Functor Biokepi_pipeline_edsl.Optimization_framework.Generic_optimizer (.ml)

module Generic_optimizer: functor (X : Transformation) -> functor (Input : Semantics.Bioinformatics_base  with type 'a repr = 'a X.from) -> sig .. end

The default, generic optimizer.

Concrete optimizers are built by overriding the interpretations of some DSL forms.

See the module Biokepi_pipeline_edsl.Transform_applications for an example of use.

Parameters:

`X`	:	`Transformation`
`Input`	:	`Semantics.Bioinformatics_base with type 'a repr = 'a X.from`

type 'a repr = 'a X.term

type 'a observation = 'a Input.observation

val lambda : ('a X.term -> 'b X.term) -> ('a -> 'b) X.term

val apply : ('a -> 'b) X.term -> 'a X.term -> 'b X.term

val observe : (unit -> 'a X.term) -> 'a Input.observation

val list : 'a X.term list -> 'a list X.term

val list_map : 'a list X.term -> f:('a -> 'b) X.term -> 'b list X.term

val to_unit : 'a X.term -> unit X.term

val pair : 'a X.term -> 'b X.term -> ('a * 'b) X.term

val pair_first : ('a * 'b) X.term -> 'a X.term

val pair_second : ('a * 'b) X.term -> 'b X.term

val input_url : string -> [ `Raw_file ] X.term

val save : name:string -> 'a X.term -> [ `Saved of 'a ] X.term

val fastq : sample_name:string ->
       ?fragment_id:string ->
       r1:[ `Raw_file ] X.term ->
       ?r2:[ `Raw_file ] X.term -> unit -> [ `Fastq ] X.term

val fastq_gz : sample_name:string ->
       ?fragment_id:string ->
       r1:[ `Raw_file ] X.term ->
       ?r2:[ `Raw_file ] X.term -> unit -> [ `Gz of [ `Fastq ] ] X.term

val bam : sample_name:string ->
       ?sorting:[ `Coordinate | `Read_name ] ->
       reference_build:string -> [ `Raw_file ] X.term -> [ `Bam ] X.term

val bed : [ `Raw_file ] X.term -> [ `Bed ] X.term

val mhc_alleles : [< `File of [ `Raw_file ] X.term | `Names of string list ] ->
       [ `MHC_alleles ] X.term

val index_bam : [ `Bam ] X.term -> [ `Bai ] X.term

val kallisto : reference_build:string ->
       ?bootstrap_samples:int -> [ `Fastq ] X.term -> [ `Kallisto_result ] X.term

val delly2 : ?configuration:Biokepi_bfx_tools.Delly2.Configuration.t ->
       normal:[ `Bam ] X.term -> tumor:[ `Bam ] X.term -> unit -> [ `Vcf ] X.term

val cufflinks : ?reference_build:string -> [ `Bam ] X.term -> [ `Cufflinks_result ] X.term

val bwa_aln : ?configuration:Biokepi_bfx_tools.Bwa.Configuration.Aln.t ->
       reference_build:Biokepi_run_environment.Reference_genome.name ->
       [ `Fastq ] X.term -> [ `Bam ] X.term

val bwa_mem : ?configuration:Biokepi_bfx_tools.Bwa.Configuration.Mem.t ->
       reference_build:Biokepi_run_environment.Reference_genome.name ->
       [ `Fastq ] X.term -> [ `Bam ] X.term

val bwa_mem_opt : ?configuration:Biokepi_bfx_tools.Bwa.Configuration.Mem.t ->
       reference_build:Biokepi_run_environment.Reference_genome.name ->
       [< `Bam of [ `Bam ] X.term * [ `PE | `SE ]
        | `Fastq of [ `Fastq ] X.term
        | `Fastq_gz of [ `Gz of [ `Fastq ] ] X.term ] ->
       [ `Bam ] X.term

val star : ?configuration:Biokepi_bfx_tools.Star.Configuration.Align.t ->
       reference_build:Biokepi_run_environment.Reference_genome.name ->
       [ `Fastq ] X.term -> [ `Bam ] X.term

val hisat : ?configuration:Biokepi_bfx_tools.Hisat.Configuration.t ->
       reference_build:Biokepi_run_environment.Reference_genome.name ->
       [ `Fastq ] X.term -> [ `Bam ] X.term

val mosaik : reference_build:Biokepi_run_environment.Reference_genome.name ->
       [ `Fastq ] X.term -> [ `Bam ] X.term

val stringtie : ?configuration:Biokepi_bfx_tools.Stringtie.Configuration.t ->
       [ `Bam ] X.term -> [ `Gtf ] X.term

val gatk_indel_realigner : ?configuration:Biokepi_bfx_tools.Gatk.Configuration.indel_realigner ->
       [ `Bam ] X.term -> [ `Bam ] X.term

val gatk_indel_realigner_joint : ?configuration:Biokepi_bfx_tools.Gatk.Configuration.indel_realigner ->
       ([ `Bam ] * [ `Bam ]) X.term -> ([ `Bam ] * [ `Bam ]) X.term

