jbrowse2: x/static/js/8965.51db703f.chunk.js.map annotate

annotate x/static/js/8965.51db703f.chunk.js.map @ 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
parents
children

rev	line source
125 49f3d3878413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5ea1f9c1eef1de76232e69aa6d34cda77d90d566 fubar parents: diff changeset	1 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{\n BaseFeatureDataAdapter,\n BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport {\n doesIntersect2,\n SimpleFeature,\n Feature,\n Region,\n} from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { readFile, parseBed } from '../util'\n\ninterface BareFeature {\n strand: number\n refName: string\n start: number\n end: number\n score: number\n name: string\n}\n\ntype Row = [BareFeature, BareFeature, number, number]\n\nexport default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {\n private setupP?: Promise<{\n assemblyNames: string[]\n feats: Row[]\n }>\n\n public static capabilities = ['getFeatures', 'getRefNames']\n\n async setup(opts: BaseOptions) {\n if (!this.setupP) {\n this.setupP = this.setupPre(opts).catch((e: unknown) => {\n this.setupP = undefined\n throw e\n })\n }\n return this.setupP\n }\n async setupPre(opts: BaseOptions) {\n const assemblyNames = this.getConf('assemblyNames') as string[]\n\n const pm = this.pluginManager\n const bed1 = openLocation(this.getConf('bed1Location'), pm)\n const bed2 = openLocation(this.getConf('bed2Location'), pm)\n const mcscan = openLocation(this.getConf('mcscanAnchorsLocation'), pm)\n const [bed1text, bed2text, mcscantext] = await Promise.all(\n [bed1, bed2, mcscan].map(r => readFile(r, opts)),\n )\n\n const bed1Map = parseBed(bed1text!)\n const bed2Map = parseBed(bed2text!)\n const feats = mcscantext!\n .split(/\\n\|\\r\\n\|\\r/)\n .filter(f => !!f && f !== '###')\n .map((line, index) => {\n const [name1, name2, score] = line.split('\\t')\n const r1 = bed1Map.get(name1)\n const r2 = bed2Map.get(name2)\n if (!r1 \|\| !r2) {\n throw new Error(`feature not found, ${name1} ${name2} ${r1} ${r2}`)\n }\n return [r1, r2, +score!, index] as Row\n })\n\n return {\n assemblyNames,\n feats,\n }\n }\n\n async hasDataForRefName() {\n // determining this properly is basically a call to getFeatures\n // so is not really that important, and has to be true or else\n // getFeatures is never called (BaseFeatureDataAdapter filters it out)\n return true\n }\n\n async getRefNames() {\n // we cannot determine this accurately\n return []\n }\n\n getFeatures(region: Region, opts: BaseOptions = {}) {\n return ObservableCreate<Feature>(async observer => {\n const { assemblyNames, feats } = await this.setup(opts)\n\n // The index of the assembly name in the region list corresponds to\n // the adapter in the subadapters list\n const index = assemblyNames.indexOf(region.assemblyName)\n if (index !== -1) {\n const flip = index === 0\n feats.forEach(f => {\n const [r1, r2, score, rowNum] = f\n const [f1, f2] = !flip ? [r2, r1] : [r1, r2]\n if (\n f1.refName === region.refName &&\n doesIntersect2(region.start, region.end, f1.start, f1.end)\n ) {\n observer.next(\n new SimpleFeature({\n ...f1,\n uniqueId: `${index}-${rowNum}`,\n syntenyId: rowNum,\n\n // note: strand would be -1 if the two features are on opposite\n // strands, indicating inverted alignment\n strand: f1.strand * f2.strand,\n assemblyName: assemblyNames[+!flip],\n score,\n mate: {\n ...f2,\n assemblyName: assemblyNames[+flip],\n },\n }),\n )\n }\n })\n }\n\n observer.complete()\n })\n }\n\n /*\n called to provide a hint that data tied to a certain region\n * will not be needed for the foreseeable future and can be purged\n * from caches, etc\n /\n freeResources(/ { region } /): void {}\n}\n","import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { GenericFilehandle } from 'generic-filehandle'\nimport { unzip } from '@gmod/bgzf-filehandle'\nimport { isGzip } from '@jbrowse/core/util'\nimport type { Buffer } from 'buffer'\n\nimport { PAFRecord } from './PAFAdapter/util'\n\nexport function parseBed(text: string) {\n return new Map(\n text\n .split(/\\n\|\\r\\n\|\\r/)\n .filter(f => !!f \|\| f.startsWith('#'))\n .map(line => {\n const [refName, start, end, name, score, strand] = line.split('\\t')\n return [\n name,\n {\n refName,\n start: +start!,\n end: +end!,\n score: +score!,\n name,\n strand: strand === '-' ? -1 : 1,\n },\n ]\n }),\n )\n}\n\nexport async function readFile(file: GenericFilehandle, opts?: BaseOptions) {\n const buffer = (await file.readFile(opts)) as Buffer\n return new TextDecoder('utf8', { fatal: true }).decode(\n isGzip(buffer) ? await unzip(buffer) : buffer,\n )\n}\n\nexport function zip(a: number[], b: number[]) {\n return a.map((e, i) => [e, b[i]] as [number, number])\n}\n\nconst decoder =\n typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined\n\nexport function parseLineByLine(\n buffer: Buffer,\n cb: (line: string) => PAFRecord,\n) {\n let blockStart = 0\n const entries = []\n while (blockStart < buffer.length) {\n const n = buffer.indexOf('\\n', blockStart)\n if (n === -1) {\n break\n }\n const b = buffer.subarray(blockStart, n)\n const line = (decoder?.decode(b) \|\| b.toString()).trim()\n if (line) {\n entries.push(cb(line))\n }\n\n blockStart = n + 1\n }\n return entries\n}\n\nexport function parsePAFLine(line: string) {\n const [\n qname,\n ,\n qstart,\n qend,\n strand,\n tname,\n ,\n tstart,\n tend,\n numMatches,\n blockLen,\n mappingQual,\n ...fields\n ] = line.split('\\t')\n\n const rest = Object.fromEntries(\n fields.map(field => {\n const r = field.indexOf(':')\n const fieldName = field.slice(0, r)\n const fieldValue = field.slice(r + 3)\n return [fieldName, fieldValue]\n }),\n )\n\n return {\n tname,\n tstart: +tstart!,\n tend: +tend!,\n qname,\n qstart: +qstart!,\n qend: +qend!,\n strand: strand === '-' ? -1 : 1,\n extra: {\n numMatches: +numMatches!,\n blockLen: +blockLen!,\n mappingQual: +mappingQual!,\n ...rest,\n },\n } as PAFRecord\n}\n\nexport function flipCigar(cigar: string[]) {\n const arr = []\n for (let i = cigar.length - 2; i >= 0; i -= 2) {\n arr.push(cigar[i])\n const op = cigar[i + 1]\n if (op === 'D') {\n arr.push('I')\n } else if (op === 'I') {\n arr.push('D')\n } else {\n arr.push(op)\n }\n }\n return arr\n}\n\nexport function swapIndelCigar(cigar: string) {\n return cigar.replaceAll('D', 'K').replaceAll('I', 'D').replaceAll('K', 'I')\n}\n","import { Buffer } from 'buffer'\n//@ts-ignore\nimport { Z_SYNC_FLUSH, Inflate } from 'pako'\n\ninterface VirtualOffset {\n blockPosition: number\n dataPosition: number\n}\ninterface Chunk {\n minv: VirtualOffset\n maxv: VirtualOffset\n}\n\n// browserify-zlib, which is the zlib shim used by default in webpacked code,\n// does not properly uncompress bgzf chunks that contain more than\n// one bgzf block, so export an unzip function that uses pako directly\n// if we are running in a browser.\nasync function unzip(inputData: Buffer) {\n try {\n let strm\n let pos = 0\n let i = 0\n const chunks = []\n let totalSize = 0\n let inflator\n do {\n const remainingInput = inputData.subarray(pos)\n inflator = new Inflate()\n //@ts-ignore\n ;({ strm } = inflator)\n inflator.push(remainingInput, Z_SYNC_FLUSH)\n if (inflator.err) {\n throw new Error(inflator.msg)\n }\n\n pos += strm.next_in\n chunks[i] = inflator.result as Uint8Array\n totalSize += chunks[i].length\n i += 1\n } while (strm.avail_in)\n\n const result = new Uint8Array(totalSize)\n for (let i = 0, offset = 0; i < chunks.length; i++) {\n result.set(chunks[i], offset)\n offset += chunks[i].length\n }\n return Buffer.from(result)\n } catch (e) {\n //cleanup error message\n if (`${e}`.match(/incorrect header check/)) {\n throw new Error(\n 'problem decompressing block: incorrect gzip header check',\n )\n }\n throw e\n }\n}\n\n// similar to pakounzip, except it does extra counting\n// to return the positions of compressed and decompressed\n// data offsets\nasync function unzipChunk(inputData: Buffer) {\n try {\n let strm\n let cpos = 0\n let dpos = 0\n const blocks = []\n const cpositions = []\n const dpositions = []\n do {\n const remainingInput = inputData.slice(cpos)\n const inflator = new Inflate()\n // @ts-ignore\n ;({ strm } = inflator)\n inflator.push(remainingInput, Z_SYNC_FLUSH)\n if (inflator.err) {\n throw new Error(inflator.msg)\n }\n\n const buffer = Buffer.from(inflator.result)\n blocks.push(buffer)\n\n cpositions.push(cpos)\n dpositions.push(dpos)\n\n cpos += strm.next_in\n dpos += buffer.length\n } while (strm.avail_in)\n\n const buffer = Buffer.concat(blocks)\n return { buffer, cpositions, dpositions }\n } catch (e) {\n //cleanup error message\n if (`${e}`.match(/incorrect header check/)) {\n throw new Error(\n 'problem decompressing block: incorrect gzip header check',\n )\n }\n throw e\n }\n}\n\n// similar to unzipChunk above but slices (0,minv.dataPosition) and\n// (maxv.dataPosition,end) off\nasync function unzipChunkSlice(inputData: Buffer, chunk: Chunk) {\n try {\n let strm\n const { minv, maxv } = chunk\n let cpos = minv.blockPosition\n let dpos = minv.dataPosition\n const chunks = []\n const cpositions = []\n const dpositions = []\n\n let totalSize = 0\n let i = 0\n do {\n const remainingInput = inputData.subarray(cpos - minv.blockPosition)\n const inflator = new Inflate()\n // @ts-ignore\n ;({ strm } = inflator)\n inflator.push(remainingInput, Z_SYNC_FLUSH)\n if (inflator.err) {\n throw new Error(inflator.msg)\n }\n\n const buffer = inflator.result\n chunks.push(buffer as Uint8Array)\n let len = buffer.length\n\n cpositions.push(cpos)\n dpositions.push(dpos)\n if (chunks.length === 1 && minv.dataPosition) {\n // this is the first chunk, trim it\n chunks[0] = chunks[0].subarray(minv.dataPosition)\n len = chunks[0].length\n }\n const origCpos = cpos\n cpos += strm.next_in\n dpos += len\n\n if (origCpos >= maxv.blockPosition) {\n // this is the last chunk, trim it and stop decompressing\n // note if it is the same block is minv it subtracts that already\n // trimmed part of the slice length\n\n chunks[i] = chunks[i].subarray(\n 0,\n maxv.blockPosition === minv.blockPosition\n ? maxv.dataPosition - minv.dataPosition + 1\n : maxv.dataPosition + 1,\n )\n\n cpositions.push(cpos)\n dpositions.push(dpos)\n totalSize += chunks[i].length\n break\n }\n totalSize += chunks[i].length\n i++\n } while (strm.avail_in)\n\n const result = new Uint8Array(totalSize)\n for (let i = 0, offset = 0; i < chunks.length; i++) {\n result.set(chunks[i], offset)\n offset += chunks[i].length\n }\n const buffer = Buffer.from(result)\n\n return { buffer, cpositions, dpositions }\n } catch (e) {\n //cleanup error message\n if (`${e}`.match(/incorrect header check/)) {\n throw new Error(\n 'problem decompressing block: incorrect gzip header check',\n )\n }\n throw e\n }\n}\n\nfunction nodeUnzip() {\n throw new Error('nodeUnzip not implemented.')