Added plots for front page of report

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

 #import(nl.lumc.sasc.biopet.core.summary.Summary)
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
+#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
+#import(java.io.File)
 <%@ var summary: Summary %>
 <%@ var sampleId: Option[String] = None %>
 <%@ var libId: Option[String] = None %>
 <%@ var sampleLevel: Boolean = false %>
 <%@ var rootPath: String %>
+<%@ var outputDir: File %>
+<%@ var showPlot: Boolean = false %>
+<%@ var showTable: Boolean = true %>
 #{
     val samples = sampleId match {
-    case Some(sample) => List(sample.toString)
-    case _ => summary.samples.toList
+        case Some(sample) => {
+            List(sample.toString)
+        }
+        case _ => summary.samples.toList
     }
 }#
+
+#if (showPlot)
+#{ BammetricsReport.alignmentSummaryPlot(outputDir, "alignmentSummary", summary, !sampleLevel, sampleId = sampleId) }#
+    <img src="alignmentSummary.png"><br>
+    <a href="alignmentSummary.tsv">Tsv file</a>
+#end
+#if (showTable)
 <table>
     <thead><tr>
         <th>Sample</th>
@@ -52,4 +66,5 @@
             #end
         #end
     </tbody>
-</table>
\ No newline at end of file
+</table>
+#end
\ No newline at end of file

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

 package nl.lumc.sasc.biopet.pipelines.bammetrics
 
+import java.io.{PrintWriter, File}
+
 import nl.lumc.sasc.biopet.core.report.{ ReportBuilder, ReportPage, ReportSection }
+import nl.lumc.sasc.biopet.core.summary.{SummaryValue, Summary}
+import nl.lumc.sasc.biopet.extensions.rscript.StackedBarPlot
 
 /**
  * Created by pjvan_thof on 3/30/15.
  */
 object BammetricsReport extends ReportBuilder {
+  // FIXME: Not yet finished
+
   val reportName = "Bam Metrics"
 
   def indexPage = ReportPage(Map(
@@ -29,5 +35,55 @@ object BammetricsReport extends ReportBuilder {
     Map()
   )
 
-  // FIXME: Not yet finished
+  def alignmentSummaryPlot(outputDir: File,
+                           prefix: String,
+                           summary: Summary,
+                           libraryLevel: Boolean = false,
+                           sampleId: 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.print("Library") else tsvWriter.print("Sample")
+    tsvWriter.println("\tMapped\tDuplicates\tUnmapped\tSecondary")
+
+    def getLine(summary: Summary, sample: String, lib: Option[String] = None): String = {
+      val mapped = new SummaryValue(List("bammetrics", "stats", "biopet_flagstat", "Mapped"),
+        summary, Some(sample), lib).value.getOrElse(0).toString.toLong
+      val duplicates = new SummaryValue(List("bammetrics", "stats", "biopet_flagstat", "Duplicates"),
+        summary, Some(sample), lib).value.getOrElse(0).toString.toLong
+      val total = new SummaryValue(List("bammetrics", "stats", "biopet_flagstat", "All"),
+        summary, Some(sample), lib).value.getOrElse(0).toString.toLong
+      val secondary = new SummaryValue(List("bammetrics", "stats", "biopet_flagstat", "NotPrimaryAlignment"),
+        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(duplicates + "\t")
+      sb.append((total - mapped - secondary) + "\t")
+      sb.append(secondary)
+      sb.toString
+    }
+
+    if (libraryLevel) {
+      for (sample <- summary.samples if (sampleId.isEmpty || sample == sampleId.get);
+           lib <- summary.libraries(sample)) {
+        tsvWriter.println(getLine(summary, sample, Some(lib)))
+      }
+    } else {
+      for (sample <- summary.samples if (sampleId.isEmpty || sample == sampleId.get)) {
+        tsvWriter.println(getLine(summary, sample))
+      }
+    }
+
+    tsvWriter.close()
+
+    val plot = new StackedBarPlot(null)
+    plot.input = tsvFile
+    plot.output = pngFile
+    plot.ylabel = Some("Reads")
+    plot.width = Some(750)
+    plot.runLocal()
+  }
+
+
 }

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala

@@ -64,7 +64,14 @@ trait RscriptCommandLineFunction extends BiopetCommandLineFunction {
   def runLocal(logger: ProcessLogger): Unit = {
     checkScript(local = true)
 
-    Process(cmdLine).run(logger)
+    this.logger.info(cmdLine)
+
+    val cmd = cmdLine.stripPrefix(" '").stripSuffix("' ").split("' *'")
+
+    this.logger.info(cmd.mkString(" "))
+
+    val process = Process(cmd.toSeq).run(logger)
+    this.logger.info(process.exitValue())
   }
 
