wuepgg3-track 2.0.0 → 2.0.1

package/dist/{SharedSystems-gfisoPIO.mjs → SharedSystems-CEwenHFK.mjs}

@@ -1,4 +1,4 @@
-import { q as Le, G as ae, t as ne, u as He, k as ie, M as v, v as oe, E as u, e as O, x as S, y as ze, z as F, F as b, R as L, H as le, I as We, s as m, S as f, h as B, w as H, J, K as Ve, b as X, B as k, i as U, L as M, j as T, N as w, O as Ne, a as je, Q as ue, V as de, W as ce, X as he, C as P, Y as $e, Z as A, D as z, _ as qe, P as Ke, c as Ye, T as Q, $ as Z, a0 as Je, a1 as Xe, a2 as Qe } from "./index-C1Sd-2Ub.mjs";
+import { q as Le, G as ae, t as ne, u as He, k as ie, M as v, v as oe, E as u, e as O, x as S, y as ze, z as F, F as b, R as L, H as le, I as We, s as m, S as f, h as B, w as H, J, K as Ve, b as X, B as k, i as U, L as M, j as T, N as w, O as Ne, a as je, Q as ue, V as de, W as ce, X as he, C as P, Y as $e, Z as A, D as z, _ as qe, P as Ke, c as Ye, T as Q, $ as Z, a0 as Je, a1 as Xe, a2 as Qe } from "./index-C4Ue5B9P.mjs";
 import { S as fe, B as pe, c as Ze } from "./colorToUniform-zJcCVLeu.mjs";
 const me = class I extends Le {
   /**

package/dist/{WebGLRenderer-DaSVYxNP.mjs → WebGLRenderer-CGEE1FYg.mjs}

@@ -1,6 +1,6 @@
-import { E as d, B, w as m, D as S, J as K, t as Be, q as U, s as b, a3 as Ae, j as $, a4 as Ne, S as p, N as H, i as A, h as N, k as F, M as z, a5 as Y, a6 as ye, a7 as Ce, a8 as q, a9 as De, A as Ie, R as Ge, e as v } from "./index-C1Sd-2Ub.mjs";
+import { E as d, B, w as m, D as S, J as K, t as Be, q as U, s as b, a3 as Ae, j as $, a4 as Ne, S as p, N as H, i as A, h as N, k as F, M as z, a5 as Y, a6 as ye, a7 as Ce, a8 as q, a9 as De, A as Ie, R as Ge, e as v } from "./index-C4Ue5B9P.mjs";
 import { S as O, b as Z } from "./colorToUniform-zJcCVLeu.mjs";
-import { e as Ue, G as Fe, c as Oe, b as Pe, U as Me, R as Le, B as J, d as y, f as He, S as we, a as Ve } from "./SharedSystems-gfisoPIO.mjs";
+import { e as Ue, G as Fe, c as Oe, b as Pe, U as Me, R as Le, B as J, d as y, f as He, S as we, a as Ve } from "./SharedSystems-CEwenHFK.mjs";
 class Q {
   constructor() {
     this._tempState = O.for2d(), this._didUploadHash = {};

package/dist/{WebGPURenderer-DhPKSrZp.mjs → WebGPURenderer--_kGet56.mjs}

@@ -1,6 +1,6 @@
-import { g as E, E as p, f as ae, D as B, S as C, B as T, b as ue, c as L, d as M, w as v, h as y, i as ce, j as de, k as A, l as w, M as k, m as D, n as he, o as pe, p as H, q as z, s as R, A as le, R as fe, e as S } from "./index-C1Sd-2Ub.mjs";
+import { g as E, E as p, f as ae, D as B, S as C, B as T, b as ue, c as L, d as M, w as v, h as y, i as ce, j as de, k as A, l as w, M as k, m as D, n as he, o as pe, p as H, q as z, s as R, A as le, R as fe, e as S } from "./index-C4Ue5B9P.mjs";
 import { S as F, l as ge, a as me } from "./colorToUniform-zJcCVLeu.mjs";
-import { c as _e, u as be, U as ye, B as xe, G as Ge, e as Be, R as Se, t as Pe, S as Te, a as Ce } from "./SharedSystems-gfisoPIO.mjs";
