npm - jbrowse-plugin-graphgenomeviewer - Versions diffs - 6.2.0 → 6.3.0 - Mend

jbrowse-plugin-graphgenomeviewer 6.2.0 → 6.3.0

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Files changed (43) hide show

package/dist/chunks/chunk-PZE3GABA.js ADDED Viewed

	@@ -0,0 +1,2 @@
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li(e,t,n,s){let o=ir(si(s,n.length>0));if(!(e.length===0\|\|t.length===0)){structuredClone(e).forEach((r,a)=>{r.seq??="",r.sequenceLength??=r.seq.length,o.nodes[a+1]=r}),o.tracks=structuredClone(t),o.reads=o.config.showReads?structuredClone(n.filter(r=>r.is_secondary!==!0)):[];for(let r=o.tracks.length-1;r>=0;r-=1){let a=o.tracks[r];if(a.type??="haplotype",a.hidden===!0){o.tracks.splice(r,1);continue}a.indexOfFirstBase!==void 0&&(o.trackForRuler=a.name)}if(o.tracks.length!==0)return mi(o,0),o.nodeMap=Qo(o),Ie(o,o.tracks),Ie(o,o.reads),rr(o),o.config.mergeNodes&&(Zo(o),on(o),rn(o),rc(o),o.nodeMap=Qo(o),rr(o),Ie(o,o.tracks),Ie(o,o.reads)),Zo(o),Bi(o),on(o),Xi(o),on(o),rn(o),Ie(o,o.reads),{options:o.config,nodes:o.nodes,tracks:o.tracks,reads:o.reads,nodeMap:o.nodeMap,maxOrder:Pi(o),trackForRuler:o.trackForRuler}}}function fi(e,{mappingQualityCutoff:t=0,focusReadNames:n=null,facet:s}){let o=n?new Set(n):null;return e.reads.filter(r=>(r.mapping_quality??0)>=t&&(o===null\|\|r.name!==void 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e.tracks[t].sequence)B(o)?s.has(F(o))\|\|n.add(F(o)):s.add(o);if(n.size!==0){for(let{sequence:o}of[...e.tracks,...e.reads])for(let r=0;r<o.length;r+=1)n.has(F(o[r]))&&(o[r]=sn(o[r]));e.nodes.forEach(o=>{n.has(o.name)&&(o.seq=an(o.seq))})}}function gi(e){e.nodesPerOrder=[];for(let n=0;n<=e.maxOrder;n+=1)e.nodesPerOrder[n]=[];let t=new Map;e.nodes.forEach(n=>{n.y!==void 0&&jo(t,n.order,n.y+n.contentHeight)}),e.tracks.forEach(n=>{n.type==="haplotype"&&n.path.forEach(s=>{jo(t,s.order,(s.y??0)+n.width)})}),e.nodes.forEach((n,s)=>{n.order>=0&&n.y===void 0&&(n.y=(t.get(n.order)??0)+25,n.contentHeight=0,e.nodesPerOrder[n.order].push(s))})}function jo(e,t,n){let s=e.get(t);s===void 0?e.set(t,n):e.set(t,Math.max(s,n))}var bt=7;function xi(e){e.nodes.forEach(t=>{t.incomingReads=[],t.outgoingReads=[],t.internalReads=[]}),e.reads.forEach((t,n)=>{if((t.width===void 0\|\|t.width===0)&&(t.width=bt),t.path.length===1){let s=t.path[0].node;s!==null&&e.nodes[s].internalReads.push(n)}else 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h!==0?h:(r.finalNodeCoverLength??0)-(a.finalNodeCoverLength??0)}function Ei(e,t){let n=e.path,s=t.path,o=0,r=0;for(;o<n.length&&r<s.length;){let a=n[o],i=s[r],c=a.order,l=i.order;if(c===l&&a.node&&i.node)return(i.y??0)-(a.y??0);c<l?o+=1:(c>l\|\|(o+=1),r+=1)}return 0}function Si(e,t,n){let s=e.reads[t],o=e.reads[n],r=s.firstNodeOffset??0,a=o.firstNodeOffset??0;if(r<a)return-1;if(r>a)return 1;let i=s.finalNodeCoverLength??0,c=o.finalNodeCoverLength??0;return i<c?-1:i>c?1:0}function Ri(e){let t=[];for(let n=0;n<=e.maxOrder;n+=1)t.push(0);return e.nodes.forEach(n=>{n.y!==void 0&&(t[n.order]=Math.max(t[n.order],n.y+n.contentHeight+20))}),e.tracks.forEach(n=>{n.path.forEach(s=>{t[s.order]=Math.max(t[s.order],(s.y??0)+n.width)})}),t}function ur(e,t){let n=[],s=(c,l)=>{n.push({order:c,isForward:l,node:null})},o=(c,l,d)=>{n.push({order:c,isForward:l,node:d})},r=Math.abs(t.indexSequence[0]),a=Ko(t.indexSequence[0]),i=e.nodes[r];o(i.order,a,r);for(let c=1;c<t.sequence.length;c+=1){let l=i,d=a;r=Math.abs(t.indexSequence[c]),a=Ko(t.indexSequence[c]),i=e.nodes[r];let{order:f}=i;if(f>l.order){d\|\|s(l.order,!0);for(let u=l.order+1;u<f;u+=1)s(u,!0);a\|\|s(f,!0)}else if(f<l.order){d&&s(l.order,!1);for(let u=l.order-1;u>f;u-=1)s(u,!1);a&&s(f,!1)}else a===d&&s(f,!a);o(f,a,r)}return n}function rn(e,t=e.reads){t.forEach(n=>{let s=0;for(;s<n.sequence.length&&n.sequence[s].startsWith("-");)s+=1;if(s===n.sequence.length){n.is_reverse=!0,n.sequence=n.sequence.reverse();for(let c=0;c<n.sequence.length;c+=1)n.sequence[c]=F(n.sequence[c]);let o=n.sequenceNew??[];o.reverse(),n.sequenceNew=o;for(let c of o)c.nodeName=F(c.nodeName),_i(c.mismatches,nn(e,c.nodeName).sequenceLength);let r=n.firstNodeOffset??0,a=nn(e,n.sequence[0]).sequenceLength;n.firstNodeOffset=a-(n.finalNodeCoverLength??0);let i=nn(e,n.sequence[n.sequence.length-1]).sequenceLength;n.finalNodeCoverLength=i-r}})}function _i(e,t){e.forEach(n=>{Object.assign(n,Ni(n,t))})}function Ni(e,t){let 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