jbrowse-plugin-graphgenomeviewer 8.0.2 → 8.2.0

package/dist/chunks/{WalkFormsAdapter-PBN7BJZW.js → WalkFormsAdapter-LTAKACZD.js}

@@ -1,2 +1,2 @@
-import{a as x,b,c as N,d as R,f as c,g as C,h as P,i as T}from"./chunk-I6F25EXY.js";import{a as k}from"./chunk-KOB7YIMR.js";import{C as $,b as l,d as g,e as w,f as h,g as p,k as y,o as B,s as F,t as S}from"./chunk-DG3E6BSX.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-5RHNR3TH.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{a as m,o as u}from"./chunk-J5RMHLFJ.js";var v=r=>`${(r/1e6).toFixed(1)} MB`,O=r=>`${(r/1e6).toFixed(1)} M`;function E(r,f){if(!(r instanceof g))return r;let t=N(f);if(r instanceof F)return new Error(`The pinned window ${t} is too large to read every walk in full for structural forms: its walks take ${O(r.steps)} steps, over the ${O(r.limit)} step budget, and about ${p(r.fitsBp)} of it fits. Pin a narrower window`);let e=`walkByteBudget, ${v(r.limit)}`;return new Error(`The pinned window ${t} is too large to cut for structural forms: ${r.zoomHelps?`about ${p(r.fitsBp)} of it fits in ${e}. Pin a narrower window or raise walkByteBudget`:`its cut fetches ${v(r.bytes??0)}, over ${e}. Raise walkByteBudget`}`)}var L=8,i=new Map;function A(r,f){let t=i.get(r),e=t??f();if(i.delete(r),i.set(r,e),!t){e.catch(()=>{i.get(r)===e&&i.delete(r)});for(let s of i.keys()){if(i.size<=L)break;i.delete(s)}}return e}var d=class extends l{constructor(){super(...arguments);this.reader=new y($(this,["walksLocation"],["walksIndex"]))}static{this.capabilities=["getFeatures","getRefNames"]}async referenceSample(t){let{references:e}=await this.reader.header(t);return e[0]??""}async getRefNames(t={}){let e=await this.reader.referenceSequences(t),s=await this.referenceSample(t),a=e.filter(o=>h(o,s)).map(o=>w(o));return a.length>0?[...new Set(a)]:e}pinned(){let t=x(this.getConf("pinned"));if(!t)throw new Error("WalkFormsAdapter needs `pinned`, the window its forms come from: { refName, start, end }");return t}forms(t){if(!this.formsRead){let e=this.pinned(),s=`${JSON.stringify(this.getConf("walksLocation"))}	${e.refName}:${e.start}-${e.end}`,a=this.getConf("walkByteBudget"),o=A(`${s}	${a}`,()=>u("Cutting walks",t.statusCallback,()=>S(this.reader,e,{byteBudget:a,partial:!1}).catch(n=>{throw E(n,e)}))).then(n=>B(n,{window:e,floorBp:b(this.getConf("floorBp")),exclude:this.getConf("exclude")}));o.catch(()=>{this.formsRead===o&&(this.formsRead=void 0)}),this.formsRead=o}return this.formsRead}maxForms(){return this.getConf("maxForms")}async getSourcesAndWarnings(t={}){let e=await this.forms(t),s=R(this.pinned());return{sources:c(e,this.maxForms()),warnings:C(e,this.maxForms()).map(a=>s+a)}}async getSources(t,e={}){return c(await this.forms(e),this.maxForms())}async onPinnedSequence(t,e){let s=await this.referenceSample(e),[a,o]=await Promise.all([this.reader.sequenceFor(s,t,e),this.reader.sequenceFor(s,this.pinned().refName,e)]);return a!==void 0&&a===o}getFeatures(t,e={}){return k(async s=>{let a=await this.forms(e),o=await this.onPinnedSequence(t.refName,e)?T(a,this.maxForms()).filter(n=>n.start<t.end&&n.end>t.start):[];for(let n of o)s.next(new m({uniqueId:`forms-${a.floorBp}-${n.id}`,refName:t.refName,start:n.start,end:n.end,name:n.name,description:n.description,type:n.type,svType:n.svType,consequence:n.consequence,REF:"N",ALT:[n.alt],INFO:{SVTYPE:[n.svType],SVLEN:[n.mark.delta]},mark:n.mark,genotypes:n.genotypes}));if(o.length===0){let n=Math.floor(t.start);s.next(new m({uniqueId:`forms-reference-${t.refName}-${n}`,refName:t.refName,start:n,end:n+1,REF:"N",ALT:["."],genotypes:P(a,this.maxForms())}))}s.complete()},e.signal)}};export{d as default};
-//# sourceMappingURL=WalkFormsAdapter-PBN7BJZW.js.map
+import{a as x,b,c as N,d as R,f as c,g as C,h as P,i as T}from"./chunk-PTOKTIQG.js";import{a as k}from"./chunk-KOB7YIMR.js";import{E as $,b as l,d as g,e as w,f as h,g as p,k as y,o as B,s as F,t as S}from"./chunk-CZXJXNZN.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-VKZALU57.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{a as m,o as u}from"./chunk-J5RMHLFJ.js";var v=r=>`${(r/1e6).toFixed(1)} MB`,O=r=>`${(r/1e6).toFixed(1)} M`;function E(r,f){if(!(r instanceof g))return r;let t=N(f);if(r instanceof F)return new Error(`The pinned window ${t} is too large to read every walk in full for structural forms: its walks take ${O(r.steps)} steps, over the ${O(r.limit)} step budget, and about ${p(r.fitsBp)} of it fits. Pin a narrower window`);let e=`walkByteBudget, ${v(r.limit)}`;return new Error(`The pinned window ${t} is too large to cut for structural forms: ${r.zoomHelps?