+import { c as _e, u as be, U as ye, B as xe, G as Ge, e as Be, R as Se, t as Pe, S as Te, a as Ce } from "./SharedSystems-CEwenHFK.mjs";
 const x = F.for2d();
 class O {
   start(e, t, r) {

package/dist/assets/{fetchDataWorker-DHBPgS4v.js → fetchDataWorker-CQEJY3Jd.js}

@@ -57,4 +57,4 @@ License: MIT
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n[3],Number.parseInt(n[4],10),Number.parseInt(n[5],10),a[3]=`${n[3]}:${n[4]}-${n[5]},${e[5]}`,`${n[0]}${n[1]}${n[2]}${e[5]}`,a}initIndex(){this.indexer=new nd(this.textData.data,this.convertToBedRecord.bind(this),1)}}let Rr={};const M2={bed:async function(e){return wn(e,"bedOrTabix")},bedgraph:async function(e){return wn(e,"bedOrTabix")},qbed:async function(e){return wn(e,"bedOrTabix")},bigbed:async function(e){return wn(e,"big")},refbed:async function(e){return wn(e,"bedOrTabix")},matplot:async function(e){return wn(e,"bedOrTabix")},bigwig:async function(e){return wn(e,"big")},categorical:async function(e){return wn(e,"bedOrTabix")},longrange:async function(e){return wn(e,"bedOrTabix")},dynseq:async function(e){return wn(e,"big")},biginteract:async function(e){return wn(e,"big")},methylc:async function(e){return wn(e,"bedOrTabix")}},P2={bed:async function(e){return Ra(e)},bedgraph:async function(e){return Ra(e)},qbed:async function(e){return Ra(e)},refbed:async function(e){return Ra(e)},longrange:async function(e){return Ra(e)}};async function Ra(t){return t.trackModel.id in Rr||(t.trackModel.type==="longrange"?Rr[`${t.trackModel.id}`]=new L2({blob:t.trackModel.fileObj,textConfig:t.trackModel.textConfig,url:""}):Rr[`${t.trackModel.id}`]=new rd({blob:t.trackModel.fileObj,textConfig:t.trackModel.textConfig,url:""})),await Rr[`${t.trackModel.id}`].getData(t.nav)}async function wn(t,e){return t.trackModel.id in Rr||(e==="big"?Rr[`${t.trackModel.id}`]=new R2(t.trackModel.fileObj):e==="bedOrTabix"&&(Rr[`${t.trackModel.id}`]=new F2(t.trackModel))),await Rr[`${t.trackModel.id}`].getData(t.nav,t.trackModel.options)}const U2={geneannotation:"",bed:"",bedcolor:"",bigwig:"",dynseq:"",methylc:"",hic:"",genomealign:"",vcf:"",categorical:"",longrange:"",biginteract:"",repeatmasker:"",bigbed:"",refbed:"",matplot:"",ruler:"",modbed:"",dynamic:"",bedgraph:"",qbed:"",boxplot:"",jaspar:"",dynamichic:"",dynamicbed:"",dbedgraph:"",dynamiclongrange:"",snp:"",bam:"",omeroidr:"",error:""};async function H2(t){if(!Array.isArray(t))throw new Error(`fetchGenomicData expects an array, but received: ${typeof t}`);const e=t.map(a=>{const f=a.primaryGenName,o=a.initial,l=[],h=a.genomicLoci,w=a.regionExpandLoci?a.regionExpandLoci:a.genomicLoci,d=a.initGenomicLoci,c=a.trackModelArr,x=a.bpRegionSize,E=a.windowWidth,y=a.trackToDrawId||{},F=a.trackDataIdx,B=a.missingIdx;a.useFineModeNav;let O=a.genomicFetchCoord||{[f]:{genomicLoci:h,regionExpandLoci:w,initGenomicLoci:d,primaryVisData:a.visData}};const H=c.filter(D=>D&&D.type!