimitError(error, nodeLimit, end - start) ?? error,\n          'lanes',\n        )\n      })\n      const gap = widestWalkGap(subgraphs, kept)\n      const context = Math.ceil(gap / 2) + 2000\n      return gap > 0 && context > baseContext\n        ? cut(path, context).catch((error: unknown) => {\n            if (error instanceof SubgraphLimitError) {\n              return subgraphs\n            }\n            throw error\n          })\n        : subgraphs\n    }\n    const subgraphs =\n      query && first && answerable.length > 0\n        ? await updateStatus(\n            pairs.length === 1\n              ? `Reading ${first.queryAssemblyName} against ${first.targetAssemblyName}`\n              : `Reading ${pairs.length} lane pairs`,\n            opts.statusCallback,\n            () => bridged(query),\n          )\n        : []\n    return subgraphs.flatMap(subgraph =>\n      answerable.flatMap(({ pair, featureSide, mateSide }) =>\n        featureSide.flatMap(target =>\n          mateSide.flatMap(mate =>\n            subgraph\n              .pairAlignments({ target, query: mate, bases: false })\n              .map(alignment =>\n                pairFeature({\n                  pair: alignment,\n                  lane: pair.queryAssemblyName,\n                  mateLane: pair.targetAssemblyName,\n                }),\n              ),\n          ),\n        ),\n      ),\n    )\n  }\n\n  getFeatures(asked: Region, opts: GbzFeatureOptions = {}) {\n    const region = wholeBp(asked)\n    return ObservableCreate<Feature>(async observer => {\n      const { db, anchor, unreadableIndex } = await this.graph(opts)\n      if (!db.hasHaplotypeIndex) {\n        throw new NoHaplotypeIndexError(unreadableIndex)\n      }\n      // the graph is indexed on its reference alone, so a window on a\n      // haplotype lane has no answer: a lane pair is read inside the anchor's\n      if (region.assemblyName === anchor) {\n        const pairs = requestedPairs(opts)\n        const features =\n          pairs.length > 0\n            ? await this.pairFeatures(region, pairs, opts)\n            : await this.anchorFeatures(region, opts)\n        for (const feature of features) {\n          observer.next(feature)\n        }\n      }\n      observer.complete()\n    }, opts.signal)\n  }\n}\n"],
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package/dist/chunks/{GraphGenomeView-NFC2XO4Z.js → GraphGenomeView-3ZJSM36D.js}

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   "sourcesContent": ["import { ErrorBanner, LoadingEllipses } from '@jbrowse/core/ui'\nimport { Button, LinearProgress, Paper, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport type { GraphPaneModel } from '../model'\n\nconst useStyles = makeStyles()({\n  paper: {\n    padding: 16,\n    margin: 8,\n    maxWidth: 560,\n    marginInline: 'auto',\n    display: 'flex',\n    flexDirection: 'column',\n    gap: 12,\n  },\n  row: {\n    display: 'flex',\n    alignItems: 'center',\n    justifyContent: 'space-between',\n    gap: 8,\n  },\n})\n\n// What a view with no graph on screen shows while its load runs, and after a\n// load of a source it can retry was canceled or failed.\nconst GraphLoadStatus = observer(function GraphLoadStatus({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const { classes } = useStyles()\n  if (model.isLoading) {\n    return (\n      <Paper className={classes.paper} data-testid=\"graph-genome-loading\">\n        <div className={classes.row}>\n          <LoadingEllipses variant=\"h6\" message={model.statusMessage} />\n          <Button\n            size=\"small\"\n            data-testid=\"graph-genome-cancel\"\n            onClick={() => {\n              model.cancelLoad()\n            }}\n          >\n            Cancel\n          </Button>\n        </div>\n        <LinearProgress variant=\"indeterminate\" />\n      </Paper>\n    )\n  }\n  if (model.error) {\n    return (\n      <Paper className={classes.paper}>\n        <ErrorBanner\n          error={model.error}\n          onReset={() => {\n            model.retryLoad()\n          }}\n        />\n      </Paper>\n    )\n  }\n  return (\n    <Paper className={classes.paper} data-testid=\"graph-genome-load-canceled\">\n      <div className={classes.row}>\n        <Typography variant=\"h6\">Loading canceled</Typography>\n        <Button\n          variant=\"contained\"\n          size=\"small\"\n          data-testid=\"graph-genome-retry\"\n          onClick={() => {\n            model.retryLoad()\n          }}\n        >\n          Retry\n        </Button>\n      </div>\n    </Paper>\n  )\n})\n\nexport default GraphLoadStatus\n", "import { useState } from 'react'\n\nimport { ErrorBanner } from '@jbrowse/core/ui'\nimport { Button, Paper, TextField, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport type { GraphPaneModel } from '../model'\n\nconst EXAMPLE_GFA = `H\\tVN:Z:1.0\nS\\t1\\tACGT\nS\\t2\\tGGCC\nS\\t3\\tTTAA\nS\\t4\\tCCGG\nL\\t1\\t+\\t2\\t+\\t0M\nL\\t1\\t+\\t3\\t+\\t0M\nL\\t2\\t+\\t4\\t+\\t0M\nL\\t3\\t+\\t4\\t+\\t0M`\n\nconst useStyles = makeStyles()({\n  column: { display: 'flex', flexDirection: 'column', gap: 8 },\n  rowEnd: { display: 'flex', gap: 8, alignItems: 'flex-end' },\n  rowCenter: { display: 'flex', gap: 8, alignItems: 'center' },\n  flex1: { flex: 1 },\n  paper: { padding: 16, margin: 8, maxWidth: 560, marginInline: 'auto' },\n  header: { marginBottom: 12 },\n  footer: { marginTop: 12, display: 'flex', justifyContent: 'flex-end' },\n})\n\nconst ImportForm = observer(function ImportForm({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const { classes } = useStyles()\n  const [url, setUrl] = useState('')\n\n  function handleUrlLoad() {\n    const uri = url.trim()\n    if (uri) {\n      void model.loadGFAFromLocation({ uri, locationType: 'UriLocation' })\n    }\n  }\n\n  function handleFileUpload(event: React.ChangeEvent<HTMLInputElement>) {\n    const file = event.target.files?.[0]\n    // or picking the same file again fires no change\n    event.target.value = ''\n    if (file) {\n      file\n        .text()\n        .then(text => model.loadGFA(text, file.name))\n        .catch((err: unknown) => {\n          model.setError(err)\n        })\n    }\n  }\n\n  return (\n    <Paper className={classes.paper}>\n      <div className={classes.header}>\n        <Typography variant=\"h6\">Load a GFA graph</Typography>\n      </div>\n\n      <div className={classes.column}>\n        <div className={classes.rowCenter}>\n          <Button variant=\"outlined\" component=\"label\" size=\"small\">\n            Choose file\n            <input\n              type=\"file\"\n              accept=\".gfa,.gfa1,.gfa2\"\n              hidden\n              onChange={event => {\n                handleFileUpload(event)\n              }}\n            />\n          </Button>\n          <Typography variant=\"caption\" color=\"text.secondary\">\n            Whole-file GFA; best for small/medium graphs.\n          </Typography>\n        </div>\n\n        <div className={classes.rowEnd}>\n          <TextField\n            size=\"small\"\n            label=\"URL\"\n            placeholder=\"https://example.com/graph.gfa\"\n            value={url}\n            onChange={e => {\n              setUrl(e.target.value)\n            }}\n            onKeyDown={e => {\n              if (e.key === 'Enter') {\n                handleUrlLoad()\n              }\n            }}\n            className={classes.flex1}\n          />\n          <Button\n            variant=\"contained\"\n            onClick={() => {\n              handleUrlLoad()\n            }}\n            disabled={!url.trim()}\n          >\n            Open\n          </Button>\n        </div>\n      </div>\n\n      <div className={classes.footer}>\n        <Button\n          size=\"small\"\n          onClick={() => {\n            void model.loadGFA(EXAMPLE_GFA, 'Example graph')\n          }}\n        >\n          Load 4-node example\n        </Button>\n      </div>\n\n      {model.error ? <ErrorBanner error={model.error} /> : null}\n    </Paper>\n  )\n})\n\nexport default ImportForm\n", "import { observer } from 'mobx-react'\n\nimport GraphCanvas from './GraphCanvas'\nimport GraphLoadStatus from './GraphLoadStatus'\nimport ImportForm from './ImportForm'\n\nimport type { GraphPaneModel } from '../model'\n\nconst GraphGenomeView = observer(function GraphGenomeView({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  if (model.hasGraph) {\n    return <GraphCanvas model={model} />\n  }\n  // A launched or restored view has a source of its own, so the import form\n  // has nothing to offer it when that source fails\n  if (model.canRetryLoad && (model.error || model.loadCanceled)) {\n    return <GraphLoadStatus model={model} />\n  }\n  // Hidden rather than unmounted, so a typed URL survives a failed load\n  return (\n    <>\n      {model.isLoading ? <GraphLoadStatus model={model} /> : null}\n      <div hidden={model.isLoading}>\n        <ImportForm model={model} />\n      </div>\n    </>\n  )\n})\n\nexport default GraphGenomeView\n"],
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 }

