Format fix

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

@@ -9,6 +9,7 @@
 #import(java.io.File)
 <%@ var summary: SummaryDb %>
 <%@ var sampleId: Option[Int] = None %>
+<%@ var multisample: Boolean = true %>
 <%@ var rootPath: String %>
 <%@ var outputDir: File %>
 <%@ var showPlot: Boolean = false %>
@@ -82,7 +83,8 @@
     #{
     fields.map(x => x -> List("total", "genotype", "general", sample.name, x)).toMap
         val statsPaths = fields.map(x => x -> List("total", "genotype", "general", sample.name, x)).toMap
-        val results = summary.getStatKeys(runId, "shivavariantcalling", "vcfstatsKey", sample = sample.id, keyValues = statsPaths)
+        val sampleQuery: SampleQuery = if (multisample) NoSample else SampleId(sampleId.get)
+        val results = summary.getStatKeys(runId, "shivavariantcalling", vcfstatsKey, sampleQuery, keyValues = statsPaths)
     }#
 
     #for (field <- fields)

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

@@ -148,7 +148,7 @@ trait ShivaReportTrait extends MultisampleMappingReportTrait {
     val samples = Await.result(summary.getSamples(runId = runId, sampleId = sampleId), Duration.Inf)
     val statsPaths = {
       (for (sample <- Await.result(summary.getSamples(runId = runId), Duration.Inf)) yield {
-        field.map(f => s"${sample.name};HomVar" -> List("total", "genotype", "general", sample.name, f)).toMap
+        field.map(f => s"${sample.name};$f" -> List("total", "genotype", "general", sample.name, f)).toMap
       }).fold(Map())(_ ++ _)
     }
 
@@ -160,7 +160,7 @@ trait ShivaReportTrait extends MultisampleMappingReportTrait {
     val results = summary.getStatKeys(runId, "shivavariantcalling", moduleName, sampleId.map(SampleId).getOrElse(NoSample), keyValues = statsPaths)
 
     for (sample <- samples if sampleId.isEmpty || sample.id == sampleId.get) {
-      tsvWriter.println(sample.name + "\t" + field.map(f => results(s"${sample.name};$f").getOrElse("")).mkString("\t"))
+      tsvWriter.println(sample.name + "\t" + field.map(f => results.get(s"${sample.name};$f").getOrElse(Some("0")).get).mkString("\t"))
     }
 
     tsvWriter.close()