=="genomealign");return Promise.all(H.map(async D=>{const R=(D==null?void 0:D.type)||(D==null?void 0:D.metadata["Track type"]),P=D.id;let V=!1;if((D.metadata.genome&&!(D.metadata.genome in O)||!(D.type in U2))&&(V=!0),V)l.push({name:R,id:P,metadata:D.metadata,trackModel:D,result:{error:"This track type is currently not supported"}});else if(R in{hic:"",dynamichic:""})l.push({name:R,id:P,metadata:D.metadata,trackModel:D});else if(R==="ruler")l.push({name:R,id:P,metadata:D.metadata,trackModel:D,result:[]});else if(R==="geneannotation"){const N=await q(D);l.push({name:R,result:N[0],id:P,metadata:D.metadata,trackModel:D})}else if(R==="bam"){let N;"genome"in D.metadata&&D.metadata.genome!==void 0&&D.metadata.genome!==f?N=O[D.metadata.genome===""?f:D.metadata.genome].queryGenomicCoord:o===1?N=d:N=Array(h),l.push({name:R,id:P,metadata:D.metadata,trackModel:D,curFetchNav:N})}else if(R in{matplot:"",dynamic:"",dynamicbed:"",dynamiclongrange:""}){let N=!1;const A=await Promise.all(D.tracks.map(async S=>{const L=(await q(S)).flat(1);return typeof L[0]=="object"&&"error"in 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ed[D.type]({genomeName:"genome"in D.metadata?D.metadata.genome:D.genome?D.genome:f,name:D.name,chr:L.chr,start:L.start,end:L.end,nav:L,trackModel:D,trackType:D.type}))):S=await Promise.all([ed[D.type]({basesPerPixel:x/E,nav:P[A],trackModel:D})]),R.push(br.flatten(S))}catch(L){console.error(`Error fetching data for track model type ${D.type}:`,L),R.push({error:"Data fetch failed. 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$2{constructor(e){Ce(this,"config");Ce(this,"url");Ce(this,"blob");Ce(this,"init",async()=>await this.processTextFile());this.config=e,this.url="",this.blob=null,e.blob&&(this.blob=e.blob),e.url&&(this.url=e.url)}processTextFile(){let e,n;return this.url.length?(n=this.url,e={download:!0,skipEmptyLines:"greedy",worker:this.config.textConfig.isFileHuge}):this.blob?(n=this.blob,e={skipEmptyLines:"greedy",worker:this.config.textConfig.isFileHuge}):console.error("no data source for TextSource, abort..."),new Promise((a,f)=>{N2.parse(n,{config:e,error:(o,l)=>{console.error(o,l),f(o)},complete:o=>{a(o)}})})}}function*Ca(t,e,n=void 0){e===void 0&&(e=t,t=0),n===void 0&&(n=1);for(let a=t;t<e?a<e:a>e;a+=n)yield a}function O2(t,e){return e-=1,t>>14===e>>14?4681+(t>>14):t>>17===e>>17?585+(t>>17):t>>20===e>>20?73+(t>>20):t>>23===e>>23?9+(t>>23):t>>26===e>>26?1+(t>>26):0}function D2(t,e){let n=[];if(n.push(0),t>=e)return n;e>=1<<29&&(e=1<<29),e-=1;for(let a of 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o)this.indexer[e].hasOwnProperty(l)&&this.indexer[e][l].forEach(h=>f.push(h));return f}}class rd{constructor(e){Ce(this,"source");Ce(this,"textData");Ce(this,"indexer");Ce(this,"ready");this.source=new $2(e),this.textData=null,this.indexer=null,this.ready=!1}convertToBedRecord(e){const n={chr:e[0],start:Number.parseInt(e[1],10),end:Number.parseInt(e[2],10)};for(let