sv-s are grouped by type also for the tables

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

@@ -7,37 +7,70 @@ import nl.lumc.sasc.biopet.utils.summary.Summary
 
 object ShivaSvCallingReport {
 
+  val histogramBinBoundaries: Array[Int] = Array(100, 1000, 10000, 100000, 1000000, 10000000)
+  val histogramText: List[String] = List("<=100bp", "0.1-1kb", "1-10kb", "10-100kb", "0.1-1Mb", "1-10Mb", ">10Mb")
+
   def parseSummaryForSvCounts(summary: Summary): Map[String, Map[String, Array[Any]]] = {
-    var result: Map[String, Map[String, Array[Any]]] = Map()
+    var delCounts, insCounts, dupCounts, invCounts: Map[String, Array[Any]] = Map()
+
     for (sampleName <- summary.samples) {
       var sampleCounts: Map[String, Any] = summary.getSampleValue(sampleName, "shivasvcalling", "stats", "variantsBySizeAndType").get.asInstanceOf[Map[String, Any]]
-      result = result + (sampleName -> sampleCounts.collect({ case (k, v: List[_]) => (k, v.toArray[Any]) }))
+      for ((svType, counts) <- sampleCounts.collect({ case (k, v: List[_]) => (k, v.toArray[Any]) })) {
+        svType match {
+          case "DEL" => delCounts = delCounts + (sampleName -> counts)
+          case "INS" => insCounts = insCounts + (sampleName -> counts)
+          case "DUP" => dupCounts = dupCounts + (sampleName -> counts)
+          case "INV" => invCounts = invCounts + (sampleName -> counts)
+        }
+      }
     }
+
+    var result: Map[String, Map[String, Array[Any]]] = Map()
+    if (!delCounts.isEmpty) result = Map("DEL" -> delCounts)
+    if (!insCounts.isEmpty) result = result + ("INS" -> insCounts)
+    if (!dupCounts.isEmpty) result = result + ("DUP" -> dupCounts)
+    if (!invCounts.isEmpty) result = result + ("INV" -> invCounts)
     result
   }
 
-  def writeTsvForPlots(counts: Map[String, Map[String, Array[Any]]], svTypes: List[SvTypeForReport], outDir: File): Unit = {
-    val sampleNames = counts.keys
+  def writeTsvFiles(sampleNames: List[String], counts: Map[String, Map[String, Array[Any]]], svTypes: List[SvTypeForReport], outFileAllTypes: String, outDir: File): Unit = {
+
+    val tsvWriter = new PrintWriter(new File(outDir, outFileAllTypes))
+    tsvWriter.print("sv_type\tsample")
+    histogramText.foreach(bin => tsvWriter.print("\t" + bin))
+    tsvWriter.println()
+
     for (sv <- svTypes) {
-      val tsvFile = new File(outDir, sv.tsvFileName)
-      val tsvWriter = new PrintWriter(tsvFile)
+      val countsForSvType: Map[String, Array[Any]] = counts.get(sv.svType).get
 
-      tsvWriter.print("binMax")
-      sampleNames.foreach(sampleName => tsvWriter.print("\t" + sampleName))
-      tsvWriter.println()
+      writeTsvFileForSvType(sv, countsForSvType, sampleNames, outDir)
 
-      for (i <- ShivaSvCalling.histogramBinBoundaries.indices) {
-        tsvWriter.print(ShivaSvCalling.histogramBinBoundaries(i))
-        sampleNames.foreach(sampleName => tsvWriter.print("\t" + counts.get(sampleName).get.get(sv.svType).get(i)))
-        tsvWriter.println()
+      for (sampleName <- sampleNames) {
+        tsvWriter.print(sv.svType + "\t" + sampleName + "\t")
+        tsvWriter.println(countsForSvType.get(sampleName).get.mkString("\t"))
       }
-      val i = ShivaSvCalling.histogramBinBoundaries.length
-      tsvWriter.print(ShivaSvCalling.histogramBinBoundaries(i - 1) * 10)
-      sampleNames.foreach(sampleName => tsvWriter.print("\t" + counts.get(sampleName).get.get(sv.svType).get(i)))
-      tsvWriter.println()
+    }
+    tsvWriter.close()
+  }
 
-      tsvWriter.close()
+  def writeTsvFileForSvType(svType: SvTypeForReport, counts: Map[String, Array[Any]], sampleNames: List[String], outDir: File): Unit = {
+    val tsvWriter = new PrintWriter(new File(outDir, svType.tsvFileName))
+
+    tsvWriter.print("histogramBin")
+    sampleNames.foreach(sampleName => tsvWriter.print("\t" + sampleName))
+    tsvWriter.println()
+
+    for (i <- histogramBinBoundaries.indices) {
+      tsvWriter.print(histogramBinBoundaries(i))
+      sampleNames.foreach(sampleName => tsvWriter.print("\t" + counts.get(sampleName).get(i)))
+      tsvWriter.println()
     }
+    val i = histogramBinBoundaries.length
+    tsvWriter.print(histogramBinBoundaries(i - 1) * 10)
+    sampleNames.foreach(sampleName => tsvWriter.print("\t" + counts.get(sampleName).get(i)))
+    tsvWriter.println()
+
+    tsvWriter.close()
   }
 
   def createPlots(svTypes: List[SvTypeForReport], outDir: File): Unit = {
@@ -45,11 +78,12 @@ object ShivaSvCallingReport {
       val tsvFile = new File(outDir, sv.tsvFileName)
       val pngFile: File = new File(outDir, sv.pngFileName)
       val plot = LinePlot(tsvFile, pngFile,
-        xlabel = Some(s"${sv.displayText} size"),
+        xlabel = Some(s"${sv.displayText.substring(0, sv.displayText.length - 1)} size"),
         ylabel = Some("Number of loci"),
-        title = Some(sv.displayText + "s"),
-        width = 600,
+        title = Some(sv.displayText),
+        width = 400,
         removeZero = false)
+      plot.height = Some(300)
       plot.llabel = Some("Sample")
       plot.xLog10 = true
       plot.yLog10 = true