Commit f2e835df authored by Peter van 't Hof's avatar Peter van 't Hof

Move package

parent 14f35a60
......@@ -7,8 +7,8 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Created by pjvanthof on 30/03/16.
*/
* Created by pjvanthof on 30/03/16.
*/
class Grep(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Input file", required = true)
var input: File = _
......
package nl.lumc.sasc.biopet.extensions.gatk.broad
package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
class AnalyzeCovariates(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
......
package nl.lumc.sasc.biopet.extensions.gatk.broad
package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.utils.VcfUtils
import org.broadinstitute.gatk.utils.commandline.Argument
import org.broadinstitute.gatk.utils.commandline.Gather
import org.broadinstitute.gatk.utils.commandline.Input
import org.broadinstitute.gatk.utils.commandline.Output
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 }
class ApplyRecalibration(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "ApplyRecalibration"
......
package nl.lumc.sasc.biopet.extensions.gatk.broad
import org.broadinstitute.gatk.queue.function.scattergather.GatherFunction
package nl.lumc.sasc.biopet.extensions.gatk
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.extensions.picard.MergeSamFiles
import org.broadinstitute.gatk.queue.function.scattergather.GatherFunction
/**
* Merges BAM files using htsjdk.samtools.MergeSamFiles.
......
package nl.lumc.sasc.biopet.extensions.gatk.broad
package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.{ TaggedFile }
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
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, _ }
//TODO: check gathering
......
package nl.lumc.sasc.biopet.extensions.gatk.broad
package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.Argument
import org.broadinstitute.gatk.utils.commandline.Gather
import org.broadinstitute.gatk.utils.commandline.Input
import org.broadinstitute.gatk.utils.commandline.Output
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Input, Output }
class CatVariants(val root: Configurable) extends BiopetJavaCommandLineFunction {
analysisName = "CatVariants"
......
package nl.lumc.sasc.biopet.extensions.gatk.broad
package nl.lumc.sasc.biopet.extensions.gatk
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
......
package nl.lumc.sasc.biopet.extensions.gatk.broad
package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
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, _ }
class CombineGVCFs(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
......
package nl.lumc.sasc.biopet.extensions.gatk.broad
package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
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, _ }
class CombineVariants(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
......
package nl.lumc.sasc.biopet.extensions.gatk.broad
package nl.lumc.sasc.biopet.extensions.gatk
import collection.JavaConversions._
import org.broadinstitute.gatk.utils.interval.IntervalUtils
import org.broadinstitute.gatk.queue.function.InProcessFunction
import org.broadinstitute.gatk.utils.interval.IntervalUtils
import scala.collection.JavaConversions._
/**
* Splits intervals by contig instead of evenly.
......
package nl.lumc.sasc.biopet.extensions.gatk.broad
package nl.lumc.sasc.biopet.extensions.gatk
import org.broadinstitute.gatk.utils.interval.IntervalUtils
import java.io.File
import org.broadinstitute.gatk.queue.extensions.gatk.GATKIntervals
import org.broadinstitute.gatk.utils.io.IOUtils
import org.broadinstitute.gatk.queue.function.scattergather.{ CloneFunction, ScatterFunction }
import org.broadinstitute.gatk.utils.commandline.{ Output, _ }
import org.broadinstitute.gatk.utils.commandline.Output
import org.broadinstitute.gatk.utils.interval.IntervalUtils
import org.broadinstitute.gatk.utils.io.IOUtils
trait GATKScatterFunction extends ScatterFunction {
/* The runtime field to set for specifying intervals. */
......
