hlarp 0.0.3 (latest) · OCaml Package

type directory = string

type scanner = directory -> (Std.sample * Std.Info.t list) list

type source = string

val to_source : string -> 'a list -> int -> source

val add_to_sample_map : 
  source_name:string ->
  scanner ->
  directory list ->
  (source * Std.Info.t list) list Std.SampleMap.t ->
  (source * Std.Info.t list) list Std.SampleMap.t

module HlarpOutputFiles : sig ... end

val hlarp_file_arg : string

val seq2hl_file_arg : string

val optitype_file_arg : string

val athlates_file_arg : string

val prohlatype_file_arg : string

val seq2HLA_source : string

val optitype_source : string

val athlates_source : string

val prohlatype_source : string

val argument_order : use_basename:bool -> string list

val nested_maps : 
  ?seqlst:directory list ->
  ?optlst:directory list ->
  ?athlst:directory list ->
  ?prolst:directory list ->
  ?filelst:source Std.List.t ->
  unit ->
  (Std.SampleMap.key * (source * Std.Info.t list) list) Std.List.t

val list_fold_over_all_pairs : 
  f:('a -> 'b -> 'b -> 'a) ->
  init:'a ->
  'b list ->
  'a

val colon_regex : Re__.Compile.re

val to_allele : ?resolution:int -> Std.Info.t -> Std.allele

module AlleleSet : sig ... end

val jaccard : ?zero_on_empty:bool -> AlleleSet.t -> AlleleSet.t -> float

val loci_prefix_filter : string -> Std.Info.t -> bool

val hla_class_filter : Std.hla_class -> Std.Info.t -> bool

val count_consecutive_doubles : 'a list -> ('a * int) list

val compress_counts : (string * int) Std.List.t -> string Std.List.t

val loci_class_filters : 
  string Std.List.t option ->
  Std.hla_class Std.List.t option ->
  (Std.Info.t -> bool) Std.List.t

val specific_grouped_view : 
  ?loci:string Std.List.t ->
  ?classes:Std.hla_class Std.List.t ->
  typer1:string ->
  ilist1:(Std.AlleleMap.key * Std.Info.t) list ->
  typer2:string ->
  ilist2:(Std.AlleleMap.key * Std.Info.t) list ->
  (Std.AlleleMap.key * string Std.List.t) list

val against_all_pairs : 
  ((string * 'a) -> (string * 'a) -> 'b) ->
  ('c * (string * 'a) list) Std.List.t ->
  ('c * (string * 'b) list) Std.List.t

type comparison = {

metrics_eval : float list;
grouped_view : (Std.allele * string list) list;

}

val args_to_projections : 
  ?loci:string Std.List.t ->
  ?classes:Std.hla_class Std.List.t ->
  (Std.Info.t list -> Std.Info.t list -> float) Std.List.t ->
  (itassoc1:(string * Std.Info.t Std.List.t) ->
    itassoc2:(string * Std.Info.t Std.List.t) ->
    (Std.allele * string list) list) ->
  ('a * (string * Std.Info.t Std.List.t) list) Std.List.t ->
  ('a * (string * comparison) list) Std.List.t

val remove_and_assoc : 'a -> ('a * 'b) list -> ('a * 'b) * ('a * 'b) list

val keyed_by_allele_info_assoc : 
  ?resolution:int ->
  ?label_homozygous:bool ->
  Std.Info.t list ->
  (Std.allele * Std.Info.t) list

val set_of_assoc_keys : (AlleleSet.elt * 'a) Std.List.t -> AlleleSet.t

val sum_confidence : ('a * Std.Info.t) Std.List.t -> float

val sum_snd : ('a * float) Std.List.t -> float

val normalize : 
  float ->
  ('a * Std.Info.t) Std.List.t ->
  ('a * float) Std.List.t

val describe_distr : (string * float) Std.List.t -> string

val to_metric : 
  [< `Jaccard | `KLDiv ] ->
  ((AlleleSet.elt * Std.Info.t) Std.List.t ->
  (AlleleSet.elt * Std.Info.t) Std.List.t ->
  float)
  * bool

val analyze_samples : 
  ?loci:string Std.List.t ->
  ?classes:Std.hla_class Std.List.t ->
  ?resolution:int ->
  ?label_homozygous:bool ->
  ?metrics:[< `Jaccard | `KLDiv Jaccard ] Std.List.t ->
  ('a * (string * Std.Info.t Std.List.t) list) Std.List.t ->
  ('a * (string * comparison) list) Std.List.t

val float_lst_to_str : sep:string -> float Std.List.t -> string

val output_aggregates : 
  ?summary_by:[< `Mean | `Median Mean ] ->
  out_channel ->
  int ->
  int list ->
  ('a * ('b * comparison) list) list ->
  unit

val output : 
  ?max_allele_rows_to_print:int ->
  ?summary_by:[< `Mean | `Median Mean ] ->
  out_channel ->
  (string * (string * comparison) Std.List.t) list ->
  unit

package hlarp