Merge remote-tracking branch 'origin/develop' into develop

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

@@ -127,9 +127,9 @@ object BammetricsReport extends ReportBuilder {
         summary, Some(sample), lib).value.getOrElse(0).toString.toLong
       val sb = new StringBuffer()
       if (lib.isDefined) sb.append(sample + "-" + lib.get + "\t") else sb.append(sample + "\t")
-      sb.append((mapped - duplicates) + "\t")
+      sb.append((mapped - duplicates - secondary) + "\t")
       sb.append(duplicates + "\t")
-      sb.append((total - mapped - secondary) + "\t")
+      sb.append((total - mapped) + "\t")
       sb.append(secondary)
       sb.toString
     }

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala

@@ -205,7 +205,7 @@ trait ReportBuilder extends ToolCommand {
 
     val pageOutputDir = new File(outputDir, path.mkString(File.separator))
     pageOutputDir.mkdirs()
-    val rootPath = "./" + Array.fill(path.size)("src/main").mkString("")
+    val rootPath = "./" + Array.fill(path.size)("../").mkString
     val pageArgs = args ++ page.args ++
       Map("page" -> page,
         "path" -> path,