npm - jbrowse-plugin-graphgenomeviewer - Versions diffs - 4.0.21 → 4.0.22 - Mend

jbrowse-plugin-graphgenomeviewer 4.0.21 → 4.0.22

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.

Files changed (42) hide show

package/dist/chunks/chunk-D7XFR2IV.js.map ADDED Viewed

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["global-externals:@jbrowse/core/util/tracks"],
+  "sourcesContent": ["module.exports = JBrowseExports[\"@jbrowse/core/util/tracks\"];"],
+  "mappings": "wCAAA,IAAAA,EAAAC,EAAA,CAAAC,EAAAC,IAAA,CAAAA,EAAO,QAAU,eAAe,2BAA2B",
+  "names": ["require_tracks", "__commonJSMin", "exports", "module"]
+}

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

@@ -0,0 +1,3 @@
+import{b as m}from"./chunk-EFVAQ2KM.js";import{a as c,b as u,c as d,d as f}from"./chunk-KULNKXPT.js";var y=new Map([["hg38","GRCh38"],["hg19","GRCh37"],["hs1","CHM13"],["t2t-chm13","CHM13"],["chm13v2","CHM13"]]);function x(t){return y.get(t.toLowerCase())}function g(t){let e=t.includes("#")?c(t):void 0;return e===void 0||u(e)?void 0:e}function h(t){return d(t)??c(t)}function l(t){let e=new Set((t.anchorPaths??[]).map(n=>n.name));for(let n of t.nodes)n.stable&&e.add(n.stable.refName);let s=new Map;for(let n of e){let r=g(n);r!==void 0&&(s.get(r)??s.set(r,new Set).get(r)).add(h(n))}return s}function b(t,e){let s=new Set(t.map(p=>g(p.refName))),[n]=s;if(s.size!==1||n===void 0)return{contigs:t,prefixes:[],named:!1};let r=new Set(t.map(p=>h(p.refName))),i=[...e.get(n)??[]].every(p=>r.has(p)),a=new Set(t.map(p=>d(p.refName))),[o]=a;return{contigs:t,prefixes:[...i?[n]:[],...a.size===1&&o?[o]:[]],named:!0}}function M(t){let e=new Map;for(let n of t.nodes)if(m(n)){let{refName:r,start:i}=n.stable,a=i+n.length,o=e.get(r);o?(o.start=Math.min(o.start,i),o.end=Math.max(o.end,a)):e.set(r,{refName:r,contig:f(r),start:i,end:a})}let s=[...e.values()];return s.length?b(s,l(t)):void 0}function S(t,e){let s=a=>[a.name,...a.aliases??[]],n=a=>o=>s(o).some(p=>p.toLowerCase()===a.toLowerCase()),r=[...t?.prefixes??[]].reverse(),i=t?.prefixes.find(a=>!a.includes("#"))?.toLowerCase();for(let a of r){let o=e.find(n(a));if(o)return o}return i===void 0?void 0:e.find(a=>s(a).some(o=>x(o)?.toLowerCase()===i))}function k(t,e){let s=l(t);return t.anchorPaths?.find(n=>S(b([{refName:n.name,contig:f(n.name),start:n.start,end:n.start+n.length}],s),[e]))}function C(t){let e=new Set(t),s=new Map;for(let n of e){let r=f(n);s.set(r,s.has(r)?void 0:n)}return n=>e.has(n)?n:s.get(n)}function q(t,e){let s=C(e.contigs.map(n=>n.refName));return t.flatMap(n=>{let r=s(n.refName);return r===void 0?[]:[r===n.refName?n:{...n,refName:r}]})}var N=/([><])([^><]+)/g;function G(t){if(!t.startsWith(">")&&!t.startsWith("<"))return;let e=[];for(let[,s,n]of t.matchAll(N))e.push({name:n,strand:s===">"?"+":"-"});return e}function w(t){let e=t.split("	");if(e.length<12||t.startsWith("#"))return;let s=G(e[5]);if(!s)return;let n,r=!1;for(let i=12;i<e.length;i++){let a=e[i];a.startsWith("cs:Z:")?n=a.slice(5):a==="tp:A:S"&&(r=!0)}return{name:e[0],queryLength:+e[1],queryStart:+e[2],queryEnd:+e[3],strand:e[4]==="-"?"-":"+",path:s,pathLength:+e[6],pathStart:+e[7],pathEnd:+e[8],matches:+e[9],blockLength:+e[10],mappingQuality:+e[11],secondary:r,...n===void 0?{}:{cs:n}}}function z(t){let e=[];for(let s of t.split(`