package/dist/chunks/GraphTrackSettingsDialog-JHKKV2S4.js

@@ -0,0 +1,6 @@
+import{b as x}from"./chunk-BQQTY3GZ.js";import{c as H}from"./chunk-EAZJJZAY.js";import{q as u}from"./chunk-OTU3GXFO.js";import"./chunk-5JKSYSN5.js";import"./chunk-VAATBXRG.js";import"./chunk-KFP5PZRE.js";import{g as h}from"./chunk-6OPB7FOJ.js";import{D as v,F as y,H as c,n as g,s as b,w as S,z as C}from"./chunk-E3WYW7Z6.js";import{b as a,c as l,d as i}from"./chunk-JMBDTNUR.js";var k=u()({section:{marginBottom:24},formControl:{minWidth:200}}),F=[{value:0,label:"None"},{value:1,label:"1 hop"},{value:2,label:"2 hops"}],M=i(function({model:e}){let{classes:t}=k();return e.adapterConfig.type==="RgfaTabixAdapter"?l("div",{className:t.section,children:[l(b,{className:t.formControl,children:[a(S,{children:"Graph context"}),a(v,{value:e.subgraphContext,label:"Graph context","data-testid":"graph-context-select",onChange:o=>{e.setSubgraphContext(o.target.value),e.cut()},children:F.map(({value:o,label:p})=>a(C,{value:o,children:p},o))})]}),a(c,{variant:"caption",component:"div",color:"text.secondary",children:"How far the cut follows links out of the region. At none, a detour that leaves the window draws as two stubs. No effect on gfa-to-tabix's default anchored index."})]}):null}),G=M;var N=u()({section:{marginBottom:24}});function P(n){let e=n.split(/[\s,]+/).map(t=>t.trim()).filter(t=>t!=="");return e.length===0?void 0:e}var T=i(function({model:e}){let[t,o]=h(e.chosenHaplotypes?.join(", ")??""),p=()=>{let r=P(t)??[];r.join(`
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+`)||(e.setSubgraphHaplotypes(r),e.cut())};return a(y,{fullWidth:!0,label:"Haplotypes",placeholder:"every haplotype",value:t,slotProps:{htmlInput:{"data-testid":"graph-haplotypes-field"}},onChange:r=>{o(r.target.value)},onBlur:()=>{p()},onKeyDown:r=>{r.key==="Enter"&&p()}})}),I=i(function({model:e,names:t}){let[o,p]=h(e.chosenHaplotypes??[]),[r,d]=h(!1),f=s=>{s.join(`
+`)!==(e.chosenHaplotypes??[]).join(`
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+//# sourceMappingURL=GraphTrackSettingsDialog-JHKKV2S4.js.map

