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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
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1 "use strict";(globalThis.webpackChunk_jbrowse_web=globalThis.webpackChunk_jbrowse_web||[]).push([[8120,7706],{47046:(e,t,n)=>{n.d(t,{A:()=>s});class i{}class r{constructor(){this.signals=new Set,this.abortController=new AbortController}addSignal(e=new i){if(this.signal.aborted)throw new Error("cannot add a signal, already aborted!");this.signals.add(e),e.aborted?this.handleAborted(e):"function"==typeof e.addEventListener&&e.addEventListener("abort",(()=>{this.handleAborted(e)}))}handleAborted(e){this.signals.delete(e),0===this.signals.size&&this.abortController.abort()}get signal(){return this.abortController.signal}abort(){this.abortController.abort()}}class a{constructor(){this.callbacks=new Set}addCallback(e=()=>{}){this.callbacks.add(e),e(this.currentMessage)}callback(e){this.currentMessage=e;for(const t of this.callbacks)t(e)}}class s{constructor({fill:e,cache:t}){if("function"!=typeof e)throw new TypeError("must pass a fill function");if("object"!=typeof t)throw new TypeError("must pass a cache object");if("function"!=typeof t.get||"function"!=typeof t.set||"function"!=typeof t.delete)throw new TypeError("cache must implement get(key), set(key, val), and and delete(key)");this.cache=t,this.fillCallback=e}static isAbortException(e){return"AbortError"===e.name||"ERR_ABORTED"===e.code||"AbortError: aborted"===e.message||"Error: aborted"===e.message}evict(e,t){this.cache.get(e)===t&&this.cache.delete(e)}fill(e,t,n,i){const s=new r,o=new a;o.addCallback(i);const l={aborter:s,promise:this.fillCallback(t,s.signal,(e=>{o.callback(e)})),settled:!1,statusReporter:o,get aborted(){return this.aborter.signal.aborted}};l.aborter.addSignal(n),l.aborter.signal.addEventListener("abort",(()=>{l.settled||this.evict(e,l)})),l.promise.then((()=>{l.settled=!0}),(()=>{l.settled=!0,this.evict(e,l)})).catch((e=>{throw console.error(e),e})),this.cache.set(e,l)}static checkSinglePromise(e,t){function n(){if(null==t?void 0:t.aborted)throw Object.assign(new Error("aborted"),{code:"ERR_ABORTED"})}return e.then((e=>(n(),e)),(e=>{throw n(),e}))}has(e){return this.cache.has(e)}get(e,t,n,i){if(!n&&t instanceof AbortSignal)throw new TypeError("second get argument appears to be an AbortSignal, perhaps you meant to pass `null` for the fill data?");const r=this.cache.get(e);return r?r.aborted&&!r.settled?(this.evict(e,r),this.get(e,t,n,i)):r.settled?r.promise:(r.aborter.addSignal(n),r.statusReporter.addCallback(i),s.checkSinglePromise(r.promise,n)):(this.fill(e,t,n,i),s.checkSinglePromise(this.cache.get(e).promise,n))}delete(e){const t=this.cache.get(e);t&&(t.settled||t.aborter.abort(),this.cache.delete(e))}clear(){const e=this.cache.keys();let t=0;for(let n=e.next();!n.done;n=e.next())this.delete(n.value),t+=1;return t}}},7706:(e,t,n)=>{n.d(t,{sG:()=>d,unzip:()=>s,i2:()=>o});var i=n(35451),r=n(45834),a=n(57864);async function s(e){try{let t,n=0,r=0;const s=[];let o,l=0;do{const i=e.subarray(n);if(o=new a.Inflate,({strm:t}=o),o.push(i,a.Z_SYNC_FLUSH),o.err)throw new