sig
module type Trans_base =
sig
type 'a from
type 'a term
val fwd :
'a Biokepi_pipeline_edsl.Optimization_framework.Trans_base.from ->
'a Biokepi_pipeline_edsl.Optimization_framework.Trans_base.term
val bwd :
'a Biokepi_pipeline_edsl.Optimization_framework.Trans_base.term ->
'a Biokepi_pipeline_edsl.Optimization_framework.Trans_base.from
end
module type Transformation =
sig
type 'a from
type 'a term
val fwd : 'a from -> 'a term
val bwd : 'a term -> 'a from
val fmap : ('a from -> 'b from) -> 'a term -> 'b term
val fmap2 :
('a from -> 'b from -> 'c from) -> 'a term -> 'b term -> 'c term
end
module Define_transformation :
functor (X : Trans_base) ->
sig
type 'a from = 'a X.from
type 'a term = 'a X.term
val fwd : 'a from -> 'a term
val bwd : 'a term -> 'a from
val fmap : ('a from -> 'b from) -> 'a term -> 'b term
val fmap2 :
('a from -> 'b from -> 'c from) -> 'a term -> 'b term -> 'c term
end
module Generic_optimizer :
functor
(X : Transformation) (Input : sig
type 'a repr = 'a X.from
val lambda :
('a repr -> 'b repr) ->
('a -> 'b) repr
val apply :
('a -> 'b) repr -> 'a repr -> 'b repr
type 'a observation
val observe :
(unit -> 'a repr) -> 'a observation
val list : 'a repr list -> 'a list repr
val list_map :
'a list repr ->
f:('a -> 'b) repr -> 'b list repr
val pair :
'a repr -> 'b repr -> ('a * 'b) repr
val pair_first :
('a * 'b) repr -> 'a repr
val pair_second :
('a * 'b) repr -> 'b repr
val to_unit : 'a repr -> unit repr
val fastq :
sample_name:string ->
?fragment_id:string ->
r1:string ->
?r2:string -> unit -> [ `Fastq ] repr
val fastq_gz :
sample_name:string ->
?fragment_id:string ->
r1:string ->
?r2:string ->
unit -> [ `Gz of [ `Fastq ] ] repr
val bam :
path:string ->
?sorting:[ `Coordinate | `Read_name ] ->
reference_build:string ->
unit -> [ `Bam ] repr
val gunzip :
[ `Gz of 'a ] repr -> 'a repr
val gunzip_concat :
[ `Gz of 'a ] list repr -> 'a repr
val concat : 'a list repr -> 'a repr
val merge_bams :
[ `Bam ] list repr -> [ `Bam ] repr
val bam_to_fastq :
sample_name:string ->
?fragment_id:string ->
[ `PE | `SE ] ->
[ `Bam ] repr -> [ `Fastq ] repr
val bwa_aln :
?configuration:Biokepi_bfx_tools.Bwa.Configuration.Aln.t ->
reference_build:Biokepi_run_environment.Reference_genome.name ->
[ `Fastq ] repr -> [ `Bam ] repr
val bwa_mem :
?configuration:Biokepi_bfx_tools.Bwa.Configuration.Mem.t ->
reference_build:Biokepi_run_environment.Reference_genome.name ->
[ `Fastq ] repr -> [ `Bam ] repr
val star :
?configuration:Biokepi_bfx_tools.Star.Configuration.Align.t ->
reference_build:Biokepi_run_environment.Reference_genome.name ->
[ `Fastq ] repr -> [ `Bam ] repr
val hisat :
?configuration:Biokepi_bfx_tools.Hisat.Configuration.t ->
reference_build:Biokepi_run_environment.Reference_genome.name ->
[ `Fastq ] repr -> [ `Bam ] repr
val mosaik :
