gosling.js 1.0.2 → 1.0.3

package/dist/exported-utils-26226ee9.js.map

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-{"version":3,"file":"exported-utils-26226ee9.js","sources":["../src/data-fetchers/utils.ts"],"sourcesContent":["import { bisector } from 'd3-array';\nimport { RemoteFile as _RemoteFile } from 'generic-filehandle';\n\nimport type * as HiGlass from '@higlass/types';\nimport type { Assembly, ChromSizes, Datum } from '@gosling-lang/gosling-schema';\n\nexport type CommonDataConfig = {\n    assembly: Assembly;\n    x?: string;\n    xe?: string;\n    x1?: string;\n    x1e?: string;\n    urlFetchOptions?: RequestInit;\n};\n\nexport class DataSource<File, Options> {\n    chromInfo: ExtendedChromInfo;\n    tilesetInfo: ReturnType<typeof tilesetInfoFromChromInfo>;\n\n    constructor(public file: File, chromSizes: ChromSizes, public options: Options) {\n        this.chromInfo = sizesToChromInfo(chromSizes);\n        this.tilesetInfo = tilesetInfoFromChromInfo(this.chromInfo);\n    }\n}\n\n/**\n * Filter data before sending to a track considering the visible genomic area in the track.\n * TODO(2022-Jul-13): Consider genomic `y` channels as well.\n */\nexport function filterUsingGenoPos(\n    data: Datum[],\n    [minX, maxX]: [number, number],\n    config: Omit<CommonDataConfig, 'assembly'>\n) {\n    const { x, xe, x1, x1e } = config;\n    const definedXFields = [x, xe, x1, x1e].filter(f => f) as string[];\n    return data.filter((d: Datum) => {\n        if (definedXFields.length === 0) {\n            // no filter applies\n            return true;\n        } else if (definedXFields.length === 1) {\n            // filter based on one genomic position\n            const value = +d[definedXFields[0]];\n            return typeof value === 'number' && minX < value && value <= maxX;\n        } else {\n            // filter based on two genomic positions, i.e., check overlaps\n            const values = definedXFields.map(f => +d[f]).filter(v => !isNaN(v));\n            const minValue = Math.min(...values);\n            const maxValue = Math.max(...values);\n            return minX <= maxValue && minValue <= maxX;\n        }\n    });\n}\n\nconst chromInfoBisector = bisector((d: { pos: number }) => d.pos).left;\n\nconst chrToAbs = (chrom: string, chromPos: number, chromInfo: HiGlass.ChromInfo) =>\n    chromInfo.chrPositions[chrom].pos + chromPos;\n\nconst absToChr = (absPosition: number, chromInfo: HiGlass.ChromInfo) => {\n    if (!chromInfo || !chromInfo.cumPositions || !chromInfo.cumPositions.length) {\n        return null;\n    }\n\n    let insertPoint = chromInfoBisector(chromInfo.cumPositions, absPosition);\n    const lastChr = chromInfo.cumPositions[chromInfo.cumPositions.length - 1].chr;\n    const lastLength = chromInfo.chromLengths[lastChr];\n\n    // @ts-expect-error\n    insertPoint -= insertPoint > 0 && 1;\n\n    let chrPosition = Math.floor(absPosition - chromInfo.cumPositions[insertPoint].pos);\n    let offset = 0;\n\n    if (chrPosition < 0) {\n        // before the start of the genome\n        offset = chrPosition - 1;\n        chrPosition = 1;\n    }\n\n    if (insertPoint === chromInfo.cumPositions.length - 1 && chrPosition > lastLength) {\n        // beyond the last chromosome\n        offset = chrPosition - lastLength;\n        chrPosition = lastLength;\n    }\n\n    return [chromInfo.cumPositions[insertPoint].chr, chrPosition, offset, insertPoint] as const;\n};\n\n/**\n * Get a chromosome name for the consistentcy, e.g., `1` --> `chr1`.