Fix insertsize plots

public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala

@@ -61,7 +61,11 @@ object BammetricsReport extends ReportBuilder {
     val wgsExecuted = summary.getValue(sampleId, libId, metricsTag, "stats", "wgs").isDefined
     val rnaExecuted = summary.getValue(sampleId, libId, metricsTag, "stats", "rna").isDefined
 
-    val insertsizeMetrics = summary.getValue(sampleId, libId, metricsTag, "stats", "CollectInsertSizeMetrics", "metrics").isDefined
+    val insertsizeMetrics = summary.getValue(sampleId, libId, metricsTag, "stats", "CollectInsertSizeMetrics", "metrics") match {
+      case Some(None) => false
+      case Some(_) => true
+      case _ => false
+    }
 
     val targets = (
       summary.getValue(sampleId, libId, metricsTag, "settings", "amplicon_name"),
@@ -81,7 +85,8 @@ object BammetricsReport extends ReportBuilder {
       List(
         "Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp")) ++
         (if (insertsizeMetrics) List("Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp", Map("showPlot" -> true))
-      ) else Nil) ++ (if (wgsExecuted) List("Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
+        )
+        else Nil) ++ (if (wgsExecuted) List("Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
           Map("showPlot" -> true)))
         else Nil) ++
         (if (rnaExecuted) List("Rna coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp",

public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BaseCounterTest.scala

@@ -4,7 +4,7 @@ import java.io.File
 import java.nio.file.Paths
 
 import com.google.common.io.Files
-import htsjdk.samtools.{SAMReadGroupRecord, SAMSequenceRecord, SAMLineParser, SAMFileHeader}
+import htsjdk.samtools.{ SAMReadGroupRecord, SAMSequenceRecord, SAMLineParser, SAMFileHeader }
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.Test
@@ -13,8 +13,8 @@ import picard.annotation.Gene
 import scala.collection.JavaConversions._
 
 /**
-  * Created by pjvan_thof on 1/29/16.
-  */
+ * Created by pjvan_thof on 1/29/16.
+ */
 class BaseCounterTest extends TestNGSuite with Matchers {
 
   import BaseCounter._
@@ -55,7 +55,7 @@ class BaseCounterTest extends TestNGSuite with Matchers {
     bamRecordBasesOverlap(read, 60, 70) shouldBe 0
   }
 
-    @Test
+  @Test
   def testBamRecordBasesOverlap(): Unit = {
     val read = BaseCounterTest.lineParser.parseLine("r02\t0\tchrQ\t50\t60\t10M\t*\t0\t0\tTACGTACGTA\tEEFFGGHHII\tRG:Z:001")
     bamRecordBasesOverlap(read, 40, 70) shouldBe 10

public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala

@@ -28,7 +28,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
 
     val wgsExecuted = summary.getSampleValues("bammetrics", "stats", "wgs").values.exists(_.isDefined)
     val rnaExecuted = summary.getSampleValues("bammetrics", "stats", "rna").values.exists(_.isDefined)
-    val insertsizeExecuted = summary.getSampleValues("bammetrics", "stats", "CollectInsertSizeMetrics", "metrics").values.exists(_.isDefined)
+    val insertsizeExecuted = summary.getSampleValues("bammetrics", "stats", "CollectInsertSizeMetrics", "metrics").values.exists(_ != Some(None))
     val flexiprepExecuted = summary.getLibraryValues("flexiprep")
       .exists { case ((sample, lib), value) => value.isDefined }
 
@@ -47,7 +47,8 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
           Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)
         )) ++
         (if (insertsizeExecuted) List("Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
-          Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)))else Nil) ++
+          Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)))
+        else Nil) ++
         (if (wgsExecuted) List("Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
           Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)))
         else Nil) ++