Added objects again

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala

@@ -5,23 +5,6 @@
  */
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
-//import java.io.File
-//
-//import nl.lumc.sasc.biopet.utils.config.Configurable
-//
-//class AnalyzeCovariates(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.AnalyzeCovariates with GatkGeneral {
-//}
-//
-//object AnalyzeCovariates {
-//  def apply(root: Configurable, before: File, after: File, plots: File): AnalyzeCovariates = {
-//    val ac = new AnalyzeCovariates(root)
-//    ac.before = before
-//    ac.after = after
-//    ac.plots = plots
-//    ac
-//  }
-//}
-
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
@@ -175,3 +158,13 @@ class AnalyzeCovariates(val root: Configurable) extends CommandLineGATK with Sca
     conditional(filter_mismatching_base_and_quals, "-filterMBQ", escape = true, format = "%s") +
     conditional(filter_bases_not_stored, "-filterNoBases", escape = true, format = "%s")
 }
+
+object AnalyzeCovariates {
+  def apply(root: Configurable, before: File, after: File, plots: File): AnalyzeCovariates = {
+    val ac = new AnalyzeCovariates(root)
+    ac.before = before
+    ac.after = after
+    ac.plots = plots
+    ac
+  }
+}

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala

@@ -15,14 +15,6 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
 //  if (config.contains("known_sites")) knownSites :+= new File(config("known_sites").asString)
 //}
 //
-//object BaseRecalibrator {
-//  def apply(root: Configurable, input: File, output: File): BaseRecalibrator = {
-//    val br = new BaseRecalibrator(root)
-//    br.input_file :+= input
-//    br.out = output
-//    br
-//  }
-//}
 
 import java.io.File
 
@@ -489,3 +481,12 @@ class BaseRecalibrator(val root: Configurable) extends CommandLineGATK /* with S
     conditional(filter_mismatching_base_and_quals, "-filterMBQ", escape = true, format = "%s") +
     conditional(filter_bases_not_stored, "-filterNoBases", escape = true, format = "%s")
 }
+
+object BaseRecalibrator {
+  def apply(root: Configurable, input: File, output: File): BaseRecalibrator = {
+    val br = new BaseRecalibrator(root)
+    br.input_file :+= input
+    br.out = output
+    br
+  }
+}

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala

@@ -34,16 +34,6 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
 //    if (out.getName.endsWith(".vcf.gz")) vcfIndex = new File(out.getAbsolutePath + ".tbi")
 //  }
 //}
-//
-//object GenotypeGVCFs {
-//  def apply(root: Configurable, gvcfFiles: List[File], output: File): GenotypeGVCFs = {
-//    val gg = new GenotypeGVCFs(root)
-//    gg.variant = gvcfFiles
-//    gg.out = output
-//    if (gg.out.getName.endsWith(".vcf.gz")) gg.vcfIndex = new File(gg.out.getAbsolutePath + ".tbi")
-//    gg
-//  }
-//}
 
 import java.io.File
 
@@ -394,3 +384,13 @@ class GenotypeGVCFs(val root: Configurable) extends CommandLineGATK with Scatter
     conditional(filter_mismatching_base_and_quals, "-filterMBQ", escape = true, format = "%s") +
     conditional(filter_bases_not_stored, "-filterNoBases", escape = true, format = "%s")
 }
+
+object GenotypeGVCFs {
+  def apply(root: Configurable, gvcfFiles: List[File], output: File): GenotypeGVCFs = {
+    val gg = new GenotypeGVCFs(root)
+    gg.variant = gvcfFiles
+    gg.out = output
+    //if (gg.out.getName.endsWith(".vcf.gz")) gg.vcfIndex = new File(gg.out.getAbsolutePath + ".tbi")
+    gg
+  }
+}

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala

@@ -57,23 +57,6 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
 //  }
 //}
 //
-//object HaplotypeCaller {
-//  def apply(root: Configurable, inputFiles: List[File], outputFile: File): HaplotypeCaller = {
-//    val hc = new HaplotypeCaller(root)
-//    hc.input_file = inputFiles
-//    hc.out = outputFile
-//    if (hc.out.getName.endsWith(".vcf.gz")) hc.vcfIndex = new File(hc.out.getAbsolutePath + ".tbi")
-//    hc
-//  }
-//
-//  def gvcf(root: Configurable, inputFile: File, outputFile: File): HaplotypeCaller = {
-//    val hc = apply(root, List(inputFile), outputFile)
-//    hc.emitRefConfidence = org.broadinstitute.gatk.tools.walkers.haplotypecaller.ReferenceConfidenceMode.GVCF
-//    hc.variant_index_type = GATKVCFIndexType.LINEAR
-//    hc.variant_index_parameter = Some(hc.config("variant_index_parameter", default = 128000).asInt)
-//    hc
-//  }
-//}
 
