biocaml
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package biocaml
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FASTQ files. The FASTQ file format is repeated sequence of 4 lines:

    \@name
    sequence
    +comment
    qualities
    ...

The name line begins with an @ character, which is omitted in the parsed item type provided by this module. Any spaces after the @ are retained, but the specification implies that there shouldn't be any such spaces. Trailing whitespace is also retained since you should not normally have such files.

The comment line, which begins with a +, is handled similarly. The purpose of the comment line is unclear and it is rarely used. Also, "comment" may not be the correct term for this line.

The name line may be structured into two parts: a sequence identifier and an optional description. We provide a function split_name to parse such a value. However, an item's name field contains the unparsed string because it is unclear whether fastq files really follow this. Also the format of the description is unspecified. When it is provided, usually it has some additional structure, so the minimal amount of parsing done by split_name isn't too useful anyway.

Illumina uses a systematic format for the name line that serves as a unique sequence identifier. Use Illumina.sequence_id_of_string to parse an item's name field when you have fastq files produced by Casava version >= 1.8. Earlier versions of Casava returned a different format, which is not currently supported in this module (it could be easily added).

The qualities line is returned as a plain string, but it is required to be decodable as either Phred or Solexa scores. Modules Phred_score and Solexa_score can be used to parse as needed.

Older FASTQ files allowed the sequence and qualities strings to span multiple lines. This is discouraged and is not supported by this module.

type item = {
  1. name : string;
  2. sequence : string;
  3. comment : string;
  4. qualities : string;
}
val sexp_of_item : item -> Ppx_sexp_conv_lib.Sexp.t
val item_of_sexp : Ppx_sexp_conv_lib.Sexp.t -> item
val 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.

module MakeIO (Future : Future.S) : sig ... end
include sig ... end
val write_file : ?perm:int -> ?append:bool -> string -> item Future_unix.Pipe.Reader.t -> unit Future_unix.Deferred.t
module Illumina : sig ... end

Low-level Printing

val 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.

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

Low-level Parsing

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