Error(o.msg);n+=t.next_in,s[r]=o.result,l+=s[r].length,r+=1}while(t.avail_in);const h=new Uint8Array(l);for(let e=0,t=0;e<s.length;e++)h.set(s[e],t),t+=s[e].length;return i.hp.from(h)}catch(e){if(`${e}`.match(/incorrect header check/))throw new Error("problem decompressing block: incorrect gzip header check");throw e}}async function o(e,t){try{let n;const{minv:r,maxv:s}=t;let o=r.blockPosition,l=r.dataPosition;const h=[],c=[],d=[];let f=0,u=0;do{const t=e.subarray(o-r.blockPosition),i=new a.Inflate;if(({strm:n}=i),i.push(t,a.Z_SYNC_FLUSH),i.err)throw new Error(i.msg);const m=i.result;h.push(m);let w=m.length;c.push(o),d.push(l),1===h.length&&r.dataPosition&&(h[0]=h[0].subarray(r.dataPosition),w=h[0].length);const b=o;if(o+=n.next_in,l+=w,b>=s.blockPosition){h[u]=h[u].subarray(0,s.blockPosition===r.blockPosition?s.dataPosition-r.dataPosition+1:s.dataPosition+1),c.push(o),d.push(l),f+=h[u].length;break}f+=h[u].length,u++}while(n.avail_in);const m=new Uint8Array(f);for(let e=0,t=0;e<h.length;e++)m.set(h[e],t),t+=h[e].length;return{buffer:i.hp.from(m),cpositions:c,dpositions:d}}catch(e){if(`${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 r.EY(t)}}_readLongWithOverflow(e,t=0,n=!0){const i=h().fromBytesLE(e.slice(t,t+8),n);if(i.greaterThan(Number.MAX_SAFE_INTEGER)||i.lessThan(Number.MIN_SAFE_INTEGER))throw new TypeError("integer overflow");return i.toNumber()}_getIndex(){return this.index||(this.index=this._readIndex()),this.index}async _readIndex(){let e=i.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 r=16*t;if(r>Number.MAX_SAFE_INTEGER)throw new TypeError("integer overflow");e=i.hp.allocUnsafe(r),await this.filehandle.read(e,0,r,8);for(let i=0;i<t;i+=1){const t=this._readLongWithOverflow(e,16*i),r=this._readLongWithOverflow(e,16*i+8);n[i+1]=[t,r]}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 i=await this._getIndex(),r=[],a=(e,n)=>{const i=e[1],r=n?n[1]:1/0;return i<=t&&r>t?0:i<t?-1:1};let s=0,o=i.length-1,l=Math.floor(i.length/2),h=a(i[l],i[l+1]);for(;0!==h;)h>0?o=l-1:h<0&&(s=l+1),l=Math.ceil((o-s)/2)+s,h=a(i[l],i[l+1]);r.push(i[l]);let c=l+1;for(;c<i.length&&(r.push(i[c]),!(i[c][1]>=n));c+=1);return r[r.length-1][1]<n&&r.push([]),r}}class d{constructor({filehandle:e,path:t,gziFilehandle:n,gziPath:i}){if(e)this.filehandle=e;else{if(!t)throw new TypeError("either filehandle or path must be defined");this.filehandle=new r.EY(t)}if(!n&&!i&&!t)throw new TypeError("either gziFilehandle or gziPath must be defined");this.gzi=new c({filehandle:n,path:n||i||!t?`${t}.gzi`:i})}async stat(){const e=await this.filehandle.stat();return Object.assign(e,{size:await this.getUncompressedFileSize(),blocks:void 0,blksize:void 0})}async getUncompressedFileSize(){const[,e]=await this.gzi.getLastBlock(),{size:t}=await this.filehandle.stat(),n=i.hp.allocUnsafe(4),{bytesRead:r}=await this.filehandle.read(n,0,4,t-28-4);if(4!