reference_build:Biokepi_run_environment.Reference_genome.name ->
[ `Fastq ] repr -> [ `Bam ] repr
val stringtie :
?configuration:Biokepi_bfx_tools.Stringtie.Configuration.t ->
[ `Bam ] repr -> [ `Gtf ] repr
val gatk_indel_realigner :
?configuration:Biokepi_bfx_tools.Gatk.Configuration.indel_realigner ->
[ `Bam ] repr -> [ `Bam ] repr
val gatk_indel_realigner_joint :
?configuration:Biokepi_bfx_tools.Gatk.Configuration.indel_realigner ->
([ `Bam ] * [ `Bam ]) repr ->
([ `Bam ] * [ `Bam ]) repr
val picard_mark_duplicates :
?configuration:Biokepi_bfx_tools.Picard.Mark_duplicates_settings.t ->
[ `Bam ] repr -> [ `Bam ] repr
val gatk_bqsr :
?configuration:Biokepi_bfx_tools.Gatk.Configuration.bqsr ->
[ `Bam ] repr -> [ `Bam ] repr
val seq2hla :
[ `Fastq ] repr ->
[ `Seq2hla_result ] repr
val optitype :
[ `DNA | `RNA ] ->
[ `Fastq ] repr ->
[ `Optitype_result ] repr
val gatk_haplotype_caller :
[ `Bam ] repr -> [ `Vcf ] repr
val mutect :
?configuration:Biokepi_bfx_tools.Mutect.Configuration.t ->
normal:[ `Bam ] repr ->
tumor:[ `Bam ] repr ->
unit -> [ `Vcf ] repr
val mutect2 :
?configuration:Biokepi_bfx_tools.Gatk.Configuration.Mutect2.t ->
normal:[ `Bam ] repr ->
tumor:[ `Bam ] repr ->
unit -> [ `Vcf ] repr
val somaticsniper :
?configuration:Biokepi_bfx_tools.Somaticsniper.Configuration.t ->
normal:[ `Bam ] repr ->
tumor:[ `Bam ] repr ->
unit -> [ `Vcf ] repr
val varscan_somatic :
?adjust_mapq:int ->
normal:[ `Bam ] repr ->
tumor:[ `Bam ] repr ->
unit -> [ `Vcf ] repr
val strelka :
?configuration:Biokepi_bfx_tools.Strelka.Configuration.t ->
normal:[ `Bam ] repr ->
tumor:[ `Bam ] repr ->
unit -> [ `Vcf ] repr
val virmid :
?configuration:Biokepi_bfx_tools.Virmid.Configuration.t ->
normal:[ `Bam ] repr ->
tumor:[ `Bam ] repr ->
unit -> [ `Vcf ] repr
val muse :
?configuration:Biokepi_bfx_tools.Muse.Configuration.t ->
normal:[ `Bam ] repr ->
tumor:[ `Bam ] repr ->
unit -> [ `Vcf ] repr
end) ->
sig
type 'a repr = 'a X.term
val lambda : ('a repr -> 'b repr) -> ('a -> 'b) repr
val apply : ('a -> 'b) repr -> 'a repr -> 'b repr
type 'a observation = 'a Input.observation
val observe : (unit -> 'a repr) -> 'a observation
val list : 'a repr list -> 'a list repr
val list_map : 'a list repr -> f:('a -> 'b) repr -> 'b list repr
val pair : 'a repr -> 'b repr -> ('a * 'b) repr
val pair_first : ('a * 'b) repr -> 'a repr
val pair_second : ('a * 'b) repr -> 'b repr
val to_unit : 'a repr -> unit repr
val fastq :
sample_name:string ->
?fragment_id:string ->
r1:string -> ?r2:string -> unit -> [ `Fastq ] repr
val fastq_gz :
sample_name:string ->
?fragment_id:string ->
r1:string -> ?r2:string -> unit -> [ `Gz of [ `Fastq ] ] repr
val bam :
path:string ->
?sorting:[ `Coordinate | `Read_name ] ->
reference_build:string -> unit -> [ `Bam ] repr
val gunzip : [ `Gz of 'a ] repr -> 'a repr
val gunzip_concat : [ `Gz of 'a ] list repr -> 'a repr
