jbrowse2: x/static/js/5461.5c8cf5d1.chunk.js.map comparison

comparison x/static/js/5461.5c8cf5d1.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

comparison

equal deleted inserted replaced

124:137e08517410	125:49f3d3878413
	1 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{ AugmentedRegion as Region } from '@jbrowse/core/util/types'\nimport { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { getTag, getTagAlt, shouldFetchReferenceSequence } from '../util'\nimport {\n parseCigar,\n getNextRefPos,\n getModificationPositions,\n getMethBins,\n Mismatch,\n} from '../MismatchParser'\nimport { doesIntersect2 } from '@jbrowse/core/util'\nimport { Bin, SkipMap } from './util'\n\nfunction mismatchLen(mismatch: Mismatch) {\n return !isInterbase(mismatch.type) ? mismatch.length : 1\n}\n\nfunction isInterbase(type: string) {\n return type === 'softclip' \|\| type === 'hardclip' \|\| type === 'insertion'\n}\n\nfunction inc(bin: any, strand: number, type: string, field: string) {\n let thisBin = bin[type][field]\n if (thisBin === undefined) {\n thisBin = bin[type][field] = {\n total: 0,\n '-1': 0,\n '0': 0,\n '1': 0,\n }\n }\n thisBin.total++\n thisBin[strand]++\n}\n\nexport default async function generateCoverageBins(\n features: Feature[],\n region: Region,\n opts: { bpPerPx?: number; colorBy?: { type: string; tag?: string } },\n fetchSequence: (arg: Region) => Promise<string>,\n) {\n const { colorBy } = opts\n const extendedRegion = {\n ...region,\n start: Math.max(0, region.start - 1),\n end: region.end + 1,\n }\n const binMax = Math.ceil(extendedRegion.end - extendedRegion.start)\n const skipmap = {} as SkipMap\n const regionSequence =\n features.length && shouldFetchReferenceSequence(opts.colorBy?.type)\n ? await fetchSequence(region)\n : undefined\n\n const bins = [] as Bin[]\n\n for (const feature of features) {\n const fstart = feature.get('start')\n const fend = feature.get('end')\n const fstrand = feature.get('strand') as -1 \| 0 \| 1\n const mismatches =\n (feature.get('mismatches') as Mismatch[] \| undefined) \|\| []\n\n for (let j = fstart; j < fend + 1; j++) {\n const i = j - region.start\n if (i >= 0 && i < binMax) {\n if (bins[i] === undefined) {\n bins[i] = {\n total: 0,\n all: 0,\n ref: 0,\n '-1': 0,\n '0': 0,\n '1': 0,\n lowqual: {},\n cov: {},\n delskips: {},\n noncov: {},\n }\n }\n if (j !== fend) {\n bins[i].total++\n bins[i].all++\n bins[i].ref++\n bins[i][fstrand]++\n }\n }\n }\n\n if (colorBy?.type === 'modifications') {\n const seq = feature.get('seq') as string \| undefined\n const mm = (getTagAlt(feature, 'MM', 'Mm') as string) \|\| ''\n const ops = parseCigar(feature.get('CIGAR'))\n const fend = feature.get('end')\n if (seq) {\n const modifications = getModificationPositions(mm, seq, fstrand)\n for (const { type, positions } of modifications) {\n const mod = `mod_${type}`\n for (const pos of getNextRefPos(ops, positions)) {\n const epos = pos + fstart - region.start\n if (epos >= 0 && epos < bins.length && pos + fstart < fend) {\n if (bins[epos] === undefined) {\n bins[epos] = {\n total: 0,\n all: 0,\n ref: 0,\n '-1': 0,\n '0': 0,\n '1': 0,\n lowqual: {},\n cov: {},\n delskips: {},\n noncov: {},\n }\n }\n const bin = bins[epos]\n inc(bin, fstrand, 'cov', mod)\n }\n }\n }\n }\n }\n\n if (colorBy?.type === 'methylation') {\n if (!regionSequence) {\n throw new Error(\n 'no region sequence detected, need sequenceAdapter configuration',\n )\n }\n const seq = feature.get('seq') as string \| undefined\n if (!seq) {\n continue\n }\n const { methBins, methProbs } = getMethBins(feature)\n const dels = mismatches.filter(f => f.type === 'deletion')\n\n // methylation based coloring takes into account both reference sequence\n // CpG detection and reads\n for (let i = 0; i < fend - fstart; i++) {\n const j = i + fstart\n const l1 = regionSequence[j - region.start + 1]?.toLowerCase()\n const l2 = regionSequence[j - region.start + 2]?.toLowerCase()\n if (l1 === 'c' && l2 === 'g') {\n const bin0 = bins[j - region.start]\n const bin1 = bins[j - region.start + 1]\n const b0 = methBins[i]\n const b1 = methBins[i + 1]\n const p0 = methProbs[i]\n const p1 = methProbs[i + 1]\n\n // color\n if (\n (b0 && (p0 !