`about ${p(r.fitsBp)} of it fits in ${e}. Pin a narrower window or raise walkByteBudget`:`its cut fetches ${v(r.bytes??0)}, over ${e}. Raise walkByteBudget`}`)}var L=8,i=new Map;function A(r,f){let t=i.get(r),e=t??f();if(i.delete(r),i.set(r,e),!t){e.catch(()=>{i.get(r)===e&&i.delete(r)});for(let s of i.keys()){if(i.size<=L)break;i.delete(s)}}return e}var d=class extends l{constructor(){super(...arguments);this.reader=new y($(this,["walksLocation"],["walksIndex"]))}static{this.capabilities=["getFeatures","getRefNames"]}async referenceSample(t){let{references:e}=await this.reader.header(t);return e[0]??""}async getRefNames(t={}){let e=await this.reader.referenceSequences(t),s=await this.referenceSample(t),a=e.filter(o=>h(o,s)).map(o=>w(o));return a.length>0?[...new Set(a)]:e}pinned(){let t=x(this.getConf("pinned"));if(!t)throw new Error("WalkFormsAdapter needs `pinned`, the window its forms come from: { refName, start, end }");return t}forms(t){if(!this.formsRead){let e=this.pinned(),s=`${JSON.stringify(this.getConf("walksLocation"))}	${e.refName}:${e.start}-${e.end}`,a=this.getConf("walkByteBudget"),o=A(`${s}	${a}`,()=>u("Cutting walks",t.statusCallback,()=>S(this.reader,e,{byteBudget:a,partial:!1}).catch(n=>{throw E(n,e)}))).then(n=>B(n,{window:e,floorBp:b(this.getConf("floorBp")),exclude:this.getConf("exclude")}));o.catch(()=>{this.formsRead===o&&(this.formsRead=void 0)}),this.formsRead=o}return this.formsRead}maxForms(){return this.getConf("maxForms")}async getSourcesAndWarnings(t={}){let e=await this.forms(t),s=R(this.pinned());return{sources:c(e,this.maxForms()),warnings:C(e,this.maxForms()).map(a=>s+a)}}async getSources(t,e={}){return c(await this.forms(e),this.maxForms())}async onPinnedSequence(t,e){let s=await this.referenceSample(e),[a,o]=await Promise.all([this.reader.sequenceFor(s,t,e),this.reader.sequenceFor(s,this.pinned().refName,e)]);return a!==void 0&&a===o}getFeatures(t,e={}){return k(async s=>{let a=await this.forms(e),o=await this.onPinnedSequence(t.refName,e)?T(a,this.maxForms()).filter(n=>n.start<t.end&&n.end>t.start):[];for(let n of o)s.next(new m({uniqueId:`forms-${a.floorBp}-${n.id}`,refName:t.refName,start:n.start,end:n.end,name:n.name,description:n.description,type:n.type,svType:n.svType,consequence:n.consequence,REF:"N",ALT:[n.alt],INFO:{SVTYPE:[n.svType],SVLEN:[n.mark.delta]},mark:n.mark,genotypes:n.genotypes}));if(o.length===0){let n=Math.floor(t.start);s.next(new m({uniqueId:`forms-reference-${t.refName}-${n}`,refName:t.refName,start:n,end:n+1,REF:"N",ALT:["."],genotypes:P(a,this.maxForms())}))}s.complete()},e.signal)}};export{d as default};
+//# sourceMappingURL=WalkFormsAdapter-LTAKACZD.js.map

package/dist/chunks/{WalkTabixSyntenyAdapter-27WDE5JF.js → WalkTabixSyntenyAdapter-B6V3YNW7.js}

@@ -1,2 +1,2 @@
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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-27WDE5JF.js.map
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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-B6V3YNW7.js.map

package/dist/chunks/chunk-5FNGR33G.js

@@ -0,0 +1,2 @@
+import{c as m}from"./chunk-3VGXCEMQ.js";import{a as p,b as l,c as h,d as A,h as a,i as g,j as d}from"./chunk-6VNDP3UB.js";import{a as T}from"./chunk-OGQ6OQDN.js";var z=5e3;function G(e){return typeof e=="string"&&/^[\w+-][\w.+-]*$/.test(e)}function x(e){return e==null}function M(e){return typeof e=="object"&&e!==null&&!Array.isArray(e)}function L(e){return M(e)&&G(e.prefix)&&typeof e.foldBelowBp=="number"&&Number.isFinite(e.foldBelowBp)&&e.foldBelowBp>0}function P(e){let n;try{n=JSON.parse(e)}catch{return}if(!M(n)||n.schema!==1)return;let{reference:i,tier:t,index:r,contig:o,bubbles:s,alleles:f}=n;if((x(i)||typeof i=="string"&&i.trim()!=="")&&(x(t)||L(t))&&[r,o,s,f].every(I=>x(I)||G(I)))return{...typeof i=="string"?{reference:i.trim()}:{},...L(t)?{tier:{prefix:t.prefix,foldBelowBp:t.foldBelowBp}}:{}}}function y(e,n){return d(e,i=>i.replace(/[^/\\]*$/,n))}function R(e){let n=a(e);return[p,l].find(i=>n.endsWith(i))}function N(e){return g(e)&&R(e)!