package hlarp

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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 = {
  1. metrics_eval : float list;
  2. 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
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