Added multisample coverage table

public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp

+#import(nl.lumc.sasc.biopet.utils.IoUtils)
+#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.core.report.ReportPage)
+#import(org.apache.commons.io.FileUtils)
+#import(java.io.File)
+<%@ var summary: Summary %>
+<%@ var sampleId: Option[String] = None %>
+<%@ var libId: Option[String] = None %>
+<%@ var sampleLevel: Boolean = true %>
+<%@ var rootPath: String %>
+<%@ var outputDir: File %>
+<%@ var metricsTag: String = "bammetrics" %>
+<%@ var target: String %>
+#{
+    val samples = sampleId match {
+        case Some(sample) => List(sample.toString)
+        case _ => summary.samples.toList
+    }
+}#
+
+
+<table class="table">
+<thead><tr>
+    <th>mean</th>
+    <th>median</th>
+    <th>max</th>
+    <th>horizontal</th>
+    <th>frac min 10x</th>
+    <th>frac min 20x</th>
+    <th>frac min 30x</th>
+    <th>frac min 40x</th>
+    <th>frac min 50x</th>
+</tr></thead>
+<tbody>
+    #for (sample <- samples.toList.sorted)
+        #{
+            val libs = (libId, sampleLevel) match {
+            case (_, true) => List("")
+            case (Some(libId), _) => List(libId.toString)
+            case _ => summary.libraries(sample).toList
+            }
+        }#
+        <tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
+        #for (libId <- libs)
+            #if (libs.head != libId) <tr> #end
+                #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td> #end
+                #{
+                    val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List(metricsTag, "stats", target + "_cov_stats", "coverage", "_all")
+                    val total = summary.getValue((prefixPath ::: List("biopet_flagstat", "All")):_*).getOrElse(0L).asInstanceOf[Long]
+                    val mapped = summary.getValue((prefixPath ::: List("biopet_flagstat", "Mapped")):_*).getOrElse(0L).asInstanceOf[Long]
+                    val duplicates = summary.getValue((prefixPath ::: List("biopet_flagstat", "Duplicates")):_*).getOrElse(0L).asInstanceOf[Long]
+                }#
+                <td>${summary.getValue((prefixPath ::: "mean" :: Nil):_*)}</td>
+                <td>${summary.getValue((prefixPath ::: "median" :: Nil):_*)}</td>
+                <td>${summary.getValue((prefixPath ::: "max" :: Nil):_*)}</td>
+                <td>${summary.getValue((prefixPath ::: "horizontal" :: Nil):_*)}</td>
+                <td>${summary.getValue((prefixPath ::: "frac_min_10x" :: Nil):_*)}</td>
+                <td>${summary.getValue((prefixPath ::: "frac_min_20x" :: Nil):_*)}</td>
+                <td>${summary.getValue((prefixPath ::: "frac_min_30x" :: Nil):_*)}</td>
+                <td>${summary.getValue((prefixPath ::: "frac_min_40x" :: Nil):_*)}</td>
+                <td>${summary.getValue((prefixPath ::: "frac_min_50x" :: Nil):_*)}</td>
+            </tr>
+        #end
+    #end
+</tbody>
+</table>

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala

@@ -58,7 +58,7 @@ object ShivaReport extends MultisampleReportBuilder {
 
     def createPage(name: String, amplicon: Boolean = false): ReportPage = {
       //TODO: get target content
-      ReportPage(Map(), List(), Map())
+      ReportPage(Map(), List("Coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp")), Map("target" -> name))
     }
 
     amplicon match {