==void 0}function F(e,n){let i=R(e)??p;return d(e,t=>`${t.slice(0,-i.length)}${n}`)}function _(e){return N(e)?F(e,".graph.json"):void 0}async function X(e,n){let i=_(e);if(i)try{let t=await T(i,n).readFile({encoding:"utf8",signal:AbortSignal.timeout(z)});return P(t)}catch{return}}var J={RgfaTabixAdapter:"Indexed GFA (gfa-to-tabix .segs.bed.gz or .graph.bed.gz)",RgfaTabixWalks:"Haplotype walks (.walks.bed.gz)",GbzBaseSyntenyAdapter:"GBZ database (.gbz.db)",MinigraphBubbleAdapter:"Minigraph bubbles (tabix BED)"},K={RgfaTabixAdapter:"Path to segments BED (.segs.bed.gz from gfa-to-tabix; the .links.bed.gz, its index and any .graph.json are read beside it), or format 2's .graph.bed.gz",RgfaTabixWalks:"Path to a walk file (<prefix>.<sample>.walks.bed.gz from gfa-to-tabix --walks, for the sample this assembly is)",GbzBaseSyntenyAdapter:"Path to the .gbz.db written by gbz-base construct",MinigraphBubbleAdapter:"Path to bubbles BED (.bed.gz from gfatools bubble)"},B="Path to tabix index (optional; the sibling .tbi is assumed, a .csi is recognised by name)",Z={RgfaTabixAdapter:B,RgfaTabixWalks:B,GbzBaseSyntenyAdapter:"Path to the haplotype index (optional; graph.haplotype-index.db beside the database is assumed)",MinigraphBubbleAdapter:B};function b(e,n){return d(e,i=>i+n)}function C(e){if(!a(e).endsWith(p))throw new Error(`Expected a segments BED ending in ${p}, got ${a(e)}`);return F(e,".links.bed.gz")}function u(e,n){return n?{location:n,indexType:m(a(n),"CSI","TBI")}:{location:b(e,".tbi"),indexType:"TBI"}}function k(e,n){return n!==void 0&&m(a(n),"CSI","TBI")==="CSI"?{location:b(e,".csi"),indexType:"CSI"}:{location:b(e,".tbi"),indexType:"TBI"}}function w(e,n){let i=n.trim();return i&&e?{assemblyNameToPanSN:{[e]:i}}:{}}function E(e,n,i){if(!i)return{};let t=y(e,`${i.prefix}${p}`),r=y(e,`${i.prefix}.links.bed.gz`);return{coarse:{foldBelowBp:i.foldBelowBp,segmentsLocation:t,segmentsIndex:k(t,n),linksLocation:r,linksIndex:k(r,n)}}}function S(e,n,i){let t=i===e?void 0:i;return w(e,n.trim()||t||"")}function W(e){return e?{readsLocation:e,...a(e).endsWith(".gz")&&g(e)?{readsIndex:{location:b(e,".tbi")}}:{}}:{}}function q(e){return e.split(/[\s,]+/).filter(n=>n!=="")}function D({choice:e,loc:n,indexLoc:i,readsLoc:t,manifest:r,assembly:o,sample:s,haplotypes:f=[]}){if(e==="RgfaTabixWalks"){if(!a(n).endsWith(h))throw new Error(`Expected a walk file ending in ${h}, got ${a(n)}`);return{type:"RgfaTabixAdapter",walksLocation:n,walksIndex:u(n,i),...S(o,s,A(n)),...f.length>0?{defaultHaplotypes:f}:{}}}if(e==="GbzBaseSyntenyAdapter")return{type:"GbzBaseSyntenyAdapter",gbzDbLocation:n,...i?{haplotypeIndexLocation:i}:{},...W(t),...w(o,s)};if(e==="MinigraphBubbleAdapter")return{type:"MinigraphBubbleAdapter",bubblesLocation:n,index:u(n,i),...w(o,s)};if(a(n).endsWith(l))return{type:"RgfaTabixAdapter",graphLocation:n,graphIndex:u(n,i),...S(o,s,r?.reference),...E(n,i,r?.tier)};let c=C(n);return{type:"RgfaTabixAdapter",segmentsLocation:n,segmentsIndex:u(n,i),linksLocation:c,linksIndex:k(c,i),...S(o,s,r?.reference),...E(n,i,r?.tier)}}function Q(e){let{choice:n,assembly:i,trackId:t,name:r}=e;return{type:n==="MinigraphBubbleAdapter"?"FeatureTrack":"GraphTrack",trackId:t,name:r,assemblyNames:[i],adapter:D(e),...n==="RgfaTabixAdapter"||n==="RgfaTabixWalks"?{displayDefaults:{labels:{name:{show:!1},description:{show:!1}}}}:{}}}export{N as a,X as b,J as c,K as d,Z as e,q as f,D as g,Q as h};
+//# sourceMappingURL=chunk-5FNGR33G.js.map

package/dist/chunks/chunk-5FNGR33G.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/GraphAddTrackWorkflow/graphManifest.ts", "../../src/GraphAddTrackWorkflow/buildTrackConfig.ts"],
+  "sourcesContent": ["import { openLocation } from '@jbrowse/core/util/io'\n\nimport {\n  GRAPH_SUFFIX,\n  SEGMENTS_SUFFIX,\n  locationName,\n  readsSiblings,\n  renamed,\n} from '../locationName'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { FileLocation } from '@jbrowse/core/util'\n\n// The part of `<prefix>.graph.json`, written by `gfa-to-tabix build`, that\n// Open track reads\nexport interface GraphManifest {\n  reference?: string\n  tier?: { prefix: string; foldBelowBp: number }\n}\n\nconst FETCH_TIMEOUT_MS = 5000\n\n// A bare file name beside the manifest: no directory, scheme or leading dot\nfunction isSiblingName(name: unknown): name is string {\n  return typeof name === 'string' && /^[\\w+-][\\w.+-]*$/.test(name)\n}\n\nfunction isAbsent(value: unknown) {\n  return value === undefined || value === null\n}\n\nfunction isPlainRecord(value: unknown): value is Record<string, unknown> {\n  return typeof value === 'object' && value !