Merge branch 'develop' into feature-report

public/bammetrics/pom.xml

@@ -39,5 +39,17 @@
             <artifactId>BiopetFramework</artifactId>
             <version>${project.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.testng</groupId>
+            <artifactId>testng</artifactId>
+            <version>6.8</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.scalatest</groupId>
+            <artifactId>scalatest_2.11</artifactId>
+            <version>2.2.1</version>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 </project>

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

@@ -18,12 +18,12 @@ 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.{ CollectInsertSizeMetrics, CollectGcBiasMetrics, CalculateHsMetrics, CollectAlignmentSummaryMetrics }
+import nl.lumc.sasc.biopet.extensions.picard._
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
 
 class BamMetrics(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
@@ -32,14 +32,13 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
   @Input(doc = "Bam File", shortName = "BAM", required = true)
   var inputBam: File = _
 
-  @Input(doc = "Bed tracks targets", shortName = "target", required = false)
-  var bedFiles: List[File] = Nil
+  /** Bed files for region of interests */
+  var roiBedFiles: List[File] = config("regions_of_interest", Nil)
 
-  @Input(doc = "Bed tracks bait", shortName = "bait", required = false)
-  var baitBedFile: File = _
+  /** Bed of amplicon that is used */
+  var ampliconBedFile: Option[File] = config("amplicon_bed")
 
-  @Argument(doc = "", required = false)
-  var wholeGenome = false
+  var rnaMetrics: Boolean = config("rna_metrcis", default = false)
 
   /** return location of summary file */
   def summaryFile = (sampleId, libId) match {
@@ -49,19 +48,16 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
   }
 
   /** returns files to store in summary */
-  def summaryFiles = Map("input_bam" -> inputBam)
+  def summaryFiles = Map("input_bam" -> inputBam) ++
+    ampliconBedFile.map("amplicon" -> _).toMap ++
+    ampliconBedFile.map(x => "roi_" + x.getName.stripSuffix(".bed") -> x).toMap
 
   /** return settings */
-  def summarySettings = Map()
+  def summarySettings = Map("amplicon_name" -> ampliconBedFile.collect { case x => x.getName.stripSuffix(".bed") },
+    "roi_name" -> roiBedFiles.map(_.getName.stripSuffix(".bed")))
 
   /** executed before script */
   def init() {
-    if (config.contains("target_bed")) {
-      for (file <- config("target_bed").asList) {
-        bedFiles +:= new File(file.toString)
-      }
-    }
-    if (baitBedFile == null && config.contains("target_bait")) baitBedFile = config("target_bait")
   }
 
   /** Script to add jobs */
@@ -72,42 +68,96 @@ 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 collectAlignmentSummaryMetrics = CollectAlignmentSummaryMetrics(this, inputBam, outputDir)
-    add(collectAlignmentSummaryMetrics)
-    addSummarizable(collectAlignmentSummaryMetrics, "alignment_metrics")
-
-    val baitIntervalFile = if (baitBedFile != null) new File(outputDir, baitBedFile.getName.stripSuffix(".bed") + ".interval") else null
-    if (baitIntervalFile != null)
-      add(BedToInterval(this, baitBedFile, inputBam, outputDir), true)
-
-    for (bedFile <- bedFiles) {
-      //TODO: Add target jobs to summary
-      val targetDir = new File(outputDir, bedFile.getName.stripSuffix(".bed"))
-      val targetFile = new File(targetDir, bedFile.getName.stripSuffix(".bed") + ".interval")
-      val targetInterval = BedToInterval(this, bedFile, inputBam, targetFile)
-      add(targetInterval, true)
-      add(CalculateHsMetrics(this, inputBam, if (baitIntervalFile != null) baitIntervalFile
-      else targetInterval.output, targetInterval.output, targetDir))
+    val multiMetrics = new CollectMultipleMetrics(this)
+    multiMetrics.input = inputBam
+    multiMetrics.outputName = new File(outputDir, inputBam.getName.stripSuffix(".bam"))
+    add(multiMetrics)
+    addSummarizable(multiMetrics, "multi_metrics")
+
+    val gcBiasMetrics = CollectGcBiasMetrics(this, inputBam, outputDir)
+    add(gcBiasMetrics)
+    addSummarizable(gcBiasMetrics, "gc_bias")
+
+    val wgsMetrics = new CollectWgsMetrics(this)
+    wgsMetrics.input = inputBam
+    wgsMetrics.output = swapExt(outputDir, inputBam, ".bam", ".wgs.metrics")
+    add(wgsMetrics)
+    addSummarizable(wgsMetrics, "wgs")
+
+    if (rnaMetrics) {
+      val rnaMetrics = new CollectRnaSeqMetrics(this)
+      rnaMetrics.input = inputBam
+      rnaMetrics.output = swapExt(outputDir, inputBam, ".bam", ".rna.metrics")
+      rnaMetrics.chartOutput = Some(swapExt(outputDir, inputBam, ".bam", ".rna.metrics.pdf"))
+      add(rnaMetrics)
+      addSummarizable(rnaMetrics, "rna")
+    }
 