\n}\n\nexport { unzip, unzipChunk, unzipChunkSlice, unzip as pakoUnzip, nodeUnzip }\n","import Long from 'long'\nimport { Buffer } from 'buffer'\nimport { LocalFile, GenericFilehandle } from 'generic-filehandle'\n\n// const COMPRESSED_POSITION = 0\nconst UNCOMPRESSED_POSITION = 1\n\nexport default class GziIndex {\n filehandle: GenericFilehandle\n\n index?: any\n\n constructor({\n filehandle,\n path,\n }: {\n filehandle?: GenericFilehandle\n path?: string\n }) {\n if (filehandle) {\n this.filehandle = filehandle\n } else if (path) {\n this.filehandle = new LocalFile(path)\n } else {\n throw new TypeError('either filehandle or path must be defined')\n }\n }\n\n _readLongWithOverflow(buf: Buffer, offset = 0, unsigned = true) {\n //@ts-ignore\n const long = Long.fromBytesLE(buf.slice(offset, offset + 8), unsigned)\n if (\n long.greaterThan(Number.MAX_SAFE_INTEGER) \|\|\n long.lessThan(Number.MIN_SAFE_INTEGER)\n ) {\n throw new TypeError('integer overflow')\n }\n\n return long.toNumber()\n }\n\n _getIndex() {\n if (!this.index) {\n this.index = this._readIndex()\n }\n return this.index\n }\n\n async _readIndex() {\n let buf = Buffer.allocUnsafe(8)\n await this.filehandle.read(buf, 0, 8, 0)\n const numEntries = this._readLongWithOverflow(buf, 0, true)\n if (!numEntries) {\n return [[0, 0]]\n }\n\n const entries = new Array(numEntries + 1)\n entries[0] = [0, 0]\n\n // TODO rewrite this to make an index-index that stays in memory\n const bufSize = 8 2 * numEntries\n if (bufSize > Number.MAX_SAFE_INTEGER) {\n throw new TypeError('integer overflow')\n }\n buf = Buffer.allocUnsafe(bufSize)\n await this.filehandle.read(buf, 0, bufSize, 8)\n for (let entryNumber = 0; entryNumber < numEntries; entryNumber += 1) {\n const compressedPosition = this._readLongWithOverflow(\n buf,\n entryNumber * 16,\n )\n const uncompressedPosition = this._readLongWithOverflow(\n buf,\n entryNumber * 16 + 8,\n )\n entries[entryNumber + 1] = [compressedPosition, uncompressedPosition]\n }\n\n return entries\n }\n\n async getLastBlock() {\n const entries = await this._getIndex()\n if (!entries.length) {\n return undefined\n }\n return entries[entries.length - 1]\n }\n\n async getRelevantBlocksForRead(length: number, position: number) {\n const endPosition = position + length\n if (length === 0) {\n return []\n }\n const entries = await this._getIndex()\n const relevant = []\n\n // binary search to find the block that the\n // read starts in and extend forward from that\n const compare = (entry: any, nextEntry: any) => {\n const uncompressedPosition = entry[UNCOMPRESSED_POSITION]\n const nextUncompressedPosition = nextEntry\n ? nextEntry[UNCOMPRESSED_POSITION]\n : Infinity\n // block overlaps read start\n if (\n uncompressedPosition <= position &&\n nextUncompressedPosition > position\n ) {\n return 0\n // block is before read start\n }\n if (uncompressedPosition < position) {\n return -1\n }\n // block is after read start\n return 1\n }\n\n let lowerBound = 0\n let upperBound = entries.length - 1\n let searchPosition = Math.floor(entries.length / 2)\n\n let comparison = compare(\n entries[searchPosition],\n entries[searchPosition + 1],\n )\n while (comparison !== 0) {\n if (comparison > 0) {\n upperBound = searchPosition - 1\n } else if (comparison < 0) {\n lowerBound = searchPosition + 1\n }\n searchPosition = Math.ceil((upperBound - lowerBound) / 2) + lowerBound\n comparison = compare(entries[searchPosition], entries[searchPosition + 1])\n }\n\n // here's where we read forward\n relevant.push(entries[searchPosition])\n let i = searchPosition + 1\n for (; i < entries.length; i += 1) {\n relevant.push(entries[i])\n if (entries[i][UNCOMPRESSED_POSITION] >= endPosition) {\n break\n }\n }\n if (relevant[relevant.length - 1][UNCOMPRESSED_POSITION] < endPosition) {\n relevant.push([])\n }\n return relevant\n }\n}\n","import { Buffer } from 'buffer'\nimport { LocalFile, GenericFilehandle } from 'generic-filehandle'\n\n// locals\nimport { unzip } from './unzip'\nimport GziIndex from './gziIndex'\n\nexport default class BgzFilehandle {\n filehandle: GenericFilehandle\n gzi: GziIndex\n\n constructor({\n filehandle,\n path,\n gziFilehandle,\n gziPath,\n }: {\n filehandle?: GenericFilehandle\n path?: string\n gziFilehandle?: GenericFilehandle\n gziPath?: string\n }) {\n if (filehandle) {\n this.filehandle = filehandle\n } else if (path) {\n this.filehandle = new LocalFile(path)\n } else {\n throw new TypeError('either filehandle or path must be defined')\n }\n\n if (!gziFilehandle && !gziPath && !path) {\n throw new TypeError('either gziFilehandle or gziPath must be defined')\n }\n\n this.gzi = new GziIndex({\n filehandle: gziFilehandle,\n path: !gziFilehandle && !gziPath && path ? gziPath : `${path}.gzi`,\n })\n }\n\n async stat() {\n const compressedStat = await this.filehandle.stat()\n return Object.assign(compressedStat, {\n size: await this.getUncompressedFileSize(),\n blocks: undefined,\n blksize: undefined,\n })\n }\n\n async getUncompressedFileSize() {\n // read the last block's ISIZE (see gzip RFC),\n // and add it to its uncompressedPosition\n const [, uncompressedPosition] = await this.gzi.getLastBlock()\n\n const { size } = await this.filehandle.stat()\n\n const buf = Buffer.allocUnsafe(4)\n // note: there should be a 28-byte EOF marker (an empty block) at\n // the end of the file, so we skip backward past that\n const { bytesRead } = await this.filehandle.read(buf, 0, 4, size - 28 - 4)\n if (bytesRead !== 4) {\n throw new Error('read error')\n }\n const lastBlockUncompressedSize = buf.readUInt32LE(0)\n return uncompressedPosition + lastBlockUncompressedSize\n }\n\n async _readAndUncompressBlock(\n blockBuffer: Buffer,\n [compressedPosition]: [number],\n [nextCompressedPosition]: [number],\n ) {\n let next = nextCompressedPosition\n if (!next) {\n next = (await this.filehandle.stat()).size\n }\n\n // read the compressed data into the block buffer\n const blockCompressedLength = next - compressedPosition\n\n await this.filehandle.read(\n blockBuffer,\n 0,\n blockCompressedLength,\n compressedPosition,\n )\n\n // uncompress it\n const unzippedBuffer = await unzip(\n blockBuffer.slice(0, blockCompressedLength),\n )\n\n return unzippedBuffer as Buffer\n }\n\n async read(buf: Buffer, offset: number, length: number, position: number) {\n // get the block positions for this read\n const blockPositions = await this.gzi.getRelevantBlocksForRead(\n length,\n position,\n )\n const blockBuffer = Buffer.allocUnsafe(32768 * 2)\n // uncompress the blocks and read from them one at a time to keep memory usage down\n let destinationOffset = offset\n let bytesRead = 0\n for (\n let blockNum = 0;\n blockNum < blockPositions.length - 1;\n blockNum += 1\n ) {\n // eslint-disable-next-line no-await-in-loop\n const uncompressedBuffer = await this._readAndUncompressBlock(\n blockBuffer,\n blockPositions[blockNum],\n blockPositions[blockNum + 1],\n )\n const [, uncompressedPosition] = blockPositions[blockNum]\n const sourceOffset =\n uncompressedPosition >= position ? 0 : position - uncompressedPosition\n const sourceEnd =\n Math.min(\n position + length,\n uncompressedPosition + uncompressedBuffer.length,\n ) - uncompressedPosition\n if (sourceOffset >= 0 && sourceOffset < uncompressedBuffer.length) {\n uncompressedBuffer.copy(buf, destinationOffset, sourceOffset, sourceEnd)\n destinationOffset += sourceEnd - sourceOffset\n bytesRead += sourceEnd - sourceOffset\n }\n }\n\n return { bytesRead, buffer: buf }\n }\n}\n"],"names":["MCScanAnchorsAdapter","BaseFeatureDataAdapter","setup","opts","this","setupP","setupPre","catch","e","undefined","assemblyNames","getConf","pm","pluginManager","bed1","openLocation","bed2","mcscan","bed1text","bed2text","mcscantext","Promise","all","map","r","readFile","bed1Map","parseBed","bed2Map","feats","split","filter","f","line","index","name1","name2","score","r1","get","r2","Error","hasDataForRefName","getRefNames","getFeatures","region","ObservableCreate","async","indexOf","assemblyName","flip","forEach","rowNum","f1","f2","refName","doesIntersect2","start","end","observer","next","SimpleFeature","uniqueId","syntenyId","strand","mate","complete","freeResources","text","Map","startsWith","name","file","buffer","TextDecoder","fatal","decode","isGzip","unzip","zip","a","b","i","decoder","parseLineByLine","cb","blockStart","entries","length","n","subarray","toString","trim","push","parsePAFLine","qname","qstart","qend","tname","tstart","tend","numMatches","blockLen","mappingQual","fields","extra","Object","fromEntries","field","slice","flipCigar","cigar","arr","op","swapIndelCigar","replaceAll","inputData","strm","pos","chunks","inflator","totalSize","remainingInput","Inflate","Z_SYNC_FLUSH","err","msg","next_in","result","avail_in","Uint8Array","offset","set","from","match","unzipChunkSlice","chunk","minv","maxv","cpos","blockPosition","dpos","dataPosition","cpositions","dpositions","len","origCpos","GziIndex","constructor","filehandle","path","TypeError","_readLongWithOverflow","buf","unsigned","long","greaterThan","Number","MAX_SAFE_INTEGER","lessThan","MIN_SAFE_INTEGER","toNumber","_getIndex","_readIndex","allocUnsafe","read","numEntries","Array","bufSize","entryNumber","compressedPosition","uncompressedPosition","getLastBlock","getRelevantBlocksForRead","position","endPosition","relevant","compare","entry","nextEntry","nextUncompressedPosition","Infinity","lowerBound","upperBound","searchPosition","Math","floor","comparison","ceil","BgzFilehandle","gziFilehandle","gziPath","gzi","stat","compressedStat","assign","size","getUncompressedFileSize","blocks","blksize","bytesRead","readUInt32LE","_readAndUncompressBlock","blockBuffer","nextCompressedPosition","blockCompressedLength","blockPositions","destinationOffset","blockNum","uncompressedBuffer","sourceOffset","sourceEnd","min","copy"],"sourceRoot":""}

