jbrowse-plugin-graphgenomeviewer 6.11.0 → 6.12.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/chunks/{GbzBaseSyntenyAdapter-SPT62NR4.js → GbzBaseSyntenyAdapter-SFTZXPG5.js} +2 -2
- package/dist/chunks/{RgfaTabixAdapter-5ZRSJMIP.js → RgfaTabixAdapter-L55JCQKS.js} +2 -2
- package/dist/chunks/WalkTabixSyntenyAdapter-G4O2572E.js +2 -0
- package/dist/chunks/WalkTabixSyntenyAdapter-G4O2572E.js.map +7 -0
- package/dist/chunks/{chunk-KROCIQJP.js → chunk-SYETHCAR.js} +5 -5
- package/dist/chunks/{chunk-KROCIQJP.js.map → chunk-SYETHCAR.js.map} +1 -1
- package/dist/chunks/chunk-WSZ6RCMI.js +2 -0
- package/dist/chunks/{chunk-TVXMEJLJ.js.map → chunk-WSZ6RCMI.js.map} +3 -3
- package/dist/jbrowse-plugin-graphgenomeviewer.esm.js +2 -2
- package/dist/jbrowse-plugin-graphgenomeviewer.esm.js.map +2 -2
- package/package.json +2 -2
- package/src/RgfaTabixAdapter/configSchema.ts +3 -2
- package/src/RgfaTabixAdapter/walkReader.ts +22 -4
- package/src/RgfaTabixAdapter/walkRows.ts +22 -0
- package/src/WalkTabixSyntenyAdapter/WalkTabixSyntenyAdapter.test.ts +79 -1
- package/src/WalkTabixSyntenyAdapter/WalkTabixSyntenyAdapter.ts +2 -2
- package/src/WalkTabixSyntenyAdapter/configSchema.ts +3 -2
- package/src/WalkTabixSyntenyAdapter/walkLanes.ts +83 -1
- package/src/version.ts +1 -1
- package/dist/chunks/WalkTabixSyntenyAdapter-2KJTYCX3.js +0 -2
- package/dist/chunks/WalkTabixSyntenyAdapter-2KJTYCX3.js.map +0 -7
- package/dist/chunks/chunk-TVXMEJLJ.js +0 -2
- /package/dist/chunks/{GbzBaseSyntenyAdapter-SPT62NR4.js.map → GbzBaseSyntenyAdapter-SFTZXPG5.js.map} +0 -0
- /package/dist/chunks/{RgfaTabixAdapter-5ZRSJMIP.js.map → RgfaTabixAdapter-L55JCQKS.js.map} +0 -0
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//# sourceMappingURL=GbzBaseSyntenyAdapter-
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import{c as J,d as K,e as q,f as ne,g as me,h as ae}from"./chunk-SYETHCAR.js";import{b as G,c as V,d as ee,e as te}from"./chunk-X4NNWAXW.js";import{a as O,b as H}from"./chunk-NU53CDGF.js";import{f as le,g as Z,h,i as B,j as z,k as R,l as M,m as k,o as E}from"./chunk-R4DSKZ5P.js";import"./chunk-PR5YUSXN.js";import{a as P}from"./chunk-OGQ6OQDN.js";import"./chunk-YBLNN5FU.js";import{e as F,f as S,g as C}from"./chunk-XKN5LH2Z.js";import"./chunk-E7J6SB5P.js";import{b as U,c as X,d as Y}from"./chunk-R3TRNF7N.js";import"./chunk-7WIBGKBU.js";import{e as W,o as $}from"./chunk-TENPGIPX.js";function A(n){let i=/\.gbz\.db$/i;return i.test(n)?n.replace(i,".haplotype-index.db"):void 0}function de(n){return X(n)&&A(U(n))?Y(n,i=>A(i)):void 0}function fe(n){return n instanceof Error&&(/\bHTTP 40[34]\b/.test(n.message)||n.code==="ENOENT")}async function re(n,i){let t=de(n);if(!t)return{};try{return await P(t,i).stat(),{location:t}}catch(e){return fe(e)?{}:{unreadable:String(e)}}}var he=5e3,ue=50*2**20,T=class extends Error{constructor(t){super(`this GAF is ${(t/2**20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`);this.name="UnindexedGafTooLargeError"}};function ge(n,i){if(n.length<=i)return n;let t=n.length/i;return Array.from({length:i},(e,a)=>n[Math.floor(a*t)])}var oe=(n,i)=>n.path.some(t=>i.has(t.name)),I=class{constructor(i,t){this.file=i;this.tabix=t;this.whole=G({setup:async({signal:i})=>{let{size:t}=await this.file.stat();if(t>ue)throw new T(t);let e=await this.file.readFile({signal:i}),a=new TextDecoder().decode(e[0]===31&&e[1]===139?await ee(e):e);return H(a)}})}async readIndexed(i,t,e){let a=1/0,r=-1/0;for(let c of t){let s=Number(c);Number.isInteger(s)&&(a=Math.min(a,s),r=Math.max(r,s))}let o=[];return a<=r&&await i.getLines("{node}",a,r+1,{signal:e,lineCallback:c=>{let s=O(c);s&&oe(s,t)&&o.push(s)}}),o}async readsOver(i,{signal:t}={}){let e=this.tabix?await this.readIndexed(this.tabix,i,t):(await this.whole({signal:t})).filter(a=>oe(a,i));return{records:ge(e,he),total:e.length}}};var v=class extends Error{constructor(t){super(t===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${t}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`);this.name="NoHaplotypeIndexError"}},D=class extends Error{constructor(t,e){super(`the graph is cut on its reference, ${e}; a window on ${t} has no reference coordinates to cut at. Open the graph from a ${e} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function se(n,i){let t=h(i);return n[t]??n[i.sample]??t}function ye(n,i){return`${h(n)}#${n.contig}@${i.start.node}.${i.start.offset}`}function be({alignment:n,assemblyName:i,refName:t,lane:e}){let{refStart:a,refEnd:r,strand:o,cigar:c}=n;if(!(!n.resolved||r<=a)){let{name:s,hapStart:p,hapEnd:m}=n,u=ye(s,n),g={uniqueId:u,assemblyName:i,refName:t,start:a,end:r,type:"match",strand:o==="-"?-1:1,CIGAR:c,syntenyId:u,mate:{refName:s.contig,start:p,end:m,assemblyName:e}};return new q(g)}}function xe({pair:n,lane:i,mateLane:t}){let e=`${h(n.target)}#${n.target.contig}:${n.targetStart}-${n.targetEnd}|${h(n.query)}#${n.query.contig}:${n.queryStart}-${n.queryEnd}`;return new q({uniqueId:e,assemblyName:i,refName:n.target.contig,start:n.targetStart,end:n.targetEnd,type:"match",strand:n.strand==="-"?