==r)throw new Error("read error");return e+n.readUInt32LE(0)}async _readAndUncompressBlock(e,[t],[n]){let i=n;i||(i=(await this.filehandle.stat()).size);const r=i-t;return await this.filehandle.read(e,0,r,t),await s(e.slice(0,r))}async read(e,t,n,r){const a=await this.gzi.getRelevantBlocksForRead(n,r),s=i.hp.allocUnsafe(65536);let o=t,l=0;for(let t=0;t<a.length-1;t+=1){const i=await this._readAndUncompressBlock(s,a[t],a[t+1]),[,h]=a[t],c=h>=r?0:r-h,d=Math.min(r+n,h+i.length)-h;c>=0&&c<i.length&&(i.copy(e,o,c,d),o+=d-c,l+=d-c)}return{bytesRead:l,buffer:e}}}},68120:(e,t,n)=>{n.d(t,{wD:()=>k});var i=n(47046),r=n(16308),a=n.n(r),s=n(35451),o=n(45834),l=n(7706);function h(e){if(e.greaterThan(Number.MAX_SAFE_INTEGER)||e.lessThan(Number.MIN_SAFE_INTEGER))throw new Error("integer overflow");return e.toNumber()}class c extends Error{}function d(e){if(e&&e.aborted){if("undefined"!=typeof DOMException)throw new DOMException("aborted","AbortError");{const e=new c("aborted");throw e.code="ERR_ABORTED",e}}}function f(e,t){const n=[];let i=null;return 0===e.length?e:(e.sort((function(e,t){const n=e.minv.blockPosition-t.minv.blockPosition;return 0!==n?n:e.minv.dataPosition-t.minv.dataPosition})),e.forEach((e=>{var r,a;(!t||e.maxv.compareTo(t)>0)&&(null===i?(n.push(e),i=e):(r=i,(a=e).minv.blockPosition-r.maxv.blockPosition<65e3&&a.maxv.blockPosition-r.minv.blockPosition<5e6?e.maxv.compareTo(i.maxv)>0&&(i.maxv=e.maxv):(n.push(e),i=e)))})),n)}var u=n(59086),m=n.n(u);class w{constructor(e,t){this.blockPosition=e,this.dataPosition=t}toString(){return`${this.blockPosition}:${this.dataPosition}`}compareTo(e){return this.blockPosition-e.blockPosition||this.dataPosition-e.dataPosition}}function b(e,t=0,n=!1){if(n)throw new Error("big-endian virtual file offsets not implemented");return new w(1099511627776*e[t+7]+4294967296*e[t+6]+16777216*e[t+5]+65536*e[t+4]+256*e[t+3]+e[t+2],e[t+1]<<8|e[t])}class p{constructor(e,t,n,i=void 0){this.minv=e,this.maxv=t,this.bin=n,this._fetchedSize=i}toUniqueString(){return`${this.minv}..${this.maxv} (bin ${this.bin}, fetchedSize ${this.fetchedSize()})`}toString(){return this.toUniqueString()}compareTo(e){return this.minv.compareTo(e.minv)||this.maxv.compareTo(e.maxv)||this.bin-e.bin}fetchedSize(){return void 0!==this._fetchedSize?this._fetchedSize:this.maxv.blockPosition+65536-this.minv.blockPosition}}class g{constructor({filehandle:e,renameRefSeqs:t=e=>e}){this.filehandle=e,this.renameRefSeq=t}async getMetadata(e={}){const{indices:t,...n}=await this.parse(e);return n}_findFirstData(e,t){return e?e.compareTo(t)>0?t:e:t}async parse(e={}){return this.parseP||(this.parseP=this._parse(e).catch((e=>{throw this.parseP=void 0,e}))),this.parseP}async hasRefSeq(e,t={}){var n;return!!(null===(n=(await this.parse(t)).indices[e])||void 0===n?void 0:n.binIndex)}}class E extends g{async lineCount(e,t={}){const n=await this.parse(t),i=n.refNameToId[e];if(void 0===i)return-1;if(!n.indices[i])return-1;const{stats:r}=n.indices[i];return r?r.lineCount:-1}async _parse(e={}){const t=await this.filehandle.readFile(e),n=await(0,l.unzip)(t);if(d(e.signal),21578324!