sv-s are grouped by type also for the tables

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

@@ -8,22 +8,28 @@
 <%@ var showIntro: Boolean = true %>
 
 #{
-    val svTypes = List(
-    SvTypeForReport("DEL", "Deletion", "svSummaryDeletions.tsv", "svSummaryDeletions.png"),
-    SvTypeForReport("DUP", "Duplication", "svSummaryDuplications.tsv", "svSummaryDuplications.png"),
-    SvTypeForReport("INS", "Insertion", "svSummaryInsertions.tsv", "svSummaryInsertions.png"),
-    SvTypeForReport("INV", "Inversion", "svSummaryInversions.tsv", "svSummaryInversions.png"))
+    val sampleNames: List[String] = summary.samples.toList.sorted
 
     val counts: Map[String, Map[String, Array[Any]]] = ShivaSvCallingReport.parseSummaryForSvCounts(summary)
 
-    ShivaSvCallingReport.writeTsvForPlots(counts, svTypes, outputDir)
+    var svTypes = List(
+    SvTypeForReport("DEL", "Deletions", "svSummaryDeletions.tsv", "svSummaryDeletions.png"),
+    SvTypeForReport("DUP", "Duplications", "svSummaryDuplications.tsv", "svSummaryDuplications.png"),
+    SvTypeForReport("INS", "Insertions", "svSummaryInsertions.tsv", "svSummaryInsertions.png"),
+    SvTypeForReport("INV", "Inversions", "svSummaryInversions.tsv", "svSummaryInversions.png"))
+    svTypes = svTypes.filter(sv => counts.contains(sv.svType))
+    val tsvAllTypes = "svSummary.tsv"
+
+    ShivaSvCallingReport.writeTsvFiles(sampleNames, counts, svTypes, tsvAllTypes, outputDir)
     ShivaSvCallingReport.createPlots(svTypes, outputDir)
 }#
 
 
 #if (showPlot)
     <div class="panel-body">
-    <img src="svSummaryDeletions.png" class="img-responsive" />
+    #for (sv <- svTypes)
+        <img src="${sv.pngFileName}" />
+    #end
     </div>
     <div class="panel-footer">
     #if (showTable)
@@ -31,49 +37,34 @@
     #else
         <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#svSummaryTable">Show table</button>
     #end
-    <i class="glyphicon glyphicon-file"></i> <a href="svSummary.tsv">tsv file</a>
+    <i class="glyphicon glyphicon-file"></i> <a href="${tsvAllTypes}">tsv file</a>
     </div>
 #end
 
 <div class="panel-body collapse #if (showTable)in#end" id="svSummaryTable">
 
+#for (sv <- svTypes)
+#{
+    val countsForSvType: Map[String, Array[Any]] = counts.get(sv.svType).get
+}#
+<h3>${sv.displayText}</h3>
 <table class="table sortable-theme-bootstrap" data-sortable>
     <thead><tr><th data-sorted="true" data-sorted-direction="ascending">Sample</th>
-        <th>Variant Type</th> <!-- TODO: use values from summary.getValue("shivasvcalling", "stats", "histBreaksForCounts")  -->
-        <th>&le;100bp</th>
-        <th>0.1-1kb</th>
-        <th>1-10kb</th>
-        <th>10-100kb</th>
-        <th>0.1-1Mb</th>
-        <th>1-10Mb</th>
-        <th>&gt;10Mb</th>
+        #for (text <- ShivaSvCallingReport.histogramText)
+            <th>${text}</th>
+         #end
     </tr></thead>
     <tbody>
-        #for (sampleName <- summary.samples.toList.sorted)
-            #{
-                val sampleCounts:Map[String, Array[Any]] = counts.get(sampleName).get
-                var firstRow = true
-            }#
-
-            #for (sv <- svTypes)
-                <tr>
-                #if (counts.contains(sv.svType))
-                    #if (firstRow)
-                        <td><a href="${rootPath}Samples/${sampleName}/index.html">${sampleName}</a></td>
-                        #{ firstRow = false }#
-                    #else
-                        <td></td>
-                    #end
-
-                        <td>${sv.displayText}</td>
-
-                    #for (countForSize <- counts.get(sv.svType).get.asInstanceOf[List[Long]])
-                        <td>${countForSize}</td>
-                    #end
-                #end
-                </tr>
+        #for (sampleName <- sampleNames)
+            <tr>
+            <td><a href="${rootPath}Samples/${sampleName}/index.html">${sampleName}</a></td>
+            #for (countForSize <- countsForSvType.get(sampleName).get)
+                <td>${countForSize}</td>
             #end
+            </tr>
         #end
     </tbody>
 </table>
+
+#end
 </div>

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala

@@ -14,11 +14,9 @@
  */
 package nl.lumc.sasc.biopet.pipelines.shiva
 
-import java.io.File
-
 import htsjdk.variant.vcf.VCFFileReader
 import nl.lumc.sasc.biopet.core.summary.{ Summarizable, SummaryQScript }
-import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, SampleLibraryTag }
+import nl.lumc.sasc.biopet.core.{ Reference, SampleLibraryTag }
 import nl.lumc.sasc.biopet.extensions.Pysvtools
 import nl.lumc.sasc.biopet.pipelines.shiva.svcallers._
 import nl.lumc.sasc.biopet.utils.config.Configurable
@@ -100,7 +98,7 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
     // sample tagging is however not available within this pipeline
 
     for ((sample, mergedResultFile) <- outputMergedVCFbySample) {
-      lazy val counts = getVariantCounts(mergedResultFile, ShivaSvCalling.histogramBinBoundaries)
+      lazy val counts = getVariantCounts(mergedResultFile, ShivaSvCallingReport.histogramBinBoundaries)
       addSummarizable(new Summarizable {
         def summaryFiles = Map.empty
         def summaryStats = counts
@@ -108,7 +106,7 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
     }
     addSummarizable(new Summarizable {
       def summaryFiles = Map.empty
-      def summaryStats = ShivaSvCalling.histogramBinBoundaries
+      def summaryStats = ShivaSvCallingReport.histogramBinBoundaries
     }, "histBreaksForCounts")
 
     addSummaryJobs()
@@ -164,13 +162,4 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
     true
   }
 
-}
-
-object ShivaSvCalling extends PipelineCommand {
-  val histogramBinBoundaries: Array[Int] = Array(100, 1000, 10000, 100000, 1000000, 10000000)
-}
-
-object StructuralVariantType extends Enumeration {
-  val Deletion = Value("DEL")
-  val Inversion = Value("INV")
 }
\ No newline at end of file