== null && !Array.isArray(value)\n}\n\nfunction isTier(tier: unknown): tier is NonNullable<GraphManifest['tier']> {\n  return (\n    isPlainRecord(tier) &&\n    isSiblingName(tier.prefix) &&\n    typeof tier.foldBelowBp === 'number' &&\n    Number.isFinite(tier.foldBelowBp) &&\n    tier.foldBelowBp > 0\n  )\n}\n\nexport function parseGraphManifest(text: string): GraphManifest | undefined {\n  let json: unknown\n  try {\n    json = JSON.parse(text)\n  } catch {\n    return undefined\n  }\n  if (!isPlainRecord(json) || json.schema !== 1) {\n    return undefined\n  }\n  const { reference, tier, index, contig, bubbles, alleles } = json\n  const valid =\n    (isAbsent(reference) ||\n      (typeof reference === 'string' && reference.trim() !== '')) &&\n    (isAbsent(tier) || isTier(tier)) &&\n    [index, contig, bubbles, alleles].every(\n      f => isAbsent(f) || isSiblingName(f),\n    )\n  if (!valid) {\n    return undefined\n  }\n  return {\n    ...(typeof reference === 'string' ? { reference: reference.trim() } : {}),\n    ...(isTier(tier)\n      ? { tier: { prefix: tier.prefix, foldBelowBp: tier.foldBelowBp } }\n      : {}),\n  }\n}\n\n// A file the manifest names, in the directory of the segments file opened\nexport function besideSegments(segs: FileLocation, fileName: string) {\n  return renamed(segs, name => name.replace(/[^/\\\\]*$/, fileName))\n}\n\n// The suffix of a gfa-to-tabix index file: format 1's segments BED or format\n// 2's graph BED\nfunction indexSuffix(loc: FileLocation) {\n  const name = locationName(loc)\n  return [SEGMENTS_SUFFIX, GRAPH_SUFFIX].find(suffix => name.endsWith(suffix))\n}\n\n// A segments BED, or format 2's graph BED, the rest of the index and the\n// manifest can be found beside\nexport function isGraphIndexLocation(loc: FileLocation) {\n  return readsSiblings(loc) && indexSuffix(loc) !== undefined\n}\n\n// `<prefix><suffix>` beside `<prefix>.segs.bed.gz` or `<prefix>.graph.bed.gz`\nexport function segmentsSibling(segs: FileLocation, suffix: string) {\n  const own = indexSuffix(segs) ?? SEGMENTS_SUFFIX\n  return renamed(segs, name => `${name.slice(0, -own.length)}${suffix}`)\n}\n\nexport function manifestLocation(segs: FileLocation) {\n  return isGraphIndexLocation(segs)\n    ? segmentsSibling(segs, '.graph.json')\n    : undefined\n}\n\n// Undefined for a manifest that is missing, unreadable or not schema 1, so\n// Open track falls back to the files beside the segments alone\nexport async function readGraphManifest(\n  segs: FileLocation,\n  pluginManager?: PluginManager,\n) {\n  const loc = manifestLocation(segs)\n  if (!loc) {\n    return undefined\n  }\n  try {\n    const text = await openLocation(loc, pluginManager).readFile({\n      encoding: 'utf8',\n      signal: AbortSignal.timeout(FETCH_TIMEOUT_MS),\n    })\n    return parseGraphManifest(text)\n  } catch {\n    return undefined\n  }\n}\n", "import { makeIndexType } from '@jbrowse/core/util/tracks'\n\nimport { besideSegments, segmentsSibling } from './graphManifest'\nimport {\n  GRAPH_SUFFIX,\n  SEGMENTS_SUFFIX,\n  WALKS_SUFFIX,\n  locationName,\n  readsSiblings,\n  renamed,\n  walkFileSample,\n} from '../locationName'\n\nimport type { GraphManifest } from './graphManifest'\nimport type { FileLocation } from '@jbrowse/core/util'\n\n// 'RgfaTabixWalks' is an RgfaTabixAdapter read from a walk file\nexport type GraphFileChoice =\n  | 'RgfaTabixAdapter'\n  | 'RgfaTabixWalks'\n  | 'GbzBaseSyntenyAdapter'\n  | 'MinigraphBubbleAdapter'\n\nexport const GRAPH_FILE_LABELS: Record<GraphFileChoice, string> = {\n  RgfaTabixAdapter: 'Indexed GFA (gfa-to-tabix .segs.bed.gz or .graph.bed.gz)',\n  RgfaTabixWalks: 'Haplotype walks (.walks.bed.gz)',\n  GbzBaseSyntenyAdapter: 'GBZ database (.gbz.db)',\n  MinigraphBubbleAdapter: 'Minigraph bubbles (tabix BED)',\n}\n\nexport const GRAPH_FILE_FIELDS: Record<GraphFileChoice, string> = {\n  RgfaTabixAdapter:\n    \"Path to segments BED (.segs.bed.gz from gfa-to-tabix; the .links.bed.gz, its index and any .graph.json are read beside it), or format 2's .graph.bed.gz\",\n  RgfaTabixWalks:\n    'Path to a walk file (<prefix>.