   /**

public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp

 #import(nl.lumc.sasc.biopet.core.summary.Summary)
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
+#import(nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport)
+#import(java.io.File)
 <%@ var summary: Summary %>
 <%@ var sampleId: Option[String] = None %>
 <%@ var libId: Option[String] = None %>
 <%@ var rootPath: String %>
+<%@ var outputDir: File %>
+<%@ var showPlot: Boolean = false %>
+<%@ var showTable: Boolean = true %>
 #{
     val samples = sampleId match {
         case Some(sample) => List(sample.toString)
         case _ => summary.samples.toList
     }
 }#
+#if (showPlot)
+    #{
+        FlexiprepReport.baseSummaryPlot(outputDir, "QC_Bases_R1","R1", summary, sampleId = sampleId)
+        FlexiprepReport.baseSummaryPlot(outputDir, "QC_Bases_R2","R2", summary, sampleId = sampleId)
+    }#
+    <table>
+        <tr><th>R1</th><th>R2</th></tr>
+        <tr>
+            <td><img src="QC_Bases_R1.png"><br><a href="QC_Bases_R1.tsv">Tsv file</a></td>
+            <td><img src="QC_Bases_R2.png"><br><a href="QC_Bases_R2.tsv">Tsv file</a></td>
+        </tr>
+    </table>
+#end
+#if (showTable)
 <table>
 <thead><tr>
     <th>Sample</th>
@@ -54,4 +73,5 @@
         #end
     #end
 </tbody>
-</table>
\ No newline at end of file
+</table>
+#end
\ No newline at end of file

public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp

 #import(nl.lumc.sasc.biopet.core.summary.Summary)
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
+#import(nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport)
+#import(java.io.File)
 <%@ var summary: Summary %>
 <%@ var sampleId: Option[String] = None %>
 <%@ var libId: Option[String] = None %>
 <%@ var rootPath: String %>
+<%@ var outputDir: File %>
+<%@ var showPlot: Boolean = false %>
+<%@ var showTable: Boolean = true %>
 #{
     val samples = sampleId match {
         case Some(sample) => List(sample.toString)
         case _ => summary.samples.toList
     }
 }#
+
+#if (showPlot)
+    #{
+        FlexiprepReport.readSummaryPlot(outputDir, "QC_Reads_R1","R1", summary, sampleId = sampleId)
+        FlexiprepReport.readSummaryPlot(outputDir, "QC_Reads_R2","R2", summary, sampleId = sampleId)
+    }#
+    <table>
+        <tr><th>R1</th><th>R2</th></tr>
+        <tr>
+            <td><img src="QC_Reads_R1.png"><br><a href="QC_Reads_R1.tsv">Tsv file</a></td>
+            <td><img src="QC_Reads_R2.png"><br><a href="QC_Reads_R2.tsv">Tsv file</a></td>
+        </tr>
+    </table>
+#end
+#if (showTable)
 <table>
 <thead><tr>
     <th>Sample</th>
@@ -56,4 +76,5 @@
         #end
     #end
 </tbody>
-</table>
\ No newline at end of file
+</table>
+#end
\ No newline at end of file

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala

 package nl.lumc.sasc.biopet.pipelines.flexiprep
 
+import java.io.{PrintWriter, File}
+
 import nl.lumc.sasc.biopet.core.report.{ ReportSection, ReportPage, ReportBuilder }
+import nl.lumc.sasc.biopet.core.summary.{SummaryValue, Summary}
+import nl.lumc.sasc.biopet.extensions.rscript.StackedBarPlot
 
 /**
  * Created by pjvan_thof on 3/30/15.
@@ -38,4 +42,88 @@ object FlexiprepReport extends ReportBuilder {
   }
 