+`)){let n=w(s.trimEnd());n&&e.push(n)}return e}var L=/:(\d+)|=([A-Za-z]+)|\*[a-zA-Z]([a-zA-Z])|\+([A-Za-z]+)|-([A-Za-z]+)|~[a-z]{2}(\d+)[a-z]{2}/g;function T(t){let e=[];for(let s of t.matchAll(L))s[1]!==void 0?e.push({op:"match",length:+s[1]}):s[2]!==void 0?e.push({op:"match",length:s[2].length}):s[3]!==void 0?e.push({op:"substitution",seq:s[3].toUpperCase()}):s[4]!==void 0?e.push({op:"insertion",seq:s[4].toUpperCase()}):s[5]!==void 0?e.push({op:"deletion",length:s[5].length}):s[6]!==void 0&&e.push({op:"match",length:+s[6]});return e}export{x as a,M as b,S as c,k as d,q as e,w as f,z as g,T as h};
+//# sourceMappingURL=chunk-DMYUVGGI.js.map

package/dist/chunks/{chunk-QSH263Y6.js.map → chunk-DMYUVGGI.js.map} RENAMED Viewed

@@ -1,7 +1,7 @@
 {
   "version": 3,
-  "sources": ["../../packages/core/src/reference.ts"],
-  "sourcesContent": ["import { isBackbone } from './anchoredNodes'\nimport {\n  isGenericSample,\n  panSNContig,\n  panSNHaplotype,\n  panSNSample,\n} from './pansn'\n\nimport type { Graph, PathOrigin } from './types'\n\n// A graph's backbone names the sample it lies on (`GRCh38#0#chr6`), not an\n// assembly, and a bare contig (`chr6`) is in every human assembly at once. A\n// backbone binds to an assembly where its PanSN prefix is that assembly's name,\n// one of its aliases, or its well-known sample. One that names no sample binds\n// only where the host knows the assembly otherwise, as a track's config does.\n\nexport interface BackboneContig {\n  // as the graph names it, `GRCh38#0#chr6`\n  refName: string\n  // as an assembly names it, `chr6`\n  contig: string\n  start: number\n  end: number\n}\n\nexport interface Backbone {\n  contigs: BackboneContig[]\n  // The PanSN prefixes that name the backbone, sample then haplotype:\n  // `GRCh38`, `GRCh38#0`. The sample drops out where the graph walks another\n  // haplotype of it, as a diploid's `HG002` names `HG002#1` and `HG002#2`.\n  prefixes: string[]\n  // Whether the contigs name one real sample: false where every contig is bare\n  // (`chr6`) or generic (`_gbwt_ref#0#chr6`), or where the samples differ\n  named: boolean\n}\n\nexport interface AssemblyNames {\n  name: string\n  aliases?: string[]\n}\n\n// The sample a reference assembly's graphs name it by, keyed by the assembly's\n// name in lower case: HPRC writes `CHM13` where UCSC's assembly is `hs1`.\nexport const WELL_KNOWN_SAMPLES: ReadonlyMap<string, string> = new Map([\n  ['hg38', 'GRCh38'],\n  ['hg19', 'GRCh37'],\n  ['hs1', 'CHM13'],\n  ['t2t-chm13', 'CHM13'],\n  ['chm13v2', 'CHM13'],\n])\n\nexport function wellKnownSample(assemblyName: string) {\n  return WELL_KNOWN_SAMPLES.get(assemblyName.toLowerCase())\n}\n\nfunction sampleOf(refName: string) {\n  const sample = refName.includes('#') ? panSNSample(refName) : undefined\n  return sample === undefined || isGenericSample(sample) ? undefined : sample\n}\n\n// `HG002#1`, or the sample of a two-part name, which states no haplotype\nfunction haplotypeOf(refName: string) {\n  return panSNHaplotype(refName) ?? panSNSample(refName)\n}\n\n// Each sample's haplotypes among the graph's walks and node refNames\nfunction graphHaplotypes(graph: Graph) {\n  const refNames = new Set((graph.anchorPaths ?? []).map(p => p.name))\n  for (const node of graph.nodes) {\n    if (node.stable) {\n      refNames.add(node.stable.refName)\n    }\n  }\n  const bySample = new Map<string, Set<string>>()\n  for (const refName of refNames) {\n    const sample = sampleOf(refName)\n    if (sample !