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Linearize Genomic Coordinate

Placeholder

TODO

Parameters

as Required
The output field or fields for linearized coordinates.
channel

Get the genome assembly from the scale of the channel.

Default: "x"

chrom Required
The chromosome/contig field
offset

An offset or offsets that allow for adjusting the numbering base. The offset is subtracted from the positions.

GenomeSpy uses internally zero-based indexing with half-open intervals. UCSC-based formats (BED, etc.) generally use this scheme. However, for example, VCF files use one-based indexing and must be adjusted by setting the offset to 1.

Default: 0

pos Required
The field or fields that contain intra-chromosomal positions

Example

{
  "type": "linearizeGenomicCoordinate",
  "chrom": "chrom",
  "pos": "start",
  "as": "_start"
}