Change method singature

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala

@@ -30,7 +30,7 @@ trait Summarizable {
   def summaryFiles: Map[String, File]
 
   /** Must returns stats to store into summary */
-  def summaryStats: Map[String, Any]
+  def summaryStats: Any
 
   /** Can be used to add additional Summarizable, this is executed at the start of WriteSummary*/
   def addToQscriptSummary(qscript: SummaryQScript, name: String) {}

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala

@@ -139,7 +139,7 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
     val stats = summarizable.summaryStats
     val files = parseFiles(summarizable.summaryFiles)
 
-    (if (stats.isEmpty) Map[String, Any]() else Map("stats" -> Map(name -> stats))) ++
+    (Map("stats" -> Map(name -> stats))) ++
       (if (files.isEmpty) Map[String, Any]() else Map("files" -> Map(name -> files)))
   }
 

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

@@ -63,7 +63,7 @@ class CalculateHsMetrics(val root: Configurable) extends Picard with Summarizabl
   def summaryFiles: Map[String, File] = Map()
 
   /** Returns stats for summary */
-  def summaryStats: Map[String, Any] = Picard.getMetrics(output).getOrElse(Map())
+  def summaryStats: Any = Picard.getMetrics(output).getOrElse(Map())
 }
 
 object CalculateHsMetrics {

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

@@ -66,7 +66,7 @@ class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with
   def summaryFiles: Map[String, File] = Map()
 
   /** Returns stats for summary */
-  def summaryStats: Map[String, Any] = Picard.getMetrics(output).getOrElse(Map())
+  def summaryStats = Picard.getMetrics(output).getOrElse(Map())
 }
 
 object CollectAlignmentSummaryMetrics {

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

@@ -71,7 +71,7 @@ class CollectGcBiasMetrics(val root: Configurable) extends Picard with Summariza
   def summaryFiles: Map[String, File] = Map()
 
   /** Returns stats for summary */
-  def summaryStats: Map[String, Any] = Picard.getMetrics(output).getOrElse(Map())
+  def summaryStats = Picard.getMetrics(output).getOrElse(Map())
 }
 
 object CollectGcBiasMetrics {

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

@@ -75,7 +75,7 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summa
   /** Returns files for summary */
   def summaryFiles: Map[String, File] = Map("output_histogram" -> outputHistogram)
 
-  def summaryStats: Map[String, Any] = Picard.getMetrics(output).getOrElse(Map())
+  def summaryStats = Picard.getMetrics(output).getOrElse(Map())
 }
 
 object CollectInsertSizeMetrics {

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

@@ -68,25 +68,25 @@ class CollectMultipleMetrics(val root: Configurable) extends Picard with Summari
 
   override def addToQscriptSummary(qscript: SummaryQScript, name: String): Unit = {
     program.foreach(p => {
-      val stats: Map[String, Any] = p match {
+      val stats: Any = p match {
         case _ if p == Programs.CollectAlignmentSummaryMetrics.toString =>
-          Picard.getMetrics(new File(outputName + ".alignment_summary_metrics")).getOrElse(Map())
+          Picard.getMetrics(new File(outputName + ".alignment_summary_metrics"), groupBy = Some("CATEGORY"))
         case _ if p == Programs.CollectInsertSizeMetrics.toString =>
           Map(
-            "metrics" -> Picard.getMetrics(new File(outputName + ".insert_size_metrics")).getOrElse(Map()),
-            "histogram" -> Picard.getMetrics(new File(outputName + ".insert_size_metrics"), "HISTOGRAM").getOrElse(Map())
+            "metrics" -> Picard.getMetrics(new File(outputName + ".insert_size_metrics")),
+            "histogram" -> Picard.getHistogram(new File(outputName + ".insert_size_metrics"))
           )
         case _ if p == Programs.QualityScoreDistribution.toString =>
-          Picard.getMetrics(new File(outputName + ".quality_distribution_metrics"), "HISTOGRAM").getOrElse(Map())
+          Picard.getHistogram(new File(outputName + ".quality_distribution_metrics"))
         case _ if p == Programs.MeanQualityByCycle.toString =>
-          Picard.getMetrics(new File(outputName + ".quality_by_cycle_metrics"), "HISTOGRAM").getOrElse(Map())
+          Picard.getHistogram(new File(outputName + ".quality_by_cycle_metrics"))
         case _ if p == Programs.CollectBaseDistributionByCycle.toString =>
-          Picard.getMetrics(new File(outputName + ".base_distribution_by_cycle_metrics")).getOrElse(Map())
-        case _ => Map()
+          Picard.getMetrics(new File(outputName + ".base_distribution_by_cycle_metrics"))
+        case _ => None
       }
       val sum = new Summarizable {
         override def summaryFiles: Map[String, File] = Map()
-        override def summaryStats: Map[String, Any] = stats
+        override def summaryStats = stats
       }
       qscript.addSummarizable(sum, p)
     })

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

@@ -84,7 +84,7 @@ class CollectRnaSeqMetrics(val root: Configurable) extends Picard with Summariza
       "output_chart" -> chartOutput
     ).collect { case (key, Some(value)) => key -> value }
 
-  def summaryStats: Map[String, Any] = Picard.getMetrics(output).getOrElse(Map())
+  def summaryStats = Picard.getMetrics(output).getOrElse(Map())
 
   override def commandLine = super.commandLine +
     required("INPUT=", input, spaceSeparated = false) +

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

@@ -51,7 +51,7 @@ class CollectTargetedPcrMetrics(val root: Configurable) extends Picard with Summ
   def summaryFiles: Map[String, File] = Map()
 
   /** Returns stats for summary */
-  def summaryStats: Map[String, Any] = Picard.getMetrics(output).getOrElse(Map())
+  def summaryStats = Picard.getMetrics(output).getOrElse(Map())
 }
 
 object CollectTargetedPcrMetrics {

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

@@ -51,5 +51,5 @@ class CollectWgsMetrics(val root: Configurable) extends Picard with Summarizable
   def summaryFiles: Map[String, File] = Map()
 
   /** Returns stats for summary */
-  def summaryStats: Map[String, Any] = Picard.getMetrics(output).getOrElse(Map())
+  def summaryStats = Picard.getMetrics(output).getOrElse(Map())
 }

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

@@ -100,7 +100,7 @@ class MarkDuplicates(val root: Configurable) extends Picard with Summarizable {
   def summaryFiles: Map[String, File] = Map()
 
   /** Returns stats for summary */
-  def summaryStats: Map[String, Any] = Picard.getMetrics(outputMetrics).getOrElse(Map())
+  def summaryStats = Picard.getMetrics(outputMetrics).getOrElse(Map())
 }
 object MarkDuplicates {
   /** Returns default MarkDuplicates */