Merge pull request #89 from biopet/fix-BIOPET-662

fixes for sv calling

biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStatsForSv.scala

@@ -36,7 +36,8 @@ class VcfStatsForSv(val parent: Configurable) extends ToolCommandFunction with S
   @Output(required = true)
   var outputFile: File = _
 
-  override def defaultCoreMemory = 1.0
+  override def defaultResidentFactor = 2.0
+  override def defaultVmemFactor = 3.0
 
   override def cmdLine = super.cmdLine +
     required("-i", inputFile) +

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStatsForSv.scala

@@ -38,8 +38,7 @@ object VcfStatsForSv extends ToolCommand {
 
     val stats: Map[String, Any] = getVariantCounts(cmdArgs.inputFile, cmdArgs.histBinBoundaries)
 
-    ConfigUtils.mapToYamlFile(stats, cmdArgs.outputFile)
-
+    ConfigUtils.mapToJsonFile(stats, cmdArgs.outputFile)
   }
 
   /** Parses a vcf-file and counts sv-s by type and size. Sv-s are divided to different size classes, the parameter histogramBinBoundaries gives the boundaries between these classes. */

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala

@@ -168,6 +168,12 @@ object ConfigUtils extends Logging {
     writer.close()
   }
 
+  def mapToJsonFile(map: Map[String, Any], outputFile: File) = {
+    val writer = new PrintWriter(outputFile)
+    writer.println(anyToJson(map).toString())
+    writer.close()
+  }
+
   /** Convert json to native scala map/values */
   def jsonToMap(json: Json): Map[String, Any] = {
     var output: Map[String, Any] = Map()

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala

@@ -20,9 +20,14 @@ import nl.lumc.sasc.biopet.extensions.Pysvtools
 import nl.lumc.sasc.biopet.extensions.tools.VcfStatsForSv
 import nl.lumc.sasc.biopet.pipelines.shiva.svcallers._
 import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
 import nl.lumc.sasc.biopet.utils.{ BamUtils, Logging }
 import org.broadinstitute.gatk.queue.QScript
 
+import scala.concurrent.Await
+import scala.concurrent.duration.Duration
+import scala.concurrent.ExecutionContext.Implicits.global
+
 /**
  * Common trait for ShivaVariantcalling
  *
@@ -43,7 +48,16 @@ class ShivaSvCalling(val parent: Configurable) extends QScript with SummaryQScri
 
   /** Executed before script */
   def init(): Unit = {
-    if (inputBamsArg.nonEmpty) inputBams = BamUtils.sampleBamMap(inputBamsArg)
+    if (inputBamsArg.nonEmpty) {
+      inputBams = BamUtils.sampleBamMap(inputBamsArg)
+
+      val db = SummaryDb.openSqliteSummary(summaryDbFile)
+      for (sampleName <- inputBams.keys) {
+        if (Await.result(db.getSampleId(summaryRunId, sampleName), Duration.Inf).isEmpty) {
+          db.createSample(sampleName, summaryRunId)
+        }
+      }
+    }
     outputMergedVCF = new File(outputDir, "allsamples.merged.vcf")
   }