xhmm discover stats file

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmDiscover.scala

@@ -2,13 +2,16 @@ package nl.lumc.sasc.biopet.extensions.xhmm
 
 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.{Argument, Input, Output}
 
+import scala.io.Source
+
 /**
   * Created by Sander Bollen on 23-11-16.
   */
-class XhmmDiscover(val root: Configurable) extends Xhmm {
+class XhmmDiscover(val root: Configurable) extends Xhmm with Summarizable {
 
   @Input
   var inputMatrix: File = _
@@ -38,4 +41,24 @@ class XhmmDiscover(val root: Configurable) extends Xhmm {
       required("-s", xhmmAnalysisName)
   }
 
+  case class XcnvLine(sample: String, cnvType: String, location: String)
+
+  def summaryFiles: Map[String, File] = Map()
+
+  def summaryStats: Map[String, Any] = {
+    val lines = Source.fromFile(outputXcnv).
+      getLines().
+      filter(p => !p.startsWith("SAMPLE")).
+      map(x => x.split("\t")).
+      map(x => XcnvLine(x(0), x(1), x(2))).toList
+
+    val samples = lines.map(_.sample)
+    samples.map{x =>
+      val sampleLines = lines.filter(_.sample == x)
+      x -> Map(
+        "DEL" -> sampleLines.count(_.cnvType == "DEL"),
+        "DUP" -> sampleLines.count(_.cnvType == "DUP"))
+    }.toMap
+  }
+
 }