one log line

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

@@ -37,13 +37,15 @@ class VcfStatsForSv(val parent: Configurable) extends ToolCommandFunction with S
   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) +
     required("-o", outputFile) +
     repeat("--histBinBoundaries", histogramBinBoundaries)
 
-  def summaryStats: Map[String, Any] = ConfigUtils.yamlToMap(outputFile)
+  def summaryStats: Map[String, Any] = ConfigUtils.fileToConfigMap(outputFile)
 
   def summaryFiles: Map[String, File] = Map.empty
 

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()