== undefined) {\n      const haplotypes =\n        bySample.get(sample) ?? bySample.set(sample, new Set()).get(sample)!\n      haplotypes.add(haplotypeOf(refName))\n    }\n  }\n  return bySample\n}\n\nfunction backboneFrom(\n  contigs: BackboneContig[],\n  haplotypes: Map<string, Set<string>>,\n): Backbone {\n  const samples = new Set(contigs.map(c => sampleOf(c.refName)))\n  const [sample] = samples\n  if (samples.size !== 1 || sample === undefined) {\n    return { contigs, prefixes: [], named: false }\n  }\n  const own = new Set(contigs.map(c => haplotypeOf(c.refName)))\n  const unique = [...(haplotypes.get(sample) ?? [])].every(h => own.has(h))\n  const shared = new Set(contigs.map(c => panSNHaplotype(c.refName)))\n  const [haplotype] = shared\n  return {\n    contigs,\n    prefixes: [\n      ...(unique ? [sample] : []),\n      ...(shared.size === 1 && haplotype ? [haplotype] : []),\n    ],\n    named: true,\n  }\n}\n\n// The rank-0 nodes' refNames and the span each covers\nexport function graphBackbone(graph: Graph): Backbone | undefined {\n  const spans = new Map<string, BackboneContig>()\n  for (const node of graph.nodes) {\n    if (isBackbone(node)) {\n      const { refName, start } = node.stable\n      const end = start + node.length\n      const span = spans.get(refName)\n      if (span) {\n        span.start = Math.min(span.start, start)\n        span.end = Math.max(span.end, end)\n      } else {\n        spans.set(refName, {\n          refName,\n          contig: panSNContig(refName),\n          start,\n          end,\n        })\n      }\n    }\n  }\n  const contigs = [...spans.values()]\n  return contigs.length\n    ? backboneFrom(contigs, graphHaplotypes(graph))\n    : undefined\n}\n\n// The assembly the backbone's haplotype names by its name or an alias, else\n// the one its sample names, else the one whose well-known sample it is. A\n// backbone with no prefix binds to none.\nexport function backboneAssembly<T extends AssemblyNames>(\n  backbone: Backbone | undefined,\n  assemblies: T[],\n): T | undefined {\n  const names = (a: T) => [a.name, ...(a.aliases ?? [])]\n  const naming = (prefix: string) => (a: T) =>\n    names(a).some(n => n.toLowerCase() === prefix.toLowerCase())\n  const prefixes = [...(backbone?.prefixes ?? [])].reverse()\n  const sample = backbone?.prefixes.find(p => !p.includes('#'))?.toLowerCase()\n  for (const prefix of prefixes) {\n    const assembly = assemblies.find(naming(prefix))\n    if (assembly) {\n      return assembly\n    }\n  }\n  return sample === undefined\n    ? undefined\n    : assemblies.find(a =>\n        names(a).some(n => wellKnownSample(n)?.toLowerCase() === sample),\n      )\n}\n\n// The first of the graph's walks that a backbone along it would bind to\n// `assembly`, for putting x on the assembly a cut was made for\nexport function assemblyWalk(\n  graph: Graph,\n  assembly: AssemblyNames,\n): PathOrigin | undefined {\n  const haplotypes = graphHaplotypes(graph)\n  return graph.anchorPaths?.find(walk =>\n    backboneAssembly(\n      backboneFrom(\n        [\n          {\n            refName: walk.name,\n            contig: panSNContig(walk.name),\n            start: walk.start,\n            end: walk.start + walk.length,\n          },\n        ],\n        haplotypes,\n      ),\n      [assembly],\n    ),\n  )\n}\n\n// Which of `refNames` a feature's refName names: the one it equals, else the\n// only one whose contig it is. A contig two refNames share names neither.