Commit 3e834749 authored by pjvan_thof's avatar pjvan_thof

Moving scatter and gather functions to a new package

parent 23f8f923
......@@ -17,8 +17,9 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.extensions.gatk.scatter.{GATKScatterFunction, LocusScatterFunction}
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Output, _}
class AnalyzeCovariates(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "AnalyzeCovariates"
......
......@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.extensions.gatk.gather.GatherVcfs
import nl.lumc.sasc.biopet.extensions.gatk.scatter.{GATKScatterFunction, LocusScatterFunction}
import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Input, Output }
import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Input, Output}
class ApplyRecalibration(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "ApplyRecalibration"
......@@ -41,7 +43,7 @@ class ApplyRecalibration(val parent: Configurable) extends CommandLineGATK with
/** The output filtered and recalibrated VCF file in which each variant is annotated with its VQSLOD value */
@Output(fullName = "out", shortName = "o", doc = "The output filtered and recalibrated VCF file in which each variant is annotated with its VQSLOD value", required = false, exclusiveOf = "", validation = "")
@Gather(classOf[CatVariantsGatherer])
@Gather(classOf[GatherVcfs])
var out: File = _
/** The truth sensitivity level at which to start filtering */
......
......@@ -17,10 +17,11 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.extensions.gatk.scatter.{ContigScatterFunction, GATKScatterFunction}
import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, Input }
import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Input, Output}
class BaseRecalibrator(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "BaseRecalibrator"
......
......@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.extensions.gatk.gather.GatherVcfs
import nl.lumc.sasc.biopet.extensions.gatk.scatter.{GATKScatterFunction, LocusScatterFunction}
import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.utils.commandline.{ Gather, Input, Output, _ }
import org.broadinstitute.gatk.utils.commandline.{Gather, Input, Output, _}
class CombineGVCFs(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "CombineGVCFs"
......@@ -45,7 +47,7 @@ class CombineGVCFs(val parent: Configurable) extends CommandLineGATK with Scatte
/** File to which the combined gVCF should be written */
@Output(fullName = "out", shortName = "o", doc = "File to which the combined gVCF should be written", required = false, exclusiveOf = "", validation = "")
@Gather(classOf[CatVariantsGatherer])
@Gather(classOf[GatherVcfs])
var out: File = _
/** If specified, convert banded gVCFs to all-sites gVCFs */
......
......@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.extensions.gatk.gather.GatherVcfs
import nl.lumc.sasc.biopet.extensions.gatk.scatter.{GATKScatterFunction, LocusScatterFunction}
import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Output, _}
class CombineVariants(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "CombineVariants"
......@@ -33,7 +35,7 @@ class CombineVariants(val parent: Configurable) extends CommandLineGATK with Sca
/** File to which variants should be written */
@Output(fullName = "out", shortName = "o", doc = "File to which variants should be written", required = false, exclusiveOf = "", validation = "")
@Gather(classOf[CatVariantsGatherer])
@Gather(classOf[GatherVcfs])
var out: File = _
/** Determines how we should merge genotype records for samples shared across the ROD files */
......
......@@ -18,11 +18,12 @@ import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.core.summary.Summarizable
import nl.lumc.sasc.biopet.extensions.gatk.scatter.{GATKScatterFunction, LocusScatterFunction}
import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
import org.broadinstitute.gatk.utils.report.{ GATKReport, GATKReportTable }
import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Output, _}
import org.broadinstitute.gatk.utils.report.{GATKReport, GATKReportTable}
class GenotypeConcordance(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction with Summarizable {
analysisName = "GenotypeConcordance"
......
......@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.extensions.gatk.gather.GatherVcfs
import nl.lumc.sasc.biopet.extensions.gatk.scatter.{GATKScatterFunction, LocusScatterFunction}
import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Output, _}
class GenotypeGVCFs(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "GenotypeGVCFs"
......@@ -33,7 +35,7 @@ class GenotypeGVCFs(val parent: Configurable) extends CommandLineGATK with Scatt
/** File to which variants should be written */
@Output(fullName = "out", shortName = "o", doc = "File to which variants should be written", required = false, exclusiveOf = "", validation = "")
@Gather(classOf[CatVariantsGatherer])
@Gather(classOf[GatherVcfs])
var out: File = _
/** Include loci found to be non-variant after genotyping */
......
......@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.extensions.gatk.gather.{CatVariantsGatherer, MergeSamFiles}
import nl.lumc.sasc.biopet.extensions.gatk.scatter.{GATKScatterFunction, LocusScatterFunction}
import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Input, Output }
import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Input, Output}
class HaplotypeCaller(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "HaplotypeCaller"
......
......@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.extensions.gatk.gather.MergeSamFiles
import nl.lumc.sasc.biopet.extensions.gatk.scatter.{ContigScatterFunction, GATKScatterFunction}
import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Output, _}
class IndelRealigner(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "IndelRealigner"
......
