Fixed single end metrics

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

@@ -16,7 +16,7 @@ package nl.lumc.sasc.biopet.extensions.picard
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{Reference, BiopetQScript}
+import nl.lumc.sasc.biopet.core.Reference
 import nl.lumc.sasc.biopet.utils.Logging
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.core.summary.{Summarizable, SummaryQScript}
@@ -36,17 +36,22 @@ class CollectMultipleMetrics(val parent: Configurable)
   override def defaultCoreMemory = 8.0
 
   @Input(doc = "The input SAM or BAM files to analyze", required = true)
-  var input: File = null
+  var input: File = _
 
   @Input(doc = "The reference file for the bam files.", shortName = "R")
-  var reference: File = null
+  var reference: File = _
 
   @Output(doc = "Base name of output files", required = true)
-  var outputName: File = null
+  var outputName: File = _
 
   @Argument(doc = "Base name of output files", required = true)
-  var program: List[String] =
-    config("metrics_programs", default = Programs.values.iterator.toList.map(_.toString))
+  var program: List[Programs.Value] = {
+    val value: List[String] = config("metrics_programs")
+    value match {
+      case Nil => Programs.values.toList
+      case list => list.flatMap(x => Programs.values.find(_.toString.toLowerCase == x.toLowerCase))
+    }
+  }
 
   @Argument(doc = "Assume alignment file is sorted by position", required = false)
   var assumeSorted: Boolean = config("assume_sorted", default = false)
@@ -61,88 +66,86 @@ class CollectMultipleMetrics(val parent: Configurable)
     super.beforeGraph()
     if (reference == null) reference = referenceFasta()
     program.foreach {
-      case p if p == Programs.CollectAlignmentSummaryMetrics.toString =>
+      case Programs.CollectAlignmentSummaryMetrics =>
         outputFiles :+= new File(outputName + ".alignment_summary_metrics")
-      case p if p == Programs.CollectInsertSizeMetrics.toString =>
+      case Programs.CollectInsertSizeMetrics =>
         outputFiles :+= new File(outputName + ".insert_size_metrics")
         outputFiles :+= new File(outputName + ".insert_size_histogram.pdf")
-      case p if p == Programs.QualityScoreDistribution.toString =>
+      case Programs.QualityScoreDistribution =>
         outputFiles :+= new File(outputName + ".quality_distribution_metrics")
         outputFiles :+= new File(outputName + ".test.quality_distribution.pdf")
-      case p if p == Programs.MeanQualityByCycle.toString =>
+      case Programs.MeanQualityByCycle =>
         outputFiles :+= new File(outputName + ".quality_by_cycle_metrics")
         outputFiles :+= new File(outputName + ".quality_by_cycle.pdf")
-      case p if p == Programs.CollectBaseDistributionByCycle.toString =>
+      case Programs.CollectBaseDistributionByCycle =>
         outputFiles :+= new File(outputName + ".base_distribution_by_cycle_metrics")
         outputFiles :+= new File(outputName + ".base_distribution_by_cycle.pdf")
       case p => Logging.addError("Program '" + p + "' does not exist for 'CollectMultipleMetrics'")
     }
   }
 
-  override def cmdLine =
+  override def cmdLine: String =
     super.cmdLine +
       required("INPUT=", input, spaceSeparated = false) +
       required("OUTPUT=", outputName, spaceSeparated = false) +
       conditional(assumeSorted, "ASSUME_SORTED=true") +
       optional("STOP_AFTER=", stopAfter, spaceSeparated = false) +
       optional("REFERENCE_SEQUENCE=", reference, spaceSeparated = false) +
-      repeat("PROGRAM=", program, spaceSeparated = false)
+      repeat("PROGRAM=", program.map(_.toString), spaceSeparated = false)
 
   override def addToQscriptSummary(qscript: SummaryQScript): Unit = {
 
     def summarizable(stats: () => Any): Summarizable = new Summarizable {
-      def summaryStats = stats()
+      def summaryStats: Any = stats()
       def summaryFiles: Map[String, File] = Map()
     }
 
