Commit e60b100f authored by akaljuvee's avatar akaljuvee

-

parent fbc8e4ab
......@@ -16,7 +16,7 @@ package nl.lumc.sasc.biopet.pipelines.shiva
import htsjdk.variant.vcf.VCFFileReader
import nl.lumc.sasc.biopet.core.summary.{ Summarizable, SummaryQScript }
import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, SampleLibraryTag }
import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference }
import nl.lumc.sasc.biopet.extensions.Pysvtools
import nl.lumc.sasc.biopet.pipelines.shiva.svcallers._
import nl.lumc.sasc.biopet.utils.config.Configurable
......@@ -28,7 +28,7 @@ import org.broadinstitute.gatk.queue.QScript
*
* Created by pjvan_thof on 2/26/15.
*/
class ShivaSvCalling(val parent: Configurable) extends QScript with SummaryQScript with SampleLibraryTag with Reference {
class ShivaSvCalling(val parent: Configurable) extends QScript with SummaryQScript with Reference {
qscript =>
def this() = this(null)
......@@ -100,7 +100,7 @@ class ShivaSvCalling(val parent: Configurable) extends QScript with SummaryQScri
for ((sample, mergedResultFile) <- outputMergedVCFbySample) {
lazy val counts = getVariantCounts(mergedResultFile, ShivaSvCallingReport.histogramBinBoundaries)
addSummarizable(new Summarizable {
def summaryFiles = Map.empty
def summaryFiles = Map("output_vcf" -> mergedResultFile)
def summaryStats = counts
}, "variantsBySizeAndType", Some(sample))
}
......@@ -119,7 +119,7 @@ class ShivaSvCalling(val parent: Configurable) extends QScript with SummaryQScri
def summarySettings = Map("sv_callers" -> configCallers.toList)
/** Files for the summary */
def summaryFiles: Map[String, File] = outputMergedVCFbySample ++ (if (inputBams.size > 1) Map("final_mergedvcf" -> outputMergedVCF) else Nil)
def summaryFiles: Map[String, File] = if (inputBams.size > 1) Map("final_mergedvcf" -> outputMergedVCF) else Map.empty
def getVariantCounts(vcfFile: File, breaks: Array[Int]): Map[String, Any] = {
val delCounts, insCounts, dupCounts, invCounts = Array.fill(breaks.size + 1) { 0 }
......
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