......@@ -3,6 +3,8 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.extensions.gatk.gather.GatherVcfs
import nl.lumc.sasc.biopet.extensions.gatk.scatter.{GATKScatterFunction, LocusScatterFunction}
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Input, Output}
......@@ -31,7 +33,7 @@ class MuTect2(val parent: Configurable) extends CommandLineGATK with ScatterGath
/** Output file of the program. */
@Output(fullName = "out", shortName = "o", required = false)
@Gather(classOf[CatVariantsGatherer])
@Gather(classOf[GatherVcfs])
var outputVcf: File = _
/**
......
......@@ -17,6 +17,8 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.extensions.gatk.gather.MergeSamFiles
import nl.lumc.sasc.biopet.extensions.gatk.scatter.{ContigScatterFunction, GATKScatterFunction}
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline._
......
......@@ -17,10 +17,11 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.extensions.gatk.scatter.{GATKScatterFunction, LocusScatterFunction}
import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Input, _ }
import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Input, _}
class RealignerTargetCreator(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "RealignerTargetCreator"
......
......@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.extensions.gatk.gather.GatherVcfs
import nl.lumc.sasc.biopet.extensions.gatk.scatter.{GATKScatterFunction, LocusScatterFunction}
import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Output, _}
class SelectVariants(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "SelectVariants"
......@@ -41,7 +43,7 @@ class SelectVariants(val parent: Configurable) extends CommandLineGATK with Scat
/** File to which variants should be written */
@Output(fullName = "out", shortName = "o", doc = "File to which variants should be written", required = false, exclusiveOf = "", validation = "")
@Gather(classOf[CatVariantsGatherer])
@Gather(classOf[GatherVcfs])
var out: File = _
/** Include genotypes from this sample */
......
......@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.extensions.gatk.gather.GatherVcfs
import nl.lumc.sasc.biopet.extensions.gatk.scatter.{GATKScatterFunction, LocusScatterFunction}
import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.utils.commandline.{ Gather, Input, Output, _ }
import org.broadinstitute.gatk.utils.commandline.{Gather, Input, Output, _}
class UnifiedGenotyper(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "UnifiedGenotyper"
......@@ -221,7 +223,7 @@ class UnifiedGenotyper(val parent: Configurable) extends CommandLineGATK with Sc
/** File to which variants should be written */
@Output(fullName = "out", shortName = "o", doc = "File to which variants should be written", required = false, exclusiveOf = "", validation = "")
@Gather(classOf[CatVariantsGatherer])
@Gather(classOf[GatherVcfs])
var out: File = _
/** If provided, only these samples will be emitted into the VCF, regardless of which samples are present in the BAM file */
......
......@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.extensions.gatk.gather.CatVariantsGatherer
import nl.lumc.sasc.biopet.extensions.gatk.scatter.{GATKScatterFunction, LocusScatterFunction}
import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Output, _}
class VariantAnnotator(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "VariantAnnotator"
......
......@@ -16,10 +16,11 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.extensions.gatk.gather.GatherVcfs
import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.utils.commandline.{ Gather, Input, Output, _ }
import org.broadinstitute.gatk.utils.commandline.{Gather, Input, Output, _}
class VariantRecalibrator(val parent: Configurable) extends CommandLineGATK {
def analysis_type = "VariantRecalibrator"
......@@ -122,7 +123,7 @@ class VariantRecalibrator(val parent: Configurable) extends CommandLineGATK {
/** The output recal file used by ApplyRecalibration */
@Output(fullName = "recal_file", shortName = "recalFile", doc = "The output recal file used by ApplyRecalibration", required = true, exclusiveOf = "", validation = "")
@Gather(classOf[CatVariantsGatherer])
@Gather(classOf[GatherVcfs])
var recal_file: File = _
/** The output tranches file used by ApplyRecalibration */
......
......@@ -12,14 +12,14 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package nl.lumc.sasc.biopet.extensions.gatk
package nl.lumc.sasc.biopet.extensions.gatk.gather
import java.io.File
import java.util
import org.broadinstitute.gatk.engine.recalibration.BQSRGatherer
import org.broadinstitute.gatk.queue.function.InProcessFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
/**
* Created by pjvanthof on 05/04/2017.
......
......@@ -12,9 +12,10 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package nl.lumc.sasc.biopet.extensions.gatk
package nl.lumc.sasc.biopet.extensions.gatk.gather
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.extensions.gatk.{CatVariants, CommandLineGATK}
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.queue.function.scattergather.GatherFunction
......
package nl.lumc.sasc.biopet.extensions.gatk.gather
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.extensions.gatk.CommandLineGATK
import nl.lumc.sasc.biopet.extensions.picard
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.queue.function.scattergather.GatherFunction
/**
* Created by pjvan_thof on 12-7-17.