a=3;a<e.length;a++)n[a]=e[a];return n}async initSource(){this.textData||(this.textData=await this.source.init())}initIndex(){this.indexer=new nd(this.textData.data,this.convertToBedRecord)}async init(){await this.initSource(),this.initIndex(),this.indexer.init(),this.ready=!0}async getData(e){this.ready||await this.init();const n=e.map(a=>this.indexer.get(a.chr,a.start,a.end));return br.flatten(n)}}class L2 extends rd{convertToBedRecord(e){const n=e[0].split(/\W+/),a={chr:n[0],start:Number.parseInt(n[1],10),end:Number.parseInt(n[2],10)};return n[3],Number.parseInt(n[4],10),Number.parseInt(n[5],10),a[3]=`${n[3]}:${n[4]}-${n[5]},${e[5]}`,`${n[0]}${n[1]}${n[2]}${e[5]}`,a}initIndex(){this.indexer=new nd(this.textData.data,this.convertToBedRecord.bind(this),1)}}let Rr={};const M2={bed:async function(e){return wn(e,"bedOrTabix")},bedgraph:async function(e){return wn(e,"bedOrTabix")},qbed:async function(e){return wn(e,"bedOrTabix")},bigbed:async function(e){return wn(e,"big")},refbed:async function(e){return wn(e,"bedOrTabix")},matplot:async function(e){return wn(e,"bedOrTabix")},bigwig:async function(e){return wn(e,"big")},categorical:async function(e){return wn(e,"bedOrTabix")},longrange:async function(e){return wn(e,"bedOrTabix")},dynseq:async function(e){return wn(e,"big")},biginteract:async function(e){return wn(e,"big")},methylc:async function(e){return wn(e,"bedOrTabix")}},P2={bed:async function(e){return Ra(e)},bedgraph:async function(e){return Ra(e)},qbed:async function(e){return Ra(e)},refbed:async function(e){return Ra(e)},longrange:async function(e){return Ra(e)}};async function Ra(t){return t.trackModel.id in Rr||(t.trackModel.type==="longrange"?Rr[`${t.trackModel.id}`]=new L2({blob:t.trackModel.fileObj,textConfig:t.trackModel.textConfig,url:""}):Rr[`${t.trackModel.id}`]=new rd({blob:t.trackModel.fileObj,textConfig:t.trackModel.textConfig,url:""})),await Rr[`${t.trackModel.id}`].getData(t.nav)}async function wn(t,e){return t.trackModel.id in Rr||(e==="big"?Rr[`${t.trackModel.id}`]=new R2(t.trackModel.fileObj):e==="bedOrTabix"&&(Rr[`${t.trackModel.id}`]=new F2(t.trackModel))),await Rr[`${t.trackModel.id}`].getData(t.nav,t.trackModel.options)}const U2={geneannotation:"",bed:"",bedcolor:"",bigwig:"",dynseq:"",methylc:"",hic:"",genomealign:"",vcf:"",categorical:"",longrange:"",biginteract:"",repeatmasker:"",bigbed:"",refbed:"",matplot:"",ruler:"",modbed:"",dynamic:"",bedgraph:"",qbed:"",boxplot:"",jaspar:"",dynamichic:"",dynamicbed:"",dbedgraph:"",dynamiclongrange:"",snp:"",bam:"",omeroidr:"",error:""};async function H2(t){if(!Array.isArray(t))throw new Error(`fetchGenomicData expects an array, but received: ${typeof t}`);const e=t.map(a=>{const f=a.primaryGenName,o=a.initial,l=[],h=a.genomicLoci,w=a.regionExpandLoci?a.regionExpandLoci:a.genomicLoci,d=a.initGenomicLoci,c=a.trackModelArr,x=a.bpRegionSize,E=a.windowWidth,y=a.trackToDrawId||{},F=a.trackDataIdx,B=a.missingIdx;a.useFineModeNav;let O=a.genomicFetchCoord||{[f]:{genomicLoci:h,regionExpandLoci:w,initGenomicLoci:d,primaryVisData:a.visData}};const H=c.filter(D=>D&&D.type!