   // FIXME: Not yet finished
+
+  def readSummaryPlot(outputDir: File,
+                         prefix: String,
+                         read: String,
+                         summary: Summary,
+                         sampleId: Option[String] = None): Unit = {
+    val tsvFile = new File(outputDir, prefix + ".tsv")
+    val pngFile = new File(outputDir, prefix + ".png")
+    val tsvWriter = new PrintWriter(tsvFile)
+    tsvWriter.println("Library\tAfter_QC\tClipping\tTrimming\tSynced")
+
+    def getLine(summary: Summary, sample: String, lib: String): String = {
+      val beforeTotal = new SummaryValue(List("flexiprep", "stats", "seqstat_" + read, "reads", "num_total"),
+        summary, Some(sample), Some(lib)).value.getOrElse(0).toString.toLong
+      val afterTotal = new SummaryValue(List("flexiprep", "stats", "seqstat_" + read + "_after", "reads", "num_total"),
+        summary, Some(sample), Some(lib)).value.getOrElse(0).toString.toLong
+      val clippingDiscardedToShort = new SummaryValue(List("flexiprep", "stats", "clipping_" + read, "num_reads_discarded_too_short"),
+        summary, Some(sample), Some(lib)).value.getOrElse(0).toString.toLong
+      val clippingDiscardedToLong = new SummaryValue(List("flexiprep", "stats", "clipping_" + read, "num_reads_discarded_too_long"),
+        summary, Some(sample), Some(lib)).value.getOrElse(0).toString.toLong
+      val trimmingDiscarded = new SummaryValue(List("flexiprep", "stats", "trimming", "num_reads_discarded_" + read),
+        summary, Some(sample), Some(lib)).value.getOrElse(0).toString.toLong
+
+      val sb = new StringBuffer()
+      sb.append(sample + "-" + lib + "\t")
+      sb.append(afterTotal + "\t")
+      sb.append((clippingDiscardedToShort + clippingDiscardedToLong) + "\t")
+      sb.append(trimmingDiscarded + "\t")
+      sb.append(beforeTotal - afterTotal - trimmingDiscarded - clippingDiscardedToShort - clippingDiscardedToLong)
+      sb.toString
+    }
+
+    for (sample <- summary.samples if (sampleId.isEmpty || sample == sampleId.get);
+         lib <- summary.libraries(sample)) {
+      tsvWriter.println(getLine(summary, sample, lib))
+    }
+
+    tsvWriter.close()
+
+    val plot = new StackedBarPlot(null)
+    plot.input = tsvFile
+    plot.output = pngFile
+    plot.ylabel = Some("Reads")
+    plot.width = Some(750)
+    plot.runLocal()
+  }
+
+  def baseSummaryPlot(outputDir: File,
+                      prefix: String,
+                      read: String,
+                      summary: Summary,
+                      sampleId: Option[String] = None): Unit = {
+    val tsvFile = new File(outputDir, prefix + ".tsv")
+    val pngFile = new File(outputDir, prefix + ".png")
+    val tsvWriter = new PrintWriter(tsvFile)
+    tsvWriter.println("Library\tAfter_QC\tDiscarded")
+
+    def getLine(summary: Summary, sample: String, lib: String): String = {
+      val beforeTotal = new SummaryValue(List("flexiprep", "stats", "seqstat_" + read, "bases", "num_total"),
+        summary, Some(sample), Some(lib)).value.getOrElse(0).toString.toLong
+      val afterTotal = new SummaryValue(List("flexiprep", "stats", "seqstat_" + read + "_after", "bases", "num_total"),
+        summary, Some(sample), Some(lib)).value.getOrElse(0).toString.toLong
+
+      val sb = new StringBuffer()
+      sb.append(sample + "-" + lib + "\t")
+      sb.append(afterTotal + "\t")
+      sb.append(beforeTotal - afterTotal)
+      sb.toString
+    }
+
+    for (sample <- summary.samples if (sampleId.isEmpty || sample == sampleId.get);
+         lib <- summary.libraries(sample)) {
+      tsvWriter.println(getLine(summary, sample, lib))
+    }
+
+    tsvWriter.close()
+
+    val plot = new StackedBarPlot(null)
+    plot.input = tsvFile
+    plot.output = pngFile
+    plot.ylabel = Some("Bases")
+    plot.width = Some(750)
+    plot.runLocal()
+  }
 }

public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp

 #import(nl.lumc.sasc.biopet.core.summary.Summary)
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
+#import(nl.lumc.sasc.biopet.pipelines.shiva.ShivaReport)
+#import(java.io.File)
 <%@ var summary: Summary %>
 <%@ var sampleId: Option[String] = None %>
 <%@ var rootPath: String %>
+<%@ var outputDir: File %>
+<%@ var showPlot: Boolean = false %>
+<%@ var showTable: Boolean = true %>
 #{
     val fields = List("Hom", "HomVar", "HomRef", "NoCall", "Variant", "NonInformative", "Total")
     val samples = sampleId match {
@@ -11,6 +16,12 @@
     }
 }#
 
+#if (showPlot)
+    #{ ShivaReport.variantSummaryPlot(outputDir, "variantSummary", summary, sampleId = sampleId) }#
+    <img src="variantSummary.png"><br>
+    <a href="variantSummary.tsv">Tsv file</a>
+#end
+#if (showTable)
 <table>
 <thead><tr><th>Sample</th>
 #for (field <- fields) <th>${field}</th> #end
@@ -24,4 +35,5 @@
         </tr>
     #end
 </tbody>
-</table>
\ No newline at end of file
+</table>
+#end
\ No newline at end of file