val concat : 'a list repr -> 'a repr
val merge_bams : [ `Bam ] list repr -> [ `Bam ] repr
val bam_to_fastq :
sample_name:string ->
?fragment_id:string ->
[ `PE | `SE ] -> [ `Bam ] repr -> [ `Fastq ] repr
val bwa_aln :
?configuration:Biokepi_bfx_tools.Bwa.Configuration.Aln.t ->
reference_build:Biokepi_run_environment.Reference_genome.name ->
[ `Fastq ] repr -> [ `Bam ] repr
val bwa_mem :
?configuration:Biokepi_bfx_tools.Bwa.Configuration.Mem.t ->
reference_build:Biokepi_run_environment.Reference_genome.name ->
[ `Fastq ] repr -> [ `Bam ] repr
val star :
?configuration:Biokepi_bfx_tools.Star.Configuration.Align.t ->
reference_build:Biokepi_run_environment.Reference_genome.name ->
[ `Fastq ] repr -> [ `Bam ] repr
val hisat :
?configuration:Biokepi_bfx_tools.Hisat.Configuration.t ->
reference_build:Biokepi_run_environment.Reference_genome.name ->
[ `Fastq ] repr -> [ `Bam ] repr
val mosaik :
reference_build:Biokepi_run_environment.Reference_genome.name ->
[ `Fastq ] repr -> [ `Bam ] repr
val stringtie :
?configuration:Biokepi_bfx_tools.Stringtie.Configuration.t ->
[ `Bam ] repr -> [ `Gtf ] repr
val gatk_indel_realigner :
?configuration:Biokepi_bfx_tools.Gatk.Configuration.indel_realigner ->
[ `Bam ] repr -> [ `Bam ] repr
val gatk_indel_realigner_joint :
?configuration:Biokepi_bfx_tools.Gatk.Configuration.indel_realigner ->
([ `Bam ] * [ `Bam ]) repr -> ([ `Bam ] * [ `Bam ]) repr
val picard_mark_duplicates :
?configuration:Biokepi_bfx_tools.Picard.Mark_duplicates_settings.t ->
[ `Bam ] repr -> [ `Bam ] repr
val gatk_bqsr :
?configuration:Biokepi_bfx_tools.Gatk.Configuration.bqsr ->
[ `Bam ] repr -> [ `Bam ] repr
val seq2hla : [ `Fastq ] repr -> [ `Seq2hla_result ] repr
val optitype :
[ `DNA | `RNA ] -> [ `Fastq ] repr -> [ `Optitype_result ] repr
val gatk_haplotype_caller : [ `Bam ] repr -> [ `Vcf ] repr
val mutect :
?configuration:Biokepi_bfx_tools.Mutect.Configuration.t ->
normal:[ `Bam ] repr ->
tumor:[ `Bam ] repr -> unit -> [ `Vcf ] repr
val mutect2 :
?configuration:Biokepi_bfx_tools.Gatk.Configuration.Mutect2.t ->
normal:[ `Bam ] repr ->
tumor:[ `Bam ] repr -> unit -> [ `Vcf ] repr
val somaticsniper :
?configuration:Biokepi_bfx_tools.Somaticsniper.Configuration.t ->
normal:[ `Bam ] repr ->
tumor:[ `Bam ] repr -> unit -> [ `Vcf ] repr
val varscan_somatic :
?adjust_mapq:int ->
normal:[ `Bam ] repr ->
tumor:[ `Bam ] repr -> unit -> [ `Vcf ] repr
val strelka :
?configuration:Biokepi_bfx_tools.Strelka.Configuration.t ->
normal:[ `Bam ] repr ->
tumor:[ `Bam ] repr -> unit -> [ `Vcf ] repr
val virmid :
?configuration:Biokepi_bfx_tools.Virmid.Configuration.t ->
normal:[ `Bam ] repr ->
tumor:[ `Bam ] repr -> unit -> [ `Vcf ] repr
val muse :
?configuration:Biokepi_bfx_tools.Muse.Configuration.t ->
normal:[ `Bam ] repr ->
tumor:[ `Bam ] repr -> unit -> [ `Vcf ] repr
end
end