*/
class GatherVcfs extends picard.GatherVcfs(null) with GatherFunction {
analysisName = "Gather_CatVariants"
override val parent = originalFunction match {
case b: BiopetCommandLineFunction => b
case _ => null
}
override def freezeFieldValues() {
val originalGATK = this.originalFunction.asInstanceOf[CommandLineGATK]
this.input = this.gatherParts.zipWithIndex map { case (input, index) => new TaggedFile(input, "input" + index) }
this.output = this.originalOutput
super.freezeFieldValues()
}
}
......@@ -12,9 +12,10 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package nl.lumc.sasc.biopet.extensions.gatk
package nl.lumc.sasc.biopet.extensions.gatk.gather
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.extensions.gatk.CommandLineGATK
import nl.lumc.sasc.biopet.extensions.picard
import org.broadinstitute.gatk.queue.function.scattergather.GatherFunction
......
......@@ -12,7 +12,7 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package nl.lumc.sasc.biopet.extensions.gatk
package nl.lumc.sasc.biopet.extensions.gatk.scatter
import org.broadinstitute.gatk.queue.function.InProcessFunction
import org.broadinstitute.gatk.utils.interval.IntervalUtils
......
......@@ -12,12 +12,13 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package nl.lumc.sasc.biopet.extensions.gatk
package nl.lumc.sasc.biopet.extensions.gatk.scatter
import java.io.File
import nl.lumc.sasc.biopet.extensions.gatk.CommandLineGATK
import org.broadinstitute.gatk.queue.extensions.gatk.GATKIntervals
import org.broadinstitute.gatk.queue.function.scattergather.{ CloneFunction, ScatterFunction }
import org.broadinstitute.gatk.queue.function.scattergather.{CloneFunction, ScatterFunction}
import org.broadinstitute.gatk.utils.commandline.Output
import org.broadinstitute.gatk.utils.interval.IntervalUtils
import org.broadinstitute.gatk.utils.io.IOUtils
......
......@@ -12,7 +12,7 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package nl.lumc.sasc.biopet.extensions.gatk
package nl.lumc.sasc.biopet.extensions.gatk.scatter
import org.broadinstitute.gatk.queue.function.InProcessFunction
import org.broadinstitute.gatk.utils.interval.IntervalUtils
......
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
class GatherVcfs(val parent: Configurable) extends Picard {
@Input(doc = "The input SAM or BAM files to analyze.", required = true)
var input: Seq[File] = Nil
@Output(doc = "The output file to bam file to", required = true)
var output: File = _
override def cmdLine =
super.cmdLine +
repeat("INPUT=", input, spaceSeparated = false) +
required("OUTPUT=", output, spaceSeparated = false)
}
......@@ -20,6 +20,7 @@ import nl.lumc.sasc.biopet.core.extensions.CheckValidateVcf
import nl.lumc.sasc.biopet.core.{PipelineCommand, Reference}
import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import nl.lumc.sasc.biopet.extensions.gatk._
import nl.lumc.sasc.biopet.extensions.gatk.gather.BqsrGather
import nl.lumc.sasc.biopet.extensions.tools.ValidateVcf
import nl.lumc.sasc.biopet.pipelines.bammetrics.TargetRegions
import nl.lumc.sasc.biopet.pipelines.kopisu.Kopisu
......
......@@ -20,7 +20,7 @@
package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
import nl.lumc.sasc.biopet.extensions.gatk
import nl.lumc.sasc.biopet.extensions.gatk.BqsrGather
import nl.lumc.sasc.biopet.extensions.gatk.gather.BqsrGather
import nl.lumc.sasc.biopet.utils.config.Configurable
/** Default mode for the haplotypecaller */
......
......@@ -20,7 +20,7 @@
package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
import nl.lumc.sasc.biopet.extensions.gatk
import nl.lumc.sasc.biopet.extensions.gatk.BqsrGather
import nl.lumc.sasc.biopet.extensions.gatk.gather.BqsrGather
import nl.lumc.sasc.biopet.utils.config.Configurable
/** Allele mode for Haplotypecaller */
......
......@@ -20,7 +20,7 @@
package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
import nl.lumc.sasc.biopet.extensions.gatk
import nl.lumc.sasc.biopet.extensions.gatk.BqsrGather
import nl.lumc.sasc.biopet.extensions.gatk.gather.BqsrGather
import nl.lumc.sasc.biopet.utils.config.Configurable
/** Default mode for UnifiedGenotyper */
......
......@@ -20,7 +20,7 @@
package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
import nl.lumc.sasc.biopet.extensions.gatk
import nl.lumc.sasc.biopet.extensions.gatk.BqsrGather
import nl.lumc.sasc.biopet.extensions.gatk.gather.BqsrGather
import nl.lumc.sasc.biopet.utils.config.Configurable
/** Allele mode for GenotyperAllele */
......
package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.somatic
import nl.lumc.sasc.biopet.extensions.bcftools.BcftoolsReheader
import nl.lumc.sasc.biopet.extensions.gatk.{BqsrGather, CombineVariants}
import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import nl.lumc.sasc.biopet.extensions._
import nl.lumc.sasc.biopet.extensions.gatk.gather.BqsrGather
import nl.lumc.sasc.biopet.utils.{IoUtils, Logging}
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
......
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