\nexport function refNameBinding(refNames: Iterable<string>) {\n  const exact = new Set(refNames)\n  const byContig = new Map<string, string | undefined>()\n  for (const refName of exact) {\n    const contig = panSNContig(refName)\n    byContig.set(contig, byContig.has(contig) ? undefined : refName)\n  }\n  return (name: string) => (exact.has(name) ? name : byContig.get(name))\n}\n\n// An assembly's features on a backbone that binds to it, each renamed to the\n// backbone's refName for it, so the assembly's `chr6` becomes the graph's\n// `GRCh38#0#chr6`. genePins and tubeMapGenes take only the renamed.\nexport function featuresOnBackbone<T extends { refName: string }>(\n  features: readonly T[],\n  backbone: Backbone,\n): T[] {\n  const bind = refNameBinding(backbone.contigs.map(c => c.refName))\n  return features.flatMap(f => {\n    const refName = bind(f.refName)\n    return refName === undefined\n      ? 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-  "names": ["WELL_KNOWN_SAMPLES", "wellKnownSample", "assemblyName", "sampleOf", "refName", "sample", "panSNSample", "isGenericSample", "haplotypeOf", "panSNHaplotype", "graphHaplotypes", "graph", "refNames", "p", "node", "bySample", "backboneFrom", "contigs", "haplotypes", "samples", "c", "own", "unique", "h", "shared", "haplotype", "graphBackbone", "spans", "isBackbone", "start", "end", "span", "panSNContig", "backboneAssembly", "backbone", "assemblies", "names", "a", "naming", "prefix", "n", "prefixes", "assembly", "assemblyWalk", "walk", "refNameBinding", "exact", "byContig", "contig", "name", "featuresOnBackbone", "features", "bind", "f"]
+  "sources": ["../../packages/core/src/reference.ts", "../../packages/core/src/gaf/parseGaf.ts"],
+  "sourcesContent": ["import { isBackbone } from './anchoredNodes'\nimport {\n  isGenericSample,\n  panSNContig,\n  panSNHaplotype,\n  panSNSample,\n} from './pansn'\n\nimport type { Graph, PathOrigin } from './types'\n\n// A graph's backbone names the sample it lies on (`GRCh38#0#chr6`), not an\n// assembly, and a bare contig (`chr6`) is in every human assembly at once. A\n// backbone binds to an assembly where its PanSN prefix is that assembly's name,\n// one of its aliases, or its well-known sample. One that names no sample binds\n// only where the host knows the assembly otherwise, as a track's config does.\n\nexport interface BackboneContig {\n  // as the graph names it, `GRCh38#0#chr6`\n  refName: string\n  // as an assembly names it, `chr6`\n  contig: string\n  start: number\n  end: number\n}\n\nexport interface Backbone {\n  contigs: BackboneContig[]\n  // The PanSN prefixes that name the backbone, sample then haplotype:\n  // `GRCh38`, `GRCh38#0`. The sample drops out where the graph walks another\n  // haplotype of it, as a diploid's `HG002` names `HG002#1` and `HG002#2`.