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

Type: string

The output field for the computed coverage.

asChrom

Type: string

The output field for the chromosome.

Default: Same as chrom

asEnd

Type: string

The output field for the end coordinate.

Default: Same as end

asStart

Type: string

The output field for the start coordinate.

Default: Same as start

chrom

Type: string (field name)

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

end Required

Type: string (field name)

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

start Required

Type: string (field name)

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

weight

Type: string (field name)

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
          }
        }
      }
    }
  ]
}