-1:1,CIGAR:n.cigar,syntenyId:e,identity:n.matches/Math.max(n.columns,1),numMatches:n.matches,blockLen:n.columns,mate:{refName:n.query.contig,start:n.queryStart,end:n.queryEnd,assemblyName:t}})}var we=12e4;function Se(n,i){let t=new Map;for(let a of n)for(let{name:r,start:o,end:c}of a.walkSpans()){let s=h(r);if(i.has(s)){let p=`${s}#${r.contig}`;t.set(p,[...t.get(p)??[],[o,c]])}}let e=0;for(let a of t.values()){a.sort((r,o)=>r[0]-o[0]);for(let r=1;r<a.length;r++){let o=a[r][0]-a[r-1][1];o>0&&o<=we&&(e=Math.max(e,o))}}return e}function _(n,i){return n instanceof Z&&(n.message=`Zoom in to about ${W(n.fitsBp)} to see ${i}`),n}var Q=n=>!("uri"in n)||n.uri!=="",j=class extends ne{constructor(){super(...arguments);this.graph=G({label:"Opening pangenome database",setup:async()=>{let t=this.getConf("gbzDbLocation"),e=this.getConf("haplotypeIndexLocation"),a=Q(e)?{location:e}:await re(t,this.pluginManager),r=a.location,o=await K.open({source:P(t,this.pluginManager),haplotypeIndex:r?P(r,this.pluginManager):void 0}),c=this.getConf("assemblyNames")[0];if(c===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let s=await z(o),p=R({configured:this.getConf("referenceSample"),anchorPrefix:S(this,c),referenceSamples:s});return{db:o,anchor:c,referenceSample:p,referenceSamples:s,unreadableIndex:a.unreadable}}});this.gaf=G({label:"Opening reads",setup:async()=>{let t=this.getConf("readsLocation"),e=this.getConf(["readsIndex","location"]);return Q(t)?new I(P(t,this.pluginManager),Q(e)?te(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(t,e){let{db:a,referenceSample:r}=await this.graph(e);return M(a,r,t)}async getHaplotypes(t={}){let{db:e,referenceSamples:a}=await this.graph(t),r=new Map;for(let o of await e.paths()){let c=h(o.name),s=r.get(c);s?s.contigs.includes(o.name.contig)||s.contigs.push(o.name.contig):r.set(c,{prefix:c,sample:o.name.sample,haplotype:o.name.haplotype,contigs:[o.name.contig],isReference:a.includes(o.name.sample)})}return[...r.values()]}async getHeader(t={}){let{anchor:e,referenceSample:a,referenceSamples:r}=await this.graph(t),o=C(this),c=[];for(let s of await this.getHaplotypes(t))s.sample!==a&&c.push({name:se(o,s),label:s.prefix,group:s.sample});return{hasCoarseTier:!1,anchorAssemblyName:e,referenceSample:a,referenceSamples:r,lanes:c}}async getRefNames(t={}){let{db:e,anchor:a,referenceSample:r}=await this.graph(t),{assemblyName:o}=t,c=o===a?void 0:S(this,o),s=(await e.paths()).filter(p=>o===a?p.isIndexed&&p.name.sample===r:F(h(p.name),c)).map(p=>p.name.contig);return[...new Set(s)]}keepPredicate(t,e){let a=t===void 0||t.length===0?void 0:t.map(r=>S(this,r));return a===void 0&&e===void 0?void 0:r=>B(r,a)&&(e===void 0||F(h(r),e))}async getSubgraph(t,e={}){let{signal:a}=e,{db:r,anchor:o,referenceSample:c,unreadableIndex:s}=await this.graph({signal:a}),{assemblyName:p,refName:m,start:u,end:g}=t;if(p!==o)throw new D(p,o);let y=await this.referenceQuery(m,{signal:a});if(!y)throw new Error(`${c} has no indexed path ${m} in this graph`);let x=this.keepPredicate(e.haplotypes);if(x!==void 0&&!r.hasHaplotypeIndex)throw new v(s);return E(r,y,u,g,{context:this.getConf("context"),snarls:e.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:e.signal,keep:x}).catch(d=>{throw _(d,"the graph")})}async getReads(t,e={}){let a=await this.gaf(e);return a?a.readsOver(new Set(t),e):{records:[],total:0}}async laneHaplotypes(t,e){let a=S(this,t);return(await this.getHaplotypes(e)).filter(r=>F(r.prefix,a))}async anchorFeatures(t,e){let{db:a}=await this.graph(e),{assemblyName:r,refName:o,start:c,end:s}=t,p=S(this,e.targetAssemblyName),m=C(this),u=this.keepPredicate(e.haplotypes,p),g=await this.referenceQuery(o,e),y=this.getConf("nodeLimit");return(g?await $(`Reading graph ${o}:${c.toLocaleString()}-${s.toLocaleString()}`,e.statusCallback,()=>a.getAlignments({path:g,start:c,end:s,context:this.getConf("context"),haplotypes:"all",limit:y,signal:e.signal,keep:u}).catch(d=>{throw _(k(d,y,s-c)??d,"lanes")})):[]).flatMap(d=>{let N=d.resolved?be({alignment:d,assemblyName:r,refName:o,lane:se(m,d.name)}):void 0;return N===void 0?[]:[N]})}async pairFeatures(t,e,a){let{db:r}=await this.graph(a),{refName:o,start:c,end:s}=t,m=(await Promise.all(e.map(async l=>({pair:l,featureSide:await this.laneHaplotypes(l.queryAssemblyName,a),mateSide:await this.laneHaplotypes(l.targetAssemblyName,a)})))).filter(({featureSide:l,mateSide:f})=>l.length>0&&f.length>0),u=new Set(m.flatMap(({featureSide:l,mateSide:f})=>[...l,...f].map(h))),g=await this.referenceQuery(o,a),y=this.getConf("nodeLimit"),x=this.getConf("context"),[d]=e,N=(l,f)=>r.getSubgraphs({path:l,start:c,end:s,context:f,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:a.signal,keep:w=>u.has(h(w))}),ie=async l=>{let f=await N(l,x).catch(b=>{throw _(k(b,y,s-c)??b,"lanes")}),w=Se(f,u),L=Math.ceil(w/2)+2e3;return w>0&&L>x?N(l,L).catch(b=>{if(b instanceof J)return f;throw b}):f};return(g&&d&&m.length>0?await $(e.length===1?`Reading ${d.queryAssemblyName} against ${d.targetAssemblyName}`:`Reading ${e.length} lane pairs`,a.statusCallback,()=>ie(g)):[]).flatMap(l=>m.flatMap(({pair:f,featureSide:w,mateSide:L})=>w.flatMap(b=>L.flatMap(ce=>l.pairAlignments({target:b,query:ce,bases:!1}).map(pe=>xe({pair:pe,lane:f.queryAssemblyName,mateLane:f.targetAssemblyName}))))))}getFeatures(t,e={}){return V(async a=>{let{db:r,anchor:o,unreadableIndex:c}=await this.graph(e);if(!r.hasHaplotypeIndex)throw new v(c);if(t.assemblyName===o){let s=ae(e),p=s.length>0?await this.pairFeatures(t,s,e):await this.anchorFeatures(t,e);for(let m of p)a.next(m)}a.complete()},e.signal)}};export{D as HaplotypeWindowError,v as NoHaplotypeIndexError,le as NoReferenceSampleError,me as PairTargetError,j as default,be as fragmentFeature,se as laneAssemblyName,xe as pairFeature,R as resolveReferenceSample,Se as widestWalkGap};