val picard_mark_duplicates : ?configuration:Biokepi_bfx_tools.Picard.Mark_duplicates_settings.t ->
       [ `Bam ] X.term -> [ `Bam ] X.term

val picard_reorder_sam : ?mem_param:string ->
       ?reference_build:string -> [ `Bam ] X.term -> [ `Bam ] X.term

val picard_clean_bam : [ `Bam ] X.term -> [ `Bam ] X.term

val gatk_bqsr : ?configuration:Biokepi_bfx_tools.Gatk.Configuration.bqsr ->
       [ `Bam ] X.term -> [ `Bam ] X.term

val seq2hla : [ `Fastq ] X.term -> [ `Seq2hla_result ] X.term

val optitype : [ `DNA | `RNA ] -> [ `Fastq ] X.term -> [ `Optitype_result ] X.term

val hlarp : [< `Optitype of [ `Optitype_result ] X.term
        | `Seq2hla of [ `Seq2hla_result ] X.term ] ->
       [ `MHC_alleles ] X.term

val filter_to_region : [ `Vcf ] X.term -> [ `Bed ] X.term -> [ `Vcf ] X.term

val gatk_haplotype_caller : [ `Bam ] X.term -> [ `Vcf ] X.term

val gunzip : [ `Gz of 'a ] X.term -> 'a X.term

val gunzip_concat : [ `Gz of 'a ] list X.term -> 'a X.term

val concat : 'a list X.term -> 'a X.term

val merge_bams : ?delete_input_on_success:'a ->
       ?attach_rg_tag:'b ->
       ?uncompressed_bam_output:'c ->
       ?compress_level_one:'d ->
       ?combine_rg_headers:'e ->
       ?combine_pg_headers:'f -> [ `Bam ] list X.term -> [ `Bam ] X.term

val bam_to_fastq : ?fragment_id:string -> [ `PE | `SE ] -> [ `Bam ] X.term -> [ `Fastq ] X.term

val bam_left_align : reference_build:string -> [ `Bam ] X.term -> [ `Bam ] X.term

val sambamba_filter : filter:Biokepi_bfx_tools.Sambamba.Filter.t ->
       [ `Bam ] X.term -> [ `Bam ] X.term

val mutect : ?configuration:Biokepi_bfx_tools.Mutect.Configuration.t ->
       normal:[ `Bam ] X.term -> tumor:[ `Bam ] X.term -> unit -> [ `Vcf ] X.term

val mutect2 : ?configuration:Biokepi_bfx_tools.Gatk.Configuration.Mutect2.t ->
       normal:[ `Bam ] X.term -> tumor:[ `Bam ] X.term -> unit -> [ `Vcf ] X.term

val somaticsniper : ?configuration:Biokepi_bfx_tools.Somaticsniper.Configuration.t ->
       normal:[ `Bam ] X.term -> tumor:[ `Bam ] X.term -> unit -> [ `Vcf ] X.term

val strelka : ?configuration:Biokepi_bfx_tools.Strelka.Configuration.t ->
       normal:[ `Bam ] X.term -> tumor:[ `Bam ] X.term -> unit -> [ `Vcf ] X.term

val varscan_somatic : ?adjust_mapq:int ->
       normal:[ `Bam ] X.term -> tumor:[ `Bam ] X.term -> unit -> [ `Vcf ] X.term

val muse : ?configuration:Biokepi_bfx_tools.Muse.Configuration.t ->
       normal:[ `Bam ] X.term -> tumor:[ `Bam ] X.term -> unit -> [ `Vcf ] X.term

val virmid : ?configuration:Biokepi_bfx_tools.Virmid.Configuration.t ->
       normal:[ `Bam ] X.term -> tumor:[ `Bam ] X.term -> unit -> [ `Vcf ] X.term

val fastqc : [ `Fastq ] X.term -> [ `Fastqc ] X.term

val flagstat : [ `Bam ] X.term -> [ `Flagstat ] X.term

val vcf_annotate_polyphen : [ `Vcf ] X.term -> [ `Vcf ] X.term

val snpeff : [ `Vcf ] X.term -> [ `Vcf ] X.term

val isovar : ?configuration:Biokepi_bfx_tools.Isovar.Configuration.t ->
       [ `Vcf ] X.term -> [ `Bam ] X.term -> [ `Isovar ] X.term

val topiary : ?configuration:Biokepi_bfx_tools.Topiary.Configuration.t ->
       [ `Vcf ] X.term list ->
       Biokepi_run_environment.Hla_utilities.predictor_type ->
       [ `MHC_alleles ] X.term -> [ `Topiary ] X.term

val vaxrank : ?configuration:Biokepi_bfx_tools.Vaxrank.Configuration.t ->
       [ `Vcf ] X.term list ->
       [ `Bam ] X.term ->
       Biokepi_run_environment.Hla_utilities.predictor_type ->
       [ `MHC_alleles ] X.term -> [ `Vaxrank ] X.term

val seqtk_shift_phred_scores : [ `Fastq ] X.term -> [ `Fastq ] X.term