jbrowse2: x/static/js/9409.c7569196.chunk.js annotate

annotate x/static/js/9409.c7569196.chunk.js @ 125:49f3d3878413 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5ea1f9c1eef1de76232e69aa6d34cda77d90d566

author	fubar
date	Sat, 05 Oct 2024 23:58:05 +0000
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49f3d3878413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5ea1f9c1eef1de76232e69aa6d34cda77d90d566

fubar

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1 "use strict";(globalThis.webpackChunk_jbrowse_web=globalThis.webpackChunk_jbrowse_web||[]).push([[9409,7706],{69409:(e,t,n)=>{n.r(t),n.d(t,{default:()=>h});var r=n(46377),a=n(99834),s=n(99546),i=n(66885),o=n(6434),l=n(78054);class h extends r.BaseFeatureDataAdapter{static capabilities=["getFeatures","getRefNames"];async setup(e){return this.setupP||(this.setupP=this.setupPre(e).catch((e=>{throw this.setupP=void 0,e}))),this.setupP}async setupPre(e){const t=this.getConf("assemblyNames"),n=this.pluginManager,r=(0,a.openLocation)(this.getConf("bed1Location"),n),s=(0,a.openLocation)(this.getConf("bed2Location"),n),i=(0,a.openLocation)(this.getConf("mcscanSimpleAnchorsLocation"),n),[o,h,c]=await Promise.all([r,s,i].map((t=>(0,l.TA)(t,e)))),d=(0,l.fY)(o),f=(0,l.fY)(h);return{assemblyNames:t,feats:c.split(/\n|\r\n|\r/).filter((e=>!!e&&"###"!==e)).map(((e,t)=>{const[n,r,a,s,i,o]=e.split("\t"),l=d.get(n),h=d.get(r),c=f.get(a),u=f.get(s);if(!(l&&h&&c&&u))throw new Error(`feature not found, ${n} ${r} ${a} ${s} ${l} ${h} ${c} ${u}`);return[l,h,c,u,+i,"-"===o?-1:1,t]}))}}async hasDataForRefName(){return!0}async getRefNames(){return[]}getFeatures(e,t={}){return(0,i.ObservableCreate)((async n=>{const{assemblyNames:r,feats:a}=await this.setup(t),i=r.indexOf(e.assemblyName);if(-1!==i){const t=0===i;a.forEach((a=>{const[i,l,h,c,d,f,u]=a;let p={refName:i.refName,start:Math.min(i.start,l.start),end:Math.max(i.end,l.end)},g={refName:h.refName,start:Math.min(h.start,c.start),end:Math.max(h.end,c.end)};t||([g,p]=[p,g]),p.refName===e.refName&&(0,s.doesIntersect2)(p.start,p.end,e.start,e.end)&&n.next(new o.A({...p,uniqueId:`${u}`,syntenyId:u,assemblyName:r[+!t],score:d,strand:f,mate:{...g,assemblyName:r[+t]}}))}))}n.complete()}))}freeResources(){}}},78054:(e,t,n)=>{n.d(t,{PX:()=>h,TA:()=>i,fY:()=>s,gJ:()=>f,qm:()=>d,xI:()=>c,yU:()=>o});var r=n(7706),a=n(99546);function s(e){return new Map(e.split(/\n|\r\n|\r/).filter((e=>!!e||e.startsWith("#"))).map((e=>{const[t,n,r,a,s,i]=e.split("\t");return[a,{refName:t,start:+n,end:+r,score:+s,name:a,strand:"-"===i?-1:1}]})))}async function i(e,t){const n=await e.readFile(t);return new TextDecoder("utf8",{fatal:!0}).decode((0,a.isGzip)(n)?await(0,r.unzip)(n):n)}function o(e,t){return e.map(((e,n)=>[e,t[n]]))}const l="undefined"!=typeof TextDecoder?new TextDecoder("utf8"):void 0;function h(e,t){let n=0;const r=[];for(;n<e.length;){const a=e.indexOf("\n",n);if(-1===a)break;const s=e.subarray(n,a),i=(l?.decode(s)||s.toString()).trim();i&&r.push(t(i)),n=a+1}return r}function c(e){const[t,,n,r,a,s,,i,o,l,h,c,...d]=e.split("\t");return{tname:s,tstart:+i,tend:+o,qname:t,qstart:+n,qend:+r,strand:"-"===a?