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import{a as u,b as v,c as P}from"./chunk-
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import{a as u,b as v,c as P}from"./chunk-WSZ6RCMI.js";import{a as B,c as F,e as N,f as I}from"./chunk-X4NNWAXW.js";import"./chunk-R4DSKZ5P.js";import"./chunk-PR5YUSXN.js";import"./chunk-OGQ6OQDN.js";import"./chunk-YBLNN5FU.js";import{c as A,f as M}from"./chunk-XKN5LH2Z.js";import{a as $,o as T}from"./chunk-TENPGIPX.js";function y(i){let e=i.split(" "),a=e.length>=8,s=a?5:0;return{anchored:a,segment:{refName:e[s],start:+e[s+1],end:+e[s+2],id:e[3],rank:+e[4],tags:e[a?8:5]??""}}}function j(i){let e=i.tags.split(" ").find(s=>s.startsWith("SM:Z:"));if(e===void 0)return;let a=e.slice(5).split(",").map(s=>s.trim()).filter(Boolean);return a.length>0?a:void 0}function O(i){return{id:i.slice(0,-1),strand:i.slice(-1)}}function x(i){let e=i.split(" "),a=O(e[3]),s=O(e[4]);return{source:a.id,sourceStrand:a.strand,target:s.id,targetStrand:s.strand,sourceSegment:{id:a.id,refName:e[5],start:+e[6],end:+e[7],rank:+e[8],tags:e[13]??""},targetSegment:{id:s.id,refName:e[9],start:+e[10],end:+e[11],rank:+e[12],tags:e[14]??""}}}function S(i){return`${i.source}${i.sourceStrand}${i.target}${i.targetStrand}`}function Z(i,e,a){let s=n=>n.rank!==0||n.refName!==a.refName?0:n.end<=a.start?-1:n.start>=a.end?1:0,t=new Map(i),r=new Map;for(let n of e)if(i.has(n.source)||i.has(n.target)||s(n.sourceSegment)*s(n.targetSegment)===-1){r.set(S(n),n);for(let o of[n.sourceSegment,n.targetSegment])t.has(o.id)||t.set(o.id,o)}for(let n of e)t.has(n.source)&&t.has(n.target)&&r.set(S(n),n);return{segments:t,links:r}}function W(i,e,a){let s=t=>t.refName!==a.refName||t.end<=a.start||t.start>=a.end;return[...G(i.filter(t=>t.rank>0),e,a.end-a.start),...G(i.filter(t=>t.rank===0&&s(t)),new Set(i.map(t=>t.id)),0)]}function G(i,e,a){let s=[...i].sort((r,n)=>R(r.refName,n.refName)||r.start-n.start),t=[];for(let r of s){let n=t.at(-1);n?.refName===r.refName&&r.start-n.end<=a?(n.needed||=r.start>n.end||e.has(r.id),n.end=Math.max(n.end,r.end)):t.push({refName:r.refName,start:r.start,end:r.end,needed:e.has(r.id)})}return t.filter(r=>r.needed).map(({refName:r,start:n,end:o})=>({refName:r,start:n,end:o}))}function H(i,e,a){let s=t=>e.has(t.id)||a.some(r=>r.refName===t.refName&&t.start>=r.start&&t.end<=r.end);return i.filter(t=>s(t.sourceSegment)&&s(t.targetSegment))}var E=/^[A-Za-z][A-Za-z0-9]:[AifZJHB]:/;function K(i){let{id:e,refName:a,start:s,end:t,rank:r,tags:n}=i,o=n.split(" ").filter(f=>E.test(f)),c=o.length===0?"":` ${o.join(" ")}`;return`S ${e} * LN:i:${t-s} SN:Z:${a} SO:i:${s} SR:i:${r}${c}`}function z(i){let{source:e,sourceStrand:a,target:s,targetStrand:t}=i;return`L ${e} ${a} ${s} ${t} 0M`}function R(i,e){return i<e?-1:i>e?1:0}function L(i,e){let a=[...i.values()].sort((t,r)=>R(t.refName,r.refName)||t.start-r.start||R(t.id,r.id)),s=[...e.keys()].sort((t,r)=>R(t,r));return["H VN:Z:1.0",...a.map(t=>K(t)),...s.map(t=>z(e.get(t)))].join(`
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`)}function _(i){return i.filter(e=>e.rank>0)}var J=1e3,C=class extends B{static{this.capabilities=["getFeatures","getRefNames"]}constructor(e,a,s){super(e,a,s),this.fine=this.openIndex([])}openIndex(e){let a=N(this,[...e,"segmentsLocation"],[...e,"segmentsIndex"]),s=this.getConf("walksLocation"),t=e.length===0&&(!("uri"in s)||s.uri!==""),r=N(this,[...e,"linksLocation"],[...e,"linksIndex"]);return{segments:a,links:r,walks:t?new P({walks:N(this,["walksLocation"],["walksIndex"]),nodes:a,links:r},this.getConf("walkChunk")):void 0,refNames:new I(a,this)}}async getHaplotypeNames(e={}){let a=await this.fine.walks?.header(e);return a?.haplotypes.length?a.haplotypes:void 0}index(e="fine"){return e==="fine"?this.fine:(this.coarse??=this.openIndex(["coarse"]),this.coarse)}async getRefNames(e={}){return this.fine.refNames.assemblyRefNames(e)}async hasDataForRefName(){return!0}getFeatures(e,a={}){let{signal:s,statusCallback:t}=a;return F(async r=>{let n=await this.fine.refNames.resolve(e,a);if(n!==void 0){let o=this.fine.walks?await this.fine.walks.queryStart(e.start,a):e.start;await T("Downloading segments",t,()=>u(this.fine.segments,n,o,e.end,{signal:s,lineCallback:c=>{let{segment:f,anchored:h}=y(c);if(h&&f.refName!