package biocaml

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The OCaml Bioinformatics Library

Install

Dune Dependency

biocaml.org Readme Edit opam file Versions (5)

Authors

Maintainers

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biocaml@googlegroups.com

Sources

v0.10.1.tar.gz

md5=4cf944bcae5d36bf47b67f6bcb2455d7

sha512=0262b5768aefd7c080f664c46c88876fce9a658cc6a87358a77b7112c49ae3042e7ab542e76be5738fbaeda853149b308b48d4897960b5c7ae3b4da71d978bd8

doc/biocaml.unix/Biocaml_unix/Seq_range/index.html

Module `Biocaml_unix.Seq_range`

Range on a sequence, where the sequence is represented by an identifier.

This datatype can be used to represent genomic regions with a triplet (chromosome, start, end) as can be found in say, BED files. The Seq_range.Make functor offers some genericity for the choice of the type representing a sequence identifier, while the module offers the most frequent case when the identifier is a simple string.

Most operations on Seq_range.t are simple extensions of operations on Range.t.

module type Identifier = sig ... end

module Make (S : Identifier) : sig ... end

include sig ... end

type t = Core_kernel.String.t * Range.t

val compare : t -> t -> int

val t_of_sexp : Sexplib0.Sexp.t -> t

val sexp_of_t : t -> Sexplib0.Sexp.t

val make : Core_kernel.String.t -> int -> int -> t Core_kernel.Or_error.t

val seq : t -> Core_kernel.String.t

val size : t -> int

val to_string : t -> string

String representation of a sequence range, as <seq>:<start>-<end>

val of_string : string -> t Core_kernel.Or_error.t

Parses a string representation of a sequence range, as <seq>:<start>-<end>