jbrowse-plugin-graphgenomeviewer 7.7.0 → 8.0.1

package/dist/chunks/{WalkTabixSyntenyAdapter-EOD4RQVU.js → WalkTabixSyntenyAdapter-NWB2OALF.js}

@@ -1,2 +1,2 @@
-import{a as K}from"./chunk-2QRCU675.js";import{b as $,d as U,e as X,f as O,g as z,h as G}from"./chunk-DDAG445J.js";import"./chunk-TUECGSVJ.js";import{a as q}from"./chunk-KOB7YIMR.js";import{p as M,q as _,r as T}from"./chunk-M2D7NUOY.js";import"./chunk-YBLNN5FU.js";import"./chunk-GK5YETAZ.js";import"./chunk-LIRBZOBX.js";import{C as D,D as H,i as j}from"./chunk-Q5H6ETNZ.js";import"./chunk-YBLNN5FU.js";import"./chunk-JRJHXLGP.js";import{a as S,c as I,d as W,g as F,h as w,i as x}from"./chunk-ODQSCM3F.js";import"./chunk-T4R3ZVEM.js";import"./chunk-7WIBGKBU.js";import"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{o as R}from"./chunk-TENPGIPX.js";var se=50;function re(r){let i=[];for(let e=0;e<r.length;e++){let[t,a]=r[e],[s,n]=r[e+1]??[];a===n&&a<=se&&(t==="I"&&s==="D"||t==="D"&&s==="I")?(i.push(["X",a]),e++):i.push([t,a])}return i}function E(r){return Array.from(r.ids,(i,e)=>2*i+r.rev[e])}function A(r,i){let e=r.get(i);return e===void 0?0:e.end-e.start}function V(r){let i=new Map,e=s=>{let n=A(r,s),o=i.get(n);return o===void 0&&(o="N".repeat(n),i.set(n,o)),o},t=new Map,a=s=>{let n=t.get(s);return n===void 0&&(n=E(s),t.set(s,n)),n};return(s,n)=>_({query:a(s),target:a(n),sequenceOf:e,bases:!1})}var B=100;function v(r,i,e){let t=r.at(-1);e>0&&(t?.[0]===i?t[1]+=e:r.push([i,e]))}function Z(r){let i=t=>A(r,t>>1),e=t=>{let a=new Float64Array(t.length+1);return t.forEach((s,n)=>{a[n+1]=a[n]+i(s)}),a};return(t,a)=>{let s=E(a),n=E(t),[o,l]=M(n,s,i),[u,f]=M(n.map(g=>g^1).reverse(),s,i),c=f>l,p=c?u:o,N=Math.max(l,f);if(N<B)return[];let h=e(s),d=e(n),y=g=>c?n.length-1-p[g][0]:p[g][0],m=[];p.forEach(([,g],k)=>{if(k>0){let[ee,te]=[y(k-1),y(k)].sort((ae,ne)=>ae-ne);v(m,"I",d[te]-d[ee+1]),v(m,"D",h[g]-h[p[k-1][1]+1])}v(m,"=",i(s[g]))});let[b,P]=[y(0),y(p.length-1)].sort((g,k)=>g-k);return[{queryStart:d[b],queryEnd:d[P+1],targetStart:h[p[0][1]],targetEnd:h[p.at(-1)[1]+1],strand:c?"-":"+",edits:m,sharedBases:N}]}}function oe(r){let i=new Map,e=new Set;r.ids.forEach((t,a)=>{i.has(t)?e.add(t):i.set(t,r.rev[a])});for(let t of e)i.delete(t);return i}function J(r){let i=new Map,e=t=>{let a=i.get(t);return a===void 0&&(a=oe(t),i.set(t,a)),a};return(t,a)=>{let s=e(a),n=0,o=0;for(let[l,u]of e(t)){let f=s.get(l);f===u?n+=A(r,l):f!==void 0&&(o+=A(r,l))}return{same:n,opposite:o}}}function Q(r){let i=Z(r),e=V(r),t=J(r);return(a,s)=>{let{same:n,opposite:o}=t(a,s);return n>=B&&o>=B?e(a,s):i(a,s)}}var ie=1e4;function Y(r){let i=Z(r),e=V(r),t=J(r);return(a,s)=>{let n=i(a,s),o=n[0]?.strand,{same:l,opposite:u}=t(a,s);return o===void 0||Math.min(l,u)<ie?n:[...n,...e(a,s).filter(f=>f.strand!==o)]}}function C({chain:r,target:i,query:e,assemblyName:t,refName:a,mateAssemblyName:s}){let n=re(r.edits);return G({target:{name:i.name,assemblyName:t,refName:a,start:i.hapStart+r.targetStart,end:i.hapStart+r.targetEnd},query:{name:e.name,assemblyName:s,refName:W(e.name),start:e.hapStart+r.queryStart,end:e.hapStart+r.queryEnd},strand:r.strand,cigar:T(n),matches:n.reduce((o,[l,u])=>o+(l==="="?u:0),0),columns:n.reduce((o,[,l])=>o+l,0)})}var me=r=>I(r.name)??r.name,L=class extends ${constructor(){super(...arguments);this.walks=new K(D(this,["walksLocation"],["walksIndex"]),this);this.refNames=new H(this.walks.file,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={}){return this.walks.haplotypeNames(e)}async getHeader(e={}){let{haplotypes:t}=await this.walks.reader.header(e),{anchor:a}=this,s=w(this,a),n=x(this);return{hasCoarseTier:!1,anchorAssemblyName:a,lanes:t.filter(o=>o!==s&&S(o)!==s).map(o=>({name:O(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}):[]}async getSubgraph(e,t={}){let a=await this.refNames.resolveForCut(e,{signal:t.signal});return this.walks.subgraph(a,e,t)}async laneWalks(e,t,a,s,n){let o=j(a,e);return R(n,s.statusCallback,()=>this.walks.reader.cut(e,t,{...this.walks.budgets(),signal:s.signal,keep:o,expand:o,links:!1}).catch(l=>{throw z(l,t.end-t.start)}))}async anchorFeatures(e,t,a){let s=a.haplotypes?.length?a.haplotypes.map(m=>w(this,m)):void 0,n=w(this,a.targetAssemblyName),o=n===void 0?s:s===void 0||s.some(m=>F(n,m)||F(m,n))?[n]:[];if(o?.length===0)return[];let{start:l,end:u}=t,{graph:f,fragments:c}=await this.laneWalks(e,t,o,a,`Reading walks ${t.refName}:${l.toLocaleString()}-${u.toLocaleString()}`),p=Y(f.nodes),N=x(this),h=c.filter(m=>m.name===e),d=m=>o===void 0?0:o.findIndex(b=>F(m.name,b));return c.filter(m=>m.name!==e&&d(m)>=0).sort((m,b)=>d(m)-d(b)).flatMap(m=>h.flatMap(b=>p(m,b).map(P=>C({chain:P,target:b,query:m,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:O(N,me(m))}))))}async pairFeatures(e,t,a,s){let n=a.map(c=>({pair:c,featurePrefix:w(this,c.queryAssemblyName),matePrefix:w(this,c.targetAssemblyName)})),{graph:o,fragments:l}=await this.laneWalks(e,t,n.flatMap(c=>[c.featurePrefix,c.matePrefix]),s,X(a)),u=Q(o.nodes),f=c=>l.filter(p=>F(p.name,c));return n.flatMap(({pair:c,featurePrefix:p,matePrefix:N})=>f(p).flatMap(h=>f(N).flatMap(d=>u(d,h).map(y=>C({chain:y,target:h,query:d,assemblyName:c.queryAssemblyName,refName:W(h.name),mateAssemblyName:c.targetAssemblyName})))))}getFeatures(e,t={}){return q(async a=>{let s=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(s!==void 0){let n=U(t),o=n.length>0?await this.pairFeatures(s,e,n,t):await this.anchorFeatures(s,e,t);for(let l of o)a.next(l)}a.complete()},t.signal)}};export{L as default};
-//# sourceMappingURL=WalkTabixSyntenyAdapter-EOD4RQVU.js.map
+import{a as K}from"./chunk-QTEWKTFE.js";import{b as $,d as U,e as X,f as O,g as z,h as G}from"./chunk-OYXKO3SL.js";import"./chunk-Q4UIYMYF.js";import{a as q}from"./chunk-KOB7YIMR.js";import{p as M,q as _,r as T}from"./chunk-M2D7NUOY.js";import"./chunk-YBLNN5FU.js";import"./chunk-UQDZNX5E.js";import"./chunk-AJX6ZXCI.js";import{C as D,D as H,i as j}from"./chunk-UDHJGXQV.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import{a as S,c as I,d as W,g as F,h as w,i as x}from"./chunk-KFZWGL76.js";import"./chunk-OTBDKJEA.js";import"./chunk-3VGXCEMQ.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{o as R}from"./chunk-J5RMHLFJ.js";var se=50;function re(r){let i=[];for(let e=0;e<r.length;e++){let[t,a]=r[e],[s,n]=r[e+1]??[];a===n&&a<=se&&(t==="I"&&s==="D"||t==="D"&&s==="I")?(i.push(["X",a]),e++):i.push([t,a])}return i}function E(r){return Array.from(r.ids,(i,e)=>2*i+r.rev[e])}function A(r,i){let e=r.get(i);return e===void 0?0:e.end-e.start}function V(r){let i=new Map,e=s=>{let n=A(r,s),o=i.get(n);return o===void 0&&(o="N".repeat(n),i.set(n,o)),o},t=new Map,a=s=>{let n=t.get(s);return n===void 0&&(n=E(s),t.set(s,n)),n};return(s,n)=>_({query:a(s),target:a(n),sequenceOf:e,bases:!1})}var B=100;function v(r,i,e){let t=r.at(-1);e>0&&(t?.[0]===i?t[1]+=e:r.push([i,e]))}function Z(r){let i=t=>A(r,t>>1),e=t=>{let a=new Float64Array(t.length+1);return t.forEach((s,n)=>{a[n+1]=a[n]+i(s)}),a};return(t,a)=>{let s=E(a),n=E(t),[o,l]=M(n,s,i),[u,f]=M(n.map(g=>g^1).reverse(),s,i),c=f>l,p=c?u:o,N=Math.max(l,f);if(N<B)return[];let h=e(s),d=e(n),y=g=>c?n.length-1-p[g][0]:p[g][0],m=[];p.forEach(([,g],k)=>{if(k>0){let[ee,te]=[y(k-1),y(k)].sort((ae,ne)=>ae-ne);v(m,"I",d[te]-d[ee+1]),v(m,"D",h[g]-h[p[k-1][1]+1])}v(m,"=",i(s[g]))});let[b,P]=[y(0),y(p.length-1)].sort((g,k)=>g-k);return[{queryStart:d[b],queryEnd:d[P+1],targetStart:h[p[0][1]],targetEnd:h[p.at(-1)[1]+1],strand:c?"-":"+",edits:m,sharedBases:N}]}}function oe(r){let i=new Map,e=new Set;r.ids.forEach((t,a)=>{i.has(t)?e.add(t):i.set(t,r.rev[a])});for(let t of e)i.delete(t);return i}function J(r){let i=new Map,e=t=>{let a=i.get(t);return a===void 0&&(a=oe(t),i.set(t,a)),a};return(t,a)=>{let s=e(a),n=0,o=0;for(let[l,u]of e(t)){let f=s.get(l);f===u?n+=A(r,l):f!==void 0&&(o+=A(r,l))}return{same:n,opposite:o}}}function Q(r){let i=Z(r),e=V(r),t=J(r);return(a,s)=>{let{same:n,opposite:o}=t(a,s);return n>=B&&o>=B?e(a,s):i(a,s)}}var ie=1e4;function Y(r){let i=Z(r),e=V(r),t=J(r);return(a,s)=>{let n=i(a,s),o=n[0]?.strand,{same:l,opposite:u}=t(a,s);return o===void 0||Math.min(l,u)<ie?n:[...n,...e(a,s).filter(f=>f.strand!==o)]}}function C({chain:r,target:i,query:e,assemblyName:t,refName:a,mateAssemblyName:s}){let n=re(r.edits);return G({target:{name:i.name,assemblyName:t,refName:a,start:i.hapStart+r.targetStart,end:i.hapStart+r.targetEnd},query:{name:e.name,assemblyName:s,refName:W(e.name),start:e.hapStart+r.queryStart,end:e.hapStart+r.queryEnd},strand:r.strand,cigar:T(n),matches:n.reduce((o,[l,u])=>o+(l==="="?u:0),0),columns:n.reduce((o,[,l])=>o+l,0)})}var me=r=>I(r.name)??r.name,L=class extends ${constructor(){super(...arguments);this.walks=new K(D(this,["walksLocation"],["walksIndex"]),this);this.refNames=new H(this.walks.file,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={}){return this.walks.haplotypeNames(e)}async getHeader(e={}){let{haplotypes:t}=await this.walks.reader.header(e),{anchor:a}=this,s=w(this,a),n=x(this);return{hasCoarseTier:!1,anchorAssemblyName:a,lanes:t.filter(o=>o!==s&&S(o)!==s).map(o=>({name:O(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}):[]}async getSubgraph(e,t={}){let a=await this.refNames.resolveForCut(e,{signal:t.signal});return this.walks.subgraph(a,e,t)}async laneWalks(e,t,a,s,n){let o=j(a,e);return R(n,s.statusCallback,()=>this.walks.reader.cut(e,t,{...this.walks.budgets(),signal:s.signal,keep:o,expand:o,links:!1}).catch(l=>{throw z(l,t.end-t.start)}))}async anchorFeatures(e,t,a){let s=a.haplotypes?.length?a.haplotypes.map(m=>w(this,m)):void 0,n=w(this,a.targetAssemblyName),o=n===void 0?s:s===void 0||s.some(m=>F(n,m)||F(m,n))?[n]:[];if(o?.length===0)return[];let{start:l,end:u}=t,{graph:f,fragments:c}=await this.laneWalks(e,t,o,a,`Reading walks ${t.refName}:${l.toLocaleString()}-${u.toLocaleString()}`),p=Y(f.nodes),N=x(this),h=c.filter(m=>m.name===e),d=m=>o===void 0?0:o.findIndex(b=>F(m.name,b));return c.filter(m=>m.name!==e&&d(m)>=0).sort((m,b)=>d(m)-d(b)).flatMap(m=>h.flatMap(b=>p(m,b).map(P=>C({chain:P,target:b,query:m,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:O(N,me(m))}))))}async pairFeatures(e,t,a,s){let n=a.map(c=>({pair:c,featurePrefix:w(this,c.queryAssemblyName),matePrefix:w(this,c.targetAssemblyName)})),{graph:o,fragments:l}=await this.laneWalks(e,t,n.flatMap(c=>[c.featurePrefix,c.matePrefix]),s,X(a)),u=Q(o.nodes),f=c=>l.filter(p=>F(p.name,c));return n.flatMap(({pair:c,featurePrefix:p,matePrefix:N})=>f(p).flatMap(h=>f(N).flatMap(d=>u(d,h).map(y=>C({chain:y,target:h,query:d,assemblyName:c.queryAssemblyName,refName:W(h.name),mateAssemblyName:c.targetAssemblyName})))))}getFeatures(e,t={}){return q(async a=>{let s=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(s!==void 0){let n=U(t),o=n.length>0?await this.pairFeatures(s,e,n,t):await this.anchorFeatures(s,e,t);for(let l of o)a.next(l)}a.complete()},t.signal)}};export{L as default};
+//# sourceMappingURL=WalkTabixSyntenyAdapter-NWB2OALF.js.map

package/dist/chunks/{chunk-E7S7PGEZ.js → chunk-3OALERH2.js}

@@ -1,2 +1,2 @@
-import{h as B,k as F,o as M}from"./chunk-O6HXOTJN.js";import{b as _,h as A}from"./chunk-22A3MS5J.js";import{K as b,Q as W,V as S}from"./chunk-EV54SYM7.js";import{e as O}from"./chunk-YU7T5WOQ.js";import{D as P,E as R,H as m,d as C,o as I,q as L,r as w,s as N,t as D,w as E,y as G,z as x}from"./chunk-UGCNPRKC.js";import{b as t,c as r,d as T}from"./chunk-JMBDTNUR.js";var f=[{value:0,label:"Fastest"},{value:1,label:"Fast"},{value:2,label:"Default"},{value:3,label:"Fine"},{value:4,label:"Best"}];function y({label:o,value:n,options:e,testId:s,size:d,sx:p,disabled:a,title:h,shown:g,onChange:Q}){let v=O();return r(N,{size:d,sx:p,disabled:a,title:h,children:[t(E,{id:v,shrink:!0,children:o}),t(P,{labelId:v,value:n,label:o,notched:!0,displayEmpty:!0,"data-testid":s,renderValue:i=>g??e.find(z=>z.value===i)?.label??i,onChange:i=>{Q(i.target.value)},children:e.map(i=>t(x,{value:i.value,disabled:i.disabled,title:i.disabled?void 0:i.description,children:t(G,{primary:i.label,secondary:i.disabled?i.description:void 0})},i.value))})]})}var u=M()({section:{marginBottom:24},group:{marginBottom:16},heading:{marginBottom:8}});function l({warn:o=!1,children:n}){return t(m,{variant:"caption",component:"div",color:o?"warning.main":"text.secondary",children:n})}function k({title:o,children:n}){let{classes:e}=u();return r("section",{className:e.group,children:[t(m,{variant:"subtitle1",className:e.heading,children:o}),n]})}function U({label:o,checked:n,onChange:e,children:s}){let{classes:d}=u();return r("div",{className:d.section,children:[t(D,{control:t(R,{checked:n,onChange:p=>{e(p.target.checked)}}),label:o}),s]})}function c({children:o,...n}){let{classes:e}=u();return r("div",{className:e.section,children:[t(y,{sx:{minWidth:200},...n}),o]})}var Y=[5e3,2e4,5e4,1e5];function $(o){return[...new Set([...Y,o])].sort((n,e)=>n-e).map(n=>({value:String(n),label:n.toLocaleString()}))}function H({label:o,choices:n,stored:e,auto:s,testId:d,onChange:p,children:a}){return n.length>0?t(c,{label:o,value:n.some(h=>h.trackId===e)?e:"",options:[{value:"",label:`Automatic (${s?.name??"none"})`},...n.map(({trackId:h,name:g})=>({value:h,label:g}))],testId:d,onChange:p,children:a}):null}var q=T(function(n){let{model:e,onClose:s,children:d}=n,{classes:p}=u();return r(C,{open:!0,onClose:s,title:"Graph settings",children:[r(w,{children:[r(k,{title:"Subgraph",children:[d,t(c,{label:"Node limit",value:String(e.maxGraphNodes),options:$(e.maxGraphNodes),testId:"graph-node-limit-select",onChange:a=>{e.setMaxGraphNodes(Number(a))},children:t(l,{children:"The most nodes a layout draws; past it the graph is declined. Walk rows take no limit."})})]}),r(k,{title:"Drawing",children:[e.anchorPaths.length>1?t(c,{label:"Reference path",value:e.activeReferencePath??"",options:e.anchorPaths.map(({name:a})=>({value:a,label:a})),testId:"graph-reference-path-select",onChange:a=>{e.setReferencePath(a),e.recomputeLayout()},children:t(l,{children:"The path the anchored layouts place x along"})}):null,t(c,{label:"Node width",value:e.nodeWidth,options:W,testId:"graph-node-width-select",onChange:a=>{e.setNodeWidth(a)},children:t(l,{children:"Depth as width. In a cut with walks, depth is how many haplotypes carry the node."})}),t(c,{label:"Link width",value:e.linkWidth,options:S,testId:"graph-link-width-select",onChange:a=>{e.setLinkWidth(a)},children:t(l,{children:"Walks as width, so a common route reads heavy and a private one thin."})}),r(U,{label:"Draw paths",checked:e.drawPaths,onChange:a=>{e.setLayer("paths",a)},children:[t(l,{children:"Color each node by the paths through it, one lane per path"}),e.drawPaths&&!e.effectiveDrawPaths?t(l,{warn:!0,children:e.pathCount>b?`Off: ${e.pathCount.toLocaleString()} paths is past the ${b} this can tell apart`:"Off: this graph states no paths"}):null]}),t(H,{label:"Gene track",choices:e.geneTrackChoices,stored:e.geneTrackId,auto:F(e.geneTrackChoices,""),testId:"graph-gene-track-select",onChange:a=>{e.setGeneTrackId(a)},children:t(l,{children:"Where genes on the backbone come from"})}),t(H,{label:"Repeat track",choices:e.repeatTrackChoices,stored:e.repeatTrackId,auto:B(e.repeatTrackChoices,""),testId:"graph-repeat-track-select",onChange:a=>{e.setRepeatTrackId(a)},children:t(l,{children:"The tandem repeat annotation walk rows measure and tile by"})})]}),r(k,{title:"Force-directed layout",children:[e.hasGraph&&!e.usesLayoutEngine?t("div",{className:p.section,children:t(l,{warn:!0,children:"No effect on the current layout until Layout is Force-directed"})}):null,t(c,{label:"Engine",value:e.layoutEngine,options:_,testId:"graph-layout-engine-select",onChange:a=>{e.setLayoutEngine(a)},children:t(l,{children:"Stress keeps the reference straight, so a zoom keeps the picture; FMMM lets the whole graph settle."})}),t(c,{label:"Layout quality",value:String(e.layoutQuality),options:f.map(a=>({value:String(a.value),label:a.label})),testId:"graph-layout-quality-select",onChange:a=>{e.setLayoutQuality(Number(a))},children:t(l,{children:"The engine's iteration budget; higher is slower"})}),t(c,{label:"Bubble spread",value:e.bubbleSpread,options:A,testId:"graph-bubble-spread-select",onChange:a=>{e.setBubbleSpread(a)},children:t(l,{children:"How far the layout opens a bubble"})}),e.layoutEngine==="stress"?null:t(U,{label:"Linear layout",checked:e.linearLayout,onChange:a=>{e.setLinearLayout(a)},children:t(l,{children:"Keeps a chain of nodes on one line where it can"})})]})]}),t(L,{children:t(I,{variant:"contained",color:"primary",onClick:s,children:"Close"})})]})}),fe=q;export{y as a,fe as b};
-//# sourceMappingURL=chunk-E7S7PGEZ.js.map
+import{i as B,l as F,p as M}from"./chunk-46CNCY7Z.js";import{b as _,h as A}from"./chunk-BH2HG6VX.js";import{K as b,Q as W,V as S}from"./chunk-ACN3SGJ3.js";import{e as O}from"./chunk-YU7T5WOQ.js";import{D as P,E as R,H as m,d as C,o as I,q as L,r as w,s as N,t as D,w as E,y as G,z as x}from"./chunk-5Z4VIKXZ.js";import{b as t,c as r,d as T}from"./chunk-JMBDTNUR.js";var f=[{value:0,label:"Fastest"},{value:1,label:"Fast"},{value:2,label:"Default"},{value:3,label:"Fine"},{value:4,label:"Best"}];function y({label:o,value:n,options:e,testId:s,size:d,sx:p,disabled:a,title:h,shown:g,onChange:Q}){let v=O();return r(N,{size:d,sx:p,disabled:a,title:h,children:[t(E,{id:v,shrink:!0,children:o}),t(P,{labelId:v,value:n,label:o,notched:!0,displayEmpty:!0,"data-testid":s,renderValue:i=>g??e.find(z=>z.value===i)?.label??i,onChange:i=>{Q(i.target.value)},children:e.map(i=>t(x,{value:i.value,disabled:i.disabled,title:i.disabled?void 0:i.description,children:t(G,{primary:i.label,secondary:i.disabled?i.description:void 0})},i.value))})]})}var u=M()({section:{marginBottom:24},group:{marginBottom:16},heading:{marginBottom:8}});function l({warn:o=!1,children:n}){return t(m,{variant:"caption",component:"div",color:o?"warning.main":"text.secondary",children:n})}function k({title:o,children:n}){let{classes:e}=u();return r("section",{className:e.group,children:[t(m,{variant:"subtitle1",className:e.heading,children:o}),n]})}function U({label:o,checked:n,onChange:e,children:s}){let{classes:d}=u();return r("div",{className:d.section,children:[t(D,{control:t(R,{checked:n,onChange:p=>{e(p.target.checked)}}),label:o}),s]})}function c({children:o,...n}){let{classes:e}=u();return r("div",{className:e.section,children:[t(y,{sx:{minWidth:200},...n}),o]})}var Y=[5e3,2e4,5e4,1e5];function $(o){return[...new Set([...Y,o])].sort((n,e)=>n-e).map(n=>({value:String(n),label:n.toLocaleString()}))}function H({label:o,choices:n,stored:e,auto:s,testId:d,onChange:p,children:a}){return n.length>0?t(c,{label:o,value:n.some(h=>h.trackId===e)?e:"",options:[{value:"",label:`Automatic (${s?.name??"none"})`},...n.map(({trackId:h,name:g})=>({value:h,label:g}))],testId:d,onChange:p,children:a}):null}var q=T(function(n){let{model:e,onClose:s,children:d}=n,{classes:p}=u();return r(C,{open:!0,onClose:s,title:"Graph settings",children:[r(w,{children:[r(k,{title:"Subgraph",children:[d,t(c,{label:"Node limit",value:String(e.maxGraphNodes),options:$(e.maxGraphNodes),testId:"graph-node-limit-select",onChange:a=>{e.setMaxGraphNodes(Number(a))},children:t(l,{children:"The most nodes a layout draws; past it the graph is declined. Walk rows take no limit."})})]}),r(k,{title:"Drawing",children:[e.anchorPaths.length>1?t(c,{label:"Reference path",value:e.activeReferencePath??"",options:e.anchorPaths.map(({name:a})=>({value:a,label:a})),testId:"graph-reference-path-select",onChange:a=>{e.setReferencePath(a),e.recomputeLayout()},children:t(l,{children:"The path the anchored layouts place x along"})}):null,t(c,{label:"Node width",value:e.nodeWidth,options:W,testId:"graph-node-width-select",onChange:a=>{e.setNodeWidth(a)},children:t(l,{children:"Depth as width. In a cut with walks, depth is how many haplotypes carry the node."})}),t(c,{label:"Link width",value:e.linkWidth,options:S,testId:"graph-link-width-select",onChange:a=>{e.setLinkWidth(a)},children:t(l,{children:"Walks as width, so a common route reads heavy and a private one thin."})}),r(U,{label:"Draw paths",checked:e.drawPaths,onChange:a=>{e.setLayer("paths",a)},children:[t(l,{children:"Color each node by the paths through it, one lane per path"}),e.drawPaths&&!e.effectiveDrawPaths?t(l,{warn:!0,children:e.pathCount>b?`Off: ${e.pathCount.toLocaleString()} paths is past the ${b} this can tell apart`:"Off: this graph states no paths"}):null]}),t(H,{label:"Gene track",choices:e.geneTrackChoices,stored:e.geneTrackId,auto:F(e.geneTrackChoices,""),testId:"graph-gene-track-select",onChange:a=>{e.setGeneTrackId(a)},children:t(l,{children:"Where genes on the backbone come from"})}),t(H,{label:"Repeat track",choices:e.repeatTrackChoices,stored:e.repeatTrackId,auto:B(e.repeatTrackChoices,""),testId:"graph-repeat-track-select",onChange:a=>{e.setRepeatTrackId(a)},children:t(l,{children:"The tandem repeat annotation walk rows measure and tile by"})})]}),r(k,{title:"Force-directed layout",children:[e.hasGraph&&!e.usesLayoutEngine?t("div",{className:p.section,children:t(l,{warn:!0,children:"No effect on the current layout until Layout is Force-directed"})}):null,t(c,{label:"Engine",value:e.layoutEngine,options:_,testId:"graph-layout-engine-select",onChange:a=>{e.setLayoutEngine(a)},children:t(l,{children:"Stress keeps the reference straight, so a zoom keeps the picture; FMMM lets the whole graph settle."})}),t(c,{label:"Layout quality",value:String(e.layoutQuality),options:f.map(a=>({value:String(a.value),label:a.label})),testId:"graph-layout-quality-select",onChange:a=>{e.setLayoutQuality(Number(a))},children:t(l,{children:"The engine's iteration budget; higher is slower"})}),t(c,{label:"Bubble spread",value:e.bubbleSpread,options:A,testId:"graph-bubble-spread-select",onChange:a=>{e.setBubbleSpread(a)},children:t(l,{children:"How far the layout opens a bubble"})}),e.layoutEngine==="stress"?null:t(U,{label:"Linear layout",checked:e.linearLayout,onChange:a=>{e.setLinearLayout(a)},children:t(l,{children:"Keeps a chain of nodes on one line where it can"})})]})]}),t(L,{children:t(I,{variant:"contained",color:"primary",onClick:s,children:"Close"})})]})}),fe=q;export{y as a,fe as b};
+//# sourceMappingURL=chunk-3OALERH2.js.map

