Added single sample coverage plot

public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.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] %>
+<%@ var libId: Option[String] = None %>
+<%@ var outputDir: File %>
+<%@ var target: String %>
+#{
+    val originalPlot = new File(summary.getLibraryValue(sampleId, libId, "bammetrics", "files", target + "_cov_stats", "plot", "path")
+        .getOrElse(throw new IllegalArgumentException("No plot found in summary")).toString)
+
+    val plot = new File(outputDir, target + "_cov_stats.png")
+
+    IoUtils.copyFile(originalPlot, plot)
+}#
+
+<img src="${plot}">

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

@@ -14,26 +14,32 @@ object BammetricsReport extends ReportBuilder {
 
   val reportName = "Bam Metrics"
 
-  def indexPage = ReportPage(Map(
-    "Bam Metrics" -> bamMetricsPage
-  ), List(
-    "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp")
-  ),
-    Map()
-  )
-
-  def bamMetricsPage = ReportPage(
-    Map(),
-    List(
-      "Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
-      "Bam Stats" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp"),
-      "Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp", Map("showPlot" -> true)),
-      "RNA (optional)" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/rna.ssp"),
-      "Target (optional)" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/target.ssp"),
-      "GC Bias" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/gcBias.ssp")
-    ),
-    Map()
-  )
+  def indexPage = ReportPage(Map(), List(), Map())
+
+  def bamMetricsPage(summary:Summary, sampleId: Option[String], libId: Option[String]) = {
+    val targets = (
+      summary.getLibraryValue(sampleId, libId, "bammetrics", "settings", "amplicon_name"),
+      summary.getLibraryValue(sampleId, libId, "bammetrics", "settings", "roi_name")
+      ) match {
+      case (Some(amplicon:String), Some(roi:List[_])) => amplicon :: roi.map(_.toString)
+      case (_, Some(roi:List[_])) => roi.map(_.toString)
+      case _ => Nil
+    }
+
+    ReportPage(
+      (if (targets.isEmpty) Map() else Map("Targets" -> ReportPage(
+        Map(),
+        targets.map(t => (t -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp", Map("target" -> t)))),
+        Map()))),
+      List(
+        "Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
+        "Bam Stats" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp"),
+        "Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp", Map("showPlot" -> true))
+      ),
+      Map()
+    )
+  }
+
 
   def alignmentSummaryPlot(outputDir: File,
                            prefix: String,
@@ -168,6 +174,5 @@ object BammetricsReport extends ReportBuilder {
     plot.removeZero = true
     plot.title = Some("Insert size")
     plot.runLocal()
-
   }
 }

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala

@@ -12,7 +12,7 @@ trait MultisampleReportBuilder extends ReportBuilder {
     )
   }
 
-  def libraryPage(libraryId: String, args: Map[String, Any]): ReportPage
+  def libraryPage(sampleId:String, libraryId: String, args: Map[String, Any]): ReportPage
 
   def libririesSections: List[(String, ReportSection)] = {
     List(
@@ -28,11 +28,13 @@ trait MultisampleReportBuilder extends ReportBuilder {
   }
 
   def generateLibraryPage(args: Map[String, Any]): ReportPage = {
-    val libPages = summary.libraries(args("sampleId") match {
+    val sampleId = args("sampleId") match {
       case Some(x) => x.toString
       case None    => throw new IllegalStateException("Sample not found")
-    })
-      .map(libId => (libId -> libraryPage(libId, args ++ Map("libId" -> Some(libId)))))
+    }
+
+    val libPages = summary.libraries(sampleId)
+      .map(libId => (libId -> libraryPage(sampleId, libId, args ++ Map("libId" -> Some(libId)))))
       .toMap
     ReportPage(libPages, libririesSections, args)
   }

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

@@ -86,7 +86,7 @@ object ShivaReport extends MultisampleReportBuilder {
   def samplePage(sampleId: String, args: Map[String, Any]) = {
     ReportPage(Map(
       "Libraries" -> generateLibraryPage(args),
-      "Alignment" -> BammetricsReport.bamMetricsPage,
+      "Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), None),
       "Files" -> filesPage
     ), List(
       "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
@@ -98,9 +98,9 @@ object ShivaReport extends MultisampleReportBuilder {
     ), args)
   }
 
-  def libraryPage(libId: String, args: Map[String, Any]) = {
+  def libraryPage(sampleId:String, libId: String, args: Map[String, Any]) = {
     ReportPage(Map(
-      "Alignment" -> BammetricsReport.bamMetricsPage,
+      "Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), Some(libId)),
       "QC" -> FlexiprepReport.flexiprepPage
     ), List(
       "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),