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in-package search v0.1.0
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
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
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
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.
val sexp_of_item : item -> Ppx_sexp_conv_lib.Sexp.t
val item_of_sexp : Ppx_sexp_conv_lib.Sexp.t -> item
Split a name string into a sequence identifier and an optional description. It is assumed that the given string is from an
name field, i.e. that it doesn't contain a leading @ char.
include sig ... end
val write : Future_unix.Writer.t -> item Future_unix.Pipe.Reader.t -> unit Future_unix.Deferred.t
val write_file : ?perm:int -> ?append:bool -> string -> item Future_unix.Pipe.Reader.t -> unit Future_unix.Deferred.t
module Illumina : sig ... end
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
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 is needed to assure the correct number of quality scores are provided. If not provided, this check is omitted.