==n.readUInt32LE(0))throw new Error("Not a TBI file");const i=n.readInt32LE(4),r=n.readInt32LE(8),a=65536&r?"zero-based-half-open":"1-based-closed",s={0:"generic",1:"SAM",2:"VCF"}[15&r];if(!s)throw new Error(`invalid Tabix preset format flags ${r}`);const o={ref:n.readInt32LE(12),start:n.readInt32LE(16),end:n.readInt32LE(20)},h=n.readInt32LE(24),c=h?String.fromCharCode(h):null,f=n.readInt32LE(28),u=n.readInt32LE(32),{refNameToId:m,refIdToName:w}=this._parseNameBytes(n.slice(36,36+u));let g,E=36+u;return{indices:new Array(i).fill(0).map((()=>{const e=n.readInt32LE(E);E+=4;const t={};let i;for(let r=0;r<e;r+=1){const e=n.readUInt32LE(E);if(E+=4,e>37450)throw new Error("tabix index contains too many bins, please use a CSI index");if(37450===e){const e=n.readInt32LE(E);E+=4,2===e&&(i=this.parsePseudoBin(n,E)),E+=16*e}else{const i=n.readInt32LE(E);E+=4;const r=new Array(i);for(let t=0;t<i;t+=1){const i=b(n,E),a=b(n,E+8);E+=16,g=this._findFirstData(g,i),r[t]=new p(i,a,e)}t[e]=r}}const r=n.readInt32LE(E);E+=4;const a=new Array(r);for(let e=0;e<r;e+=1)a[e]=b(n,E),E+=8,g=this._findFirstData(g,a[e]);return{binIndex:t,linearIndex:a,stats:i}})),metaChar:c,maxBinNumber:37449,maxRefLength:536870912,skipLines:f,firstDataLine:g,columnNumbers:o,coordinateType:a,format:s,refIdToName:w,refNameToId:m,maxBlockSize:65536}}parsePseudoBin(e,t){return{lineCount:h(m().fromBytesLE(e.slice(t+16,t+24),!0))}}_parseNameBytes(e){let t=0,n=0;const i=[],r={};for(let a=0;a<e.length;a+=1)if(!e[a]){if(n<a){let s=e.toString("utf8",n,a);s=this.renameRefSeq(s),i[t]=s,r[s]=t}n=a+1,t+=1}return{refNameToId:r,refIdToName:i}}async blocksForRange(e,t,n,i={}){t<0&&(t=0);const r=await this.parse(i),a=r.refNameToId[e];if(void 0===a)return[];const s=r.indices[a];if(!s)return[];(s.linearIndex.length?s.linearIndex[t>>14>=s.linearIndex.length?s.linearIndex.length-1:t>>14]:new w(0,0))||console.warn("querying outside of possible tabix range");const o=(l=t,h=n,[[0,0],[1+((l+=1)>>26),1+((h-=1)>>26)],[9+(l>>23),9+(h>>23)],[73+(l>>20),73+(h>>20)],[585+(l>>17),585+(h>>17)],[4681+(l>>14),4681+(h>>14)]]);var l,h;const c=[];for(const[e,t]of o)for(let n=e;n<=t;n++)if(s.binIndex[n])for(const e of s.binIndex[n])c.push(new p(e.minv,e.maxv,n));const d=s.linearIndex.length;let u=null;const m=Math.min(t>>14,d-1),b=Math.min(n>>14,d-1);for(let e=m;e<=b;++e){const t=s.linearIndex[e];t&&(!u||t.compareTo(u)<0)&&(u=t)}return f(c,u)}}function x(e,t){return Math.floor(e/2**t)}class v extends g{constructor(e){super(e),this.maxBinNumber=0,this.depth=0,this.minShift=0}async lineCount(e,t={}){const n=await this.parse(t),i=n.refNameToId[e];if(void 0===i)return-1;if(!n.indices[i])return-1;const{stats:r}=n.indices[i];return r?r.lineCount:-1}indexCov(){throw new Error("CSI indexes do not support indexcov")}parseAuxData(e,t){const n=e.readInt32LE(t),i=65536&n?"zero-based-half-open":"1-based-closed",r={0:"generic",1:"SAM",2:"VCF"}[15&n];if(!r)throw new Error(`invalid Tabix preset format flags ${n}`);const a={ref:e.readInt32LE(t+4),start:e.readInt32LE(t+8),end:e.readInt32LE(t+12)},s=e.readInt32LE(t+16),o=s?String.fromCharCode(s):null,l=e.readInt32LE(t+20),h=e.readInt32LE(t+24),{refIdToName:c,refNameToId:d}=this._parseNameBytes(e.slice(t+28,t+28+h));return{refIdToName:c,refNameToId:d,skipLines:l,metaChar:o,columnNumbers:a,format:r,coordinateType:i}}_parseNameBytes(e){let t=0,n=0;const i=[],r={};for(let a=0;a<e.length;a+=1)if(!e[a]){if(n<a){let s=e.toString("utf8",n,a);s=this.renameRefSeq(s),i[t]=s,r[s]=t}n=a+1,t+=1}return{refNameToId:r,refIdToName:i}}async _parse(e={}){const t=await(0,l.unzip)(await this.filehandle.readFile(e));let n;if(21582659===t.readUInt32LE(0))n=1;else{if(38359875!