sig
type vcf_id = string
type vcf_description = string
type vcf_number =
Biocaml_vcf.vcf_number =
Number of int
| OnePerAllele
| OnePerGenotype
| Unknown
type vcf_format_type =
[ `character_value | `float_value | `integer_value | `string_value ]
type vcf_info_type =
[ `character_value
| `flag_value
| `float_value
| `integer_value
| `string_value ]
type vcf_info_meta =
Biocaml_vcf.vcf_info_meta =
Info of vcf_number * vcf_info_type * vcf_description
type vcf_filter_meta =
Biocaml_vcf.vcf_filter_meta =
Filter of vcf_description
type vcf_format_meta =
Biocaml_vcf.vcf_format_meta =
Format of vcf_number * vcf_format_type * vcf_description
type vcf_alt_meta = Biocaml_vcf.vcf_alt_meta = Alt of vcf_description
type vcf_meta =
Biocaml_vcf.vcf_meta = {
vcfm_version : string;
vcfm_id_cache : vcf_id Biocaml_internal_pervasives.Set.Poly.t;
vcfm_info : (vcf_id, vcf_info_meta) Biocaml_internal_pervasives.Hashtbl.t;
vcfm_filters : (vcf_id * vcf_filter_meta) list;
vcfm_format :
(vcf_id, vcf_format_meta) Biocaml_internal_pervasives.Hashtbl.t;
vcfm_alt : (string, vcf_alt_meta) Biocaml_internal_pervasives.Hashtbl.t;
vcfm_arbitrary : (string, string) Biocaml_internal_pervasives.Hashtbl.t;
vcfm_header : string list;
vcfm_samples : string list;
}
type vcf_format =
[ `character of char
| `float of float
| `integer of int
| `missing
| `string of string ]
type vcf_info =
[ `character of char
| `flag of string
| `float of float
| `integer of int
| `missing
| `string of string ]
type vcf_row =
Biocaml_vcf.vcf_row = {
vcfr_chrom : string;
vcfr_pos : int;
vcfr_ids : string list;
vcfr_ref : string;
vcfr_alts : string list;
vcfr_qual : float option;
vcfr_filter : vcf_id list;
vcfr_info : (vcf_id, vcf_info list) Biocaml_internal_pervasives.Hashtbl.t;
vcfr_samples :
(vcf_id, (vcf_id * vcf_format list) list)
Biocaml_internal_pervasives.Hashtbl.t;
}
type item = vcf_row
module Pos :
sig
type t =
Biocaml_vcf.Pos.t = private {
file : string option;
line : int option;
col : int option;
}
exception Bad of string
exception Undefined
val make : ?file:string -> ?line:int -> ?col:int -> unit -> t
val f : string -> t
val l : int -> t
val fl : string -> int -> t
val lc : int -> int -> t
val flc : string -> int -> int -> t
val unknown : t
val file_exn : t -> string
val line_exn : t -> int
val col_exn : t -> int
val set_file : t -> string -> t
val set_line : t -> int -> t
val set_col : t -> int -> t
val incrl : t -> int -> t
val to_string : t -> string
val t_of_sexp : Sexplib.Sexp.t -> t
val sexp_of_t : t -> Sexplib.Sexp.t
end
type vcf_parse_row_error =
[ `duplicate_ids of vcf_id list
| `format_type_coersion_failure of vcf_format_type * string
| `info_type_coersion_failure of vcf_info_type * string
| `invalid_arguments_length of vcf_id * int * int
| `invalid_dna of string
| `invalid_float of string
| `invalid_int of string
| `invalid_row_length of int * int
| `malformed_sample of string
| `unknown_alt of string
| `unknown_filter of vcf_id
| `unknown_format of vcf_id
| `unknown_info of vcf_id ]
type vcf_parse_error =
[ `incomplete_input of Pos.t * string list * string option
| `malformed_header of Pos.t * string
| `malformed_meta of Pos.t * string
| `malformed_row of Pos.t * vcf_parse_row_error * string
| `not_ready ]
val parse_error_to_string : vcf_parse_error -> string
module Transform :
sig
val string_to_item :
?filename:string ->
unit ->
(string, (item, vcf_parse_error) Core.Result.t) Biocaml_transform.t
end
end