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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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{\n BaseFeatureDataAdapter,\n BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport {\n doesIntersect2,\n SimpleFeature,\n Feature,\n Region,\n} from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { readFile, parseBed } from '../util'\n\ninterface BareFeature {\n strand: number\n refName: string\n start: number\n end: number\n score: number\n name: string\n}\n\ntype Row = [BareFeature, BareFeature, number, number]\n\nexport default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {\n private setupP?: Promise<{\n assemblyNames: string[]\n feats: Row[]\n }>\n\n public static capabilities = ['getFeatures', 'getRefNames']\n\n async setup(opts: BaseOptions) {\n if (!this.setupP) {\n this.setupP = this.setupPre(opts).catch((e: unknown) => {\n this.setupP = undefined\n throw e\n })\n }\n return this.setupP\n }\n async setupPre(opts: BaseOptions) {\n const assemblyNames = this.getConf('assemblyNames') as string[]\n\n const pm = this.pluginManager\n const bed1 = openLocation(this.getConf('bed1Location'), pm)\n const bed2 = openLocation(this.getConf('bed2Location'), pm)\n const mcscan = openLocation(this.getConf('mcscanAnchorsLocation'), pm)\n const [bed1text, bed2text, mcscantext] = await Promise.all(\n [bed1, bed2, mcscan].map(r => readFile(r, opts)),\n )\n\n const bed1Map = parseBed(bed1text!)\n const bed2Map = parseBed(bed2text!)\n const feats = mcscantext!\n .split(/\\n|\\r\\n|\\r/)\n .filter(f => !!f && f !== '###')\n .map((line, index) => {\n const [name1, name2, score] = line.split('\\t')\n const r1 = bed1Map.get(name1)\n const r2 = bed2Map.get(name2)\n if (!r1 || !r2) {\n throw new Error(`feature not found, ${name1} ${name2} ${r1} ${r2}`)\n }\n return [r1, r2, +score!, index] as Row\n })\n\n return {\n assemblyNames,\n feats,\n }\n }\n\n async hasDataForRefName() {\n // determining this properly is basically a call to getFeatures\n // so is not really that important, and has to be true or else\n // getFeatures is never called (BaseFeatureDataAdapter filters it out)\n return true\n }\n\n async getRefNames() {\n // we cannot determine this accurately\n return []\n }\n\n getFeatures(region: Region, opts: BaseOptions = {}) {\n return ObservableCreate<Feature>(async observer => {\n const { assemblyNames, feats } = await this.setup(opts)\n\n // The index of the assembly name in the region list corresponds to\n // the adapter in the subadapters list\n const index = assemblyNames.indexOf(region.assemblyName)\n if (index !== -1) {\n const flip = index === 0\n feats.forEach(f => {\n const [r1, r2, score, rowNum] = f\n const [f1, f2] = !flip ? [r2, r1] : [r1, r2]\n if (\n f1.refName === region.refName &&\n doesIntersect2(region.start, region.end, f1.start, f1.end)\n ) {\n observer.next(\n new SimpleFeature({\n ...f1,\n uniqueId: `${index}-${rowNum}`,\n syntenyId: rowNum,\n\n // note: strand would be -1 if the two features are on opposite\n // strands, indicating inverted alignment\n strand: f1.strand * f2.strand,\n assemblyName: assemblyNames[+!flip],\n score,\n mate: {\n ...f2,\n assemblyName: assemblyNames[+flip],\n },\n }),\n )\n }\n })\n }\n\n observer.complete()\n })\n }\n\n /**\n * called to provide a hint that data tied to a certain region\n * will not be needed for the foreseeable future and can be purged\n * from caches, etc\n */\n freeResources(/* { region } */): void {}\n}\n","import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { GenericFilehandle } from 'generic-filehandle'\nimport { unzip } from '@gmod/bgzf-filehandle'\nimport { isGzip } from '@jbrowse/core/util'\nimport type { Buffer } from 'buffer'\n\nimport { PAFRecord } from './PAFAdapter/util'\n\nexport function parseBed(text: string) {\n return new Map(\n text\n .split(/\\n|\\r\\n|\\r/)\n .filter(f => !!f || f.startsWith('#'))\n .map(line => {\n const [refName, start, end, name, score, strand] = line.split('\\t')\n return [\n name,\n {\n refName,\n start: +start!,\n end: +end!,\n score: +score!,\n name,\n strand: strand === '-' ? -1 : 1,\n },\n ]\n }),\n )\n}\n\nexport async function readFile(file: GenericFilehandle, opts?: BaseOptions) {\n const buffer = (await file.readFile(opts)) as Buffer\n return new TextDecoder('utf8', { fatal: true }).decode(\n isGzip(buffer) ? await unzip(buffer) : buffer,\n )\n}\n\nexport function zip(a: number[], b: number[]) {\n return a.map((e, i) => [e, b[i]] as [number, number])\n}\n\nconst decoder =\n typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined\n\nexport function parseLineByLine(\n buffer: Buffer,\n cb: (line: string) => PAFRecord,\n) {\n let blockStart = 0\n const entries = []\n while (blockStart < buffer.length) {\n const n = buffer.indexOf('\\n', blockStart)\n if (n === -1) {\n break\n }\n const b = buffer.subarray(blockStart, n)\n const line = (decoder?.decode(b) || b.toString()).trim()\n if (line) {\n entries.push(cb(line))\n }\n\n blockStart = n + 1\n }\n return entries\n}\n\nexport function parsePAFLine(line: string) {\n