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  "plugins": [
    { "name": "UMDLocPlugin", "umdLoc": { "uri": "umd_plugin.js" } },
    { "name": "UMDUrlPlugin", "umdUrl": "umd_plugin.js" }
  ],
  "assemblies": [
    {
      "name": "volvox",
      "aliases": ["vvx"],
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "volvox_refseq",
        "metadata": {
          "date": "2020-08-20"
        },
        "formatAbout": {
          "hideUris": true,
          "config": "jexl:{extraField:'important data'}"
        },
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            "uri": "volvox.2bit",
            "locationType": "UriLocation"
          }
        }
      },
      "refNameAliases": {
        "adapter": {
          "type": "FromConfigAdapter",
          "adapterId": "W6DyPGJ0UU",
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            {
              "refName": "ctgA",
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              "aliases": ["A", "contigA"]
            },
            {
              "refName": "ctgB",
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              "aliases": ["B", "contigB"]
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          ]
        }
      }
    },
    {
      "name": "volvox2",
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          "type": "TwoBitAdapter",
          "twoBitLocation": {
            "uri": "volvox.2bit",
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          }
        }
      }
    },
    {
      "name": "volvox404",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "volvox_refseq404",
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          "type": "TwoBitAdapter",
          "twoBitLocation": {
            "uri": "volvox.2bit_404",
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          }
        }
      }
    },
    {
      "name": "volvox_del",
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        "type": "ReferenceSequenceTrack",
        "trackId": "volvox_del-ReferenceSequenceTrack",
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            "uri": "volvox_del.fa",
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            "uri": "volvox_del.fa.fai",
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          }
        }
      }
    },
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      "name": "volvox_ins",
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  "connections": [],
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        "id": "integration_test",
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        "bpPerPx": 0.05,
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            "refName": "ctgA",
            "start": 0,
            "end": 50001,
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      "type": "VariantTrack",
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        "type": "VcfTabixAdapter",
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        }
      }
    },
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      "type": "AlignmentsTrack",
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        "type": "CramAdapter",
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          "uri": "volvox-sorted-altname.cram",
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        "source": "We generated 150bp paired end reads from a <i>Volvox mythicus</i>, an imaginary species, for this jbrowse demo"
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        "type": "CramAdapter",
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          "type": "LinearPileupDisplay",
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      "type": "AlignmentsTrack",
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      "type": "AlignmentsTrack",
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      "type": "AlignmentsTrack",
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      "type": "AlignmentsTrack",
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      "name": "volvox-sorted.bam (contigA LinearSNPCoverageDisplay)",
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      "type": "AlignmentsTrack",
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              }
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          }
        }
      ]
    },
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      "type": "VariantTrack",
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      "assemblyNames": ["volvox"],
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    },
    {
      "type": "FeatureTrack",
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      "name": "nclist with long names/descriptions",
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      "type": "AlignmentsTrack",
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    },
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      "type": "MultiQuantitativeTrack",
      "trackId": "volvox_microarray_multi",
      "name": "MultiWig",
      "assemblyNames": ["volvox"],
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            "name": "k1",
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            "name": "k3",
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            "name": "k4",
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    },
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      "type": "QuantitativeTrack",
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    },
    {
      "type": "QuantitativeTrack",
      "trackId": "dropbox_bigwig",
      "name": "Dropbox BigWig",
      "category": ["Authentication"],
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          "locationType": "UriLocation",
          "internetAccountId": "dropboxOAuth"
        }
      }
    },
    {
      "type": "QuantitativeTrack",
      "trackId": "google_bigwig",
      "name": "Google Drive BigWig",
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      "assemblyNames": ["volvox"],
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        "type": "BigWigAdapter",
        "bigWigLocation": {
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      }
    },
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      "type": "QuantitativeTrack",
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      ]
    },
    {
      "type": "QuantitativeTrack",
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      },
      "displays": [
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          "type": "LinearWiggleDisplay",
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      ]
    },
    {
      "type": "QuantitativeTrack",
      "trackId": "volvox_microarray_density_altname",
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      "category": ["Integration test", "Wiggle"],
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      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "lollipop_track",
      "name": "FromConfig Track (defaults to LinearLollipopDisplay)",
      "assemblyNames": ["volvox"],
      "category": ["Miscellaneous"],
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        "type": "FromConfigAdapter",
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            "refName": "ctgA",