package nl.lumc.sasc.biopet.extensions.gatk.broad
package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
......@@ -7,8 +7,8 @@ import nl.lumc.sasc.biopet.core.summary.Summarizable
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 root: Configurable) extends CommandLineGATK with ScatterGatherableFunction with Summarizable {
analysisName = "GenotypeConcordance"
......@@ -17,48 +17,48 @@ class GenotypeConcordance(val root: Configurable) extends CommandLineGATK with S
setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = false }
/** The variants and genotypes to evaluate */
@Input(fullName="eval", shortName="eval", doc="The variants and genotypes to evaluate", required=true, exclusiveOf="", validation="")
@Input(fullName = "eval", shortName = "eval", doc = "The variants and genotypes to evaluate", required = true, exclusiveOf = "", validation = "")
var eval: File = _
/** The variants and genotypes to compare against */
@Input(fullName="comp", shortName="comp", doc="The variants and genotypes to compare against", required=true, exclusiveOf="", validation="")
@Input(fullName = "comp", shortName = "comp", doc = "The variants and genotypes to compare against", required = true, exclusiveOf = "", validation = "")
var comp: File = _
/** Filters will be ignored */
@Argument(fullName="ignoreFilters", shortName="", doc="Filters will be ignored", required=false, exclusiveOf="", validation="")
@Argument(fullName = "ignoreFilters", shortName = "", doc = "Filters will be ignored", required = false, exclusiveOf = "", validation = "")
var ignoreFilters: Boolean = config("ignoreFilters", default = false)
/** One or more criteria to use to set EVAL genotypes to no-call. These genotype-level filters are only applied to the EVAL rod. */
@Argument(fullName="genotypeFilterExpressionEval", shortName="gfe", doc="One or more criteria to use to set EVAL genotypes to no-call. These genotype-level filters are only applied to the EVAL rod.", required=false, exclusiveOf="", validation="")
@Argument(fullName = "genotypeFilterExpressionEval", shortName = "gfe", doc = "One or more criteria to use to set EVAL genotypes to no-call. These genotype-level filters are only applied to the EVAL rod.", required = false, exclusiveOf = "", validation = "")
var genotypeFilterExpressionEval: List[String] = config("genotypeFilterExpressionEval", default = Nil)
/** One or more criteria to use to set COMP genotypes to no-call. These genotype-level filters are only applied to the COMP rod. */
@Argument(fullName="genotypeFilterExpressionComp", shortName="gfc", doc="One or more criteria to use to set COMP genotypes to no-call. These genotype-level filters are only applied to the COMP rod.", required=false, exclusiveOf="", validation="")
@Argument(fullName = "genotypeFilterExpressionComp", shortName = "gfc", doc = "One or more criteria to use to set COMP genotypes to no-call. These genotype-level filters are only applied to the COMP rod.", required = false, exclusiveOf = "", validation = "")
var genotypeFilterExpressionComp: Seq[String] = config("genotypeFilterExpressionComp", default = Nil)
/** Molten rather than tabular output */
@Argument(fullName="moltenize", shortName="moltenize", doc="Molten rather than tabular output", required=false, exclusiveOf="", validation="")
@Argument(fullName = "moltenize", shortName = "moltenize", doc = "Molten rather than tabular output", required = false, exclusiveOf = "", validation = "")
var moltenize: Boolean = config("moltenize", default = true)
/** File to output the discordant sites and genotypes. */
@Output(fullName="printInterestingSites", shortName="sites", doc="File to output the discordant sites and genotypes.", required=false, exclusiveOf="", validation="")
@Output(fullName = "printInterestingSites", shortName = "sites", doc = "File to output the discordant sites and genotypes.", required = false, exclusiveOf = "", validation = "")
var printInterestingSites: Option[File] = None
/** An output file created by the walker. Will overwrite contents if file exists */
@Output(fullName="out", shortName="o", doc="An output file created by the walker. Will overwrite contents if file exists", required=false, exclusiveOf="", validation="")
@Output(fullName = "out", shortName = "o", doc = "An output file created by the walker. Will overwrite contents if file exists", required = false, exclusiveOf = "", validation = "")
@Gather(classOf[org.broadinstitute.gatk.queue.function.scattergather.SimpleTextGatherFunction])
var out: File = _
/** Filter out reads with CIGAR containing the N operator, instead of failing with an error */
@Argument(fullName="filter_reads_with_N_cigar", shortName="filterRNC", doc="Filter out reads with CIGAR containing the N operator, instead of failing with an error", required=false, exclusiveOf="", validation="")
@Argument(fullName = "filter_reads_with_N_cigar", shortName = "filterRNC", doc = "Filter out reads with CIGAR containing the N operator, instead of failing with an error", required = false, exclusiveOf = "", validation = "")
var filter_reads_with_N_cigar: Boolean = config("filter_reads_with_N_cigar", default = false)
/** Filter out reads with mismatching numbers of bases and base qualities, instead of failing with an error */
@Argument(fullName="filter_mismatching_base_and_quals", shortName="filterMBQ", doc="Filter out reads with mismatching numbers of bases and base qualities, instead of failing with an error", required=false, exclusiveOf="", validation="")
@Argument(fullName = "filter_mismatching_base_and_quals", shortName = "filterMBQ", doc = "Filter out reads with mismatching numbers of bases and base qualities, instead of failing with an error", required = false, exclusiveOf = "", validation = "")