\n * @param chrName A chromosome name to be sanitized\n * @param assembly A genome assembly of the data\n * @param chromosomePrefix A prefix string that can be replaced to 'chr'\n * @returns\n */\nexport function sanitizeChrName(chrName: string, assembly: Assembly, chromosomePrefix?: string) {\n    if (Array.isArray(assembly)) {\n        // this is a custom assembly, so use this as is\n        return chrName;\n    }\n\n    // For assemblies in Gosling, we use the `chr` prefix consistently\n    if (chromosomePrefix) {\n        // `hs1` --> `chr1`\n        chrName = chrName.replace(chromosomePrefix, 'chr');\n    } else if (!chrName.includes('chr')) {\n        // `1` --> `chr1`\n        chrName = `chr${chrName}`;\n    }\n    return chrName;\n}\n\nexport type ExtendedChromInfo = HiGlass.ChromInfo & {\n    absToChr(absPos: number): ReturnType<typeof absToChr> | null;\n    chrToAbs(chr: [name: string, pos: number]): number | null;\n};\n\nexport function tilesetInfoFromChromInfo(chromInfo: ExtendedChromInfo, tileSize = 1024) {\n    return {\n        tile_size: tileSize,\n        bins_per_dimension: tileSize,\n        max_zoom: Math.ceil(Math.log(chromInfo.totalLength / tileSize) / Math.log(2)),\n        max_width: chromInfo.totalLength,\n        min_pos: [0],\n        max_pos: [chromInfo.totalLength]\n    };\n}\n\nexport function sizesToChromInfo(sizes: [string, number][]): ExtendedChromInfo {\n    const info: HiGlass.ChromInfo = {\n        cumPositions: [],\n        chromLengths: {},\n        chrPositions: {},\n        totalLength: 0\n    };\n\n    sizes.forEach(([chr, length], i) => {\n        const chrPosition = { id: i, chr, pos: info.totalLength };\n        info.chrPositions[chr] = chrPosition;\n        info.chromLengths[chr] = length;\n        info.cumPositions.push(chrPosition);\n        info.totalLength += length;\n    });\n\n    return {\n        ...info,\n        absToChr: absPos => (info.chrPositions ? absToChr(absPos, info) : null),\n        chrToAbs: ([chrName, chrPos]) => (info.chrPositions ? chrToAbs(chrName, chrPos, info) : null)\n    };\n}\n\nexport class RemoteFile extends _RemoteFile {\n    // Overrides `read` to eagerly read 200 or 206 response\n    // from https://github.com/GMOD/generic-filehandle/blob/0e8209be25e3097307bd15e964edd8c017e808d7/src/remoteFile.ts#L100-L162\n    public read: _RemoteFile['read'] = async (\n        buffer,\n        offset = 0,\n        length,\n        position = 0,\n        opts = {}\n    ): Promise<{ bytesRead: number; buffer: Buffer }> => {\n        const { headers = {}, signal, overrides = {} } = opts;\n\n        if (length < Infinity) {\n            headers.range = `bytes=${position}-${position + length}`;\n        } else if (length === Infinity && position !== 0) {\n            headers.range = `bytes=${position}-`;\n        }\n        const args = {\n            // @ts-expect-error private property\n            ...this.baseOverrides,\n            ...overrides,\n            headers: {\n                ...headers,\n                ...overrides.headers,\n                // @ts-expect-error private property\n                ...this.baseOverrides.headers\n            },\n            method: 'GET',\n            redirect: 'follow',\n            mode: 'cors',\n            signal\n        };\n        const response = await this.fetch(this.url, args);\n\n        if (!response.ok) {\n            throw new Error(`HTTP ${response.status} ${response.statusText} ${this.url}`);\n        }\n\n        // Just read the response if it was successful.\n        if 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package/dist/src/alias/buffer-shim.d.ts

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-export { Buffer } from "buffer/";
-//# sourceMappingURL=buffer-shim.d.ts.map

package/dist/src/alias/buffer-shim.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"buffer-shim.d.ts","sourceRoot":"","sources":["../../../src/alias/buffer-shim.js"],"names":[],"mappings":""}