Coverage

The "coverage" transform computes coverage for overlapping segments. The result is a new list of non-overlapping segments with the coverage values. The segments must be sorted by their start coordinates before passing them to the coverage transform.

Parameters

as

The output field for the computed coverage.

asChrom

The output field for the chromosome.

Default: Same as chrom

asEnd

The output field for the end coordinate.

Default: Same as end

asStart

The output field for the start coordinate.

Default: Same as start

chrom

An optional chromosome field that is passed through. TODO: groupby

end Required

The field representing the end coordinate of the segment (exclusive).

start Required

The field representing the start coordinate of the segment (inclusive).

weight

A field representing an optional weight for the segment. Can be used with copy ratios, for example.

Example

Given the following data:

start	end
0	4
1	3

... and configuration:

{
  "type": "coverage",
  "start": "startpos",
  "end": "endpos"
}

A new list of segments is produced:

start	end	coverage
0	1	1
1	3	2
3	4	1

Interactive example

The following example demonstrates both "coverage" and "pileup" transforms.

{
  "data": {
    "sequence": {
      "start": 1,
      "stop": 100,
      "as": "start"
    }
  },
  "transform": [
    {
      "type": "formula",
      "expr": "datum.start + ceil(random() * 20)",
      "as": "end"
    }
  ],
  "resolve": { "scale": { "x": "shared" } },
  "vconcat": [
    {
      "transform": [
        {
          "type": "coverage",
          "start": "start",
          "end": "end",
          "as": "coverage"
        }
      ],
      "mark": "rect",
      "encoding": {
        "x": { "field": "start", "type": "index" },
        "x2": { "field": "end" },
        "y": { "field": "coverage", "type": "quantitative" }
      }
    },
    {
      "transform": [
        {
          "type": "pileup",
          "start": "start",
          "end": "end",
          "as": "lane"
        }
      ],
      "mark": "rect",
      "encoding": {
        "x": { "field": "start", "type": "index" },
        "x2": { "field": "end" },
        "y": {
          "field": "lane",
          "type": "index",
          "scale": {
            "padding": 0.2,
            "reverse": true,
            "zoom": false
          }
        }
      }
    }
  ]
}