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biopet.biopet
Commit 7abb542a authored by Peter van 't Hof's avatar Peter van 't Hof
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protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala
View file @ 7abb542a
......@@ -8,7 +8,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.{CatVariantsGatherer, GATKScatterFunction, LocusScatterFunction, TaggedFile}
import org.broadinstitute.gatk.queue.extensions.gatk.{ CatVariantsGatherer, GATKScatterFunction, LocusScatterFunction, TaggedFile }
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.utils.VcfUtils
import org.broadinstitute.gatk.utils.commandline.Argument
......
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala
View file @ 7abb542a
......@@ -8,10 +8,10 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.{GATKScatterFunction, ReadScatterFunction, TaggedFile}
import org.broadinstitute.gatk.queue.extensions.gatk.{ GATKScatterFunction, ReadScatterFunction, TaggedFile }
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.utils.VcfUtils
import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Output, _}
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
//TODO: check gathering
class BaseRecalibrator(val root: Configurable) extends CommandLineGATK /* with ScatterGatherableFunction */ {
......@@ -22,7 +22,7 @@ class BaseRecalibrator(val root: Configurable) extends CommandLineGATK /* with S
/** A database of known polymorphic sites */
@Input(fullName = "knownSites", shortName = "knownSites", doc = "A database of known polymorphic sites", required = false, exclusiveOf = "", validation = "")
var knownSites: List[File] = config("known_sites")
var knownSites: List[File] = config("known_sites", default = Nil)
/** Dependencies on any indexes of knownSites */
@Input(fullName = "knownSitesIndexes", shortName = "", doc = "Dependencies on any indexes of knownSites", required = false, exclusiveOf = "", validation = "")
......
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala
View file @ 7abb542a
......@@ -8,10 +8,10 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.{CatVariantsGatherer, GATKScatterFunction, LocusScatterFunction, TaggedFile}
import org.broadinstitute.gatk.queue.extensions.gatk.{ CatVariantsGatherer, GATKScatterFunction, LocusScatterFunction, TaggedFile }
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.utils.VcfUtils
import org.broadinstitute.gatk.utils.commandline.{Gather, Input, Output, _}
import org.broadinstitute.gatk.utils.commandline.{ Gather, Input, Output, _ }
class CombineGVCFs(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "CombineGVCFs"
......
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineVariants.scala
View file @ 7abb542a
......@@ -8,10 +8,10 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.{CatVariantsGatherer, GATKScatterFunction, LocusScatterFunction, TaggedFile}
import org.broadinstitute.gatk.queue.extensions.gatk.{ CatVariantsGatherer, GATKScatterFunction, LocusScatterFunction, TaggedFile }
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.utils.VcfUtils
import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Output, _}
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
class CombineVariants(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "CombineVariants"
......
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala
View file @ 7abb542a
......@@ -8,10 +8,10 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.{CatVariantsGatherer, GATKScatterFunction, LocusScatterFunction, TaggedFile}
import org.broadinstitute.gatk.queue.extensions.gatk.{ CatVariantsGatherer, GATKScatterFunction, LocusScatterFunction, TaggedFile }
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.utils.VcfUtils
import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Output, _}
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
class GenotypeGVCFs(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "GenotypeGVCFs"
......
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala
View file @ 7abb542a
......@@ -277,7 +277,7 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
/** GQ thresholds for reference confidence bands */
@Argument(fullName = "GVCFGQBands", shortName = "GQB", doc = "GQ thresholds for reference confidence bands", required = false, exclusiveOf = "", validation = "")
var GVCFGQBands: List[Int] = config("GVCFGQBands")
var GVCFGQBands: List[Int] = config("GVCFGQBands", default = Nil)
/** The size of an indel to check for in the reference model */
@Argument(fullName = "indelSizeToEliminateInRefModel", shortName = "ERCIS", doc = "The size of an indel to check for in the reference model", required = false, exclusiveOf = "", validation = "")
......@@ -402,7 +402,7 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
if (out != null && !org.broadinstitute.gatk.utils.io.IOUtils.isSpecialFile(out))
if (!org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptor.isCompressed(out.getPath))
outputFiles :+= VcfUtils.getVcfIndexFile(out)
dbsnp.foreach(deps :+= VcfUtils.getVcfIndexFile(_))
dbsnp.foreach(deps :+= VcfUtils.getVcfIndexFile(_))
deps ++= comp.filter(orig => orig != null && (!orig.getName.endsWith(".list"))).map(orig => new File(orig.getPath + ".idx"))
if (bamOutput != null && !org.broadinstitute.gatk.utils.io.IOUtils.isSpecialFile(bamOutput))
if (!disable_bam_indexing)
......