\n  prefixes: string[]\n  // Whether the contigs name one real sample: false where every contig is bare\n  // (`chr6`) or generic (`_gbwt_ref#0#chr6`), or where the samples differ\n  named: boolean\n}\n\nexport interface AssemblyNames {\n  name: string\n  aliases?: string[]\n}\n\n// The sample a reference assembly's graphs name it by, keyed by the assembly's\n// name in lower case: HPRC writes `CHM13` where UCSC's assembly is `hs1`.\nexport const WELL_KNOWN_SAMPLES: ReadonlyMap<string, string> = new Map([\n  ['hg38', 'GRCh38'],\n  ['hg19', 'GRCh37'],\n  ['hs1', 'CHM13'],\n  ['t2t-chm13', 'CHM13'],\n  ['chm13v2', 'CHM13'],\n])\n\nexport function wellKnownSample(assemblyName: string) {\n  return WELL_KNOWN_SAMPLES.get(assemblyName.toLowerCase())\n}\n\nfunction sampleOf(refName: string) {\n  const sample = refName.includes('#') ? panSNSample(refName) : undefined\n  return sample === undefined || isGenericSample(sample) ? undefined : sample\n}\n\n// `HG002#1`, or the sample of a two-part name, which states no haplotype\nfunction haplotypeOf(refName: string) {\n  return panSNHaplotype(refName) ?? panSNSample(refName)\n}\n\n// Each sample's haplotypes among the graph's walks and node refNames\nfunction graphHaplotypes(graph: Graph) {\n  const refNames = new Set((graph.anchorPaths ?? []).map(p => p.name))\n  for (const node of graph.nodes) {\n    if (node.stable) {\n      refNames.add(node.stable.refName)\n    }\n  }\n  const bySample = new Map<string, Set<string>>()\n  for (const refName of refNames) {\n    const sample = sampleOf(refName)\n    if (sample !== undefined) {\n      const haplotypes =\n        bySample.get(sample) ?? bySample.set(sample, new Set()).get(sample)!\n      haplotypes.add(haplotypeOf(refName))\n    }\n  }\n  return bySample\n}\n\nfunction backboneFrom(\n  contigs: BackboneContig[],\n  haplotypes: Map<string, Set<string>>,\n): Backbone {\n  const samples = new Set(contigs.map(c => sampleOf(c.refName)))\n  const [sample] = samples\n  if (samples.size !== 1 || sample === undefined) {\n    return { contigs, prefixes: [], named: false }\n  }\n  const own = new Set(contigs.map(c => haplotypeOf(c.refName)))\n  const unique = [...(haplotypes.get(sample) ?? [])].every(h => own.has(h))\n  const shared = new Set(contigs.map(c => panSNHaplotype(c.refName)))\n  const [haplotype] = shared\n  return {\n    contigs,\n    prefixes: [\n      ...(unique ? [sample] : []),\n      ...(shared.size === 1 && haplotype ? 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 }

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Set(t),r=e.nodes.filter(a=>n.has(a.name)),o=new Set(r.map(a=>a.id)),s=e.paths?.map(a=>({...a,nodeIds:a.nodeIds.filter(i=>o.has(i))})).filter(a=>a.nodeIds.length>0);return{name:e.name,nodes:r,edges:e.edges.filter(a=>o.has(a.from)&&o.has(a.to)),...s?.length?{paths:s}:{},anchorPaths:e.anchorPaths,pathVisits:e.pathVisits,anchoredBy:e.anchoredBy,referencePath:e.referencePath}}function hi(e,t,n){let r=new Map;for(let s of e.nodes)if(v(s)){let{refName:a}=s.stable;if(n[s.id]?.length){let i=r.get(a)??r.set(a,{nodes:[],reach:0}).get(a);i.nodes.push(s),i.reach=Math.max(i.reach,s.length)}}for(let{nodes:s}of r.values())s.sort((a,i)=>a.stable.start-i.stable.start);let o=[];for(let s of t){let a=r.get(s.refName);if(!a)continue;let i=[],c,d=1/0,p=0,u=(s.start+s.end)/2,{nodes:l,reach:f}=a;for(let