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

 package nl.lumc.sasc.biopet.pipelines.shiva
 
+import java.io.{PrintWriter, File}
+
 import nl.lumc.sasc.biopet.core.report.{ ReportSection, MultisampleReportBuilder, ReportPage }
+import nl.lumc.sasc.biopet.core.summary.{SummaryValue, Summary}
+import nl.lumc.sasc.biopet.extensions.rscript.StackedBarPlot
 import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
 import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
 
@@ -8,32 +12,47 @@ import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
  * Created by pjvan_thof on 3/30/15.
  */
 object ShivaReport extends MultisampleReportBuilder {
-  def indexPage = ReportPage(
-    Map(
-      /*"General" -> ReportPage(Map(), List(
-        "Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp"),
-        "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp", Map("sampleLevel" -> true)),
-        "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
-        "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
-      ), Map()),*/
-      "Samples" -> generateSamplesPage(pageArgs)
-    ),
-    List(
-      "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp"),
-      "Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp"),
-      "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp", Map("sampleLevel" -> true)),
-      "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
-      "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
-    ),
-    pageArgs
-  )
+
+  // FIXME: Not yet finished
+
+  def indexPage = {
+    ReportPage(
+      Map(
+        "MultiSample" -> ReportPage(Map(), List(
+          "Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp",
+            Map("showPlot" -> true, "showTable" -> true)),
+          "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
+            Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> true)),
+          "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",
+            Map("showPlot" -> true, "showTable" -> true)),
+          "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
+            Map("showPlot" -> true, "showTable" -> true))
+        ), Map()),
+        "Samples" -> generateSamplesPage(pageArgs)
+      ),
+      List(
+        "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp"),
+        "Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp",
+          Map("showPlot" -> true, "showTable" -> false)),
+        "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
+          Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)
+        ),
+        "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",
+          Map("showPlot" -> true, "showTable" -> false)),
+        "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
+          Map("showPlot" -> true, "showTable" -> false))
+      ),
+      pageArgs
+    )
+  }
 
   def samplePage(sampleId: String, args: Map[String, Any]) = {
     ReportPage(Map(
       "Libraries" -> generateLibraryPage(args),
       "Alignment" -> BammetricsReport.bamMetricsPage
     ), List(
-      "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
+      "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
+        if (summary.libraries(sampleId).size > 1) Map("showPlot" -> true) else Map()),
       "Preprocessing" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp", Map("sampleLevel" -> true)),
       "Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp"),
       "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
@@ -54,5 +73,53 @@ object ShivaReport extends MultisampleReportBuilder {
 
   def reportName = "Shiva Report"
 
-  // FIXME: Not yet finished
+  def variantSummaryPlot(outputDir: File,
+                           prefix: String,
+                           summary: Summary,
+                           libraryLevel: Boolean = false,
+                           sampleId: 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.print("Library") else tsvWriter.print("Sample")
+    tsvWriter.println("\tHomVar\tHet\tHomRef\tNoCall")
+
+    def getLine(summary: Summary, sample: String, lib: Option[String] = None): String = {
+      val homVar = new SummaryValue(List("shivavariantcalling", "stats", "multisample-vcfstats-final", "genotype", "HomVar"),
+        summary, Some(sample), lib).value.getOrElse(0).toString.toLong
+      val homRef = new SummaryValue(List("shivavariantcalling", "stats", "multisample-vcfstats-final", "genotype", "HomRef"),
+        summary, Some(sample), lib).value.getOrElse(0).toString.toLong
+      val noCall = new SummaryValue(List("shivavariantcalling", "stats", "multisample-vcfstats-final", "genotype", "NoCall"),
+        summary, Some(sample), lib).value.getOrElse(0).toString.toLong
+      val het = new SummaryValue(List("shivavariantcalling", "stats", "multisample-vcfstats-final", "genotype", "Het"),
+        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(homVar + "\t")
+      sb.append(het + "\t")
+      sb.append(homRef + "\t")
+      sb.append(noCall)
+      sb.toString
+    }
+
+    if (libraryLevel) {
+      for (sample <- summary.samples if (sampleId.isEmpty || sample == sampleId.get);
+           lib <- summary.libraries(sample)) {
+        tsvWriter.println(getLine(summary, sample, Some(lib)))
+      }
+    } else {
+      for (sample <- summary.samples if (sampleId.isEmpty || sample == sampleId.get)) {
+        tsvWriter.println(getLine(summary, sample))
+      }
+    }
+
+    tsvWriter.close()
+
+    val plot = new StackedBarPlot(null)
+    plot.input = tsvFile
+    plot.output = pngFile
+    plot.ylabel = Some("VCF records")
+    plot.width = Some(750)
+    plot.runLocal()
+  }
 }