<sample>.walks.bed.gz from gfa-to-tabix --walks, for the sample this assembly is)',\n  GbzBaseSyntenyAdapter: 'Path to the .gbz.db written by gbz-base construct',\n  MinigraphBubbleAdapter: 'Path to bubbles BED (.bed.gz from gfatools bubble)',\n}\n\nconst TABIX_INDEX_FIELD =\n  'Path to tabix index (optional; the sibling .tbi is assumed, a .csi is recognised by name)'\n\nexport const GRAPH_INDEX_FIELDS: Record<GraphFileChoice, string> = {\n  RgfaTabixAdapter: TABIX_INDEX_FIELD,\n  RgfaTabixWalks: TABIX_INDEX_FIELD,\n  GbzBaseSyntenyAdapter:\n    'Path to the haplotype index (optional; graph.haplotype-index.db beside the database is assumed)',\n  MinigraphBubbleAdapter: TABIX_INDEX_FIELD,\n}\n\nfunction sibling(loc: FileLocation, suffix: string) {\n  return renamed(loc, name => name + suffix)\n}\n\nfunction linksLocation(loc: FileLocation) {\n  if (!locationName(loc).endsWith(SEGMENTS_SUFFIX)) {\n    throw new Error(\n      `Expected a segments BED ending in ${SEGMENTS_SUFFIX}, got ${locationName(loc)}`,\n    )\n  }\n  return segmentsSibling(loc, '.links.bed.gz')\n}\n\nfunction tabixIndex(loc: FileLocation, indexLoc: FileLocation | undefined) {\n  return indexLoc\n    ? {\n        location: indexLoc,\n        indexType: makeIndexType(locationName(indexLoc), 'CSI', 'TBI'),\n      }\n    : { location: sibling(loc, '.tbi'), indexType: 'TBI' }\n}\n\n// The links file's index is assumed beside it, of the kind the segments' is.\nfunction siblingIndex(loc: FileLocation, indexLoc: FileLocation | undefined) {\n  const csi =\n    indexLoc !== undefined &&\n    makeIndexType(locationName(indexLoc), 'CSI', 'TBI') === 'CSI'\n  return csi\n    ? { location: sibling(loc, '.csi'), indexType: 'CSI' }\n    : { location: sibling(loc, '.tbi'), indexType: 'TBI' }\n}\n\n// none for a guessed config, which knows no assembly yet; see withWalkReference\nfunction panSN(assembly: string, sample: string) {\n  const name = sample.trim()\n  return name && assembly ? { assemblyNameToPanSN: { [assembly]: name } } : {}\n}\n\nfunction coarseTier(\n  loc: FileLocation,\n  indexLoc: FileLocation | undefined,\n  tier: GraphManifest['tier'],\n) {\n  if (!tier) {\n    return {}\n  }\n  const segs = besideSegments(loc, `${tier.prefix}${SEGMENTS_SUFFIX}`)\n  const links = besideSegments(loc, `${tier.prefix}.links.bed.gz`)\n  return {\n    coarse: {\n      foldBelowBp: tier.foldBelowBp,\n      segmentsLocation: segs,\n      segmentsIndex: siblingIndex(segs, indexLoc),\n      linksLocation: links,\n      linksIndex: siblingIndex(links, indexLoc),\n    },\n  }\n}\n\n// The user's sample wins; the reference the graph's files name (a manifest's,\n// or a walk file's own) stands in when blank\nfunction referencePanSN(\n  assembly: string,\n  sample: string,\n  reference: string | undefined,\n) {\n  const fromManifest = reference === assembly ? undefined : reference\n  return panSN(assembly, sample.trim() || fromManifest || '')\n}\n\n// a bgzipped GAF is read by its tabix index, a plain one whole\nfunction readsConfig(readsLoc: FileLocation | undefined) {\n  return readsLoc\n    ? {\n        readsLocation: readsLoc,\n        ...(locationName(readsLoc).endsWith('.gz') && readsSiblings(readsLoc)\n          ? { readsIndex: { location: sibling(readsLoc, '.tbi') } }\n          : {}),\n      }\n    : {}\n}\n\n// Names typed as a list, by comma or space\nexport function parseHaplotypes(text: string) {\n  return text.split(/[\\s,]+/).filter(name => name !== '')\n}\n\nexport function buildAdapterConfig({\n  choice,\n  loc,\n  indexLoc,\n  readsLoc,\n  manifest,\n  assembly,\n  sample,\n  haplotypes = [],\n}: {\n  choice: GraphFileChoice\n  loc: FileLocation\n  indexLoc: FileLocation | undefined\n  // a GBZ track's GAF reads, which no other choice takes\n  readsLoc?: FileLocation\n  // the `.graph.json` beside an rGFA segments file\n  manifest?: GraphManifest\n  assembly: string\n  sample: string\n  // a walk file's haplotypes to cut for until the user picks others\n  haplotypes?: string[]\n}) {\n  if (choice === 'RgfaTabixWalks') {\n    if (!locationName(loc).endsWith(WALKS_SUFFIX)) {\n      throw new Error(\n        `Expected a walk file ending in ${WALKS_SUFFIX}, got ${locationName(loc)}`,\n      )\n    }\n    return {\n      type: 'RgfaTabixAdapter',\n      walksLocation: loc,\n      walksIndex: tabixIndex(loc, indexLoc),\n      ...referencePanSN(assembly, sample, walkFileSample(loc)),\n      ...(haplotypes.length > 0 ? { defaultHaplotypes: haplotypes } : {}),\n    }\n  }\n  if (choice === 'GbzBaseSyntenyAdapter') {\n    return {\n      type: 'GbzBaseSyntenyAdapter',\n      gbzDbLocation: loc,\n      ...