package/dist/chunks/{chunk-E7S7PGEZ.js.map → chunk-3OALERH2.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.19.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-K5SIJGAE.js", "../../src/GraphGenomeView/components/LabelledSelect.tsx", "../../src/GraphGenomeView/components/GraphSettingsDialog.tsx"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@12.0.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-K5SIJGAE.js", "../../src/GraphGenomeView/components/LabelledSelect.tsx", "../../src/GraphGenomeView/components/GraphSettingsDialog.tsx"],
   "sourcesContent": ["// src/layoutQualities.ts\nvar LAYOUT_QUALITIES = [\n  { value: 0, label: \"Fastest\" },\n  { value: 1, label: \"Fast\" },\n  { value: 2, label: \"Default\" },\n  { value: 3, label: \"Fine\" },\n  { value: 4, label: \"Best\" }\n];\n\nexport {\n  LAYOUT_QUALITIES\n};\n", "import { useId } from 'react'\n\nimport {\n  FormControl,\n  InputLabel,\n  ListItemText,\n  MenuItem,\n  Select,\n} from '@mui/material'\n\nimport type { SxProps } from '@mui/material'\n\ninterface SelectOption<T extends string> {\n  value: T\n  label: string\n  // an option's tooltip, and the reason under a disabled one, whose tooltip\n  // cannot open\n  description?: string\n  disabled?: boolean\n}\n\n// One dropdown with its label tied to it, so a screen reader names the combobox\nexport default function LabelledSelect<T extends string>({\n  label,\n  value,\n  options,\n  testId,\n  size,\n  sx,\n  disabled,\n  title,\n  shown,\n  onChange,\n}: {\n  label: string\n  value: T\n  options: readonly SelectOption<T>[]\n  testId?: string\n  size?: 'small' | 'medium'\n  sx?: SxProps\n  disabled?: boolean\n  title?: string\n  // what the closed select reads, when not the picked option's label\n  shown?: string\n  onChange: (value: T) => void\n}) {\n  const labelId = useId()\n  return (\n    <FormControl size={size} sx={sx} disabled={disabled} title={title}>\n      <InputLabel id={labelId} shrink>\n        {label}\n      </InputLabel>\n      <Select\n        labelId={labelId}\n        value={value}\n        label={label}\n        notched\n        displayEmpty\n        data-testid={testId}\n        renderValue={picked =>\n          shown ?? options.find(o => o.value === picked)?.label ?? picked\n        }\n        onChange={e => {\n          onChange(e.target.value as T)\n        }}\n      >\n        {options.map(o => (\n          <MenuItem\n            key={o.value}\n            value={o.value}\n            disabled={o.disabled}\n            title={o.disabled ? undefined : o.description}\n          >\n            <ListItemText\n              primary={o.label}\n              secondary={o.disabled ? o.description : undefined}\n            />\n          </MenuItem>\n        ))}\n      </Select>\n    </FormControl>\n  )\n}\n", "import type { ReactNode } from 'react'\n\nimport { BUBBLE_SPREADS } from '@jbrowse/bandage-core/bubbleSpreads'\nimport { EDGE_WIDTHS } from '@jbrowse/bandage-core/edgeWidths'\nimport { LAYOUT_ENGINES } from '@jbrowse/bandage-core/layoutEngines'\nimport { LAYOUT_QUALITIES } from '@jbrowse/bandage-core/layoutQualities'\nimport { NODE_WIDTHS } from '@jbrowse/bandage-core/nodeWidths'\nimport { MAX_PATH_COLORS } from '@jbrowse/bandage-core/pathColors'\nimport { Dialog } from '@jbrowse/core/ui'\nimport {\n  Button,\n  DialogActions,\n  DialogContent,\n  FormControlLabel,\n  Switch,\n  Typography,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport LabelledSelect from './LabelledSelect'\nimport { pickGeneTrack } from '../genes/geneFeatures'\nimport { pickRepeatTrack } from '../repeats/repeatFeatures'\n\nimport type { GraphPaneModel } from '../model'\n\nconst useStyles = makeStyles()({\n  section: {\n    marginBottom: 24,\n  },\n  group: {\n    marginBottom: 16,\n  },\n  heading: {\n    marginBottom: 8,\n  },\n})\n\nfunction Caption({\n  warn = false,\n  children,\n}: {\n  warn?: boolean\n  children: ReactNode\n}) {\n  return (\n    <Typography\n      variant=\"caption\"\n      component=\"div\"\n      color={warn ? 'warning.main' : 'text.secondary'}\n    >\n      {children}\n    </Typography>\n  )\n}\n\nfunction Group({ title, children }: { title: string; children: ReactNode }) {\n  const { classes } = useStyles()\n  return (\n    <section className={classes.group}>\n      <Typography variant=\"subtitle1\" className={classes.heading}>\n        {title}\n      </Typography>\n      {children}\n    </section>\n  )\n}\n\nfunction SettingSwitch({\n  label,\n  checked,\n  onChange,\n  children,\n}: {\n  label: string\n  checked: boolean\n  onChange: (checked: boolean) => void\n  children?: ReactNode\n}) {\n  const { classes } = useStyles()\n  return (\n    <div className={classes.section}>\n      <FormControlLabel\n        control={\n          <Switch\n            checked={checked}\n            onChange={e => {\n              onChange(e.target.checked)\n            }}\n          />\n        }\n        label={label}\n      />\n      {children}\n    </div>\n  )\n}\n\n// one dropdown setting, at the dialog's width, and its caption\nfunction SettingSelect<T extends string>({\n  children,\n  ...props\n}: Omit<Parameters<typeof LabelledSelect<T>>[0], 'size' | 'sx'> & {\n  children?: ReactNode\n}) {\n  const { classes } = useStyles()\n  return (\n    <div className={classes.section}>\n      <LabelledSelect sx={{ minWidth: 200 }} {...props} />\n      {children}\n    </div>\n  )\n}\n\nconst NODE_LIMITS = [5000, 20_000, 50_000, 100_000]\n\n// the presets, with a limit a session states among them\nfunction nodeLimitOptions(current: number) {\n  return [...new Set([...NODE_LIMITS, current])]\n    .sort((a, b) => a - b)\n    .map(limit => ({ value: String(limit), label: limit.toLocaleString() }))\n}\n\ninterface NamedTrack {\n  trackId: string\n  name: string\n}\n\n// '' leaves the pick to the heuristic, so a session can go back to it\nfunction TrackPickSetting({\n  label,\n  choices,\n  stored,\n  auto,\n  testId,\n  onChange,\n  children,\n}: {\n  label: string\n  choices: NamedTrack[]\n  stored: string\n  auto: NamedTrack | undefined\n  testId: string\n  onChange: (trackId: string) => void\n  children: ReactNode\n}) {\n  return choices.length > 0 ? (\n    <SettingSelect\n      label={label}\n      value={choices.some(t => t.trackId === stored) ? stored : ''}\n      options={[\n        { value: '', label: `Automatic (${auto?.name ?? 'none'})` },\n        ...choices.map(({ trackId, name }) => ({\n          value: trackId,\n          label: name,\n        })),\n      ]}\n      testId={testId}\n      onChange={onChange}\n    >\n      {children}\n    </SettingSelect>\n  ) : null\n}\n\n// Toggles the menus already offer (halos, genes, color) stay out of here.\n// `children` is the host's own part of the subgraph group.\nconst GraphSettingsDialog = observer(function GraphSettingsDialog(props: {\n  model: GraphPaneModel\n  onClose: () => void\n  children?: ReactNode\n}) {\n  const { model, onClose, children } = props\n  const { classes } = useStyles()\n\n  return (\n    <Dialog open onClose={onClose} title=\"Graph settings\">\n      <DialogContent>\n        <Group title=\"Subgraph\">\n          {children}\n          <SettingSelect\n            label=\"Node limit\"\n            value={String(model.maxGraphNodes)}\n            options={nodeLimitOptions(model.maxGraphNodes)}\n            testId=\"graph-node-limit-select\"\n            onChange={limit => {\n              model.setMaxGraphNodes(Number(limit))\n            }}\n          >\n            <Caption>\n              The most nodes a layout draws; past it the graph is declined. Walk\n              rows take no limit.\n            </Caption>\n          </SettingSelect>\n        </Group>\n\n        <Group title=\"Drawing\">\n          {model.anchorPaths.length > 1 ? (\n            <SettingSelect\n              label=\"Reference path\"\n              value={model.activeReferencePath ?? ''}\n              options={model.anchorPaths.map(({ name }) => ({\n                value: name,\n                label: name,\n              }))}\n              testId=\"graph-reference-path-select\"\n              onChange={name => {\n                model.setReferencePath(name)\n                void model.recomputeLayout()\n              }}\n            >\n              <Caption>The path the anchored layouts place x along</Caption>\n            </SettingSelect>\n          ) : null}\n\n          <SettingSelect\n            label=\"Node width\"\n            value={model.nodeWidth}\n            options={NODE_WIDTHS}\n            testId=\"graph-node-width-select\"\n            onChange={width => {\n              model.setNodeWidth(width)\n            }}\n          >\n            <Caption>\n              Depth as width. In a cut with walks, depth is how many haplotypes\n              carry the node.\n            </Caption>\n          </SettingSelect>\n\n          <SettingSelect\n            label=\"Link width\"\n            value={model.linkWidth}\n            options={EDGE_WIDTHS}\n            testId=\"graph-link-width-select\"\n            onChange={links => {\n              model.setLinkWidth(links)\n            }}\n          >\n            <Caption>\n              Walks as width, so a common route reads heavy and a private one\n              thin.\n            </Caption>\n          </SettingSelect>\n\n          <SettingSwitch\n            label=\"Draw paths\"\n            checked={model.drawPaths}\n            onChange={draw => {\n              model.setLayer('paths', draw)\n            }}\n          >\n            <Caption>\n              Color each node by the paths through it, one lane per path\n            </Caption>\n            {model.drawPaths && !model.effectiveDrawPaths ? (\n              <Caption warn>\n                {model.pathCount > MAX_PATH_COLORS\n                  ? `Off: ${model.pathCount.toLocaleString()} paths is past the ${MAX_PATH_COLORS} this can tell apart`\n                  : 'Off: this graph states no paths'}\n              </Caption>\n            ) : null}\n          </SettingSwitch>\n\n          <TrackPickSetting\n            label=\"Gene track\"\n            choices={model.geneTrackChoices}\n            stored={model.geneTrackId}\n            auto={pickGeneTrack(model.geneTrackChoices, '')}\n            testId=\"graph-gene-track-select\"\n            onChange={trackId => {\n              model.setGeneTrackId(trackId)\n            }}\n          >\n            <Caption>Where genes on the backbone come from</Caption>\n          </TrackPickSetting>\n\n          <TrackPickSetting\n            label=\"Repeat track\"\n            choices={model.repeatTrackChoices}\n            stored={model.repeatTrackId}\n            auto={pickRepeatTrack(model.repeatTrackChoices, '')}\n            testId=\"graph-repeat-track-select\"\n            onChange={trackId => {\n              model.setRepeatTrackId(trackId)\n            }}\n          >\n            <Caption>\n              The tandem repeat annotation walk rows measure and tile by\n            </Caption>\n          </TrackPickSetting>\n        </Group>\n\n        <Group title=\"Force-directed layout\">\n          {model.hasGraph && !model.usesLayoutEngine ? (\n            <div className={classes.section}>\n              <Caption warn>\n                No effect on the current layout until Layout is Force-directed\n              </Caption>\n            </div>\n          ) : null}\n\n          <SettingSelect\n            label=\"Engine\"\n            value={model.layoutEngine}\n            options={LAYOUT_ENGINES}\n            testId=\"graph-layout-engine-select\"\n            onChange={engine => {\n              model.setLayoutEngine(engine)\n            }}\n          >\n            <Caption>\n              Stress keeps the reference straight, so a zoom keeps the picture;\n              FMMM lets the whole graph settle.\n            </Caption>\n          </SettingSelect>\n\n          <SettingSelect\n            label=\"Layout quality\"\n            value={String(model.layoutQuality)}\n            options={LAYOUT_QUALITIES.map(q => ({\n              value: String(q.value),\n              label: q.label,\n            }))}\n            testId=\"graph-layout-quality-select\"\n            onChange={quality => {\n              model.setLayoutQuality(Number(quality))\n            }}\n          >\n            <Caption>\n              The engine&apos;s iteration budget; higher is slower\n            </Caption>\n          </SettingSelect>\n\n          <SettingSelect\n            label=\"Bubble spread\"\n            value={model.bubbleSpread}\n            options={BUBBLE_SPREADS}\n            testId=\"graph-bubble-spread-select\"\n            onChange={spread => {\n              model.setBubbleSpread(spread)\n            }}\n          >\n            <Caption>How far the layout opens a bubble</Caption>\n          </SettingSelect>\n\n          {model.layoutEngine === 'stress' ? null : (\n            <SettingSwitch\n              label=\"Linear layout\"\n              checked={model.linearLayout}\n              onChange={linear => {\n                model.setLinearLayout(linear)\n              }}\n            >\n              <Caption>Keeps a chain of nodes on one line where it can</Caption>\n            </SettingSwitch>\n          )}\n        </Group>\n      </DialogContent>\n\n      <DialogActions>\n        <Button variant=\"contained\" color=\"primary\" onClick={onClose}>\n          Close\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n})\n\nexport default GraphSettingsDialog\n"],
   "mappings": "8WACA,IAAIA,EAAmB,CACrB,CAAE,MAAO,EAAG,MAAO,SAAU,EAC7B,CAAE,MAAO,EAAG,MAAO,MAAO,EAC1B,CAAE,MAAO,EAAG,MAAO,SAAU,EAC7B,CAAE,MAAO,EAAG,MAAO,MAAO,EAC1B,CAAE,MAAO,EAAG,MAAO,MAAO,CAC5B,ECee,SAARC,EAAkD,CACvD,MAAAC,EACA,MAAAC,EACA,QAAAC,EACA,OAAAC,EACA,KAAAC,EACA,GAAAC,EACA,SAAAC,EACA,MAAAC,EACA,MAAAC,EACA,SAAAC,CACF,EAYG,CACD,IAAMC,EAAUC,EAAM,EACtB,OACEC,EAACC,EAAA,CAAY,KAAMT,EAAM,GAAIC,EAAI,SAAUC,EAAU,MAAOC,EAC1D,UAAAO,EAACC,EAAA,CAAW,GAAIL,EAAS,OAAM,GAC5B,SAAAV,EACH,EACAc,EAACE,EAAA,CACC,QAASN,EACT,MAAOT,EACP,MAAOD,EACP,QAAO,GACP,aAAY,GACZ,cAAaG,EACb,YAAac,GACXT,GAASN,EAAQ,KAAKgB,GAAKA,EAAE,QAAUD,CAAM,GAAG,OAASA,EAE3D,SAAUE,GAAK,CACbV,EAASU,EAAE,OAAO,KAAU,CAC9B,EAEC,SAAAjB,EAAQ,IAAIgB,GACXJ,EAACM,EAAA,CAEC,MAAOF,EAAE,MACT,SAAUA,EAAE,SACZ,MAAOA,EAAE,SAAW,OAAYA,EAAE,YAElC,SAAAJ,EAACO,EAAA,CACC,QAASH,EAAE,MACX,UAAWA,EAAE,SAAWA,EAAE,YAAc,OAC1C,GARKA,EAAE,KAST,CACD,EACH,GACF,CAEJ,CCxDA,IAAMI,EAAYC,EAAW,EAAE,CAC7B,QAAS,CACP,aAAc,EAChB,EACA,MAAO,CACL,aAAc,EAChB,EACA,QAAS,CACP,aAAc,CAChB,CACF,CAAC,EAED,SAASC,EAAQ,CACf,KAAAC,EAAO,GACP,SAAAC,CACF,EAGG,CACD,OACEC,EAACC,EAAA,CACC,QAAQ,UACR,UAAU,MACV,MAAOH,EAAO,eAAiB,iBAE9B,SAAAC,EACH,CAEJ,CAEA,SAASG,EAAM,CAAE,MAAAC,EAAO,SAAAJ,CAAS,EAA2C,CAC1E,GAAM,CAAE,QAAAK,CAAQ,EAAIT,EAAU,EAC9B,OACEU,EAAC,WAAQ,UAAWD,EAAQ,MAC1B,UAAAJ,EAACC,EAAA,CAAW,QAAQ,YAAY,UAAWG,EAAQ,QAChD,SAAAD,EACH,EACCJ,GACH,CAEJ,CAEA,SAASO,EAAc,CACrB,MAAAC,EACA,QAAAC,EACA,SAAAC,EACA,SAAAV,CACF,EAKG,CACD,GAAM,CAAE,QAAAK,CAAQ,EAAIT,EAAU,EAC9B,OACEU,EAAC,OAAI,UAAWD,EAAQ,QACtB,UAAAJ,EAACU,EAAA,CACC,QACEV,EAACW,EAAA,CACC,QAASH,EACT,SAAUI,GAAK,CACbH,EAASG,EAAE,OAAO,OAAO,CAC3B,EACF,EAEF,MAAOL,EACT,EACCR,GACH,CAEJ,CAGA,SAASc,EAAgC,CACvC,SAAAd,EACA,GAAGe,CACL,EAEG,CACD,GAAM,CAAE,QAAAV,CAAQ,EAAIT,EAAU,EAC9B,OACEU,EAAC,OAAI,UAAWD,EAAQ,QACtB,UAAAJ,EAACe,EAAA,CAAe,GAAI,CAAE,SAAU,GAAI,EAAI,GAAGD,EAAO,EACjDf,GACH,CAEJ,CAEA,IAAMiB,EAAc,CAAC,IAAM,IAAQ,IAAQ,GAAO,EAGlD,SAASC,EAAiBC,EAAiB,CACzC,MAAO,CAAC,GAAG,IAAI,IAAI,CAAC,GAAGF,EAAaE,CAAO,CAAC,CAAC,EAC1C,KAAK,CAACC,EAAGC,IAAMD,EAAIC,CAAC,EACpB,IAAIC,IAAU,CAAE,MAAO,OAAOA,CAAK,EAAG,MAAOA,EAAM,eAAe,CAAE,EAAE,CAC3E,CAQA,SAASC,EAAiB,CACxB,MAAAf,EACA,QAAAgB,EACA,OAAAC,EACA,KAAAC,EACA,OAAAC,EACA,SAAAjB,EACA,SAAAV,CACF,EAQG,CACD,OAAOwB,EAAQ,OAAS,EACtBvB,EAACa,EAAA,CACC,MAAON,EACP,MAAOgB,EAAQ,KAAKI,GAAKA,EAAE,UAAYH,CAAM,EAAIA,EAAS,GAC1D,QAAS,CACP,CAAE,MAAO,GAAI,MAAO,cAAcC,GAAM,MAAQ,MAAM,GAAI,EAC1D,GAAGF,EAAQ,IAAI,CAAC,CAAE,QAAAK,EAAS,KAAAC,CAAK,KAAO,CACrC,MAAOD,EACP,MAAOC,CACT,EAAE,CACJ,EACA,OAAQH,EACR,SAAUjB,EAET,SAAAV,EACH,EACE,IACN,CAIA,IAAM+B,EAAsBC,EAAS,SAA6BjB,EAI/D,CACD,GAAM,CAAE,MAAAkB,EAAO,QAAAC,EAAS,SAAAlC,CAAS,EAAIe,EAC/B,CAAE,QAAAV,CAAQ,EAAIT,EAAU,EAE9B,OACEU,EAAC6B,EAAA,CAAO,KAAI,GAAC,QAASD,EAAS,MAAM,iBACnC,UAAA5B,EAAC8B,EAAA,CACC,UAAA9B,EAACH,EAAA,CAAM,MAAM,WACV,UAAAH,EACDC,EAACa,EAAA,CACC,MAAM,aACN,MAAO,OAAOmB,EAAM,aAAa,EACjC,QAASf,EAAiBe,EAAM,aAAa,EAC7C,OAAO,0BACP,SAAUX,GAAS,CACjBW,EAAM,iBAAiB,OAAOX,CAAK,CAAC,CACtC,EAEA,SAAArB,EAACH,EAAA,CAAQ,kGAGT,EACF,GACF,EAEAQ,EAACH,EAAA,CAAM,MAAM,UACV,UAAA8B,EAAM,YAAY,OAAS,EAC1BhC,EAACa,EAAA,CACC,MAAM,iBACN,MAAOmB,EAAM,qBAAuB,GACpC,QAASA,EAAM,YAAY,IAAI,CAAC,CAAE,KAAAH,CAAK,KAAO,CAC5C,MAAOA,EACP,MAAOA,CACT,EAAE,EACF,OAAO,8BACP,SAAUA,GAAQ,CAChBG,EAAM,iBAAiBH,CAAI,EACtBG,EAAM,gBAAgB,CAC7B,EAEA,SAAAhC,EAACH,EAAA,CAAQ,uDAA2C,EACtD,EACE,KAEJG,EAACa,EAAA,CACC,MAAM,aACN,MAAOmB,EAAM,UACb,QAASI,EACT,OAAO,0BACP,SAAUC,GAAS,CACjBL,EAAM,aAAaK,CAAK,CAC1B,EAEA,SAAArC,EAACH,EAAA,CAAQ,6FAGT,EACF,EAEAG,EAACa,EAAA,CACC,MAAM,aACN,MAAOmB,EAAM,UACb,QAASM,EACT,OAAO,0BACP,SAAUC,GAAS,CACjBP,EAAM,aAAaO,CAAK,CAC1B,EAEA,SAAAvC,EAACH,EAAA,CAAQ,iFAGT,EACF,EAEAQ,EAACC,EAAA,CACC,MAAM,aACN,QAAS0B,EAAM,UACf,SAAUQ,GAAQ,CAChBR,EAAM,SAAS,QAASQ,CAAI,CAC9B,EAEA,UAAAxC,EAACH,EAAA,CAAQ,sEAET,EACCmC,EAAM,WAAa,CAACA,EAAM,mBACzBhC,EAACH,EAAA,CAAQ,KAAI,GACV,SAAAmC,EAAM,UAAYS,EACf,QAAQT,EAAM,UAAU,eAAe,CAAC,sBAAsBS,CAAe,uBAC7E,kCACN,EACE,MACN,EAEAzC,EAACsB,EAAA,CACC,MAAM,aACN,QAASU,EAAM,iBACf,OAAQA,EAAM,YACd,KAAMU,EAAcV,EAAM,iBAAkB,EAAE,EAC9C,OAAO,0BACP,SAAUJ,GAAW,CACnBI,EAAM,eAAeJ,CAAO,CAC9B,EAEA,SAAA5B,EAACH,EAAA,CAAQ,iDAAqC,EAChD,EAEAG,EAACsB,EAAA,CACC,MAAM,eACN,QAASU,EAAM,mBACf,OAAQA,EAAM,cACd,KAAMW,EAAgBX,EAAM,mBAAoB,EAAE,EAClD,OAAO,4BACP,SAAUJ,GAAW,CACnBI,EAAM,iBAAiBJ,CAAO,CAChC,EAEA,SAAA5B,EAACH,EAAA,CAAQ,sEAET,EACF,GACF,EAEAQ,EAACH,EAAA,CAAM,MAAM,wBACV,UAAA8B,EAAM,UAAY,CAACA,EAAM,iBACxBhC,EAAC,OAAI,UAAWI,EAAQ,QACtB,SAAAJ,EAACH,EAAA,CAAQ,KAAI,GAAC,0EAEd,EACF,EACE,KAEJG,EAACa,EAAA,CACC,MAAM,SACN,MAAOmB,EAAM,aACb,QAASY,EACT,OAAO,6BACP,SAAUC,GAAU,CAClBb,EAAM,gBAAgBa,CAAM,CAC9B,EAEA,SAAA7C,EAACH,EAAA,CAAQ,+GAGT,EACF,EAEAG,EAACa,EAAA,CACC,MAAM,iBACN,MAAO,OAAOmB,EAAM,aAAa,EACjC,QAASc,EAAiB,IAAIC,IAAM,CAClC,MAAO,OAAOA,EAAE,KAAK,EACrB,MAAOA,EAAE,KACX,EAAE,EACF,OAAO,8BACP,SAAUC,GAAW,CACnBhB,EAAM,iBAAiB,OAAOgB,CAAO,CAAC,CACxC,EAEA,SAAAhD,EAACH,EAAA,CAAQ,2DAET,EACF,EAEAG,EAACa,EAAA,CACC,MAAM,gBACN,MAAOmB,EAAM,aACb,QAASiB,EACT,OAAO,6BACP,SAAUC,GAAU,CAClBlB,EAAM,gBAAgBkB,CAAM,CAC9B,EAEA,SAAAlD,EAACH,EAAA,CAAQ,6CAAiC,EAC5C,EAECmC,EAAM,eAAiB,SAAW,KACjChC,EAACM,EAAA,CACC,MAAM,gBACN,QAAS0B,EAAM,aACf,SAAUmB,GAAU,CAClBnB,EAAM,gBAAgBmB,CAAM,CAC9B,EAEA,SAAAnD,EAACH,EAAA,CAAQ,2DAA+C,EAC1D,GAEJ,GACF,EAEAG,EAACoD,EAAA,CACC,SAAApD,EAACqD,EAAA,CAAO,QAAQ,YAAY,MAAM,UAAU,QAASpB,EAAS,iBAE9D,EACF,GACF,CAEJ,CAAC,EAEMqB,GAAQxB",
   "names": ["LAYOUT_QUALITIES", "LabelledSelect", "label", "value", "options", "testId", "size", "sx", "disabled", "title", "shown", "onChange", "labelId", "useId", "jsxs", "FormControl", "jsx", "InputLabel", "Select", "picked", "o", "e", "MenuItem", "ListItemText", "useStyles", "makeStyles", "Caption", "warn", "children", "jsx", "Typography", "Group", "title", "classes", "jsxs", "SettingSwitch", "label", "checked", "onChange", "FormControlLabel", "Switch", "e", "SettingSelect", "props", "LabelledSelect", "NODE_LIMITS", "nodeLimitOptions", "current", "a", "b", "limit", "TrackPickSetting", "choices", "stored", "auto", "testId", "t", "trackId", "name", "GraphSettingsDialog", "observer", "model", "onClose", "Dialog", "DialogContent", "NODE_WIDTHS", "width", "EDGE_WIDTHS", "links", "draw", "MAX_PATH_COLORS", "pickGeneTrack", "pickRepeatTrack", "LAYOUT_ENGINES", "engine", "LAYOUT_QUALITIES", "q", "quality", "BUBBLE_SPREADS", "spread", "linear", "DialogActions", "Button", "GraphSettingsDialog_default"]

package/dist/chunks/chunk-3VGXCEMQ.js

@@ -0,0 +1,2 @@
+var e=JBrowseExports["@jbrowse/core/util/tracks"],t=o=>e!=null&&o in Object(e)?e[o]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+o+"' from '@jbrowse/core/util/tracks' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:o});var s=t("getConfAssemblyNamesOrNone");var r=t("getTrackName");var n=t("makeIndexType");var a=t("toTrackConfigEntry");var c=e&&e.__esModule?e.default:e;export{s as a,r as b,n as c,a as d};
+//# sourceMappingURL=chunk-3VGXCEMQ.js.map

package/dist/chunks/{chunk-7WIBGKBU.js.map → chunk-3VGXCEMQ.js.map}

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["host:@jbrowse/core/util/tracks"],
-  "sourcesContent": ["const host = JBrowseExports[\"@jbrowse/core/util/tracks\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\n            \"This JBrowse does not provide '\" + name + \"' from '\" + \"@jbrowse/core/util/tracks\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const UNKNOWN = /* @__PURE__ */ read(\"UNKNOWN\")\nexport const UNSUPPORTED = /* @__PURE__ */ read(\"UNSUPPORTED\")\nexport const addAdapterGuesser = /* @__PURE__ */ read(\"addAdapterGuesser\")\nexport const addTrackTypeGuesser = /* @__PURE__ */ read(\"addTrackTypeGuesser\")\nexport const allSessionTracks = /* @__PURE__ */ read(\"allSessionTracks\")\nexport const annotationTrackIds = /* @__PURE__ */ read(\"annotationTrackIds\")\nexport const canonicalAssemblyNames = /* @__PURE__ */ read(\"canonicalAssemblyNames\")\nexport const clearFileFromCache = /* @__PURE__ */ read(\"clearFileFromCache\")\nexport const ensureFileHandleReady = /* @__PURE__ */ read(\"ensureFileHandleReady\")\nexport const expandLooseTrackConfig = /* @__PURE__ */ read(\"expandLooseTrackConfig\")\nexport const filterTracks = /* @__PURE__ */ read(\"filterTracks\")\nexport const findFileHandleIds = /* @__PURE__ */ read(\"findFileHandleIds\")\nexport const generateUnknownTrackConf = /* @__PURE__ */ read(\"generateUnknownTrackConf\")\nexport const generateUnsupportedTrackConf = /* @__PURE__ */ read(\"generateUnsupportedTrackConf\")\nexport const getBlob = /* @__PURE__ */ read(\"getBlob\")\nexport const getBlobMap = /* @__PURE__ */ read(\"getBlobMap\")\nexport const getConfAssemblyNames = /* @__PURE__ */ read(\"getConfAssemblyNames\")\nexport const getConfAssemblyNamesOrNone = /* @__PURE__ */ read(\"getConfAssemblyNamesOrNone\")\nexport const getConfRpcSessionId = /* @__PURE__ */ read(\"getConfRpcSessionId\")\nexport const getFileFromCache = /* @__PURE__ */ read(\"getFileFromCache\")\nexport const getFileName = /* @__PURE__ */ read(\"getFileName\")\nexport const getRpcSessionId = /* @__PURE__ */ read(\"getRpcSessionId\")\nexport const getTrackAssemblyNames = /* @__PURE__ */ read(\"getTrackAssemblyNames\")\nexport const getTrackName = /* @__PURE__ */ read(\"getTrackName\")\nexport const guessAdapter = /* @__PURE__ */ read(\"guessAdapter\")\nexport const guessTabixIndex = /* @__PURE__ */ read(\"guessTabixIndex\")\nexport const guessTrackConf = /* @__PURE__ */ read(\"guessTrackConf\")\nexport const guessTrackConfForLocation = /* @__PURE__ */ read(\"guessTrackConfForLocation\")\nexport const guessTrackType = /* @__PURE__ */ read(\"guessTrackType\")\nexport const hasFileHandlesInCache = /* @__PURE__ */ read(\"hasFileHandlesInCache\")\nexport const hideTrackGeneric = /* @__PURE__ */ read(\"hideTrackGeneric\")\nexport const isLooseTrackConfig = /* @__PURE__ */ read(\"isLooseTrackConfig\")\nexport const isSameAssemblyName = /* @__PURE__ */ read(\"isSameAssemblyName\")\nexport const launchToggleTrackGeneric = /* @__PURE__ */ read(\"launchToggleTrackGeneric\")\nexport const launchTrackGeneric = /* @__PURE__ */ read(\"launchTrackGeneric\")\nexport const makeIndex = /* @__PURE__ */ read(\"makeIndex\")\nexport const makeIndexType = /* @__PURE__ */ read(\"makeIndexType\")\nexport const normalizeTrackInit = /* @__PURE__ */ read(\"normalizeTrackInit\")\nexport const offeredTracks = /* @__PURE__ */ read(\"offeredTracks\")\nexport const openAssemblyInLinearView = /* @__PURE__ */ read(\"openAssemblyInLinearView\")\nexport const openMateLabel = /* @__PURE__ */ read(\"openMateLabel\")\nexport const pickDisplayForView = /* @__PURE__ */ read(\"pickDisplayForView\")\nexport const restoreFileHandles = /* @__PURE__ */ read(\"restoreFileHandles\")\nexport const restoreFileHandlesFromSnapshot = /* @__PURE__ */ read(\"restoreFileHandlesFromSnapshot\")\nexport const setBlobMap = /* @__PURE__ */ read(\"setBlobMap\")\nexport const setFileInCache = /* @__PURE__ */ read(\"setFileInCache\")\nexport const showTrackGeneric = /* @__PURE__ */ read(\"showTrackGeneric\")\nexport const storeBlobLocation = /* @__PURE__ */ read(\"storeBlobLocation\")\nexport const storeFileHandleLocation = /* @__PURE__ */ read(\"storeFileHandleLocation\")\nexport const stripFileExtension = /* @__PURE__ */ read(\"stripFileExtension\")\nexport const stripTrackIds = /* @__PURE__ */ read(\"stripTrackIds\")\nexport const toggleTrackGeneric = /* @__PURE__ */ read(\"toggleTrackGeneric\")\nexport const viewCanDisplayTrack = /* @__PURE__ */ read(\"viewCanDisplayTrack\")\nexport const viewDisplayNames = /* @__PURE__ */ read(\"viewDisplayNames\")\nexport const warmTrackDisplayGeneric = /* @__PURE__ */ read(\"warmTrackDisplayGeneric\")\nexport default host && host.__esModule ? host.default : host"],
-  "mappings": "AAAA,IAAMA,EAAO,eAAe,2BAA2B,EACjDC,EAAOC,GACXF,GAAQ,MAAQE,KAAQ,OAAOF,CAAI,EAC/BA,EAAKE,CAAI,EACT,OAAO,OACL,UAAY,CACV,MAAM,IAAI,MACR,kCAAoCA,EAAO,2IAC7C,CACF,EACA,CAAE,mBAAoBA,CAAK,CAC7B,EAwBC,IAAMC,EAA+BC,EAAK,cAAc,EAaxD,IAAMC,EAAgCC,EAAK,eAAe,EAmBjE,IAAOC,EAAQC,GAAQA,EAAK,WAAaA,EAAK,QAAUA",
-  "names": ["host", "read", "name", "getTrackName", "read", "makeIndexType", "read", "tracks_default", "host"]
+  "sourcesContent": ["const host = JBrowseExports[\"@jbrowse/core/util/tracks\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\n            \"This JBrowse does not provide '\" + name + \"' from '\" + \"@jbrowse/core/util/tracks\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const UNKNOWN = /* @__PURE__ */ read(\"UNKNOWN\")\nexport const UNSUPPORTED = /* @__PURE__ */ read(\"UNSUPPORTED\")\nexport const addAdapterGuesser = /* @__PURE__ */ read(\"addAdapterGuesser\")\nexport const addTrackTypeGuesser = /* @__PURE__ */ read(\"addTrackTypeGuesser\")\nexport const allSessionTracks = /* @__PURE__ */ read(\"allSessionTracks\")\nexport const annotationTrackIds = /* @__PURE__ */ read(\"annotationTrackIds\")\nexport const canonicalAssemblyNames = /* @__PURE__ */ read(\"canonicalAssemblyNames\")\nexport const clearFileFromCache = /* @__PURE__ */ read(\"clearFileFromCache\")\nexport const ensureFileHandleReady = /* @__PURE__ */ read(\"ensureFileHandleReady\")\nexport const expandLooseTrackConfig = /* @__PURE__ */ read(\"expandLooseTrackConfig\")\nexport const filterTracks = /* @__PURE__ */ read(\"filterTracks\")\nexport const findFileHandleIds = /* @__PURE__ */ read(\"findFileHandleIds\")\nexport const generateUnknownTrackConf = /* @__PURE__ */ read(\"generateUnknownTrackConf\")\nexport const generateUnsupportedTrackConf = /* @__PURE__ */ read(\"generateUnsupportedTrackConf\")\nexport const getBlob = /* @__PURE__ */ read(\"getBlob\")\nexport const getBlobMap = /* @__PURE__ */ read(\"getBlobMap\")\nexport const getConfAssemblyNames = /* @__PURE__ */ read(\"getConfAssemblyNames\")\nexport const getConfAssemblyNamesOrNone = /* @__PURE__ */ read(\"getConfAssemblyNamesOrNone\")\nexport const getConfRpcSessionId = /* @__PURE__ */ read(\"getConfRpcSessionId\")\nexport const getFileFromCache = /* @__PURE__ */ read(\"getFileFromCache\")\nexport const getFileName = /* @__PURE__ */ read(\"getFileName\")\nexport const getRpcSessionId = /* @__PURE__ */ read(\"getRpcSessionId\")\nexport const getTrackAssemblyNames = /* @__PURE__ */ read(\"getTrackAssemblyNames\")\nexport const getTrackName = /* @__PURE__ */ read(\"getTrackName\")\nexport const guessAdapter = /* @__PURE__ */ read(\"guessAdapter\")\nexport const guessTabixIndex = /* @__PURE__ */ read(\"guessTabixIndex\")\nexport const guessTrackConf = /* @__PURE__ */ read(\"guessTrackConf\")\nexport const guessTrackConfForLocation = /* @__PURE__ */ read(\"guessTrackConfForLocation\")\nexport const guessTrackType = /* @__PURE__ */ read(\"guessTrackType\")\nexport const hasFileHandlesInCache = /* @__PURE__ */ read(\"hasFileHandlesInCache\")\nexport const hideTrackGeneric = /* @__PURE__ */ read(\"hideTrackGeneric\")\nexport const isLooseTrackConfig = /* @__PURE__ */ read(\"isLooseTrackConfig\")\nexport const isSameAssemblyName = /* @__PURE__ */ read(\"isSameAssemblyName\")\nexport const launchToggleTrackGeneric = /* @__PURE__ */ read(\"launchToggleTrackGeneric\")\nexport const launchTrackGeneric = /* @__PURE__ */ read(\"launchTrackGeneric\")\nexport const makeIndex = /* @__PURE__ */ read(\"makeIndex\")\nexport const makeIndexType = /* @__PURE__ */ read(\"makeIndexType\")\nexport const normalizeTrackInit = /* @__PURE__ */ read(\"normalizeTrackInit\")\nexport const offeredTracks = /* @__PURE__ */ read(\"offeredTracks\")\nexport const openAssemblyInLinearView = /* @__PURE__ */ read(\"openAssemblyInLinearView\")\nexport const openMateLabel = /* @__PURE__ */ read(\"openMateLabel\")\nexport const pickDisplayForView = /* @__PURE__ */ read(\"pickDisplayForView\")\nexport const restoreFileHandles = /* @__PURE__ */ read(\"restoreFileHandles\")\nexport const restoreFileHandlesFromSnapshot = /* @__PURE__ */ read(\"restoreFileHandlesFromSnapshot\")\nexport const setBlobMap = /* @__PURE__ */ read(\"setBlobMap\")\nexport const setFileInCache = /* @__PURE__ */ read(\"setFileInCache\")\nexport const showTrackGeneric = /* @__PURE__ */ read(\"showTrackGeneric\")\nexport const storeBlobLocation = /* @__PURE__ */ read(\"storeBlobLocation\")\nexport const storeFileHandleLocation = /* @__PURE__ */ read(\"storeFileHandleLocation\")\nexport const stripFileExtension = /* @__PURE__ */ read(\"stripFileExtension\")\nexport const stripTrackIds = /* @__PURE__ */ read(\"stripTrackIds\")\nexport const toTrackConfigEntry = /* @__PURE__ */ read(\"toTrackConfigEntry\")\nexport const toggleTrackGeneric = /* @__PURE__ */ read(\"toggleTrackGeneric\")\nexport const trackCatalog = /* @__PURE__ */ read(\"trackCatalog\")\nexport const trackCatalogEntry = /* @__PURE__ */ read(\"trackCatalogEntry\")\nexport const trackDisplayType = /* @__PURE__ */ read(\"trackDisplayType\")\nexport const viewCanDisplayTrack = /* @__PURE__ */ read(\"viewCanDisplayTrack\")\nexport const viewDisplayNames = /* @__PURE__ */ read(\"viewDisplayNames\")\nexport const warmTrackDisplayGeneric = /* @__PURE__ */ read(\"warmTrackDisplayGeneric\")\nexport default host && host.__esModule ? host.default : host"],
+  "mappings": "AAAA,IAAMA,EAAO,eAAe,2BAA2B,EACjDC,EAAOC,GACXF,GAAQ,MAAQE,KAAQ,OAAOF,CAAI,EAC/BA,EAAKE,CAAI,EACT,OAAO,OACL,UAAY,CACV,MAAM,IAAI,MACR,kCAAoCA,EAAO,2IAC7C,CACF,EACA,CAAE,mBAAoBA,CAAK,CAC7B,EAkBC,IAAMC,EAA6CC,EAAK,4BAA4B,EAMpF,IAAMC,EAA+BC,EAAK,cAAc,EAaxD,IAAMC,EAAgCC,EAAK,eAAe,EAe1D,IAAMC,EAAqCC,EAAK,oBAAoB,EAQ3E,IAAOC,EAAQC,GAAQA,EAAK,WAAaA,EAAK,QAAUA",
+  "names": ["host", "read", "name", "getConfAssemblyNamesOrNone", "read", "getTrackName", "read", "makeIndexType", "read", "toTrackConfigEntry", "read", "tracks_default", "host"]
 }

