config.json

{
  "BACKEND_URL": false,
  "DATA_SOURCES": [
    {
      "name": "snp1kg-BRCA1",
      "tracks": [
        {"trackFile": "exampleData/internal/snp1kg-BRCA1.vg.xg", "trackType": "graph", "trackColorSettings": {"mainPalette": "greys", "auxPalette": "ygreys"}},
        {"trackFile": "exampleData/internal/NA12878-BRCA1.sorted.gam", "trackType": "read"}
      ],
      "region": "17:1-100",
      "bedFile": "exampleData/internal/snp1kg-BRCA1.bed",
      "dataType": "built-in",
      "simplify": false,
      "removeSequences": false
    },
    {
      "name": "vg \"small\" example",
      "tracks": [
        {"trackFile": "exampleData/x.vg.xg", "trackType": "graph"},
        {"trackFile": "exampleData/x.vg.gbwt", "trackType": "haplotype"}
      ],
      "dataType": "built-in",
      "region": "x:1-100"
    },
    {
      "name": "cactus",
      "tracks": [
        {"trackFile": "exampleData/cactus.vg.xg", "trackType": "graph"},
        {"trackFile": "exampleData/cactus-NA12879.sorted.gam", "trackType": "read"}
      ],
      "bedFile": "exampleData/cactus.bed",
      "region": "ref:1-100",
      "dataType": "built-in"
    },
    {
      "name": "cactus multiple reads",
      "tracks": [
        {"trackFile": "exampleData/cactus.vg.xg", "trackType": "graph"},
        {"trackFile": "exampleData/cactus0_10.sorted.gam", "trackType": "read"},
        {"trackFile": "exampleData/cactus10_20.sorted.gam", "trackType": "read"}
      ],
      "bedFile": "exampleData/cactus.bed",
      "region": "ref:1-100",
      "dataType": "built-in"
    }
  ],
  "vgPath": "",
  "dataPath": "exampleData",
  "internalDataPath": "exampleData/internal/",
  "tempDirPath": "temp",
  "fetchTimeout": 15,
  "maxFileSizeBytes": 1000000000,

  "defaultGraphColorPalette" : {
    "mainPalette": "#000000", 
    "auxPalette": "greys", 
    "colorReadsByMappingQuality": false
  },

  "defaultHaplotypeColorPalette" : {
    "mainPalette": "plainColors", 
    "auxPalette": "lightColors", 
    "colorReadsByMappingQuality": false
  },
  
  "defaultReadColorPalette" : {
    "mainPalette": "blues", 
    "auxPalette": "reds", 
    "colorReadsByMappingQuality": false
  },

  "defaultTrackProps" : {
    "trackType": "graph",
    "trackColorSettings": {
      "mainPalette": "#000000",
      "auxPalette": "greys",
      "colorReadsByMappingQuality": false
    }
  },

  "fileTypeToExtensions": {
    "graph": ".xg,.vg,.hg,.gbz,.pg,.db",
    "haplotype": ".gbwt,.gbz",
    "read": ".gam"
  },

  "MAXUPLOADSIZE": 5242880,
  "pickerTypeOptions": ["mounted", "upload"],
  "fileExpirationTime": 86400


}