(indexLoc ? { haplotypeIndexLocation: indexLoc } : {}),\n      ...readsConfig(readsLoc),\n      ...panSN(assembly, sample),\n    }\n  }\n  if (choice === 'MinigraphBubbleAdapter') {\n    return {\n      type: 'MinigraphBubbleAdapter',\n      bubblesLocation: loc,\n      index: tabixIndex(loc, indexLoc),\n      ...panSN(assembly, sample),\n    }\n  }\n  if (locationName(loc).endsWith(GRAPH_SUFFIX)) {\n    return {\n      type: 'RgfaTabixAdapter',\n      graphLocation: loc,\n      graphIndex: tabixIndex(loc, indexLoc),\n      ...referencePanSN(assembly, sample, manifest?.reference),\n      ...coarseTier(loc, indexLoc, manifest?.tier),\n    }\n  }\n  const links = linksLocation(loc)\n  return {\n    type: 'RgfaTabixAdapter',\n    segmentsLocation: loc,\n    segmentsIndex: tabixIndex(loc, indexLoc),\n    linksLocation: links,\n    linksIndex: siblingIndex(links, indexLoc),\n    ...referencePanSN(assembly, sample, manifest?.reference),\n    ...coarseTier(loc, indexLoc, manifest?.tier),\n  }\n}\n\nexport function buildTrackConfig(args: {\n  choice: GraphFileChoice\n  loc: FileLocation\n  indexLoc: FileLocation | undefined\n  readsLoc?: FileLocation\n  manifest?: GraphManifest\n  assembly: string\n  sample: string\n  haplotypes?: string[]\n  trackId: string\n  name: string\n}) {\n  const { choice, assembly, trackId, name } = args\n  return {\n    type: choice === 'MinigraphBubbleAdapter' ? 'FeatureTrack' : 'GraphTrack',\n    trackId,\n    name,\n    assemblyNames: [assembly],\n    adapter: buildAdapterConfig(args),\n    ...(choice === 'RgfaTabixAdapter' || choice === 'RgfaTabixWalks'\n      ? {\n          displayDefaults: {\n            labels: { name: { show: false }, description: { show: false } },\n          },\n        }\n      : {}),\n  }\n}\n"],
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+  "names": ["FETCH_TIMEOUT_MS", "isSiblingName", "name", "isAbsent", "value", "isPlainRecord", "isTier", "tier", "parseGraphManifest", "text", "json", "reference", "index", "contig", "bubbles", "alleles", "f", "besideSegments", "segs", "fileName", "renamed", "indexSuffix", "loc", "locationName", "SEGMENTS_SUFFIX", "GRAPH_SUFFIX", "suffix", "isGraphIndexLocation", "readsSiblings", "segmentsSibling", "own", "manifestLocation", "readGraphManifest", "pluginManager", "openLocation", "GRAPH_FILE_LABELS", "GRAPH_FILE_FIELDS", "TABIX_INDEX_FIELD", "GRAPH_INDEX_FIELDS", "sibling", "loc", "suffix", "renamed", "name", "linksLocation", "locationName", "SEGMENTS_SUFFIX", "segmentsSibling", "tabixIndex", "indexLoc", "makeIndexType", "siblingIndex", "panSN", "assembly", "sample", "coarseTier", "tier", "segs", "besideSegments", "links", "referencePanSN", "reference", "fromManifest", "readsConfig", "readsLoc", "readsSiblings", "parseHaplotypes", "text", "buildAdapterConfig", "choice", "manifest", "haplotypes", "WALKS_SUFFIX", "walkFileSample", "GRAPH_SUFFIX", "buildTrackConfig", "args", "trackId"]
+}

package/dist/chunks/chunk-6VNDP3UB.js

@@ -0,0 +1,2 @@
+var s=".segs.bed.gz",u=".graph.bed.gz",r=".walks.bed.gz";function l(e){let n=a(e).replace(/^.*[/\\]/,"");if(!n.endsWith(r))return;let t=n.slice(0,-r.length),i=t.lastIndexOf(".");return i===-1?void 0:t.slice(i+1)||void 0}function c(e){return!("uri"in e)||e.uri!==""}function p(e){return typeof e=="object"&&e!==null&&Object.entries(e).some(([n,t])=>["uri","localPath","blobId"].includes(n)&&typeof t=="string"&&t!=="")}function o(e){let n=e.search(/[?#]/);return n===-1?{name:e,query:""}:{name:e.slice(0,n),query:e.slice(n)}}function a(e){return"uri"in e?o(e.uri).name:"localPath"in e?e.localPath:e.name}function d(e){return"uri"in e||"localPath"in e}function f(e,n){if("uri"in e){let{name:t,query:i}=o(e.uri);return{...e,uri:n(t)+i}}else{if("localPath"in e)return{...e,localPath:n(e.localPath)};throw new Error(`${e.name} was picked in the browser, which reads no file beside it; open it by URL`)}}export{s as a,u as b,r as c,l as d,c as e,p as f,o as g,a as h,d as i,f as j};
+//# sourceMappingURL=chunk-6VNDP3UB.js.map

package/dist/chunks/chunk-6VNDP3UB.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/locationName.ts"],