package/dist/chunks/GraphTrackSettingsDialog-JHKKV2S4.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/LinearGraphDisplay/components/SubgraphContextSelect.tsx", "../../src/LinearGraphDisplay/components/SubgraphHaplotypesField.tsx", "../../src/LinearGraphDisplay/components/GraphTrackSettingsDialog.tsx"],
+  "sourcesContent": ["import {\n  FormControl,\n  InputLabel,\n  MenuItem,\n  Select,\n  Typography,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport type { LinearGraphCutModel } from '../model'\n\nconst useStyles = makeStyles()({\n  section: {\n    marginBottom: 24,\n  },\n  formControl: {\n    minWidth: 200,\n  },\n})\n\n// Only an rGFA cut reads hops; a GBZ cut widens by its adapter's bp `context`.\n// Hops past the region's own segments, each costing a tabix query per\n// off-reference segment already reached. One is the default: at none a single\n// detour draws as two unrelated stubs, which is a wrong picture of the graph\n// rather than a cheaper one. Two exists for a graph whose alleles have alleles\n// (HPRC's amylase window keeps growing at 2, the E. coli paa locus does not), and\n// it stops there because a frontier is still not a bubble decomposition. Cut an\n// exact slice with gfatools when that is what is wanted.\nconst SUBGRAPH_CONTEXTS = [\n  { value: 0, label: 'None' },\n  { value: 1, label: '1 hop' },\n  { value: 2, label: '2 hops' },\n]\n\nconst SubgraphContextSelect = observer(function SubgraphContextSelect({\n  model,\n}: {\n  model: LinearGraphCutModel\n}) {\n  const { classes } = useStyles()\n  return model.adapterConfig.type === 'RgfaTabixAdapter' ? (\n    <div className={classes.section}>\n      <FormControl className={classes.formControl}>\n        <InputLabel>Graph context</InputLabel>\n        <Select\n          value={model.subgraphContext}\n          label=\"Graph context\"\n          data-testid=\"graph-context-select\"\n          onChange={e => {\n            model.setSubgraphContext(e.target.value)\n            void model.cut()\n          }}\n        >\n          {SUBGRAPH_CONTEXTS.map(({ value, label }) => (\n            <MenuItem key={value} value={value}>\n              {label}\n            </MenuItem>\n          ))}\n        </Select>\n      </FormControl>\n      <Typography variant=\"caption\" component=\"div\" color=\"text.secondary\">\n        How far the cut follows links out of the region. At none, a detour that\n        leaves the window draws as two stubs. No effect on gfa-to-tabix&apos;s\n        default anchored index.\n      </Typography>\n    </div>\n  ) : null\n})\n\nexport default SubgraphContextSelect\n", "import { useState } from 'react'\n\nimport { Autocomplete, TextField, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport { cutsByHaplotype } from '../../graphTrackConfig'\n\nimport type { LinearGraphCutModel } from '../model'\n\nconst useStyles = makeStyles()({\n  section: {\n    marginBottom: 24,\n  },\n})\n\nexport function parseHaplotypeList(text: string) {\n  const names = text\n    .split(/[\\s,]+/)\n    .map(name => name.trim())\n    .filter(name => name !== '')\n  return names.length === 0 ? undefined : names\n}\n\nconst HaplotypeListField = observer(function HaplotypeListField({\n  model,\n}: {\n  model: LinearGraphCutModel\n}) {\n  const [draft, setDraft] = useState(model.chosenHaplotypes?.join(', ') ?? '')\n  const apply = () => {\n    const parsed = parseHaplotypeList(draft) ?? []\n    const unchanged =\n      parsed.join('\\n') === (model.chosenHaplotypes ?? []).join('\\n')\n    if (!unchanged) {\n      model.setSubgraphHaplotypes(parsed)\n      void model.cut()\n    }\n  }\n  return (\n    <TextField\n      fullWidth\n      label=\"Haplotypes\"\n      placeholder=\"every haplotype\"\n      value={draft}\n      slotProps={{ htmlInput: { 'data-testid': 'graph-haplotypes-field' } }}\n      onChange={e => {\n        setDraft(e.target.value)\n      }}\n      onBlur={() => {\n        apply()\n      }}\n      onKeyDown={e => {\n        if (e.key === 'Enter') {\n          apply()\n        }\n      }}\n    />\n  )\n})\n\n// The haplotypes a walk-indexed graph's header names, searched as typed. A\n// typed prefix the list lacks (HG002 for both haplotypes) is kept too. The\n// set applies when the list closes or, with the list closed, as it changes.\nconst HaplotypePickField = observer(function HaplotypePickField({\n  model,\n  names,\n}: {\n  model: LinearGraphCutModel\n  names: string[]\n}) {\n  const [draft, setDraft] = useState(model.chosenHaplotypes ?? [])\n  const [open, setOpen] = useState(false)\n  const apply = (haplotypes: string[]) => {\n    if (haplotypes.join('\\n') !== (model.chosenHaplotypes ?? []).join('\\n')) {\n      model.setSubgraphHaplotypes(haplotypes)\n      void model.cut()\n    }\n  }\n  return (\n    <Autocomplete\n      multiple\n      freeSolo\n      disableCloseOnSelect\n      options={names}\n      value={draft}\n      open={open}\n      onOpen={() => {\n        setOpen(true)\n      }}\n      onClose={() => {\n        setOpen(false)\n        apply(draft)\n      }}\n      onChange={(_, value) => {\n        setDraft(value)\n        if (!open) {\n          apply(value)\n        }\n      }}\n      renderInput={params => (\n        <TextField\n          {...params}\n          label=\"Haplotypes\"\n          placeholder={draft.length === 0 ? 'every haplotype' : undefined}\n          slotProps={{\n            ...params.slotProps,\n            htmlInput: {\n              ...params.slotProps.htmlInput,\n              'data-testid': 'graph-haplotypes-field',\n            },\n          }}\n        />\n      )}\n    />\n  )\n})\n\n// Only a GBZ cut and a walk-indexed rGFA cut read the set. The inner field is\n// keyed on it so an outside change (a restored session, a launch) resets the\n// draft rather than fighting it.\nconst SubgraphHaplotypesField = observer(function SubgraphHaplotypesField({\n  model,\n}: {\n  model: LinearGraphCutModel\n}) {\n  const { classes } = useStyles()\n  const names = model.haplotypeNames\n  const key = model.chosenHaplotypes?.join(',') ?? ''\n  return cutsByHaplotype(model.adapterConfig) ? (\n    <div className={classes.section}>\n      {names ? (\n        <HaplotypePickField key={key} model={model} names={names} />\n      ) : (\n        <HaplotypeListField key={key} model={model} />\n      )}\n      <Typography variant=\"caption\" component=\"div\" color=\"text.secondary\">\n        {names\n          ? `Which of the graph's ${names.length.toLocaleString()} haplotypes to cut, or a PanSN prefix (HG002 for both).`\n          : 'Which haplotypes to cut, as lane assembly names or PanSN prefixes (HG002#1, or HG002 for both) separated by commas.'}{' '}\n        Empty is every haplotype.\n      </Typography>\n    </div>\n  ) : null\n})\n\nexport default SubgraphHaplotypesField\n", "import SubgraphContextSelect from './SubgraphContextSelect'\nimport SubgraphHaplotypesField from './SubgraphHaplotypesField'\nimport GraphSettingsDialog from '../../GraphGenomeView/components/GraphSettingsDialog'\n\nimport type { LinearGraphCutModel } from '../model'\n\nexport default function GraphTrackSettingsDialog({\n  model,\n  open,\n  onClose,\n}: {\n  model: LinearGraphCutModel\n  open: boolean\n  onClose: () => void\n}) {\n  return (\n    <GraphSettingsDialog model={model} open={open} onClose={onClose}>\n      <SubgraphContextSelect model={model} />\n      <SubgraphHaplotypesField model={model} />\n    </GraphSettingsDialog>\n  )\n}\n"],
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+  "names": ["useStyles", "makeStyles", "SUBGRAPH_CONTEXTS", "SubgraphContextSelect", "observer", "model", "classes", "jsxs", "FormControl", "jsx", "InputLabel", "Select", "e", "value", "label", "MenuItem", "Typography", "SubgraphContextSelect_default", "useStyles", "makeStyles", "parseHaplotypeList", "text", "names", "name", "HaplotypeListField", "observer", "model", "draft", "setDraft", "useState", "apply", "parsed", "jsx", "TextField", "e", "HaplotypePickField", "open", "setOpen", "haplotypes", "Autocomplete", "_", "value", "params", "SubgraphHaplotypesField", "classes", "key", "cutsByHaplotype", "jsxs", "Typography", "SubgraphHaplotypesField_default", "GraphTrackSettingsDialog", "model", "open", "onClose", "jsxs", "GraphSettingsDialog_default", "jsx", "SubgraphContextSelect_default", "SubgraphHaplotypesField_default"]
+}

