jbrowse-plugin-graphgenomeviewer 7.0.0 → 7.1.1

package/dist/chunks/{WalkTabixSyntenyAdapter-H5NDC7U5.js → WalkTabixSyntenyAdapter-I6E6HAN4.js}

@@ -1,2 +1,2 @@
-import{b as q,c as D,d as H,e as G}from"./chunk-GHL7VXRC.js";import{a as _}from"./chunk-LUTMKRXY.js";import{a as T,b as I,d as j,e as B}from"./chunk-RKOQVSZG.js";import{a as R}from"./chunk-KOB7YIMR.js";import{p as W,q as L}from"./chunk-IXQK7JAW.js";import"./chunk-TXI43PEN.js";import{f as $,g as v}from"./chunk-ECZOKJYP.js";import"./chunk-YBLNN5FU.js";import"./chunk-MVVXRZXV.js";import{a as P,c as F,d as A,e as k,f as N,g as x}from"./chunk-OUN4BNWJ.js";import"./chunk-E7J6SB5P.js";import"./chunk-7WIBGKBU.js";import"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{o as C}from"./chunk-TENPGIPX.js";var Z=50;function ee(m){let e=[];for(let t=0;t<m.length;t++){let[r,s]=m[t],[n,a]=m[t+1]??[];s===a&&s<=Z&&(r==="I"&&n==="D"||r==="D"&&n==="I")?(e.push(["X",s]),t++):e.push([r,s])}return e}function te(m){return m.map(([e,t])=>`${t}${e}`).join("")}function U(m){let e=new Map,t=n=>{let a=m.get(n),i=a===void 0?0:a.end-a.start,p=e.get(i);return p===void 0&&(p="N".repeat(i),e.set(i,p)),p},r=new Map,s=n=>{let a=r.get(n);return a===void 0&&(a=Array.from(n.ids,(i,p)=>2*i+n.rev[p]),r.set(n,a)),a};return(n,a)=>L({query:s(n),target:s(a),sequenceOf:t,bases:!1})}var ae=100;function E(m,e,t){let r=m.at(-1);t>0&&(r?.[0]===e?r[1]+=t:m.push([e,t]))}function X(m){let e=s=>{let n=m.get(s>>1);return n===void 0?0:n.end-n.start},t=s=>{let n=new Float64Array(s.length+1);return s.forEach((a,i)=>{n[i+1]=n[i]+e(a)}),n},r=s=>Array.from(s.ids,(n,a)=>2*n+s.rev[a]);return(s,n)=>{let a=r(n),i=r(s),[p,y]=W(i,a,e),[h,l]=W(i.map(b=>b^1).reverse(),a,e),d=l>y,c=d?h:p,f=Math.max(y,l);if(f<ae)return[];let u=t(a),o=t(i),g=b=>d?i.length-1-c[b][0]:c[b][0],w=[];c.forEach(([,b],S)=>{if(S>0){let[K,Q]=[g(S-1),g(S)].sort((V,Y)=>V-Y);E(w,"I",o[Q]-o[K+1]),E(w,"D",u[b]-u[c[S-1][1]+1])}E(w,"=",e(a[b]))});let[z,J]=[g(0),g(c.length-1)].sort((b,S)=>b-S);return[{queryStart:o[z],queryEnd:o[J+1],targetStart:u[c[0][1]],targetEnd:u[c.at(-1)[1]+1],strand:d?"-":"+",edits:w,sharedBases:f}]}}function O({chain:m,target:e,query:t,assemblyName:r,refName:s,mateAssemblyName:n}){let a=e.hapStart+m.targetStart,i=e.hapStart+m.targetEnd,p=t.hapStart+m.queryStart,y=t.hapStart+m.queryEnd,h=ee(m.edits),l=h.reduce((f,[u,o])=>f+(u==="="?o:0),0),d=h.reduce((f,[,u])=>f+u,0),c=`${e.name}:${a}-${i}|${t.name}:${p}-${y}`;return new T({uniqueId:c,assemblyName:r,refName:s,start:a,end:i,type:"match",strand:m.strand==="-"?