Switch to multi metrics

public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -63,15 +63,12 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
     add(biopetFlagstat)
     addSummarizable(biopetFlagstat, "biopet_flagstat")
 
-    add(CollectGcBiasMetrics(this, inputBam, outputDir))
-
-    val collectInsertSizeMetrics = CollectInsertSizeMetrics(this, inputBam, outputDir)
-    add(collectInsertSizeMetrics)
-    addSummarizable(collectInsertSizeMetrics, "insert_size_metrics")
+    val multiMetrics = new CollectMultipleMetrics(this)
+    multiMetrics.input = inputBam
+    multiMetrics.outputName = new File(outputDir, inputBam.getName.stripSuffix(".bam"))
+    add(multiMetrics)
 
-    val collectAlignmentSummaryMetrics = CollectAlignmentSummaryMetrics(this, inputBam, outputDir)
-    add(collectAlignmentSummaryMetrics)
-    addSummarizable(collectAlignmentSummaryMetrics, "alignment_metrics")
+    add(CollectGcBiasMetrics(this, inputBam, outputDir))
 
     case class Intervals(bed: File, intervals: File)
 
@@ -135,7 +132,7 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
 }
 
 object BamMetrics extends PipelineCommand {
-  /** Make default implementation of BamMetrics */
+  /** Make default implementation of BamMetrics and runs script already */
   def apply(root: Configurable, bamFile: File, outputDir: File): BamMetrics = {
     val bamMetrics = new BamMetrics(root)
     bamMetrics.inputBam = bamFile

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

+package nl.lumc.sasc.biopet.extensions.picard
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.BiopetQScript
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Output, Argument, Input }
+
+/**
+ * Created by pjvan_thof on 4/16/15.
+ */
+class CollectMultipleMetrics(val root: Configurable) extends Picard {
+  import CollectMultipleMetrics._
+
+  javaMainClass = new picard.analysis.CollectMultipleMetrics().getClass.getName
+
+  @Input(doc = "The input SAM or BAM files to analyze", required = true)
+  var input: File = null
+
+  @Output(doc = "Base name of output files", required = true)
+  var outputName: File = null
+
+  @Argument(doc = "Base name of output files", required = true)
+  var program: List[String] = config("metrics_programs",
+    default = Programs.values.iterator.toList.map(_.toString))
+
+  @Argument(doc = "Assume alignment file is sorted by position", required = false)
+  var assumeSorted: Boolean = config("assume_sorted", default = false)
+
+  @Argument(doc = "Stop after processing N reads", required = false)
+  var stopAfter: Option[Long] = config("stop_after")
+
+  @Output
+  protected var outputFiles: List[File] = Nil
+
+  override def beforeGraph: Unit = {
+    program.foreach(p => p match {
+      case _ if p == Programs.CollectAlignmentSummaryMetrics.toString => {
+        outputFiles :+= new File(outputName + ".alignment_summary_metrics")
+      }
+      case _ if p == Programs.CollectInsertSizeMetrics.toString => {
+        outputFiles :+= new File(outputName + ".insert_size_metrics")
+        outputFiles :+= new File(outputName + ".insert_size_Histogram.pdf")
+      }
+      case _ if p == Programs.QualityScoreDistribution.toString => {
+        outputFiles :+= new File(outputName + ".quality_distribution_metrics")
+        outputFiles :+= new File(outputName + ".test.quality_distribution.pdf")
+      }
+      case _ if p == Programs.MeanQualityByCycle.toString => {
+        outputFiles :+= new File(outputName + ".quality_by_cycle_metrics")
+        outputFiles :+= new File(outputName + ".quality_by_cycle.pdf")
+      }
+      case _ if p == Programs.CollectBaseDistributionByCycle.toString => {
+        outputFiles :+= new File(outputName + ".base_distribution_by_cycle_metrics")
+        outputFiles :+= new File(outputName + ".base_distribution_by_cycle.pdf")
+      }
+      case _ => BiopetQScript.addError("Program '" + p + "' does not exist for 'CollectMultipleMetrics'")
+    })
+  }
+
+  override def commandLine = super.commandLine +
+    required("INPUT=", input, spaceSeparated = false) +
+    required("OUTPUT=", outputName, spaceSeparated = false) +
+    required("ASSUME_SORTED=", assumeSorted, spaceSeparated = false) +
+    required("STOP_AFTER=", stopAfter, spaceSeparated = false) +
+    repeat("PROGRAM=", program, spaceSeparated = false)
+}
+
+object CollectMultipleMetrics {
+  object Programs extends Enumeration {
+    val CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics, QualityScoreDistribution, MeanQualityByCycle, CollectBaseDistributionByCycle = Value
+  }
+}
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