package/dist/chunks/chunk-3WG3GF2A.js

@@ -0,0 +1,2 @@
+var e=JBrowseExports["mobx-state-tree"],t=o=>e!=null&&o in Object(e)?e[o]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+o+"' from 'mobx-state-tree' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:o}),n=t("addDisposer");var s=t("flow");var r=t("getEnv");var p=t("getRoot");var c=t("isAlive");var i=t("types");var a=e&&e.__esModule?e.default:e;export{n as a,s as b,r as c,p as d,c as e,i as f};
+//# sourceMappingURL=chunk-3WG3GF2A.js.map

package/dist/chunks/{chunk-NDRLCGPC.js.map → chunk-3WG3GF2A.js.map}

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["host:@jbrowse/mobx-state-tree"],
-  "sourcesContent": ["const host = JBrowseExports[\"mobx-state-tree\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\n            \"This JBrowse does not provide '\" + name + \"' from '\" + \"mobx-state-tree\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const addDisposer = /* @__PURE__ */ read(\"addDisposer\")\nexport const addMiddleware = /* @__PURE__ */ read(\"addMiddleware\")\nexport const applyAction = /* @__PURE__ */ read(\"applyAction\")\nexport const applyPatch = /* @__PURE__ */ read(\"applyPatch\")\nexport const applySnapshot = /* @__PURE__ */ read(\"applySnapshot\")\nexport const asArrayType = /* @__PURE__ */ read(\"asArrayType\")\nexport const asMapType = /* @__PURE__ */ read(\"asMapType\")\nexport const asModelType = /* @__PURE__ */ read(\"asModelType\")\nexport const cannotDetermineSubtype = /* @__PURE__ */ read(\"cannotDetermineSubtype\")\nexport const cast = /* @__PURE__ */ read(\"cast\")\nexport const castFlowReturn = /* @__PURE__ */ read(\"castFlowReturn\")\nexport const castToReferenceSnapshot = /* @__PURE__ */ read(\"castToReferenceSnapshot\")\nexport const castToSnapshot = /* @__PURE__ */ read(\"castToSnapshot\")\nexport const clone = /* @__PURE__ */ read(\"clone\")\nexport const createActionTrackingMiddleware = /* @__PURE__ */ read(\"createActionTrackingMiddleware\")\nexport const createActionTrackingMiddleware2 = /* @__PURE__ */ read(\"createActionTrackingMiddleware2\")\nexport const decorate = /* @__PURE__ */ read(\"decorate\")\nexport const destroy = /* @__PURE__ */ read(\"destroy\")\nexport const detach = /* @__PURE__ */ read(\"detach\")\nexport const escapeJsonPath = /* @__PURE__ */ read(\"escapeJsonPath\")\nexport const extendInstance = /* @__PURE__ */ read(\"extendInstance\")\nexport const flow = /* @__PURE__ */ read(\"flow\")\nexport const getChildType = /* @__PURE__ */ read(\"getChildType\")\nexport const getEnv = /* @__PURE__ */ read(\"getEnv\")\nexport const getIdentifier = /* @__PURE__ */ read(\"getIdentifier\")\nexport const getLivelinessChecking = /* @__PURE__ */ read(\"getLivelinessChecking\")\nexport const getMembers = /* @__PURE__ */ read(\"getMembers\")\nexport const getNodeId = /* @__PURE__ */ read(\"getNodeId\")\nexport const getParent = /* @__PURE__ */ read(\"getParent\")\nexport const getParentOfType = /* @__PURE__ */ read(\"getParentOfType\")\nexport const getPath = /* @__PURE__ */ read(\"getPath\")\nexport const getPathParts = /* @__PURE__ */ read(\"getPathParts\")\nexport const getPropertyMembers = /* @__PURE__ */ read(\"getPropertyMembers\")\nexport const getRelativePath = /* @__PURE__ */ read(\"getRelativePath\")\nexport const getRoot = /* @__PURE__ */ read(\"getRoot\")\nexport const getRunningActionContext = /* @__PURE__ */ read(\"getRunningActionContext\")\nexport const getSnapshot = /* @__PURE__ */ read(\"getSnapshot\")\nexport const getType = /* @__PURE__ */ read(\"getType\")\nexport const getUnionSubtypes = /* @__PURE__ */ read(\"getUnionSubtypes\")\nexport const getWrappedType = /* @__PURE__ */ read(\"getWrappedType\")\nexport const hasParent = /* @__PURE__ */ read(\"hasParent\")\nexport const hasParentOfType = /* @__PURE__ */ read(\"hasParentOfType\")\nexport const isActionContextChildOf = /* @__PURE__ */ read(\"isActionContextChildOf\")\nexport const isActionContextThisOrChildOf = /* @__PURE__ */ read(\"isActionContextThisOrChildOf\")\nexport const isAlive = /* @__PURE__ */ read(\"isAlive\")\nexport const isArrayType = /* @__PURE__ */ read(\"isArrayType\")\nexport const isFrozenType = /* @__PURE__ */ read(\"isFrozenType\")\nexport const isIdentifierType = /* @__PURE__ */ read(\"isIdentifierType\")\nexport const isLateType = /* @__PURE__ */ read(\"isLateType\")\nexport const isLiteralType = /* @__PURE__ */ read(\"isLiteralType\")\nexport const isMapType = /* @__PURE__ */ read(\"isMapType\")\nexport const isModelType = /* @__PURE__ */ read(\"isModelType\")\nexport const isOptionalType = /* @__PURE__ */ read(\"isOptionalType\")\nexport const isPrimitiveType = /* @__PURE__ */ read(\"isPrimitiveType\")\nexport const isProtected = /* @__PURE__ */ read(\"isProtected\")\nexport const isReferenceType = /* @__PURE__ */ read(\"isReferenceType\")\nexport const isRefinementType = /* @__PURE__ */ read(\"isRefinementType\")\nexport const isRoot = /* @__PURE__ */ read(\"isRoot\")\nexport const isStateTreeNode = /* @__PURE__ */ read(\"isStateTreeNode\")\nexport const isType = /* @__PURE__ */ read(\"isType\")\nexport const isUnionType = /* @__PURE__ */ read(\"isUnionType\")\nexport const isValidReference = /* @__PURE__ */ read(\"isValidReference\")\nexport const joinJsonPath = /* @__PURE__ */ read(\"joinJsonPath\")\nexport const onAction = /* @__PURE__ */ read(\"onAction\")\nexport const onPatch = /* @__PURE__ */ read(\"onPatch\")\nexport const onSnapshot = /* @__PURE__ */ read(\"onSnapshot\")\nexport const protect = /* @__PURE__ */ read(\"protect\")\nexport const recordActions = /* @__PURE__ */ read(\"recordActions\")\nexport const recordPatches = /* @__PURE__ */ read(\"recordPatches\")\nexport const resolveIdentifier = /* @__PURE__ */ read(\"resolveIdentifier\")\nexport const resolvePath = /* @__PURE__ */ read(\"resolvePath\")\nexport const setDevMode = /* @__PURE__ */ read(\"setDevMode\")\nexport const setLivelinessChecking = /* @__PURE__ */ read(\"setLivelinessChecking\")\nexport const setLivelynessChecking = /* @__PURE__ */ read(\"setLivelynessChecking\")\nexport const setTypeChecking = /* @__PURE__ */ read(\"setTypeChecking\")\nexport const splitJsonPath = /* @__PURE__ */ read(\"splitJsonPath\")\nexport const t = /* @__PURE__ */ read(\"t\")\nexport const toGenerator = /* @__PURE__ */ read(\"toGenerator\")\nexport const toGeneratorFunction = /* @__PURE__ */ read(\"toGeneratorFunction\")\nexport const tryReference = /* @__PURE__ */ read(\"tryReference\")\nexport const tryResolve = /* @__PURE__ */ read(\"tryResolve\")\nexport const typecheck = /* @__PURE__ */ read(\"typecheck\")\nexport const types = /* @__PURE__ */ read(\"types\")\nexport const unescapeJsonPath = /* @__PURE__ */ read(\"unescapeJsonPath\")\nexport const unprotect = /* @__PURE__ */ read(\"unprotect\")\nexport const unwrapType = /* @__PURE__ */ read(\"unwrapType\")\nexport const walk = /* @__PURE__ */ read(\"walk\")\nexport default host && host.__esModule ? host.default : host"],
-  "mappings": "AAAA,IAAMA,EAAO,eAAe,iBAAiB,EACvCC,EAAOC,GACXF,GAAQ,MAAQE,KAAQ,OAAOF,CAAI,EAC/BA,EAAKE,CAAI,EACT,OAAO,OACL,UAAY,CACV,MAAM,IAAI,MACR,kCAAoCA,EAAO,iIAC7C,CACF,EACA,CAAE,mBAAoBA,CAAK,CAC7B,EACOC,EAA8BF,EAAK,aAAa,EAqBtD,IAAMG,EAAuBC,EAAK,MAAM,EAExC,IAAMC,EAAyBC,EAAK,QAAQ,EAW5C,IAAMC,EAA0BC,EAAK,SAAS,EAU9C,IAAMC,EAA0BC,EAAK,SAAS,EAc9C,IAAMC,EAAkCC,EAAK,iBAAiB,EAwB9D,IAAMC,EAAwBC,EAAK,OAAO,EAKjD,IAAOC,EAAQC,GAAQA,EAAK,WAAaA,EAAK,QAAUA",
-  "names": ["host", "read", "name", "addDisposer", "flow", "read", "getEnv", "read", "getRoot", "read", "isAlive", "read", "isStateTreeNode", "read", "types", "read", "mobx_state_tree_default", "host"]
+  "sourcesContent": ["const host = JBrowseExports[\"mobx-state-tree\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\n            \"This JBrowse does not provide '\" + name + \"' from '\" + \"mobx-state-tree\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const addDisposer = /* @__PURE__ */ read(\"addDisposer\")\nexport const addMiddleware = /* @__PURE__ */ read(\"addMiddleware\")\nexport const applyAction = /* @__PURE__ */ read(\"applyAction\")\nexport const applyPatch = /* @__PURE__ */ read(\"applyPatch\")\nexport const applySnapshot = /* @__PURE__ */ read(\"applySnapshot\")\nexport const asArrayType = /* @__PURE__ */ read(\"asArrayType\")\nexport const asMapType = /* @__PURE__ */ read(\"asMapType\")\nexport const asModelType = /* @__PURE__ */ read(\"asModelType\")\nexport const cannotDetermineSubtype = /* @__PURE__ */ read(\"cannotDetermineSubtype\")\nexport const cast = /* @__PURE__ */ read(\"cast\")\nexport const castFlowReturn = /* @__PURE__ */ read(\"castFlowReturn\")\nexport const castToReferenceSnapshot = /* @__PURE__ */ read(\"castToReferenceSnapshot\")\nexport const castToSnapshot = /* @__PURE__ */ read(\"castToSnapshot\")\nexport const clone = /* @__PURE__ */ read(\"clone\")\nexport const createActionTrackingMiddleware = /* @__PURE__ */ read(\"createActionTrackingMiddleware\")\nexport const createActionTrackingMiddleware2 = /* @__PURE__ */ read(\"createActionTrackingMiddleware2\")\nexport const decorate = /* @__PURE__ */ read(\"decorate\")\nexport const destroy = /* @__PURE__ */ read(\"destroy\")\nexport const detach = /* @__PURE__ */ read(\"detach\")\nexport const escapeJsonPath = /* @__PURE__ */ read(\"escapeJsonPath\")\nexport const extendInstance = /* @__PURE__ */ read(\"extendInstance\")\nexport const findParent = /* @__PURE__ */ read(\"findParent\")\nexport const flow = /* @__PURE__ */ read(\"flow\")\nexport const getChildType = /* @__PURE__ */ read(\"getChildType\")\nexport const getEnv = /* @__PURE__ */ read(\"getEnv\")\nexport const getIdentifier = /* @__PURE__ */ read(\"getIdentifier\")\nexport const getLivelinessChecking = /* @__PURE__ */ read(\"getLivelinessChecking\")\nexport const getMembers = /* @__PURE__ */ read(\"getMembers\")\nexport const getNodeId = /* @__PURE__ */ read(\"getNodeId\")\nexport const getParent = /* @__PURE__ */ read(\"getParent\")\nexport const getParentOfType = /* @__PURE__ */ read(\"getParentOfType\")\nexport const getPath = /* @__PURE__ */ read(\"getPath\")\nexport const getPathParts = /* @__PURE__ */ read(\"getPathParts\")\nexport const getPropertyMembers = /* @__PURE__ */ read(\"getPropertyMembers\")\nexport const getRelativePath = /* @__PURE__ */ read(\"getRelativePath\")\nexport const getRoot = /* @__PURE__ */ read(\"getRoot\")\nexport const getRunningActionContext = /* @__PURE__ */ read(\"getRunningActionContext\")\nexport const getSnapshot = /* @__PURE__ */ read(\"getSnapshot\")\nexport const getType = /* @__PURE__ */ read(\"getType\")\nexport const getUnionSubtypes = /* @__PURE__ */ read(\"getUnionSubtypes\")\nexport const getWrappedType = /* @__PURE__ */ read(\"getWrappedType\")\nexport const hasParent = /* @__PURE__ */ read(\"hasParent\")\nexport const hasParentOfType = /* @__PURE__ */ read(\"hasParentOfType\")\nexport const isActionContextChildOf = /* @__PURE__ */ read(\"isActionContextChildOf\")\nexport const isActionContextThisOrChildOf = /* @__PURE__ */ read(\"isActionContextThisOrChildOf\")\nexport const isAlive = /* @__PURE__ */ read(\"isAlive\")\nexport const isArrayType = /* @__PURE__ */ read(\"isArrayType\")\nexport const isFrozenType = /* @__PURE__ */ read(\"isFrozenType\")\nexport const isIdentifierType = /* @__PURE__ */ read(\"isIdentifierType\")\nexport const isLateType = /* @__PURE__ */ read(\"isLateType\")\nexport const isLiteralType = /* @__PURE__ */ read(\"isLiteralType\")\nexport const isMapType = /* @__PURE__ */ read(\"isMapType\")\nexport const isModelType = /* @__PURE__ */ read(\"isModelType\")\nexport const isOptionalType = /* @__PURE__ */ read(\"isOptionalType\")\nexport const isPrimitiveType = /* @__PURE__ */ read(\"isPrimitiveType\")\nexport const isProtected = /* @__PURE__ */ read(\"isProtected\")\nexport const isReferenceType = /* @__PURE__ */ read(\"isReferenceType\")\nexport const isRefinementType = /* @__PURE__ */ read(\"isRefinementType\")\nexport const isRoot = /* @__PURE__ */ read(\"isRoot\")\nexport const isStateTreeNode = /* @__PURE__ */ read(\"isStateTreeNode\")\nexport const isType = /* @__PURE__ */ read(\"isType\")\nexport const isUnionType = /* @__PURE__ */ read(\"isUnionType\")\nexport const isValidReference = /* @__PURE__ */ read(\"isValidReference\")\nexport const joinJsonPath = /* @__PURE__ */ read(\"joinJsonPath\")\nexport const onAction = /* @__PURE__ */ read(\"onAction\")\nexport const onPatch = /* @__PURE__ */ read(\"onPatch\")\nexport const onSnapshot = /* @__PURE__ */ read(\"onSnapshot\")\nexport const protect = /* @__PURE__ */ read(\"protect\")\nexport const recordActions = /* @__PURE__ */ read(\"recordActions\")\nexport const recordPatches = /* @__PURE__ */ read(\"recordPatches\")\nexport const resolveIdentifier = /* @__PURE__ */ read(\"resolveIdentifier\")\nexport const resolvePath = /* @__PURE__ */ read(\"resolvePath\")\nexport const setDevMode = /* @__PURE__ */ read(\"setDevMode\")\nexport const setLivelinessChecking = /* @__PURE__ */ read(\"setLivelinessChecking\")\nexport const setLivelynessChecking = /* @__PURE__ */ read(\"setLivelynessChecking\")\nexport const setTypeChecking = /* @__PURE__ */ read(\"setTypeChecking\")\nexport const splitJsonPath = /* @__PURE__ */ read(\"splitJsonPath\")\nexport const t = /* @__PURE__ */ read(\"t\")\nexport const toGenerator = /* @__PURE__ */ read(\"toGenerator\")\nexport const toGeneratorFunction = /* @__PURE__ */ read(\"toGeneratorFunction\")\nexport const tryReference = /* @__PURE__ */ read(\"tryReference\")\nexport const tryResolve = /* @__PURE__ */ read(\"tryResolve\")\nexport const typecheck = /* @__PURE__ */ read(\"typecheck\")\nexport const types = /* @__PURE__ */ read(\"types\")\nexport const unescapeJsonPath = /* @__PURE__ */ read(\"unescapeJsonPath\")\nexport const unprotect = /* @__PURE__ */ read(\"unprotect\")\nexport const unwrapType = /* @__PURE__ */ read(\"unwrapType\")\nexport const walk = /* @__PURE__ */ read(\"walk\")\nexport default host && host.__esModule ? host.default : host"],
+  "mappings": "AAAA,IAAMA,EAAO,eAAe,iBAAiB,EACvCC,EAAOC,GACXF,GAAQ,MAAQE,KAAQ,OAAOF,CAAI,EAC/BA,EAAKE,CAAI,EACT,OAAO,OACL,UAAY,CACV,MAAM,IAAI,MACR,kCAAoCA,EAAO,iIAC7C,CACF,EACA,CAAE,mBAAoBA,CAAK,CAC7B,EACOC,EAA8BF,EAAK,aAAa,EAsBtD,IAAMG,EAAuBC,EAAK,MAAM,EAExC,IAAMC,EAAyBC,EAAK,QAAQ,EAW5C,IAAMC,EAA0BC,EAAK,SAAS,EAU9C,IAAMC,EAA0BC,EAAK,SAAS,EAsC9C,IAAMC,EAAwBC,EAAK,OAAO,EAKjD,IAAOC,EAAQC,GAAQA,EAAK,WAAaA,EAAK,QAAUA",
+  "names": ["host", "read", "name", "addDisposer", "flow", "read", "getEnv", "read", "getRoot", "read", "isAlive", "read", "types", "read", "mobx_state_tree_default", "host"]
 }

package/dist/chunks/chunk-46CNCY7Z.js

@@ -0,0 +1,2 @@
+import{d as A}from"./chunk-ROZPEXN4.js";import{a as x,d as O}from"./chunk-3VGXCEMQ.js";import{e as I}from"./chunk-IKJZPPOA.js";function G(e){return Array.isArray(e)&&e.every(t=>typeof t=="string")}function oe(e){let t=x(e).slice(1);return t.length>0?t:void 0}function P(e){return e.type==="WalkTabixSyntenyAdapter"||e.type==="RgfaTabixAdapter"&&(typeof e.walksUri=="string"&&e.walksUri!==""||I(e.walksLocation))}function se(e){return e.type==="GbzBaseSyntenyAdapter"||P(e)}function ie(e){let{defaultHaplotypes:t}=e;return P(e)&&G(t)&&t.length>0?t:void 0}function ae(e){return x(e)[0]}function ce(e){return O(e).adapter}function ue(e,t){return e===void 0||e===t?void 0:`The graph is cut on its reference, ${e}: open it from a view of ${e}`}function i(e,t){return typeof e.get=="function"?e.get(t):e[t]}function T(e,t){return e.find(n=>n.trackId===t)}function g(e){return`${e.trackId} ${e.name??""}`}var U=new Set(["BedAdapter","BedTabixAdapter","BigBedAdapter","VcfAdapter","VcfTabixAdapter"]),R=/repeat|tandem|\bstr\b|vntr|trf|trgt|vamos|expansion|microsat/i;function Ze(e,t){let n=t?T(e,t):void 0;return n||e.filter(o=>U.has(o.adapterType)).find(o=>R.test(g(o)))}var D=/^\w+=[^;]*(;\w+=[^;]*)*$/;function H(e){let t=i(e,"name");if(!(typeof t!="string"||!D.test(t)))return Object.fromEntries(t.split(";").map(n=>{let r=n.indexOf("=");return[n.slice(0,r),n.slice(r+1)]}))}function d(e,t){let n=i(e,t);return n!==void 0?n:i(e,"INFO")?.[t]??H(e)?.[t]}var M=["RUS","MOTIFS","RU","motifs","motif","sequence","consensus"],v=["RUL","period","PERIOD","consensusSize","unit","unitLength"],j=["TRID","REPID","VARID","ID","name","id"];function y(e,t){for(let n of t){let r=d(e,n),o=String((Array.isArray(r)?r[0]:r)??"").split(",")[0].trim();if(o!==""&&o!==".")return o}}var B=/^[ACGTURYSWKMBDHVN]+$/i;function V(e){let t=Number(y(e,v));if(Number.isFinite(t)&&t>0)return Math.round(t);let n=y(e,M);return n&&B.test(n)?n.length:void 0}function m(e){return(Array.isArray(e)?e:String(e??"").split(",")).map(n=>{let r=n===""||n===null||n===void 0?NaN:Number(n);return Number.isFinite(r)?r:void 0})}function N(e){return(Array.isArray(e)?e:String(e??"").split(",")).map(n=>{let r=String(n??"").trim();return r===""||r==="."?void 0:r})}var w="<CNV:TR>";function W(e){let t=N(i(e,"ALT"));if(!t.includes(w))return;let n=m(d(e,"RN")),r=N(d(e,"RUS")),o=m(d(e,"RUL")),s=m(d(e,"RUC")),a=m(d(e,"RB")),c=0;return t.map((u,f)=>{let p=n[f]??(u===w?1:0),h=0,F=0;for(let S=0;S<p;S++,c++){let b=r[c],L=o[c]??(b&&B.test(b)?b.length:void 0),_=s[c],C=a[c]??(L&&_!==void 0?Math.round(L*_):void 0);C!==void 0&&(h+=C,F++)}return u===w&&p>0&&F===p?h:void 0})}function K(e,t,n){let r=e?.includes("|");return(e??"").split(/[/|]/).flatMap((o,s)=>{let a=o===""?NaN:Number(o),c=a>0?t[a-1]:n;return!Number.isInteger(a)||c===void 0?[]:[{bp:c,...r?{haplotype:s+1}:{}}]})}function q(e,t,n){let r=i(e,"samples"),o={};for(let[s,a]of Object.entries(r??{})){let c=m(a.SD),u=m(a.AL).flatMap((p,h)=>p!==void 0&&p>0?[c[h]===void 0?{bp:p}:{bp:p,spanningReads:c[h]}]:[]),f=u.length>0||!t?u:K(N(a.GT)[0],t,n);f.length>0&&(o[s]=f)}return Object.keys(o).length>0?o:void 0}function Y(e,t){let n=d(e,"start"),r=d(e,"end"),o=m(d(e,"SVLEN"))[0];return t&&o!==void 0?{start:n+1,end:n+1+o}:{start:n,end:r}}function en(e){let t=[];for(let n of e){let r=W(n),{start:o,end:s}=Y(n,r!==void 0),a=V(n);if(!(s>o)||a===void 0)continue;let c=d(n,"refName"),u=y(n,M),f=y(n,j);t.push({key:`${c}:${o}-${s}`,name:(f&&!D.test(f)?f:void 0)??(u&&u.length<=12?`(${u})n`:`${c}:${(o+1).toLocaleString("en-US")}-${s.toLocaleString("en-US")}`),refName:c,start:o,end:s,unit:a,motif:u,calls:q(n,r,s-o)})}return t.sort((n,r)=>n.start-r.start)}function k(e){let t=[];for(let n of[...e].sort((r,o)=>r.start-o.start)){let r=t.at(-1);r&&n.start<=r.end?r.end=Math.max(r.end,n.end):t.push({...n})}return t}function E(e){let t=[],n=new Map;for(let r of[...e].sort((o,s)=>o.start-s.start)){let o=`${r.refName}	${r.strand}	${r.name}`,s=n.get(o);if(s&&r.start<s.end)s.end=Math.max(s.end,r.end),s.exons=k([...s.exons,...r.exons]);else{let a={...r,exons:k(r.exons)};t.push(a),n.set(o,a)}}return t}var J=new Set(["Gff3TabixAdapter","Gff3Adapter","BedTabixAdapter","BedAdapter","GtfTabixAdapter","GtfAdapter","BigBedAdapter","NCListAdapter"]),z=/gene|refseq|gencode|ensembl|annotation/i,X=new Set(["BedTabixAdapter","BedAdapter"]);function mn(e,t){let n=t?T(e,t):void 0;if(n)return n;let r=e.filter(o=>J.has(o.adapterType)&&!R.test(g(o)));return r.find(o=>z.test(g(o)))??r.find(o=>!X.has(o.adapterType))}var Q=/\bTEs?\b|transpos/i;function ln(e){return e&&Q.test(g(e))?"TE":"gene"}function gn(e,t){let n=e.tracks?.find(r=>A(r.configuration,"trackId")===t)?.displays[0];return n?A(n.configuration,"filter")??[]:[]}var Z=new Set(["chromosome","region","contig","supercontig","scaffold"]),ee=new Set(["exon","CDS","five_prime_UTR","three_prime_UTR","UTR"]);function $(e,t){let n=i(e,"type");typeof n=="string"&&ee.has(n)&&t.push({start:i(e,"start"),end:i(e,"end")});let r=i(e,"subfeatures");for(let o of r??[])$(o,t)}function hn(e){let t=[];for(let n of e){let r=i(n,"gene_name")??i(n,"name")??i(n,"gene")??i(n,"gene_id"),o=i(n,"start"),s=i(n,"end");if(!r||!(s>o)||Z.has(i(n,"type")))continue;let a=[];$(n,a),t.push({name:r,refName:i(n,"refName"),start:o,end:s,strand:i(n,"strand")??0,exons:a.length?k(a):[{start:o,end:s}]})}return E(t)}var l=JBrowseExports["tss-react/mui"],ne=e=>l!=null&&e in Object(l)?l[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from 'tss-react/mui' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e});var Tn=ne("makeStyles"),yn=l&&l.__esModule?l.default:l;export{oe as a,P as b,se as c,ie as d,ae as e,ce as f,ue as g,U as h,Ze as i,en as j,J as k,mn as l,ln as m,gn as n,hn as o,Tn as p};
+//# sourceMappingURL=chunk-46CNCY7Z.js.map