==n)return;let l=j(f);r.next(new $({uniqueId:f.id,refName:e.refName,start:f.start,end:f.end,name:f.id,type:"segment",rank:f.rank,stableName:f.refName,...l&&{samples:l,sampleCount:l.length}}))}}))}r.complete()},s)}async getSubgraph(e,a={}){let{hops:s=0,signal:t,tier:r}=a,n=this.index(r),o=new Map,c=new Map,f=await n.refNames.resolve(e,{signal:t}),h=async(p,m,g)=>{let d=[];return await u(n.links,p,m,g,{signal:t,lineCallback:D=>{let k=x(D);c.set(S(k),k);for(let b of[k.sourceSegment,k.targetSegment])o.has(b.id)||(o.set(b.id,b),d.push(b))}}),d};if(f===void 0)throw new Error(`${e.assemblyName} ${e.refName} is not in this graph's index; a graph with PanSN names (GRCh38#0#chr1) needs ${e.assemblyName} mapped to its prefix in assemblyNameToPanSN`);if(n.walks)return this.walkSubgraph(n.walks,f,e,a);let l={anchored:!1};if(await u(n.segments,f,e.start,e.end,{signal:t,lineCallback:p=>{let m=y(p);l.anchored||=m.anchored,o.set(m.segment.id,m.segment)}}),l.anchored){let p=[];await u(n.links,f,e.start,e.end,{signal:t,lineCallback:g=>{p.push(x(g))}});let m=Z(o,p,{refName:f,start:e.start,end:e.end});return L(m.segments,m.links)}let w=_(await h(f,e.start,e.end));for(let p=0;p<s;p++){let m=await Promise.all(w.map(g=>h(g.refName,g.start,g.end)));w=_(m.flat())}if(s>0){let p=W([...o.values()],new Set(w.map(g=>g.id)),{refName:f,start:e.start,end:e.end}),m=[];await Promise.all(p.map(g=>u(n.links,g.refName,g.start,g.end,{signal:t,lineCallback:d=>{m.push(x(d))}})));for(let g of H(m,o,p)){c.set(S(g),g);for(let d of[g.sourceSegment,g.targetSegment])o.has(d.id)||o.set(d.id,d)}}return L(o,c)}async walkSubgraph(e,a,s,t){let{graph:r,kept:n,fragments:o}=await e.cut(a,s,{signal:t.signal,keep:v(t.haplotypes?.map(c=>M(this,c)),A(a)),stepBudget:this.getConf("walkStepBudget"),byteBudget:this.getConf("walkByteBudget"),context:J});return r.tables(n,o)}};export{C as default};
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import{b as C,c as j}from"./chunk-WSZ6RCMI.js";import{a as O,b as $,e as I,f as _,h as q}from"./chunk-SYETHCAR.js";import{c as v,e as x,f as T}from"./chunk-X4NNWAXW.js";import{g as R}from"./chunk-R4DSKZ5P.js";import"./chunk-PR5YUSXN.js";import"./chunk-OGQ6OQDN.js";import"./chunk-YBLNN5FU.js";import{a as S,c as P,d as F,e as A,f as N,g as W}from"./chunk-XKN5LH2Z.js";import"./chunk-E7J6SB5P.js";import"./chunk-7WIBGKBU.js";import{o as L}from"./chunk-TENPGIPX.js";var V=50;function Y(i){let e=[];for(let t=0;t<i.length;t++){let[r,s]=i[t],[a,n]=i[t+1]??[];s===n&&s<=V&&(r==="I"&&a==="D"||r==="D"&&a==="I")?(e.push(["X",s]),t++):e.push([r,s])}return e}function Z(i){return i.map(([e,t])=>`${t}${e}`).join("")}function D(i){let e=new Map,t=a=>{let n=i.get(a),o=n===void 0?0:n.end-n.start,p=e.get(o);return p===void 0&&(p="N".repeat(o),e.set(o,p)),p},r=new Map,s=a=>{let n=r.get(a);return n===void 0&&(n=Array.from(a.ids,(o,p)=>2*o+a.rev[p]),r.set(a,n)),n};return(a,n)=>$({query:s(a),target:s(n),sequenceOf:t,bases:!1})}var ee=100;function E(i,e,t){let r=i.at(-1);t>0&&(r?.[0]===e?r[1]+=t:i.push([e,t]))}function H(i){let e=s=>{let a=i.get(s>>1);return a===void 0?0:a.end-a.start},t=s=>{let a=new Float64Array(s.length+1);return s.forEach((n,o)=>{a[o+1]=a[o]+e(n)}),a},r=s=>Array.from(s.ids,(a,n)=>2*a+s.rev[n]);return(s,a)=>{let n=r(a),o=r(s),[p,h]=O(o,n,e),[g,l]=O(o.map(b=>b^1).reverse(),n,e),f=l>h,c=f?g:p,d=Math.max(h,l);if(d<ee)return[];let u=t(n),m=t(o),y=b=>f?o.length-1-c[b][0]:c[b][0],w=[];c.forEach(([,b],k)=>{if(k>0){let[K,U]=[y(k-1),y(k)].sort((J,Q)=>J-Q);E(w,"I",m[U]-m[K+1]),E(w,"D",u[b]-u[c[k-1][1]+1])}E(w,"=",e(n[b]))});let[G,z]=[y(0),y(c.length-1)].sort((b,k)=>b-k);return[{queryStart:m[G],queryEnd:m[z+1],targetStart:u[c[0][1]],targetEnd:u[c.at(-1)[1]+1],strand:f?"-":"+",edits:w,sharedBases:d}]}}function M({chain:i,target:e,query:t,assemblyName:r,refName:s,mateAssemblyName:a}){let n=e.hapStart+i.targetStart,o=e.hapStart+i.targetEnd,p=t.hapStart+i.queryStart,h=t.hapStart+i.queryEnd,g=Y(i.edits),l=g.reduce((d,[u,m])=>d+(u==="="?m:0),0),f=g.reduce((d,[,u])=>d+u,0),c=`${e.name}:${n}-${o}|${t.name}:${p}-${h}`;return new I({uniqueId:c,assemblyName:r,refName:s,start:n,end:o,type:"match",strand:i.strand==="-"?-1:1,CIGAR:Z(g),syntenyId:c,identity:l/Math.max(f,1),numMatches:l,blockLen:f,mate:{refName:F(t.name),start:p,end:h,assemblyName:a}})}var te=1e3;function X(i,e){return i[e]??i[S(e)]??e}var ae=i=>P(i.name)??i.name,B=class extends _{constructor(e,t,r){super(e,t,r);let s=x(this,["nodesLocation"],["nodesIndex"]);this.reader=new j({walks:x(this,["walksLocation"],["walksIndex"]),nodes:s,links:x(this,["linksLocation"],["linksIndex"])},this.getConf("walkChunk")),this.refNames=new T(s,this)}get anchor(){let e=this.getConf("assemblyNames")[0];if(e===void 0)throw new Error("WalkTabixSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");return e}async getHaplotypeNames(e={}){let{haplotypes:t}=await this.reader.header(e);return t.length>0?t:void 0}async getHeader(e={}){let{haplotypes:t,references:r}=await this.reader.header(e),{anchor:s}=this,a=N(this,s),n=W(this);return{hasCoarseTier:!1,anchorAssemblyName:s,referenceSamples:r,lanes:t.filter(o=>o!==a&&S(o)!