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala
View file @ 7abb542a
......@@ -8,10 +8,10 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.{BamGatherFunction, GATKScatterFunction, ReadScatterFunction, TaggedFile}
import org.broadinstitute.gatk.queue.extensions.gatk.{ BamGatherFunction, GATKScatterFunction, ReadScatterFunction, TaggedFile }
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.utils.VcfUtils
import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Output, _}
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
class IndelRealigner(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "IndelRealigner"
......
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/RealignerTargetCreator.scala
View file @ 7abb542a
......@@ -8,10 +8,10 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.{GATKScatterFunction, LocusScatterFunction, TaggedFile}
import org.broadinstitute.gatk.queue.extensions.gatk.{ GATKScatterFunction, LocusScatterFunction, TaggedFile }
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.utils.VcfUtils
import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Input, _}
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Input, _ }
class RealignerTargetCreator(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "RealignerTargetCreator"
......
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala
View file @ 7abb542a
......@@ -8,10 +8,10 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.{CatVariantsGatherer, GATKScatterFunction, LocusScatterFunction, TaggedFile}
import org.broadinstitute.gatk.queue.extensions.gatk.{ CatVariantsGatherer, GATKScatterFunction, LocusScatterFunction, TaggedFile }
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.utils.VcfUtils
import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Output, _}
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
class SelectVariants(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "SelectVariants"
......
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala
View file @ 7abb542a
......@@ -48,10 +48,10 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.{CatVariantsGatherer, GATKScatterFunction, LocusScatterFunction, TaggedFile}
import org.broadinstitute.gatk.queue.extensions.gatk.{ CatVariantsGatherer, GATKScatterFunction, LocusScatterFunction, TaggedFile }
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.utils.VcfUtils
import org.broadinstitute.gatk.utils.commandline.{Gather, Input, Output, _}
import org.broadinstitute.gatk.utils.commandline.{ Gather, Input, Output, _ }
class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "UnifiedGenotyper"
......@@ -293,9 +293,9 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat
override def freezeFieldValues() {
super.freezeFieldValues()
reference_sample_calls.foreach( deps :+= VcfUtils.getVcfIndexFile(_))
alleles.foreach( deps :+= VcfUtils.getVcfIndexFile(_))
dbsnp.foreach( deps :+= VcfUtils.getVcfIndexFile(_))
reference_sample_calls.foreach(deps :+= VcfUtils.getVcfIndexFile(_))
alleles.foreach(deps :+= VcfUtils.getVcfIndexFile(_))
dbsnp.foreach(deps :+= VcfUtils.getVcfIndexFile(_))
deps ++= comp.filter(orig => orig != null && (!orig.getName.endsWith(".list"))).map(orig => VcfUtils.getVcfIndexFile(orig))
if (out != null && !org.broadinstitute.gatk.utils.io.IOUtils.isSpecialFile(out))
if (!org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptor.isCompressed(out.getPath))
......
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala
View file @ 7abb542a
......@@ -10,8 +10,8 @@ import java.io.File
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.{CatVariantsGatherer, GATKScatterFunction, LocusScatterFunction, TaggedFile}
import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Output, _}
import org.broadinstitute.gatk.queue.extensions.gatk.{ CatVariantsGatherer, GATKScatterFunction, LocusScatterFunction, TaggedFile }
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
class VariantAnnotator(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "VariantAnnotator"
......
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantRecalibrator.scala
View file @ 7abb542a
......@@ -9,8 +9,8 @@ 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.{CatVariantsGatherer, TaggedFile}
import org.broadinstitute.gatk.utils.commandline.{Gather, Input, Output, _}
import org.broadinstitute.gatk.queue.extensions.gatk.{ CatVariantsGatherer, TaggedFile }
import org.broadinstitute.gatk.utils.commandline.{ Gather, Input, Output, _ }
class VariantRecalibrator(val root: Configurable) extends CommandLineGATK {
def analysis_type = "VariantRecalibrator"
......
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