package/dist/chunks/chunk-46CNCY7Z.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/graphTrackConfig.ts", "../../src/GraphGenomeView/trackFeatures.ts", "../../src/GraphGenomeView/repeats/repeatFeatures.ts", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.0.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-EQDQ7P4Y.js", "../../src/GraphGenomeView/genes/geneFeatures.ts", "host:tss-react/mui"],
+  "sourcesContent": ["import {\n  getConfAssemblyNamesOrNone,\n  toTrackConfigEntry,\n} from '@jbrowse/core/util/tracks'\n\nimport { snapshotNamesFile } from './locationName.ts'\n\nimport type { AnyTrackConfig } from '@jbrowse/core/configuration'\n\nfunction isStringArray(value: unknown): value is string[] {\n  return Array.isArray(value) && value.every(item => typeof item === 'string')\n}\n\n// The assemblies the track names after its reference, which is what core's\n// MultiWaySyntenyDisplay opens a lane-declaring source on.\nexport function trackLanes(track: AnyTrackConfig) {\n  const lanes = getConfAssemblyNamesOrNone(track).slice(1)\n  return lanes.length > 0 ? lanes : undefined\n}\n\n// Whether a track names a walk file, by the `walksUri` shorthand as written\n// or the location it expands to: an rGFA track may, and a\n// WalkTabixSyntenyAdapter one does\nexport function walkIndexed(adapterConfig: Record<string, unknown>) {\n  return (\n    adapterConfig.type === 'WalkTabixSyntenyAdapter' ||\n    (adapterConfig.type === 'RgfaTabixAdapter' &&\n      ((typeof adapterConfig.walksUri === 'string' &&\n        adapterConfig.walksUri !== '') ||\n        snapshotNamesFile(adapterConfig.walksLocation)))\n  )\n}\n\n// Whether a track's cut reads `haplotypes`: a GBZ cut does, and so does an\n// rGFA one with a walk file\nexport function cutsByHaplotype(adapterConfig: Record<string, unknown>) {\n  return (\n    adapterConfig.type === 'GbzBaseSyntenyAdapter' || walkIndexed(adapterConfig)\n  )\n}\n\n// The haplotypes a walk-indexed track's config names to cut for until the\n// user picks others\nexport function configHaplotypes(adapterConfig: Record<string, unknown>) {\n  const { defaultHaplotypes } = adapterConfig\n  return walkIndexed(adapterConfig) &&\n    isStringArray(defaultHaplotypes) &&\n    defaultHaplotypes.length > 0\n    ? defaultHaplotypes\n    : undefined\n}\n\n// A graph is cut on the first assembly its track names, the rule\n// GbzBaseSyntenyAdapter states for its anchor. Every other assembly the track\n// names holds its sequence as rank>0 alleles off that reference's backbone, so\n// a window on one has no reference coordinates to frame the cut by.\nexport function graphReferenceAssembly(track: AnyTrackConfig) {\n  return getConfAssemblyNamesOrNone(track)[0]\n}\n\n// A track's adapter config, from a live node or a session's frozen entry\nexport function trackAdapterSnapshot(track: AnyTrackConfig) {\n  return toTrackConfigEntry(track).adapter as Record<string, unknown>\n}\n\nexport function offReferenceProblem(\n  referenceAssembly: string | undefined,\n  assemblyName: string,\n) {\n  return referenceAssembly === undefined || referenceAssembly === assemblyName\n    ? undefined\n    : `The graph is cut on its reference, ${referenceAssembly}: open it from a view of ${referenceAssembly}`\n}\n", "import type { Feature } from '@jbrowse/core/util'\n\nexport type FeatureLike = Feature | Record<string, unknown>\n\nexport function ownField(f: FeatureLike, name: string): unknown {\n  return typeof (f as Feature).get === 'function'\n    ? (f as Feature).get(name)\n    : (f as Record<string, unknown>)[name]\n}\n\nexport interface TrackChoice {\n  trackId: string\n  name?: string\n  adapterType: string\n}\n\nexport function namedTrack<T extends TrackChoice>(tracks: T[], named: string) {\n  return tracks.find(t => t.trackId === named)\n}\n\n// what a track-name hint such as /repeat|tandem/ is matched against\nexport function trackLabel(t: TrackChoice) {\n  return `${t.trackId} ${t.name ?? ''}`\n}\n", "import { namedTrack, ownField, trackLabel } from '../trackFeatures'\n\nimport type { FeatureLike, TrackChoice } from '../trackFeatures'\n\nexport interface RepeatCall {\n  bp: number\n  // TRGT's `SD`. Zero means the allele is a copy of the one the reads did\n  // support, so its length states nothing about a second haplotype; absent\n  // where the genotyper writes no such field.\n  spanningReads?: number\n  // the PanSN haplotype a phased genotype puts this allele on\n  haplotype?: number\n}\n\n// A tandem repeat array as the walk rows need it: its span on the reference,\n// which is what the bars measure between, and its unit length, which is what\n// they tile by. Read off whatever repeat annotation the session has, since the\n// tools all state the same two facts under different names: VCF 4.5's\n// `<CNV:TR>` allele gives `RUL` and `RUS` (one entry per repeat sequence,\n// grouped by `RN`), UCSC simpleRepeat and TRF give `period` and the consensus\n// `sequence`, TRGT gives `MOTIFS` and `TRID`, ExpansionHunter `RU` and `REPID`,\n// HipSTR and GangSTR `PERIOD`, vamos its `motifs`. A VCF record's INFO is\n// searched as well as its top level, and a list's first entry is the unit the\n// bars tile by: for a compound array that is the first repeat sequence, which\n// is the expanding one at every such locus in the common catalogues.\nexport interface RepeatArray {\n  key: string\n  name: string\n  refName: string\n  start: number\n  end: number\n  unit: number\n  motif?: string\n  // Each sample's genotyped alleles, from a genotyper's per-sample `AL`\n  // (TRGT) or a genotype over VCF 4.5 <CNV:TR> alleles; absent from a\n  // catalogue.\n  calls?: Record<string, RepeatCall[]>\n}\n\nexport const REPEAT_ADAPTER_TYPES = new Set([\n  'BedAdapter',\n  'BedTabixAdapter',\n  'BigBedAdapter',\n  'VcfAdapter',\n  'VcfTabixAdapter',\n])\n\nexport const REPEAT_TRACK_HINT =\n  /repeat|tandem|\\bstr\\b|vntr|trf|trgt|vamos|expansion|microsat/i\n\nexport function pickRepeatTrack<T extends TrackChoice>(\n  tracks: T[],\n  named: string,\n) {\n  const chosen = named ? namedTrack(tracks, named) : undefined\n  if (chosen) {\n    return chosen\n  }\n  const candidates = tracks.filter(t => REPEAT_ADAPTER_TYPES.has(t.adapterType))\n  return candidates.find(t => REPEAT_TRACK_HINT.test(trackLabel(t)))\n}\n\n// A TRGT repeat catalogue is a BED whose name column packs the record:\n// `ID=HTT;MOTIFS=CAG,CCG;STRUC=(CAG)nCAACAG(CCG)n`. Read as fields when it\n// has that shape.\nconst PACKED_NAME = /^\\w+=[^;]*(;\\w+=[^;]*)*$/\n\nfunction packedName(f: FeatureLike) {\n  const name = ownField(f, 'name')\n  if (typeof name !== 'string' || !PACKED_NAME.test(name)) {\n    return undefined\n  }\n  return Object.fromEntries(\n    name.split(';').map(pair => {\n      const i = pair.indexOf('=')\n      return [pair.slice(0, i), pair.slice(i + 1)]\n    }),\n  )\n}\n\n// A field at the feature's top level, in a VCF record's INFO, or in a packed\n// name column, in that order.\nfunction field(f: FeatureLike, name: string): unknown {\n  const top = ownField(f, name)\n  if (top !== undefined) {\n    return top\n  }\n  const info = ownField(f, 'INFO') as Record<string, unknown> | undefined\n  return info?.[name] ?? packedName(f)?.[name]\n}\n\nconst MOTIF_FIELDS = [\n  'RUS',\n  'MOTIFS',\n  'RU',\n  'motifs',\n  'motif',\n  'sequence',\n  'consensus',\n]\nconst PERIOD_FIELDS = [\n  'RUL',\n  'period',\n  'PERIOD',\n  'consensusSize',\n  'unit',\n  'unitLength',\n]\nconst NAME_FIELDS = ['TRID', 'REPID', 'VARID', 'ID', 'name', 'id']\n\n// The first entry of a list-valued field, whether it arrived parsed or as\n// the comma-joined text a VCF INFO or a BED column holds; VCF's missing \".\"\n// counts as absent.\nfunction first(f: FeatureLike, names: string[]) {\n  for (const name of names) {\n    const value = field(f, name)\n    const one = String((Array.isArray(value) ? value[0] : value) ?? '')\n      .split(',')[0]!\n      .trim()\n    if (one !== '' && one !== '.') {\n      return one\n    }\n  }\n  return undefined\n}\n\nconst IUPAC = /^[ACGTURYSWKMBDHVN]+$/i\n\n// The unit in bp: a stated period, else the length of the first motif.\nexport function repeatUnitOf(f: FeatureLike) {\n  const period = Number(first(f, PERIOD_FIELDS))\n  if (Number.isFinite(period) && period > 0) {\n    return Math.round(period)\n  }\n  const motif = first(f, MOTIF_FIELDS)\n  return motif && IUPAC.test(motif) ? motif.length : undefined\n}\n\n// A per-sample list field, parsed or as the comma-joined text a VCF column\n// holds. A missing entry stays missing: read as 0, an absent `SD` would make\n// every allele of every genotyper that writes no such field unspanned.\nfunction numbers(value: unknown) {\n  const raw: unknown[] = Array.isArray(value)\n    ? value\n    : String(value ?? '').split(',')\n  return raw.map(one => {\n    const n =\n      one === '' || one === null || one === undefined ? NaN : Number(one)\n    return Number.isFinite(n) ? n : undefined\n  })\n}\n\nfunction strings(value: unknown) {\n  const raw: unknown[] = Array.isArray(value)\n    ? value\n    : String(value ?? '').split(',')\n  return raw.map(one => {\n    const text = String(one ?? '').trim()\n    return text === '' || text === '.' ? undefined : text\n  })\n}\n\nconst TANDEM_REPEAT = '<CNV:TR>'\n\n// Each ALT allele's length, off VCF 4.5's flattened list-of-lists: RN says how\n// many RUS/RUL/RUC/RB entries each allele takes, and the allele's bases are\n// its runs' RB, or unit length times count where RB is missing. An allele that\n// is not <CNV:TR>, or has a run stating neither, has none.\nfunction tandemAlleleBp(f: FeatureLike) {\n  const alts = strings(ownField(f, 'ALT'))\n  if (!alts.includes(TANDEM_REPEAT)) {\n    return undefined\n  }\n  const rn = numbers(field(f, 'RN'))\n  const rus = strings(field(f, 'RUS'))\n  const rul = numbers(field(f, 'RUL'))\n  const ruc = numbers(field(f, 'RUC'))\n  const rb = numbers(field(f, 'RB'))\n  let k = 0\n  return alts.map((alt, i) => {\n    const n = rn[i] ?? (alt === TANDEM_REPEAT ? 1 : 0)\n    let bp = 0\n    let known = 0\n    for (let j = 0; j < n; j++, k++) {\n      const motif = rus[k]\n      const unitLength =\n        rul[k] ?? (motif && IUPAC.test(motif) ? motif.length : undefined)\n      const count = ruc[k]\n      const runBp =\n        rb[k] ??\n        (unitLength && count !== undefined\n          ? Math.round(unitLength * count)\n          : undefined)\n      if (runBp !== undefined) {\n        bp += runBp\n        known++\n      }\n    }\n    return alt === TANDEM_REPEAT && n > 0 && known === n ? bp : undefined\n  })\n}\n\n// A sample's alleles through its genotype: 0 is the reference's, an index\n// past it the ALT allele's. A phased genotype's k-th allele is PanSN\n// haplotype k, the order vg deconstruct writes an assembly's haplotypes in.\nfunction genotyped(\n  gt: string | undefined,\n  alleleBp: (number | undefined)[],\n  referenceBp: number,\n) {\n  const phased = gt?.includes('|')\n  return (gt ?? '').split(/[/|]/).flatMap((index, k): RepeatCall[] => {\n    const i = index === '' ? NaN : Number(index)\n    const bp = i > 0 ? alleleBp[i - 1] : referenceBp\n    if (!Number.isInteger(i) || bp === undefined) {\n      return []\n    }\n    return [{ bp, ...(phased ? { haplotype: k + 1 } : {}) }]\n  })\n}\n\nfunction callsOf(\n  f: FeatureLike,\n  alleleBp: (number | undefined)[] | undefined,\n  referenceBp: number,\n) {\n  const samples = ownField(f, 'samples') as\n    Record<string, Record<string, unknown>> | undefined\n  const called: Record<string, RepeatCall[]> = {}\n  for (const [sample, fields] of Object.entries(samples ?? {})) {\n    const reads = numbers(fields.SD)\n    const lengths = numbers(fields.AL).flatMap((bp, i) =>\n      bp !== undefined && bp > 0\n        ? [reads[i] === undefined ? { bp } : { bp, spanningReads: reads[i] }]\n        : [],\n    )\n    const calls =\n      lengths.length > 0 || !alleleBp\n        ? lengths\n        : genotyped(strings(fields.GT)[0], alleleBp, referenceBp)\n    if (calls.length > 0) {\n      called[sample] = calls\n    }\n  }\n  return Object.keys(called).length > 0 ? called : undefined\n}\n\n// A <CNV:TR> record's POS is the base before the array and SVLEN the\n// reference allele's length, while a VCF feature starts at that padding base.\nfunction spanOf(f: FeatureLike, tandem: boolean) {\n  const start = field(f, 'start') as number\n  const end = field(f, 'end') as number\n  const svlen = numbers(field(f, 'SVLEN'))[0]\n  return tandem && svlen !== undefined\n    ? { start: start + 1, end: start + 1 + svlen }\n    : { start, end }\n}\n\nexport function repeatArraysFrom(features: FeatureLike[]): RepeatArray[] {\n  const arrays: RepeatArray[] = []\n  for (const f of features) {\n    const alleleBp = tandemAlleleBp(f)\n    const { start, end } = spanOf(f, alleleBp !== undefined)\n    const unit = repeatUnitOf(f)\n    if (!(end > start) || unit === undefined) {\n      continue\n    }\n    const refName = field(f, 'refName') as string\n    const motif = first(f, MOTIF_FIELDS)\n    const stated = first(f, NAME_FIELDS)\n    arrays.push({\n      key: `${refName}:${start}-${end}`,\n      name:\n        (stated && !PACKED_NAME.test(stated) ? stated : undefined) ??\n        (motif && motif.length <= 12\n          ? `(${motif})n`\n          : `${refName}:${(start + 1).toLocaleString('en-US')}-${end.toLocaleString('en-US')}`),\n      refName,\n      start,\n      end,\n      unit,\n      motif,\n      calls: callsOf(f, alleleBp, end - start),\n    })\n  }\n  return arrays.sort((a, b) => a.start - b.start)\n}\n", "// src/genes/geneFiles.ts\nvar GENE_TYPE = /(gene|gene_segment|RNA|transcript)$/i;\nvar isGene = (type) => GENE_TYPE.test(type) || type === \"CDS\" || type === \"exon\";\nfunction mergedIntervals(intervals) {\n  const out = [];\n  for (const iv of [...intervals].sort((a, b) => a.start - b.start)) {\n    const last = out.at(-1);\n    if (last && iv.start <= last.end) {\n      last.end = Math.max(last.end, iv.end);\n    } else {\n      out.push({ ...iv });\n    }\n  }\n  return out;\n}\nfunction strandOf(s) {\n  return s === \"+\" ? 1 : s === \"-\" ? -1 : 0;\n}\nfunction unescape(value) {\n  try {\n    return decodeURIComponent(value);\n  } catch {\n    return value;\n  }\n}\nfunction attributes(column) {\n  const out = /* @__PURE__ */ new Map();\n  for (const pair of column.split(\";\")) {\n    const eq = pair.indexOf(\"=\");\n    if (eq > 0) {\n      out.set(pair.slice(0, eq).trim(), unescape(pair.slice(eq + 1).trim()));\n    }\n  }\n  return out;\n}\nfunction gff3Row(line) {\n  const cols = line.split(\"\t\");\n  const start = Number(cols[3]);\n  const end = Number(cols[4]);\n  if (cols.length < 9 || !Number.isInteger(start) || !Number.isInteger(end)) {\n    return void 0;\n  }\n  return {\n    refName: cols[0],\n    type: cols[2],\n    start: start - 1,\n    end,\n    strand: strandOf(cols[6]),\n    attrs: attributes(cols[8])\n  };\n}\nfunction genesFromGff3Lines(lines) {\n  const rows = [];\n  for (const line of lines) {\n    if (line.startsWith(\"##FASTA\")) {\n      break;\n    }\n    const row = line.startsWith(\"#\") ? void 0 : gff3Row(line);\n    if (row) {\n      rows.push(row);\n    }\n  }\n  const parentOf = /* @__PURE__ */ new Map();\n  for (const { attrs } of rows) {\n    const id = attrs.get(\"ID\");\n    const parent = attrs.get(\"Parent\")?.split(\",\")[0];\n    if (id && parent) {\n      parentOf.set(id, parent);\n    }\n  }\n  const rootOf = (row) => {\n    let id = row.attrs.get(\"Parent\")?.split(\",\")[0] ?? row.attrs.get(\"ID\");\n    if (!id) {\n      return row.attrs.get(\"gene_id\");\n    }\n    const seen = /* @__PURE__ */ new Set();\n    while (id && parentOf.has(id) && !seen.has(id)) {\n      seen.add(id);\n      id = parentOf.get(id);\n    }\n    return id;\n  };\n  const groups = /* @__PURE__ */ new Map();\n  rows.forEach((row, i) => {\n    const root = rootOf(row) ?? `#${i}`;\n    const key = `${row.refName}\t${root}`;\n    const group = groups.get(key) ?? groups.set(key, { rows: [] }).get(key);\n    group.rows.push(row);\n    if (!row.attrs.has(\"Parent\") && !group.top) {\n      group.top = row;\n    }\n  });\n  const genes = [];\n  for (const [key, { top, rows: rows2 }] of groups) {\n    if (top && !isGene(top.type)) {\n      continue;\n    }\n    const first = top ?? rows2[0];\n    const start = top?.start ?? Math.min(...rows2.map((r) => r.start));\n    const end = top?.end ?? Math.max(...rows2.map((r) => r.end));\n    const a = first.attrs;\n    const spans = (type) => rows2.filter((r) => r.type === type).map((r) => ({ start: r.start, end: r.end }));\n    const exons = spans(\"exon\");\n    const coding = spans(\"CDS\");\n    const transcribed = rows2.some(\n      (r) => r !== top && r.type !== \"exon\" && r.type !== \"CDS\"\n    );\n    genes.push({\n      name: a.get(\"Name\") ?? a.get(\"gene_name\") ?? a.get(\"gene\") ?? a.get(\"gene_id\") ?? key.split(\"\t\")[1],\n      refName: first.refName,\n      start,\n      end,\n      strand: first.strand,\n      // A range read holds only the rows over its window, so a gene with\n      // transcripts but no exon or CDS there is intronic in it. Only a gene\n      // with no transcripts, as a bacterium's gene and CDS, is one exon.\n      exons: exons.length ? mergedIntervals(exons) : transcribed ? mergedIntervals(coding) : [{ start, end }]\n    });\n  }\n  return genes;\n}\nfunction mergeOverlappingByName(genes) {\n  const out = [];\n  const open = /* @__PURE__ */ new Map();\n  for (const g of [...genes].sort((a, b) => a.start - b.start)) {\n    const key = `${g.refName}\t${g.strand}\t${g.name}`;\n    const last = open.get(key);\n    if (last && g.start < last.end) {\n      last.end = Math.max(last.end, g.end);\n      last.exons = mergedIntervals([...last.exons, ...g.exons]);\n    } else {\n      const gene = { ...g, exons: mergedIntervals(g.exons) };\n      out.push(gene);\n      open.set(key, gene);\n    }\n  }\n  return out;\n}\nvar BED_HEADER = /^(#|track\\s|browser\\s)/;\nfunction genesFromBed(text) {\n  const rows = [];\n  for (const line of text.split(\"\\n\")) {\n    const cols = line.replace(/\\r$/, \"\").split(\"\t\");\n    const start = Number(cols[1]);\n    const end = Number(cols[2]);\n    if (BED_HEADER.test(line) || cols.length < 3 || !Number.isInteger(start) || !(end > start)) {\n      continue;\n    }\n    const refName = cols[0];\n    const name = cols[3] && cols[3] !== \".\" ? cols[3] : `${refName}:${start + 1}-${end}`;\n    const sizes = cols[10]?.split(\",\").filter((s) => s !== \"\").map(Number);\n    const starts = cols[11]?.split(\",\").filter((s) => s !== \"\").map(Number);\n    const blocks = sizes?.length && sizes.length === starts?.length ? sizes.map((size, i) => ({\n      start: start + starts[i],\n      end: start + starts[i] + size\n    })) : [{ start, end }];\n    rows.push({\n      name,\n      refName,\n      start,\n      end,\n      strand: strandOf(cols[5]),\n      exons: blocks\n    });\n  }\n  return mergeOverlappingByName(rows);\n}\nfunction sniffedFormat(text) {\n  const first = text.split(\"\\n\", 1e3).find((l) => l.trim() !== \"\" && !BED_HEADER.test(l));\n  const cols = first?.split(\"\t\") ?? [];\n  return /^\\d+$/.test(cols[1] ?? \"\") && /^\\d+$/.test(cols[2] ?? \"\") ? \"bed\" : \"gff3\";\n}\nfunction genesFromText(text, format = sniffedFormat(text)) {\n  return format === \"bed\" ? genesFromBed(text) : genesFromGff3Lines(text.split(/\\r?\\n/));\n}\n\nexport {\n  mergedIntervals,\n  genesFromGff3Lines,\n  mergeOverlappingByName,\n  genesFromBed,\n  genesFromText\n};\n", "import {\n  mergeOverlappingByName,\n  mergedIntervals,\n} from '@jbrowse/bandage-core/genes/geneFiles'\nimport { readConfObject } from '@jbrowse/core/configuration'\n\nimport { REPEAT_TRACK_HINT } from '../repeats/repeatFeatures'\nimport { namedTrack, ownField, trackLabel } from '../trackFeatures'\n\nimport type { FeatureLike, TrackChoice } from '../trackFeatures'\nimport type { GeneModel } from '@jbrowse/bandage-core/genes/genePins'\nimport type { AnyConfigurationModel } from '@jbrowse/core/configuration'\n\n// The adapters whose tracks hold gene models, in the order the session's\n// tracks are searched when no track is named.\nexport const GENE_ADAPTER_TYPES = new Set([\n  'Gff3TabixAdapter',\n  'Gff3Adapter',\n  'BedTabixAdapter',\n  'BedAdapter',\n  'GtfTabixAdapter',\n  'GtfAdapter',\n  'BigBedAdapter',\n  'NCListAdapter',\n])\n\nconst GENE_TRACK_HINT = /gene|refseq|gencode|ensembl|annotation/i\n\n// A BED track is as often peaks or repeats as genes, so one counts only where\n// its name says it is annotation\nconst BED_ADAPTER_TYPES = new Set(['BedTabixAdapter', 'BedAdapter'])\n\n// Which of the session's tracks to read genes from: the named one while the\n// assembly has it (a saved pick can name a track since removed), else the\n// first gene-bearing track on the assembly whose name says it is annotation,\n// else the first non-BED gene-bearing track. A track whose name says repeats is\n// never picked unnamed, as \"RepeatMasker annotation\" would be.\nexport function pickGeneTrack<T extends TrackChoice>(\n  tracks: T[],\n  named: string,\n) {\n  const chosen = named ? namedTrack(tracks, named) : undefined\n  if (chosen) {\n    return chosen\n  }\n  const candidates = tracks.filter(\n    t =>\n      GENE_ADAPTER_TYPES.has(t.adapterType) &&\n      !REPEAT_TRACK_HINT.test(trackLabel(t)),\n  )\n  return (\n    candidates.find(t => GENE_TRACK_HINT.test(trackLabel(t))) ??\n    candidates.find(t => !BED_ADAPTER_TYPES.has(t.adapterType))\n  )\n}\n\nconst TE_TRACK_HINT = /\\bTEs?\\b|transpos/i\n\n// What a walk row's boxes are, for the key: TEs where the annotation track's\n// name says so, else genes\nexport function annotationNoun(track: TrackChoice | undefined) {\n  return track && TE_TRACK_HINT.test(trackLabel(track)) ? 'TE' : 'gene'\n}\n\ninterface LaneView {\n  tracks?: readonly {\n    configuration: AnyConfigurationModel\n    displays: readonly { configuration: AnyConfigurationModel }[]\n  }[]\n}\n\n// The `filter` of the gene track's lane in the view the graph is drawn in, so\n// the chips name what the lane draws. None where the view shows no such lane,\n// or has no tracks, as a graph genome view of its own.\nexport function laneFilters(view: object, trackId: string | undefined) {\n  const lane = (view as LaneView).tracks?.find(\n    t => readConfObject(t.configuration, 'trackId') === trackId,\n  )?.displays[0]\n  return lane\n    ? ((readConfObject(lane.configuration, 'filter') as string[] | undefined) ??\n        [])\n    : []\n}\n\n// Records spanning a whole sequence, the types the GFF3 adapter declines to\n// widen a fetch for. RefSeq opens every molecule with a `region` named\n// ANONYMOUS.\nconst WHOLE_SEQUENCE_TYPES = new Set([\n  'chromosome',\n  'region',\n  'contig',\n  'supercontig',\n  'scaffold',\n])\n\n// JBrowse's BED parser splits a coding BED12 block into CDS and UTR parts and\n// keeps `exon` for non-coding ones, so all of them are exon\nconst EXON_PARTS = new Set([\n  'exon',\n  'CDS',\n  'five_prime_UTR',\n  'three_prime_UTR',\n  'UTR',\n])\n\nfunction exonsOf(f: FeatureLike, into: { start: number; end: number }[]) {\n  const type = ownField(f, 'type')\n  if (typeof type === 'string' && EXON_PARTS.has(type)) {\n    into.push({\n      start: ownField(f, 'start') as number,\n      end: ownField(f, 'end') as number,\n    })\n  }\n  const children = ownField(f, 'subfeatures') as FeatureLike[] | undefined\n  for (const child of children ?? []) {\n    exonsOf(child, into)\n  }\n}\n\n// Genes from a track's features: every top-level feature but a whole-sequence\n// record, named by the first of gene_name, name, gene and gene_id it carries,\n// with the exons found anywhere under it merged. A feature with no exons is one exon,\n// its whole span. A BED track gives one feature per transcript, so a name's\n// overlapping features merge, while its copies down the contig stay apart.\n// UCSC's ncbiRefSeq.gff gene records carry their symbol only as gene_id. A\n// feature with none of those names is left out: its raw ID, RefSeq's\n// `id-NC_000913.3:1978503..1979270`, only restates where it is.\nexport function geneModelsFrom(features: FeatureLike[]): GeneModel[] {\n  const genes: GeneModel[] = []\n  for (const f of features) {\n    const name =\n      (ownField(f, 'gene_name') as string | undefined) ??\n      (ownField(f, 'name') as string | undefined) ??\n      (ownField(f, 'gene') as string | undefined) ??\n      (ownField(f, 'gene_id') as string | undefined)\n    const start = ownField(f, 'start') as number\n    const end = ownField(f, 'end') as number\n    if (\n      !name ||\n      !(end > start) ||\n      WHOLE_SEQUENCE_TYPES.has(ownField(f, 'type') as string)\n    ) {\n      continue\n    }\n    const exons: { start: number; end: number }[] = []\n    exonsOf(f, exons)\n    genes.push({\n      name,\n      refName: ownField(f, 'refName') as string,\n      start,\n      end,\n      strand: (ownField(f, 'strand') as number | undefined) ?? 0,\n      exons: exons.length ? mergedIntervals(exons) : [{ start, end }],\n    })\n  }\n  return mergeOverlappingByName(genes)\n}\n", "const host = JBrowseExports[\"tss-react/mui\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\n            \"This JBrowse does not provide '\" + name + \"' from '\" + \"tss-react/mui\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const cx = /* @__PURE__ */ read(\"cx\")\nexport const keyframes = /* @__PURE__ */ read(\"keyframes\")\nexport const makeStyles = /* @__PURE__ */ read(\"makeStyles\")\nexport default host && host.__esModule ? host.default : host"],
+  "mappings": "+HASA,SAASA,EAAcC,EAAmC,CACxD,OAAO,MAAM,QAAQA,CAAK,GAAKA,EAAM,MAAMC,GAAQ,OAAOA,GAAS,QAAQ,CAC7E,CAIO,SAASC,GAAWC,EAAuB,CAChD,IAAMC,EAAQC,EAA2BF,CAAK,EAAE,MAAM,CAAC,EACvD,OAAOC,EAAM,OAAS,EAAIA,EAAQ,MACpC,CAKO,SAASE,EAAYC,EAAwC,CAClE,OACEA,EAAc,OAAS,2BACtBA,EAAc,OAAS,qBACpB,OAAOA,EAAc,UAAa,UAClCA,EAAc,WAAa,IAC3BC,EAAkBD,EAAc,aAAa,EAErD,CAIO,SAASE,GAAgBF,EAAwC,CACtE,OACEA,EAAc,OAAS,yBAA2BD,EAAYC,CAAa,CAE/E,CAIO,SAASG,GAAiBH,EAAwC,CACvE,GAAM,CAAE,kBAAAI,CAAkB,EAAIJ,EAC9B,OAAOD,EAAYC,CAAa,GAC9BR,EAAcY,CAAiB,GAC/BA,EAAkB,OAAS,EACzBA,EACA,MACN,CAMO,SAASC,GAAuBT,EAAuB,CAC5D,OAAOE,EAA2BF,CAAK,EAAE,CAAC,CAC5C,CAGO,SAASU,GAAqBV,EAAuB,CAC1D,OAAOW,EAAmBX,CAAK,EAAE,OACnC,CAEO,SAASY,GACdC,EACAC,EACA,CACA,OAAOD,IAAsB,QAAaA,IAAsBC,EAC5D,OACA,sCAAsCD,CAAiB,4BAA4BA,CAAiB,EAC1G,CCpEO,SAASE,EAASC,EAAgBC,EAAuB,CAC9D,OAAO,OAAQD,EAAc,KAAQ,WAChCA,EAAc,IAAIC,CAAI,EACtBD,EAA8BC,CAAI,CACzC,CAQO,SAASC,EAAkCC,EAAaC,EAAe,CAC5E,OAAOD,EAAO,KAAKE,GAAKA,EAAE,UAAYD,CAAK,CAC7C,CAGO,SAASE,EAAWD,EAAgB,CACzC,MAAO,GAAGA,EAAE,OAAO,IAAIA,EAAE,MAAQ,EAAE,EACrC,CCgBO,IAAME,EAAuB,IAAI,IAAI,CAC1C,aACA,kBACA,gBACA,aACA,iBACF,CAAC,EAEYC,EACX,gEAEK,SAASC,GACdC,EACAC,EACA,CACA,IAAMC,EAASD,EAAQE,EAAWH,EAAQC,CAAK,EAAI,OACnD,OAAIC,GAGeF,EAAO,OAAOI,GAAKP,EAAqB,IAAIO,EAAE,WAAW,CAAC,EAC3D,KAAKA,GAAKN,EAAkB,KAAKO,EAAWD,CAAC,CAAC,CAAC,CACnE,CAKA,IAAME,EAAc,2BAEpB,SAASC,EAAWC,EAAgB,CAClC,IAAMC,EAAOC,EAASF,EAAG,MAAM,EAC/B,GAAI,SAAOC,GAAS,UAAY,CAACH,EAAY,KAAKG,CAAI,GAGtD,OAAO,OAAO,YACZA,EAAK,MAAM,GAAG,EAAE,IAAIE,GAAQ,CAC1B,IAAMC,EAAID,EAAK,QAAQ,GAAG,EAC1B,MAAO,CAACA,EAAK,MAAM,EAAGC,CAAC,EAAGD,EAAK,MAAMC,EAAI,CAAC,CAAC,CAC7C,CAAC,CACH,CACF,CAIA,SAASC,EAAML,EAAgBC,EAAuB,CACpD,IAAMK,EAAMJ,EAASF,EAAGC,CAAI,EAC5B,OAAIK,IAAQ,OACHA,EAEIJ,EAASF,EAAG,MAAM,IACjBC,CAAI,GAAKF,EAAWC,CAAC,IAAIC,CAAI,CAC7C,CAEA,IAAMM,EAAe,CACnB,MACA,SACA,KACA,SACA,QACA,WACA,WACF,EACMC,EAAgB,CACpB,MACA,SACA,SACA,gBACA,OACA,YACF,EACMC,EAAc,CAAC,OAAQ,QAAS,QAAS,KAAM,OAAQ,IAAI,EAKjE,SAASC,EAAMV,EAAgBW,EAAiB,CAC9C,QAAWV,KAAQU,EAAO,CACxB,IAAMC,EAAQP,EAAML,EAAGC,CAAI,EACrBY,EAAM,QAAQ,MAAM,QAAQD,CAAK,EAAIA,EAAM,CAAC,EAAIA,IAAU,EAAE,EAC/D,MAAM,GAAG,EAAE,CAAC,EACZ,KAAK,EACR,GAAIC,IAAQ,IAAMA,IAAQ,IACxB,OAAOA,CAEX,CAEF,CAEA,IAAMC,EAAQ,yBAGP,SAASC,EAAaf,EAAgB,CAC3C,IAAMgB,EAAS,OAAON,EAAMV,EAAGQ,CAAa,CAAC,EAC7C,GAAI,OAAO,SAASQ,CAAM,GAAKA,EAAS,EACtC,OAAO,KAAK,MAAMA,CAAM,EAE1B,IAAMC,EAAQP,EAAMV,EAAGO,CAAY,EACnC,OAAOU,GAASH,EAAM,KAAKG,CAAK,EAAIA,EAAM,OAAS,MACrD,CAKA,SAASC,EAAQN,EAAgB,CAI/B,OAHuB,MAAM,QAAQA,CAAK,EACtCA,EACA,OAAOA,GAAS,EAAE,EAAE,MAAM,GAAG,GACtB,IAAIC,GAAO,CACpB,IAAMM,EACJN,IAAQ,IAAMA,IAAQ,MAAQA,IAAQ,OAAY,IAAM,OAAOA,CAAG,EACpE,OAAO,OAAO,SAASM,CAAC,EAAIA,EAAI,MAClC,CAAC,CACH,CAEA,SAASC,EAAQR,EAAgB,CAI/B,OAHuB,MAAM,QAAQA,CAAK,EACtCA,EACA,OAAOA,GAAS,EAAE,EAAE,MAAM,GAAG,GACtB,IAAIC,GAAO,CACpB,IAAMQ,EAAO,OAAOR,GAAO,EAAE,EAAE,KAAK,EACpC,OAAOQ,IAAS,IAAMA,IAAS,IAAM,OAAYA,CACnD,CAAC,CACH,CAEA,IAAMC,EAAgB,WAMtB,SAASC,EAAevB,EAAgB,CACtC,IAAMwB,EAAOJ,EAAQlB,EAASF,EAAG,KAAK,CAAC,EACvC,GAAI,CAACwB,EAAK,SAASF,CAAa,EAC9B,OAEF,IAAMG,EAAKP,EAAQb,EAAML,EAAG,IAAI,CAAC,EAC3B0B,EAAMN,EAAQf,EAAML,EAAG,KAAK,CAAC,EAC7B2B,EAAMT,EAAQb,EAAML,EAAG,KAAK,CAAC,EAC7B4B,EAAMV,EAAQb,EAAML,EAAG,KAAK,CAAC,EAC7B6B,EAAKX,EAAQb,EAAML,EAAG,IAAI,CAAC,EAC7B8B,EAAI,EACR,OAAON,EAAK,IAAI,CAACO,EAAK3B,IAAM,CAC1B,IAAMe,EAAIM,EAAGrB,CAAC,IAAM2B,IAAQT,EAAgB,EAAI,GAC5CU,EAAK,EACLC,EAAQ,EACZ,QAASC,EAAI,EAAGA,EAAIf,EAAGe,IAAKJ,IAAK,CAC/B,IAAMb,EAAQS,EAAII,CAAC,EACbK,EACJR,EAAIG,CAAC,IAAMb,GAASH,EAAM,KAAKG,CAAK,EAAIA,EAAM,OAAS,QACnDmB,EAAQR,EAAIE,CAAC,EACbO,EACJR,EAAGC,CAAC,IACHK,GAAcC,IAAU,OACrB,KAAK,MAAMD,EAAaC,CAAK,EAC7B,QACFC,IAAU,SACZL,GAAMK,EACNJ,IAEJ,CACA,OAAOF,IAAQT,GAAiBH,EAAI,GAAKc,IAAUd,EAAIa,EAAK,MAC9D,CAAC,CACH,CAKA,SAASM,EACPC,EACAC,EACAC,EACA,CACA,IAAMC,EAASH,GAAI,SAAS,GAAG,EAC/B,OAAQA,GAAM,IAAI,MAAM,MAAM,EAAE,QAAQ,CAACI,EAAOb,IAAoB,CAClE,IAAM1B,EAAIuC,IAAU,GAAK,IAAM,OAAOA,CAAK,EACrCX,EAAK5B,EAAI,EAAIoC,EAASpC,EAAI,CAAC,EAAIqC,EACrC,MAAI,CAAC,OAAO,UAAUrC,CAAC,GAAK4B,IAAO,OAC1B,CAAC,EAEH,CAAC,CAAE,GAAAA,EAAI,GAAIU,EAAS,CAAE,UAAWZ,EAAI,CAAE,EAAI,CAAC,CAAG,CAAC,CACzD,CAAC,CACH,CAEA,SAASc,EACP5C,EACAwC,EACAC,EACA,CACA,IAAMI,EAAU3C,EAASF,EAAG,SAAS,EAE/B8C,EAAuC,CAAC,EAC9C,OAAW,CAACC,EAAQC,CAAM,IAAK,OAAO,QAAQH,GAAW,CAAC,CAAC,EAAG,CAC5D,IAAMI,EAAQ/B,EAAQ8B,EAAO,EAAE,EACzBE,EAAUhC,EAAQ8B,EAAO,EAAE,EAAE,QAAQ,CAAChB,EAAI5B,IAC9C4B,IAAO,QAAaA,EAAK,EACrB,CAACiB,EAAM7C,CAAC,IAAM,OAAY,CAAE,GAAA4B,CAAG,EAAI,CAAE,GAAAA,EAAI,cAAeiB,EAAM7C,CAAC,CAAE,CAAC,EAClE,CAAC,CACP,EACM+C,EACJD,EAAQ,OAAS,GAAK,CAACV,EACnBU,EACAZ,EAAUlB,EAAQ4B,EAAO,EAAE,EAAE,CAAC,EAAGR,EAAUC,CAAW,EACxDU,EAAM,OAAS,IACjBL,EAAOC,CAAM,EAAII,EAErB,CACA,OAAO,OAAO,KAAKL,CAAM,EAAE,OAAS,EAAIA,EAAS,MACnD,CAIA,SAASM,EAAOpD,EAAgBqD,EAAiB,CAC/C,IAAMC,EAAQjD,EAAML,EAAG,OAAO,EACxBuD,EAAMlD,EAAML,EAAG,KAAK,EACpBwD,EAAQtC,EAAQb,EAAML,EAAG,OAAO,CAAC,EAAE,CAAC,EAC1C,OAAOqD,GAAUG,IAAU,OACvB,CAAE,MAAOF,EAAQ,EAAG,IAAKA,EAAQ,EAAIE,CAAM,EAC3C,CAAE,MAAAF,EAAO,IAAAC,CAAI,CACnB,CAEO,SAASE,GAAiBC,EAAwC,CACvE,IAAMC,EAAwB,CAAC,EAC/B,QAAW3D,KAAK0D,EAAU,CACxB,IAAMlB,EAAWjB,EAAevB,CAAC,EAC3B,CAAE,MAAAsD,EAAO,IAAAC,CAAI,EAAIH,EAAOpD,EAAGwC,IAAa,MAAS,EACjDoB,EAAO7C,EAAaf,CAAC,EAC3B,GAAI,EAAEuD,EAAMD,IAAUM,IAAS,OAC7B,SAEF,IAAMC,EAAUxD,EAAML,EAAG,SAAS,EAC5BiB,EAAQP,EAAMV,EAAGO,CAAY,EAC7BuD,EAASpD,EAAMV,EAAGS,CAAW,EACnCkD,EAAO,KAAK,CACV,IAAK,GAAGE,CAAO,IAAIP,CAAK,IAAIC,CAAG,GAC/B,MACGO,GAAU,CAAChE,EAAY,KAAKgE,CAAM,EAAIA,EAAS,UAC/C7C,GAASA,EAAM,QAAU,GACtB,IAAIA,CAAK,KACT,GAAG4C,CAAO,KAAKP,EAAQ,GAAG,eAAe,OAAO,CAAC,IAAIC,EAAI,eAAe,OAAO,CAAC,IACtF,QAAAM,EACA,MAAAP,EACA,IAAAC,EACA,KAAAK,EACA,MAAA3C,EACA,MAAO2B,EAAQ5C,EAAGwC,EAAUe,EAAMD,CAAK,CACzC,CAAC,CACH,CACA,OAAOK,EAAO,KAAK,CAACI,EAAGC,IAAMD,EAAE,MAAQC,EAAE,KAAK,CAChD,CC3RA,SAASC,EAAgBC,EAAW,CAClC,IAAMC,EAAM,CAAC,EACb,QAAWC,IAAM,CAAC,GAAGF,CAAS,EAAE,KAAK,CAACG,EAAGC,IAAMD,EAAE,MAAQC,EAAE,KAAK,EAAG,CACjE,IAAMC,EAAOJ,EAAI,GAAG,EAAE,EAClBI,GAAQH,EAAG,OAASG,EAAK,IAC3BA,EAAK,IAAM,KAAK,IAAIA,EAAK,IAAKH,EAAG,GAAG,EAEpCD,EAAI,KAAK,CAAE,GAAGC,CAAG,CAAC,CAEtB,CACA,OAAOD,CACT,CA2GA,SAASK,EAAuBC,EAAO,CACrC,IAAMC,EAAM,CAAC,EACPC,EAAuB,IAAI,IACjC,QAAWC,IAAK,CAAC,GAAGH,CAAK,EAAE,KAAK,CAACI,EAAGC,IAAMD,EAAE,MAAQC,EAAE,KAAK,EAAG,CAC5D,IAAMC,EAAM,GAAGH,EAAE,OAAO,IAAIA,EAAE,MAAM,IAAIA,EAAE,IAAI,GACxCI,EAAOL,EAAK,IAAII,CAAG,EACzB,GAAIC,GAAQJ,EAAE,MAAQI,EAAK,IACzBA,EAAK,IAAM,KAAK,IAAIA,EAAK,IAAKJ,EAAE,GAAG,EACnCI,EAAK,MAAQC,EAAgB,CAAC,GAAGD,EAAK,MAAO,GAAGJ,EAAE,KAAK,CAAC,MACnD,CACL,IAAMM,EAAO,CAAE,GAAGN,EAAG,MAAOK,EAAgBL,EAAE,KAAK,CAAE,EACrDF,EAAI,KAAKQ,CAAI,EACbP,EAAK,IAAII,EAAKG,CAAI,CACpB,CACF,CACA,OAAOR,CACT,CC1HO,IAAMS,EAAqB,IAAI,IAAI,CACxC,mBACA,cACA,kBACA,aACA,kBACA,aACA,gBACA,eACF,CAAC,EAEKC,EAAkB,0CAIlBC,EAAoB,IAAI,IAAI,CAAC,kBAAmB,YAAY,CAAC,EAO5D,SAASC,GACdC,EACAC,EACA,CACA,IAAMC,EAASD,EAAQE,EAAWH,EAAQC,CAAK,EAAI,OACnD,GAAIC,EACF,OAAOA,EAET,IAAME,EAAaJ,EAAO,OACxBK,GACET,EAAmB,IAAIS,EAAE,WAAW,GACpC,CAACC,EAAkB,KAAKC,EAAWF,CAAC,CAAC,CACzC,EACA,OACED,EAAW,KAAKC,GAAKR,EAAgB,KAAKU,EAAWF,CAAC,CAAC,CAAC,GACxDD,EAAW,KAAKC,GAAK,CAACP,EAAkB,IAAIO,EAAE,WAAW,CAAC,CAE9D,CAEA,IAAMG,EAAgB,qBAIf,SAASC,GAAeC,EAAgC,CAC7D,OAAOA,GAASF,EAAc,KAAKD,EAAWG,CAAK,CAAC,EAAI,KAAO,MACjE,CAYO,SAASC,GAAYC,EAAcC,EAA6B,CACrE,IAAMC,EAAQF,EAAkB,QAAQ,KACtCP,GAAKU,EAAeV,EAAE,cAAe,SAAS,IAAMQ,CACtD,GAAG,SAAS,CAAC,EACb,OAAOC,EACDC,EAAeD,EAAK,cAAe,QAAQ,GAC3C,CAAC,EACH,CAAC,CACP,CAKA,IAAME,EAAuB,IAAI,IAAI,CACnC,aACA,SACA,SACA,cACA,UACF,CAAC,EAIKC,GAAa,IAAI,IAAI,CACzB,OACA,MACA,iBACA,kBACA,KACF,CAAC,EAED,SAASC,EAAQC,EAAgBC,EAAwC,CACvE,IAAMC,EAAOC,EAASH,EAAG,MAAM,EAC3B,OAAOE,GAAS,UAAYJ,GAAW,IAAII,CAAI,GACjDD,EAAK,KAAK,CACR,MAAOE,EAASH,EAAG,OAAO,EAC1B,IAAKG,EAASH,EAAG,KAAK,CACxB,CAAC,EAEH,IAAMI,EAAWD,EAASH,EAAG,aAAa,EAC1C,QAAWK,KAASD,GAAY,CAAC,EAC/BL,EAAQM,EAAOJ,CAAI,CAEvB,CAUO,SAASK,GAAeC,EAAsC,CACnE,IAAMC,EAAqB,CAAC,EAC5B,QAAWR,KAAKO,EAAU,CACxB,IAAME,EACHN,EAASH,EAAG,WAAW,GACvBG,EAASH,EAAG,MAAM,GAClBG,EAASH,EAAG,MAAM,GAClBG,EAASH,EAAG,SAAS,EAClBU,EAAQP,EAASH,EAAG,OAAO,EAC3BW,EAAMR,EAASH,EAAG,KAAK,EAC7B,GACE,CAACS,GACD,EAAEE,EAAMD,IACRb,EAAqB,IAAIM,EAASH,EAAG,MAAM,CAAW,EAEtD,SAEF,IAAMY,EAA0C,CAAC,EACjDb,EAAQC,EAAGY,CAAK,EAChBJ,EAAM,KAAK,CACT,KAAAC,EACA,QAASN,EAASH,EAAG,SAAS,EAC9B,MAAAU,EACA,IAAAC,EACA,OAASR,EAASH,EAAG,QAAQ,GAA4B,EACzD,MAAOY,EAAM,OAASC,EAAgBD,CAAK,EAAI,CAAC,CAAE,MAAAF,EAAO,IAAAC,CAAI,CAAC,CAChE,CAAC,CACH,CACA,OAAOG,EAAuBN,CAAK,CACrC,CC5JA,IAAMO,EAAO,eAAe,eAAe,EACrCC,GAAOC,GACXF,GAAQ,MAAQE,KAAQ,OAAOF,CAAI,EAC/BA,EAAKE,CAAI,EACT,OAAO,OACL,UAAY,CACV,MAAM,IAAI,MACR,kCAAoCA,EAAO,+HAC7C,CACF,EACA,CAAE,mBAAoBA,CAAK,CAC7B,EAGC,IAAMC,GAA6BC,GAAK,YAAY,EACpDC,GAAQC,GAAQA,EAAK,WAAaA,EAAK,QAAUA",
+  "names": ["isStringArray", "value", "item", "trackLanes", "track", "lanes", "getConfAssemblyNamesOrNone", "walkIndexed", "adapterConfig", "snapshotNamesFile", "cutsByHaplotype", "configHaplotypes", "defaultHaplotypes", "graphReferenceAssembly", "trackAdapterSnapshot", "toTrackConfigEntry", "offReferenceProblem", "referenceAssembly", "assemblyName", "ownField", "f", "name", "namedTrack", "tracks", "named", "t", "trackLabel", "REPEAT_ADAPTER_TYPES", "REPEAT_TRACK_HINT", "pickRepeatTrack", "tracks", "named", "chosen", "namedTrack", "t", "trackLabel", "PACKED_NAME", "packedName", "f", "name", "ownField", "pair", "i", "field", "top", "MOTIF_FIELDS", "PERIOD_FIELDS", "NAME_FIELDS", "first", "names", "value", "one", "IUPAC", "repeatUnitOf", "period", "motif", "numbers", "n", "strings", "text", "TANDEM_REPEAT", "tandemAlleleBp", "alts", "rn", "rus", "rul", "ruc", "rb", "k", "alt", "bp", "known", "j", "unitLength", "count", "runBp", "genotyped", "gt", "alleleBp", "referenceBp", "phased", "index", "callsOf", "samples", "called", "sample", "fields", "reads", "lengths", "calls", "spanOf", "tandem", "start", "end", "svlen", "repeatArraysFrom", "features", "arrays", "unit", "refName", "stated", "a", "b", "mergedIntervals", "intervals", "out", "iv", "a", "b", "last", "mergeOverlappingByName", "genes", "out", "open", "g", "a", "b", "key", "last", "mergedIntervals", "gene", "GENE_ADAPTER_TYPES", "GENE_TRACK_HINT", "BED_ADAPTER_TYPES", "pickGeneTrack", "tracks", "named", "chosen", "namedTrack", "candidates", "t", "REPEAT_TRACK_HINT", "trackLabel", "TE_TRACK_HINT", "annotationNoun", "track", "laneFilters", "view", "trackId", "lane", "readConfObject", "WHOLE_SEQUENCE_TYPES", "EXON_PARTS", "exonsOf", "f", "into", "type", "ownField", "children", "child", "geneModelsFrom", "features", "genes", "name", "start", "end", "exons", "mergedIntervals", "mergeOverlappingByName", "host", "read", "name", "makeStyles", "read", "mui_default", "host"]
+}

