Module Biokepi_bfx_tools.Varscan (.ml)

module Varscan: sig .. end

module Remove: Biokepi_run_environment.Workflow_utilities.Remove

Expects the tool "varscan" to provide the environment variable "$VARSCAN_JAR".

val empty_vcf : string

val somatic_on_region : run_with:Biokepi_run_environment.Machine.t ->
       ?adjust_mapq:int ->
       normal:Biokepi_run_environment.Common.KEDSL.bam_file
              Biokepi_run_environment.Common.KEDSL.workflow_node ->
       tumor:Biokepi_run_environment.Common.KEDSL.bam_file
             Biokepi_run_environment.Common.KEDSL.workflow_node ->
       result_prefix:string ->
       [< `Chromosome of string | `Chromosome_interval of string * int * int | `Full ] ->
       < as_single_file : Biokepi_run_environment.Common.KEDSL.single_file
                          Biokepi_run_environment.Common.KEDSL.product;
         host : Biokepi_run_environment.Common.KEDSL.Host.t;
         is_done : Biokepi_run_environment.Common.KEDSL.Condition.t option;
         path : string; reference_build : string >
       Biokepi_run_environment.Common.KEDSL.workflow_node

val somatic_map_reduce : ?more_edges:Biokepi_run_environment.Common.KEDSL.workflow_edge list ->
       run_with:Biokepi_run_environment.Machine.t ->
       ?adjust_mapq:int ->
       normal:Biokepi_run_environment.Common.KEDSL.bam_file
              Biokepi_run_environment.Common.KEDSL.workflow_node ->
       tumor:Biokepi_run_environment.Common.KEDSL.bam_file
             Biokepi_run_environment.Common.KEDSL.workflow_node ->
       result_prefix:string ->
       unit ->
       < as_single_file : Biokepi_run_environment.Common.KEDSL.single_file
                          Biokepi_run_environment.Common.KEDSL.product;
         host : Biokepi_run_environment.Common.KEDSL.Host.t;
         is_done : Biokepi_run_environment.Common.KEDSL.Condition.t option;
         path : string; reference_build : string >
       Biokepi_run_environment.Common.KEDSL.workflow_node