==t.readUInt32LE(0))throw new Error("Not a CSI file");n=2}this.minShift=t.readInt32LE(4),this.depth=t.readInt32LE(8),this.maxBinNumber=((1<<3*(this.depth+1))-1)/7;const i=2**(this.minShift+3*this.depth),r=t.readInt32LE(12),a=r&&r>=30?this.parseAuxData(t,16):{refIdToName:[],refNameToId:{},metaChar:null,columnNumbers:{ref:0,start:1,end:2},coordinateType:"zero-based-half-open",format:"generic"},s=t.readInt32LE(16+r);let o,h=16+r+4;const c=new Array(s).fill(0).map((()=>{const e=t.readInt32LE(h);h+=4;const n={};let i;for(let r=0;r<e;r+=1){const e=t.readUInt32LE(h);if(e>this.maxBinNumber)i=this.parsePseudoBin(t,h+4),h+=48;else{const i=b(t,h+4);o=this._findFirstData(o,i);const r=t.readInt32LE(h+12);h+=16;const a=new Array(r);for(let n=0;n<r;n+=1){const i=b(t,h),r=b(t,h+8);h+=16,a[n]=new p(i,r,e)}n[e]=a}}return{binIndex:n,stats:i}}));return{...a,csi:!0,refCount:s,maxBlockSize:65536,firstDataLine:o,csiVersion:n,indices:c,depth:this.depth,maxBinNumber:this.maxBinNumber,maxRefLength:i}}parsePseudoBin(e,t){return{lineCount:h(m().fromBytesLE(e.slice(t+28,t+36),!0))}}async blocksForRange(e,t,n,i={}){t<0&&(t=0);const r=await this.parse(i),a=r.refNameToId[e];if(void 0===a)return[];const s=r.indices[a];if(!s)return[];const o=this.reg2bins(t,n),l=[];for(const[e,t]of o)for(let n=e;n<=t;n++)if(s.binIndex[n])for(const e of s.binIndex[n])l.push(new p(e.minv,e.maxv,n));return f(l,new w(0,0))}reg2bins(e,t){(e-=1)<1&&(e=1),t>2**50&&(t=2**34),t-=1;let n=0,i=0,r=this.minShift+3*this.depth;const a=[];for(;n<=this.depth;r-=3,i+=1*2**(3*n),n+=1){const n=i+x(e,r),s=i+x(t,r);if(s-n+a.length>this.maxBinNumber)throw new Error(`query ${e}-${t} is too large for current binning scheme (shift ${this.minShift}, depth ${this.depth}), try a smaller query or a coarser index binning scheme`);a.push([n,s])}return a}}const y="undefined"!=typeof TextDecoder?new TextDecoder("utf8"):void 0;function I(e){return new Promise((t=>setTimeout(t,e)))}class k{constructor({path:e,filehandle:t,url:n,tbiPath:r,tbiUrl:s,tbiFilehandle:l,csiPath:h,csiUrl:c,csiFilehandle:d,yieldTime:f=500,renameRefSeqs:u=e=>e,chunkCacheSize:m=5242880}){if(t)this.filehandle=t;else if(e)this.filehandle=new o.EY(e);else{if(!n)throw new TypeError("must provide either filehandle or path");this.filehandle=new o.Tx(n)}if(l)this.index=new E({filehandle:l,renameRefSeqs:u});else if(d)this.index=new v({filehandle:d,renameRefSeqs:u});else if(r)this.index=new E({filehandle:new o.EY(r),renameRefSeqs:u});else if(h)this.index=new v({filehandle:new o.EY(h),renameRefSeqs:u});else if(e)this.index=new E({filehandle:new o.EY(`${e}.tbi`),renameRefSeqs:u});else if(c)this.index=new v({filehandle:new o.Tx(c)});else if(s)this.index=new E({filehandle:new o.Tx(s)});else{if(!n)throw new TypeError("must provide one of tbiFilehandle, tbiPath, csiFilehandle, csiPath, tbiUrl, csiUrl");this.index=new E({filehandle:new o.Tx(`${n}.tbi`)})}this.renameRefSeq=u,this.yieldTime=f,this.chunkCache=new i.A({cache:new(a())({maxSize:Math.floor(m/65536)}),fill:(e,t)=>this.readChunk(e,{signal:t})})}async getLines(e,t,n,i){var r;let a,s,o={};"function"==typeof i?s=i:(o=i,s=i.lineCallback,a=i.signal);const l=await this.index.getMetadata(o);d(a);const h=null!