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config.example.js
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config.example.js
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/*
* config.js
*
* This file configures the dataset that this EpiVar node is responsible for hosting.
*/
const ASSAY_RNA_SEQ = "RNA-seq";
const ASSAY_ATAC_SEQ = "ATAC-seq";
const ASSAY_H3K4ME1 = "H3K4me1";
const ASSAY_H3K4ME3 = "H3K4me3";
const ASSAY_H3K27AC = "H3K27ac";
const ASSAY_H3K27ME3 = "H3K27me3";
// noinspection JSUnusedGlobalSymbols
module.exports = {
title: "Aracena 𝘦𝘵 𝘢𝘭.",
assembly: "hg19",
// availableAssays must be a subset or the set of assays supported by EpiVar:
availableAssays: [
ASSAY_RNA_SEQ,
ASSAY_ATAC_SEQ,
ASSAY_H3K4ME1,
ASSAY_H3K4ME3,
ASSAY_H3K27AC,
ASSAY_H3K27ME3,
],
conditions: [
{id: "NI", name: "Non-infected"},
{id: "Flu", name: "Flu"},
],
ethnicities: [
{id: "AF", name: "African-American", plotColor: "#5100FF", plotBoxColor: "rgba(81, 0, 255, 0.6)"},
{id: "EU", name: "European-American", plotColor: "#FF8A00", plotBoxColor: "rgba(255, 138, 0, 0.6)"},
],
samples: {
/*
* Additional filter for variants - limit to just first SNP. The VCF might contain variants that we don't want to
* see, this removes them without having to clean it. The following filter is the default value:
*/
vcfFindFn: (line) => line.REF.length === 1 && line.ALT.every((a) => a.length === 1),
/*
* The current VCF for Aracena et al. contains names as "Epi_realName_flu_xxx".
* We need to extract "realName" to make it easier for the rest (where "realName" corresponds to
* the metadata.json "donor" property).
*/
vcfSampleNameConverter: name => name.split('_')[1], // name => name
/*
* When given a contig from a peak as input, produce a contig compatible with the genotype VCF.
* For example, peak contigs may be in the format chr1, chr2, ..., whereas VCF contigs may be
* formatted without the 'chr' prefix (1, 2, ...). Stripping the chr prefix gives the correct
* VCF contig value.
*/
vcfChrTransform: (chr) => chr.replace(/^chr/, ""), // e.g., chr1 => 1
// bigWigChrTransform: TODO,
},
};