var filter_mismatching_base_and_quals: Boolean = config("filter_mismatching_base_and_quals", default = false)
/** Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error */
@Argument(fullName="filter_bases_not_stored", shortName="filterNoBases", doc="Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error", required=false, exclusiveOf="", validation="")
@Argument(fullName = "filter_bases_not_stored", shortName = "filterNoBases", doc = "Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error", required = false, exclusiveOf = "", validation = "")
var filter_bases_not_stored: Boolean = config("filter_bases_not_stored", default = false)
def summaryFiles = Map("output" -> out)
......@@ -100,7 +100,6 @@ class GenotypeConcordance(val root: Configurable) extends CommandLineGATK with S
)
}
override def beforeGraph() {
super.beforeGraph()
if (eval != null) deps :+= VcfUtils.getVcfIndexFile(eval)
......@@ -108,15 +107,15 @@ class GenotypeConcordance(val root: Configurable) extends CommandLineGATK with S
}
override def cmdLine = super.cmdLine +
required(TaggedFile.formatCommandLineParameter("-eval", eval), eval, spaceSeparated=true, escape=true, format="%s") +
required(TaggedFile.formatCommandLineParameter("-comp", comp), comp, spaceSeparated=true, escape=true, format="%s") +
conditional(ignoreFilters, "--ignoreFilters", escape=true, format="%s") +
repeat("-gfe", genotypeFilterExpressionEval, spaceSeparated=true, escape=true, format="%s") +
repeat("-gfc", genotypeFilterExpressionComp, spaceSeparated=true, escape=true, format="%s") +
conditional(moltenize, "-moltenize", escape=true, format="%s") +
optional("-sites", printInterestingSites, spaceSeparated=true, escape=true, format="%s") +
optional("-o", out, spaceSeparated=true, escape=true, format="%s") +
conditional(filter_reads_with_N_cigar, "-filterRNC", escape=true, format="%s") +
conditional(filter_mismatching_base_and_quals, "-filterMBQ", escape=true, format="%s") +
conditional(filter_bases_not_stored, "-filterNoBases", escape=true, format="%s")
required(TaggedFile.formatCommandLineParameter("-eval", eval), eval, spaceSeparated = true, escape = true, format = "%s") +
required(TaggedFile.formatCommandLineParameter("-comp", comp), comp, spaceSeparated = true, escape = true, format = "%s") +
conditional(ignoreFilters, "--ignoreFilters", escape = true, format = "%s") +
repeat("-gfe", genotypeFilterExpressionEval, spaceSeparated = true, escape = true, format = "%s") +
repeat("-gfc", genotypeFilterExpressionComp, spaceSeparated = true, escape = true, format = "%s") +
conditional(moltenize, "-moltenize", escape = true, format = "%s") +
optional("-sites", printInterestingSites, spaceSeparated = true, escape = true, format = "%s") +
optional("-o", out, spaceSeparated = true, escape = true, format = "%s") +
conditional(filter_reads_with_N_cigar, "-filterRNC", escape = true, format = "%s") +
conditional(filter_mismatching_base_and_quals, "-filterMBQ", escape = true, format = "%s") +
conditional(filter_bases_not_stored, "-filterNoBases", escape = true, format = "%s")
}
package nl.lumc.sasc.biopet.extensions.gatk.broad
package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
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, _ }
class GenotypeGVCFs(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
......
package nl.lumc.sasc.biopet.extensions.gatk.broad
package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
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 }
......
package nl.lumc.sasc.biopet.extensions.gatk.broad
package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
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, _ }
class IndelRealigner(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
......
package nl.lumc.sasc.biopet.extensions.gatk.broad
package nl.lumc.sasc.biopet.extensions.gatk
import collection.JavaConversions._
import org.broadinstitute.gatk.utils.interval.IntervalUtils
import org.broadinstitute.gatk.queue.function.InProcessFunction
import org.broadinstitute.gatk.utils.interval.IntervalUtils
import scala.collection.JavaConversions._
/**
* A scatter function that divides down to the locus level.
......
package nl.lumc.sasc.biopet.extensions.gatk.broad
package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline._
class PrintReads(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
......
package nl.lumc.sasc.biopet.extensions.gatk.broad
package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.{ TaggedFile }
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
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, _ }
class RealignerTargetCreator(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
......
package nl.lumc.sasc.biopet.extensions.gatk.broad
package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
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, _ }
class SelectVariants(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
......
package nl.lumc.sasc.biopet.extensions.gatk.broad
package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
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, _ }
class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
......
package nl.lumc.sasc.biopet.extensions.gatk.broad
package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import java.io.File
import org.broadinstitute.gatk.utils.commandline.Argument
import org.broadinstitute.gatk.utils.commandline.Gather
import org.broadinstitute.gatk.utils.commandline.Input
import org.broadinstitute.gatk.utils.commandline.Output
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Input, Output }
class VariantEval(val root: Configurable) extends CommandLineGATK {
def analysis_type = "VariantEval"
......
