{
  "$schema": "https://vega.github.io/schema/vega-lite/v5.json",
  
  "config": {
    "axis": {"grid": true, "tickBand": "extent"}
  },
  "datasets": {
    "variants": [],
    "haplotype_variants": [],
    "haplotype_fractions": [],
    "covered_variants": [],
    "allele_frequency_distribution": []
  },
  "vconcat":[
    {
      "layer": [
        {
          "data": {"name": "haplotype_variants"},
          "transform": [
            {
              "lookup": "haplotype",
              "from": {
                "data": {"name": "haplotype_fractions"},
                "key": "haplotype",
                "fields": ["fraction"]
              }
            }
          ],
          "mark": {"type": "bar", "tooltip": true},
          "encoding": {
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            "y": {"aggregate": "sum", "type": "quantitative", "field": "fraction", "axis": {"titleFontSize": 16}},
            "color": {
              "field": "haplotype",
              "type": "nominal",
              "legend": {"titleFontSize": 16, "labelFontSize": 14},
              "scale": {"scheme": "category20"}
            }
          }
        },
        {
          "data": {"name": "variants"},
          "mark": {"type": "point", "tooltip": true},
          "encoding": {
            "x": {"field": "variant", "type": "ordinal", "axis": {"labels": true, "title": null, "labelFontSize": 12}},
            "y": {
              "field": "vaf",
              "type": "quantitative",
              "axis": {"titleFontSize": 16, "labelFontSize": 12},
              "scale": {"domain": [0, 1]}
            },
            "color": {"value": "black"}
          }
        }
      ]
  },
  {
    "data": {"name": "haplotype_variants"},
    "mark": {"type":"rect", "tooltip": true},
    "encoding": {
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    "x": {"field": "variant", "type": "ordinal", "axis": {"titleFontSize": 16, "labels": true, "labelFontSize": 12}},
    "color": {
      "field": "haplotype",
      "scale": {"scheme": "category20"},
      "legend": null
    }
    }
  },
  {
    "data": {"name": "covered_variants"},
    "mark": {"type": "rect", "tooltip": true},
    "encoding": {
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    "x": {"field": "variant", "type": "ordinal", "axis": {"titleFontSize": 16, "labels": true, "labelFontSize": 12}},
    "color": {
      "field": "haplotype",
      "scale": {"scheme": "category20"},
      "legend": null
    }
    }
  },
  {
    "data": {"name": "allele_frequency_distribution"},
    "mark": {"type": "circle", "tooltip": true},
    "encoding": {
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        "field": "variant",
        "type": "ordinal",
        "title": "Variant",
        "axis": {"labelFontSize": 12, "titleFontSize": 16}
      },
      "y": {
        "field": "allele_freq",
        "type": "quantitative",
        "title": "Allele frequency",
        "axis": {"labelFontSize": 12, "titleFontSize": 16}
      },
      "color": {
        "field": "probability",
        "type": "quantitative",
        "legend": {
          "title": null
        }
      },
      "size": {
        "field": "probability",
        "type": "quantitative",
        "legend": {
          "title": null
        }
      }
    }
  }
]
}