Added target variants to report

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

@@ -10,7 +10,7 @@
 <%@ var rootPath: String %>
 <%@ var outputDir: File %>
 <%@ var metricsTag: String = "bammetrics" %>
-<%@ var target: String %>
+<%@ var target: Option[String] %>
 #{
     val samples = sampleId match {
         case Some(sample) => List(sample.toString)
@@ -46,7 +46,7 @@
             #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 prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List(metricsTag, "stats", target.get + "_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]

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

@@ -70,7 +70,7 @@ object BammetricsReport extends ReportBuilder {
       if (targets.isEmpty) List()
       else List("Targets" -> ReportPage(
         List(),
-        targets.map(t => t -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp", Map("target" -> t))),
+        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"),

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

@@ -8,13 +8,20 @@
 <%@ var outputDir: File %>
 <%@ var showPlot: Boolean = false %>
 <%@ var showTable: Boolean = true %>
-<%@ var showIntro: Boolean = true%>
+<%@ var showIntro: Boolean = true %>
+<%@ var target: Option[String] = None %>
+<%@ var caller: String = "final" %>
+
 #{
     val fields = List("Hom", "HomVar", "Het", "HomRef", "NoCall", "Variant", "Total")
     val samples = sampleId match {
         case Some(sample) => List(sample.toString)
         case _ => summary.samples.toList
     }
+    val vcfstatsKey = target match {
+        case Some(t) => s"multisample-vcfstats-$caller-$t"
+        case _ => s"multisample-vcfstats-$caller"
+    }
 }#
 
 #if (showIntro)
@@ -70,7 +77,7 @@
     #for (sample <- samples.toList.sorted)
     <tr><td><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
         #for (field <- fields)
-        <td>${summary.getSampleValue(sample, "shivavariantcalling", "stats", "multisample-vcfstats-final", "genotype", field)}</td>
+        <td>${summary.getSampleValue(sample, "shivavariantcalling", "stats", vcfstatsKey, "genotype", field)}</td>
         #end
     </tr>
     #end

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

@@ -107,14 +107,16 @@ object ShivaReport extends MultisampleReportBuilder {
     }
 
     if (regionPages.nonEmpty) Some("Regions" -> ReportPage(
-      List(),
-      regionPages.map(p => p._1 -> ReportSection(
-        "/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp",
-        Map("target" -> p._1.stripSuffix(" (Amplicon)"))
+      regionPages.map(p => p._1 -> ReportPage(Nil,
+        List(
+          "Variants" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp"),
+          "Coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp")
+        ),
+        Map("target" -> Some(p._1.stripSuffix(" (Amplicon)")))
       )).toList.sortBy(_._1),
+      List(),
       Map())
-    )
-    else None
+    ) else None
   }
 
   /** Files page, can be used general or at sample level */
@@ -178,7 +180,9 @@ object ShivaReport extends MultisampleReportBuilder {
                          prefix: String,
                          summary: Summary,
                          libraryLevel: Boolean = false,
-                         sampleId: Option[String] = None): Unit = {
+                         sampleId: Option[String] = None,
+                         caller: String = "final",
+                         target: Option[String] = None): Unit = {
     val tsvFile = new File(outputDir, prefix + ".tsv")
     val pngFile = new File(outputDir, prefix + ".png")
     val tsvWriter = new PrintWriter(tsvFile)
@@ -186,14 +190,14 @@ object ShivaReport extends MultisampleReportBuilder {
     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 path = target match {
+        case Some(t) => List("shivavariantcalling", "stats", s"multisample-vcfstats-$caller-$t", "genotype")
+        case _ => List("shivavariantcalling", "stats", s"multisample-vcfstats-$caller", "genotype")
+      }
+      val homVar = new SummaryValue(path :+ "HomVar", summary, Some(sample), lib).value.getOrElse(0).toString.toLong
+      val homRef = new SummaryValue(path :+ "HomRef", summary, Some(sample), lib).value.getOrElse(0).toString.toLong
+      val noCall = new SummaryValue(path :+ "NoCall", summary, Some(sample), lib).value.getOrElse(0).toString.toLong
+      val het = new SummaryValue(path :+ "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")

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

@@ -19,7 +19,7 @@ import htsjdk.samtools.SamReaderFactory
 import nl.lumc.sasc.biopet.core.{ MultiSampleQScript, Reference }
 import nl.lumc.sasc.biopet.extensions.Ln
 import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, MarkDuplicates, SamToFastq }
-import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
+import nl.lumc.sasc.biopet.pipelines.bammetrics.{TargetRegions, BamMetrics}
 import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
 import nl.lumc.sasc.biopet.pipelines.toucan.Toucan
 import nl.lumc.sasc.biopet.utils.Logging
@@ -32,7 +32,7 @@ import scala.collection.JavaConversions._
  *
  * Created by pjvan_thof on 2/26/15.
  */
-trait ShivaTrait extends MultiSampleQScript with Reference { qscript: QScript =>
+trait ShivaTrait extends MultiSampleQScript with Reference with TargetRegions { qscript: QScript =>
 
   /** Executed before running the script */
   def init(): Unit = {
@@ -355,11 +355,13 @@ trait ShivaTrait extends MultiSampleQScript with Reference { qscript: QScript =>
 
   /** Settings of pipeline for summary */
   def summarySettings = Map(
-      "reference" -> referenceSummary,
-      "annotation" -> annotation.isDefined,
-      "multisample_variantcalling" -> multisampleVariantCalling.isDefined,
-      "sv_calling" -> svCalling.isDefined
-    )
+    "reference" -> referenceSummary,
+    "annotation" -> annotation.isDefined,
+    "multisample_variantcalling" -> multisampleVariantCalling.isDefined,
+    "sv_calling" -> svCalling.isDefined,
+    "regions_of_interest" -> roiBedFiles.map(_.getName.stripSuffix(".bed")),
+    "amplicon_bed" -> ampliconBedFile.map(_.getName.stripSuffix(".bed"))
+  )
 
   /** Files for the summary */
   def summaryFiles = Map("referenceFasta" -> referenceFasta())