==a).map(o=>({name:X(n,o),label:o,group:S(o)}))}}async getRefNames(e={}){let{assemblyName:t}=e;return t===void 0||t===this.anchor?this.refNames.assemblyRefNames({...e,assemblyName:this.anchor}):[]}budgets(){return{stepBudget:this.getConf("walkStepBudget"),byteBudget:this.getConf("walkByteBudget"),context:te}}async getSubgraph(e,t={}){let{signal:r,haplotypes:s}=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`);let{graph:n,kept:o,fragments:p}=await this.reader.cut(a,e,{...this.budgets(),signal:r,keep:C(s?.map(h=>N(this,h)),P(a))});return n.tables(o,p)}async laneWalks(e,t,r,s,a){return L(a,s.statusCallback,()=>this.reader.cut(e,t,{...this.budgets(),signal:s.signal,keep:C(r,P(e)),links:!1}).catch(n=>{throw n instanceof R&&(n.message=n.message.replace("to see the graph","to see lanes")),n}))}async anchorFeatures(e,t,r){let s=r.haplotypes?.length?r.haplotypes.map(m=>N(this,m)):void 0,a=N(this,r.targetAssemblyName),n=a===void 0?s:s===void 0||s.some(m=>A(a,m)||A(m,a))?[a]:[];if(n?.length===0)return[];let{start:o,end:p}=t,{graph:h,fragments:g}=await this.laneWalks(e,t,n,r,`Reading walks ${t.refName}:${o.toLocaleString()}-${p.toLocaleString()}`),l=H(h.nodes),f=W(this),c=g.filter(m=>m.name===e),d=m=>n===void 0?0:n.findIndex(y=>A(m.name,y));return g.filter(m=>m.name!==e&&d(m)>=0).sort((m,y)=>d(m)-d(y)).flatMap(m=>c.flatMap(y=>l(m,y).map(w=>M({chain:w,target:y,query:m,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:X(f,ae(m))}))))}async pairFeatures(e,t,r,s){let[a]=r,n=r.map(l=>({pair:l,featurePrefix:N(this,l.queryAssemblyName),matePrefix:N(this,l.targetAssemblyName)})),{graph:o,fragments:p}=await this.laneWalks(e,t,n.flatMap(l=>[l.featurePrefix,l.matePrefix]),s,r.length===1&&a?`Reading ${a.queryAssemblyName} against ${a.targetAssemblyName}`:`Reading ${r.length} lane pairs`),h=D(o.nodes),g=l=>p.filter(f=>A(f.name,l));return n.flatMap(({pair:l,featurePrefix:f,matePrefix:c})=>g(f).flatMap(d=>g(c).flatMap(u=>h(u,d).map(m=>M({chain:m,target:d,query:u,assemblyName:l.queryAssemblyName,refName:F(d.name),mateAssemblyName:l.targetAssemblyName})))))}getFeatures(e,t={}){return v(async r=>{let s=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(s!==void 0){let a=q(t),n=a.length>0?await this.pairFeatures(s,e,a,t):await this.anchorFeatures(s,e,t);for(let o of n)r.next(o)}r.complete()},t.signal)}};export{B as default,X as laneOf};
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"sources": ["../../src/WalkTabixSyntenyAdapter/walkLanes.ts", "../../src/WalkTabixSyntenyAdapter/WalkTabixSyntenyAdapter.ts"],
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"sourcesContent": ["import { pairAlignments, weightedLcs } from '@gmod/gbz-base'\nimport { panSNContig } from '@jbrowse/bandage-core/pansn'\n\nimport SyntenyFeature from '../synteny/SyntenyFeature.ts'\n\nimport type { WalkFragment, WalkNode } from '../RgfaTabixAdapter/walkRows.ts'\nimport type { PairChain, PairEdit } from '@gmod/gbz-base'\n\n// The longest bubble with equal bases on both sides that is written as\n// mismatches; a longer one stays an insertion and a deletion\nconst BALANCED_BUBBLE_MAX_BP = 50\n\n/**\n * A chain's edits with each short balanced bubble as `X`. The walks carry no\n * bases, so two walks differ wherever they leave a shared node, and a SNP is\n * one base inserted and one deleted until it is read as the mismatch it is.\n */\nexport function bubblesAsMismatches(edits: PairEdit[]) {\n const out: PairEdit[] = []\n for (let i = 0; i < edits.length; i++) {\n const [op, len] = edits[i]!\n const [nextOp, nextLen] = edits[i + 1] ?? []\n if (\n len === nextLen &&\n len <= BALANCED_BUBBLE_MAX_BP &&\n ((op === 'I' && nextOp === 'D') || (op === 'D' && nextOp === 'I'))\n ) {\n out.push(['X', len])\n i++\n } else {\n out.push([op, len])\n }\n }\n return out\n}\n\nfunction cigarOf(edits: PairEdit[]) {\n return edits.map(([op, len]) => `${len}${op}`).join('')\n}\n\n/**\n * Aligns one walk fragment to another on the nodes both visit, from node\n * lengths alone: the fragments' steps as the handles gbz-base's chainer reads,\n * and a stand-in sequence of each node's length.\n */\nexport function walkAligner(nodes: Map<number, WalkNode>) {\n const standIn = new Map<number, string>()\n const sequenceOf = (id: number) => {\n const node = nodes.get(id)\n const length = node === undefined ? 0 : node.end - node.start\n let sequence = standIn.get(length)\n if (sequence === undefined) {\n sequence = 'N'.repeat(length)\n standIn.set(length, sequence)\n }\n return sequence\n }\n const handles = new Map<WalkFragment, number[]>()\n const handlesOf = (fragment: WalkFragment) => {\n let steps = handles.get(fragment)\n if (steps === undefined) {\n steps = Array.from(fragment.ids, (id, i) => 2 * id + fragment.rev[i]!)\n handles.set(fragment, steps)\n }\n return steps\n }\n return (query: WalkFragment, target: WalkFragment) =>\n pairAlignments({\n query: handlesOf(query),\n target: handlesOf(target),\n sequenceOf,\n bases: false,\n })\n}\n\n// The fewest bases on shared nodes a record against the reference keeps,\n// gbz-base's floor for a pair record\nconst MIN_MATCH_BP = 100\n\nfunction appendEdit(edits: PairEdit[], op: PairEdit[0], len: number) {\n const last = edits.at(-1)\n if (len > 0) {\n if (last?.