     program
-      .foreach { p =>
-        p match {
-          case _ if p == Programs.CollectAlignmentSummaryMetrics.toString =>
-            qscript.addSummarizable(
-              summarizable(
-                () =>
-                  Picard.getMetrics(new File(outputName + ".alignment_summary_metrics"),
-                                    groupBy = Some("CATEGORY"))),
-              p,
-              forceSingle = true)
-          case _ if p == Programs.CollectInsertSizeMetrics.toString =>
-            qscript.addSummarizable(
-              summarizable(
-                () =>
-                  if (new File(outputName + ".insert_size_metrics").exists())
-                    Map(
-                      "metrics" -> Picard.getMetrics(
-                        new File(outputName + ".insert_size_metrics")),
-                      "histogram" -> Picard.getHistogram(
-                        new File(outputName + ".insert_size_metrics"))
-                    )
-                  else Map()),
-              p,
-              forceSingle = true
-            )
-          case _ if p == Programs.QualityScoreDistribution.toString =>
-            qscript.addSummarizable(
-              summarizable(
-                () => Picard.getHistogram(new File(outputName + ".quality_distribution_metrics"))),
-              p,
-              forceSingle = true)
-          case _ if p == Programs.MeanQualityByCycle.toString =>
-            qscript.addSummarizable(
-              summarizable(
-                () => Picard.getHistogram(new File(outputName + ".quality_by_cycle_metrics"))),
-              p,
-              forceSingle = true)
-          case _ if p == Programs.CollectBaseDistributionByCycle.toString =>
-            qscript.addSummarizable(
-              summarizable(
-                () =>
-                  Picard.getHistogram(new File(outputName + ".base_distribution_by_cycle_metrics"),
-                                      tag = "METRICS CLASS")),
-              p,
-              forceSingle = true)
-          case _ => None
-        }
+      .foreach {
+        case Programs.CollectAlignmentSummaryMetrics =>
+          qscript.addSummarizable(
+            summarizable(
+              () =>
+                Picard.getMetrics(new File(outputName + ".alignment_summary_metrics"),
+                  groupBy = Some("CATEGORY"))),
+            Programs.CollectAlignmentSummaryMetrics.toString,
+            forceSingle = true)
+        case Programs.CollectInsertSizeMetrics =>
+          qscript.addSummarizable(
+            summarizable(
+              () =>
+                if (new File(outputName + ".insert_size_metrics").exists())
+                  Map(
+                    "metrics" -> Picard.getMetrics(
+                      new File(outputName + ".insert_size_metrics")),
+                    "histogram" -> Picard.getHistogram(
+                      new File(outputName + ".insert_size_metrics"))
+                  )
+                else Map()),
+            Programs.CollectInsertSizeMetrics.toString,
+            forceSingle = true
+          )
+        case Programs.QualityScoreDistribution =>
+          qscript.addSummarizable(
+            summarizable(
+              () => Picard.getHistogram(new File(outputName + ".quality_distribution_metrics"))),
+            Programs.QualityScoreDistribution.toString,
+            forceSingle = true)
+        case Programs.MeanQualityByCycle =>
+          qscript.addSummarizable(
+            summarizable(
+              () => Picard.getHistogram(new File(outputName + ".quality_by_cycle_metrics"))),
+            Programs.MeanQualityByCycle.toString,
+            forceSingle = true)
+        case Programs.CollectBaseDistributionByCycle =>
+          qscript.addSummarizable(
+            summarizable(
+              () =>
+                Picard.getHistogram(new File(outputName + ".base_distribution_by_cycle_metrics"),
+                  tag = "METRICS CLASS")),
+            Programs.CollectBaseDistributionByCycle.toString,
+            forceSingle = true)
+        case _ => None
       }
   }
 
@@ -151,10 +154,10 @@ class CollectMultipleMetrics(val parent: Configurable)
   def summaryFiles: Map[String, File] = {
     program
       .map {
-        case p if p == Programs.CollectInsertSizeMetrics.toString =>
+        case Programs.CollectInsertSizeMetrics =>
           Map("insert_size_histogram" -> new File(outputName + ".insert_size_histogram.pdf"),
               "insert_size_metrics" -> new File(outputName + ".insert_size_metrics"))
-        case otherwise => Map()
+        case _ => Map()
       }
       .foldLeft(Map.empty[String, File]) { case (acc, m) => acc ++ m }
   }