package biotk

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package biotk
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Module Biotk.BedSource

BED format

BED (Browser Extensible Data) format is used to describe a collection of genomic features. It is a tabulated format. See the {https://genome.ucsc.edu/FAQ/FAQformat.html#format1specification

}

. Several variants exist, depending on the number of fields, and they are accordingly named BED3, BED4, etc. This module offers one representation per variant, including a general-purpose representation only assuming 3 fields.

Sourcetype strand = [
  1. | `Plus
  2. | `Minus
  3. | `Not_relevant
  4. | `Unknown
]
Sourceval parse_strand : string -> (strand, string) result
Sourceval unparse_strand : strand -> string
Sourcemodule type Item = sig ... end
Sourcemodule type S = sig ... end
Sourcemodule Item : Item with type t = GLoc.t * string list
include S with type item := Item.t
Sourceval load : string -> Item.t list
Sourceval load_as_lmap : string -> Item.t GAnnot.LMap.t
Sourceval save : Item.t list -> string -> unit
Sourcemodule Bed3 : sig ... end
Sourcemodule Bed4 : sig ... end
Sourcemodule Bed5 : sig ... end
Sourcemodule Bed6 : sig ... end
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