package/dist/chunks/{HighlightColorDialog-6B3HM5K5.js → HighlightColorDialog-H6AGVINB.js}

@@ -1,2 +1,2 @@
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+//# sourceMappingURL=HighlightColorDialog-H6AGVINB.js.map

package/dist/chunks/{LinearGraphDisplay-77UBGSWR.js → LinearGraphDisplay-RTMEWTK4.js}

@@ -1,2 +1,2 @@
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package/dist/chunks/{MinigraphBubbleAdapter-OEOJKDBZ.js → MinigraphBubbleAdapter-FKDOLLD3.js}

@@ -1,2 +1,2 @@
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package/dist/chunks/{RgfaTabixAdapter-Q2URYHKT.js → RgfaTabixAdapter-SMDO5VX7.js}

@@ -1,3 +1,3 @@
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+//# sourceMappingURL=RgfaTabixAdapter-SMDO5VX7.js.map

package/dist/chunks/{TrackWarningsDialog-XBUQM2ZH.js → TrackWarningsDialog-QT4YEXGD.js}

@@ -1,2 +1,2 @@
-import{G as i,g as o,l as a}from"./chunk-ECD5B2ZM.js";import{c as r,d as e}from"./chunk-JMBDTNUR.js";var u=e(function({model:n,title:s,children:l,handleClose:m}){return r(o,{open:!0,title:s,onClose:()=>{m()},children:[l,n.trackWarnings.flatMap(({name:f,warnings:g},p)=>g.map((t,c)=>r(a,{severity:"warning",style:{marginBottom:8},children:[r(i,{variant:"subtitle2",children:[f,": ",t.message]}),t.effect]},`${p}_${c}`)))]})}),x=u;export{x as default};
-//# sourceMappingURL=TrackWarningsDialog-XBUQM2ZH.js.map
+import{H as i,g as o,m as a}from"./chunk-E3WYW7Z6.js";import{c as r,d as e}from"./chunk-JMBDTNUR.js";var u=e(function({model:n,title:s,children:l,handleClose:m}){return r(o,{open:!0,title:s,onClose:()=>{m()},children:[l,n.trackWarnings.flatMap(({name:f,warnings:g},p)=>g.map((t,c)=>r(a,{severity:"warning",style:{marginBottom:8},children:[r(i,{variant:"subtitle2",children:[f,": ",t.message]}),t.effect]},`${p}_${c}`)))]})}),x=u;export{x as default};
+//# sourceMappingURL=TrackWarningsDialog-QT4YEXGD.js.map

