added target pcr metrics

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

@@ -18,9 +18,9 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.scripts.CoverageStats
 import org.broadinstitute.gatk.queue.QScript
-import nl.lumc.sasc.biopet.core.{ SampleLibraryTag, BiopetQScript, PipelineCommand }
+import nl.lumc.sasc.biopet.core.{ SampleLibraryTag, PipelineCommand }
 import java.io.File
-import nl.lumc.sasc.biopet.tools.{ BedToInterval, BiopetFlagstat }
+import nl.lumc.sasc.biopet.tools.BiopetFlagstat
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsIntersect }
 import nl.lumc.sasc.biopet.extensions.picard._
@@ -103,7 +103,9 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
           List(ampIntervals), ampIntervals :: roiIntervals.map(_.intervals), outputDir)
         add(chsMetrics)
 
-        //TODO: target pcr metrics
+        val pcrMetrics = CollectTargetedPcrMetrics(this, inputBam,
+          ampIntervals, ampIntervals :: roiIntervals.map(_.intervals), outputDir)
+        add(pcrMetrics)
 
         Intervals(ampliconBedFile, ampIntervals)
       }
@@ -133,7 +135,7 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
       val coverageFile = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".coverage")
 
       //FIXME:should use piping
-      add(BedtoolsCoverage(this, inputBam, intervals.bed, coverageFile, true), true)
+      add(BedtoolsCoverage(this, inputBam, intervals.bed, coverageFile, depth = true), isIntermediate = true)
       add(CoverageStats(this, coverageFile, targetDir))
     }
 
@@ -148,8 +150,8 @@ object BamMetrics extends PipelineCommand {
     bamMetrics.inputBam = bamFile
     bamMetrics.outputDir = outputDir
 
-    bamMetrics.init
-    bamMetrics.biopetScript
-    return bamMetrics
+    bamMetrics.init()
+    bamMetrics.biopetScript()
+    bamMetrics
   }
 }

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

@@ -61,13 +61,17 @@ class CalculateHsMetrics(val root: Configurable) extends Picard {
 
 object CalculateHsMetrics {
   /** Returns default CalculateHsMetrics */
-  def apply(root: Configurable, input: File, baitIntervals: List[File], targetIntervals: List[File], outputDir: File): CalculateHsMetrics = {
+  def apply(root: Configurable,
+            input: File,
+            baitIntervals: List[File],
+            targetIntervals: List[File],
+            outputDir: File): CalculateHsMetrics = {
     val calculateHsMetrics = new CalculateHsMetrics(root)
     calculateHsMetrics.input = input
     calculateHsMetrics.baitIntervals = baitIntervals
     calculateHsMetrics.targetIntervals = targetIntervals
-    calculateHsMetrics.output = new File(outputDir, input.getName.stripSuffix(".bam") + ".capmetrics")
-    calculateHsMetrics.perTargetCoverage = new File(outputDir, input.getName.stripSuffix(".bam") + ".per_target_coverage")
-    return calculateHsMetrics
+    calculateHsMetrics.output = new File(outputDir, input.getName.stripSuffix(".bam") + ".HsMetrics")
+    calculateHsMetrics.perTargetCoverage = new File(outputDir, input.getName.stripSuffix(".bam") + ".HsMetrics.per_target_coverage")
+    calculateHsMetrics
   }
 }
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectTargetedPcrMetrics.scala

+package nl.lumc.sasc.biopet.extensions.picard
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{Argument, Output, Input}
+
+/**
+ * Created by pjvan_thof on 4/16/15.
+ */
+class CollectTargetedPcrMetrics(val root: Configurable) extends Picard {
+
+  javaMainClass = new picard.analysis.directed.CollectTargetedPcrMetrics().getClass.getName
+
+  @Input(doc = "The input SAM or BAM files to analyze.  Must be coordinate sorted.", required = true)
+  var input: File = _
+
+  @Input(doc = "AMPLICON_INTERVALS", required = true)
+  var ampliconIntervals: File = _
+
+  @Input(doc = "TARGET_INTERVALS", required = true)
+  var targetIntervals: List[File] = Nil
+
+  @Output(doc = "The output file to write statistics to", required = true)
+  var output: File = _
+
+  @Output(doc = "PER_TARGET_COVERAGE", required = false)
+  var perTargetCoverage: File = _
+
+  @Argument(doc = "METRIC_ACCUMULATION_LEVEL", required = false)
+  var metricAccumulationLevel: List[String] = config("metricaccumulationlevel", default = Nil)
+
+  @Argument(doc = "CUSTOM_AMPLICON_SET_NAME", required = false)
+  var customAmpliconSetName: Option[String] = config("custom_amplicon_set_name")
+
+  override def commandLine = super.commandLine +
+    required("INPUT=", input, spaceSeparated = false) +
+    required("OUTPUT=", output, spaceSeparated = false) +
+    repeat("METRIC_ACCUMULATION_LEVEL=", metricAccumulationLevel, spaceSeparated = false) +
+    required("AMPLICON_INTERVALS=", ampliconIntervals, spaceSeparated = false) +
+    repeat("TARGET_INTERVALS=", targetIntervals, spaceSeparated = false) +
+    optional("PER_TARGET_COVERAGE=", perTargetCoverage, spaceSeparated = false) +
+    optional("CUSTOM_AMPLICON_SET_NAME=", customAmpliconSetName, spaceSeparated = false)
+}
+
+object CollectTargetedPcrMetrics {
+  def apply(root: Configurable,
+            input: File,
+            ampliconIntervals: File,
+            targetIntervals: List[File],
+            outputDir: File): CollectTargetedPcrMetrics = {
+    val pcrMetrics = new CollectTargetedPcrMetrics(root)
+    pcrMetrics.input = input
+    pcrMetrics.ampliconIntervals = ampliconIntervals
+    pcrMetrics.targetIntervals = targetIntervals
+    pcrMetrics.output = new File(outputDir, input.getName.stripSuffix(".bam") + ".TargetedPcrMetrics")
+    pcrMetrics.perTargetCoverage = new File(outputDir, input.getName.stripSuffix(".bam") + ".TargetedPcrMetrics.per_target_coverage")
+    pcrMetrics
+  }
+}
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