package/dist/chunks/{chunk-KY6GXBXU.js → chunk-4KVQOJHH.js}

@@ -1,4 +1,4 @@
-import{a as ce,b as N,c as Ee,d as Q,e as ee,f as Ft,g as Ue,h as We,i as qt,j as zt,k as He,l as Oe,m as Pe,n as Dt,o as jt,p as Ut,q as Wt,r as Vt}from"./chunk-M2D7NUOY.js";import{a as _t,g as Tt}from"./chunk-PT3WV5ED.js";import{c as Ot}from"./chunk-LIRBZOBX.js";import{a as Ct,g as Bt}from"./chunk-ODQSCM3F.js";var Ln=4096;function pt(a){let e=[];for(let t of a){let n=e[e.length-1];n&&t-n[1]<=Ln?n[1]=t:e.push([t,t])}return e}var Hn=32768,Gt={mostChosenPaths:32},lt=class{byNode=new Map;get(e){return this.byNode.get(e.node)?.get(e.offset)}set(e,t){let n=this.byNode.get(e.node);n||(n=new Map,this.byNode.set(e.node,n)),n.set(e.offset,t)}},re=class extends Error{};function Ve(a,e,t,n){return a==="forward"?e+t:e-n}function Qt(a,e,t,n){return a==="forward"?e-n:e+t}function Kt(a){return Pe(ee(a.handles[a.handles.length-1]),ee(a.handles[0]))}function Ce(a){return`${a.pathHandle}:${a.hapStart}:${a.hapEnd}`}async function Zt(a){let{db:e,records:t,signal:n}=a,s=performance.now(),o=()=>{let w=performance.now(),S=w-s;return s=w,S},r={spacing:await e.haplotypeAnchorSpacing(),anchors:void 0,anchorsRead:0,chosenPaths:0,scans:[],scanRows:0,strays:void 0,pieces:0,sources:{reference:0,section:0,stray:0,chain:0,twin:0},walks:{},twins:{tried:0,found:0},graphFetches:0,fallback:void 0,ms:{scan:0,walks:0,check:0,twins:0}},i=(w,S)=>{let A=`${w}: ${S}`;r.walks[A]=(r.walks[A]??0)+1},h=await e.haplotypeSampleInterval()??4096,c=new Map,d=async w=>{let S=t.get(w)??c.get(w);if(S)return S;let A=await e.getRecord(w);if(r.graphFetches+=1,!A)throw new Error(`Node record ${w} is missing from the database`);return c.set(w,A),A},f=w=>t.get(w).sequenceLen,p=await e.pathsByHandle(),y=w=>{let S=p.get(w);return S!==void 0&&a.keep(S.name)},g=[],l=new lt,b=new Map,x=new Set,P=new Set,E=async w=>{let S=(await d(w.node)).gbwt().lf(w.offset);return S===void 0||S.node===0?void 0:S},R=async(w,S)=>{let A=(await d(ee(w.node))).gbwt().predecessorAt(w.offset);if(A===void 0||S!==void 0&&!S.has(A))return;let M=(await d(A)).gbwt().offsetTo(w);if(M===void 0)throw new Error(`No offset in ${A} leads to ${w.node}:${w.offset}`);return{node:A,offset:M}},m=(w,S,A,M)=>{let B=A.map(W=>W.pos.node),U=A.map(W=>W.pos.offset),J=0;for(let W of B)J+=f(W);let O=S==="forward"?A[0].left:A[A.length-1].left,L=g.length;g.push({pathHandle:w,orientation:S,handles:B,offsets:U,len:J,hapStart:O,hapEnd:O+J,canonical:Pe(B[0],B[B.length-1]),source:M});for(let W of A)l.set(W.pos,L);let G=b.get(w);return G?G.push(L):b.set(w,[L]),L},I=async(w,S,A,M)=>{let B=[],U=w;for(;;){n?.throwIfAborted();let O=await R(U.pos,t);if(!O)break;U={pos:O,left:Qt(A,U.left,f(U.pos.node),f(O.node))},B.push(U)}B.reverse();let J=[w];for(U=w;;){n?.throwIfAborted();let O=await E(U.pos);if(!O||!t.has(O.node))break;U={pos:O,left:Ve(A,U.left,f(U.pos.node),f(O.node))},J.push(U)}return m(S,A,[...B,...J],M)},$=async(w,S,A,M)=>g[l.get(w.pos)??await I(w,S,A,M)],F=w=>{let S=w.handles[w.handles.length-1];return{pos:{node:S,offset:w.offsets[w.offsets.length-1]},left:w.orientation==="forward"?w.hapEnd-f(S):w.hapStart}},_=w=>{let S=w.handles[0];return{pos:{node:S,offset:w.offsets[0]},left:w.orientation==="forward"?w.hapStart:w.hapEnd-f(S)}},D=await I({pos:a.referencePos,left:a.referenceLeft},a.referenceHandle,"forward","reference"),C=g[D],H=()=>{if(r.fallback!==void 0)return{reference:C,pieces:[],stats:r};let w=new Map;g.forEach((A,M)=>{M!==D&&w.set(Ce(A),[...w.get(Ce(A))??[],A])});let S=[];for(let A of w.values()){let M=new Set;for(let B of A)B.canonical&&!M.has(B.orientation)&&(M.add(B.orientation),S.push(B),r.sources[B.source]+=1)}return r.sources.reference=1,r.pieces=S.length+1,{reference:C,pieces:S,stats:r}},k=async(w,S)=>{let A=S?x:P,M=S?P:x,B=w;for(;;){if(A.has(B))return;A.add(B);let U=g[B],J=S?F(U):_(U),O=0,L;for(;L===void 0;){n?.throwIfAborted();let G=S?await E(J.pos):await R(J.pos);if(!G){L="endmarker";break}let W=(await d(J.pos.node)).sequenceLen,ue=(await d(G.node)).sequenceLen,se=S?Ve(U.orientation,J.left,W,ue):Qt(U.orientation,J.left,W,ue);if(t.has(G.node)){let Y=l.get(G);Y===void 0?(B=await I({pos:G,left:se},U.pathHandle,U.orientation,"chain"),M.add(B),L="landed"):(M.add(Y),L="merge")}else O>Hn?L="bound":(O+=ue,J={pos:G,left:se})}if(i("chain",L),L!=="landed")return}},j=async w=>{if(a.context>w.context)throw new re(`the context of ${a.context} bp exceeds the ${w.context} bp the haplotype index's stray rows cover`);let S=r.spacing;if(S===void 0)throw new re("the haplotype index has no anchors");let{bin:A,bound:M}=w,{fills:B,inserted:U}=a.snarls;if(a.snarls.mode==="overlapping"&&B.length>0)throw new re("the haplotype index's stray rows cover contained snarls only");for(let u of B){if(u.inserted>0&&u.low===u.high)throw new re(`the haplotype index's stray rows leave out the snarl bounded by node ${u.low} at both ends`);if(u.inserted>0&&(w.snarlNodes===void 0||u.nodes>w.snarlNodes))throw new re(w.snarlNodes===void 0?"the haplotype index's stray rows leave snarls out":`a snarl of ${u.nodes} nodes exceeds the ${w.snarlNodes} the haplotype index's stray rows cover`)}let J=Math.floor(a.window.start/A),O=Math.floor((a.window.end-1)/A),L=J*A,G=(O+1)*A,W=new Map,ue=async(u,v)=>{let z=await e.haplotypeAnchorsBetween(a.referenceHandle,u*S,v*S);for(let T of z)W.set(T.anchorOffset/S,T)},se=Math.max(0,Math.floor((L-M)/S)-1),Y=Math.ceil((G+M)/S)+1,[{listed:De,strays:ae}]=await Promise.all([e.haplotypeBinData(a.referenceHandle,J,O),ue(se,Y)]);for(let u of t.keys()){let v=N(u);if(!Q(u)&&!De(v)&&!U.has(v))throw new re(`the haplotype index lists node ${v} of the subgraph in no bin that the window touches`)}r.scans=pt([...t.keys()].sort((u,v)=>u-v));let ie=Promise.all(r.scans.map(([u,v])=>e.haplotypeSamplesInRange(u,v)));for(ie.catch(()=>{});se>0&&(W.get(se)?.pathOffset??Number.POSITIVE_INFINITY)>=L-M;)se-=1,await ue(se,se);for(;W.has(Y)&&W.get(Y).pathOffset<=G+M;)Y+=1,await ue(Y,Y);let pe=[...W.keys()].sort((u,v)=>u-v),ye=W.get(pe[0]??-1);if(!ye)throw new re("the haplotype index has no anchors on this path");let he=u=>W.get(u).pathOffset,Ne=new Map;for(let u of pe){let v=N(W.get(u).node);Ne.set(v,[...Ne.get(v)??[],u])}let ct=[...Ne.keys()],Et=ct.map(u=>W.get(Ne.get(u)[0]).visits);if(!Et[ct.indexOf(N(ye.node))].some(u=>u.pathHandle===a.referenceHandle&&u.orientation==="forward"&&u.pathOffset===ye.pathOffset))throw new Error(`The haplotype index has no anchor row for the reference path ${a.referenceHandle} at offset ${ye.pathOffset} (node ${N(ye.node)}); it does not match this graph`);let kt=pe.filter(u=>he(u)<=a.window.start),$n=pe.filter(u=>he(u)>=a.window.end);r.anchors=[he(kt[kt.length-1]??pe[0]),he($n[0]??pe[pe.length-1])],r.anchorsRead=pe.length;let dt=new Map,vt=new Set;if(ct.forEach((u,v)=>{let z=Ne.get(u),T=z.length===1?z[0]:void 0;for(let q of Et[v])vt.add(q.pathHandle),q.orientation==="forward"&&y(q.pathHandle)&&dt.set(q.pathHandle,[...dt.get(q.pathHandle)??[],{k:T,row:q}])}),r.chosenPaths=[...vt].filter(y).length,r.chosenPaths>Gt.mostChosenPaths)throw new re(`${r.chosenPaths} chosen paths pass the anchors, more than ${Gt.mostChosenPaths}`);let je=[],Ie=Number.POSITIVE_INFINITY,be=0;for(let[u,v]of dt){v.sort((z,T)=>z.row.pathOffset-T.row.pathOffset);for(let z=0;z+1<v.length;z++){let T=v[z],q=v[z+1];if(T.k===void 0||q.k===void 0||Math.abs(T.k-q.k)!==1)continue;let[Z,te]=he(T.k)<=he(q.k)?[T,q]:[q,T],ne=he(Z.k),oe=he(te.k);ne<G&&oe>=L?(je.push({pathHandle:u,from:T.row,to:q.row}),Ie=Math.min(Ie,ne-M),be=Math.max(be,oe+M)):ne>=G&&ne-G<=M?(je.push({pathHandle:u,from:Z.row,to:void 0}),Ie=Math.min(Ie,ne-M),be=Math.max(be,ne+M)):oe<L&&L-oe<=M&&(je.push({pathHandle:u,from:te.row,to:void 0}),Ie=Math.min(Ie,oe-M),be=Math.max(be,oe+M))}}let Rn=new Set(B.map(u=>`${u.low}:${u.high}`)),Nn=ae.filter(u=>y(u.pathHandle)&&(u.snarl===void 0||Rn.has(`${u.snarl[0]}:${u.snarl[1]}`))).sort((u,v)=>u.pathHandle-v.pathHandle||u.pathStart-v.pathStart);r.strays={bins:O-J+1,rows:ae.length,walked:0,outsideBp:0},be>0&&await a.prefetchReferenceRange(a.referenceHandle,Math.max(0,Ie),be+1),r.ms.scan=o();let Pt=8*S+2*(a.window.end-a.window.start),At=r.strays,Me=0,$t=u=>{if(At.outsideBp+=u,Me+=u,Me>Pt)throw new re(`a walk of a chosen path near the window went past its cap of ${Pt} bp`)},ft=new Map,Rt=(u,v,z)=>(ft.get(u)??[]).some(([T,q])=>T<=v&&z<q),Nt=(u,v,z)=>{ft.set(u,[...ft.get(u)??[],[v,z]])},Mt=async(u,v,z,T,q)=>{let Z=v,te=z,ne=te;for(;Z&&te<=T;){n?.throwIfAborted();let oe;if(t.has(Z.node)){let Le=await $({pos:Z,left:te},u,"forward",q),Ht=F(Le);Z=Ht.pos,te=Ht.left,oe=f(Z.node),ne=Math.max(ne,Le.hapEnd)}else oe=(await d(Z.node)).sequenceLen,$t(oe),ne=Math.max(ne,te+oe);Z=await E(Z),te+=oe}return ne},Mn=async(u,v,z,T)=>{let q={pos:v,left:z},Z=z;for(;q.left>T;){n?.throwIfAborted();let te=await R(q.pos);if(!te)break;let ne=(await d(te.node)).sequenceLen,oe=q.left-ne;if(t.has(te.node)){let Le=await $({pos:te,left:oe},u,"forward","section");q=_(Le),Z=Math.min(Z,Le.hapStart)}else $t(ne),q={pos:te,left:oe},Z=Math.min(Z,oe)}return Z};for(let{pathHandle:u,from:v,to:z}of je){let T=v.pathOffset,q=(z??v).pathOffset+M;if(Rt(u,T-M,q))continue;let Z={node:v.node,offset:v.offset};Me=0;let te=await Mt(u,Z,T,q,"section");Me=0;let ne=await Mn(u,Z,T,T-M);Nt(u,Math.min(ne,T-M),Math.max(te,q+1)),i(z?"section":"visit",z?"past the far anchor":"bound")}for(let u of Nn){if(Rt(u.pathHandle,u.pathStart,u.pathEnd))continue;Me=0;let v=await Mt(u.pathHandle,{node:u.node,offset:u.offset},u.pathStart,u.pathEnd,"stray");Nt(u.pathHandle,u.pathStart,Math.max(v,u.pathEnd+1)),At.walked+=1}r.ms.walks=o();let Lt=[];for(let u of await ie)for(let v of u)if(r.scanRows+=1,t.has(v.node)&&y(v.pathHandle)){if(!(b.get(v.pathHandle)??[]).some(z=>{let T=g[z];return T.hapStart<=v.pathOffset&&v.pathOffset<T.hapEnd}))throw new re(`chosen path ${v.pathHandle} has a sample at ${v.pathOffset} on the window's nodes that no walk reached`);v.orientation==="reverse"&&Lt.push(v)}for(let u of Lt)await $({pos:{node:u.node,offset:u.offset},left:u.pathOffset},u.pathHandle,"reverse","twin");r.ms.check=o()},X=async()=>{let w=new Map,S=O=>{let L=Ce(O),G=w.get(L);G?G.add(O.orientation):w.set(L,new Set([O.orientation]))},A=0,M=()=>{for(;A<g.length;A++)S(g[A])};M();let B=O=>(w.get(Ce(O))?.size??0)>1,U=2*h,J=(O,L)=>L===D?y(a.referenceHandle)&&Kt(O):!O.canonical||Kt(O);for(let O=0;O<g.length;O++){let L=g[O];if(B(L)||!J(L,O))continue;r.twins.tried+=1;let G=L.orientation==="forward"?"reverse":"forward",W=F(L),ue=0,se;for(;!se&&ue<=U;){n?.throwIfAborted();let ae=await E(W.pos);if(!ae)break;let ie=(await d(ae.node)).sequenceLen,pe=Ve(L.orientation,W.left,(await d(W.pos.node)).sequenceLen,ie),ye=ee(ae.node);se=(await e.haplotypeSamplesInRange(ye,ye)).find(he=>he.pathHandle===L.pathHandle&&he.orientation===G&&he.pathOffset===pe),ue+=ie,W={pos:ae,left:pe}}let Y=se&&{pos:{node:se.node,offset:se.offset},left:se.pathOffset},De=0;for(;Y&&!B(L)&&De<=U+L.len;){if(n?.throwIfAborted(),t.has(Y.pos.node)){let ae=await $(Y,L.pathHandle,G,"twin"),ie=g.indexOf(ae);await k(ie,!0),await k(ie,!1),M(),Y=F(ae)}if(!B(L)){let ae=(await d(Y.pos.node)).sequenceLen;De+=ae;let ie=await E(Y.pos);Y=ie?{pos:ie,left:Ve(G,Y.left,ae,(await d(ie.node)).sequenceLen)}:void 0}}if(M(),!B(L))throw new re(`piece ${Ce(L)} was found in one orientation where extractPaths keeps the other`);r.twins.found+=1}r.ms.twins=o()};try{let w=await e.haplotypeStrayOptions();if(w===void 0)throw new re("the haplotype index has no stray rows; gbz-haplotype-index 0.2.0 writes them");await j(w),await X()}catch(w){if(!(w instanceof re))throw w;r.fallback=w.message}return H()}function Xt(a,e){return a.handles[0]-e.handles[0]||a.offsets[0]-e.offsets[0]}var On=Uint32Array.from([1116352408,1899447441,3049323471,3921009573,961987163,1508970993,2453635748,2870763221,3624381080,310598401,607225278,1426881987,1925078388,2162078206,2614888103,3248222580,3835390401,4022224774,264347078,604807628,770255983,1249150122,1555081692,1996064986,2554220882,2821834349,2952996808,3210313671,3336571891,3584528711,113926993,338241895,666307205,773529912,1294757372,1396182291,1695183700,1986661051,2177026350,2456956037,2730485921,2820302411,3259730800,3345764771,3516065817,3600352804,4094571909,275423344,430227734,506948616,659060556,883997877,958139571,1322822218,1537002063,1747873779,1955562222,2024104815,2227730452,2361852424,2428436474,2756734187,3204031479,3329325298]),we=(a,e)=>a>>>e|a<<32-e;function Jt(a){let e=Math.ceil((a.length+9)/64),t=new Uint8Array(e*64);t.set(a),t[a.length]=128;let n=new DataView(t.buffer),s=a.length*8;n.setUint32(t.length-8,Math.floor(s/2**32)),n.setUint32(t.length-4,s>>>0);let o=Uint32Array.from([1779033703,3144134277,1013904242,2773480762,1359893119,2600822924,528734635,1541459225]),r=new Uint32Array(64);for(let c=0;c<e;c++){for(let P=0;P<16;P++)r[P]=n.getUint32(c*64+P*4);for(let P=16;P<64;P++){let E=r[P-15],R=r[P-2],m=we(E,7)^we(E,18)^E>>>3,I=we(R,17)^we(R,19)^R>>>10;r[P]=r[P-16]+m+r[P-7]+I}let d=o[0],f=o[1],p=o[2],y=o[3],g=o[4],l=o[5],b=o[6],x=o[7];for(let P=0;P<64;P++){let E=we(g,6)^we(g,11)^we(g,25),R=g&l^~g&b,m=x+E+R+On[P]+r[P]|0,I=we(d,2)^we(d,13)^we(d,22),$=d&f^d&p^f&p;x=b,b=l,l=g,g=y+m|0,y=p,p=f,f=d,d=m+I+$|0}[d,f,p,y,g,l,b,x].forEach((P,E)=>{o[E]=o[E]+P})}let i=new Uint8Array(32),h=new DataView(i.buffer);for(let c=0;c<8;c++)h.setUint32(c*4,o[c]);return i}function Yt(a,e){let t=new Map;if(a!==void 0)for(let n of a.split(";")){let s=n.split(","),[o,r]=s;if(s.length!==2||!o||!r)throw new Error(`Invalid ${e} relationship: ${n}`);let i=t.get(o);i||(i=new Set,t.set(o,i)),i.add(r)}return t}function nn(a){return{name:a.get("pggname"),subgraph:Yt(a.get("subgraph"),"subgraph"),translation:Yt(a.get("translation"),"translation")}}function en(a,e){for(let[t,n]of e){let s=a.get(t);s||(s=new Set,a.set(t,s));for(let o of n)s.add(o)}}function sn(a,e){let t={name:a,subgraph:new Map,translation:new Map};return e.name!==void 0&&(t.subgraph.set(a,new Set([e.name])),en(t.subgraph,e.subgraph),en(t.translation,e.translation)),t}function tn(a){return[...a.entries()].sort(([e],[t])=>e<t?-1:e>t?1:0).flatMap(([e,t])=>[...t].sort().map(n=>[e,n]))}function on(a){let e=[];a.name!==void 0&&e.push(`H	NM:Z:${a.name}`);for(let[t,n]of tn(a.subgraph))e.push(`H	SG:Z:${t},${n}`);for(let[t,n]of tn(a.translation))e.push(`H	TL:Z:${t},${n}`);return e}async function rn(a){let e=a.reduce((r,i)=>r+i.length,0),t=new Uint8Array(e),n=0;for(let r of a)t.set(r,n),n+=r.length;let s=globalThis.crypto?.subtle;return[...s?new Uint8Array(await s.digest("SHA-256",t)):Jt(t)].map(r=>r.toString(16).padStart(2,"0")).join("")}var Cn="_gbwt_ref";function fe(a){let e=`${a.sample}#${a.haplotype}#${a.contig}`;return a.end===void 0?e:`${e}[${a.fragment}-${a.end}]`}var Bn=/^([^#]+)#(\d+)#([^#]+?)(?:\[\d+-\d+\])?$/,_n=/^([^#]+?)(?:\[\d+-\d+\])?$/;function Tn(a){let e=Bn.exec(a);if(e)return{sample:e[1],haplotype:Number(e[2]),contig:e[3]};let t=_n.exec(a);if(t)return{contig:t[1]};throw new Error(`"${a}" is not a path name; expected "sample#haplotype#contig" or a bare contig`)}function Ae(a){return typeof a=="string"?Tn(a):a}function $e(a,e){return{sample:a.sample??Cn,contig:a.contig,haplotype:a.haplotype??0,fragment:e}}var le=class extends Error{name="SubgraphLimitError";limit;windowBp;walkedBp;constructor(e,t){super(t===void 0?`Subgraph size limit of ${e} nodes exceeded`:`Subgraph size limit of ${e} nodes exceeded ${t.walkedBp} bp into a ${t.windowBp} bp window`),this.limit=e,this.windowBp=t?.windowBp,this.walkedBp=t?.walkedBp}};function ut(a,e){return a[0]<e[0]||a[0]===e[0]&&(a[1]<e[1]||a[1]===e[1]&&a[2]<e[2])}var _e=class{heap=[];push(e,t,n){let s=this.heap;s.push([e,t,n]);let o=s.length-1;for(;o>0;){let r=o-1>>1;if(ut(s[o],s[r]))[s[o],s[r]]=[s[r],s[o]],o=r;else break}}pop(){let e=this.heap,t=e[0],n=e.pop();if(e.length>0&&n!==void 0){e[0]=n;let s=0;for(;;){let o=2*s+1,r=o+1,i=s;if(o<e.length&&ut(e[o],e[i])&&(i=o),r<e.length&&ut(e[r],e[i])&&(i=r),i===s)break;[e[s],e[i]]=[e[i],e[s]],s=i}}return t}get size(){return this.heap.length}};function Fn(a){let e=new Int32Array(a.length),t=new Int32Array(a.length);return a.forEach(([n,s],o)=>{e[o]=n,t[o]=s}),{pathAt:e,refAt:t,count:a.length}}function qn(a,e){let t=0,n=a.length;for(;t<n;){let s=t+n>>1;a[s]>e?n=s:t=s+1}return a[t]}function ke(a){return`${a.node}:${a.offset}`}function Be(a){return a.map(e=>ee(e)).reverse()}function zn(a,e){let t=e.identity.hapStart-a.identity.hapEnd,n=a.strand==="+"?e.refStart-a.refEnd:a.refStart-e.refEnd;return a.strand===e.strand&&t>=0&&n>=0?{insertion:t,deletion:n}:void 0}function Dn(a,e,t){let[n,s]=a.strand==="+"?[a,e]:[e,a],o=n.edits.map(([c,d])=>[c,d]);hn(o,t.insertion,t.deletion);for(let[c,d]of s.edits)K(o,c,d);let r=a.identity.walkForward,[i,h]=r?[a,e]:[e,a];return{strand:a.strand,refStart:n.refStart,refEnd:s.refEnd,edits:o,weight:void 0,path:[...i.path,...h.path],start:i.start,pieces:[...i.pieces,...h.pieces],soloAligned:[...i.soloAligned,...h.soloAligned],identity:{pathHandle:a.identity.pathHandle,name:a.identity.name,hapStart:a.identity.hapStart,hapEnd:e.identity.hapEnd,walkForward:r}}}function jn(a,e,t){if(a.some(r=>r.weight!==void 0))return a;let n=new Map;a.forEach((r,i)=>{if(r.identity){let h=n.get(r.identity.pathHandle);h?h.push(i):n.set(r.identity.pathHandle,[i])}});let s=new Map,o=new Set;for(let r of n.values()){r.sort((d,f)=>a[d].identity.hapStart-a[f].identity.hapStart);let i=r[0],h=a[i],c=[];for(let d of r.slice(1)){let f=a[d],p=c.length===0?zn(h,f):void 0;if(p){h=Dn(h,f,p),o.add(d);continue}if(!e(f)){c.push(d);continue}let y=e(h)?t([h,...c.map(g=>a[g]),f]):void 0;if(y){h=y;for(let g of[...c,d])o.add(g)}else s.set(i,h),i=d,h=f;c=[]}s.set(i,h)}return a.flatMap((r,i)=>o.has(i)?[]:[s.get(i)??r])}function Ge(a,e){return{node:a.path[e],offset:a.offsets[e]}}var Un=32768;function Wn(a){let e=[...a].sort((n,s)=>n-s),t=[];for(let n of e){let s=t[t.length-1];s&&n-s[1]<=Un?s[1]=n:t.push([n,n])}return t}var Te=class a{records=new Map;paths=[];twinStarts=new Set;twinDeferred=!1;unsettled;refId;refPath;refHandle;refInterval;refIndexCache;refPrefixCache;walkedBp;snarlMode="none";snarlFills=[];snarlNodes=new Set;stats={orderedAlignments:0,lcsAlignments:0,snarls:{fills:0,inserted:0},identificationSteps:0,identificationFetches:0,identification:{interval:0,scans:[],windowSamples:0,fragmentLengths:[],companionSeeks:0,companionMisses:0,graphLookups:0,graphFetches:0,chains:[]},keep:void 0};db;limit;signal;constructor(e,t){this.db=e,this.limit=t.limit,this.signal=t.signal}static create(e,t={}){return new a(e,t)}get nodeCount(){return this.records.size/2}get pathCount(){return this.settleDeferred(),this.paths.length}get referenceInterval(){return this.refInterval&&this.refPath?{name:this.refPath,start:this.refPath.fragment+this.refInterval[0],end:this.refPath.fragment+this.refInterval[1]}:void 0}hasNode(e){return this.records.has(ce(e,"forward"))}hasHandle(e){return this.records.has(e)}record(e){let t=this.records.get(e);if(!t)throw new Error(`Subgraph has no record for handle ${e}`);return t}sortedHandles(){return[...this.records.keys()].sort((e,t)=>e-t)}async addNode(e){if(this.signal?.throwIfAborted(),this.limit!==void 0&&this.nodeCount>=this.limit)throw new le(this.limit);let t=await this.db.getRecord(ce(e,"forward")),n=await this.db.getRecord(ce(e,"reverse"));if(!t||!n)throw new Error(`Node ${e} does not exist in the graph`);this.records.set(t.handle,t),this.records.set(n.handle,n)}async ensureNode(e){this.hasNode(e)||await this.addNode(e)}clearPaths(){this.paths=[],this.twinStarts.clear(),this.twinDeferred=!1,this.unsettled=void 0,this.refId=void 0,this.refPath=void 0,this.refHandle=void 0,this.refInterval=void 0,this.refIndexCache=void 0,this.refPrefixCache=void 0}async pathPosition(e){let t=await this.db.findPath(e);if(!t)throw new Error(`Cannot find a path covering offset ${e.fragment} of ${fe(e)}`);if(!t.isIndexed)throw new Error(`The fragment of ${fe(t.name)} at ${t.name.fragment} has not been indexed for random access`);let n=e.fragment-t.name.fragment,s=await this.db.indexedPosition(t.handle,n);if(!s)throw new Error(`The fragment of ${fe(t.name)} at ${t.name.fragment} has not been indexed for random access`);return this.findPathPosition(t,n,s.pathOffset,s.pos)}async findPathPosition(e,t,n,s){let o=n,r=s;for(;;){await this.ensureNode(N(r.node));let i=this.record(r.node);if(o+i.sequenceLen>t)return{position:{seqOffset:t,handle:r.node,nodeOffset:t-o,gbwtOffset:r.offset},name:e.name,handle:e.handle};o+=i.sequenceLen;let h=i.gbwt().lf(r.offset);if(!h)throw new Error(`The fragment of ${fe(e.name)} at ${e.name.fragment} does not contain offset ${t}`);r=h}}async aroundPosition(e,t,n){let s=N(e);await this.ensureNode(s);let o=this.record(e),r=Ee(e),i=new _e;return i.push(t,s,Ue(r)),i.push(o.sequenceLen-t-1,s,We(r)),this.insertContext(i,n)}prefetchReferenceWalk(e,t){return this.prefetchReferenceRange(e.handle,e.position.seqOffset,e.position.seqOffset+t)}async prefetchReferenceRange(e,t,n){let[s,o]=await Promise.all([this.db.indexedPosition(e,t),this.db.indexedPosition(e,n)]);if(s&&o){let r=s.pos.node,i=o.pos.node;if(!await this.db.prefetchRecords([[Math.min(r,i),Math.max(r,i)+1]])){let c=await this.db.indexedPositionsBetween(e,t,n);await this.db.prefetchRecords(Wn(c.map(d=>d.pos.node)).map(([d,f])=>[d,f+2]),!0)}}return s}async aroundInterval(e,t,n){if(!