Adding clipping and mapping quality plots to report

bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.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("mean_insert_size", "standard_deviation", "median_insert_size")%>
+<%@ 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>
+        #if (sampleId.isDefined && libId.isDefined)
+            This plot shows the clipping distribution for all libraries combined in sample <b>${sampleId}</b>.
+        #elseif(sampleId.isDefined)
+            This plot shows the clipping distribution for the libraries of sample <b>${sampleId}</b>.
+        #else
+            This plot shows the clipping distribution for each of the <b>${samples.size}</b> samples.
+        #end
+        </p>
+    </div>
+    </div>
+#end
+
+#if (showPlot)
+    #{ BammetricsReport.clippingPlot(outputDir, "clipping", summary, !sampleLevel, sampleId = sampleId, libId = libId) }#
+
+    <div class="panel-body">
+    <img src="clipping.png" class="img-responsive" />
+    </div>
+    <div class="panel-footer">
+        #if (showTable)
+            <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#clippingTable">
+                <i class="glyphicon glyphicon-eye-close"></i> Hide table</button>
+        #else
+            <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#clippingTable">
+            <i class="glyphicon glyphicon-eye-open"></i> Show table</button>
+        #end
+        <button type="button" class="btn btn-info"><i class="glyphicon glyphicon-cloud-download"> <a href="clipping.tsv">tsv file</a></i></button>
+
+    </div>
+#end
+
+<div class="panel-body collapse #if (showTable)in#end" id="clippingTable">
+<!-- Table -->
+<table class="table">
+    <thead><tr>
+        <th data-sorted="true" data-sorted-direction="ascending">Sample</th>
+        #if (!sampleLevel) <th>Library</th> #end
+        #for (field <- fields)
+            <th>${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("CollectInsertSizeMetrics", "metrics", field.toUpperCase)):_*).getOrElse("N/A")
+                        }
+                    }#
+                    #for (value <- fieldValues)
+                        <td>${value}</td>
+                    #end
+                </tr>
+            #end
+        #end
+    </tbody>
+</table>
+
+</div>

bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.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("mean_insert_size", "standard_deviation", "median_insert_size")%>
+<%@ 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>
+        #if (sampleId.isDefined && libId.isDefined)
+            This plot shows the mapping quality distribution for all libraries combined in sample <b>${sampleId}</b>.
+        #elseif(sampleId.isDefined)
+            This plot shows the mapping quality distribution for the libraries of sample <b>${sampleId}</b>.
+        #else
+            This plot shows the mapping quality distribution for each of the <b>${samples.size}</b> samples.
+        #end
+        </p>
+    </div>
+    </div>
+#end
+
+#if (showPlot)
+    #{ BammetricsReport.mappingQualityPlot(outputDir, "mapping_quality", summary, !sampleLevel, sampleId = sampleId, libId = libId) }#
+
+    <div class="panel-body">
+    <img src="mapping_quality.png" class="img-responsive" />
+    </div>
+    <div class="panel-footer">
+        #if (showTable)
+            <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#mapping_qualityTable">
+                <i class="glyphicon glyphicon-eye-close"></i> Hide table</button>
+        #else
+            <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#mapping_qualityTable">
+            <i class="glyphicon glyphicon-eye-open"></i> Show table</button>
+        #end
+        <button type="button" class="btn btn-info"><i class="glyphicon glyphicon-cloud-download"> <a href="mapping_quality.tsv">tsv file</a></i></button>
+
+    </div>
+#end
+
+<div class="panel-body collapse #if (showTable)in#end" id="mapping_qualityTable">
+<!-- Table -->
+<table class="table">
+    <thead><tr>
+        <th data-sorted="true" data-sorted-direction="ascending">Sample</th>
+        #if (!sampleLevel) <th>Library</th> #end
+        #for (field <- fields)
+            <th>${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("CollectInsertSizeMetrics", "metrics", field.toUpperCase)):_*).getOrElse("N/A")
+                        }
+                    }#
+                    #for (value <- fieldValues)
+                        <td>${value}</td>
+                    #end
+                </tr>
+            #end
+        #end
+    </tbody>
+</table>
+
+</div>

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

@@ -82,7 +82,9 @@ object BammetricsReport extends ReportBuilder {
         targets.map(t => t -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp", Map("target" -> Some(t)))),
         Map())),
       List(
-        "Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp")) ++
+        "Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
+        "Mapping Quality" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp", Map("showPlot" -> true)),
+        "Clipping" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp", Map("showPlot" -> true))) ++
         (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",
@@ -196,6 +198,62 @@ object BammetricsReport extends ReportBuilder {
       removeZero = true).runLocal()
   }
 
+  def mappingQualityPlot(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")
+
+    def paths(name: String) = Map(
+      "mapping_quality" -> List("bammetrics", "stats", "bamstats", "mapping_quality", "value"),
+      name -> List("bammetrics", "stats", "bamstats", "mapping_quality", "count")
+    )
+
+    val tables = getSampleLibraries(summary, sampleId, libId, libraryLevel)
+      .map {
+        case (sample, lib) =>
+          getTableFromSummary(summary, paths(lib.map(l => s"$sample-$l").getOrElse(sample)), Some(sample), lib)
+      }
+    writeTableToTsv(tsvFile, mergeTables(tables.toArray, "mapping_quality"), "mapping_quality")
+
+    LinePlot(tsvFile, pngFile,
+      xlabel = Some("Mapping Quality"),
+      ylabel = Some("Reads"),
+      title = Some("Mapping Quality"),
+      removeZero = true).runLocal()
+  }
+
+  def clippingPlot(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")
+
+    def paths(name: String) = Map(
+      "clipping" -> List("bammetrics", "stats", "bamstats", "clipping", "value"),
+      name -> List("bammetrics", "stats", "bamstats", "clipping", "count")
+    )
+
+    val tables = getSampleLibraries(summary, sampleId, libId, libraryLevel)
+      .map {
+        case (sample, lib) =>
+          getTableFromSummary(summary, paths(lib.map(l => s"$sample-$l").getOrElse(sample)), Some(sample), lib)
+      }
+    writeTableToTsv(tsvFile, mergeTables(tables.toArray, "clipping"), "clipping")
+
+    LinePlot(tsvFile, pngFile,
+      xlabel = Some("Clipping"),
+      ylabel = Some("Reads"),
+      title = Some("Clipping"),
+      removeZero = true).runLocal()
+  }
+
   /**
    * Generate a line plot for wgs coverage
    *