m=kt(l,s.start-f);m<l.length&&l[m].stable.start<s.end;m++){let h=l[m],b=h.stable.start,g=b+h.length;if(g<=s.start)continue;let y=n[h.id];p+=Math.min(g,s.end)-Math.max(b,s.start);for(let S of s.exons){let 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K=`${T.id}${V}	${z.node.id}${z.strand}`,q=w.get(K);q?q.pathIds.push(x.name):w.set(K,{from:T.id,to:z.node.id,fromStrand:V,toStrand:z.strand,pathIds:[x.name]})}}),g.push({...x,nodeIds:k.map(T=>T.node.id)}),b.set(x.name,P)}let S=[...d.map(x=>x.node),...m.values()].filter(x=>M.has(x.id)).map(x=>({...x,depth:M.get(x.id)}));return{graph:{...e,nodes:S,edges:[...w.values()],paths:g,pathVisits:y,reads:void 0},members:l,coarseOf:f,deviations:b,cuts:i}}var ip=e=>e.bp1>e.bp0;function xi(e,t){let n=e.filter(ip);if(n.length===0){let s=e[0];return s?[{tx:s.x0,sx:t(s.bp0)}]:[]}let r=n.map(s=>({c:s,s0:t(s.bp0),s1:t(s.bp1),trimLeft:0,trimRight:0}));for(let s=0;s+1<r.length;s++){let a=r[s],i=r[s+1],d=Math.min(i.c.x0-a.c.x1,24)-(i.s0-a.s1);if(d>0){let p=(a.s1-a.s0)/2,u=(i.s1-i.s0)/2,l=Math.min(d/2,p),f=Math.min(d-l,u);l=Math.min(d-f,p),a.trimRight=l,i.trimLeft=f}}let o=[];for(let{c:s,s0:a,s1:i,trimLeft:c,trimRight:d}of r)o.push({tx:s.x0,sx:a+c},{tx:s.x1,sx:i-d});return o}function wi(e,t){let n=e.length;if(n===0)return t;let r=e[0],o=e[n-1];if(t<=r.tx)return r.sx+(t-r.tx);if(t>=o.tx)return o.sx+(t-o.tx);let s=0,a=n-1;for(;a-s>1;){let p=s+a>>1;e[p].tx<=t?s=p:a=p}let i=e[s],c=e[a],d=c.tx-i.tx;return d>0?i.sx+(t-i.tx)/d*(c.sx-i.sx):i.sx}var cp=.05,cn=9;function dp(e,t){let{minY:n,maxY:r}=e.layout.bounds,o=r-n;return e.columns&&o>0?Math.max(cp,Math.min(1,t/o)):1}function Mi(e,t){let{scaleX:n,translateX:r,translateY:o}=t,s=t.scaleY*dp(e,t.usableHeight),a=c=>(c-e.yOffset)*s+o,{columns:i}=e;if(i){let c=xi(i,d=>d*n+r);return{x:d=>wi(c,d),y:a,yScale:s}}return{x:c=>c*n+r,y:a,yScale:s}}function Si(e,{x:t,y:n},r,o){let s=null;return e.layout.nodes.forEach(a=>{a.order>=0&&t(a.x-cn)<=r&&r<=t(a.x+a.pixelWidth+cn)&&n(a.y-cn)<=o&&o<=n(a.y+a.contentHeight+cn)&&(s=a.name)}),s}function Ri(e){return e.referencePath?e.paths?.find(t=>j(t.name).name===e.referencePath):void 0}function up(e,t){let n=e.paths?.find(f=>f.name===t);if(!n)return;let r=new Map(e.nodes.map(f=>[f.id,f])),o=new 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pp(e,t){let n=Ri(e),r=new Set,o=0;if(!n||t.reference)return{reversed:r,bp:o};let s=j(t.name).name,a=j(n.name).name,i=new Map(e.nodes.map(c=>[c.id,c]));for(let c of t.progress.keys()){let d=i.get(c),p=d?e.pathVisits?.get(d.name):void 0,u=p?.find(f=>f.path===s)?.strand,l=p?.find(f=>f.path===a)?.strand;u&&l&&u!==l&&(r.add(c),o+=d.length)}return{reversed:r,bp:o}}function Nr(e,t,n){let r=new Set,o=t.filter(i=>!r.has(i.walk)&&r.add(i.walk)).flatMap(i=>{let c=up(e,i.walk);return c?[{walk:c,layer:i}]:[]}).sort((i,c)=>Number(c.walk.reference)-Number(i.walk.reference));if(o.length===0)return;let s=0,a=o.map(({walk:i,layer:c})=>{let d=cs(c,i.reference,i.reference?0:s++,o.length===1),{reversed:p,bp:u}=pp(e,i);return{...i,encoding:d,colors:lp(e,i,d,n),reversed:p,reversedBp:u}});return{walks:a,referenceDomain:n?{start:n.start,end:n.start+n.span}:void 0,nodeIds:new Set(a.flatMap(i=>[...i.nodeIds])),edgeIndexes:new Set(a.flatMap(i=>[...i.edgeIndexes])),names:new Set(a.map(i=>i.name))}}var 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