......@@ -24,14 +24,14 @@ import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, BiopetQScript, Pipe
import nl.lumc.sasc.biopet.extensions._
import nl.lumc.sasc.biopet.extensions.bowtie.{ Bowtie2Build, BowtieBuild }
import nl.lumc.sasc.biopet.extensions.bwa.BwaIndex
import nl.lumc.sasc.biopet.extensions.gatk.broad.CombineVariants
import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import nl.lumc.sasc.biopet.extensions.gmap.GmapBuild
import nl.lumc.sasc.biopet.extensions.picard.CreateSequenceDictionary
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFaidx
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QScript
import scala.language.reflectiveCalls
import scala.language.reflectiveCalls
import scala.collection.JavaConversions._
class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript {
......
......@@ -6,7 +6,7 @@ import java.util
import htsjdk.samtools.reference.FastaSequenceFile
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand, Reference }
import nl.lumc.sasc.biopet.extensions.Snptest
import nl.lumc.sasc.biopet.extensions.gatk.broad.{ CatVariants, SelectVariants }
import nl.lumc.sasc.biopet.extensions.gatk.{ CatVariants, SelectVariants }
import nl.lumc.sasc.biopet.extensions.tools.{ GensToVcf, SnptestToVcf }
import nl.lumc.sasc.biopet.pipelines.gwastest.impute.ImputeOutput
import nl.lumc.sasc.biopet.utils.Logging
......@@ -105,7 +105,7 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
bedFile.deleteOnExit()
val sv = new SelectVariants(this)
sv.variant :+= chrVcfFiles.getOrElse(region.chr, vcfFile)
sv.variant = chrVcfFiles.getOrElse(region.chr, vcfFile)
sv.out = new File(regionDir, s"$name.vcf.gz")
sv.intervals :+= bedFile
sv.isIntermediate = true
......
......@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.shiva
import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference }
import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import nl.lumc.sasc.biopet.extensions.gatk.broad._
import nl.lumc.sasc.biopet.extensions.gatk._
import nl.lumc.sasc.biopet.pipelines.bammetrics.TargetRegions
import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingTrait
import nl.lumc.sasc.biopet.pipelines.toucan.Toucan
......
......@@ -15,15 +15,15 @@
*/
package nl.lumc.sasc.biopet.pipelines.shiva
import nl.lumc.sasc.biopet.core.{PipelineCommand, Reference, SampleLibraryTag}
import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, SampleLibraryTag }
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.Tabix
import nl.lumc.sasc.biopet.extensions.gatk.broad.{CombineVariants, GenotypeConcordance}
import nl.lumc.sasc.biopet.extensions.gatk.{ CombineVariants, GenotypeConcordance }
import nl.lumc.sasc.biopet.extensions.tools.VcfStats
import nl.lumc.sasc.biopet.extensions.vt.{VtDecompose, VtNormalize}
import nl.lumc.sasc.biopet.extensions.vt.{ VtDecompose, VtNormalize }
import nl.lumc.sasc.biopet.pipelines.bammetrics.TargetRegions
import nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.{VarscanCnsSingleSample, _}
import nl.lumc.sasc.biopet.utils.{BamUtils, Logging}
import nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.{ VarscanCnsSingleSample, _ }
import nl.lumc.sasc.biopet.utils.{ BamUtils, Logging }
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
......@@ -88,7 +88,7 @@ class ShivaVariantcalling(val root: Configurable) extends QScript
val cv = new CombineVariants(qscript)
cv.out = finalFile
cv.setKey = "VariantCaller"
cv.setKey = Some("VariantCaller")
cv.genotypemergeoption = Some("PRIORITIZE")
cv.rod_priority_list = Some(callers.map(_.name).mkString(","))
for (caller <- callers) {
......
......@@ -16,7 +16,7 @@
package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
import nl.lumc.sasc.biopet.extensions.delly.DellyCaller
import nl.lumc.sasc.biopet.extensions.gatk.broad.CatVariants
import nl.lumc.sasc.biopet.extensions.gatk.CatVariants
import nl.lumc.sasc.biopet.utils.config.Configurable
/** Script for sv caller delly */
......
