From 10d4ca7915b788feb185fa0b3a177c194f12a9b0 Mon Sep 17 00:00:00 2001
From: rhpvorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 31 Jul 2017 17:26:11 +0200
Subject: [PATCH] Started defuturing mappingQuality.ssp

---
 .../pipelines/bammetrics/mappingQuality.ssp   |  3 +-
 .../bammetrics/BammetricsReport.scala         | 46 +++++++++----------
 .../mapping/MultisampleMappingReport.scala    |  2 +-
 3 files changed, 25 insertions(+), 26 deletions(-)

diff --git a/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp b/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp
index ecd74eefd..68ae56428 100644
--- a/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp
+++ b/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp
@@ -18,6 +18,7 @@
 <%@ var fields: List[String] = List("min", "max", "mean", "median", "modal")%>
 <%@ var allSamples: Seq[Sample] %>
 <%@ var allLibraries: Seq[Library] %>
+<%@ var mappingQualityPlotTables: Array[Map[String, Array[Any]]] %>
 #{
     val samples = sampleId match {
     case Some(id) => allSamples.filter(_.id == id).toList
@@ -43,7 +44,7 @@
 #end
 
 #if (showPlot)
-    #{ BammetricsReport.mappingQualityPlot(outputDir, "mapping_quality", summary, !sampleLevel, sampleId = sampleId, libraryId = libId) }#
+    #{ BammetricsReport.mappingQualityPlot(outputDir, "mapping_quality", mappingQualityPlotTables)}#
 
     <div class="panel-body">
     <img src="mapping_quality.png" class="img-responsive" />
diff --git a/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala b/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
index 1a481bbb0..90ec0a382 100644
--- a/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+++ b/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
@@ -17,12 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics
 import java.io.{File, PrintWriter}
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.report.{
-  ReportBuilder,
-  ReportBuilderExtension,
-  ReportPage,
-  ReportSection
-}
+import nl.lumc.sasc.biopet.core.report.{ReportBuilder, ReportBuilderExtension, ReportPage, ReportSection}
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import nl.lumc.sasc.biopet.utils.rscript.{LinePlot, StackedBarPlot}
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
@@ -534,19 +529,16 @@ object BammetricsReport extends ReportBuilder {
     }
     writer.close()
   }
-}
-
-object BamMetricsAlignmentReport {
-  def values(summary: SummaryDb,
-             runId: Int,
-             allSamples: Seq[Sample],
-             allLibraries: Seq[Library],
-             sampleId: Option[Int] = None,
-             libId: Option[Int] = None,
-             sampleLevel: Boolean = false,
-             showPlot: Boolean = false,
-             showIntro: Boolean = true,
-             showTable: Boolean = true): Map[String, Any] = {
+  def alignmentReportValues(summary: SummaryDb,
+                            runId: Int,
+                            allSamples: Seq[Sample],
+                            allLibraries: Seq[Library],
+                            sampleId: Option[Int] = None,
+                            libId: Option[Int] = None,
+                            sampleLevel: Boolean = false,
+                            showPlot: Boolean = false,
+                            showIntro: Boolean = true,
+                            showTable: Boolean = true): Map[String, Any] = {
 
     val statsPaths = Map(
       "All" -> List("flagstats", "All"),
@@ -571,9 +563,7 @@ object BamMetricsAlignmentReport {
       "libId" -> libId
     )
   }
-}
-object BamMetricsMappingQuality {
-  def values(summary: SummaryDb,
+  def mappingQualityValues(summary: SummaryDb,
              runId: Int,
              allSamples: Seq[Sample],
              allLibraries: Seq[Library],
@@ -582,11 +572,19 @@ object BamMetricsMappingQuality {
              sampleLevel: Boolean = false,
              showPlot: Boolean = false,
              showIntro: Boolean = true,
-             showTable: Boolean = true): Map[String, Any] = {
+             showTable: Boolean = true
+               : Map[String, Any] = {
 
     val samples = sampleId match {
       case Some(id) => allSamples.filter(_.id == id).toList
       case _ => allSamples.toList
     }
+    val mapQualityPlotTables = mappingQualityPlotTables(summary,!sampleLevel,sampleId,libId)
+    Map("mappingQualityPlotTables" -> mapQualityPlotTables,
+    "showIntro" -> showIntro,
+    "showTable" -> showTable,
+      "showPlot" -> showPlot,
+      "sampleId" -> sampleId,
+    "libId" -> libId)
   }
-}
+}
\ No newline at end of file
diff --git a/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala b/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
index bb3344197..f69fa38a2 100644
--- a/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
+++ b/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
@@ -124,7 +124,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
                                                          libraries,
                                                          sampleId,
                                                          libId)
-    val alignmentSummary = BamMetricsAlignmentReport.values(summary,
+    val alignmentSummary = BammetricsReport.alignmentReportValues(summary,
                                                             runId,
                                                             samples,
                                                             libraries,
-- 
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