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          {
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            "refName": "ctgA",
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            "end": 192,
            "type": "bar",
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            "note": "note for theresa"
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          {
            "uniqueId": "three",
            "refName": "ctgA",
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            "end": 211,
            "type": "baz",
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            "name": "Nigel",
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          },
          {
            "uniqueId": "four",
            "refName": "ctgA",
            "start": 220,
            "end": 221,
            "score": 2,
            "type": "quux",
            "name": "Geoffray",
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          }
        ]
      },
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          "type": "LinearLollipopDisplay",
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        }
      ]
    },
    {
      "type": "AlignmentsTrack",
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      "name": "volvox-long reads with SV",
      "assemblyNames": ["volvox"],
      "category": ["Alignments"],
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        "type": "BamAdapter",
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          "uri": "volvox-long-reads-sv.bam",
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        "index": {
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        }
      }
    },
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        "sequenceAdapter": {
          "type": "TwoBitAdapter",
          "twoBitLocation": {
            "uri": "volvox.2bit",
            "locationType": "UriLocation"
          }
        }
      },
      "displays": [
        {
          "type": "LinearAlignmentsDisplay",
          "displayId": "deep_seq_alignments",
          "pileupDisplay": {
            "type": "LinearPileupDisplay",
            "displayId": "deep_seq_pileup",
            "renderers": {
              "PileupRenderer": {
                "type": "PileupRenderer",
                "maxHeight": 10000
              }
            }
          }
        }
      ]
    },
    {
      "type": "FeatureTrack",
      "trackId": "arc_track",
      "name": "FromConfig Track (defaults to LinearArcDisplay)",
      "assemblyNames": ["volvox"],
      "category": ["Miscellaneous"],
      "adapter": {
        "type": "FromConfigAdapter",
        "adapterId": "Y4yJ6gAC2E",
        "features": [
          {
            "uniqueId": "arc-one",
            "refName": "ctgA",
            "start": 190,
            "end": 200,
            "type": "foo",
            "score": 2,
            "name": "SE_001"
          },
          {
            "uniqueId": "arc-two",
            "refName": "ctgA",
            "start": 191,
            "end": 192,
            "type": "bar",
            "score": 5,
            "name": "SE_002"
          },
          {
            "uniqueId": "arc-three",
            "refName": "ctgA",
            "start": 210,
            "end": 290,
            "type": "baz",
            "score": 50,
            "name": "SE_003"
          },
          {
            "uniqueId": "arc-four",
            "refName": "ctgA",
            "start": 180,
            "end": 189,
            "score": 200,
            "type": "quux",
            "name": "SE_004, and some other characters that make the name extra long"
          }
        ]
      },
      "displays": [
        {
          "type": "LinearArcDisplay",
          "displayId": "arc_track_linear",
          "renderer": {
            "type": "ArcRenderer"
          }
        }
      ]
    },
    {
      "type": "AlignmentsTrack",
      "trackId": "spliced",
      "name": "volvox-rnaseq demo",
      "category": ["Alignments"],
      "assemblyNames": ["volvox"],
      "adapter": {
        "type": "BamAdapter",
        "bamLocation": {
          "uri": "spliced.bam",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "spliced.bam.bai",
            "locationType": "UriLocation"
          },
          "indexType": "BAI"
        },
        "sequenceAdapter": {
          "type": "TwoBitAdapter",
          "twoBitLocation": {
            "uri": "volvox.2bit",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "volvox.filtered.lowercase",
      "name": "volvox.filtered.lowercase",
      "adapter": {
        "type": "VcfAdapter",
        "vcfLocation": {
          "uri": "volvox.filtered.lowercase.vcf",
          "locationType": "UriLocation"
        }
      },
      "category": ["Integration test"],
      "assemblyNames": ["volvox"]
    },
    {
      "type": "SyntenyTrack",
      "trackId": "volvox_del.paf-1658813720770",
      "name": "volvox_del.paf",
      "assemblyNames": ["volvox", "volvox_del"],
      "adapter": {
        "type": "PAFAdapter",
        "targetAssembly": "volvox",
        "queryAssembly": "volvox_del",
        "pafLocation": {
          "uri": "volvox_del.paf"
        }
      }
    },
    {
      "type": "SyntenyTrack",
      "trackId": "volvox_ins.paf-1658813720770",
      "name": "volvox_ins.paf",
      "assemblyNames": ["volvox", "volvox_ins"],
      "adapter": {
        "type": "PAFAdapter",
        "targetAssembly": "volvox",
        "queryAssembly": "volvox_ins",
        "pafLocation": {
          "uri": "volvox_ins.paf"
        }
      }
    },

    {
      "type": "VariantTrack",
      "trackId": "variant_effect_demo_data",
      "name": "Ensembl VEP example",
      "adapter": {
        "type": "VcfAdapter",
        "vcfLocation": {
          "uri": "variant_effect_demo_data.vcf",
          "locationType": "UriLocation"
        }
      },
      "category": ["VCF"],
      "assemblyNames": ["volvox"]
    },
    {
      "type": "VariantTrack",
      "trackId": "variant_effect_demo_jannovar",
      "name": "Jannovar example",
      "adapter": {
        "type": "VcfAdapter",
        "vcfLocation": {
          "uri": "volvox_vcf_jannovar.vcf",
          "locationType": "UriLocation"
        }
      },
      "category": ["VCF"],
      "assemblyNames": ["volvox"]
    }
  ],
  "aggregateTextSearchAdapters": [
    {
      "type": "TrixTextSearchAdapter",
      "textSearchAdapterId": "volvox-index",
      "ixFilePath": {
        "uri": "trix/volvox.ix",
        "locationType": "UriLocation"
      },
      "ixxFilePath": {
        "uri": "trix/volvox.ixx",
        "locationType": "UriLocation"
      },
      "metaFilePath": {
        "uri": "trix/volvox_meta.json",
        "locationType": "UriLocation"
      },
      "assemblyNames": ["volvox"]
    }
  ],
  "internetAccounts": [
    {
      "type": "DropboxOAuthInternetAccount",
      "internetAccountId": "dropboxOAuth",
      "name": "Dropbox",
      "description": "Account to access Dropbox files",
      "clientId": "50knr6xrjfc39sk"
    },
    {
      "type": "GoogleDriveOAuthInternetAccount",
      "internetAccountId": "googleOAuth",
      "name": "Google Drive",
      "description": "Account to access Google Drive files",
      "clientId": "109518325434-udfch80a0v70mgu65d5fejqsq5kvhm1b.apps.googleusercontent.com"
    }
  ]
}