-1:1,CIGAR:te(h),syntenyId:c,identity:l/Math.max(d,1),numMatches:l,blockLen:d,mate:{refName:A(t.name),start:p,end:y,assemblyName:n}})}var ne=m=>F(m.name)??m.name,M=class extends I{constructor(e,t,r){super(e,t,r);let s=$(this,["walksLocation"],["walksIndex"]);this.reader=new D(s),this.refNames=new v(s,this)}get anchor(){let e=this.getConf("assemblyNames")[0];if(e===void 0)throw new Error("WalkTabixSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");return e}async getHaplotypeNames(e={}){let{haplotypes:t}=await this.reader.header(e);return t.length>0?t:void 0}async getHeader(e={}){let{haplotypes:t,references:r}=await this.reader.header(e),{anchor:s}=this,n=N(this,s),a=x(this);return{hasCoarseTier:!1,anchorAssemblyName:s,referenceSamples:r,lanes:t.filter(i=>i!==n&&P(i)!==n).map(i=>({name:B(a,i),label:i,group:P(i)}))}}async getRefNames(e={}){let{assemblyName:t}=e;return t===void 0||t===this.anchor?this.refNames.assemblyRefNames({...e,assemblyName:this.anchor}):[]}budgets(){return{stepBudget:this.getConf("walkStepBudget"),byteBudget:this.getConf("walkByteBudget"),budgetNames:H}}async getSubgraph(e,t={}){let{signal:r,haplotypes:s,walkRows:n}=t,a=await this.refNames.resolve(e,{signal:r});if(a===void 0)throw new Error(`${e.assemblyName} ${e.refName} is not in this graph's index; the graph is cut on ${this.anchor}, mapped to its PanSN prefix in assemblyNameToPanSN`);return G(this.reader,a,e,{...this.budgets(),signal:r,prefixes:s?.map(i=>N(this,i)),walkRows:n})}async laneWalks(e,t,r,s,n){return C(n,s.statusCallback,()=>this.reader.cut(e,t,{...this.budgets(),signal:s.signal,keep:q(r,F(e)),links:!1}).catch(a=>{throw _(a)&&a instanceof Error&&(a.message=a.message.replace("to see the graph","to see lanes")),a}))}async anchorFeatures(e,t,r){let s=r.haplotypes?.length?r.haplotypes.map(o=>N(this,o)):void 0,n=N(this,r.targetAssemblyName),a=n===void 0?s:s===void 0||s.some(o=>k(n,o)||k(o,n))?[n]:[];if(a?.length===0)return[];let{start:i,end:p}=t,{graph:y,fragments:h}=await this.laneWalks(e,t,a,r,`Reading walks ${t.refName}:${i.toLocaleString()}-${p.toLocaleString()}`),l=X(y.nodes),d=x(this),c=h.filter(o=>o.name===e),f=o=>a===void 0?0:a.findIndex(g=>k(o.name,g));return h.filter(o=>o.name!==e&&f(o)>=0).sort((o,g)=>f(o)-f(g)).flatMap(o=>c.flatMap(g=>l(o,g).map(w=>O({chain:w,target:g,query:o,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:B(d,ne(o))}))))}async pairFeatures(e,t,r,s){let[n]=r,a=r.map(l=>({pair:l,featurePrefix:N(this,l.queryAssemblyName),matePrefix:N(this,l.targetAssemblyName)})),{graph:i,fragments:p}=await this.laneWalks(e,t,a.flatMap(l=>[l.featurePrefix,l.matePrefix]),s,r.length===1&&n?`Reading ${n.queryAssemblyName} against ${n.targetAssemblyName}`:`Reading ${r.length} lane pairs`),y=U(i.nodes),h=l=>p.filter(d=>k(d.name,l));return a.flatMap(({pair:l,featurePrefix:d,matePrefix:c})=>h(d).flatMap(f=>h(c).flatMap(u=>y(u,f).map(o=>O({chain:o,target:f,query:u,assemblyName:l.queryAssemblyName,refName:A(f.name),mateAssemblyName:l.targetAssemblyName})))))}getFeatures(e,t={}){return R(async r=>{let s=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(s!==void 0){let n=j(t),a=n.length>0?await this.pairFeatures(s,e,n,t):await this.anchorFeatures(s,e,t);for(let i of a)r.next(i)}r.complete()},t.signal)}};export{M as default};