const [\n qname,\n ,\n qstart,\n qend,\n strand,\n tname,\n ,\n tstart,\n tend,\n numMatches,\n blockLen,\n mappingQual,\n ...fields\n ] = line.split('\\t')\n\n const rest = Object.fromEntries(\n fields.map(field => {\n const r = field.indexOf(':')\n const fieldName = field.slice(0, r)\n const fieldValue = field.slice(r + 3)\n return [fieldName, fieldValue]\n }),\n )\n\n return {\n tname,\n tstart: +tstart!,\n tend: +tend!,\n qname,\n qstart: +qstart!,\n qend: +qend!,\n strand: strand === '-' ? -1 : 1,\n extra: {\n numMatches: +numMatches!,\n blockLen: +blockLen!,\n mappingQual: +mappingQual!,\n ...rest,\n },\n } as PAFRecord\n}\n\nexport function flipCigar(cigar: string[]) {\n const arr = []\n for (let i = cigar.length - 2; i >= 0; i -= 2) {\n arr.push(cigar[i])\n const op = cigar[i + 1]\n if (op === 'D') {\n arr.push('I')\n } else if (op === 'I') {\n arr.push('D')\n } else {\n arr.push(op)\n }\n }\n return arr\n}\n\nexport function swapIndelCigar(cigar: string) {\n return cigar.replaceAll('D', 'K').replaceAll('I', 'D').replaceAll('K', 'I')\n}\n","import { Buffer } from 'buffer'\n//@ts-ignore\nimport { Z_SYNC_FLUSH, Inflate } from 'pako'\n\ninterface VirtualOffset {\n blockPosition: number\n dataPosition: number\n}\ninterface Chunk {\n minv: VirtualOffset\n maxv: VirtualOffset\n}\n\n// browserify-zlib, which is the zlib shim used by default in webpacked code,\n// does not properly uncompress bgzf chunks that contain more than\n// one bgzf block, so export an unzip function that uses pako directly\n// if we are running in a browser.\nasync function unzip(inputData: Buffer) {\n try {\n let strm\n let pos = 0\n let i = 0\n const chunks = []\n let totalSize = 0\n let inflator\n do {\n const remainingInput = inputData.subarray(pos)\n inflator = new Inflate()\n //@ts-ignore\n ;({ strm } = inflator)\n inflator.push(remainingInput, Z_SYNC_FLUSH)\n if (inflator.err) {\n throw new Error(inflator.msg)\n }\n\n pos += strm.next_in\n chunks[i] = inflator.result as Uint8Array\n totalSize += chunks[i].length\n i += 1\n } while (strm.avail_in)\n\n const result = new Uint8Array(totalSize)\n for (let i = 0, offset = 0; i < chunks.length; i++) {\n result.set(chunks[i], offset)\n offset += chunks[i].length\n }\n return Buffer.from(result)\n } catch (e) {\n //cleanup error message\n if (`${e}`.match(/incorrect header check/)) {\n throw new Error(\n 'problem decompressing block: incorrect gzip header check',\n )\n }\n throw e\n }\n}\n\n// similar to pakounzip, except it does extra counting\n// to return the positions of compressed and decompressed\n// data offsets\nasync function unzipChunk(inputData: Buffer) {\n try {\n let strm\n let cpos = 0\n let dpos = 0\n const blocks = []\n const cpositions = []\n const dpositions = []\n do {\n const remainingInput = inputData.slice(cpos)\n const inflator = new Inflate()\n // @ts-ignore\n ;({ strm } = inflator)\n inflator.push(remainingInput, Z_SYNC_FLUSH)\n if (inflator.err) {\n throw new Error(inflator.msg)\n }\n\n const buffer = Buffer.from(inflator.result)\n blocks.push(buffer)\n\n cpositions.push(cpos)\n dpositions.push(dpos)\n\n cpos += strm.next_in\n dpos += buffer.length\n } while (strm.avail_in)\n\n const buffer = Buffer.concat(blocks)\n return { buffer, cpositions, dpositions }\n } catch (e) {\n //cleanup error message\n if (`${e}`.match(/incorrect header check/)) {\n throw new Error(\n 'problem decompressing block: incorrect gzip header check',\n )\n }\n throw e\n }\n}\n\n// similar to unzipChunk above but slices (0,minv.dataPosition) and\n// (maxv.dataPosition,end) off\nasync function unzipChunkSlice(inputData: Buffer, chunk: Chunk) {\n try {\n let strm\n const { minv, maxv } = chunk\n let cpos = minv.blockPosition\n let dpos = minv.dataPosition\n const chunks = []\n const cpositions = []\n const dpositions = []\n\n let totalSize = 0\n let i = 0\n do {\n const remainingInput = inputData.subarray(cpos - minv.blockPosition)\n const inflator = new Inflate()\n // @ts-ignore\n ;({ strm } = inflator)\n inflator.push(remainingInput, Z_SYNC_FLUSH)\n if (inflator.err) {\n throw new Error(inflator.msg)\n }\n\n const buffer = inflator.result\n chunks.push(buffer as Uint8Array)\n let len = buffer.length\n\n cpositions.push(cpos)\n dpositions.push(dpos)\n if (chunks.length === 1 && minv.dataPosition) {\n // this is the first chunk, trim it\n chunks[0] = chunks[0].subarray(minv.dataPosition)\n len = chunks[0].length\n }\n const origCpos = cpos\n cpos += strm.next_in\n dpos += len\n\n if (origCpos >= maxv.blockPosition) {\n // this is the last chunk, trim it and stop decompressing\n // note if it is the same block is minv it subtracts that already\n // trimmed part of the slice length\n\n chunks[i] = chunks[i].subarray(\n 0,\n maxv.blockPosition === minv.blockPosition\n ? maxv.dataPosition - minv.dataPosition + 1\n : maxv.dataPosition + 1,\n )\n\n cpositions.push(cpos)\n dpositions.push(dpos)\n totalSize += chunks[i].length\n break\n }\n totalSize += chunks[i].length\n i++\n } while (strm.avail_in)\n\n const result = new Uint8Array(totalSize)\n for (let i = 0, offset = 0; i < chunks.length; i++) {\n result.set(chunks[i], offset)\n offset += chunks[i].length\n }\n const buffer = Buffer.from(result)\n\n return { buffer, cpositions, dpositions }\n } catch (e) {\n //cleanup error message\n if (`${e}`.match(/incorrect header check/)) {\n throw new Error(\n 'problem decompressing block: incorrect gzip header check',\n )\n }\n throw e\n }\n}\n\nfunction nodeUnzip() {\n throw new Error('nodeUnzip not implemented.')