{
  "assemblies": [
    {
      "name": "volvox",
      "aliases": ["vvx"],
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "volvox_refseq",
        "metadata": {
          "date": "2020-08-20"
        },
        "formatAbout": {
          "hideUris": true,
          "config": "jexl:{extraField:'important data'}"
        },
        "adapter": {
          "type": "TwoBitAdapter",
          "twoBitLocation": {
            "uri": "volvox.2bit",
            "locationType": "UriLocation"
          }
        }
      }
    }
  ],
  "configuration": {
    "theme": {
      "palette": {
        "tertiary": {
          "main": "#9da9b6"
        },
        "secondary": {
          "main": "#29405F"
        }
      }
    },
    "extraThemes": {
      "darkWild": {
        "name": "Dark (wild)",
        "palette": {
          "primary": {
            "main": "#444"
          },
          "secondary": {
            "main": "#335"
          },
          "tertiary": {
            "main": "#250"
          },
          "quaternary": {
            "main": "#535"
          },
          "mode": "dark"
        }
      }
    }
  },
  "defaultSession": {
    "name": "Integration test example",
    "views": [
      {
        "id": "integration_test",
        "type": "LinearGenomeView",
        "offsetPx": 2000,
        "bpPerPx": 0.05,
        "displayedRegions": [
          {
            "refName": "ctgA",
            "start": 0,
            "end": 50001,
            "assemblyName": "volvox"
          }
        ]
      }
    ],
    "widgets": {
      "hierarchicalTrackSelector": {
        "id": "hierarchicalTrackSelector",
        "type": "HierarchicalTrackSelectorWidget",
        "filterText": "",
        "view": "integration_test"
      }
    },
    "activeWidgets": {
      "hierarchicalTrackSelector": "hierarchicalTrackSelector"
    }
  },
  "tracks": [
    {
      "type": "VariantTrack",
      "trackId": "volvox_sv_test",
      "name": "volvox structural variant test",
      "category": ["VCF"],
      "assemblyNames": ["volvox"],
      "adapter": {
        "type": "VcfTabixAdapter",
        "vcfGzLocation": {
          "uri": "volvox.dup.vcf.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "volvox.dup.vcf.gz.tbi",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "type": "VariantTrack",
      "trackId": "volvox_sv_test_renamed",
      "name": "volvox structural variant test w/renamed refs",
      "category": ["VCF"],
      "assemblyNames": ["volvox"],
      "adapter": {
        "type": "VcfTabixAdapter",
        "vcfGzLocation": {
          "uri": "volvox.dup.renamed.vcf.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "volvox.dup.renamed.vcf.gz.tbi",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "type": "AlignmentsTrack",
      "trackId": "volvox_cram_alignments",
      "name": "volvox-sorted.cram (contigA, default display)",
      "category": ["Integration test"],
      "assemblyNames": ["volvox"],
      "adapter": {
        "type": "CramAdapter",
        "cramLocation": {
          "uri": "volvox-sorted-altname.cram",
          "locationType": "UriLocation"
        },
        "craiLocation": {
          "uri": "volvox-sorted-altname.cram.crai",
          "locationType": "UriLocation"
        },
        "sequenceAdapter": {
          "type": "TwoBitAdapter",
          "twoBitLocation": {
            "uri": "volvox.2bit",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "type": "AlignmentsTrack",
      "trackId": "volvox_cram_pileup",
      "name": "volvox-sorted.cram (contigA, LinearPileupDisplay)",
      "category": ["Integration test"],
      "metadata": {
        "source": "We generated 150bp paired end reads from a <i>Volvox mythicus</i>, an imaginary species, for this jbrowse demo"
      },
      "assemblyNames": ["volvox"],
      "adapter": {
        "type": "CramAdapter",
        "cramLocation": {
          "uri": "volvox-sorted-altname.cram",
          "locationType": "UriLocation"
        },
        "craiLocation": {
          "uri": "volvox-sorted-altname.cram.crai",
          "locationType": "UriLocation"
        },
        "sequenceAdapter": {
          "type": "TwoBitAdapter",
          "twoBitLocation": {
            "uri": "volvox.2bit",
            "locationType": "UriLocation"
          }
        },
        "fetchSizeLimit": 1000
      },
      "displays": [
        {
          "type": "LinearPileupDisplay",
          "displayId": "volvox_cram_pileup_pileup"
        }
      ]
    },
    {
      "type": "AlignmentsTrack",
      "trackId": "volvox_cram_snpcoverage",
      "name": "volvox-sorted.cram (contigA, LinearSNPCoverageDisplay)",
      "category": ["Integration test"],
      "assemblyNames": ["volvox"],
      "adapter": {
        "type": "CramAdapter",
        "cramLocation": {
          "uri": "volvox-sorted-altname.cram",
          "locationType": "UriLocation"
        },
        "craiLocation": {
          "uri": "volvox-sorted-altname.cram.crai",
          "locationType": "UriLocation"
        },
        "sequenceAdapter": {
          "type": "TwoBitAdapter",
          "twoBitLocation": {
            "uri": "volvox.2bit",
            "locationType": "UriLocation"