=t?t:0,c=null!=n?n:l.maxRefLength;if(!(h<=c))throw new TypeError("invalid start and end coordinates. start must be less than or equal to end");if(h===c)return;const f=await this.index.blocksForRange(e,h,c,o);d(a);let u=Date.now();for(const t of f){let n;const{buffer:i,cpositions:o,dpositions:f}=await this.chunkCache.get(t.toString(),t,a);d(a);let m=0,w=0;for(;m<i.length;){const b=i.indexOf("\n",m);if(-1===b)break;const p=i.slice(m,b),g=null!==(r=null==y?void 0:y.decode(p))&&void 0!==r?r:p.toString();if(f){for(;m+t.minv.dataPosition>=f[w++];);w--}const{startCoordinate:E,overlaps:x}=this.checkLine(l,e,h,c,g);if(void 0!==n&&void 0!==E&&n>E)throw new Error(`Lines not sorted by start coordinate (${n} > ${E}), this file is not usable with Tabix.`);if(n=E,x)s(g.trim(),256*o[w]+(m-f[w])+t.minv.dataPosition+1);else if(void 0!==E&&E>=c)return;this.yieldTime&&u-Date.now()>this.yieldTime&&(u=Date.now(),d(a),await I(1)),m=b+1}}}async getMetadata(e={}){return this.index.getMetadata(e)}async getHeaderBuffer(e={}){const{firstDataLine:t,metaChar:n,maxBlockSize:i}=await this.getMetadata(e);d(e.signal);const r=((null==t?void 0:t.blockPosition)||0)+i,a=await this._readRegion(0,r,e),s=await(0,l.unzip)(a);if(n){let e=-1;const t="\n".charCodeAt(0),i=n.charCodeAt(0);for(let n=0;n<s.length&&(n!==e+1||s[n]===i);n+=1)s[n]===t&&(e=n);return s.slice(0,e+1)}return s}async getHeader(e={}){return(await this.getHeaderBuffer(e)).toString("utf8")}async getReferenceSequenceNames(e={}){return(await this.getMetadata(e)).refIdToName}checkLine(e,t,n,i,r){const{columnNumbers:a,metaChar:s,coordinateType:o,format:l}=e;if(s&&r.startsWith(s))return{overlaps:!1};let{ref:h,start:c,end:d}=a;h||(h=0),c||(c=0),d||(d=0),"VCF"===l&&(d=8);const f=Math.max(h,c,d);let u=1,m=0,w="",b=-1/0;for(let e=0;e<r.length+1;e+=1)if("\t"===r[e]||e===r.length){if(u===h){if(this.renameRefSeq(r.slice(m,e))!==t)return{overlaps:!1}}else if(u===c){if(b=parseInt(r.slice(m,e),10),"1-based-closed"===o&&(b-=1),b>=i)return{startCoordinate:b,overlaps:!1};if((0===d||d===c)&&b+1<=n)return{startCoordinate:b,overlaps:!1}}else if("VCF"===l&&4===u)w=r.slice(m,e);else if(u===d&&("VCF"===l?this._getVcfEnd(b,w,r.slice(m,e)):parseInt(r.slice(m,e),10))<=n)return{overlaps:!1};if(m=e+1,u+=1,u>f)break}return{startCoordinate:b,overlaps:!0}}_getVcfEnd(e,t,n){let i=e+t.length;const r=n.includes("SVTYPE=TRA");if("."===n[0]||r){if(r)return e+1}else{let e=";";for(let t=0;t<n.length;t+=1){if(";"===e&&"END="===n.slice(t,t+4)){let e=n.indexOf(";",t);-1===e&&(e=n.length),i=parseInt(n.slice(t+4,e),10);break}e=n[t]}}return i}async lineCount(e,t={}){return this.index.lineCount(e,t)}async _readRegion(e,t,n={}){const i=s.hp.alloc(t),{bytesRead:r,buffer:a}=await this.filehandle.read(i,0,t,e,n);return a.slice(0,r)}async readChunk(e,t={}){const n=await this._readRegion(e.minv.blockPosition,e.fetchedSize(),t);return(0,l.i2)(n,e)}}}}]);
49f3d3878413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5ea1f9c1eef1de76232e69aa6d34cda77d90d566
fubar
parents:
diff changeset
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