\n}\n\nexport { unzip, unzipChunk, unzipChunkSlice, unzip as pakoUnzip, nodeUnzip }\n","import Long from 'long'\nimport { Buffer } from 'buffer'\nimport { LocalFile, GenericFilehandle } from 'generic-filehandle'\n\n// const COMPRESSED_POSITION = 0\nconst UNCOMPRESSED_POSITION = 1\n\nexport default class GziIndex {\n filehandle: GenericFilehandle\n\n index?: any\n\n constructor({\n filehandle,\n path,\n }: {\n filehandle?: GenericFilehandle\n path?: string\n }) {\n if (filehandle) {\n this.filehandle = filehandle\n } else if (path) {\n this.filehandle = new LocalFile(path)\n } else {\n throw new TypeError('either filehandle or path must be defined')\n }\n }\n\n _readLongWithOverflow(buf: Buffer, offset = 0, unsigned = true) {\n //@ts-ignore\n const long = Long.fromBytesLE(buf.slice(offset, offset + 8), unsigned)\n if (\n long.greaterThan(Number.MAX_SAFE_INTEGER) ||\n long.lessThan(Number.MIN_SAFE_INTEGER)\n ) {\n throw new TypeError('integer overflow')\n }\n\n return long.toNumber()\n }\n\n _getIndex() {\n if (!this.index) {\n this.index = this._readIndex()\n }\n return this.index\n }\n\n async _readIndex() {\n let buf = Buffer.allocUnsafe(8)\n await this.filehandle.read(buf, 0, 8, 0)\n const numEntries = this._readLongWithOverflow(buf, 0, true)\n if (!numEntries) {\n return [[0, 0]]\n }\n\n const entries = new Array(numEntries + 1)\n entries[0] = [0, 0]\n\n // TODO rewrite this to make an index-index that stays in memory\n const bufSize = 8 * 2 * numEntries\n if (bufSize > Number.MAX_SAFE_INTEGER) {\n throw new TypeError('integer overflow')\n }\n buf = Buffer.allocUnsafe(bufSize)\n await this.filehandle.read(buf, 0, bufSize, 8)\n for (let entryNumber = 0; entryNumber < numEntries; entryNumber += 1) {\n const compressedPosition = this._readLongWithOverflow(\n buf,\n entryNumber * 16,\n )\n const uncompressedPosition = this._readLongWithOverflow(\n buf,\n entryNumber * 16 + 8,\n )\n entries[entryNumber + 1] = [compressedPosition, uncompressedPosition]\n }\n\n return entries\n }\n\n async getLastBlock() {\n const entries = await this._getIndex()\n if (!entries.length) {\n return undefined\n }\n return entries[entries.length - 1]\n }\n\n async getRelevantBlocksForRead(length: number, position: number) {\n const endPosition = position + length\n if (length === 0) {\n return []\n }\n const entries = await this._getIndex()\n const relevant = []\n\n // binary search to find the block that the\n // read starts in and extend forward from that\n const compare = (entry: any, nextEntry: any) => {\n const uncompressedPosition = entry[UNCOMPRESSED_POSITION]\n const nextUncompressedPosition = nextEntry\n ? nextEntry[UNCOMPRESSED_POSITION]\n : Infinity\n // block overlaps read start\n if (\n uncompressedPosition <= position &&\n nextUncompressedPosition > position\n ) {\n return 0\n // block is before read start\n }\n if (uncompressedPosition < position) {\n return -1\n }\n // block is after read start\n return 1\n }\n\n let lowerBound = 0\n let upperBound = entries.length - 1\n let searchPosition = Math.floor(entries.length / 2)\n\n let comparison = compare(\n entries[searchPosition],\n entries[searchPosition + 1],\n )\n while (comparison !== 0) {\n if (comparison > 0) {\n upperBound = searchPosition - 1\n } else if (comparison < 0) {\n lowerBound = searchPosition + 1\n }\n searchPosition = Math.ceil((upperBound - lowerBound) / 2) + lowerBound\n comparison = compare(entries[searchPosition], entries[searchPosition + 1])\n }\n\n // here's where we read forward\n relevant.push(entries[searchPosition])\n let i = searchPosition + 1\n for (; i < entries.length; i += 1) {\n relevant.push(entries[i])\n if (entries[i][UNCOMPRESSED_POSITION] >= endPosition) {\n break\n }\n }\n if (relevant[relevant.length - 1][UNCOMPRESSED_POSITION] < endPosition) {\n relevant.push([])\n }\n return relevant\n }\n}\n","import { Buffer } from 'buffer'\nimport { LocalFile, GenericFilehandle } from 'generic-filehandle'\n\n// locals\nimport { unzip } from './unzip'\nimport GziIndex from './gziIndex'\n\nexport default class BgzFilehandle {\n filehandle: GenericFilehandle\n gzi: GziIndex\n\n constructor({\n filehandle,\n path,\n gziFilehandle,\n gziPath,\n }: {\n filehandle?: GenericFilehandle\n path?: string\n gziFilehandle?: GenericFilehandle\n gziPath?: string\n }) {\n if (filehandle) {\n this.filehandle = filehandle\n } else if (path) {\n this.filehandle = new LocalFile(path)\n } else {\n throw new TypeError('either filehandle or path must be defined')\n }\n\n if (!gziFilehandle && !gziPath && !path) {\n throw new TypeError('either gziFilehandle or gziPath must be defined')\n }\n\n this.gzi = new GziIndex({\n filehandle: gziFilehandle,\n path: !gziFilehandle && !gziPath && path ? gziPath : `${path}.gzi`,\n })\n }\n\n async stat() {\n const compressedStat = await this.filehandle.stat()\n return Object.assign(compressedStat, {\n size: await this.getUncompressedFileSize(),\n blocks: undefined,\n blksize: undefined,\n })\n }\n\n async getUncompressedFileSize() {\n // read the last block's ISIZE (see gzip RFC),\n // and add it to its uncompressedPosition\n const [, uncompressedPosition] = await this.gzi.getLastBlock()\n\n const { size } = await this.filehandle.stat()\n\n const buf = Buffer.allocUnsafe(4)\n // note: there should be a 28-byte EOF marker (an empty block) at\n // the end of the file, so we skip backward past that\n const { bytesRead } = await this.filehandle.read(buf, 0, 4, size - 28 - 4)\n if (bytesRead !