[0] === op) {\n last[1] += len\n } else {\n edits.push([op, len])\n }\n }\n}\n\n/**\n * Aligns a haplotype's walk fragment to the reference's as gbz-base aligns a\n * walk to its reference path: the heaviest common subsequence of their steps,\n * each node weighing its length, read in whichever direction shares more. A\n * pair chain leaves out every node either walk passes twice, which is the\n * whole of a collapsed copy-number array (amylase, KIV-2); the subsequence\n * matches one pass over it, and the other copies are insertions.\n */\nexport function referenceAligner(nodes: Map<number, WalkNode>) {\n const lengthOf = (handle: number) => {\n const node = nodes.get(handle >> 1)\n return node === undefined ? 0 : node.end - node.start\n }\n const offsets = (handles: number[]) => {\n const out = new Float64Array(handles.length + 1)\n handles.forEach((handle, i) => {\n out[i + 1] = out[i]! + lengthOf(handle)\n })\n return out\n }\n const handlesOf = (fragment: WalkFragment) =>\n Array.from(fragment.ids, (id, i) => 2 * id + fragment.rev[i]!)\n\n return (query: WalkFragment, target: WalkFragment): PairChain[] => {\n const ref = handlesOf(target)\n const hap = handlesOf(query)\n const [same, sameWeight] = weightedLcs(hap, ref, lengthOf)\n const [turned, turnedWeight] = weightedLcs(\n hap.map(handle => handle ^ 1).reverse(),\n ref,\n lengthOf,\n )\n const reverse = turnedWeight > sameWeight\n const pairs = reverse ? turned : same\n const sharedBases = Math.max(sameWeight, turnedWeight)\n if (sharedBases < MIN_MATCH_BP) {\n return []\n }\n const refAt = offsets(ref)\n const hapAt = offsets(hap)\n // a pair's haplotype step, counted along the haplotype\n const stepOf = (k: number) =>\n reverse ? hap.length - 1 - pairs[k]![0] : pairs[k]![0]\n const edits: PairEdit[] = []\n pairs.forEach(([, r], k) => {\n if (k > 0) {\n const [lo, hi] = [stepOf(k - 1), stepOf(k)].sort((x, y) => x - y)\n appendEdit(edits, 'I', hapAt[hi!]! - hapAt[lo! + 1]!)\n appendEdit(edits, 'D', refAt[r]! - refAt[pairs[k - 1]![1] + 1]!)\n }\n appendEdit(edits, '=', lengthOf(ref[r]!))\n })\n const [lo, hi] = [stepOf(0), stepOf(pairs.length - 1)].sort((x, y) => x - y)\n return [\n {\n queryStart: hapAt[lo!]!,\n queryEnd: hapAt[hi! + 1]!,\n targetStart: refAt[pairs[0]![1]]!,\n targetEnd: refAt[pairs.at(-1)![1] + 1]!,\n strand: reverse ? '-' : '+',\n edits,\n sharedBases,\n },\n ]\n }\n}\n\n/**\n * One record of a walk aligned to another: on the target walk's contig, with\n * the query walk as its mate and the CIGAR read along the target, a `D` being\n * target bases the query lacks.\n */\nexport function chainFeature({\n chain,\n target,\n query,\n assemblyName,\n refName,\n mateAssemblyName,\n}: {\n chain: PairChain\n target: WalkFragment\n query: WalkFragment\n assemblyName: string\n refName: string\n mateAssemblyName: string\n}) {\n const start = target.hapStart + chain.targetStart\n const end = target.hapStart + chain.targetEnd\n const mateStart = query.hapStart + chain.queryStart\n const mateEnd = query.hapStart + chain.queryEnd\n const edits = bubblesAsMismatches(chain.edits)\n const matches = edits.reduce((sum, [op, n]) => sum + (op === '=' ? n : 0), 0)\n const columns = edits.reduce((sum, [, n]) => sum + n, 0)\n const id = `${target.name}:${start}-${end}|${query.name}:${mateStart}-${mateEnd}`\n return new SyntenyFeature({\n uniqueId: id,\n assemblyName,\n refName,\n start,\n end,\n type: 'match',\n strand: chain.strand === '-' ? -1 : 1,\n CIGAR: cigarOf(edits),\n syntenyId: id,\n identity: matches / Math.max(columns, 1),\n numMatches: matches,\n blockLen: columns,\n mate: {\n refName: panSNContig(query.name),\n start: mateStart,\n end: mateEnd,\n assemblyName: mateAssemblyName,\n },\n })\n}\n", "import { NodeLimitError } from '@jbrowse/bandage-core/gbzWindow'\nimport {\n assemblyByPanSNPrefix,\n panSNContig,\n panSNHaplotype,\n panSNMatchesPrefix,\n panSNSample,\n resolvePanSNPrefix,\n} from '@jbrowse/bandage-core/pansn'\nimport { updateStatus } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\n\nimport { chainFeature, referenceAligner, walkAligner } from './walkLanes.ts'\nimport { WalkReader } from '../RgfaTabixAdapter/walkReader.ts'\nimport { walkNameFilter } from '../RgfaTabixAdapter/walkRows.ts'\nimport { PanSNRefNames, openTabixSlot } from '../panSNTabix.ts'\nimport { ComparativeAdapterBase } from '../synteny/ComparativeAdapterBase.ts'\nimport { requestedPairs } from '../synteny/lanePairs.ts'\n\nimport type { WalkTabixSyntenyAdapterConfig } from './configSchema.ts'\nimport type { SubgraphAdapterOptions } from '../GetSubgraph.ts'\nimport type { WalkFragment } from '../RgfaTabixAdapter/walkRows.ts'\nimport type { LaneFeatureOptions, LanePair } from '../synteny/lanePairs.ts'\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { Region } from '@jbrowse/core/util/types'\n\n// How much graph a cut keeps around the window, on the