-1:1,extra:{numMatches:+l,blockLen:+h,mappingQual:+c,...Object.fromEntries(d.map((e=>{const t=e.indexOf(":");return[e.slice(0,t),e.slice(t+3)]})))}}}function d(e){const t=[];for(let n=e.length-2;n>=0;n-=2){t.push(e[n]);const r=e[n+1];"D"===r?t.push("I"):"I"===r?t.push("D"):t.push(r)}return t}function f(e){return e.replaceAll("D","K").replaceAll("I","D").replaceAll("K","I")}},7706:(e,t,n)=>{n.d(t,{sG:()=>d,unzip:()=>i,i2:()=>o});var r=n(35451),a=n(45834),s=n(57864);async function i(e){try{let t,n=0,a=0;const i=[];let o,l=0;do{const r=e.subarray(n);if(o=new s.Inflate,({strm:t}=o),o.push(r,s.Z_SYNC_FLUSH),o.err)throw new Error(o.msg);n+=t.next_in,i[a]=o.result,l+=i[a].length,a+=1}while(t.avail_in);const h=new Uint8Array(l);for(let e=0,t=0;e<i.length;e++)h.set(i[e],t),t+=i[e].length;return r.hp.from(h)}catch(e){if(`${e}`.match(/incorrect header check/))throw new Error("problem decompressing block: incorrect gzip header check");throw e}}async function o(e,t){try{let n;const{minv:a,maxv:i}=t;let o=a.blockPosition,l=a.dataPosition;const h=[],c=[],d=[];let f=0,u=0;do{const t=e.subarray(o-a.blockPosition),r=new s.Inflate;if(({strm:n}=r),r.push(t,s.Z_SYNC_FLUSH),r.err)throw new Error(r.msg);const p=r.result;h.push(p);let g=p.length;c.push(o),d.push(l),1===h.length&&a.dataPosition&&(h[0]=h[0].subarray(a.dataPosition),g=h[0].length);const m=o;if(o+=n.next_in,l+=g,m>=i.blockPosition){h[u]=h[u].subarray(0,i.blockPosition===a.blockPosition?i.dataPosition-a.dataPosition+1:i.dataPosition+1),c.push(o),d.push(l),f+=h[u].length;break}f+=h[u].length,u++}while(n.avail_in);const p=new Uint8Array(f);for(let e=0,t=0;e<h.length;e++)p.set(h[e],t),t+=h[e].length;return{buffer:r.hp.from(p),cpositions:c,dpositions:d}}catch(e){if(`${e}`.match(/incorrect header check/))throw new Error("problem decompressing block: incorrect gzip header check");throw e}}var l=n(59086),h=n.n(l);class c{constructor({filehandle:e,path:t}){if(e)this.filehandle=e;else{if(!t)throw new TypeError("either filehandle or path must be defined");this.filehandle=new a.EY(t)}}_readLongWithOverflow(e,t=0,n=!0){const r=h().fromBytesLE(e.slice(t,t+8),n);if(r.greaterThan(Number.MAX_SAFE_INTEGER)||r.lessThan(Number.MIN_SAFE_INTEGER))throw new TypeError("integer overflow");return r.toNumber()}_getIndex(){return this.index||(this.index=this._readIndex()),this.index}async _readIndex(){let e=r.hp.allocUnsafe(8);await this.filehandle.read(e,0,8,0);const t=this._readLongWithOverflow(e,0,!0);if(!t)return[[0,0]];const n=new Array(t+1);n[0]=[0,0];const a=16*t;if(a>Number.MAX_SAFE_INTEGER)throw new TypeError("integer overflow");e=r.hp.allocUnsafe(a),await this.filehandle.read(e,0,a,8);for(let r=0;r<t;r+=1){const t=this._readLongWithOverflow(e,16*r),a=this._readLongWithOverflow(e,16*r+8);n[r+1]=[t,a]}return n}async getLastBlock(){const e=await this._getIndex();if(e.length)return e[e.length-1]}async getRelevantBlocksForRead(e,t){const n=t+e;if(0===e)return[];const r=await this._getIndex(),a=[],s=(e,n)=>{const r=e[1],a=n?n[1]:1/0;return r<=t&&a>t?0:r<t?-1:1};let 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49f3d3878413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5ea1f9c1eef1de76232e69aa6d34cda77d90d566

fubar

parents:

2 //# sourceMappingURL=9409.c7569196.chunk.js.map