+  "sourcesContent": ["import type { FileLocation } from '@jbrowse/core/util'\n\nexport const SEGMENTS_SUFFIX = '.segs.bed.gz'\n// gfa-to-tabix's format 2: segments and links in one file\nexport const GRAPH_SUFFIX = '.graph.bed.gz'\nexport const WALKS_SUFFIX = '.walks.bed.gz'\n\n// The reference sample `gfa-to-tabix --walks` names a walk file after:\n// GRCh38 in `chr22.GRCh38.walks.bed.gz`\nexport function walkFileSample(loc: FileLocation) {\n  const name = locationName(loc).replace(/^.*[/\\\\]/, '')\n  if (!name.endsWith(WALKS_SUFFIX)) {\n    return undefined\n  }\n  const prefix = name.slice(0, -WALKS_SUFFIX.length)\n  const dot = prefix.lastIndexOf('.')\n  return dot === -1 ? undefined : prefix.slice(dot + 1) || undefined\n}\n\n// A schema's unset file slot defaults to an empty uri\nexport function locationIsSet(loc: FileLocation) {\n  return !('uri' in loc) || loc.uri !== ''\n}\n\n// Whether a location as a config snapshot writes it names a file\nexport function snapshotNamesFile(location: unknown) {\n  return (\n    typeof location === 'object' &&\n    location !== null &&\n    Object.entries(location).some(\n      ([key, value]) =>\n        ['uri', 'localPath', 'blobId'].includes(key) &&\n        typeof value === 'string' &&\n        value !== '',\n    )\n  )\n}\n\n// A url's query string (a presigned signature, a token) follows the file name\nexport function splitUri(uri: string) {\n  const end = uri.search(/[?#]/)\n  return end === -1\n    ? { name: uri, query: '' }\n    : { name: uri.slice(0, end), query: uri.slice(end) }\n}\n\nexport function locationName(loc: FileLocation) {\n  return 'uri' in loc\n    ? splitUri(loc.uri).name\n    : 'localPath' in loc\n      ? loc.localPath\n      : loc.name\n}\n\n// A file picked in the browser comes without the directory it sat in\nexport function readsSiblings(loc: FileLocation) {\n  return 'uri' in loc || 'localPath' in loc\n}\n\nexport function renamed(loc: FileLocation, rename: (name: string) => string) {\n  if ('uri' in loc) {\n    const { name, query } = splitUri(loc.uri)\n    return { ...loc, uri: rename(name) + query }\n  } else if ('localPath' in loc) {\n    return { ...loc, localPath: rename(loc.localPath) }\n  } else {\n    throw new Error(\n      `${loc.name} was picked in the browser, which reads no file beside it; open it by URL`,\n    )\n  }\n}\n"],
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+  "names": ["SEGMENTS_SUFFIX", "GRAPH_SUFFIX", "WALKS_SUFFIX", "walkFileSample", "loc", "name", "locationName", "prefix", "dot", "locationIsSet", "snapshotNamesFile", "location", "key", "value", "splitUri", "uri", "end", "readsSiblings", "renamed", "rename", "query"]
+}

package/dist/chunks/{chunk-CJAV55QB.js → chunk-BJHWGRMP.js}

@@ -1,2 +1,2 @@
 function o(t){return t===void 0||t==="*"?void 0:t}function s(t){let e=t.split("	");return{refName:e[0],start:+e[1],end:+e[2],segmentCount:+e[3],pathCount:+e[4],inversion:e[5]==="1",shortestAlleleLength:+e[6],longestAlleleLength:+e[7],segments:e[11],shortestAllele:o(e[12]),longestAllele:o(e[13])}}function u(t,e){return t.key!==void 0||e.key!==void 0?t.key===e.key:t.refName===e.refName&&t.start===e.start&&t.end===e.end}function i(t){return t.key??`${t.refName}:${t.start}-${t.end}`}function b(t){let{shortestAlleleLength:e,longestAlleleLength:n}=t;return e===n?`${n.toLocaleString()} bp`:`${e.toLocaleString()}-${n.toLocaleString()} bp`}var r=2147483647;function a(t){let{pathCount:e,segmentCount:n,inversion:l}=t;return[`${n} segments`,e===r?"more paths than gfatools counts":`up to ${e.toLocaleString()} paths`,...l?["inversion"]:[]].join(", ")}export{s as a,u as b,i as c,b as d,r as e,a as f};
-//# sourceMappingURL=chunk-CJAV55QB.js.map
+//# sourceMappingURL=chunk-BJHWGRMP.js.map

package/dist/chunks/{chunk-CJAV55QB.js.map → chunk-BJHWGRMP.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@12.0.2/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-FX4RDMDN.js"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-FX4RDMDN.js"],
   "sourcesContent": ["// src/bubbles/bubbleLine.ts\nfunction sequence(field) {\n  return field === void 0 || field === \"*\" ? void 0 : field;\n}\nfunction parseBubbleLine(line) {\n  const cols = line.split(\"\t\");\n  return {\n    refName: cols[0],\n    start: +cols[1],\n    end: +cols[2],\n    segmentCount: +cols[3],\n    pathCount: +cols[4],\n    inversion: cols[5] === \"1\",\n    shortestAlleleLength: +cols[6],\n    longestAlleleLength: +cols[7],\n    segments: cols[11],\n    shortestAllele: sequence(cols[12]),\n    longestAllele: sequence(cols[13])\n  };\n}\nfunction sameBubble(a, b) {\n  return a.key !== void 0 || b.key !== void 0 ? a.key === b.key : a.refName === b.refName && a.start === b.start && a.end === b.end;\n}\nfunction bubbleKey(b) {\n  return b.key ?? `${b.refName}:${b.start}-${b.end}`;\n}\nfunction bubbleLabel(bubble) {\n  const { shortestAlleleLength: min, longestAlleleLength: max } = bubble;\n  return min === max ? `${max.toLocaleString()} bp` : `${min.toLocaleString()}-${max.toLocaleString()} bp`;\n}\nvar SATURATED_PATH_COUNT = 2147483647;\nfunction bubbleDescription(bubble) {\n  const { pathCount, segmentCount, inversion } = bubble;\n  return [\n    `${segmentCount} segments`,\n    pathCount === SATURATED_PATH_COUNT ? \"more paths than gfatools counts\" : `up to ${pathCount.toLocaleString()} paths`,\n    ...inversion ? [\"inversion\"] : []\n  ].join(\", \");\n}\n\nexport {\n  parseBubbleLine,\n  sameBubble,\n  bubbleKey,\n  bubbleLabel,\n  SATURATED_PATH_COUNT,\n  bubbleDescription\n};\n"],
