Added Alignment Metrics

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

+package nl.lumc.sasc.biopet.function.picard
+
+import java.io.File
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
+
+class CollectAlignmentSummaryMetrics(val root:Configurable) extends Picard {
+  javaMainClass = "picard.analysis.CollectAlignmentSummaryMetrics"
+  
+  @Input(doc="The input SAM or BAM files to analyze.  Must be coordinate sorted.", required = true)
+  var input: File = _
+  
+  @Argument(doc="MAX_INSERT_SIZE", required = false)
+  var maxInstertSize: Int = config("maxInstertSize", 100000)
+  
+  @Argument(doc="ADAPTER_SEQUENCE", required = false)
+  var adapterSequence: List[String] = config("adapterSequence", Nil)
+  
+  @Argument(doc="IS_BISULFITE_SEQUENCED", required = false)
+  var isBisulfiteSequenced: Boolean = config("isBisulfiteSequenced", false)
+  
+  @Output(doc="The output file to write statistics to", required = true)
+  var output: File = _
+  
+  @Argument(doc="Reference file", required = false)
+  var reference: File = config("reference", "")
+  
+  @Argument(doc="ASSUME_SORTED", required = false)
+  var assumeSorted: Boolean = config("assumeSorted", false)
+  
+  @Argument(doc="METRIC_ACCUMULATION_LEVEL", required=false)
+  var metricAccumulationLevel: List[String] = config("metricaccumulationlevel", List())
+  
+  @Argument(doc="STOP_AFTER", required = false)
+  var stopAfter: Long = config("stopAfter", 0)
+  
+  override def commandLine = super.commandLine +
+    required("INPUT=", input, spaceSeparated=false) +
+    required("OUTPUT=", output, spaceSeparated=false) +
+    optional("REFERENCE_SEQUENCE=", reference, spaceSeparated=false) + 
+    repeat("METRIC_ACCUMULATION_LEVEL=", metricAccumulationLevel, spaceSeparated=false) +
+    required("MAX_INSERT_SIZE=", maxInstertSize, spaceSeparated=false) + 
+    required("IS_BISULFITE_SEQUENCED=", isBisulfiteSequenced, spaceSeparated=false) +
+    optional("ASSUME_SORTED=", assumeSorted, spaceSeparated=false) +
+    optional("STOP_AFTER=", stopAfter, spaceSeparated=false)
+}
+
+object CollectAlignmentSummaryMetrics {
+  def apply(root:Configurable, input:File, outputDir:String) : CollectAlignmentSummaryMetrics = {
+    val collectAlignmentSummaryMetrics = new CollectAlignmentSummaryMetrics(root)
+    collectAlignmentSummaryMetrics.input = input
+    collectAlignmentSummaryMetrics.output = new File(outputDir, input.getName.stripSuffix(".bam") + ".alignmentMetrics")
+    return collectAlignmentSummaryMetrics
+  }
+}
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