(t>0))throw new Error("Interval length must be greater than 0");this.walkedBp=0;try{return await this.walkInterval(e,t,n)}catch(s){throw s instanceof le&&s.windowBp===void 0?new le(s.limit,{windowBp:t,walkedBp:this.walkedBp}):s}}get referenceWalkedBp(){return this.walkedBp}async walkInterval(e,t,n){let s={node:e.handle,offset:e.gbwtOffset},o=e.nodeOffset,r=t,i=new _e;for(;;){let h=N(s.node),c=Ee(s.node);this.walkedBp=t-r,await this.ensureNode(h);let d=this.record(s.node);if(o>=d.sequenceLen)throw new Error(`Offset ${o} in node ${h} of length ${d.sequenceLen}`);i.push(o,h,Ue(c));let f=d.sequenceLen-o;if(r<=f){i.push(r===f?0:f-r-1,h,We(c));break}i.push(0,h,We(c));let p=d.gbwt().lf(s.offset);if(!p)throw new Error(`No successor for GBWT position (${s.node}, ${s.offset})`);s=p,o=0,r-=f}return this.walkedBp=t,this.insertContext(i,n)}async aroundNodes(e,t){let n=new _e;for(let s of e)await this.ensureNode(s),n.push(0,s,"left"),n.push(0,s,"right");return this.insertContext(n,t)}async insertContext(e,t){this.clearPaths(),this.snarlMode="none",this.snarlFills=[],this.snarlNodes.clear(),this.stats.snarls={fills:0,inserted:0};let n=new Set,s=new Set;for(let r of this.records.keys())s.add(N(r));let o=0;for(;e.size>0;){let[r,i,h]=e.pop(),c=`${i}:${h}`;if(n.has(c))continue;n.add(c),s.delete(i),this.hasNode(i)||(await this.addNode(i),o+=1);let d=Ft(h);if(!n.has(`${i}:${d}`)){let y=this.record(ce(i,qt(h))),g=r+y.sequenceLen-1;g<=t&&e.push(g,i,d)}let f=this.record(ce(i,zt(h))),p=r+1;if(p<=t)for(let y of f.successors()){let g=N(y),l=Ue(Ee(y));n.has(`${g}:${l}`)||e.push(p,g,l)}}for(let r of s)this.records.delete(ce(r,"forward")),this.records.delete(ce(r,"reverse"));return{inserted:o,removed:s.size}}async betweenNodes(e,t){return(await this.fillBetween(e,t)).inserted.length}async fillBetween(e,t){this.clearPaths();let n=[e,ee(t)],s=new Set([N(e),N(t)]),o=[];for(;n.length>0;){let r=n.pop(),i=N(r);this.hasNode(i)||(await this.addNode(i),o.push(i));for(let h of this.record(r).successors()){let c=N(h);s.has(c)||(n.push(h,ee(h)),s.add(c))}}return{inserted:o,nodes:s.size-2}}async extractSnarls(e){let t=0;this.snarlMode=e;for(let[n,s]of await this.overlappingSnarls(e)){let{inserted:o,nodes:r}=await this.fillBetween(n,s),i=N(n),h=N(s);this.snarlFills.push({low:Math.min(i,h),high:Math.max(i,h),nodes:r,inserted:o.length});for(let c of o)this.snarlNodes.add(c);t+=o.length}return this.stats.snarls={fills:this.snarlFills.length,inserted:this.snarlNodes.size},t}async overlappingSnarls(e){let t=[];if(e!=="none"){let n=!1;for(let s of this.sortedHandles()){let o=this.record(s),r=o.next;r!==void 0&&(n=!0,this.hasHandle(r)?He(s,r)&&t.push([s,r]):e==="overlapping"&&this.isSnarlEntryInSubgraph(o)&&t.push([s,r]))}if(!n&&e==="overlapping"&&await this.db.hasChainLinks()){let s=await this.findCoveringSnarl();s&&t.push(s)}}return t}isSnarlEntryInSubgraph(e){let t=e.successors(),n=t.find(s=>this.hasHandle(s));return n===void 0?!1:t.length>1||this.record(ee(n)).successors().length>1}recordReader(e){let t=new Map;return async n=>{let s=this.records.get(n);if(s)return s;let o=t.get(n);if(!o){if(o=await this.db.getRecord(n),e?.(),!o)throw new Error(`Node record ${n} is missing from the database`);t.set(n,o)}return o}}async findCoveringSnarl(){let e=this.recordReader(),t=async h=>{let c=h.successors(),d=c[0];return d===void 0?!1:c.length>1||(await e(ee(d))).successors().length>1},n=async h=>{let c=await e(ee(h));return c.next!==void 0?await t(c)?{kind:"snarl-exit",snarl:[ee(h),c.next]}:{kind:"chain"}:(await e(h)).next!==void 0?{kind:"chain"}:{kind:"regular"}},s=new Set,o=this.sortedHandles().flatMap(h=>this.record(h).successors()),r,i=!1;for(;!i&&o.length>0;){let h=o.shift(),c=N(h);if(!this.hasHandle(h)&&!s.has(c)){s.add(c);let d=await n(h);if(d.kind==="snarl-exit")r=d.snarl,i=!0;else if(d.kind==="chain")i=!0;else for(let f of["forward","reverse"])o.push(...(await e(ce(c,f))).successors())}}return r}extractPaths(e,t){if(this.clearPaths(),t==="none")return;let n=e?.position;this.refPath=e?.name,this.refHandle=e?.handle;let s=this.sortedHandles(),o=s.length,r=new Map;s.forEach((m,I)=>r.set(m,I));let i=new Int32Array(o+1),h=new Int32Array(o),c=[];for(let m=0;m<o;m++){let I=this.record(s[m]),$=I.gbwt().decompressArrays();h[m]=I.sequenceLen,c.push($),i[m+1]=i[m]+$.nodes.length}let d=i[o],f=new Int32Array(d),p=new Int32Array(d),y=new Uint8Array(d);for(let m=0;m<o;m++){let I=c[m];f.set(I.nodes,i[m]),p.set(I.offsets,i[m])}c.length=0;for(let m=0;m<d;m++){let I=r.get(f[m]);I===void 0?f[m]=-1:(f[m]=I,y[i[I]+p[m]]=1)}let g=n===void 0?void 0:r.get(n.handle),l=n?.gbwtOffset,b,x=(m,I,$)=>{let F=[],_=0,D=0,C=-1,H=m,k=I;for(;;){H===g&&k===l&&(C=_),$&&($.push(s[H]),F.push(k)),_+=1,D+=h[H];let j=i[H]+k,X=f[j];if(X<0)break;k=p[j],H=X}return{offsets:F,len:D,refAt:C,last:H}},P=(m,I,$,F)=>{F>=0&&(this.refId=this.paths.length,b=F),this.paths.push({path:m,offsets:I,len:$,weight:void 0,identity:void 0})},E=new Int32Array(o);for(let m=0;m<o;m++){let I=s[m];if(!Q(I)){let $=i[m],F=i[m+1]-$;for(let _=0;_<F;_++)if(y[$+_]===0){let D=[],{offsets:C,len:H,refAt:k,last:j}=x(m,_,D),X=s[j];if(k>=0||Pe(I,X)){if(P(D,C,H,k),!Q(X)){let w=r.get(ee(X));E[w]=E[w]+1}}else this.twinStarts.add(ke({node:I,offset:_}))}}}for(let m=0;m<o;m++){let I=s[m];if(Q(I)){let $=i[m],F=i[m+1]-$,_=0;for(let C=0;C<F;C++)y[$+C]===0&&(_+=1);let D=(g===void 0||b!==void 0)&&_===E[m];for(let C=0;C<F;C++)if(y[$+C]===0){let H=D?void 0:x(m,C,void 0);if(H&&(H.refAt>=0||Pe(I,s[H.last]))){let k=[],{offsets:j,len:X,refAt:w}=x(m,C,k);P(k,j,X,w)}else this.twinStarts.add(ke({node:I,offset:C}))}}}let R=this.refId===void 0?void 0:this.paths[this.refId];if(this.paths.sort((m,I)=>m.path[0]-I.path[0]||m.offsets[0]-I.offsets[0]),R&&(this.refId=this.paths.indexOf(R)),n){if(b===void 0||this.refId===void 0)throw this.clearPaths(),new Error("Could not find the reference path");let m=this.paths[this.refId],I=n.nodeOffset;for(let F of m.path.slice(0,b))I+=this.record(F).sequenceLen;let $=n.seqOffset-I;this.refInterval=[$,$+m.len],m.identity={pathHandle:e.handle,name:e.name,orientation:"forward",hapStart:$,hapEnd:$+m.len}}if(t==="distinct")this.distinctPaths(!0);else if(t==="reference-only"){if(this.refId===void 0)throw new Error("Reference path is required for reference-only output");this.paths=[this.paths[this.refId]],this.refId=0}}distinctPaths(e){let t=this.refId===void 0?void 0:this.paths[this.refId],n=t?.path,s=n&&!Oe(n)?Be(n):void 0,o=c=>s!==void 0&&wt(c,s)===0||Oe(Be(c)),r=e&&this.db.hasHaplotypeIndex;this.twinDeferred=!1,this.paths.sort((c,d)=>wt(c.path,d.path)||c.len-d.len||(c===t?-1:d===t?1:0));let i=[],h;for(let c of this.paths){let d=i[i.length-1],f=r&&c!==t&&o(c.path);this.twinDeferred||=f,d&&wt(d.path,c.path)===0&&!f?d.weight=(d.weight??1)+(c.weight??1):(c===t&&(h=i.length),i.push({...c,weight:c.weight??1}))}this.paths=i,this.refId=h}mergeDistinct(){this.twinDeferred?this.settleDeferred():this.distinctPaths(!1)}settleDeferred(){this.twinDeferred&&(this.unsettled={paths:[...this.paths],refId:this.refId},this.distinctPaths(!1))}dropTwins(){let e=this.refId===void 0?void 0:this.paths[this.refId],t=this.refInterval,n=r=>`${r.pathHandle}:${r.hapStart}-${r.hapEnd}`,s=new Set;e?.identity&&t&&s.add(n({...e.identity,hapStart:t[0],hapEnd:t[1]}));for(let r of this.paths)r!==e&&r.identity?.orientation==="forward"&&s.add(n(r.identity));let o=this.paths.filter(r=>r===e||r.identity?.orientation!=="reverse"||!s.has(n(r.identity)));o.length<this.paths.length&&(this.paths=o,this.refId=e===void 0?void 0:o.indexOf(e)),this.twinDeferred&&this.distinctPaths(!1)}keepHaplotypes(e){if(this.paths.some(r=>r.weight!==void 0))throw new Error("keepHaplotypes needs one walk per haplotype: extract with haplotypes 'all', then call mergeDistinct()");let t=this.paths.filter((r,i)=>i!==this.refId&&r.identity===void 0).length;if(t>0)throw new Error(`${t} of the window's ${this.paths.length} walks have no name, so the haplotypes to keep cannot be told from the rest; call identifyPaths() first, and check that the haplotype index was built for this graph`);let n=this.refId===void 0?void 0:this.paths[this.refId],s=this.paths.filter((r,i)=>i===this.refId||r.identity!==void 0&&e(r.identity.name)),o=new Set;for(let r of s)for(let i of r.path)o.add(N(i));for(let r of[...this.records.keys()])o.has(N(r))||this.records.delete(r);this.paths=s,this.refId=n===void 0?void 0:s.indexOf(n)}async extractChosenPaths(e,t,n,s){this.clearPaths();let o=e.position.seqOffset,r=await Zt({db:this.db,records:this.records,referenceHandle:e.handle,referencePos:{node:e.position.handle,offset:e.position.gbwtOffset},referenceLeft:o-e.position.nodeOffset,window:{start:o,end:o+t},context:s,snarls:{mode:this.snarlMode,fills:this.snarlFills,inserted:this.snarlNodes},keep:n,signal:this.signal,prefetchReferenceRange:(d,f,p)=>this.prefetchReferenceRange(d,f,p)});if(this.stats.keep=r.stats,r.stats.fallback!==void 0)return!1;let i=await this.db.pathsByHandle(),h=d=>({path:d.handles,offsets:d.offsets,len:d.len,weight:void 0,identity:{pathHandle:d.pathHandle,name:d===r.reference?e.name:i.get(d.pathHandle).name,orientation:d.orientation,hapStart:d.hapStart,hapEnd:d.hapEnd}}),c=[r.reference,...r.pieces].sort(Xt);return this.paths=c.map(h),this.refId=c.indexOf(r.reference),this.refPath=e.name,this.refHandle=e.handle,this.refInterval=[r.reference.hapStart,r.reference.hapEnd],this.dropTwins(),!0}async identifyPaths(){if(!this.db.hasHaplotypeIndex)throw new Error("The database has no HaplotypeSamples table; run gbz-haplotype-index on it");this.unsettled&&({paths:this.paths,refId:this.refId}=this.unsettled,this.unsettled=void 0,this.twinDeferred=!0);let e=await this.db.haplotypeSampleGap()??4096,t=pt(this.sortedHandles());if(t.length===0)return;let n=new Map,s=await Promise.all(t.map(([l,b])=>this.db.haplotypeSamplesInRange(l,b)));for(let l of s.flat())n.set(ke(l),l);let o=l=>{let b=0,x=t.length-1;for(;b<x;){let E=b+x+1>>1;t[E][0]<=l?b=E:x=E-1}let P=t[b];return P[0]<=l&&l<=P[1]},r=new Map;this.paths.forEach((l,b)=>{l.path.length>0&&b!==this.refId&&r.set(ke(Ge(l,0)),b)});let i=this.stats.identification;i.interval=e,i.scans=t,i.windowSamples=n.size,this.paths.forEach((l,b)=>{b!==this.refId&&i.fragmentLengths.push(l.len)});let h=this.recordReader(()=>{this.stats.identificationFetches+=1,i.graphFetches+=1}),c=l=>(i.graphLookups+=1,h(l)),d=async(l,b)=>{if(o(l.node))return n.get(ke(l));this.stats.identificationFetches+=1,i.companionSeeks+=1,b.seeks+=1;let x=await this.db.haplotypeSampleAt(l.node,l.offset);return x||(i.companionMisses+=1),x},f=new Map,p=async l=>{let b=f.get(l);if(!b){let x=await this.db.getPath(l);if(!x)throw new Error(`Path ${l} is missing from the database`);b=x.name,f.set(l,b)}return b},y=(l,b,x)=>l.orientation==="forward"?{pathHandle:l.pathHandle,orientation:"forward",base:l.pathOffset-b}:{pathHandle:l.pathHandle,orientation:"reverse",base:l.pathOffset+b+x},g=(l,b)=>l.orientation==="forward"?{pathHandle:l.pathHandle,orientation:"forward",base:l.hapStart-b}:{pathHandle:l.pathHandle,orientation:"reverse",base:l.hapEnd+b};for(let l=0;l<this.paths.length;l++){let b=this.paths[l];if(l===this.refId||b.identity)continue;let x=[],P=new Set,E={fragments:0,steps:0,seeks:0,reentries:0,twinLandings:0,end:"endmarker",pathHandle:void 0};i.chains.push(E);let R,m=0,I=l,$;for(;R===void 0;){if(this.signal?.throwIfAborted(),I!==void 0){if(P.has(I)){E.end="cycle";break}P.add(I);let H=this.paths[I];x.push({index:I,startBp:m}),E.fragments+=1;let k=m;for(let X=0;X<H.path.length;X++){let w=Ge(H,X),S=n.get(ke(w)),A=this.record(w.node).sequenceLen;if(S){R=y(S,k,A);break}k+=A}if(m+=H.len,R){E.end="in-fragment sample";break}let j=Ge(H,H.path.length-1);$=this.record(j.node).gbwt().lf(j.offset),I=void 0}if($===void 0||$.node===0){E.end="endmarker";break}let F=ke($),_=r.get(F);if(_!==void 0){let H=this.paths[_].identity;if(H){R=g(H,m),E.end="identified sibling";break}I=_;continue}this.records.has($.node)&&(E.reentries+=1),this.twinStarts.has(F)&&(E.twinLandings+=1);let D=await d($,E),C=await c($.node);if(D){R=y(D,m,C.sequenceLen),E.end="out-of-window sample";break}if(this.stats.identificationSteps+=1,E.steps+=1,m-x[x.length-1].startBp>4*e+4*C.sequenceLen){E.end="bound";break}m+=C.sequenceLen,$=C.gbwt().lf($.offset)}if(R){E.pathHandle=R.pathHandle;let F=await p(R.pathHandle);for(let{index:_,startBp:D}of x){let C=this.paths[_];C.identity=R.orientation==="forward"?{pathHandle:R.pathHandle,name:F,orientation:"forward",hapStart:R.base+D,hapEnd:R.base+D+C.len}:{pathHandle:R.pathHandle,name:F,orientation:"reverse",hapStart:R.base-D-C.len,hapEnd:R.base-D}}}}this.dropTwins()}refIndex(e){if(this.refIndexCache===void 0){let t=new Map;e.forEach((n,s)=>{let o=t.get(n);o?o.push(s):t.set(n,[s])}),this.refIndexCache=t}return this.refIndexCache}refPrefix(e){if(this.refPrefixCache===void 0){let t=[0];e.forEach((n,s)=>{t.push(t[s]+this.record(n).sequenceLen)}),this.refPrefixCache=t}return this.refPrefixCache}orderedMatches(e,t){let n=this.refIndex(t),s=new Int32Array(e.length),o=new Int32Array(e.length),r=0,i=-1;for(let h=0;h<e.length;h++){let c=n.get(e[h]);if(c){let d=qn(c,i);if(d===void 0)return;s[r]=h,o[r]=d,r+=1,i=d}}return{pathAt:s,refAt:o,count:r}}pathLen(e){let t=0;for(let n of e)t+=this.record(n).sequenceLen;return t}prefixMatches(e,t){let n=0,s=0,o=0,r=0,i=0;for(;s<e.length&&o<t.length;){let h=this.record(e[s]).sequence,c=this.record(t[o]).sequence;for(;r<h.length&&i<c.length;){if(h[r]!==c[i])return n;r+=1,i+=1,n+=1}r===h.length&&(s+=1,r=0),i===c.length&&(o+=1,i=0)}return n}suffixMatches(e,t){let n=0,s=0,o=0,r=0,i=0;for(;s<e.length&&o<t.length;){let h=this.record(e[e.length-s-1]).sequence,c=this.record(t[t.length-o-1]).sequence;for(;r<h.length&&i<c.length;){if(h[h.length-r-1]!==c[c.length-i-1])return n;r+=1,i+=1,n+=1}r===h.length&&(s+=1,r=0),i===c.length&&(o+=1,i=0)}return n}align(e,t,n){let s=this.pathLen(e),o=this.pathLen(t),r=this.prefixMatches(e,t),i=this.suffixMatches(e,t);r+i>s&&(i=s-r),r+i>o&&(i=o-r),K(n,"M",r),hn(n,s-r-i,o-r-i),K(n,"M",i)}sharedWeight(e,t){let n=this.refIndex(t),s=0;for(let o of e)n.has(o)&&(s+=this.record(o).sequenceLen);return s}editsAgainst(e,t){let n=this.orderedMatches(e,t);n?this.stats.orderedAlignments+=1:this.stats.lcsAlignments+=1;let s=n??Fn(Ut(e,t,f=>this.record(f).sequenceLen)[0]),o=[],r=this.refPrefix(t),i=(f,p,y,g)=>{f===p?K(o,"D",r[g]-r[y]):y===g?K(o,"I",this.pathLen(e.slice(f,p))):this.align(e.slice(f,p),t.slice(y,g),o)},h=0,c=0,d=0;for(let f=0;f<s.count;f++){let p=s.pathAt[f],y=s.refAt[f];(c!==p||d!==y)&&i(c,p,d,y);let g=this.record(e[p]).sequenceLen;K(o,"M",g),h+=g,c=p+1,d=y+1}return i(c,e.length,d,t.length),{edits:o,matched:h,matches:s}}alignment(e){let t=this.paths[e];if(this.refId===void 0||e===this.refId||!t)return;let n=this.paths[this.refId].path,s;if(Oe(n)&&(t.identity===void 0||!Oe(Be(t.path))))s={...this.editsAgainst(t.path,n),flipped:!1};else{let o=Be(t.path),r=this.sharedWeight(t.path,n);if(this.sharedWeight(o,n)===0)s={...this.editsAgainst(t.path,n),flipped:!1};else if(r===0)s={...this.editsAgainst(o,n),flipped:!0};else{let h=this.editsAgainst(t.path,n),c=this.editsAgainst(o,n);s=c.matched>h.matched?{...c,flipped:!0}:{...h,flipped:!1}}}return s}alignToRef(e){return this.settleDeferred(),this.alignment(e)?.edits.map(([t,n])=>`${n}${t}`).join("")}alignments(){this.settleDeferred();let e=this.referenceInterval;if(this.refId===void 0||!e)throw new Error("Alignments need a reference path");let t=this.paths[this.refId].path,n=this.refPrefix(t)[t.length],s=(d,f,p,y)=>{let g=Gn(d),l=this.paths[p[0]],b=this.paths[p[p.length-1]],x=l.identity,P=x?.orientation==="forward",[E,R]=P?[l,b]:[b,l];return{strand:f,refStart:e.start+g.leading,refEnd:e.start+n-g.trailing,edits:g.edits,weight:l.weight,path:p.flatMap(m=>this.paths[m].path),start:Ge(l,0),pieces:p,soloAligned:y,identity:x===void 0?void 0:{pathHandle:x.pathHandle,name:x.name,hapStart:x.name.fragment+E.identity.hapStart,hapEnd:x.name.fragment+R.identity.hapEnd,walkForward:P}}},o=d=>d.soloAligned.reduce((f,p)=>f+p,0),r=d=>d.pieces.reduce((f,p)=>f+this.paths[p].len,0),i=d=>2*o(d)>=r(d),h=d=>{let f=d[0],p=d[d.length-1],y=f.identity.walkForward;if(d.some((k,j)=>k.strand!==f.strand||k.identity.walkForward!==y||j>0&&k.identity.hapStart<d[j-1].identity.hapEnd))return;let g=y?d:[...d].reverse(),l=g.flatMap(k=>k.pieces),b=g.flatMap(k=>k.soloAligned),x=f.strand==="+"!==y,P=l.map(k=>this.paths[k]),E=P.slice(1).map((k,j)=>{let X=P[j].identity;return y?k.identity.hapStart-X.hapEnd:X.hapStart-k.identity.hapEnd}),R=x?[...P].reverse():P,m=x?[...E].reverse():E,I=R.flatMap(k=>x?Be(k.path):k.path),{edits:$}=this.editsAgainst(I,t),F=an($,R.map(k=>k.len)),_=new Map((x?[...l].reverse():l).map((k,j)=>[k,F[j]])),D=k=>2*k.pieces.reduce((j,X)=>j+_.get(X),0)>=o(k);if(!D(f)||!D(p))return;let C=[],H=0;return R.slice(0,-1).forEach((k,j)=>{H+=k.len,C.push([H,m[j]])}),s(Qn($,C),f.strand,l,b)},c=[];return this.paths.forEach((d,f)=>{if(f===this.refId)return;let{edits:p,flipped:y}=this.alignment(f),g=d.identity,l=g?g.orientation==="forward"!==y:!y;c.push(s(p,l?"+":"-",[f],an(p,[d.len])))}),jn(c,i,h).map(d=>{let{edits:f,identity:p,pieces:y,soloAligned:g,...l}=d,b={...l,cigar:Kn(f)};return p?{...b,resolved:!0,name:p.name,label:fe({...p.name,fragment:p.hapStart,end:p.hapEnd}),pathHandle:p.pathHandle,hapStart:p.hapStart,hapEnd:p.hapEnd}:{...b,resolved:!1}})}pairAlignments(e){let{target:t,query:n,...s}=e,o=this.paths.flatMap(d=>{let{identity:f}=d;return f?[{name:f.name,start:f.name.fragment+f.hapStart,steps:Ke(d,f)}]:[]}),r=d=>f=>f.sample===d.sample&&f.haplotype===d.haplotype,i=r(t),h=n?r(n):d=>!i(d),c=d=>this.record(ce(d,"forward")).sequence;return o.filter(d=>i(d.name)).flatMap(d=>o.filter(f=>h(f.name)).flatMap(f=>Wt({...s,query:f.steps,target:d.steps,sequenceOf:c}).map(p=>({query:f.name,queryStart:f.start+p.queryStart,queryEnd:f.start+p.queryEnd,strand:p.strand,target:d.name,targetStart:d.start+p.targetStart,targetEnd:d.start+p.targetEnd,cigar:Vt(p.edits),matches:p.edits.reduce((y,[g,l])=>y+(g==="="?l:0),0),columns:p.edits.reduce((y,[,g])=>y+g,0),sharedBases:p.sharedBases}))))}canonicalEdges(e){let t=[];for(let n of["forward","reverse"]){let s=ce(e,n);for(let o of this.record(s).successors())this.hasHandle(o)&&He(s,o)&&t.push([n==="reverse"?1:0,N(o),Q(o)?1:0])}return t.sort((n,s)=>n[0]-s[0]||n[1]-s[1]||n[2]-s[2]),t.filter((n,s)=>s===0||n[0]!==t[s-1][0]||n[1]!==t[s-1][1]||n[2]!==t[s-1][2])}async stableName(){let e=new TextEncoder,t=[];for(let n of this.sortedHandles())if(!Q(n)){let s=N(n),o=`S	${s}	${this.record(n).sequence}