== undefined ? p0 > 0.5 : true)) \|\|\n (b1 && (p1 !== undefined ? p1 > 0.5 : true))\n ) {\n if (bin0) {\n inc(bin0, fstrand, 'cov', 'meth')\n bin0.ref--\n bin0[fstrand]--\n }\n if (bin1) {\n inc(bin1, fstrand, 'cov', 'meth')\n bin1.ref--\n bin1[fstrand]--\n }\n } else {\n if (bin0) {\n if (\n !dels.some(d =>\n doesIntersect2(\n j,\n j + 1,\n d.start + fstart,\n d.start + fstart + d.length,\n ),\n )\n ) {\n inc(bin0, fstrand, 'cov', 'unmeth')\n bin0.ref--\n bin0[fstrand]--\n }\n }\n if (bin1) {\n if (\n !dels.some(d =>\n doesIntersect2(\n j + 1,\n j + 2,\n d.start + fstart,\n d.start + fstart + d.length,\n ),\n )\n ) {\n inc(bin1, fstrand, 'cov', 'unmeth')\n bin1.ref--\n bin1[fstrand]--\n }\n }\n }\n }\n }\n }\n\n // normal SNP based coloring\n const colorSNPs =\n colorBy?.type !== 'modifications' && colorBy?.type !== 'methylation'\n\n for (const mismatch of mismatches) {\n const mstart = fstart + mismatch.start\n const mlen = mismatchLen(mismatch)\n const mend = mstart + mlen\n for (let j = mstart; j < mstart + mlen; j++) {\n const epos = j - region.start\n if (epos >= 0 && epos < bins.length) {\n const bin = bins[epos]!\n const { base, type } = mismatch\n const interbase = isInterbase(type)\n if (!interbase) {\n bin.ref--\n bin[fstrand]--\n } else {\n inc(bin, fstrand, 'noncov', type)\n }\n\n if (type === 'deletion' \|\| type === 'skip') {\n inc(bin, fstrand, 'delskips', type)\n bin.total--\n } else if (!interbase && colorSNPs) {\n inc(bin, fstrand, 'cov', base)\n bin.refbase = mismatch.altbase\n }\n }\n }\n\n if (mismatch.type === 'skip') {\n const hash = `${mstart}_${mend}_${fstrand}`\n if (skipmap[hash] === undefined) {\n skipmap[hash] = {\n feature: feature,\n start: mstart,\n end: mend,\n strand: fstrand,\n xs: getTag(feature, 'XS') \|\| getTag(feature, 'TS'),\n score: 0,\n }\n }\n skipmap[hash].score++\n }\n }\n }\n\n return { bins, skipmap }\n}\n","import {\n BaseFeatureDataAdapter,\n BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { AugmentedRegion as Region } from '@jbrowse/core/util/types'\nimport SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { toArray } from 'rxjs/operators'\nimport { firstValueFrom } from 'rxjs'\n\n// locals\nimport generateCoverageBins from './generateCoverageBins'\nimport { fetchSequence } from '../util'\n\nexport default class SNPCoverageAdapter extends BaseFeatureDataAdapter {\n protected async configure() {\n const subadapterConfig = this.getConf('subadapter')\n const sequenceConf = subadapterConfig.sequenceAdapter\n const dataAdapter = await this.getSubAdapter?.(subadapterConfig)\n\n const sequenceAdapter = sequenceConf\n ? await this.getSubAdapter?.(sequenceConf)\n : undefined\n\n if (!dataAdapter) {\n throw new Error('Failed to get subadapter')\n }\n\n return {\n subadapter: dataAdapter.dataAdapter as BaseFeatureDataAdapter,\n sequenceAdapter: sequenceAdapter?.dataAdapter as\n \| BaseFeatureDataAdapter\n \| undefined,\n }\n }\n\n async fetchSequence(region: Region) {\n const { sequenceAdapter } = await this.configure()\n if (!sequenceAdapter) {\n return undefined\n }\n\n return fetchSequence(region, sequenceAdapter)\n }\n\n getFeatures(region: Region, opts: BaseOptions = {}) {\n return ObservableCreate<Feature>(async observer => {\n const { subadapter } = await this.configure()\n const feats = await firstValueFrom(\n subadapter.getFeatures(region, opts).pipe(toArray()),\n )\n\n const { bins, skipmap } = await generateCoverageBins(\n feats,\n region,\n opts,\n arg => this.fetchSequence(arg),\n )\n\n bins.forEach((bin, index) => {\n const start = region.start + index\n observer.next(\n new SimpleFeature({\n id: `${this.id}-${start}`,\n data: {\n score: bin.total,\n snpinfo: bin,\n start,\n end: start + 1,\n refName: region.refName,\n },\n }),\n )\n })\n\n // make fake features from the coverage\n Object.entries(skipmap).forEach(([key, skip]) => {\n observer.next(\n new SimpleFeature({\n id: key,\n data: {\n type: 'skip',\n start: skip.start,\n end: skip.end,\n strand: skip.strand,\n score: skip.score,\n xs: skip.xs,\n },\n }),\n )\n })\n\n observer.complete()\n }, opts.signal)\n }\n\n async getMultiRegionFeatureDensityStats(\n regions: Region[],\n opts?: BaseOptions,\n ) {\n const { subadapter } = await this.configure()\n return subadapter.getMultiRegionFeatureDensityStats(regions, opts)\n }\n\n async getRefNames(opts: BaseOptions = {}) {\n const { subadapter } = await this.configure()\n return subadapter.getRefNames(opts)\n }\n\n freeResources(/* { region } */): void 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{ AugmentedRegion as Region } from '@jbrowse/core/util/types'\nimport { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { getTag, getTagAlt, shouldFetchReferenceSequence } from '../util'\nimport {\n parseCigar,\n getNextRefPos,\n getModificationPositions,\n getMethBins,\n Mismatch,\n} from '../MismatchParser'\nimport { doesIntersect2 } from '@jbrowse/core/util'\nimport { Bin, SkipMap } from './util'\n\nfunction mismatchLen(mismatch: Mismatch) {\n return !isInterbase(mismatch.type) ? mismatch.length : 1\n}\n\nfunction isInterbase(type: string) {\n return type === 'softclip' || type === 'hardclip' || type === 'insertion'\n}\n\nfunction inc(bin: any, strand: number, type: string, field: string) {\n let thisBin = bin[type][field]\n if (thisBin === undefined) {\n thisBin = bin[type][field] = {\n total: 0,\n '-1': 0,\n '0': 0,\n '1': 0,\n }\n }\n thisBin.total++\n thisBin[strand]++\n}\n\nexport default async function generateCoverageBins(\n features: Feature[],\n region: Region,\n opts: { bpPerPx?: number; colorBy?: { type: string; tag?: string } },\n fetchSequence: (arg: Region) => Promise<string>,\n) {\n const { colorBy } = opts\n const extendedRegion = {\n ...region,\n start: Math.max(0, region.start - 1),\n end: region.end + 1,\n }\n const binMax = Math.ceil(extendedRegion.end - extendedRegion.start)\n const skipmap = {} as SkipMap\n const regionSequence =\n features.length && shouldFetchReferenceSequence(opts.colorBy?.type)\n ? await fetchSequence(region)\n : undefined\n\n const bins = [] as Bin[]\n\n for (const feature of features) {\n const fstart = feature.get('start')\n const fend = feature.get('end')\n const fstrand = feature.get('strand') as -1 | 0 | 1\n const mismatches =\n (feature.get('mismatches') as Mismatch[] | undefined) || []\n\n for (let j = fstart; j < fend + 1; j++) {\n const i = j - region.start\n if (i >= 0 && i < binMax) {\n if (bins[i] === undefined) {\n bins[i] = {\n total: 0,\n all: 0,\n ref: 0,\n '-1': 0,\n '0': 0,\n '1': 0,\n lowqual: {},\n cov: {},\n delskips: {},\n noncov: {},\n }\n }\n if (j !