sig
type item = {
name : string;
sequence : string;
comment : string;
qualities : string;
}
module Error :
sig
type fasta_pair_to_fastq =
[ `cannot_convert_to_phred_score of int list
| `sequence_names_mismatch of string * string ]
type parsing =
[ `incomplete_input of Biocaml_pos.t * string list * string option
| `sequence_and_qualities_do_not_match of
Biocaml_pos.t * string * string
| `wrong_comment_line of Biocaml_pos.t * string
| `wrong_name_line of Biocaml_pos.t * string ]
type t =
[ `cannot_convert_to_phred_score of int list
| `incomplete_input of Biocaml_pos.t * string list * string option
| `sequence_and_qualities_do_not_match of
Biocaml_pos.t * string * string
| `sequence_names_mismatch of string * string
| `wrong_comment_line of Biocaml_pos.t * string
| `wrong_name_line of Biocaml_pos.t * string ]
val t_of_sexp : Sexplib.Sexp.t -> Biocaml_fastq.Error.t
val sexp_of_t : Biocaml_fastq.Error.t -> Sexplib.Sexp.t
val t_to_string : Biocaml_fastq.Error.t -> string
end
exception Error of Biocaml_fastq.Error.t
val in_channel_to_item_stream :
?buffer_size:int ->
?filename:string ->
Pervasives.in_channel ->
(Biocaml_fastq.item, [> Biocaml_fastq.Error.parsing ]) Core.Result.t
Stream.t
val in_channel_to_item_stream_exn :
?buffer_size:int ->
?filename:string -> Pervasives.in_channel -> Biocaml_fastq.item Stream.t
val item_to_string : Biocaml_fastq.item -> string
module Transform :
sig
val string_to_item :
?filename:string ->
unit ->
(string,
(Biocaml_fastq.item, [> Biocaml_fastq.Error.parsing ]) Core.Result.t)
Biocaml_transform.t
val item_to_string :
unit -> (Biocaml_fastq.item, string) Biocaml_transform.t
val trim :
[ `beginning of int | `ending of int ] ->
(Biocaml_fastq.item,
(Biocaml_fastq.item, [> `invalid_size of int ]) Core.Result.t)
Biocaml_transform.t
val fasta_pair_to_fastq :
?phred_score_offset:[ `offset33 | `offset64 ] ->
unit ->
(Biocaml_fasta.char_seq Biocaml_fasta.item *
Biocaml_fasta.int_seq Biocaml_fasta.item,
(Biocaml_fastq.item, [> Biocaml_fastq.Error.fasta_pair_to_fastq ])
Core.Result.t)
Biocaml_transform.t
val fastq_to_fasta_pair :
?phred_score_offset:[ `offset33 | `offset64 ] ->
unit ->
(Biocaml_fastq.item,
(Biocaml_fasta.char_seq Biocaml_fasta.item *
Biocaml_fasta.int_seq Biocaml_fasta.item,
[> `cannot_convert_ascii_phred_score of string ])
Core.Result.t)
Biocaml_transform.t
end
val item_of_sexp : Sexplib.Sexp.t -> Biocaml_fastq.item
val sexp_of_item : Biocaml_fastq.item -> Sexplib.Sexp.t
end