Module Biocaml_lwt.FastqSource

include module type of struct include Biocaml_unix.Fastq end
Sourcetype item = Biocaml_unix.Fastq.item = {
  1. name : string;
  2. sequence : string;
  3. comment : string;
  4. 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.

include sig ... end

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.

Sourceval 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
Sourceval comment_of_line : ?pos:Biocaml_unix.Pos.t -> Biocaml_unix.Line.t -> string Core_kernel.Or_error.t
Sourceval 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
Sourceval read : Future_lwt.Reader.t -> Biocaml_unix__Fastq.item Core_kernel.Or_error.t Future_lwt.Pipe.Reader.t
Sourceval write : Future_lwt.Writer.t -> Biocaml_unix__Fastq.item Future_lwt.Pipe.Reader.t -> unit Future_lwt.Deferred.t
Sourceval write_file : ?perm:int -> ?append:bool -> string -> Biocaml_unix__Fastq.item Future_lwt.Pipe.Reader.t -> unit Future_lwt.Deferred.t