== fend) {\n bins[i].total++\n bins[i].all++\n bins[i].ref++\n bins[i][fstrand]++\n }\n }\n }\n\n if (colorBy?.type === 'modifications') {\n const seq = feature.get('seq') as string | undefined\n const mm = (getTagAlt(feature, 'MM', 'Mm') as string) || ''\n const ops = parseCigar(feature.get('CIGAR'))\n const fend = feature.get('end')\n if (seq) {\n const modifications = getModificationPositions(mm, seq, fstrand)\n for (const { type, positions } of modifications) {\n const mod = `mod_${type}`\n for (const pos of getNextRefPos(ops, positions)) {\n const epos = pos + fstart - region.start\n if (epos >= 0 && epos < bins.length && pos + fstart < fend) {\n if (bins[epos] === undefined) {\n bins[epos] = {\n total: 0,\n all: 0,\n ref: 0,\n '-1': 0,\n '0': 0,\n '1': 0,\n lowqual: {},\n cov: {},\n delskips: {},\n noncov: {},\n }\n }\n const bin = bins[epos]\n inc(bin, fstrand, 'cov', mod)\n }\n }\n }\n }\n }\n\n if (colorBy?.type === 'methylation') {\n if (!regionSequence) {\n throw new Error(\n 'no region sequence detected, need sequenceAdapter configuration',\n )\n }\n const seq = feature.get('seq') as string | undefined\n if (!seq) {\n continue\n }\n const { methBins, methProbs } = getMethBins(feature)\n const dels = mismatches.filter(f => f.type === 'deletion')\n\n // methylation based coloring takes into account both reference sequence\n // CpG detection and reads\n for (let i = 0; i < fend - fstart; i++) {\n const j = i + fstart\n const l1 = regionSequence[j - region.start + 1]?.toLowerCase()\n const l2 = regionSequence[j - region.start + 2]?.toLowerCase()\n if (l1 === 'c' && l2 === 'g') {\n const bin0 = bins[j - region.start]\n const bin1 = bins[j - region.start + 1]\n const b0 = methBins[i]\n const b1 = methBins[i + 1]\n const p0 = methProbs[i]\n const p1 = methProbs[i + 1]\n\n // color\n if (\n (b0 && (p0 !== undefined ? p0 > 0.5 : true)) ||\n (b1 && (p1 !== undefined ? p1 > 0.5 : true))\n ) {\n if (bin0) {\n inc(bin0, fstrand, 'cov', 'meth')\n bin0.ref--\n bin0[fstrand]--\n }\n if (bin1) {\n inc(bin1, fstrand, 'cov', 'meth')\n bin1.ref--\n bin1[fstrand]--\n }\n } else {\n if (bin0) {\n if (\n !dels.some(d =>\n doesIntersect2(\n j,\n j + 1,\n d.start + fstart,\n d.start + fstart + d.length,\n ),\n )\n ) {\n inc(bin0, fstrand, 'cov', 'unmeth')\n bin0.ref--\n bin0[fstrand]--\n }\n }\n if (bin1) {\n if (\n !dels.some(d =>\n doesIntersect2(\n j + 1,\n j + 2,\n d.start + fstart,\n d.start + fstart + d.length,\n ),\n )\n ) {\n inc(bin1, fstrand, 'cov', 'unmeth')\n bin1.ref--\n bin1[fstrand]--\n }\n }\n }\n }\n }\n }\n\n // normal SNP based coloring\n const colorSNPs =\n colorBy?.type !== 'modifications' && colorBy?.type !== 'methylation'\n\n for (const mismatch of mismatches) {\n const mstart = fstart + mismatch.start\n const mlen = mismatchLen(mismatch)\n const mend = mstart + mlen\n for (let j = mstart; j < mstart + mlen; j++) {\n const epos = j - region.start\n if (epos >= 0 && epos < bins.length) {\n const bin = bins[epos]!\n const { base, type } = mismatch\n const interbase = isInterbase(type)\n if (!interbase) {\n bin.ref--\n bin[fstrand]--\n } else {\n inc(bin, fstrand, 'noncov', type)\n }\n\n if (type === 'deletion' || type === 'skip') {\n inc(bin, fstrand, 'delskips', type)\n bin.total--\n } else if (!interbase && colorSNPs) {\n inc(bin, fstrand, 'cov', base)\n bin.refbase = mismatch.altbase\n }\n }\n }\n\n if (mismatch.type === 'skip') {\n const hash = `${mstart}_${mend}_${fstrand}`\n if (skipmap[hash] === undefined) {\n skipmap[hash] = {\n feature: feature,\n start: mstart,\n end: mend,\n strand: fstrand,\n xs: getTag(feature, 'XS') || getTag(feature, 'TS'),\n score: 0,\n }\n }\n skipmap[hash].score++\n }\n }\n }\n\n return { bins, skipmap }\n}\n","import {\n BaseFeatureDataAdapter,\n BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { AugmentedRegion as Region } from '@jbrowse/core/util/types'\nimport SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { toArray } from 'rxjs/operators'\nimport { firstValueFrom } from 'rxjs'\n\n// locals\nimport generateCoverageBins from './generateCoverageBins'\nimport { fetchSequence } from '../util'\n\nexport default class SNPCoverageAdapter extends BaseFeatureDataAdapter {\n protected async configure() {\n const subadapterConfig = this.getConf('subadapter')\n const sequenceConf = subadapterConfig.sequenceAdapter\n const dataAdapter = await this.getSubAdapter?.