=="genomealign");return Promise.all(H.map(async D=>{const R=(D==null?void 0:D.type)||(D==null?void 0:D.metadata["Track type"]),P=D.id;let V=!1;if((D.metadata.genome&&!(D.metadata.genome in O)||!(D.type in U2))&&(V=!0),V)l.push({name:R,id:P,metadata:D.metadata,trackModel:D,result:{error:"This track type is currently not supported"}});else if(R in{hic:"",dynamichic:""})l.push({name:R,id:P,metadata:D.metadata,trackModel:D});else if(R==="ruler")l.push({name:R,id:P,metadata:D.metadata,trackModel:D,result:[]});else if(R==="geneannotation"){const N=await q(D);l.push({name:R,result:N[0],id:P,metadata:D.metadata,trackModel:D})}else if(R==="bam"){let N;"genome"in D.metadata&&D.metadata.genome!==void 0&&D.metadata.genome!==f?N=O[D.metadata.genome===""?f:D.metadata.genome].queryGenomicCoord:o===1?N=d:N=Array(h),l.push({name:R,id:P,metadata:D.metadata,trackModel:D,curFetchNav:N})}else if(R in{matplot:"",dynamic:"",dynamicbed:"",dynamiclongrange:""}){let N=!1;const A=await Promise.all(D.tracks.map(async S=>{const L=(await q(S)).flat(1);return typeof L[0]=="object"&&"error"in L[0]&&(N=!0),L}));l.push({name:R,result:N?{error:"Fetch failed: data source is not valid"}:A,id:P,metadata:D.metadata,trackModel:D})}else{const N=await q(D);l.push({name:R,result:N[0],id:P,metadata:D.metadata,trackModel:D})}})).then(()=>({fetchResults:l,trackDataIdx:F,genomicFetchCoord:O,trackToDrawId:y,missingIdx:B}));async function q(D){let R=[],P;const{genome:V}=D.metadata;V&&V!==""&&V!==f?P=O[V].queryGenomicCoord:D.type==="longrange"||D.type==="biginteract"?P=Array(w):P=Array(h);const N=D.fileObj instanceof File;if(N&&D.url==="")for(let A=0;A<P.length;A++){const S=D.isText?await P2[D.type]({basesPerPixel:x/E,nav:P[A],trackModel:D}):await M2[D.type]({basesPerPixel:x/E,nav:P[A],trackModel:D});S&&typeof S=="object"&&S.hasOwnProperty("error")?R.push({error:S.message}):R.push(S)}else if(N)R.push({error:"Fetch failed: data source is not valid"});else for(let A=0;A<P.length;A++){let S;try{D.type in{geneannotation:"",snp:""}?S=await Promise.all(P[A].map(async L=>await ed[D.type]({genomeName:"genome"in D.metadata?D.metadata.genome:D.genome?D.genome:f,name:D.name,chr:L.chr,start:L.start,end:L.end,nav:L,trackModel:D,trackType:D.type}))):S=await Promise.all([ed[D.type]({basesPerPixel:x/E,nav:P[A],trackModel:D})]),R.push(br.flatten(S))}catch(L){console.error(`Error fetching data for track model type ${D.type}:`,L),R.push({error:"Data fetch failed. Reload page or change view to retry"})}}return R}});return await Promise.all(e)}typeof self<"u"&&"postMessage"in self&&"onmessage"in self&&typeof self.importScripts<"u"&&(self.onmessage=async t=>{try{const e=await H2(t.data);postMessage(e)}catch(e){postMessage({error:e instanceof Error?e.message:"Unknown error"})}})})();