package/dist/chunks/WalkTabixSyntenyAdapter-L2E7QSX2.js

@@ -0,0 +1,2 @@
+import{b as O,c as D}from"./chunk-TH3R5SGF.js";import{a as _,b as q,d as j}from"./chunk-LCODIX3W.js";import{c as v,e as x,f as T}from"./chunk-HHADQLAY.js";import{a as C,b as L,f as $}from"./chunk-3GI2K2L7.js";import{h as I}from"./chunk-6NKKRJ2C.js";import"./chunk-VAATBXRG.js";import"./chunk-YBLNN5FU.js";import{a as S,c as P,d as F,e as A,f as N,g as W}from"./chunk-KFP5PZRE.js";import"./chunk-E7J6SB5P.js";import"./chunk-7WIBGKBU.js";import"./chunk-OGQ6OQDN.js";import{o as R}from"./chunk-TENPGIPX.js";var Y=50;function Z(i){let e=[];for(let t=0;t<i.length;t++){let[r,s]=i[t],[a,n]=i[t+1]??[];s===n&&s<=Y&&(r==="I"&&a==="D"||r==="D"&&a==="I")?(e.push(["X",s]),t++):e.push([r,s])}return e}function ee(i){return i.map(([e,t])=>`${t}${e}`).join("")}function H(i){let e=new Map,t=a=>{let n=i.get(a),o=n===void 0?0:n.end-n.start,p=e.get(o);return p===void 0&&(p="N".repeat(o),e.set(o,p)),p},r=new Map,s=a=>{let n=r.get(a);return n===void 0&&(n=Array.from(a.ids,(o,p)=>2*o+a.rev[p]),r.set(a,n)),n};return(a,n)=>L({query:s(a),target:s(n),sequenceOf:t,bases:!1})}var te=100;function E(i,e,t){let r=i.at(-1);t>0&&(r?.[0]===e?r[1]+=t:i.push([e,t]))}function X(i){let e=s=>{let a=i.get(s>>1);return a===void 0?0:a.end-a.start},t=s=>{let a=new Float64Array(s.length+1);return s.forEach((n,o)=>{a[o+1]=a[o]+e(n)}),a},r=s=>Array.from(s.ids,(a,n)=>2*a+s.rev[n]);return(s,a)=>{let n=r(a),o=r(s),[p,g]=C(o,n,e),[f,l]=C(o.map(b=>b^1).reverse(),n,e),u=l>g,c=u?f:p,d=Math.max(g,l);if(d<te)return[];let h=t(n),m=t(o),y=b=>u?o.length-1-c[b][0]:c[b][0],w=[];c.forEach(([,b],k)=>{if(k>0){let[U,J]=[y(k-1),y(k)].sort((Q,V)=>Q-V);E(w,"I",m[J]-m[U+1]),E(w,"D",h[b]-h[c[k-1][1]+1])}E(w,"=",e(n[b]))});let[z,K]=[y(0),y(c.length-1)].sort((b,k)=>b-k);return[{queryStart:m[z],queryEnd:m[K+1],targetStart:h[c[0][1]],targetEnd:h[c.at(-1)[1]+1],strand:u?"-":"+",edits:w,sharedBases:d}]}}function M({chain:i,target:e,query:t,assemblyName:r,refName:s,mateAssemblyName:a}){let n=e.hapStart+i.targetStart,o=e.hapStart+i.targetEnd,p=t.hapStart+i.queryStart,g=t.hapStart+i.queryEnd,f=Z(i.edits),l=f.reduce((d,[h,m])=>d+(h==="="?m:0),0),u=f.reduce((d,[,h])=>d+h,0),c=`${e.name}:${n}-${o}|${t.name}:${p}-${g}`;return new _({uniqueId:c,assemblyName:r,refName:s,start:n,end:o,type:"match",strand:i.strand==="-"?-1:1,CIGAR:ee(f),syntenyId:c,identity:l/Math.max(u,1),numMatches:l,blockLen:u,mate:{refName:F(t.name),start:p,end:g,assemblyName:a}})}var ae=1e3;function G(i,e){return i[e]??i[S(e)]??e}var ne=i=>P(i.name)??i.name,B=class extends q{constructor(e,t,r){super(e,t,r);let s=x(this,["nodesLocation"],["nodesIndex"]);this.reader=new D({walks:x(this,["walksLocation"],["walksIndex"]),nodes:s,links:x(this,["linksLocation"],["linksIndex"])},this.getConf("walkChunk")),this.refNames=new T(s,this)}get anchor(){let e=this.getConf("assemblyNames")[0];if(e===void 0)throw new Error("WalkTabixSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");return e}async getHaplotypeNames(e={}){let{haplotypes:t}=await this.reader.header(e);return t.length>0?t:void 0}async getHeader(e={}){let{haplotypes:t,references:r}=await this.reader.header(e),{anchor:s}=this,a=N(this,s),n=W(this);return{hasCoarseTier:!1,anchorAssemblyName:s,referenceSamples:r,lanes:t.filter(o=>o!==a&&S(o)!==a).map(o=>({name:G(n,o),label:o,group:S(o)}))}}async getRefNames(e={}){let{assemblyName:t}=e;return t===void 0||t===this.anchor?this.refNames.assemblyRefNames({...e,assemblyName:this.anchor}):[]}budgets(e){return{stepBudget:e?1/0:this.getConf("walkStepBudget"),byteBudget:this.getConf("walkByteBudget"),context:ae}}async getSubgraph(e,t={}){let{signal:r,haplotypes:s,walkRows:a}=t,n=await this.refNames.resolve(e,{signal:r});if(n===void 0)throw new Error(`${e.assemblyName} ${e.refName} is not in this graph's index; the graph is cut on ${this.anchor}, mapped to its PanSN prefix in assemblyNameToPanSN`);let{graph:o,kept:p,fragments:g}=await this.reader.cut(n,e,{...this.budgets(a),signal:r,keep:O(s?.map(f=>N(this,f)),P(n))});return I(o.tables(p,g),e,a)}async laneWalks(e,t,r,s,a){return R(a,s.statusCallback,()=>this.reader.cut(e,t,{...this.budgets(),signal:s.signal,keep:O(r,P(e)),links:!1}).catch(n=>{throw n instanceof $&&(n.message=n.message.replace("to see the graph","to see lanes")),n}))}async anchorFeatures(e,t,r){let s=r.haplotypes?.length?r.haplotypes.map(m=>N(this,m)):void 0,a=N(this,r.targetAssemblyName),n=a===void 0?s:s===void 0||s.some(m=>A(a,m)||A(m,a))?[a]:[];if(n?.length===0)return[];let{start:o,end:p}=t,{graph:g,fragments:f}=await this.laneWalks(e,t,n,r,`Reading walks ${t.refName}:${o.toLocaleString()}-${p.toLocaleString()}`),l=X(g.nodes),u=W(this),c=f.filter(m=>m.name===e),d=m=>n===void 0?0:n.findIndex(y=>A(m.name,y));return f.filter(m=>m.name!==e&&d(m)>=0).sort((m,y)=>d(m)-d(y)).flatMap(m=>c.flatMap(y=>l(m,y).map(w=>M({chain:w,target:y,query:m,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:G(u,ne(m))}))))}async pairFeatures(e,t,r,s){let[a]=r,n=r.map(l=>({pair:l,featurePrefix:N(this,l.queryAssemblyName),matePrefix:N(this,l.targetAssemblyName)})),{graph:o,fragments:p}=await this.laneWalks(e,t,n.flatMap(l=>[l.featurePrefix,l.matePrefix]),s,r.length===1&&a?`Reading ${a.queryAssemblyName} against ${a.targetAssemblyName}`:`Reading ${r.length} lane pairs`),g=H(o.nodes),f=l=>p.filter(u=>A(u.name,l));return n.flatMap(({pair:l,featurePrefix:u,matePrefix:c})=>f(u).flatMap(d=>f(c).flatMap(h=>g(h,d).map(m=>M({chain:m,target:d,query:h,assemblyName:l.queryAssemblyName,refName:F(d.name),mateAssemblyName:l.targetAssemblyName})))))}getFeatures(e,t={}){return v(async r=>{let s=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(s!==void 0){let a=j(t),n=a.length>0?await this.pairFeatures(s,e,a,t):await this.anchorFeatures(s,e,t);for(let o of n)r.next(o)}r.complete()},t.signal)}};export{B as default,G as laneOf};
+//# sourceMappingURL=WalkTabixSyntenyAdapter-L2E7QSX2.js.map

package/dist/chunks/{WalkTabixSyntenyAdapter-RXTCCCDB.js.map → WalkTabixSyntenyAdapter-L2E7QSX2.js.map}

