Module Biocaml.Fastq (.ml)

module Fastq: Biocaml_fastq

type item = {

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

}

Type of FASTQ items.

module Error: sig .. end

val in_channel_to_item_stream : ?buffer_size:int ->
       ?filename:string ->
       Pervasives.in_channel ->
       (item, Error.t) Core.Result.t Stream.t

module Exceptionful: sig .. end

module Transform: sig .. end

val item_of_sexp : Sexplib.Sexp.t -> item

val sexp_of_item : item -> Sexplib.Sexp.t

Type of FASTQ items.

Errors. All errors generated by any function in the Fastq module are defined here.

`sequence_and_qualities_do_not_match (position, sequence, qualities) - given sequence and qualities at given position are of different lengths.

`wrong_name_line x - name line x does not start with '@'

`wrong_comment_line _ - comment line does not start with '+'

`incomplete_input (position, lines, s) - the input ended prematurely. Trailing contents, which cannot be used to fully construct an item, are provided: lines is any complete lines parsed and s is any final string not ending in a newline.

Transform error to a human-readable string.

Create a full stoppable Biocaml_transform.t from arbitrary strings to item values.

Create a full stoppable Biocaml_transform.t from item values to strings.

Create a full stoppable Biocaml_transform.t that trims FASTQ items.