package biocaml

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The OCaml Bioinformatics Library

Install

Dune Dependency

biocaml.org Readme Edit opam file Versions (5)

Authors

Maintainers

B

biocaml@googlegroups.com

Sources

v0.11.1.tar.gz

md5=e292efa2f61fec33dad63ec897106f59

sha512=35519bf3b1e67a9191ef9bb74eba0dae941e0d05bad89076a36f507dc5c2d105a03c1c917d5a3f7ed9d1da4acbf3199582f78c308aa2a5a22c21f743945c852b

doc/biocaml.lwt/Biocaml_lwt/Fastq/index.html

Module `Biocaml_lwt.Fastq`Source

include module type of struct include Biocaml_unix.Fastq end

Sourcetype item = Biocaml_unix.Fastq.item = {

name : string;
sequence : string;
comment : string;
qualities : string;

}

Sourceval sexp_of_item : item -> Ppx_sexp_conv_lib.Sexp.t

Sourceval item_of_sexp : Ppx_sexp_conv_lib.Sexp.t -> item

Sourceval split_name : string -> string * string option

Split a name string into a sequence identifier and an optional description. It is assumed that the given string is from an item's name field, i.e. that it doesn't contain a leading @ char.

Sourcemodule MakeIO = Biocaml_unix.Fastq.MakeIO

include sig ... end

Sourcemodule Illumina = Biocaml_unix.Fastq.Illumina

Low-level Printing

Sourceval item_to_string : item -> string

This function converts item values to strings that can be dumped to a file, i.e. they contain full-lines, including all end-of-line characters.

Source

val name_of_line : 
  ?pos:Biocaml_unix.Pos.t ->
  Biocaml_unix.Line.t ->
  string Core_kernel.Or_error.t

Low-level Parsing

Sourceval sequence_of_line : ?pos:Biocaml_unix.Pos.t -> Biocaml_unix.Line.t -> string

Source

val comment_of_line : 
  ?pos:Biocaml_unix.Pos.t ->
  Biocaml_unix.Line.t ->
  string Core_kernel.Or_error.t

Source

val qualities_of_line : 
  ?pos:Biocaml_unix.Pos.t ->
  ?sequence:string ->
  Biocaml_unix.Line.t ->
  string Core_kernel.Or_error.t

qualities sequence line parses given qualities line in the context of a previously parsed sequence. The sequence is needed to assure the correct number of quality scores are provided. If not provided, this check is omitted.

include sig ... end

Source

val read : 
  Future_lwt.Reader.t ->
  Biocaml_unix__Fastq.item Core_kernel.Or_error.t Future_lwt.Pipe.Reader.t

Source

val write : 
  Future_lwt.Writer.t ->
  Biocaml_unix__Fastq.item Future_lwt.Pipe.Reader.t ->
  unit Future_lwt.Deferred.t

Source

val write_file : 
  ?perm:int ->
  ?append:bool ->
  string ->
  Biocaml_unix__Fastq.item Future_lwt.Pipe.Reader.t ->
  unit Future_lwt.Deferred.t

package biocaml

Install

Dune Dependency

Authors

Maintainers

Sources

doc/biocaml.lwt/Biocaml_lwt/Fastq/index.html

Module Biocaml_lwt.FastqSource

Low-level Printing

Module `Biocaml_lwt.Fastq`Source