@@ -2,6 +2,6 @@
   "version": 3,
   "sources": ["../../src/WalkTabixSyntenyAdapter/walkLanes.ts", "../../src/WalkTabixSyntenyAdapter/WalkTabixSyntenyAdapter.ts"],
   "sourcesContent": ["import { weightedLcs } from '@gmod/gbz-base/lcs'\nimport { pairAlignments } from '@gmod/gbz-base/pairAlignment'\nimport { panSNContig } from '@jbrowse/bandage-core/pansn'\n\nimport SyntenyFeature from '../synteny/SyntenyFeature.ts'\n\nimport type { WalkFragment, WalkNode } from '../RgfaTabixAdapter/walkRows.ts'\nimport type { PairChain, PairEdit } from '@gmod/gbz-base/pairAlignment'\n\n// The longest bubble with equal bases on both sides that is written as\n// mismatches; a longer one stays an insertion and a deletion\nconst BALANCED_BUBBLE_MAX_BP = 50\n\n/**\n * A chain's edits with each short balanced bubble as `X`. The walks carry no\n * bases, so two walks differ wherever they leave a shared node, and a SNP is\n * one base inserted and one deleted until it is read as the mismatch it is.\n */\nexport function bubblesAsMismatches(edits: PairEdit[]) {\n  const out: PairEdit[] = []\n  for (let i = 0; i < edits.length; i++) {\n    const [op, len] = edits[i]!\n    const [nextOp, nextLen] = edits[i + 1] ?? []\n    if (\n      len === nextLen &&\n      len <= BALANCED_BUBBLE_MAX_BP &&\n      ((op === 'I' && nextOp === 'D') || (op === 'D' && nextOp === 'I'))\n    ) {\n      out.push(['X', len])\n      i++\n    } else {\n      out.push([op, len])\n    }\n  }\n  return out\n}\n\nfunction cigarOf(edits: PairEdit[]) {\n  return edits.map(([op, len]) => `${len}${op}`).join('')\n}\n\n/**\n * Aligns one walk fragment to another on the nodes both visit, from node\n * lengths alone: the fragments' steps as the handles gbz-base's chainer reads,\n * and a stand-in sequence of each node's length.\n */\nexport function walkAligner(nodes: Map<number, WalkNode>) {\n  const standIn = new Map<number, string>()\n  const sequenceOf = (id: number) => {\n    const node = nodes.get(id)\n    const length = node === undefined ? 0 : node.end - node.start\n    let sequence = standIn.get(length)\n    if (sequence === undefined) {\n      sequence = 'N'.repeat(length)\n      standIn.set(length, sequence)\n    }\n    return sequence\n  }\n  const handles = new Map<WalkFragment, number[]>()\n  const handlesOf = (fragment: WalkFragment) => {\n    let steps = handles.get(fragment)\n    if (steps === undefined) {\n      steps = Array.from(fragment.ids, (id, i) => 2 * id + fragment.rev[i]!)\n      handles.set(fragment, steps)\n    }\n    return steps\n  }\n  return (query: WalkFragment, target: WalkFragment) =>\n    pairAlignments({\n      query: handlesOf(query),\n      target: handlesOf(target),\n      sequenceOf,\n      bases: false,\n    })\n}\n\n// The fewest bases on shared nodes a record against the reference keeps,\n// gbz-base's floor for a pair record\nconst MIN_MATCH_BP = 100\n\nfunction appendEdit(edits: PairEdit[], op: PairEdit[0], len: number) {\n  const last = edits.at(-1)\n  if (len > 0) {\n    if (last?.[0] === op) {\n      last[1] += len\n    } else {\n      edits.push([op, len])\n    }\n  }\n}\n\n/**\n * Aligns a haplotype's walk fragment to the reference's as gbz-base aligns a\n * walk to its reference path: the heaviest common subsequence of their steps,\n * each node weighing its length, read in whichever direction shares more. A\n * pair chain leaves out every node either walk passes twice, which is the\n * whole of a collapsed copy-number array (amylase, KIV-2); the subsequence\n * matches one pass over it, and the other copies are insertions.\n */\nexport function referenceAligner(nodes: Map<number, WalkNode>) {\n  const lengthOf = (handle: number) => {\n    const node = nodes.get(handle >> 1)\n    return node === undefined ? 0 : node.end - node.start\n  }\n  const offsets = (handles: number[]) => {\n    const out = new Float64Array(handles.length + 1)\n    handles.forEach((handle, i) => {\n      out[i + 1] = out[i]! + lengthOf(handle)\n    })\n    return out\n  }\n  const handlesOf = (fragment: WalkFragment) =>\n    Array.from(fragment.ids, (id, i) => 2 * id + fragment.rev[i]!)\n\n  return (query: WalkFragment, target: WalkFragment): PairChain[] => {\n    const ref = handlesOf(target)\n    const hap = handlesOf(query)\n    const [same, sameWeight] = weightedLcs(hap, ref, lengthOf)\n    const [turned, turnedWeight] = weightedLcs(\n      hap.map(handle => handle ^ 1).reverse(),\n      ref,\n      lengthOf,\n    )\n    const reverse = turnedWeight > sameWeight\n    const pairs = reverse ? turned : same\n    const sharedBases = Math.max(sameWeight, turnedWeight)\n    if (sharedBases < MIN_MATCH_BP) {\n      return []\n    }\n    const refAt = offsets(ref)\n    const hapAt = offsets(hap)\n    // a pair's haplotype step, counted along the haplotype\n    const stepOf = (k: number) =>\n      reverse ? hap.length - 1 - pairs[k]![0] : pairs[k]![0]\n    const edits: PairEdit[] = []\n    pairs.forEach(([, r], k) => {\n      if (k > 0) {\n        const [lo, hi] = [stepOf(k - 1), stepOf(k)].sort((x, y) => x - y)\n        appendEdit(edits, 'I', hapAt[hi!]! - hapAt[lo! + 1]!)\n        appendEdit(edits, 'D', refAt[r]! - refAt[pairs[k - 1]![1] + 1]!)\n      }\n      appendEdit(edits, '=', lengthOf(ref[r]!))\n    })\n    const [lo, hi] = [stepOf(0), stepOf(pairs.length - 1)].sort((x, y) => x - y)\n    return [\n      {\n        queryStart: hapAt[lo!]!,\n        queryEnd: hapAt[hi! + 1]!,\n        targetStart: refAt[pairs[0]![1]]!,\n        targetEnd: refAt[pairs.at(-1)![1] + 1]!,\n        strand: reverse ? '-' : '+',\n        edits,\n        sharedBases,\n      },\n    ]\n  }\n}\n\n/**\n * One record of a walk aligned to another: on the target walk's contig, with\n * the query walk as its mate and the CIGAR read along the target, a `D` being\n * target bases the query lacks.