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Configuration

 {
   genomes: string or array,
   igvConfig: object
   clientId: string
   urlShortener:  function or object

}

---

genomes

Array of igv reference objects, or URL to a json file containing such an array.

Examples:

genomes: "https://s3.amazonaws.com/igv.org.genomes/genomes.json"

genomes: [
   {
      id: "hg38",
      name: "Human (GRCh38/hg38)",
      fastaURL: "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa",
      indexURL: "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.fai",
      cytobandURL: "https://s3.amazonaws.com/igv.org.genomes/hg38/annotations/cytoBandIdeo.txt.gz",
      tracks: [
          {
              name: "Refseq Genes",
              format: "refgene",
              url: "https://s3.amazonaws.com/igv.org.genomes/hg38/refGene.sorted.txt.gz",
              indexURL: "https://s3.amazonaws.com/igv.org.genomes/hg38/refGene.sorted.txt.gz.tbi",
              visibilityWindow: -1,
              order: 1000000
          }
      ]
   }
]

---

igvConfig

an igv.js configuration object (see https://github.com/igvteam/igv.js/wiki/Browser-Configuration-2.0)

Example:

igvConfig:  {
         queryParametersSupported: true,
         showChromosomeWidget: true,
         genome: "hg38",
         apiKey: "YOUR GOOGLE API KEY"  
}

---

clientId

Optional. A Google client_id. If present a Google file picker will be added to the genomes and tracks menus.

---

urlShortener

Optional. A function taking 1 argument, a URL. Returns a shortened URL used by the "Share" features (email, twitter).

Factory functions are provided to create urlShortenerFunctions for Bitly or Google services. To use these you must obtain an accessToken (Bitly) or apiKey (Google) for your site

bitlyShortener(accessToken)
googleShortener(apiKey)