-//# sourceMappingURL=WalkTabixSyntenyAdapter-H5NDC7U5.js.map
+import{b as q,c as D,d as H,e as G}from"./chunk-2QQDYK5V.js";import{a as _}from"./chunk-LUTMKRXY.js";import{a as T,b as I,d as j,e as B}from"./chunk-WI7LRX6I.js";import{a as R}from"./chunk-KOB7YIMR.js";import{p as W,q as L}from"./chunk-T4HOC6O3.js";import"./chunk-TXI43PEN.js";import{f as $,g as v}from"./chunk-4IJKHORO.js";import"./chunk-YBLNN5FU.js";import"./chunk-MVVXRZXV.js";import{a as P,c as F,d as A,e as k,f as N,g as x}from"./chunk-IIGYYZI5.js";import"./chunk-E7J6SB5P.js";import"./chunk-7WIBGKBU.js";import"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{o as C}from"./chunk-TENPGIPX.js";var Z=50;function ee(m){let e=[];for(let t=0;t<m.length;t++){let[r,s]=m[t],[n,a]=m[t+1]??[];s===a&&s<=Z&&(r==="I"&&n==="D"||r==="D"&&n==="I")?(e.push(["X",s]),t++):e.push([r,s])}return e}function te(m){return m.map(([e,t])=>`${t}${e}`).join("")}function U(m){let e=new Map,t=n=>{let a=m.get(n),i=a===void 0?0:a.end-a.start,p=e.get(i);return p===void 0&&(p="N".repeat(i),e.set(i,p)),p},r=new Map,s=n=>{let a=r.get(n);return a===void 0&&(a=Array.from(n.ids,(i,p)=>2*i+n.rev[p]),r.set(n,a)),a};return(n,a)=>L({query:s(n),target:s(a),sequenceOf:t,bases:!1})}var ae=100;function E(m,e,t){let r=m.at(-1);t>0&&(r?.[0]===e?r[1]+=t:m.push([e,t]))}function X(m){let e=s=>{let n=m.get(s>>1);return n===void 0?0:n.end-n.start},t=s=>{let n=new Float64Array(s.length+1);return s.forEach((a,i)=>{n[i+1]=n[i]+e(a)}),n},r=s=>Array.from(s.ids,(n,a)=>2*n+s.rev[a]);return(s,n)=>{let a=r(n),i=r(s),[p,y]=W(i,a,e),[h,l]=W(i.map(b=>b^1).reverse(),a,e),d=l>y,c=d?h:p,f=Math.max(y,l);if(f<ae)return[];let u=t(a),o=t(i),g=b=>d?i.length-1-c[b][0]:c[b][0],w=[];c.forEach(([,b],S)=>{if(S>0){let[K,Q]=[g(S-1),g(S)].sort((V,Y)=>V-Y);E(w,"I",o[Q]-o[K+1]),E(w,"D",u[b]-u[c[S-1][1]+1])}E(w,"=",e(a[b]))});let[z,J]=[g(0),g(c.length-1)].sort((b,S)=>b-S);return[{queryStart:o[z],queryEnd:o[J+1],targetStart:u[c[0][1]],targetEnd:u[c.at(-1)[1]+1],strand:d?"-":"+",edits:w,sharedBases:f}]}}function O({chain:m,target:e,query:t,assemblyName:r,refName:s,mateAssemblyName:n}){let a=e.hapStart+m.targetStart,i=e.hapStart+m.targetEnd,p=t.hapStart+m.queryStart,y=t.hapStart+m.queryEnd,h=ee(m.edits),l=h.reduce((f,[u,o])=>f+(u==="="?o:0),0),d=h.reduce((f,[,u])=>f+u,0),c=`${e.name}:${a}-${i}|${t.name}:${p}-${y}`;return new T({uniqueId:c,assemblyName:r,refName:s,start:a,end:i,type:"match",strand:m.strand==="-"?-1:1,CIGAR:te(h),syntenyId:c,identity:l/Math.max(d,1),numMatches:l,blockLen:d,mate:{refName:A(t.name),start:p,end:y,assemblyName:n}})}var ne=m=>F(m.name)??m.name,M=class extends I{constructor(e,t,r){super(e,t,r);let s=$(this,["walksLocation"],["walksIndex"]);this.reader=new D(s),this.refNames=new v(s,this)}get anchor(){let e=this.getConf("assemblyNames")[0];if(e===void 0)throw new Error("WalkTabixSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");return e}async getHaplotypeNames(e={}){let{haplotypes:t}=await this.reader.header(e);return t.length>0?t:void 0}async getHeader(e={}){let{haplotypes:t,references:r}=await this.reader.header(e),{anchor:s}=this,n=N(this,s),a=x(this);return{hasCoarseTier:!1,anchorAssemblyName:s,referenceSamples:r,lanes:t.filter(i=>i!