+import{a as ce,b as N,c as Ee,d as Q,e as ee,f as Ft,g as Ue,h as We,i as qt,j as zt,k as He,l as Oe,m as Pe,n as Dt,o as jt,p as Ut,q as Wt,r as Vt}from"./chunk-M2D7NUOY.js";import{a as _t,g as Tt}from"./chunk-NEWN556N.js";import{c as Ot}from"./chunk-AJX6ZXCI.js";import{a as Ct,g as Bt}from"./chunk-KFZWGL76.js";var Ln=4096;function pt(a){let e=[];for(let t of a){let n=e[e.length-1];n&&t-n[1]<=Ln?n[1]=t:e.push([t,t])}return e}var Hn=32768,Gt={mostChosenPaths:32},lt=class{byNode=new Map;get(e){return this.byNode.get(e.node)?.get(e.offset)}set(e,t){let n=this.byNode.get(e.node);n||(n=new Map,this.byNode.set(e.node,n)),n.set(e.offset,t)}},re=class extends Error{};function Ve(a,e,t,n){return a==="forward"?e+t:e-n}function Qt(a,e,t,n){return a==="forward"?e-n:e+t}function Kt(a){return Pe(ee(a.handles[a.handles.length-1]),ee(a.handles[0]))}function Ce(a){return`${a.pathHandle}:${a.hapStart}:${a.hapEnd}`}async function Zt(a){let{db:e,records:t,signal:n}=a,s=performance.now(),o=()=>{let w=performance.now(),S=w-s;return s=w,S},r={spacing:await e.haplotypeAnchorSpacing(),anchors:void 0,anchorsRead:0,chosenPaths:0,scans:[],scanRows:0,strays:void 0,pieces:0,sources:{reference:0,section:0,stray:0,chain:0,twin:0},walks:{},twins:{tried:0,found:0},graphFetches:0,fallback:void 0,ms:{scan:0,walks:0,check:0,twins:0}},i=(w,S)=>{let A=`${w}: ${S}`;r.walks[A]=(r.walks[A]??0)+1},h=await e.haplotypeSampleInterval()??4096,c=new Map,d=async w=>{let S=t.get(w)??c.get(w);if(S)return S;let A=await e.getRecord(w);if(r.graphFetches+=1,!A)throw new Error(`Node record ${w} is missing from the database`);return c.set(w,A),A},f=w=>t.get(w).sequenceLen,p=await e.pathsByHandle(),y=w=>{let S=p.get(w);return S!==void 0&&a.keep(S.name)},g=[],l=new lt,b=new Map,x=new Set,P=new Set,E=async w=>{let S=(await d(w.node)).gbwt().lf(w.offset);return S===void 0||S.node===0?void 0:S},R=async(w,S)=>{let A=(await d(ee(w.node))).gbwt().predecessorAt(w.offset);if(A===void 0||S!==void 0&&!S.has(A))return;let M=(await d(A)).gbwt().offsetTo(w);if(M===void 0)throw new Error(`No offset in ${A} leads to ${w.node}:${w.offset}`);return{node:A,offset:M}},m=(w,S,A,M)=>{let B=A.map(W=>W.pos.node),U=A.map(W=>W.pos.offset),J=0;for(let W of B)J+=f(W);let O=S==="forward"?A[0].left:A[A.length-1].left,L=g.length;g.push({pathHandle:w,orientation:S,handles:B,offsets:U,len:J,hapStart:O,hapEnd:O+J,canonical:Pe(B[0],B[B.length-1]),source:M});for(let W of A)l.set(W.pos,L);let G=b.get(w);return G?G.push(L):b.set(w,[L]),L},I=async(w,S,A,M)=>{let B=[],U=w;for(;;){n?.throwIfAborted();let O=await R(U.pos,t);if(!O)break;U={pos:O,left:Qt(A,U.left,f(U.pos.node),f(O.node))},B.push(U)}B.reverse();let J=[w];for(U=w;;){n?.throwIfAborted();let O=await E(U.pos);if(!O||!t.has(O.node))break;U={pos:O,left:Ve(A,U.left,f(U.pos.node),f(O.node))},J.push(U)}return m(S,A,[...B,...J],M)},$=async(w,S,A,M)=>g[l.get(w.pos)??await I(w,S,A,M)],F=w=>{let S=w.handles[w.handles.length-1];return{pos:{node:S,offset:w.offsets[w.offsets.length-1]},left:w.orientation==="forward"?w.hapEnd-f(S):w.hapStart}},_=w=>{let S=w.handles[0];return{pos:{node:S,offset:w.offsets[0]},left:w.orientation==="forward"?w.hapStart:w.hapEnd-f(S)}},D=await I({pos:a.referencePos,left:a.referenceLeft},a.referenceHandle,"forward","reference"),C=g[D],H=()=>{if(r.fallback!==void 0)return{reference:C,pieces:[],stats:r};let w=new Map;g.forEach((A,M)=>{M!==D&&w.set(Ce(A),[...w.get(Ce(A))??[],A])});let S=[];for(let A of w.values()){let M=new Set;for(let B of A)B.canonical&&!M.has(B.orientation)&&(M.add(B.orientation),S.push(B),r.sources[B.source]+=1)}return r.sources.reference=1,r.pieces=S.length+1,{reference:C,pieces:S,stats:r}},k=async(w,S)=>{let A=S?x:P,M=S?P:x,B=w;for(;;){if(A.has(B))return;A.add(B);let U=g[B],J=S?F(U):_(U),O=0,L;for(;L===void 0;){n?.throwIfAborted();let G=S?await E(J.pos):await R(J.pos);if(!G){L="endmarker";break}let W=(await d(J.pos.node)).sequenceLen,ue=(await d(G.node)).sequenceLen,se=S?Ve(U.orientation,J.left,W,ue):Qt(U.orientation,J.left,W,ue);if(t.has(G.node)){let Y=l.get(G);Y===void 0?(B=await I({pos:G,left:se},U.pathHandle,U.orientation,"chain"),M.add(B),L="landed"):(M.add(Y),L="merge")}else O>Hn?L="bound":(O+=ue,J={pos:G,left:se})}if(i("chain",L),L!=="landed")return}},j=async w=>{if(a.context>w.context)throw new re(`the context of ${a.context} bp exceeds the ${w.context} bp the haplotype index's stray rows cover`);let S=r.spacing;if(S===void 0)throw new re("the haplotype index has no anchors");let{bin:A,bound:M}=w,{fills:B,inserted:U}=a.snarls;if(a.snarls.mode==="overlapping"&&B.length>0)throw new re("the haplotype index's stray rows cover contained snarls only");for(let u of B){if(u.inserted>0&&u.low===u.high)throw new re(`the haplotype index's stray rows leave out the snarl bounded by node ${u.low} at both ends`);if(u.inserted>0&&(w.snarlNodes===void 0||u.nodes>w.snarlNodes))throw new re(w.snarlNodes===void 0?"the haplotype index's stray rows leave snarls out":`a snarl of ${u.nodes} nodes exceeds the ${w.snarlNodes} the haplotype index's stray rows cover`)}let J=Math.floor(a.window.start/A),O=Math.floor((a.window.end-1)/A),L=J*A,G=(O+1)*A,W=new Map,ue=async(u,v)=>{let z=await e.haplotypeAnchorsBetween(a.referenceHandle,u*S,v*S);for(let T of z)W.set(T.anchorOffset/S,T)},se=Math.max(0,Math.floor((L-M)/S)-1),Y=Math.ceil((G+M)/S)+1,[{listed:De,strays:ae}]=await Promise.all([e.haplotypeBinData(a.referenceHandle,J,O),ue(se,Y)]);for(let u of t.keys()){let v=N(u);if(!Q(u)&&!De(v)&&!U.has(v))throw new re(`the haplotype index lists node ${v} of the subgraph in no bin that the window touches`)}r.scans=pt([...t.keys()].sort((u,v)=>u-v));let ie=Promise.all(r.scans.map(([u,v])=>e.haplotypeSamplesInRange(u,v)));for(ie.catch(()=>{});se>0&&(W.get(se)?.pathOffset??Number.POSITIVE_INFINITY)>=L-M;)se-=1,await ue(se,se);for(;W.has(Y)&&W.get(Y).pathOffset<=G+M;)Y+=1,await ue(Y,Y);let pe=[...W.keys()].sort((u,v)=>u-v),ye=W.get(pe[0]??-1);if(!ye)throw new re("the haplotype index has no anchors on this path");let he=u=>W.get(u).pathOffset,Ne=new Map;for(let u of pe){let v=N(W.get(u).node);Ne.set(v,[...Ne.get(v)??[],u])}let ct=[...Ne.keys()],Et=ct.map(u=>W.get(Ne.get(u)[0]).visits);if(!Et[ct.indexOf(N(ye.node))].some(u=>u.pathHandle===a.referenceHandle&&u.orientation==="forward"&&u.pathOffset===ye.pathOffset))throw new Error(`The haplotype index has no anchor row for the reference path ${a.referenceHandle} at offset ${ye.pathOffset} (node ${N(ye.node)}); it does not match this graph`);let kt=pe.filter(u=>he(u)<=a.window.start),$n=pe.filter(u=>he(u)>=a.window.end);r.anchors=[he(kt[kt.length-1]??pe[0]),he($n[0]??pe[pe.length-1])],r.anchorsRead=pe.length;let dt=new Map,vt=new Set;if(ct.forEach((u,v)=>{let z=Ne.get(u),T=z.length===1?z[0]:void 0;for(let q of Et[v])vt.add(q.pathHandle),q.orientation==="forward"&&y(q.pathHandle)&&dt.set(q.pathHandle,[...dt.get(q.pathHandle)??[],{k:T,row:q}])}),r.chosenPaths=[...vt].filter(y).length,r.chosenPaths>Gt.mostChosenPaths)throw new re(`${r.chosenPaths} chosen paths pass the anchors, more than ${Gt.mostChosenPaths}`);let je=[],Ie=Number.POSITIVE_INFINITY,be=0;for(let[u,v]of dt){v.sort((z,T)=>z.row.pathOffset-T.row.pathOffset);for(let z=0;z+1<v.length;z++){let T=v[z],q=v[z+1];if(T.k===void 0||q.k===void 0||Math.abs(T.k-q.k)!==1)continue;let[Z,te]=he(T.k)<=he(q.k)?[T,q]:[q,T],ne=he(Z.k),oe=he(te.k);ne<G&&oe>=L?(je.push({pathHandle:u,from:T.row,to:q.row}),Ie=Math.min(Ie,ne-M),be=Math.max(be,oe+M)):ne>=G&&ne-G<=M?(je.push({pathHandle:u,from:Z.row,to:void 0}),Ie=Math.min(Ie,ne-M),be=Math.max(be,ne+M)):oe<L&&L-oe<=M&&(je.push({pathHandle:u,from:te.row,to:void 0}),Ie=Math.min(Ie,oe-M),be=Math.max(be,oe+M))}}let Rn=new Set(B.map(u=>`${u.low}:${u.high}`)),Nn=ae.filter(u=>y(u.pathHandle)&&(u.snarl===void 0||Rn.has(`${u.snarl[0]}:${u.snarl[1]}`))).sort((u,v)=>u.pathHandle-v.pathHandle||u.pathStart-v.pathStart);r.strays={bins:O-J+1,rows:ae.length,walked:0,outsideBp:0},be>0&&await a.prefetchReferenceRange(a.referenceHandle,Math.max(0,Ie),be+1),r.ms.scan=o();let Pt=8*S+2*(a.window.end-a.window.start),At=r.strays,Me=0,$t=u=>{if(At.outsideBp+=u,Me+=u,Me>Pt)throw new re(`a walk of a chosen path near the window went past its cap of ${Pt} bp`)},ft=new Map,Rt=(u,v,z)=>(ft.get(u)??[]).some(([T,q])=>T<=v&&z<q),Nt=(u,v,z)=>{ft.set(u,[...ft.get(u)??[],[v,z]])},Mt=async(u,v,z,T,q)=>{let Z=v,te=z,ne=te;for(;Z&&te<=T;){n?.throwIfAborted();let oe;if(t.has(Z.node)){let Le=await $({pos:Z,left:te},u,"forward",q),Ht=F(Le);Z=Ht.pos,te=Ht.left,oe=f(Z.node),ne=Math.max(ne,Le.hapEnd)}else oe=(await d(Z.node)).sequenceLen,$t(oe),ne=Math.max(ne,te+oe);Z=await E(Z),te+=oe}return ne},Mn=async(u,v,z,T)=>{let q={pos:v,left:z},Z=z;for(;q.left>T;){n?.throwIfAborted();let te=await R(q.pos);if(!te)break;let ne=(await d(te.node)).sequenceLen,oe=q.left-ne;if(t.has(te.node)){let Le=await $({pos:te,left:oe},u,"forward","section");q=_(Le),Z=Math.min(Z,Le.hapStart)}else $t(ne),q={pos:te,left:oe},Z=Math.min(Z,oe)}return Z};for(let{pathHandle:u,from:v,to:z}of je){let T=v.pathOffset,q=(z??v).pathOffset+M;if(Rt(u,T-M,q))continue;let Z={node:v.node,offset:v.offset};Me=0;let te=await Mt(u,Z,T,q,"section");Me=0;let ne=await Mn(u,Z,T,T-M);Nt(u,Math.min(ne,T-M),Math.max(te,q+1)),i(z?"section":"visit",z?"past the far anchor":"bound")}for(let u of Nn){if(Rt(u.pathHandle,u.pathStart,u.pathEnd))continue;Me=0;let v=await Mt(u.pathHandle,{node:u.node,offset:u.offset},u.pathStart,u.pathEnd,"stray");Nt(u.pathHandle,u.pathStart,Math.max(v,u.pathEnd+1)),At.walked+=1}r.ms.walks=o();let Lt=[];for(let u of await ie)for(let v of u)if(r.scanRows+=1,t.has(v.node)&&y(v.pathHandle)){if(!(b.get(v.pathHandle)??[]).some(z=>{let T=g[z];return T.hapStart<=v.pathOffset&&v.pathOffset<T.hapEnd}))throw new re(`chosen path ${v.pathHandle} has a sample at ${v.pathOffset} on the window's nodes that no walk reached`);v.orientation==="reverse"&&Lt.push(v)}for(let u of Lt)await $({pos:{node:u.node,offset:u.offset},left:u.pathOffset},u.pathHandle,"reverse","twin");r.ms.check=o()},X=async()=>{let w=new Map,S=O=>{let L=Ce(O),G=w.get(L);G?G.add(O.orientation):w.set(L,new Set([O.orientation]))},A=0,M=()=>{for(;A<g.length;A++)S(g[A])};M();let B=O=>(w.get(Ce(O))?.size??0)>1,U=2*h,J=(O,L)=>L===D?y(a.referenceHandle)&&Kt(O):!O.canonical||Kt(O);for(let O=0;O<g.length;O++){let L=g[O];if(B(L)||!J(L,O))continue;r.twins.tried+=1;let G=L.orientation==="forward"?"reverse":"forward",W=F(L),ue=0,se;for(;!se&&ue<=U;){n?.throwIfAborted();let ae=await E(W.pos);if(!ae)break;let ie=(await d(ae.node)).sequenceLen,pe=Ve(L.orientation,W.left,(await d(W.pos.node)).sequenceLen,ie),ye=ee(ae.node);se=(await e.haplotypeSamplesInRange(ye,ye)).find(he=>he.pathHandle===L.pathHandle&&he.orientation===G&&he.pathOffset===pe),ue+=ie,W={pos:ae,left:pe}}let Y=se&&{pos:{node:se.node,offset:se.offset},left:se.pathOffset},De=0;for(;Y&&!B(L)&&De<=U+L.len;){if(n?.throwIfAborted(),t.has(Y.pos.node)){let ae=await $(Y,L.pathHandle,G,"twin"),ie=g.indexOf(ae);await k(ie,!0),await k(ie,!1),M(),Y=F(ae)}if(!B(L)){let ae=(await d(Y.pos.node)).sequenceLen;De+=ae;let ie=await E(Y.pos);Y=ie?{pos:ie,left:Ve(G,Y.left,ae,(await d(ie.node)).sequenceLen)}:void 0}}if(M(),!B(L))throw new re(`piece ${Ce(L)} was found in one orientation where extractPaths keeps the other`);r.twins.found+=1}r.ms.twins=o()};try{let w=await e.haplotypeStrayOptions();if(w===void 0)throw new re("the haplotype index has no stray rows; gbz-haplotype-index 0.2.0 writes them");await j(w),await X()}catch(w){if(!(w instanceof re))throw w;r.fallback=w.message}return H()}function Xt(a,e){return a.handles[0]-e.handles[0]||a.offsets[0]-e.offsets[0]}var On=Uint32Array.from([1116352408,1899447441,3049323471,3921009573,961987163,1508970993,2453635748,2870763221,3624381080,310598401,607225278,1426881987,1925078388,2162078206,2614888103,3248222580,3835390401,4022224774,264347078,604807628,770255983,1249150122,1555081692,1996064986,2554220882,2821834349,2952996808,3210313671,3336571891,3584528711,113926993,338241895,666307205,773529912,1294757372,1396182291,1695183700,1986661051,2177026350,2456956037,2730485921,2820302411,3259730800,3345764771,3516065817,3600352804,4094571909,275423344,430227734,506948616,659060556,883997877,958139571,1322822218,1537002063,1747873779,1955562222,2024104815,2227730452,2361852424,2428436474,2756734187,3204031479,3329325298]),we=(a,e)=>a>>>e|a<<32-e;function Jt(a){let e=Math.ceil((a.length+9)/64),t=new Uint8Array(e*64);t.set(a),t[a.length]=128;let n=new DataView(t.buffer),s=a.length*8;n.setUint32(t.length-8,Math.floor(s/2**32)),n.setUint32(t.length-4,s>>>0);let o=Uint32Array.from([1779033703,3144134277,1013904242,2773480762,1359893119,2600822924,528734635,1541459225]),r=new Uint32Array(64);for(let c=0;c<e;c++){for(let P=0;P<16;P++)r[P]=n.getUint32(c*64+P*4);for(let P=16;P<64;P++){let E=r[P-15],R=r[P-2],m=we(E,7)^we(E,18)^E>>>3,I=we(R,17)^we(R,19)^R>>>10;r[P]=r[P-16]+m+r[P-7]+I}let d=o[0],f=o[1],p=o[2],y=o[3],g=o[4],l=o[5],b=o[6],x=o[7];for(let P=0;P<64;P++){let E=we(g,6)^we(g,11)^we(g,25),R=g&l^~g&b,m=x+E+R+On[P]+r[P]|0,I=we(d,2)^we(d,13)^we(d,22),$=d&f^d&p^f&p;x=b,b=l,l=g,g=y+m|0,y=p,p=f,f=d,d=m+I+$|0}[d,f,p,y,g,l,b,x].forEach((P,E)=>{o[E]=o[E]+P})}let i=new Uint8Array(32),h=new DataView(i.buffer);for(let c=0;c<8;c++)h.setUint32(c*4,o[c]);return i}function Yt(a,e){let t=new Map;if(a!==void 0)for(let n of a.split(";")){let s=n.split(","),[o,r]=s;if(s.length!==2||!o||!r)throw new Error(`Invalid ${e} relationship: ${n}`);let i=t.get(o);i||(i=new Set,t.set(o,i)),i.add(r)}return t}function nn(a){return{name:a.get("pggname"),subgraph:Yt(a.get("subgraph"),"subgraph"),translation:Yt(a.get("translation"),"translation")}}function en(a,e){for(let[t,n]of e){let s=a.get(t);s||(s=new Set,a.set(t,s));for(let o of n)s.add(o)}}function sn(a,e){let t={name:a,subgraph:new Map,translation:new Map};return e.name!==void 0&&(t.subgraph.set(a,new Set([e.name])),en(t.subgraph,e.subgraph),en(t.translation,e.translation)),t}function tn(a){return[...a.entries()].sort(([e],[t])=>e<t?-1:e>t?1:0).flatMap(([e,t])=>[...t].sort().map(n=>[e,n]))}function on(a){let e=[];a.name!==void 0&&e.push(`H	NM:Z:${a.name}`);for(let[t,n]of tn(a.subgraph))e.push(`H	SG:Z:${t},${n}`);for(let[t,n]of tn(a.translation))e.push(`H	TL:Z:${t},${n}`);return e}async function rn(a){let e=a.reduce((r,i)=>r+i.length,0),t=new Uint8Array(e),n=0;for(let r of a)t.set(r,n),n+=r.length;let s=globalThis.crypto?.subtle;return[...s?new Uint8Array(await s.digest("SHA-256",t)):Jt(t)].map(r=>r.toString(16).padStart(2,"0")).join("")}var Cn="_gbwt_ref";function fe(a){let e=`${a.sample}#${a.haplotype}#${a.contig}`;return a.end===void 0?e:`${e}[${a.fragment}-${a.end}]`}var Bn=/^([^#]+)#(\d+)#([^#]+?)(?:\[\d+-\d+\])?$/,_n=/^([^#]+?)(?:\[\d+-\d+\])?$/;function Tn(a){let e=Bn.exec(a);if(e)return{sample:e[1],haplotype:Number(e[2]),contig:e[3]};let t=_n.exec(a);if(t)return{contig:t[1]};throw new Error(`"${a}" is not a path name; expected "sample#haplotype#contig" or a bare contig`)}function Ae(a){return typeof a=="string"?Tn(a):a}function $e(a,e){return{sample:a.sample??Cn,contig:a.contig,haplotype:a.haplotype??0,fragment:e}}var le=class extends Error{name="SubgraphLimitError";limit;windowBp;walkedBp;constructor(e,t){super(t===void 0?`Subgraph size limit of ${e} nodes exceeded`:`Subgraph size limit of ${e} nodes exceeded ${t.walkedBp} bp into a ${t.windowBp} bp window`),this.limit=e,this.windowBp=t?.windowBp,this.walkedBp=t?.walkedBp}};function ut(a,e){return a[0]<e[0]||a[0]===e[0]&&(a[1]<e[1]||a[1]===e[1]&&a[2]<e[2])}var _e=class{heap=[];push(e,t,n){let s=this.heap;s.push([e,t,n]);let o=s.length-1;for(;o>0;){let r=o-1>>1;if(ut(s[o],s[r]))[s[o],s[r]]=[s[r],s[o]],o=r;else break}}pop(){let e=this.heap,t=e[0],n=e.pop();if(e.length>0&&n!==void 0){e[0]=n;let s=0;for(;;){let o=2*s+1,r=o+1,i=s;if(o<e.length&&ut(e[o],e[i])&&(i=o),r<e.length&&ut(e[r],e[i])&&(i=r),i===s)break;[e[s],e[i]]=[e[i],e[s]],s=i}}return t}get size(){return this.heap.length}};function Fn(a){let e=new Int32Array(a.length),t=new Int32Array(a.length);return a.forEach(([n,s],o)=>{e[o]=n,t[o]=s}),{pathAt:e,refAt:t,count:a.length}}function qn(a,e){let t=0,n=a.length;for(;t<n;){let s=t+n>>1;a[s]>e?n=s:t=s+1}return a[t]}function ke(a){return`${a.node}:${a.offset}`}function Be(a){return a.map(e=>ee(e)).reverse()}function zn(a,e){let t=e.identity.hapStart-a.identity.hapEnd,n=a.strand==="+"?e.refStart-a.refEnd:a.refStart-e.refEnd;return a.strand===e.strand&&t>=0&&n>=0?{insertion:t,deletion:n}:void 0}function Dn(a,e,t){let[n,s]=a.strand==="+"?[a,e]:[e,a],o=n.edits.map(([c,d])=>[c,d]);hn(o,t.insertion,t.deletion);for(let[c,d]of s.edits)K(o,c,d);let r=a.identity.walkForward,[i,h]=r?[a,e]:[e,a];return{strand:a.strand,refStart:n.refStart,refEnd:s.refEnd,edits:o,weight:void 0,path:[...i.path,...h.path],start:i.start,pieces:[...i.pieces,...h.pieces],soloAligned:[...i.soloAligned,...h.soloAligned],identity:{pathHandle:a.identity.pathHandle,name:a.identity.name,hapStart:a.identity.hapStart,hapEnd:e.identity.hapEnd,walkForward:r}}}function jn(a,e,t){if(a.some(r=>r.weight!==void 0))return a;let n=new Map;a.forEach((r,i)=>{if(r.identity){let h=n.get(r.identity.pathHandle);h?h.push(i):n.set(r.identity.pathHandle,[i])}});let s=new Map,o=new Set;for(let r of n.values()){r.sort((d,f)=>a[d].identity.hapStart-a[f].identity.hapStart);let i=r[0],h=a[i],c=[];for(let d of r.slice(1)){let f=a[d],p=c.length===0?zn(h,f):void 0;if(p){h=Dn(h,f,p),o.add(d);continue}if(!e(f)){c.push(d);continue}let y=e(h)?t([h,...c.map(g=>a[g]),f]):void 0;if(y){h=y;for(let g of[...c,d])o.add(g)}else s.set(i,h),i=d,h=f;c=[]}s.set(i,h)}return a.flatMap((r,i)=>o.has(i)?[]:[s.get(i)??r])}function Ge(a,e){return{node:a.path[e],offset:a.offsets[e]}}var Un=32768;function Wn(a){let e=[...a].sort((n,s)=>n-s),t=[];for(let n of e){let s=t[t.length-1];s&&n-s[1]<=Un?s[1]=n:t.push([n,n])}return t}var Te=class a{records=new Map;paths=[];twinStarts=new Set;twinDeferred=!1;unsettled;refId;refPath;refHandle;refInterval;refIndexCache;refPrefixCache;walkedBp;snarlMode="none";snarlFills=[];snarlNodes=new Set;stats={orderedAlignments:0,lcsAlignments:0,snarls:{fills:0,inserted:0},identificationSteps:0,identificationFetches:0,identification:{interval:0,scans:[],windowSamples:0,fragmentLengths:[],companionSeeks:0,companionMisses:0,graphLookups:0,graphFetches:0,chains:[]},keep:void 0};db;limit;signal;constructor(e,t){this.db=e,this.limit=t.limit,this.signal=t.signal}static create(e,t={}){return new a(e,t)}get nodeCount(){return this.records.size/2}get pathCount(){return this.settleDeferred(),this.paths.length}get referenceInterval(){return this.refInterval&&this.refPath?{name:this.refPath,start:this.refPath.fragment+this.refInterval[0],end:this.refPath.fragment+this.refInterval[1]}:void 0}hasNode(e){return this.records.has(ce(e,"forward"))}hasHandle(e){return this.records.has(e)}record(e){let t=this.records.get(e);if(!t)throw new Error(`Subgraph has no record for handle ${e}`);return t}sortedHandles(){return[...this.records.keys()].sort((e,t)=>e-t)}async addNode(e){if(this.signal?.throwIfAborted(),this.limit!==void 0&&this.nodeCount>=this.limit)throw new le(this.limit);let t=await this.db.getRecord(ce(e,"forward")),n=await this.db.getRecord(ce(e,"reverse"));if(!t||!n)throw new Error(`Node ${e} does not exist in the graph`);this.records.set(t.handle,t),this.records.set(n.handle,n)}async ensureNode(e){this.hasNode(e)||await this.addNode(e)}clearPaths(){this.paths=[],this.twinStarts.clear(),this.twinDeferred=!1,this.unsettled=void 0,this.refId=void 0,this.refPath=void 0,this.refHandle=void 0,this.refInterval=void 0,this.refIndexCache=void 0,this.refPrefixCache=void 0}async pathPosition(e){let t=await this.db.findPath(e);if(!t)throw new Error(`Cannot find a path covering offset ${e.fragment} of ${fe(e)}`);if(!t.isIndexed)throw new Error(`The fragment of ${fe(t.name)} at ${t.name.fragment} has not been indexed for random access`);let n=e.fragment-t.name.fragment,s=await this.db.indexedPosition(t.handle,n);if(!s)throw new Error(`The fragment of ${fe(t.name)} at ${t.name.fragment} has not been indexed for random access`);return this.findPathPosition(t,n,s.pathOffset,s.pos)}async findPathPosition(e,t,n,s){let o=n,r=s;for(;;){await this.ensureNode(N(r.node));let i=this.record(r.node);if(o+i.sequenceLen>t)return{position:{seqOffset:t,handle:r.node,nodeOffset:t-o,gbwtOffset:r.offset},name:e.name,handle:e.handle};o+=i.sequenceLen;let h=i.gbwt().lf(r.offset);if(!h)throw new Error(`The fragment of ${fe(e.name)} at ${e.name.fragment} does not contain offset ${t}`);r=h}}async aroundPosition(e,t,n){let s=N(e);await this.ensureNode(s);let o=this.record(e),r=Ee(e),i=new _e;return i.push(t,s,Ue(r)),i.push(o.sequenceLen-t-1,s,We(r)),this.insertContext(i,n)}prefetchReferenceWalk(e,t){return this.prefetchReferenceRange(e.handle,e.position.seqOffset,e.position.seqOffset+t)}async prefetchReferenceRange(e,t,n){let[s,o]=await Promise.all([this.db.indexedPosition(e,t),this.db.indexedPosition(e,n)]);if(s&&o){let r=s.pos.node,i=o.pos.node;if(!await this.db.prefetchRecords([[Math.min(r,i),Math.max(r,i)+1]])){let c=await this.db.indexedPositionsBetween(e,t,n);await this.db.prefetchRecords(Wn(c.map(d=>d.pos.node)).map(([d,f])=>[d,f+2]),!0)}}return s}async aroundInterval(e,t,n){if(!(t>0))throw new Error("Interval length must be greater than 0");this.walkedBp=0;try{return await this.walkInterval(e,t,n)}catch(s){throw s instanceof le&&s.windowBp===void 0?new le(s.limit,{windowBp:t,walkedBp:this.walkedBp}):s}}get referenceWalkedBp(){return this.walkedBp}async walkInterval(e,t,n){let s={node:e.handle,offset:e.gbwtOffset},o=e.nodeOffset,r=t,i=new _e;for(;;){let h=N(s.node),c=Ee(s.node);this.walkedBp=t-r,await this.ensureNode(h);let d=this.record(s.node);if(o>=d.sequenceLen)throw new Error(`Offset ${o} in node ${h} of length ${d.sequenceLen}`);i.push(o,h,Ue(c));let f=d.sequenceLen-o;if(r<=f){i.push(r===f?0:f-r-1,h,We(c));break}i.push(0,h,We(c));let p=d.gbwt().lf(s.offset);if(!p)throw new Error(`No successor for GBWT position (${s.node}, ${s.offset})`);s=p,o=0,r-=f}return this.walkedBp=t,this.insertContext(i,n)}async aroundNodes(e,t){let n=new _e;for(let s of e)await this.ensureNode(s),n.push(0,s,"left"),n.push(0,s,"right");return this.insertContext(n,t)}async insertContext(e,t){this.clearPaths(),this.snarlMode="none",this.snarlFills=[],this.snarlNodes.clear(),this.stats.snarls={fills:0,inserted:0};let n=new Set,s=new Set;for(let r of this.records.keys())s.add(N(r));let o=0;for(;e.size>0;){let[r,i,h]=e.pop(),c=`${i}:${h}`;if(n.has(c))continue;n.add(c),s.delete(i),this.hasNode(i)||(await this.addNode(i),o+=1);let d=Ft(h);if(!n.has(`${i}:${d}`)){let y=this.record(ce(i,qt(h))),g=r+y.sequenceLen-1;g<=t&&e.push(g,i,d)}let f=this.record(ce(i,zt(h))),p=r+1;if(p<=t)for(let y of f.successors()){let g=N(y),l=Ue(Ee(y));n.has(`${g}:${l}`)||e.push(p,g,l)}}for(let r of s)this.records.delete(ce(r,"forward")),this.records.delete(ce(r,"reverse"));return{inserted:o,removed:s.size}}async betweenNodes(e,t){return(await this.fillBetween(e,t)).inserted.length}async fillBetween(e,t){this.clearPaths();let n=[e,ee(t)],s=new Set([N(e),N(t)]),o=[];for(;n.length>0;){let r=n.pop(),i=N(r);this.hasNode(i)||(await this.addNode(i),o.push(i));for(let h of this.record(r).successors()){let c=N(h);s.has(c)||(n.push(h,ee(h)),s.add(c))}}return{inserted:o,nodes:s.size-2}}async extractSnarls(e){let t=0;this.snarlMode=e;for(let[n,s]of await this.overlappingSnarls(e)){let{inserted:o,nodes:r}=await this.fillBetween(n,s),i=N(n),h=N(s);this.snarlFills.push({low:Math.min(i,h),high:Math.max(i,h),nodes:r,inserted:o.length});for(let c of o)this.snarlNodes.add(c);t+=o.length}return this.stats.snarls={fills:this.snarlFills.length,inserted:this.snarlNodes.size},t}async overlappingSnarls(e){let t=[];if(e!=="none"){let n=!1;for(let s of this.sortedHandles()){let o=this.record(s),r=o.next;r!==void 0&&(n=!0,this.hasHandle(r)?He(s,r)&&t.push([s,r]):e==="overlapping"&&this.isSnarlEntryInSubgraph(o)&&t.push([s,r]))}if(!n&&e==="overlapping"&&await this.db.hasChainLinks()){let s=await this.findCoveringSnarl();s&&t.push(s)}}return t}isSnarlEntryInSubgraph(e){let t=e.successors(),n=t.find(s=>this.hasHandle(s));return n===void 0?!1:t.length>1||this.record(ee(n)).successors().length>1}recordReader(e){let t=new Map;return async n=>{let s=this.records.get(n);if(s)return s;let o=t.get(n);if(!o){if(o=await this.db.getRecord(n),e?.