\n */\nexport function chainFeature({\n  chain,\n  target,\n  query,\n  assemblyName,\n  refName,\n  mateAssemblyName,\n}: {\n  chain: PairChain\n  target: WalkFragment\n  query: WalkFragment\n  assemblyName: string\n  refName: string\n  mateAssemblyName: string\n}) {\n  const start = target.hapStart + chain.targetStart\n  const end = target.hapStart + chain.targetEnd\n  const mateStart = query.hapStart + chain.queryStart\n  const mateEnd = query.hapStart + chain.queryEnd\n  const edits = bubblesAsMismatches(chain.edits)\n  const matches = edits.reduce((sum, [op, n]) => sum + (op === '=' ? n : 0), 0)\n  const columns = edits.reduce((sum, [, n]) => sum + n, 0)\n  const id = `${target.name}:${start}-${end}|${query.name}:${mateStart}-${mateEnd}`\n  return new SyntenyFeature({\n    uniqueId: id,\n    assemblyName,\n    refName,\n    start,\n    end,\n    type: 'match',\n    strand: chain.strand === '-' ? -1 : 1,\n    CIGAR: cigarOf(edits),\n    syntenyId: id,\n    identity: matches / Math.max(columns, 1),\n    numMatches: matches,\n    blockLen: columns,\n    mate: {\n      refName: panSNContig(query.name),\n      start: mateStart,\n      end: mateEnd,\n      assemblyName: mateAssemblyName,\n    },\n  })\n}\n", "import { NodeLimitError } from '@jbrowse/bandage-core/gbzWindow'\nimport {\n  assemblyByPanSNPrefix,\n  panSNContig,\n  panSNHaplotype,\n  panSNMatchesPrefix,\n  panSNSample,\n  resolvePanSNPrefix,\n} from '@jbrowse/bandage-core/pansn'\nimport { updateStatus } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\n\nimport { chainFeature, referenceAligner, walkAligner } from './walkLanes.ts'\nimport { WalkReader } from '../RgfaTabixAdapter/walkReader.ts'\nimport { walkCutFor } from '../RgfaTabixAdapter/walkRowRuns.ts'\nimport { walkNameFilter } from '../RgfaTabixAdapter/walkRows.ts'\nimport { PanSNRefNames, openTabixSlot } from '../panSNTabix.ts'\nimport { ComparativeAdapterBase } from '../synteny/ComparativeAdapterBase.ts'\nimport { requestedPairs } from '../synteny/lanePairs.ts'\n\nimport type { WalkTabixSyntenyAdapterConfig } from './configSchema.ts'\nimport type { SubgraphAdapterOptions } from '../GetSubgraph.ts'\nimport type { WalkFragment } from '../RgfaTabixAdapter/walkRows.ts'\nimport type { LaneFeatureOptions, LanePair } from '../synteny/lanePairs.ts'\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { Region } from '@jbrowse/core/util/types'\n\n// How much graph a cut keeps around the window, on the reference\nconst WALK_CONTEXT = 1000\n\n/**\n * The lane a haplotype draws on: the JBrowse assembly the config maps to it at\n * haplotype or sample depth, else its own PanSN prefix\n */\nexport function laneOf(asmByPrefix: Record<string, string>, prefix: string) {\n  return asmByPrefix[prefix] ?? asmByPrefix[panSNSample(prefix)] ?? prefix\n}\n\nconst haplotypeOf = (fragment: WalkFragment) =>\n  panSNHaplotype(fragment.name) ?? fragment.name\n\nexport default class WalkTabixSyntenyAdapter extends ComparativeAdapterBase<WalkTabixSyntenyAdapterConfig> {\n  private readonly reader\n  private readonly refNames\n\n  public constructor(\n    config: WalkTabixSyntenyAdapterConfig,\n    getSubAdapter?: getSubAdapterType,\n    pluginManager?: PluginManager,\n  ) {\n    super(config, getSubAdapter, pluginManager)\n    const nodes = openTabixSlot(this, ['nodesLocation'], ['nodesIndex'])\n    this.reader = new WalkReader(\n      {\n        walks: openTabixSlot(this, ['walksLocation'], ['walksIndex']),\n        nodes,\n        links: openTabixSlot(this, ['linksLocation'], ['linksIndex']),\n      },\n      this.getConf('walkChunk'),\n    )\n    this.refNames = new PanSNRefNames(nodes, this)\n  }\n\n  private get anchor() {\n    const anchor = this.getConf('assemblyNames')[0]\n    if (anchor === undefined) {\n      throw new Error(\n        'WalkTabixSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as',\n      )\n    }\n    return anchor\n  }\n\n  /**\n   * The haplotypes the walk file's header names, `sample#haplotype` in byte\n   * order, or undefined when it names none\n   */\n  async getHaplotypeNames(opts: BaseOptions = {}) {\n    const { haplotypes } = await this.reader.header(opts)\n    return haplotypes.length > 0 ? haplotypes : undefined\n  }\n\n  /**\n   * `lanes` is every haplotype the header names but the anchor's own,\n   * declared up front so the display can offer the whole graph's haplotypes\n   * before a fetch has placed any of them\n   */\n  async getHeader(opts: BaseOptions = {}) {\n    const { haplotypes, references } = await this.reader.header(opts)\n    const { anchor } = this\n    const anchorPrefix = resolvePanSNPrefix(this, anchor)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    return {\n      hasCoarseTier: false,\n      anchorAssemblyName: anchor,\n      referenceSamples: references,\n      lanes: haplotypes\n        .filter(\n          prefix =>\n            prefix !== anchorPrefix && panSNSample(prefix) !== anchorPrefix,\n        )\n        .map(prefix => ({\n          name: laneOf(asmByPrefix, prefix),\n          label: prefix,\n          group: panSNSample(prefix),\n        })),\n    }\n  }\n\n  // A lane's contigs are named only in its walk rows, so only the anchor's\n  // are listed\n  async getRefNames(opts: BaseOptions = {}) {\n    const { assemblyName } = opts\n    return assemblyName === undefined || assemblyName === this.anchor\n      ? this.refNames.assemblyRefNames({ ...opts, assemblyName: this.anchor })\n      : []\n  }\n\n  private budgets(walkRows?: boolean) {\n    return {\n      stepBudget: walkRows ? Infinity : this.getConf('walkStepBudget'),\n      byteBudget: this.getConf('walkByteBudget'),\n      context: WALK_CONTEXT,\n    }\n  }\n\n  /**\n   * The graph display's cut of the window, as RgfaTabixAdapter cuts a\n   * walk-indexed graph: the reference walk first, then the walks `haplotypes`\n   * asks for, and the nodes and links they visit\n   */\n  async getSubgraph(region: Region, opts: SubgraphAdapterOptions = {}) {\n    const { signal, haplotypes, walkRows } = opts\n    const refName = await this.refNames.resolve(region, { signal })\n    if (refName === undefined) {\n      throw new Error(\n        `${region.assemblyName} ${region.refName} is not in this graph's