==n&&P(i)!==n).map(i=>({name:B(a,i),label:i,group:P(i)}))}}async getRefNames(e={}){let{assemblyName:t}=e;return t===void 0||t===this.anchor?this.refNames.assemblyRefNames({...e,assemblyName:this.anchor}):[]}budgets(){return{stepBudget:this.getConf("walkStepBudget"),byteBudget:this.getConf("walkByteBudget"),budgetNames:H}}async getSubgraph(e,t={}){let{signal:r,haplotypes:s,walkRows:n}=t,a=await this.refNames.resolve(e,{signal:r});if(a===void 0)throw new Error(`${e.assemblyName} ${e.refName} is not in this graph's index; the graph is cut on ${this.anchor}, mapped to its PanSN prefix in assemblyNameToPanSN`);return G(this.reader,a,e,{...this.budgets(),signal:r,prefixes:s?.map(i=>N(this,i)),walkRows:n})}async laneWalks(e,t,r,s,n){return C(n,s.statusCallback,()=>this.reader.cut(e,t,{...this.budgets(),signal:s.signal,keep:q(r,F(e)),links:!1}).catch(a=>{throw _(a)&&a instanceof Error&&(a.message=a.message.replace("to see the graph","to see lanes")),a}))}async anchorFeatures(e,t,r){let s=r.haplotypes?.length?r.haplotypes.map(o=>N(this,o)):void 0,n=N(this,r.targetAssemblyName),a=n===void 0?s:s===void 0||s.some(o=>k(n,o)||k(o,n))?[n]:[];if(a?.length===0)return[];let{start:i,end:p}=t,{graph:y,fragments:h}=await this.laneWalks(e,t,a,r,`Reading walks ${t.refName}:${i.toLocaleString()}-${p.toLocaleString()}`),l=X(y.nodes),d=x(this),c=h.filter(o=>o.name===e),f=o=>a===void 0?0:a.findIndex(g=>k(o.name,g));return h.filter(o=>o.name!==e&&f(o)>=0).sort((o,g)=>f(o)-f(g)).flatMap(o=>c.flatMap(g=>l(o,g).map(w=>O({chain:w,target:g,query:o,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:B(d,ne(o))}))))}async pairFeatures(e,t,r,s){let[n]=r,a=r.map(l=>({pair:l,featurePrefix:N(this,l.queryAssemblyName),matePrefix:N(this,l.targetAssemblyName)})),{graph:i,fragments:p}=await this.laneWalks(e,t,a.flatMap(l=>[l.featurePrefix,l.matePrefix]),s,r.length===1&&n?`Reading ${n.queryAssemblyName} against ${n.targetAssemblyName}`:`Reading ${r.length} lane pairs`),y=U(i.nodes),h=l=>p.filter(d=>k(d.name,l));return a.flatMap(({pair:l,featurePrefix:d,matePrefix:c})=>h(d).flatMap(f=>h(c).flatMap(u=>y(u,f).map(o=>O({chain:o,target:f,query:u,assemblyName:l.queryAssemblyName,refName:A(f.name),mateAssemblyName:l.targetAssemblyName})))))}getFeatures(e,t={}){return R(async r=>{let s=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(s!==void 0){let n=j(t),a=n.length>0?await this.pairFeatures(s,e,n,t):await this.anchorFeatures(s,e,t);for(let i of a)r.next(i)}r.complete()},t.signal)}};export{M as default};
+//# sourceMappingURL=WalkTabixSyntenyAdapter-I6E6HAN4.js.map