Module All_downloads.Ref_genome (.ml)

module Ref_genome: Biokepi_run_environment.Reference_genome

type name = string

module Specification: sig .. end

type t = {

	`specification : Specification.t;`
	`location : Biokepi_run_environment.Common.KEDSL.file_workflow;`
	`cosmic : Biokepi_run_environment.Common.KEDSL.file_workflow option;`
	`dbsnp : Biokepi_run_environment.Common.KEDSL.file_workflow option;`
	`known_indels : Biokepi_run_environment.Common.KEDSL.file_workflow option;`
	`gtf : Biokepi_run_environment.Common.KEDSL.file_workflow option;`
	`cdna : Biokepi_run_environment.Common.KEDSL.file_workflow option;`
	`whess : Biokepi_run_environment.Common.KEDSL.file_workflow option;`

}

A reference genome has a name (for display/matching) and a cluster-dependent path. Corresponding Cosmic and dbSNP databases (VCFs) can be added to the mix.

val create : ?cosmic:Biokepi_run_environment.Common.KEDSL.file_workflow ->
       ?dbsnp:Biokepi_run_environment.Common.KEDSL.file_workflow ->
       ?known_indels:Biokepi_run_environment.Common.KEDSL.file_workflow ->
       ?gtf:Biokepi_run_environment.Common.KEDSL.file_workflow ->
       ?cdna:Biokepi_run_environment.Common.KEDSL.file_workflow ->
       ?whess:Biokepi_run_environment.Common.KEDSL.file_workflow ->
       Specification.t ->
       Biokepi_run_environment.Common.KEDSL.file_workflow ->
       t

val name : t -> string

val ensembl : t -> int

val species : t -> string

val snpeff_name_exn : t -> string

val path : t -> string

val cosmic_path_exn : t -> string

val dbsnp_path_exn : t -> string

val known_indels_path_exn : t -> string

val gtf_path_exn : t -> string

val cdna_path_exn : t -> string

val whess_path_exn : t -> string

val fasta : t ->
       Biokepi_run_environment.Common.KEDSL.file_workflow

val cosmic_exn : t ->
       Biokepi_run_environment.Common.KEDSL.file_workflow

val dbsnp_exn : t ->
       Biokepi_run_environment.Common.KEDSL.file_workflow

val known_indels_exn : t ->
       Biokepi_run_environment.Common.KEDSL.file_workflow

val gtf_exn : t ->
       Biokepi_run_environment.Common.KEDSL.file_workflow

val gtf : t ->
       Biokepi_run_environment.Common.KEDSL.file_workflow option

val cdna_exn : t ->
       Biokepi_run_environment.Common.KEDSL.file_workflow

val whess_exn : t ->
       Biokepi_run_environment.Common.KEDSL.file_workflow

val major_contigs : t -> Region.t list