module Make_serializer: functor (How : sig
type
val input_value : string ->
(string * string) list -> var_count:int -> t
val function_call : string ->
(string * t) list ->
t
val string : string -> t
end) -> sig .. end
| Parameters: |
How |
: |
sig
type t
val input_value :
string -> (string * string) list -> var_count:int -> t
val function_call :
string -> (string * t) list -> t
val string : string -> t
end
|
|
val fastq : sample_name:string ->
?fragment_id:string ->
r1:string -> ?r2:string -> unit -> var_count:int -> How.t
val fastq_gz : sample_name:string ->
?fragment_id:string ->
r1:string -> ?r2:string -> unit -> var_count:int -> How.t
val bam : path:string ->
?sorting:[< `Coordinate | `Read_name ] ->
reference_build:string -> unit -> var_count:int -> How.t
val pair : (var_count:int -> How.t) ->
(var_count:int -> How.t) -> var_count:int -> How.t
val pair_first : (var_count:int -> How.t) -> var_count:int -> How.t
val pair_second : (var_count:int -> How.t) -> var_count:int -> How.t
val aligner : string ->
string ->
reference_build:string -> (var_count:int -> How.t) -> var_count:int -> How.t
val one_to_one : string -> string -> (var_count:int -> How.t) -> var_count:int -> How.t
val bwa_aln : ?configuration:Tools.Bwa.Configuration.Aln.t ->
reference_build:string -> (var_count:int -> How.t) -> var_count:int -> How.t
val bwa_mem : ?configuration:Tools.Bwa.Configuration.Mem.t ->
reference_build:string -> (var_count:int -> How.t) -> var_count:int -> How.t
val gunzip : (var_count:int -> How.t) -> var_count:int -> How.t
val gunzip_concat : (var_count:int -> How.t) -> var_count:int -> How.t
val concat : (var_count:int -> How.t) -> var_count:int -> How.t
val merge_bams : (var_count:int -> How.t) -> var_count:int -> How.t
val star : ?configuration:Tools.Star.Configuration.Align.t ->
reference_build:string -> (var_count:int -> How.t) -> var_count:int -> How.t
val hisat : ?configuration:Tools.Hisat.Configuration.t ->
reference_build:string -> (var_count:int -> How.t) -> var_count:int -> How.t
val mosaik : reference_build:string -> (var_count:int -> How.t) -> var_count:int -> How.t
val stringtie : ?configuration:Tools.Stringtie.Configuration.t ->
(var_count:int -> How.t) -> var_count:int -> How.t
val indel_real_config : Tools.Gatk.Configuration.Indel_realigner.t *
Tools.Gatk.Configuration.Realigner_target_creator.t -> string
val gatk_indel_realigner : ?configuration:Tools.Gatk.Configuration.Indel_realigner.t *
Tools.Gatk.Configuration.Realigner_target_creator.t ->
(var_count:int -> How.t) -> var_count:int -> How.t
val gatk_indel_realigner_joint : ?configuration:Tools.Gatk.Configuration.Indel_realigner.t *
Tools.Gatk.Configuration.Realigner_target_creator.t ->
(var_count:int -> How.t) -> var_count:int -> How.t
val picard_mark_duplicates : ?configuration:Tools.Picard.Mark_duplicates_settings.t ->
(var_count:int -> How.t) -> var_count:int -> How.t
val gatk_bqsr : ?configuration:Tools.Gatk.Configuration.Bqsr.t *
Tools.Gatk.Configuration.Print_reads.t ->
(var_count:int -> How.t) -> var_count:int -> How.t
val seq2hla : (var_count:int -> How.t) -> var_count:int -> How.t
val optitype : [< `DNA | `RNA ] -> (var_count:int -> How.t) -> var_count:int -> How.t
val gatk_haplotype_caller : (var_count:int -> How.t) -> var_count:int -> How.t
val bam_to_fastq : sample_name:string ->
?fragment_id:string ->
[< `PE | `SE ] -> (var_count:int -> How.t) -> var_count:int -> How.t
val variant_caller : string ->
string ->
normal:(var_count:int -> How.t) ->
tumor:(var_count:int -> How.t) -> unit -> var_count:int -> How.t
val mutect : ?configuration:Tools.Mutect.Configuration.t ->
normal:(var_count:int -> How.t) ->
tumor:(var_count:int -> How.t) -> unit -> var_count:int -> How.t
val mutect2 : ?configuration:Tools.Gatk.Configuration.Mutect2.t ->
normal:(var_count:int -> How.t) ->
tumor:(var_count:int -> How.t) -> unit -> var_count:int -> How.t
val somaticsniper : ?configuration:Tools.Somaticsniper.Configuration.t ->
normal:(var_count:int -> How.t) ->
tumor:(var_count:int -> How.t) -> unit -> var_count:int -> How.t
val strelka : ?configuration:Tools.Strelka.Configuration.t ->
normal:(var_count:int -> How.t) ->
tumor:(var_count:int -> How.t) -> unit -> var_count:int -> How.t
val varscan_somatic : ?adjust_mapq:int ->
normal:(var_count:int -> How.t) ->
tumor:(var_count:int -> How.t) -> unit -> var_count:int -> How.t
val muse : ?configuration:Tools.Muse.Configuration.t ->
normal:(var_count:int -> How.t) ->
tumor:(var_count:int -> How.t) -> unit -> var_count:int -> How.t
val virmid : ?configuration:Tools.Virmid.Configuration.t ->
normal:(var_count:int -> How.t) ->
tumor:(var_count:int -> How.t) -> unit -> var_count:int -> How.t