index; the graph is cut on ${this.anchor}, mapped to its PanSN prefix in assemblyNameToPanSN`,\n      )\n    }\n    const { graph, kept, fragments } = await this.reader.cut(refName, region, {\n      ...this.budgets(walkRows),\n      signal,\n      keep: walkNameFilter(\n        haplotypes?.map(lane => resolvePanSNPrefix(this, lane)),\n        panSNHaplotype(refName),\n      ),\n    })\n    return walkCutFor(graph.tables(kept, fragments), region, walkRows)\n  }\n\n  // The window's walks for the haplotypes named and the reference, with no\n  // link read; a window past a budget fails as a zoom-in notice for lanes\n  private async laneWalks(\n    refName: string,\n    region: Region,\n    prefixes: string[] | undefined,\n    opts: LaneFeatureOptions,\n    status: string,\n  ) {\n    return updateStatus(status, opts.statusCallback, () =>\n      this.reader\n        .cut(refName, region, {\n          ...this.budgets(),\n          signal: opts.signal,\n          keep: walkNameFilter(prefixes, panSNHaplotype(refName)),\n          links: false,\n        })\n        .catch((error: unknown) => {\n          if (error instanceof NodeLimitError) {\n            error.message = error.message.replace(\n              'to see the graph',\n              'to see lanes',\n            )\n          }\n          throw error\n        }),\n    )\n  }\n\n  /**\n   * One record per stretch a haplotype's walk shares with the reference's,\n   * on the reference with the haplotype as its mate\n   */\n  private async anchorFeatures(\n    refName: string,\n    region: Region,\n    opts: LaneFeatureOptions,\n  ) {\n    const wanted = opts.haplotypes?.length\n      ? opts.haplotypes.map(lane => resolvePanSNPrefix(this, lane))\n      : undefined\n    const target = resolvePanSNPrefix(this, opts.targetAssemblyName)\n    const prefixes =\n      target === undefined\n        ? wanted\n        : wanted === undefined ||\n            wanted.some(\n              prefix =>\n                panSNMatchesPrefix(target, prefix) ||\n                panSNMatchesPrefix(prefix, target),\n            )\n          ? [target]\n          : []\n    if (prefixes?.length === 0) {\n      return []\n    }\n    const { start, end } = region\n    const { graph, fragments } = await this.laneWalks(\n      refName,\n      region,\n      prefixes,\n      opts,\n      `Reading walks ${region.refName}:${start.toLocaleString()}-${end.toLocaleString()}`,\n    )\n    const align = referenceAligner(graph.nodes)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    const references = fragments.filter(f => f.name === refName)\n    // lanes come back in the order the fetch names them, which is the order\n    // the display stacks lanes of equal weight in\n    const rank = (fragment: WalkFragment) =>\n      prefixes === undefined\n        ? 0\n        : prefixes.findIndex(prefix =>\n            panSNMatchesPrefix(fragment.name, prefix),\n          )\n    const shown = fragments\n      .filter(fragment => fragment.name !== refName && rank(fragment) >= 0)\n      .sort((a, b) => rank(a) - rank(b))\n    return shown.flatMap(query =>\n      references.flatMap(reference =>\n        align(query, reference).map(chain =>\n          chainFeature({\n            chain,\n            target: reference,\n            query,\n            assemblyName: region.assemblyName,\n            refName: region.refName,\n            mateAssemblyName: laneOf(asmByPrefix, haplotypeOf(query)),\n          }),\n        ),\n      ),\n    )\n  }\n\n  /**\n   * Each pair's two lanes read out of the anchor window, all pairs in one\n   * read, and each walk of a pair's query lane aligned to each walk of its\n   * target lane. A pair's records sit on its query lane's contigs, the lane\n   * the display draws on top.\n   */\n  private async pairFeatures(\n    refName: string,\n    region: Region,\n    pairs: LanePair[],\n    opts: LaneFeatureOptions,\n  ) {\n    const [first] = pairs\n    const sides = pairs.map(pair => ({\n      pair,\n      featurePrefix: resolvePanSNPrefix(this, pair.queryAssemblyName),\n      matePrefix: resolvePanSNPrefix(this, pair.targetAssemblyName),\n    }))\n    const { graph, fragments } = await this.laneWalks(\n      refName,\n      region,\n      sides.flatMap(side => [side.featurePrefix, side.matePrefix]),\n      opts,\n      pairs.length === 1 && first\n        ? `Reading ${first.queryAssemblyName} against ${first.targetAssemblyName}`\n        : `Reading ${pairs.length} lane pairs`,\n    )\n    const align = walkAligner(graph.nodes)\n    const walksOf = (prefix: string) =>\n      fragments.filter(f => panSNMatchesPrefix(f.name, prefix))\n    return sides.flatMap(({ pair, featurePrefix, matePrefix }) =>\n      walksOf(featurePrefix).flatMap(target =>\n        walksOf(matePrefix).flatMap(query =>\n          align(query, target).map(chain =>\n            chainFeature({\n              chain,\n              target,\n              query,\n              assemblyName: pair.queryAssemblyName,\n              refName: panSNContig(target.name),\n              mateAssemblyName: pair.targetAssemblyName,\n            }),\n          ),\n        ),\n      ),\n    )\n  }\n\n  // The files are filed under the reference alone, so a window on a\n  // haplotype lane has no answer: a lane pair is read inside the anchor's\n  getFeatures(region: Region, opts: LaneFeatureOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      const refName =\n        region.assemblyName === this.anchor\n          ? await this.refNames.resolve(region, opts)\n          : undefined\n      if (refName !== undefined) {\n        const pairs = requestedPairs(opts)\n        const features =\n          pairs.length > 0\n            ? await this.pairFeatures(refName, region, pairs, opts)\n            : await this.anchorFeatures(refName, region, opts)\n        for (const feature of features) {\n          observer.next(feature)\n        }\n      }\n      observer.complete()\n    }, opts.signal)\n  }\n}\n"],
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 }