== 4) {\n throw new Error('read error')\n }\n const lastBlockUncompressedSize = buf.readUInt32LE(0)\n return uncompressedPosition + lastBlockUncompressedSize\n }\n\n async _readAndUncompressBlock(\n blockBuffer: Buffer,\n [compressedPosition]: [number],\n [nextCompressedPosition]: [number],\n ) {\n let next = nextCompressedPosition\n if (!next) {\n next = (await this.filehandle.stat()).size\n }\n\n // read the compressed data into the block buffer\n const blockCompressedLength = next - compressedPosition\n\n await this.filehandle.read(\n blockBuffer,\n 0,\n blockCompressedLength,\n compressedPosition,\n )\n\n // uncompress it\n const unzippedBuffer = await unzip(\n blockBuffer.slice(0, blockCompressedLength),\n )\n\n return unzippedBuffer as Buffer\n }\n\n async read(buf: Buffer, offset: number, length: number, position: number) {\n // get the block positions for this read\n const blockPositions = await this.gzi.getRelevantBlocksForRead(\n length,\n position,\n )\n const blockBuffer = Buffer.allocUnsafe(32768 * 2)\n // uncompress the blocks and read from them one at a time to keep memory usage down\n let destinationOffset = offset\n let bytesRead = 0\n for (\n let blockNum = 0;\n blockNum < blockPositions.length - 1;\n blockNum += 1\n ) {\n // eslint-disable-next-line no-await-in-loop\n const uncompressedBuffer = await this._readAndUncompressBlock(\n blockBuffer,\n blockPositions[blockNum],\n blockPositions[blockNum + 1],\n )\n const [, uncompressedPosition] = blockPositions[blockNum]\n const sourceOffset =\n uncompressedPosition >= position ? 0 : position - uncompressedPosition\n const sourceEnd =\n Math.min(\n position + length,\n uncompressedPosition + uncompressedBuffer.length,\n ) - uncompressedPosition\n if (sourceOffset >= 0 && sourceOffset < uncompressedBuffer.length) {\n uncompressedBuffer.copy(buf, destinationOffset, sourceOffset, sourceEnd)\n destinationOffset += sourceEnd - sourceOffset\n bytesRead += sourceEnd - sourceOffset\n }\n }\n\n return { bytesRead, buffer: buf }\n }\n}\n"],"names":["MCScanAnchorsAdapter","BaseFeatureDataAdapter","setup","opts","this","setupP","setupPre","catch","e","undefined","assemblyNames","getConf","pm","pluginManager","bed1","openLocation","bed2","mcscan","bed1text","bed2text","mcscantext","Promise","all","map","r","readFile","bed1Map","parseBed","bed2Map","feats","split","filter","f","line","index","name1","name2","score","r1","get","r2","Error","hasDataForRefName","getRefNames","getFeatures","region","ObservableCreate","async","indexOf","assemblyName","flip","forEach","rowNum","f1","f2","refName","doesIntersect2","start","end","observer","next","SimpleFeature","uniqueId","syntenyId","strand","mate","complete","freeResources","text","Map","startsWith","name","file","buffer","TextDecoder","fatal","decode","isGzip","unzip","zip","a","b","i","decoder","parseLineByLine","cb","blockStart","entries","length","n","subarray","toString","trim","push","parsePAFLine","qname","qstart","qend","tname","tstart","tend","numMatches","blockLen","mappingQual","fields","extra","Object","fromEntries","field","slice","flipCigar","cigar","arr","op","swapIndelCigar","replaceAll","inputData","strm","pos","chunks","inflator","totalSize","remainingInput","Inflate","Z_SYNC_FLUSH","err","msg","next_in","result","avail_in","Uint8Array","offset","set","from","match","unzipChunkSlice","chunk","minv","maxv","cpos","blockPosition","dpos","dataPosition","cpositions","dpositions","len","origCpos","GziIndex","constructor","filehandle","path","TypeError","_readLongWithOverflow","buf","unsigned","long","greaterThan","Number","MAX_SAFE_INTEGER","lessThan","MIN_SAFE_INTEGER","toNumber","_getIndex","_readIndex","allocUnsafe","read","numEntries","Array","bufSize","entryNumber","compressedPosition","uncompressedPosition","getLastBlock","getRelevantBlocksForRead","position","endPosition","relevant","compare","entry","nextEntry","nextUncompressedPosition","Infinity","lowerBound","upperBound","searchPosition","Math","floor","comparison","ceil","BgzFilehandle","gziFilehandle","gziPath","gzi","stat","compressedStat","assign","size","getUncompressedFileSize","blocks","blksize","bytesRead","readUInt32LE","_readAndUncompressBlock","blockBuffer","nextCompressedPosition","blockCompressedLength","blockPositions","destinationOffset","blockNum","uncompressedBuffer","sourceOffset","sourceEnd","min","copy"],"sourceRoot":""}

Mercurial > repos > fubar > jbrowse2

annotate x/static/js/8965.51db703f.chunk.js.map @ 125:49f3d3878413 draft