Added GenotypeConcordance to shiva

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeConcordance.scala

@@ -20,7 +20,7 @@ import java.io.File
 import nl.lumc.sasc.biopet.core.summary.Summarizable
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
-import org.broadinstitute.gatk.utils.report.{GATKReportTable, GATKReport}
+import org.broadinstitute.gatk.utils.report.{ GATKReportTable, GATKReport }
 
 /**
  * Extension for CombineVariants from GATK
@@ -54,8 +54,7 @@ class GenotypeConcordance(val root: Configurable) extends Gatk with Summarizable
     val samples = for (i <- 0 until genotypeSummary.getNumRows) yield genotypeSummary.get(i, "Sample").toString
 
     def getMap(table: GATKReportTable, column: String) = samples.distinct.map(sample => sample -> {
-      (for (i <- 0 until table.getNumRows if table.get(i, "Sample") == sample) yield
-        s"${table.get(i, "Eval_Genotype")}__${table.get(i, "Comp_Genotype")}" -> table.get(i, column)).toMap
+      (for (i <- 0 until table.getNumRows if table.get(i, "Sample") == sample) yield s"${table.get(i, "Eval_Genotype")}__${table.get(i, "Comp_Genotype")}" -> table.get(i, column)).toMap
     }).toMap
 
     Map(

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala

@@ -20,7 +20,7 @@ import java.io.File
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.core.{ Reference, SampleLibraryTag }
 import nl.lumc.sasc.biopet.extensions.bcftools.{ BcftoolsCall, BcftoolsMerge }
-import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
+import nl.lumc.sasc.biopet.extensions.gatk.{ GenotypeConcordance, CombineVariants }
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
 import nl.lumc.sasc.biopet.extensions.tools.{ MpileupToVcf, VcfFilter, VcfStats }
 import nl.lumc.sasc.biopet.extensions.{ Bgzip, Tabix }
@@ -38,6 +38,10 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag with
   @Input(doc = "Bam files (should be deduped bams)", shortName = "BAM", required = true)
   var inputBams: List[File] = Nil
 
+  var referenceVcf: Option[File] = config("reference_vcf")
+
+  var referenceVcfRegions: Option[File] = config("reference_vcf_regions")
+
   /** Name prefix, can override this methods if neeeded */
   def namePrefix: String = {
     (sampleId, libId) match {
@@ -85,6 +89,16 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag with
       vcfStats.setOutputDir(new File(caller.outputDir, "vcfstats"))
       add(vcfStats)
       addSummarizable(vcfStats, namePrefix + "-vcfstats-" + caller.name)
+
+      referenceVcf.foreach(referenceVcfFile => {
+        val gc = new GenotypeConcordance(this)
+        gc.evalFile = caller.outputFile
+        gc.compFile = referenceVcfFile
+        gc.outputFile = new File(caller.outputDir, s"$namePrefix-genotype_concordance.${caller.name}.txt")
+        referenceVcfRegions.foreach(gc.intervals ::= _)
+        add(gc)
+        addSummarizable(gc, s"$namePrefix-genotype_concordance_${caller.name}")
+      })
     }
     add(cv)
 
@@ -95,6 +109,16 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag with
     add(vcfStats)
     addSummarizable(vcfStats, namePrefix + "-vcfstats-final")
 
+    referenceVcf.foreach(referenceVcfFile => {
+      val gc = new GenotypeConcordance(this)
+      gc.evalFile = finalFile
+      gc.compFile = referenceVcfFile
+      gc.outputFile = new File(outputDir, s"$namePrefix-genotype_concordance.final.txt")
+      referenceVcfRegions.foreach(gc.intervals ::= _)
+      add(gc)
+      addSummarizable(gc, s"$namePrefix-genotype_concordance_final")
+    })
+
     addSummaryJobs()
   }