          }
        }
      },
      "displays": [
        {
          "type": "LinearSNPCoverageDisplay",
          "displayId": "volvox_cram_snpcoverage_snpcoverage"
        }
      ]
    },
    {
      "type": "AlignmentsTrack",
      "trackId": "volvox_cram_alignments_ctga",
      "name": "volvox-sorted.cram (ctgA, default display)",
      "category": ["Integration test"],
      "assemblyNames": ["volvox"],
      "adapter": {
        "type": "CramAdapter",
        "cramLocation": {
          "uri": "volvox-sorted.cram",
          "locationType": "UriLocation"
        },
        "craiLocation": {
          "uri": "volvox-sorted.cram.crai",
          "locationType": "UriLocation"
        },
        "sequenceAdapter": {
          "type": "TwoBitAdapter",
          "twoBitLocation": {
            "uri": "volvox.2bit",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "type": "AlignmentsTrack",
      "trackId": "volvox_cram_pileup_ctga",
      "name": "volvox-sorted.cram (ctgA, LinearPileupDisplay)",
      "category": ["Integration test"],
      "assemblyNames": ["volvox"],
      "adapter": {
        "type": "CramAdapter",
        "cramLocation": {
          "uri": "volvox-sorted.cram",
          "locationType": "UriLocation"
        },
        "craiLocation": {
          "uri": "volvox-sorted.cram.crai",
          "locationType": "UriLocation"
        },
        "sequenceAdapter": {
          "type": "TwoBitAdapter",
          "twoBitLocation": {
            "uri": "volvox.2bit",
            "locationType": "UriLocation"
          }
        }
      },
      "displays": [
        {
          "type": "LinearPileupDisplay",
          "displayId": "volvox_cram_pileup_ctga_pileup"
        }
      ]
    },
    {
      "type": "AlignmentsTrack",
      "trackId": "volvox_cram_snpcoverage_ctga",
      "name": "volvox-sorted.cram (ctgA, LinearSNPCoverageDisplay)",
      "category": ["Integration test"],
      "assemblyNames": ["volvox"],
      "adapter": {
        "type": "CramAdapter",
        "cramLocation": {
          "uri": "volvox-sorted.cram",
          "locationType": "UriLocation"
        },
        "craiLocation": {
          "uri": "volvox-sorted.cram.crai",
          "locationType": "UriLocation"
        },
        "sequenceAdapter": {
          "type": "TwoBitAdapter",
          "twoBitLocation": {
            "uri": "volvox.2bit",
            "locationType": "UriLocation"
          }
        }
      },
      "displays": [
        {
          "type": "LinearSNPCoverageDisplay",
          "displayId": "volvox_cram_pileup_ctga_snpcoverage"
        }
      ]
    },
    {
      "type": "AlignmentsTrack",
      "trackId": "volvox_alignments",
      "name": "volvox-sorted.bam (ctgA)",
      "category": ["Integration test"],
      "assemblyNames": ["volvox", "volvox2"],
      "adapter": {
        "type": "BamAdapter",
        "bamLocation": {
          "uri": "volvox-sorted.bam",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "volvox-sorted.bam.bai",
            "locationType": "UriLocation"
          }
        }
      },
      "displays": [
        {
          "type": "LinearAlignmentsDisplay",
          "displayId": "volvox_alignments_alignments",
          "pileupDisplay": {
            "type": "LinearPileupDisplay",
            "displayId": "volvox_bam_altname_alignments_pileup"
          }
        }
      ]
    },
    {
      "type": "AlignmentsTrack",
      "trackId": "volvox_bam_snpcoverage",
      "name": "volvox-sorted.bam (contigA LinearSNPCoverageDisplay)",
      "category": ["Integration test"],
      "assemblyNames": ["volvox"],
      "adapter": {
        "type": "BamAdapter",
        "bamLocation": {
          "uri": "volvox-sorted-altname.bam",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "volvox-sorted-altname.bam.bai",
            "locationType": "UriLocation"
          }
        }
      },
      "displays": [
        {
          "type": "LinearSNPCoverageDisplay",
          "displayId": "volvox_bam_snpcoverage_snpcoverage"
        }
      ]
    },
    {
      "type": "AlignmentsTrack",
      "trackId": "volvox_bam_pileup",
      "name": "volvox-sorted.bam (contigA LinearPileupDisplay)",
      "category": ["Integration test"],
      "assemblyNames": ["volvox"],
      "adapter": {
        "type": "BamAdapter",
        "bamLocation": {
          "uri": "volvox-sorted-altname.bam",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "volvox-sorted-altname.bam.bai",
            "locationType": "UriLocation"
          }
        }
      },
      "displays": [
        {
          "type": "LinearPileupDisplay",
          "displayId": "volvox_bam_pileup_pileup"
        }
      ]
    },
    {
      "type": "AlignmentsTrack",
      "trackId": "volvox_alignments_pileup_coverage",
      "name": "volvox-sorted.bam (ctgA, canvas)",
      "category": ["Integration test"],
      "assemblyNames": ["volvox"],
      "adapter": {
        "type": "BamAdapter",
        "bamLocation": {
          "uri": "volvox-sorted.bam",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "volvox-sorted.bam.bai",
            "locationType": "UriLocation"
          }
        }
      }
    }
  ]
}