 import java.io.File
 
@@ -81,6 +64,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.extensions.gatk._
 import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Input, _ }
+import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType
 
 class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
   analysisName = "HaplotypeCaller"
@@ -1131,3 +1115,21 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
     conditional(filter_mismatching_base_and_quals, "-filterMBQ", escape = true, format = "%s") +
     conditional(filter_bases_not_stored, "-filterNoBases", escape = true, format = "%s")
 }
+
+object HaplotypeCaller {
+  def apply(root: Configurable, inputFiles: List[File], outputFile: File): HaplotypeCaller = {
+    val hc = new HaplotypeCaller(root)
+    hc.input_file = inputFiles
+    hc.out = outputFile
+    //if (hc.out.getName.endsWith(".vcf.gz")) hc.vcfIndex = new File(hc.out.getAbsolutePath + ".tbi")
+    hc
+  }
+
+  def gvcf(root: Configurable, inputFile: File, outputFile: File): HaplotypeCaller = {
+    val hc = apply(root, List(inputFile), outputFile)
+    hc.emitRefConfidence = "GVCF"
+    hc.variant_index_type = GATKVCFIndexType.LINEAR
+    hc.variant_index_parameter = Some(hc.config("variant_index_parameter", default = 128000).asInt)
+    hc
+  }
+}

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala

@@ -5,31 +5,6 @@
  */
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
-//import java.io.File
-//
-//import nl.lumc.sasc.biopet.utils.config.Configurable
-//import org.broadinstitute.gatk.utils.commandline.{ Gather, Output }
-//
-//class IndelRealigner(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.IndelRealigner with GatkGeneral {
-//
-//  @Gather(enabled = false)
-//  @Output
-//  protected var bamIndex: File = _
-//
-//  if (config.contains("scattercount")) scatterCount = config("scattercount")
-//}
-//
-//object IndelRealigner {
-//  def apply(root: Configurable, input: File, targetIntervals: File, outputDir: File): IndelRealigner = {
-//    val ir = new IndelRealigner(root)
-//    ir.input_file :+= input
-//    ir.targetIntervals = targetIntervals
-//    ir.out = new File(outputDir, input.getName.stripSuffix(".bam") + ".realign.bam")
-//    ir.bamIndex = new File(outputDir, input.getName.stripSuffix(".bam") + ".realign.bai")
-//    ir
-//  }
-//}
-
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
@@ -430,3 +405,14 @@ class IndelRealigner(val root: Configurable) extends CommandLineGATK with Scatte
     conditional(filter_mismatching_base_and_quals, "-filterMBQ", escape = true, format = "%s") +
     conditional(filter_bases_not_stored, "-filterNoBases", escape = true, format = "%s")
 }
+
+object IndelRealigner {
+  def apply(root: Configurable, input: File, targetIntervals: File, outputDir: File): IndelRealigner = {
+    val ir = new IndelRealigner(root)
+    ir.input_file :+= input
+    ir.targetIntervals = targetIntervals
+    ir.out = new File(outputDir, input.getName.stripSuffix(".bam") + ".realign.bam")
+    ir.deps :+= new File(outputDir, input.getName.stripSuffix(".bam") + ".realign.bai")
+    ir
+  }
+}

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala

@@ -5,23 +5,6 @@
  */
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
-//import java.io.File
-//
-//import nl.lumc.sasc.biopet.utils.config.Configurable
-//
-//class PrintReads(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.PrintReads with GatkGeneral {
-//  if (config.contains("scattercount")) scatterCount = config("scattercount")
-//}
-//
-//object PrintReads {
-//  def apply(root: Configurable, input: File, output: File): PrintReads = {
-//    val br = new PrintReads(root)
-//    br.input_file :+= input
-//    br.out = output
-//    br
-//  }
-//}
-
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
@@ -221,3 +204,12 @@ class PrintReads(val root: Configurable) extends CommandLineGATK with ScatterGat
     conditional(filter_mismatching_base_and_quals, "-filterMBQ", escape = true, format = "%s") +
     conditional(filter_bases_not_stored, "-filterNoBases", escape = true, format = "%s")
 }
+
+object PrintReads {
+  def apply(root: Configurable, input: File, output: File): PrintReads = {
+    val br = new PrintReads(root)
+    br.input_file :+= input
+    br.out = output
+    br
+  }
+}