   "mappings": "AACA,SAASA,EAASC,EAAO,CACvB,OAAOA,IAAU,QAAUA,IAAU,IAAM,OAASA,CACtD,CACA,SAASC,EAAgBC,EAAM,CAC7B,IAAMC,EAAOD,EAAK,MAAM,GAAG,EAC3B,MAAO,CACL,QAASC,EAAK,CAAC,EACf,MAAO,CAACA,EAAK,CAAC,EACd,IAAK,CAACA,EAAK,CAAC,EACZ,aAAc,CAACA,EAAK,CAAC,EACrB,UAAW,CAACA,EAAK,CAAC,EAClB,UAAWA,EAAK,CAAC,IAAM,IACvB,qBAAsB,CAACA,EAAK,CAAC,EAC7B,oBAAqB,CAACA,EAAK,CAAC,EAC5B,SAAUA,EAAK,EAAE,EACjB,eAAgBJ,EAASI,EAAK,EAAE,CAAC,EACjC,cAAeJ,EAASI,EAAK,EAAE,CAAC,CAClC,CACF,CACA,SAASC,EAAWC,EAAGC,EAAG,CACxB,OAAOD,EAAE,MAAQ,QAAUC,EAAE,MAAQ,OAASD,EAAE,MAAQC,EAAE,IAAMD,EAAE,UAAYC,EAAE,SAAWD,EAAE,QAAUC,EAAE,OAASD,EAAE,MAAQC,EAAE,GAChI,CACA,SAASC,EAAUD,EAAG,CACpB,OAAOA,EAAE,KAAO,GAAGA,EAAE,OAAO,IAAIA,EAAE,KAAK,IAAIA,EAAE,GAAG,EAClD,CACA,SAASE,EAAYC,EAAQ,CAC3B,GAAM,CAAE,qBAAsBC,EAAK,oBAAqBC,CAAI,EAAIF,EAChE,OAAOC,IAAQC,EAAM,GAAGA,EAAI,eAAe,CAAC,MAAQ,GAAGD,EAAI,eAAe,CAAC,IAAIC,EAAI,eAAe,CAAC,KACrG,CACA,IAAIC,EAAuB,WAC3B,SAASC,EAAkBJ,EAAQ,CACjC,GAAM,CAAE,UAAAK,EAAW,aAAAC,EAAc,UAAAC,CAAU,EAAIP,EAC/C,MAAO,CACL,GAAGM,CAAY,YACfD,IAAcF,EAAuB,kCAAoC,SAASE,EAAU,eAAe,CAAC,SAC5G,GAAGE,EAAY,CAAC,WAAW,EAAI,CAAC,CAClC,EAAE,KAAK,IAAI,CACb",
   "names": ["sequence", "field", "parseBubbleLine", "line", "cols", "sameBubble", "a", "b", "bubbleKey", "bubbleLabel", "bubble", "min", "max", "SATURATED_PATH_COUNT", "bubbleDescription", "pathCount", "segmentCount", "inversion"]

package/dist/chunks/{chunk-IAXUZMOX.js → chunk-CNCYMJ5E.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-FY7X6253.js";import{c as Ot}from"./chunk-JMRW3IGK.js";import{a as Ct,g as Bt}from"./chunk-5RHNR3TH.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 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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 ${u.low} at both ends`);if(u.inserted>0&&(w.snarlNodes===void 0||u.nodes>w.snarlNodes))throw new 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Et[v])vt.add(q.pathHandle),q.orientation==="forward"&&y(q.pathHandle)&&dt.set(q.pathHandle,[...dt.get(q.pathHandle)??[],{k:T,row:q}])}),r.chosenPaths=[...vt].filter(y).length,r.chosenPaths>Gt.mostChosenPaths)throw new re(`${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}:${u.high}`)),Nn=ae.filter(u=>y(u.pathHandle)&&(u.snarl===void 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nn(a){return{name:a.get("pggname"),subgraph:Yt(a.get("subgraph"),"subgraph"),translation:Yt(a.get("translation"),"translation")}}function en(a,e){for(let[t,n]of e){let s=a.get(t);s||(s=new Set,a.set(t,s));for(let o of n)s.add(o)}}function sn(a,e){let t={name:a,subgraph:new Map,translation:new Map};return e.name!==void 0&&(t.subgraph.set(a,new Set([e.name])),en(t.subgraph,e.subgraph),en(t.translation,e.translation)),t}function tn(a){return[...a.entries()].sort(([e],[t])=>e<t?-1:e>t?1:0).flatMap(([e,t])=>[...t].sort().map(n=>[e,n]))}function on(a){let e=[];a.name!==void 0&&e.push(`H	NM:Z:${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}	${this.record(n).sequence}
+import{a as ce,b as N,c as Ee,d as Q,e as ee,f as Ft,g as Ue,h as We,i as qt,j as zt,k as He,l as Oe,m as Pe,n as Dt,o as jt,p as Ut,q as Wt,r as Vt}from"./chunk-M2D7NUOY.js";import{a as _t,g as Tt}from"./chunk-OGXVDZPS.js";import{c as Ot}from"./chunk-IK3MQ4ZJ.js";import{a as Ct,g as Bt}from"./chunk-VKZALU57.js";var Ln=4096;function pt(a){let e=[];for(let t of a){let n=e[e.length-1];n&&t-n[1]<=Ln?n[1]=t:e.push([t,t])}return e}var Hn=32768,Gt={mostChosenPaths:32},lt=class{byNode=new Map;get(e){return this.byNode.get(e.node)?.get(e.offset)}set(e,t){let n=this.byNode.get(e.node);n||(n=new Map,this.byNode.set(e.node,n)),n.set(e.offset,t)}},re=class extends Error{};function Ve(a,e,t,n){return a==="forward"?e+t:e-n}function Qt(a,e,t,n){return a==="forward"?e-n:e+t}function Kt(a){return Pe(ee(a.handles[a.handles.length-1]),ee(a.handles[0]))}function Ce(a){return`${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};
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