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

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 {
......
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