(),!o)throw new Error(`Node record ${n} is missing from the database`);t.set(n,o)}return o}}async findCoveringSnarl(){let e=this.recordReader(),t=async h=>{let c=h.successors(),d=c[0];return d===void 0?!1:c.length>1||(await e(ee(d))).successors().length>1},n=async h=>{let c=await e(ee(h));return c.next!==void 0?await t(c)?{kind:"snarl-exit",snarl:[ee(h),c.next]}:{kind:"chain"}:(await e(h)).next!==void 0?{kind:"chain"}:{kind:"regular"}},s=new Set,o=this.sortedHandles().flatMap(h=>this.record(h).successors()),r,i=!1;for(;!i&&o.length>0;){let h=o.shift(),c=N(h);if(!this.hasHandle(h)&&!s.has(c)){s.add(c);let d=await n(h);if(d.kind==="snarl-exit")r=d.snarl,i=!0;else if(d.kind==="chain")i=!0;else for(let f of["forward","reverse"])o.push(...(await e(ce(c,f))).successors())}}return r}extractPaths(e,t){if(this.clearPaths(),t==="none")return;let n=e?.position;this.refPath=e?.name,this.refHandle=e?.handle;let s=this.sortedHandles(),o=s.length,r=new Map;s.forEach((m,I)=>r.set(m,I));let i=new Int32Array(o+1),h=new Int32Array(o),c=[];for(let m=0;m<o;m++){let I=this.record(s[m]),$=I.gbwt().decompressArrays();h[m]=I.sequenceLen,c.push($),i[m+1]=i[m]+$.nodes.length}let d=i[o],f=new Int32Array(d),p=new Int32Array(d),y=new Uint8Array(d);for(let m=0;m<o;m++){let I=c[m];f.set(I.nodes,i[m]),p.set(I.offsets,i[m])}c.length=0;for(let m=0;m<d;m++){let I=r.get(f[m]);I===void 0?f[m]=-1:(f[m]=I,y[i[I]+p[m]]=1)}let g=n===void 0?void 0:r.get(n.handle),l=n?.gbwtOffset,b,x=(m,I,$)=>{let F=[],_=0,D=0,C=-1,H=m,k=I;for(;;){H===g&&k===l&&(C=_),$&&($.push(s[H]),F.push(k)),_+=1,D+=h[H];let j=i[H]+k,X=f[j];if(X<0)break;k=p[j],H=X}return{offsets:F,len:D,refAt:C,last:H}},P=(m,I,$,F)=>{F>=0&&(this.refId=this.paths.length,b=F),this.paths.push({path:m,offsets:I,len:$,weight:void 0,identity:void 0})},E=new Int32Array(o);for(let m=0;m<o;m++){let I=s[m];if(!Q(I)){let $=i[m],F=i[m+1]-$;for(let _=0;_<F;_++)if(y[$+_]===0){let D=[],{offsets:C,len:H,refAt:k,last:j}=x(m,_,D),X=s[j];if(k>=0||Pe(I,X)){if(P(D,C,H,k),!Q(X)){let w=r.get(ee(X));E[w]=E[w]+1}}else this.twinStarts.add(ke({node:I,offset:_}))}}}for(let m=0;m<o;m++){let I=s[m];if(Q(I)){let $=i[m],F=i[m+1]-$,_=0;for(let C=0;C<F;C++)y[$+C]===0&&(_+=1);let D=(g===void 0||b!==void 0)&&_===E[m];for(let C=0;C<F;C++)if(y[$+C]===0){let H=D?void 0:x(m,C,void 0);if(H&&(H.refAt>=0||Pe(I,s[H.last]))){let k=[],{offsets:j,len:X,refAt:w}=x(m,C,k);P(k,j,X,w)}else this.twinStarts.add(ke({node:I,offset:C}))}}}let R=this.refId===void 0?void 0:this.paths[this.refId];if(this.paths.sort((m,I)=>m.path[0]-I.path[0]||m.offsets[0]-I.offsets[0]),R&&(this.refId=this.paths.indexOf(R)),n){if(b===void 0||this.refId===void 0)throw this.clearPaths(),new Error("Could not find the reference path");let m=this.paths[this.refId],I=n.nodeOffset;for(let F of m.path.slice(0,b))I+=this.record(F).sequenceLen;let $=n.seqOffset-I;this.refInterval=[$,$+m.len],m.identity={pathHandle:e.handle,name:e.name,orientation:"forward",hapStart:$,hapEnd:$+m.len}}if(t==="distinct")this.distinctPaths(!0);else if(t==="reference-only"){if(this.refId===void 0)throw new Error("Reference path is required for reference-only output");this.paths=[this.paths[this.refId]],this.refId=0}}distinctPaths(e){let t=this.refId===void 0?void 0:this.paths[this.refId],n=t?.path,s=n&&!Oe(n)?Be(n):void 0,o=c=>s!==void 0&&wt(c,s)===0||Oe(Be(c)),r=e&&this.db.hasHaplotypeIndex;this.twinDeferred=!1,this.paths.sort((c,d)=>wt(c.path,d.path)||c.len-d.len||(c===t?-1:d===t?1:0));let i=[],h;for(let c of this.paths){let d=i[i.length-1],f=r&&c!==t&&o(c.path);this.twinDeferred||=f,d&&wt(d.path,c.path)===0&&!f?d.weight=(d.weight??1)+(c.weight??1):(c===t&&(h=i.length),i.push({...c,weight:c.weight??1}))}this.paths=i,this.refId=h}mergeDistinct(){this.twinDeferred?this.settleDeferred():this.distinctPaths(!1)}settleDeferred(){this.twinDeferred&&(this.unsettled={paths:[...this.paths],refId:this.refId},this.distinctPaths(!1))}dropTwins(){let e=this.refId===void 0?void 0:this.paths[this.refId],t=this.refInterval,n=r=>`${r.pathHandle}:${r.hapStart}-${r.hapEnd}`,s=new Set;e?.identity&&t&&s.add(n({...e.identity,hapStart:t[0],hapEnd:t[1]}));for(let r of this.paths)r!==e&&r.identity?.orientation==="forward"&&s.add(n(r.identity));let o=this.paths.filter(r=>r===e||r.identity?.orientation!=="reverse"||!s.has(n(r.identity)));o.length<this.paths.length&&(this.paths=o,this.refId=e===void 0?void 0:o.indexOf(e)),this.twinDeferred&&this.distinctPaths(!1)}keepHaplotypes(e){if(this.paths.some(r=>r.weight!==void 0))throw new Error("keepHaplotypes needs one walk per haplotype: extract with haplotypes 'all', then call mergeDistinct()");let t=this.paths.filter((r,i)=>i!==this.refId&&r.identity===void 0).length;if(t>0)throw new Error(`${t} of the window's ${this.paths.length} walks have no name, so the haplotypes to keep cannot be told from the rest; call identifyPaths() first, and check that the haplotype index was built for this graph`);let n=this.refId===void 0?void 0:this.paths[this.refId],s=this.paths.filter((r,i)=>i===this.refId||r.identity!==void 0&&e(r.identity.name)),o=new Set;for(let r of s)for(let i of r.path)o.add(N(i));for(let r of[...this.records.keys()])o.has(N(r))||this.records.delete(r);this.paths=s,this.refId=n===void 0?void 0:s.indexOf(n)}async extractChosenPaths(e,t,n,s){this.clearPaths();let o=e.position.seqOffset,r=await Zt({db:this.db,records:this.records,referenceHandle:e.handle,referencePos:{node:e.position.handle,offset:e.position.gbwtOffset},referenceLeft:o-e.position.nodeOffset,window:{start:o,end:o+t},context:s,snarls:{mode:this.snarlMode,fills:this.snarlFills,inserted:this.snarlNodes},keep:n,signal:this.signal,prefetchReferenceRange:(d,f,p)=>this.prefetchReferenceRange(d,f,p)});if(this.stats.keep=r.stats,r.stats.fallback!==void 0)return!1;let i=await this.db.pathsByHandle(),h=d=>({path:d.handles,offsets:d.offsets,len:d.len,weight:void 0,identity:{pathHandle:d.pathHandle,name:d===r.reference?e.name:i.get(d.pathHandle).name,orientation:d.orientation,hapStart:d.hapStart,hapEnd:d.hapEnd}}),c=[r.reference,...r.pieces].sort(Xt);return this.paths=c.map(h),this.refId=c.indexOf(r.reference),this.refPath=e.name,this.refHandle=e.handle,this.refInterval=[r.reference.hapStart,r.reference.hapEnd],this.dropTwins(),!0}async identifyPaths(){if(!this.db.hasHaplotypeIndex)throw new Error("The database has no HaplotypeSamples table; run gbz-haplotype-index on it");this.unsettled&&({paths:this.paths,refId:this.refId}=this.unsettled,this.unsettled=void 0,this.twinDeferred=!0);let e=await this.db.haplotypeSampleGap()??4096,t=pt(this.sortedHandles());if(t.length===0)return;let n=new Map,s=await Promise.all(t.map(([l,b])=>this.db.haplotypeSamplesInRange(l,b)));for(let l of s.flat())n.set(ke(l),l);let o=l=>{let b=0,x=t.length-1;for(;b<x;){let E=b+x+1>>1;t[E][0]<=l?b=E:x=E-1}let P=t[b];return P[0]<=l&&l<=P[1]},r=new Map;this.paths.forEach((l,b)=>{l.path.length>0&&b!==this.refId&&r.set(ke(Ge(l,0)),b)});let i=this.stats.identification;i.interval=e,i.scans=t,i.windowSamples=n.size,this.paths.forEach((l,b)=>{b!==this.refId&&i.fragmentLengths.push(l.len)});let h=this.recordReader(()=>{this.stats.identificationFetches+=1,i.graphFetches+=1}),c=l=>(i.graphLookups+=1,h(l)),d=async(l,b)=>{if(o(l.node))return n.get(ke(l));this.stats.identificationFetches+=1,i.companionSeeks+=1,b.seeks+=1;let x=await this.db.haplotypeSampleAt(l.node,l.offset);return x||(i.companionMisses+=1),x},f=new Map,p=async l=>{let b=f.get(l);if(!b){let x=await this.db.getPath(l);if(!x)throw new Error(`Path ${l} is missing from the database`);b=x.name,f.set(l,b)}return b},y=(l,b,x)=>l.orientation==="forward"?{pathHandle:l.pathHandle,orientation:"forward",base:l.pathOffset-b}:{pathHandle:l.pathHandle,orientation:"reverse",base:l.pathOffset+b+x},g=(l,b)=>l.orientation==="forward"?{pathHandle:l.pathHandle,orientation:"forward",base:l.hapStart-b}:{pathHandle:l.pathHandle,orientation:"reverse",base:l.hapEnd+b};for(let l=0;l<this.paths.length;l++){let b=this.paths[l];if(l===this.refId||b.identity)continue;let x=[],P=new Set,E={fragments:0,steps:0,seeks:0,reentries:0,twinLandings:0,end:"endmarker",pathHandle:void 0};i.chains.push(E);let R,m=0,I=l,$;for(;R===void 0;){if(this.signal?.throwIfAborted(),I!==void 0){if(P.has(I)){E.end="cycle";break}P.add(I);let H=this.paths[I];x.push({index:I,startBp:m}),E.fragments+=1;let k=m;for(let X=0;X<H.path.length;X++){let w=Ge(H,X),S=n.get(ke(w)),A=this.record(w.node).sequenceLen;if(S){R=y(S,k,A);break}k+=A}if(m+=H.len,R){E.end="in-fragment sample";break}let j=Ge(H,H.path.length-1);$=this.record(j.node).gbwt().lf(j.offset),I=void 0}if($===void 0||$.node===0){E.end="endmarker";break}let F=ke($),_=r.get(F);if(_!==void 0){let H=this.paths[_].identity;if(H){R=g(H,m),E.end="identified sibling";break}I=_;continue}this.records.has($.node)&&(E.reentries+=1),this.twinStarts.has(F)&&(E.twinLandings+=1);let D=await d($,E),C=await c($.node);if(D){R=y(D,m,C.sequenceLen),E.end="out-of-window sample";break}if(this.stats.identificationSteps+=1,E.steps+=1,m-x[x.length-1].startBp>4*e+4*C.sequenceLen){E.end="bound";break}m+=C.sequenceLen,$=C.gbwt().lf($.offset)}if(R){E.pathHandle=R.pathHandle;let F=await p(R.pathHandle);for(let{index:_,startBp:D}of x){let C=this.paths[_];C.identity=R.orientation==="forward"?{pathHandle:R.pathHandle,name:F,orientation:"forward",hapStart:R.base+D,hapEnd:R.base+D+C.len}:{pathHandle:R.pathHandle,name:F,orientation:"reverse",hapStart:R.base-D-C.len,hapEnd:R.base-D}}}}this.dropTwins()}refIndex(e){if(this.refIndexCache===void 0){let t=new Map;e.forEach((n,s)=>{let o=t.get(n);o?o.push(s):t.set(n,[s])}),this.refIndexCache=t}return this.refIndexCache}refPrefix(e){if(this.refPrefixCache===void 0){let t=[0];e.forEach((n,s)=>{t.push(t[s]+this.record(n).sequenceLen)}),this.refPrefixCache=t}return this.refPrefixCache}orderedMatches(e,t){let n=this.refIndex(t),s=new Int32Array(e.length),o=new Int32Array(e.length),r=0,i=-1;for(let h=0;h<e.length;h++){let c=n.get(e[h]);if(c){let d=qn(c,i);if(d===void 0)return;s[r]=h,o[r]=d,r+=1,i=d}}return{pathAt:s,refAt:o,count:r}}pathLen(e){let t=0;for(let n of e)t+=this.record(n).sequenceLen;return t}prefixMatches(e,t){let n=0,s=0,o=0,r=0,i=0;for(;s<e.length&&o<t.length;){let h=this.record(e[s]).sequence,c=this.record(t[o]).sequence;for(;r<h.length&&i<c.length;){if(h[r]!==c[i])return n;r+=1,i+=1,n+=1}r===h.length&&(s+=1,r=0),i===c.length&&(o+=1,i=0)}return n}suffixMatches(e,t){let n=0,s=0,o=0,r=0,i=0;for(;s<e.length&&o<t.length;){let h=this.record(e[e.length-s-1]).sequence,c=this.record(t[t.length-o-1]).sequence;for(;r<h.length&&i<c.length;){if(h[h.length-r-1]!==c[c.length-i-1])return n;r+=1,i+=1,n+=1}r===h.length&&(s+=1,r=0),i===c.length&&(o+=1,i=0)}return n}align(e,t,n){let s=this.pathLen(e),o=this.pathLen(t),r=this.prefixMatches(e,t),i=this.suffixMatches(e,t);r+i>s&&(i=s-r),r+i>o&&(i=o-r),K(n,"M",r),hn(n,s-r-i,o-r-i),K(n,"M",i)}sharedWeight(e,t){let n=this.refIndex(t),s=0;for(let o of e)n.has(o)&&(s+=this.record(o).sequenceLen);return s}editsAgainst(e,t){let n=this.orderedMatches(e,t);n?this.stats.orderedAlignments+=1:this.stats.lcsAlignments+=1;let s=n??Fn(Ut(e,t,f=>this.record(f).sequenceLen)[0]),o=[],r=this.refPrefix(t),i=(f,p,y,g)=>{f===p?K(o,"D",r[g]-r[y]):y===g?K(o,"I",this.pathLen(e.slice(f,p))):this.align(e.slice(f,p),t.slice(y,g),o)},h=0,c=0,d=0;for(let f=0;f<s.count;f++){let p=s.pathAt[f],y=s.refAt[f];(c!==p||d!==y)&&i(c,p,d,y);let g=this.record(e[p]).sequenceLen;K(o,"M",g),h+=g,c=p+1,d=y+1}return i(c,e.length,d,t.length),{edits:o,matched:h,matches:s}}alignment(e){let t=this.paths[e];if(this.refId===void 0||e===this.refId||!t)return;let n=this.paths[this.refId].path,s;if(Oe(n)&&(t.identity===void 0||!Oe(Be(t.path))))s={...this.editsAgainst(t.path,n),flipped:!1};else{let o=Be(t.path),r=this.sharedWeight(t.path,n);if(this.sharedWeight(o,n)===0)s={...this.editsAgainst(t.path,n),flipped:!1};else if(r===0)s={...this.editsAgainst(o,n),flipped:!0};else{let h=this.editsAgainst(t.path,n),c=this.editsAgainst(o,n);s=c.matched>h.matched?{...c,flipped:!0}:{...h,flipped:!1}}}return s}alignToRef(e){return this.settleDeferred(),this.alignment(e)?.edits.map(([t,n])=>`${n}${t}`).join("")}alignments(){this.settleDeferred();let e=this.referenceInterval;if(this.refId===void 0||!e)throw new Error("Alignments need a reference path");let t=this.paths[this.refId].path,n=this.refPrefix(t)[t.length],s=(d,f,p,y)=>{let g=Gn(d),l=this.paths[p[0]],b=this.paths[p[p.length-1]],x=l.identity,P=x?.orientation==="forward",[E,R]=P?[l,b]:[b,l];return{strand:f,refStart:e.start+g.leading,refEnd:e.start+n-g.trailing,edits:g.edits,weight:l.weight,path:p.flatMap(m=>this.paths[m].path),start:Ge(l,0),pieces:p,soloAligned:y,identity:x===void 0?void 0:{pathHandle:x.pathHandle,name:x.name,hapStart:x.name.fragment+E.identity.hapStart,hapEnd:x.name.fragment+R.identity.hapEnd,walkForward:P}}},o=d=>d.soloAligned.reduce((f,p)=>f+p,0),r=d=>d.pieces.reduce((f,p)=>f+this.paths[p].len,0),i=d=>2*o(d)>=r(d),h=d=>{let f=d[0],p=d[d.length-1],y=f.identity.walkForward;if(d.some((k,j)=>k.strand!==f.strand||k.identity.walkForward!==y||j>0&&k.identity.hapStart<d[j-1].identity.hapEnd))return;let g=y?d:[...d].reverse(),l=g.flatMap(k=>k.pieces),b=g.flatMap(k=>k.soloAligned),x=f.strand==="+"!==y,P=l.map(k=>this.paths[k]),E=P.slice(1).map((k,j)=>{let X=P[j].identity;return y?k.identity.hapStart-X.hapEnd:X.hapStart-k.identity.hapEnd}),R=x?[...P].reverse():P,m=x?[...E].reverse():E,I=R.flatMap(k=>x?Be(k.path):k.path),{edits:$}=this.editsAgainst(I,t),F=an($,R.map(k=>k.len)),_=new Map((x?[...l].reverse():l).map((k,j)=>[k,F[j]])),D=k=>2*k.pieces.reduce((j,X)=>j+_.get(X),0)>=o(k);if(!D(f)||!D(p))return;let C=[],H=0;return R.slice(0,-1).forEach((k,j)=>{H+=k.len,C.push([H,m[j]])}),s(Qn($,C),f.strand,l,b)},c=[];return this.paths.forEach((d,f)=>{if(f===this.refId)return;let{edits:p,flipped:y}=this.alignment(f),g=d.identity,l=g?g.orientation==="forward"!==y:!y;c.push(s(p,l?"+":"-",[f],an(p,[d.len])))}),jn(c,i,h).map(d=>{let{edits:f,identity:p,pieces:y,soloAligned:g,...l}=d,b={...l,cigar:Kn(f)};return p?{...b,resolved:!0,name:p.name,label:fe({...p.name,fragment:p.hapStart,end:p.hapEnd}),pathHandle:p.pathHandle,hapStart:p.hapStart,hapEnd:p.hapEnd}:{...b,resolved:!1}})}pairAlignments(e){let{target:t,query:n,...s}=e,o=this.paths.flatMap(d=>{let{identity:f}=d;return f?[{name:f.name,start:f.name.fragment+f.hapStart,steps:Ke(d,f)}]:[]}),r=d=>f=>f.sample===d.sample&&f.haplotype===d.haplotype,i=r(t),h=n?r(n):d=>!i(d),c=d=>this.record(ce(d,"forward")).sequence;return o.filter(d=>i(d.name)).flatMap(d=>o.filter(f=>h(f.name)).flatMap(f=>Wt({...s,query:f.steps,target:d.steps,sequenceOf:c}).map(p=>({query:f.name,queryStart:f.start+p.queryStart,queryEnd:f.start+p.queryEnd,strand:p.strand,target:d.name,targetStart:d.start+p.targetStart,targetEnd:d.start+p.targetEnd,cigar:Vt(p.edits),matches:p.edits.reduce((y,[g,l])=>y+(g==="="?l:0),0),columns:p.edits.reduce((y,[,g])=>y+g,0),sharedBases:p.sharedBases}))))}canonicalEdges(e){let t=[];for(let n of["forward","reverse"]){let s=ce(e,n);for(let o of this.record(s).successors())this.hasHandle(o)&&He(s,o)&&t.push([n==="reverse"?1:0,N(o),Q(o)?1:0])}return t.sort((n,s)=>n[0]-s[0]||n[1]-s[1]||n[2]-s[2]),t.filter((n,s)=>s===0||n[0]!==t[s-1][0]||n[1]!==t[s-1][1]||n[2]!==t[s-1][2])}async stableName(){let e=new TextEncoder,t=[];for(let n of this.sortedHandles())if(!Q(n)){let s=N(n),o=`S	${s}	${this.record(n).sequence}
 `;for(let[r,i,h]of this.canonicalEdges(s))o+=`L	${s}	${r?"-":"+"}	${i}	${h?"-":"+"}
 `;t.push(e.encode(o))}return rn(t)}async toGFA(e={}){this.settleDeferred();let t=e.cigar??!1,n=[this.refPath?`H	VN:Z:1.1	RS:Z:${this.refPath.sample}`:"H	VN:Z:1.1",...on(sn(await this.stableName(),await this.db.graphName()))],s=this.sortedHandles();for(let c of s)Q(c)||n.push(`S	${N(c)}	${this.record(c).sequence}`);let o=c=>Q(c)?"-":"+";for(let c of s)for(let d of this.record(c).successors())this.hasHandle(d)&&He(c,d)&&n.push(`L	${N(c)}	${o(c)}	${N(d)}	${o(d)}	0M`);let r=(c,d,f,p,y)=>{let g=Ke(c,d).map(x=>`${Q(x)?"<":">"}${N(x)}`).join(""),l=c.weight===void 0?"":`	WT:i:${c.weight}`,b=y===void 0?"":`	CG:Z:${y}`;return`W	${f.sample}	${f.haplotype}	${f.contig}	${f.fragment}	${p}	${g}${l}${b}`},i=this.refPath?.contig??"unknown";this.refId!==void 0&&this.refPath&&this.refInterval&&n.push(r(this.paths[this.refId],void 0,{...this.refPath,fragment:this.refPath.fragment+this.refInterval[0]},this.refPath.fragment+this.refInterval[1],void 0));let h=1;return this.paths.forEach((c,d)=>{if(d!==this.refId){let f=e.names!=="anonymous"?c.identity:void 0,p=t?this.alignToRef(d):void 0;n.push(f?r(c,f,{...f.name,fragment:f.name.fragment+f.hapStart},f.name.fragment+f.hapEnd,p):r(c,void 0,{sample:"unknown",contig:i,haplotype:h,fragment:0},c.len,p)),h+=1}}),`${n.join(`
 `)}
@@ -6,4 +6,4 @@ import{a as ce,b as N,c as Ee,d as Q,e as ee,f as Ft,g as Ue,h as We,i as qt,j a
 `).filter(p=>p!=="")),n=(f,p)=>f.filter(y=>y.startsWith(`${p}	`)),s=cs(t.flat()),o=0,r=t.map(f=>{let p=n(f,"W").map(hs),y=o;for(let g of p.filter(l=>l.fields[1]===is)){let l=+g.fields[2]+y;g.fields[2]=String(l),g.name=g.fields.slice(1,4).join("	"),o=Math.max(o,l)}return p}),h=[...Ot([...r.flatMap(f=>f.slice(0,1)),...r.flatMap(f=>f.slice(1))],f=>f.name).values()].flatMap(f=>fs(f,s,e)),c=new Set(t.flatMap(f=>n(f,"L")));for(let f of h)for(let p of ls(f))!c.has(p.forward)&&!c.has(p.reverse)&&c.add(p.forward);return`${[...new Set([...n(t[0],"H"),...t.flatMap(f=>n(f,"S")),...c,...h.map(f=>f.fields.join("	"))])].join(`
 `)}
 `}var In=class extends Error{constructor(a,e){super(e.length===0?`the graph names no reference sample (gbwt_reference_samples) and the anchor "${a}" maps to none; set referenceSample`:`the anchor "${a}" is none of the graph's reference samples (${e.join(", ")}); set referenceSample or map it through assemblyNameToPanSN`),this.name="NoReferenceSampleError"}},En=class extends Error{constructor(a,e,t){super(`this ${e.toLocaleString()} bp window reads more than nodeLimit (${a.toLocaleString()}) graph nodes; zoom in to about ${t.toLocaleString()} bp or raise nodeLimit`),this.fitsBp=t,this.name="NodeLimitError",this.regionTooLarge=!0}};function kn(a){return`${a.sample}#${a.haplotype}`}function ps(a,e){let t=kn(a);return e===void 0||e.some(n=>Bt(t,n))}async function us(a){return(await a.tag("gbwt_reference_samples")??"").split(/\s+/).filter(e=>e!=="")}function vn(a,e){let t=a.toLowerCase(),n=_t(a)?.toLowerCase();return e.find(s=>s===a)??e.find(s=>s.toLowerCase()===t)??e.find(s=>s.toLowerCase()===n)}function ws({configured:a,anchorPrefix:e,referenceSamples:t}){if(a!=="")return a;let n=vn(Ct(e),t)??(t.length===1?t[0]:void 0);if(n===void 0)throw new In(e,t);return n}async function gs(a,e,t){let n=(await a.paths()).find(s=>s.isIndexed&&s.name.sample===e&&s.name.contig===t);return n?{sample:n.name.sample,contig:t,haplotype:n.name.haplotype}:void 0}function Pn(a,e,t){if(a instanceof Error&&(a.name==="SubgraphLimitError"||/^Subgraph size limit of \d+ nodes exceeded/.test(a.message))){let s=a.walkedBp,o=typeof s=="number"&&s>0?Math.floor(s*.8):Math.floor(t/2);return new En(e,t,Math.max(o,1))}else return}var ms={context:1e3,snarls:"contained",limit:1e5};async function ys(a,e,t,n,s){return a.getSubgraphs({...s,path:e,start:t,end:n,haplotypes:"all"}).catch(o=>{throw Pn(o,s.limit,n-t)??o})}async function bs(a,e){let t=await a.paths();return Sn(await Promise.all(e.map(n=>n.toGFA())),(n,s,o,r)=>t.some(({name:i})=>i.sample===n&&i.haplotype===s&&i.contig===o&&i.fragment===r))}async function xs(a,e,t,n,s){if(!e)return"";let o=await ys(a,e,t,n,s);if(o.length===1)return An(o[0].toCompactSubgraph());let r=await bs(a,o);return r&&Tt(r)||r}function Ss(a,e){let t=1/0,n=-1/0;for(let i of a)t=Math.min(t,i),n=Math.max(n,i);let s=n-t+1,o=a.length>0&&s<=16*a.length?new Int32Array(s).fill(-1):void 0,r=new Map;return a.forEach((i,h)=>{o?o[i-t]=h:r.set(i,h)}),i=>{let h=N(i),c=o!==void 0&&h>=t&&h<=n,d=c?o[h-t]:r.get(h)??-1;return d>=0?d:(c?o[h-t]=e.length:r.set(h,e.length),e.push(String(h)),e.length-1)}}var Is=/^(.*)\[(\d+)-(\d+)\]$/;function An(a){let e=Array.from(a.nodeIds,String),t=Ss(a.nodeIds,e),n=a.nodeIds.length,s=a.edges.length/2,o=new Int32Array(s),r=new Int32Array(s),i=new Uint8Array(s);for(let l=0;l<s;l++){let b=a.edges[2*l],x=a.edges[2*l+1];o[l]=t(b),r[l]=t(x),i[l]=(Q(b)?1:0)|(Q(x)?2:0)}let h=a.paths.filter(l=>l.steps.length>0),c=new Int32Array(h.length+1);h.forEach((l,b)=>{c[b+1]=c[b]+l.steps.length});let d=new Int32Array(c[h.length]),f=new Uint8Array(d.length),p=new Float64Array(h.length),y=new Float64Array(h.length),g=h.map((l,b)=>{let x=Is.exec(l.name);p[b]=x?+x[2]:0,y[b]=x?+x[3]:-1;let P=c[b];for(let E of l.steps)d[P]=t(E),f[P++]=Q(E)?1:0;return x?x[1]:l.name});return{nodes:{names:e,lengths:Int32Array.from(a.nodeSequences,l=>l.length),refs:new Int32Array(n).fill(-1),starts:new Float64Array(n),ranks:new Int32Array(n),refNames:[]},links:{from:o,to:r,strands:i},walks:{names:g,starts:p,ends:y,offsets:c,steps:d,reversed:f}}}export{le as a,St as b,En as c,kn as d,ps as e,us as f,ws as g,gs as h,Pn as i,ms as j,xs as k};
-//# sourceMappingURL=chunk-KY6GXBXU.js.map
+//# sourceMappingURL=chunk-4KVQOJHH.js.map