(subadapterConfig)\n\n const sequenceAdapter = sequenceConf\n ? await this.getSubAdapter?.(sequenceConf)\n : undefined\n\n if (!dataAdapter) {\n throw new Error('Failed to get subadapter')\n }\n\n return {\n subadapter: dataAdapter.dataAdapter as BaseFeatureDataAdapter,\n sequenceAdapter: sequenceAdapter?.dataAdapter as\n | BaseFeatureDataAdapter\n | undefined,\n }\n }\n\n async fetchSequence(region: Region) {\n const { sequenceAdapter } = await this.configure()\n if (!sequenceAdapter) {\n return undefined\n }\n\n return fetchSequence(region, sequenceAdapter)\n }\n\n getFeatures(region: Region, opts: BaseOptions = {}) {\n return ObservableCreate<Feature>(async observer => {\n const { subadapter } = await this.configure()\n const feats = await firstValueFrom(\n subadapter.getFeatures(region, opts).pipe(toArray()),\n )\n\n const { bins, skipmap } = await generateCoverageBins(\n feats,\n region,\n opts,\n arg => this.fetchSequence(arg),\n )\n\n bins.forEach((bin, index) => {\n const start = region.start + index\n observer.next(\n new SimpleFeature({\n id: `${this.id}-${start}`,\n data: {\n score: bin.total,\n snpinfo: bin,\n start,\n end: start + 1,\n refName: region.refName,\n },\n }),\n )\n })\n\n // make fake features from the coverage\n Object.entries(skipmap).forEach(([key, skip]) => {\n observer.next(\n new SimpleFeature({\n id: key,\n data: {\n type: 'skip',\n start: skip.start,\n end: skip.end,\n strand: skip.strand,\n score: skip.score,\n xs: skip.xs,\n },\n }),\n )\n })\n\n observer.complete()\n }, opts.signal)\n }\n\n async getMultiRegionFeatureDensityStats(\n regions: Region[],\n opts?: BaseOptions,\n ) {\n const { subadapter } = await this.configure()\n return subadapter.getMultiRegionFeatureDensityStats(regions, opts)\n }\n\n async getRefNames(opts: BaseOptions = {}) {\n const { subadapter } = await this.configure()\n return subadapter.getRefNames(opts)\n }\n\n freeResources(/* { region } */): void {}\n}\n"],"names":["mismatchLen","mismatch","isInterbase","type","length","inc","bin","strand","field","thisBin","undefined","total","SNPCoverageAdapter","BaseFeatureDataAdapter","configure","subadapterConfig","this","getConf","sequenceConf","sequenceAdapter","dataAdapter","getSubAdapter","Error","subadapter","fetchSequence","region","getFeatures","opts","ObservableCreate","async","feats","firstValueFrom","pipe","toArray","bins","skipmap","features","colorBy","extendedRegion","start","Math","max","end","binMax","ceil","regionSequence","shouldFetchReferenceSequence","feature","fstart","get","fend","fstrand","mismatches","j","i","all","ref","lowqual","cov","delskips","noncov","seq","mm","getTagAlt","ops","parseCigar","modifications","getModificationPositions","positions","mod","pos","getNextRefPos","epos","methBins","methProbs","getMethBins","dels","filter","f","l1","toLowerCase","l2","bin0","bin1","b0","b1","p0","p1","some","d","doesIntersect2","colorSNPs","mstart","mlen","mend","base","interbase","refbase","altbase","hash","xs","getTag","score","generateCoverageBins","arg","forEach","index","observer","next","SimpleFeature","id","data","snpinfo","refName","Object","entries","key","skip","complete","signal","getMultiRegionFeatureDensityStats","regions","getRefNames","freeResources"],"sourceRoot":""}

Mercurial > repos > fubar > jbrowse2

comparison x/static/js/5461.5c8cf5d1.chunk.js.map @ 125:49f3d3878413 draft