Added rna metrics plot

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

+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
+#import(nl.lumc.sasc.biopet.core.report.ReportPage)
+#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
+#import(java.io.File)
+#import(org.apache.commons.io.FileUtils)
+<%@ var summary: Summary %>
+<%@ var sampleId: Option[String] = None %>
+<%@ var libId: Option[String] = None %>
+<%@ var rootPath: String %>
+<%@ var metricsTag: String = "bammetrics" %>
+<%@ var sampleLevel: Boolean = false %>
+<%@ var outputDir: File %>
+<%@ var fields: List[String] = List()%>
+<%@ var showPlot: Boolean = false %>
+<%@ var showTable: Boolean = true %>
+<%@ var showIntro: Boolean = true%>
+#{
+    val samples = sampleId match {
+    case Some(sample) => {
+    List(sample.toString)
+    }
+    case _ => summary.samples.toList
+    }
+}#
+
+#if (showIntro)
+    <br/>
+    <div class="row">
+    <div class="col-md-1"></div>
+    <div class="col-md-6">
+        <p>
+            Here we show the total number of positions in the reference that are covered with a given coverage. This plot is whole-genome based, and will therefore be highly skewed in the case of an exome or targeted approach.
+        </p>
+    </div>
+    </div>
+#end
+
+#if (showPlot)
+    #{ BammetricsReport.rnaHistogramPlot(outputDir, "rna", summary, !sampleLevel, sampleId = sampleId, libId = libId) }#
+
+    <div class="panel-body">
+    <img src="rna.png" class="img-responsive" />
+    </div>
+    <div class="panel-footer">
+        #if (showTable)
+            <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#rnaTable">Hide table</button>
+        #else
+            <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#rnaTable">Show table</button>
+        #end
+        <i class="glyphicon glyphicon-file"></i> <a href="rna.tsv">tsv file</a>
+    </div>
+#end
+
+<div class="panel-body collapse #if (showTable)in#end" id="rnaTable">
+<!-- Table -->
+<table class="table sortable-theme-bootstrap" data-sortable>
+    <thead><tr>
+        <th data-sorted="true" data-sorted-direction="ascending">Sample</th>
+        #if (!sampleLevel) <th>Library</th> #end
+        #for (field <- fields)
+            <th>${field.replaceAll("_", " ")}</th>
+        #end
+    </tr></thead>
+    <tbody>
+        #for (sample <- samples.toList.sorted)
+            #{
+                val libs = (libId, sampleLevel) match {
+                case (_, true) => List("")
+                case (Some(libId), _) => List(libId.toString)
+                case _ => summary.libraries(sample).toList
+                }
+            }#
+            <tr><td rowspan="${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">${libId}</a></td> #end
+                    #{
+                        val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List("bammetrics", "stats")
+
+                        val fieldValues = for (field <- fields) yield {
+                            summary.getValue((prefixPath ::: List("rna", "metrics", field.toUpperCase)):_*).getOrElse(prefixPath ::: metricsTag :: Nil)
+                        }
+                    }#
+                    #for (value <- fieldValues)
+                        <td>${value}</td>
+                    #end
+                </tr>
+            #end
+        #end
+    </tbody>
+</table>
+
+</div>

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

@@ -321,4 +321,94 @@ object BammetricsReport extends ReportBuilder {
     plot.title = Some("Whole genome coverage")
     plot.runLocal()
   }
+
+  /**
+    * Generate a line plot for rna coverage
+    * @param outputDir OutputDir for the tsv and png file
+    * @param prefix Prefix of the tsv and png file
+    * @param summary Summary class
+    * @param libraryLevel Default false, when set true plot will be based on library stats instead of sample stats
+    * @param sampleId Default it selects all sampples, when sample is giving it limits to selected sample
+    */
+  def rnaHistogramPlot(outputDir: File,
+                       prefix: String,
+                       summary: Summary,
+                       libraryLevel: Boolean = false,
+                       sampleId: Option[String] = None,
+                       libId: Option[String] = None): Unit = {
+    val tsvFile = new File(outputDir, prefix + ".tsv")
+    val pngFile = new File(outputDir, prefix + ".png")
+    val tsvWriter = new PrintWriter(tsvFile)
+    if (libraryLevel) {
+      tsvWriter.println((for (
+        sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample;
+        lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib
+      ) yield s"$sample-$lib")
+        .mkString("library\t", "\t", ""))
+    } else {
+      sampleId match {
+        case Some(sample) => tsvWriter.println("\t" + sample)
+        case _            => tsvWriter.println(summary.samples.mkString("Sample\t", "\t", ""))
+      }
+    }
+
+    var map: Map[Int, Map[String, Double]] = Map()
+
+    def fill(sample: String, lib: Option[String]): Unit = {
+
+      val insertSize = new SummaryValue(List("bammetrics", "stats", "rna", "histogram", "normalized_position"),
+        summary, Some(sample), lib).value.getOrElse(List())
+      val counts = new SummaryValue(List("bammetrics", "stats", "rna", "histogram", "All_Reads.normalized_coverage"),
+        summary, Some(sample), lib).value.getOrElse(List())
+
+      (insertSize, counts) match {
+        case (l: List[_], l2: List[_]) =>
+          l.zip(l2).foreach(i => {
+            val insertSize = i._1.toString.toInt
+            val count = i._2.toString.toDouble
+            val old = map.getOrElse(insertSize, Map())
+            if (libraryLevel) map += insertSize -> (old + ((s"$sample-" + lib.get) -> count))
+            else map += insertSize -> (old + (sample -> count))
+          })
+        case _ => throw new IllegalStateException("Must be a list")
+      }
+    }
+
+    if (libraryLevel) {
+      for (
+        sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample;
+        lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib
+      ) fill(sample, Some(lib))
+    } else if (sampleId.isDefined) fill(sampleId.get, None)
+    else summary.samples.foreach(fill(_, None))
+
+    for ((insertSize, counts) <- map) {
+      tsvWriter.print(insertSize)
+      if (libraryLevel) {
+        for (
+          sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample;
+          lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib
+        ) {
+          tsvWriter.print("\t" + counts.getOrElse(s"$sample-$lib", "0"))
+        }
+      } else {
+        for (sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample) {
+          tsvWriter.print("\t" + counts.getOrElse(sample, "0"))
+        }
+      }
+      tsvWriter.println()
+    }
+
+    tsvWriter.close()
+
+    val plot = new LinePlot(null)
+    plot.input = tsvFile
+    plot.output = pngFile
+    plot.ylabel = Some("Reletive position")
+    plot.xlabel = Some("Coverage")
+    plot.width = Some(1200)
+    plot.removeZero = true
+    plot.title = Some("Rna coverage")
+    plot.runLocal()
+  }
 }

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

@@ -27,6 +27,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
   def indexPage = {
 
     val wgsExecuted = summary.getSampleValues("bammetrics", "stats", "wgs").values.exists(_.isDefined)
+    val rnaExecuted = summary.getSampleValues("bammetrics", "stats", "rna").values.exists(_.isDefined)
 
     ReportPage(
       List("Samples" -> generateSamplesPage(pageArgs)) ++
@@ -44,7 +45,9 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
         ),
         "Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
           Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false))) ++
-        ( if (wgsExecuted) List("Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
+        (if (wgsExecuted) List("Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
+          Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false))) else Nil) ++
+        (if (rnaExecuted) List("Rna coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp",
           Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false))) else Nil) ++
         List("QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",
           Map("showPlot" -> true, "showTable" -> false)),