......@@ -5,7 +5,7 @@
*/
package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
import nl.lumc.sasc.biopet.extensions.gatk.broad
import nl.lumc.sasc.biopet.extensions.gatk
import nl.lumc.sasc.biopet.utils.config.Configurable
/** Default mode for the haplotypecaller */
......@@ -14,7 +14,7 @@ class HaplotypeCaller(val root: Configurable) extends Variantcaller {
protected def defaultPrio = 1
def biopetScript() {
val hc = broad.HaplotypeCaller(this, inputBams.values.toList, outputFile)
val hc = gatk.HaplotypeCaller(this, inputBams.values.toList, outputFile)
add(hc)
}
}
......
......@@ -5,7 +5,7 @@
*/
package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
import nl.lumc.sasc.biopet.extensions.gatk.broad
import nl.lumc.sasc.biopet.extensions.gatk
import nl.lumc.sasc.biopet.utils.config.Configurable
/** Allele mode for Haplotypecaller */
......@@ -14,7 +14,7 @@ class HaplotypeCallerAllele(val root: Configurable) extends Variantcaller {
protected def defaultPrio = 5
def biopetScript() {
val hc = broad.HaplotypeCaller(this, inputBams.values.toList, outputFile)
val hc = gatk.HaplotypeCaller(this, inputBams.values.toList, outputFile)
hc.alleles = config("input_alleles")
hc.genotyping_mode = Some("GENOTYPE_GIVEN_ALLELES")
add(hc)
......
......@@ -5,7 +5,7 @@
*/
package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
import nl.lumc.sasc.biopet.extensions.gatk.broad
import nl.lumc.sasc.biopet.extensions.gatk
import nl.lumc.sasc.biopet.utils.config.Configurable
/** Gvcf mode for haplotypecaller */
......@@ -15,12 +15,12 @@ class HaplotypeCallerGvcf(val root: Configurable) extends Variantcaller {
def biopetScript() {
val gvcfFiles = for ((sample, inputBam) <- inputBams) yield {
val hc = broad.HaplotypeCaller.gvcf(this, inputBam, new File(outputDir, sample + ".gvcf.vcf.gz"))
val hc = gatk.HaplotypeCaller.gvcf(this, inputBam, new File(outputDir, sample + ".gvcf.vcf.gz"))
add(hc)
hc.out
}
val genotypeGVCFs = broad.GenotypeGVCFs(this, gvcfFiles.toList, outputFile)
val genotypeGVCFs = gatk.GenotypeGVCFs(this, gvcfFiles.toList, outputFile)
add(genotypeGVCFs)
}
}
......@@ -15,11 +15,9 @@
*/
package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
import java.io.File
import nl.lumc.sasc.biopet.extensions.gatk.broad.CombineVariants
import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
import nl.lumc.sasc.biopet.extensions.tools.{ VcfFilter, MpileupToVcf }
import nl.lumc.sasc.biopet.extensions.tools.{ MpileupToVcf, VcfFilter }
import nl.lumc.sasc.biopet.utils.config.Configurable
/** Makes a vcf file from a mpileup without statistics */
......@@ -62,7 +60,7 @@ class RawVcf(val root: Configurable) extends Variantcaller {
val cv = new CombineVariants(this)
cv.variant = rawFiles.toList
cv.out = outputFile
cv.setKey = "null"
cv.setKey = Some("null")
cv.excludeNonVariants = !keepRefCalls
add(cv)
}
......
......@@ -5,7 +5,7 @@
*/
package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
import nl.lumc.sasc.biopet.extensions.gatk.broad
import nl.lumc.sasc.biopet.extensions.gatk
import nl.lumc.sasc.biopet.utils.config.Configurable
/** Default mode for UnifiedGenotyper */
......@@ -14,7 +14,7 @@ class UnifiedGenotyper(val root: Configurable) extends Variantcaller {
protected def defaultPrio = 20
def biopetScript() {
val ug = broad.UnifiedGenotyper(this, inputBams.values.toList, outputFile)
val ug = gatk.UnifiedGenotyper(this, inputBams.values.toList, outputFile)
add(ug)
}
}
......@@ -5,7 +5,7 @@
*/
package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
import nl.lumc.sasc.biopet.extensions.gatk.broad
import nl.lumc.sasc.biopet.extensions.gatk
import nl.lumc.sasc.biopet.utils.config.Configurable
/** Allele mode for GenotyperAllele */
......@@ -14,7 +14,7 @@ class UnifiedGenotyperAllele(val root: Configurable) extends Variantcaller {
protected def defaultPrio = 9
def biopetScript() {