reference\nconst WALK_CONTEXT = 1000\n\n/**\n * The lane a haplotype draws on: the JBrowse assembly the config maps to it at\n * haplotype or sample depth, else its own PanSN prefix\n */\nexport function laneOf(asmByPrefix: Record<string, string>, prefix: string) {\n return asmByPrefix[prefix] ?? asmByPrefix[panSNSample(prefix)] ?? prefix\n}\n\nconst haplotypeOf = (fragment: WalkFragment) =>\n panSNHaplotype(fragment.name) ?? fragment.name\n\nexport default class WalkTabixSyntenyAdapter extends ComparativeAdapterBase<WalkTabixSyntenyAdapterConfig> {\n private readonly reader\n private readonly refNames\n\n public constructor(\n config: WalkTabixSyntenyAdapterConfig,\n getSubAdapter?: getSubAdapterType,\n pluginManager?: PluginManager,\n ) {\n super(config, getSubAdapter, pluginManager)\n const nodes = openTabixSlot(this, ['nodesLocation'], ['nodesIndex'])\n this.reader = new WalkReader(\n {\n walks: openTabixSlot(this, ['walksLocation'], ['walksIndex']),\n nodes,\n links: openTabixSlot(this, ['linksLocation'], ['linksIndex']),\n },\n this.getConf('walkChunk'),\n )\n this.refNames = new PanSNRefNames(nodes, this)\n }\n\n private get anchor() {\n const anchor = this.getConf('assemblyNames')[0]\n if (anchor === undefined) {\n throw new Error(\n 'WalkTabixSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as',\n )\n }\n return anchor\n }\n\n /**\n * The haplotypes the walk file's header names, `sample#haplotype` in byte\n * order, or undefined when it names none\n */\n async getHaplotypeNames(opts: BaseOptions = {}) {\n const { haplotypes } = await this.reader.header(opts)\n return haplotypes.length > 0 ? haplotypes : undefined\n }\n\n /**\n * `lanes` is every haplotype the header names but the anchor's own,\n * declared up front so the display can offer the whole graph's haplotypes\n * before a fetch has placed any of them\n */\n async getHeader(opts: BaseOptions = {}) {\n const { haplotypes, references } = await this.reader.header(opts)\n const { anchor } = this\n const anchorPrefix = resolvePanSNPrefix(this, anchor)\n const asmByPrefix = assemblyByPanSNPrefix(this)\n return {\n hasCoarseTier: false,\n anchorAssemblyName: anchor,\n referenceSamples: references,\n lanes: haplotypes\n .filter(\n prefix =>\n prefix !== anchorPrefix && panSNSample(prefix) !== anchorPrefix,\n )\n .map(prefix => ({\n name: laneOf(asmByPrefix, prefix),\n label: prefix,\n group: panSNSample(prefix),\n })),\n }\n }\n\n // A lane's contigs are named only in its walk rows, so only the anchor's\n // are listed\n async getRefNames(opts: BaseOptions = {}) {\n const { assemblyName } = opts\n return assemblyName === undefined || assemblyName === this.anchor\n ? this.refNames.assemblyRefNames({ ...opts, assemblyName: this.anchor })\n : []\n }\n\n private budgets() {\n return {\n stepBudget: this.getConf('walkStepBudget'),\n byteBudget: this.getConf('walkByteBudget'),\n context: WALK_CONTEXT,\n }\n }\n\n /**\n * The graph display's cut of the window, as RgfaTabixAdapter cuts a\n * walk-indexed graph: the reference walk first, then the walks `haplotypes`\n * asks for, and the nodes and links they visit\n */\n async getSubgraph(region: Region, opts: SubgraphAdapterOptions = {}) {\n const { signal, haplotypes } = opts\n const refName = await this.refNames.resolve(region, { signal })\n if (refName === undefined) {\n throw new Error(\n `${region.assemblyName} ${region.refName} is not in this graph's index; the graph is cut on ${this.anchor}, mapped to its PanSN prefix in assemblyNameToPanSN`,\n )\n }\n const { graph, kept, fragments } = await this.reader.cut(refName, region, {\n ...this.budgets(),\n signal,\n keep: walkNameFilter(\n haplotypes?.map(lane => resolvePanSNPrefix(this, lane)),\n panSNHaplotype(refName),\n ),\n })\n return graph.tables(kept, fragments)\n }\n\n // The window's walks for the haplotypes named and the reference, with no\n // link read; a window past a budget fails as a zoom-in notice for lanes\n private async laneWalks(\n refName: string,\n region: Region,\n prefixes: string[] | undefined,\n opts: LaneFeatureOptions,\n status: string,\n ) {\n return updateStatus(status, opts.statusCallback, () =>\n this.reader\n .cut(refName, region, {\n ...this.budgets(),\n signal: opts.signal,\n keep: walkNameFilter(prefixes, panSNHaplotype(refName)),\n links: false,\n })\n .catch((error: unknown) => {\n if (error instanceof NodeLimitError) {\n error.message = error.message.replace(\n 'to see the graph',\n 'to see lanes',\n )\n }\n throw error\n }),\n )\n }\n\n /**\n * One record per stretch a haplotype's walk shares with the reference's,\n * on the reference with the haplotype as its mate\n */\n private async anchorFeatures(\n refName: string,\n region: Region,\n opts: LaneFeatureOptions,\n ) {\n const wanted = opts.haplotypes?.length\n ? opts.haplotypes.map(lane => resolvePanSNPrefix(this, lane))\n : undefined\n const target = resolvePanSNPrefix(this, opts.targetAssemblyName)\n const prefixes =\n target === undefined\n ? wanted\n : wanted === undefined ||\n wanted.some(\n prefix =>\n panSNMatchesPrefix(target, prefix) ||\n panSNMatchesPrefix(prefix, target),\n )\n ? [target]\n : []\n if (prefixes?.length === 0) {\n return []\n }\n const { start, end } = region\n const { graph, fragments } = await this.laneWalks(\n refName,\n region,\n prefixes,\n opts,\n `Reading walks ${region.refName}:${start.toLocaleString()}-${end.toLocaleString()}`,\n )\n const align = referenceAligner(graph.nodes)\n const asmByPrefix = assemblyByPanSNPrefix(this)\n const references = fragments.filter(f => f.name === refName)\n // lanes come back in the order the fetch names them, which is the order\n // the display stacks lanes of equal weight in\n const rank = (fragment: WalkFragment) =>\n prefixes === undefined\n ? 