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/RealignerTargetCreator.scala

@@ -5,25 +5,6 @@
  */
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
-//import java.io.File
-//
-//import nl.lumc.sasc.biopet.utils.config.Configurable
-//
-//class RealignerTargetCreator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.RealignerTargetCreator with GatkGeneral {
-//  if (config.contains("scattercount")) scatterCount = config("scattercount")
-//
-//  if (config.contains("known")) known ++= config("known").asFileList
-//}
-//
-//object RealignerTargetCreator {
-//  def apply(root: Configurable, input: File, outputDir: File): RealignerTargetCreator = {
-//    val re = new RealignerTargetCreator(root)
-//    re.input_file :+= input
-//    re.out = new File(outputDir, input.getName.stripSuffix(".bam") + ".realign.intervals")
-//    re
-//  }
-//}
-
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
@@ -194,3 +175,12 @@ class RealignerTargetCreator(val root: Configurable) extends CommandLineGATK wit
     conditional(filter_mismatching_base_and_quals, "-filterMBQ", escape = true, format = "%s") +
     conditional(filter_bases_not_stored, "-filterNoBases", escape = true, format = "%s")
 }
+
+object RealignerTargetCreator {
+  def apply(root: Configurable, input: File, outputDir: File): RealignerTargetCreator = {
+    val re = new RealignerTargetCreator(root)
+    re.input_file :+= input
+    re.out = new File(outputDir, input.getName.stripSuffix(".bam") + ".realign.intervals")
+    re
+  }
+}

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala

@@ -44,17 +44,6 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
 //    memoryLimit = Option(nct.getOrElse(1) * memoryLimit.getOrElse(2.0))
 //  }
 //}
-//
-//object UnifiedGenotyper {
-//  def apply(root: Configurable, inputFiles: List[File], outputFile: File): UnifiedGenotyper = {
-//    val ug = new UnifiedGenotyper(root)
-//    ug.input_file = inputFiles
-//    ug.out = outputFile
-//    if (ug.out.getName.endsWith(".vcf.gz")) ug.vcfIndex = new File(ug.out.getAbsolutePath + ".tbi")
-//    ug
-//  }
-//
-//}
 
 import java.io.File
 
@@ -892,3 +881,13 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat
     conditional(filter_mismatching_base_and_quals, "-filterMBQ", escape = true, format = "%s") +
     conditional(filter_bases_not_stored, "-filterNoBases", escape = true, format = "%s")
 }
+
+object UnifiedGenotyper {
+  def apply(root: Configurable, inputFiles: List[File], outputFile: File): UnifiedGenotyper = {
+    val ug = new UnifiedGenotyper(root)
+    ug.input_file = inputFiles
+    ug.out = outputFile
+    //if (ug.out.getName.endsWith(".vcf.gz")) ug.vcfIndex = new File(ug.out.getAbsolutePath + ".tbi")
+    ug
+  }
+}

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala

@@ -28,8 +28,8 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
 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 {
   analysisName = "VariantAnnotator"

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/HaplotypeCallerAllele.scala

@@ -17,7 +17,7 @@ class HaplotypeCallerAllele(val root: Configurable) extends Variantcaller {
   def biopetScript() {
     val hc = broad.HaplotypeCaller(this, inputBams.values.toList, outputFile)
     hc.alleles = config("input_alleles")
-    hc.genotyping_mode = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES
+    hc.genotyping_mode = "GENOTYPE_GIVEN_ALLELES"
     add(hc)
   }
 }

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/UnifiedGenotyperAllele.scala

@@ -17,7 +17,7 @@ class UnifiedGenotyperAllele(val root: Configurable) extends Variantcaller {
   def biopetScript() {
     val ug = broad.UnifiedGenotyper(this, inputBams.values.toList, outputFile)
     ug.alleles = config("input_alleles")
-    ug.genotyping_mode = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES
+    ug.genotyping_mode = "GENOTYPE_GIVEN_ALLELES"
     add(ug)
   }
 }

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ScatterGatherableFunction.scala

 package nl.lumc.sasc.biopet.core
 
 /**
-  * Created by pjvan_thof on 4/26/16.
-  */
+ * Created by pjvan_thof on 4/26/16.
+ */
 trait ScatterGatherableFunction extends BiopetCommandLineFunction
   with org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction {
   scatterCount = config("scatter_count", freeVar = true)