0\n : prefixes.findIndex(prefix =>\n panSNMatchesPrefix(fragment.name, prefix),\n )\n const shown = fragments\n .filter(fragment => fragment.name !== refName && rank(fragment) >= 0)\n .sort((a, b) => rank(a) - rank(b))\n return shown.flatMap(query =>\n references.flatMap(reference =>\n align(query, reference).map(chain =>\n chainFeature({\n chain,\n target: reference,\n query,\n assemblyName: region.assemblyName,\n refName: region.refName,\n mateAssemblyName: laneOf(asmByPrefix, haplotypeOf(query)),\n }),\n ),\n ),\n )\n }\n\n /**\n * Each pair's two lanes read out of the anchor window, all pairs in one\n * read, and each walk of a pair's query lane aligned to each walk of its\n * target lane. A pair's records sit on its query lane's contigs, the lane\n * the display draws on top.\n */\n private async pairFeatures(\n refName: string,\n region: Region,\n pairs: LanePair[],\n opts: LaneFeatureOptions,\n ) {\n const [first] = pairs\n const sides = pairs.map(pair => ({\n pair,\n featurePrefix: resolvePanSNPrefix(this, pair.queryAssemblyName),\n matePrefix: resolvePanSNPrefix(this, pair.targetAssemblyName),\n }))\n const { graph, fragments } = await this.laneWalks(\n refName,\n region,\n sides.flatMap(side => [side.featurePrefix, side.matePrefix]),\n opts,\n pairs.length === 1 && first\n ? `Reading ${first.queryAssemblyName} against ${first.targetAssemblyName}`\n : `Reading ${pairs.length} lane pairs`,\n )\n const align = walkAligner(graph.nodes)\n const walksOf = (prefix: string) =>\n fragments.filter(f => panSNMatchesPrefix(f.name, prefix))\n return sides.flatMap(({ pair, featurePrefix, matePrefix }) =>\n walksOf(featurePrefix).flatMap(target =>\n walksOf(matePrefix).flatMap(query =>\n align(query, target).map(chain =>\n chainFeature({\n chain,\n target,\n query,\n assemblyName: pair.queryAssemblyName,\n refName: panSNContig(target.name),\n mateAssemblyName: pair.targetAssemblyName,\n }),\n ),\n ),\n ),\n )\n }\n\n // The files are filed under the reference alone, so a window on a\n // haplotype lane has no answer: a lane pair is read inside the anchor's\n getFeatures(region: Region, opts: LaneFeatureOptions = {}) {\n return ObservableCreate<Feature>(async observer => {\n const refName =\n region.assemblyName === this.anchor\n ? await this.refNames.resolve(region, opts)\n : undefined\n if (refName !== undefined) {\n const pairs = requestedPairs(opts)\n const features =\n pairs.length > 0\n ? await this.pairFeatures(refName, region, pairs, opts)\n : await this.anchorFeatures(refName, region, opts)\n for (const feature of features) {\n observer.next(feature)\n }\n }\n observer.complete()\n }, opts.signal)\n }\n}\n"],
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|
|
6
|
+
"names": ["BALANCED_BUBBLE_MAX_BP", "bubblesAsMismatches", "edits", "out", "i", "op", "len", "nextOp", "nextLen", "cigarOf", "walkAligner", "nodes", "standIn", "sequenceOf", "id", "node", "length", "sequence", "handles", "handlesOf", "fragment", "steps", "query", "target", "pairAlignments", "MIN_MATCH_BP", "appendEdit", "last", "referenceAligner", "lengthOf", "handle", "offsets", "ref", "hap", "same", "sameWeight", "weightedLcs", "turned", "turnedWeight", "reverse", "pairs", "sharedBases", "refAt", "hapAt", "stepOf", "k", "r", "lo", "hi", "x", "y", "chainFeature", "chain", "assemblyName", "refName", "mateAssemblyName", "start", "end", "mateStart", "mateEnd", "matches", "sum", "n", "columns", "SyntenyFeature", "panSNContig", "WALK_CONTEXT", "laneOf", "asmByPrefix", "prefix", "panSNSample", "haplotypeOf", "fragment", "panSNHaplotype", "WalkTabixSyntenyAdapter", "ComparativeAdapterBase", "config", "getSubAdapter", "pluginManager", "nodes", "openTabixSlot", "WalkReader", "PanSNRefNames", "anchor", "opts", "haplotypes", "references", "anchorPrefix", "resolvePanSNPrefix", "assemblyByPanSNPrefix", "assemblyName", "region", "signal", "refName", "graph", "kept", "fragments", "walkNameFilter", "lane", "prefixes", "status", "updateStatus", "error", "NodeLimitError", "wanted", "target", "panSNMatchesPrefix", "start", "end", "align", "referenceAligner", "f", "rank", "a", "b", "query", "reference", "chain", "chainFeature", "pairs", "first", "sides", "pair", "side", "walkAligner", "walksOf", "featurePrefix", "matePrefix", "panSNContig", "ObservableCreate", "observer", "requestedPairs", "features", "feature"]
|
|
7
|
+
}
|