-      val strictOutputBam = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.strict.bam")
-      add(BedtoolsIntersect(this, inputBam, bedFile, strictOutputBam, minOverlap = config("strictintersectoverlap", default = 1.0)), true)
-      add(SamtoolsFlagstat(this, strictOutputBam, targetDir))
-      add(BiopetFlagstat(this, strictOutputBam, targetDir))
+    case class Intervals(bed: File, intervals: File)
+
+    // Create temp jobs to convert bed files to intervals lists
+    val roiIntervals = roiBedFiles.map(roiBedFile => {
+      val roiIntervals = swapExt(outputDir, roiBedFile, ".bed", ".intervals")
+      val ampBedToInterval = BedToIntervalList(this, roiBedFile, roiIntervals)
+      ampBedToInterval.isIntermediate = true
+      add(ampBedToInterval)
+      Intervals(roiBedFile, roiIntervals)
+    })
+
+    // Metrics that require a amplicon bed file
+    val ampIntervals = ampliconBedFile.collect {
+      case ampliconBedFile => {
+        val ampIntervals = swapExt(outputDir, ampliconBedFile, ".bed", ".intervals")
+        val ampBedToInterval = BedToIntervalList(this, ampliconBedFile, ampIntervals)
+        ampBedToInterval.isIntermediate = true
+        add(ampBedToInterval)
+
+        val chsMetrics = CalculateHsMetrics(this, inputBam,
+          List(ampIntervals), ampIntervals :: roiIntervals.map(_.intervals), outputDir)
+        add(chsMetrics)
+        addSummarizable(chsMetrics, "hs_metrics")
+
+        val pcrMetrics = CollectTargetedPcrMetrics(this, inputBam,
+          ampIntervals, ampIntervals :: roiIntervals.map(_.intervals), outputDir)
+        add(pcrMetrics)
+        addSummarizable(chsMetrics, "targeted_pcr_metrics")
+
+        Intervals(ampliconBedFile, ampIntervals)
+      }
+    }
 
-      val looseOutputBam = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.loose.bam")
-      add(BedtoolsIntersect(this, inputBam, bedFile, looseOutputBam, minOverlap = config("looseintersectoverlap", default = 0.01)), true)
-      add(SamtoolsFlagstat(this, looseOutputBam, targetDir))
-      add(BiopetFlagstat(this, looseOutputBam, targetDir))
+    // Create stats and coverage plot for each bed/interval file
+    for (intervals <- roiIntervals ++ ampIntervals) {
+      val targetName = intervals.bed.getName.stripSuffix(".bed")
+      val targetDir = new File(outputDir, targetName)
+
+      val biStrict = BedtoolsIntersect(this, inputBam, intervals.bed,
+        output = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.strict.bam"),
+        minOverlap = config("strict_intersect_overlap", default = 1.0))
+      biStrict.isIntermediate = true
+      add(biStrict)
+      add(SamtoolsFlagstat(this, biStrict.output, targetDir))
+      val biopetFlagstatStrict = BiopetFlagstat(this, biStrict.output, targetDir)
+      add(biopetFlagstatStrict)
+      addSummarizable(biopetFlagstatStrict, targetName + "_biopet_flagstat_strict")
+
+      val biLoose = BedtoolsIntersect(this, inputBam, intervals.bed,
+        output = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.loose.bam"),
+        minOverlap = config("loose_intersect_overlap", default = 0.01))
+      biLoose.isIntermediate = true
+      add(biLoose)
+      add(SamtoolsFlagstat(this, biLoose.output, targetDir))
+      val biopetFlagstatLoose = BiopetFlagstat(this, biLoose.output, targetDir)
+      add(biopetFlagstatLoose)
+      addSummarizable(biopetFlagstatLoose, targetName + "_biopet_flagstat_loose")
 
       val coverageFile = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".coverage")
-      add(BedtoolsCoverage(this, inputBam, bedFile, coverageFile, true), true)
-      add(CoverageStats(this, coverageFile, targetDir))
+
+      //FIXME:should use piping
+      add(BedtoolsCoverage(this, inputBam, intervals.bed, coverageFile, depth = true), true)
+      val covStats = CoverageStats(this, coverageFile, targetDir)
+      add(covStats)
+      addSummarizable(covStats, "cov_stats")
     }
 
     addSummaryJobs
@@ -115,20 +165,14 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
 }
 
 object BamMetrics extends PipelineCommand {
-  /**
-   * Make default implementation of BamMetrics
-   * @param root
-   * @param bamFile
-   * @param outputDir
-   * @return
-   */
+  /** 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
     bamMetrics.outputDir = outputDir
 
-    bamMetrics.init
-    bamMetrics.biopetScript
-    return bamMetrics
+    bamMetrics.init()
+    bamMetrics.biopetScript()
+    bamMetrics
   }
 }

public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala

+package nl.lumc.sasc.biopet.pipelines.bammetrics
+
+import java.io.File
+
+import com.google.common.io.Files
+import nl.lumc.sasc.biopet.core.config.Config
+import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsIntersect }
+import nl.lumc.sasc.biopet.extensions.picard._
+import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
+import nl.lumc.sasc.biopet.scripts.CoverageStats
+import nl.lumc.sasc.biopet.tools.BiopetFlagstat
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+import org.apache.commons.io.FileUtils
+import org.broadinstitute.gatk.queue.QSettings
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.{ Test, DataProvider, AfterClass }
+
+/**
+ * Created by pjvan_thof on 4/30/15.
+ */
+class BamMetricsTest extends TestNGSuite with Matchers {
+
+  def initPipeline(map: Map[String, Any]): BamMetrics = {
+    new BamMetrics() {
+      override def configName = "bammetrics"
+      override def globalConfig = new Config(map)
+      qSettings = new QSettings
+      qSettings.runName = "test"
+    }
+  }
+
+  @DataProvider(name = "bammetricsOptions")
+  def bammetricsOptions = {
+    val rois = Array(0, 1, 2, 3)
+    val amplicon = Array(true, false)
+    val rna = Array(true, false)
+
+    for (
+      rois <- rois;
+      amplicon <- amplicon;
+      rna <- rna
+    ) yield Array(rois, amplicon, rna)
+  }
+
+  @Test(dataProvider = "bammetricsOptions")
+  def testFlexiprep(rois: Int, amplicon: Boolean, rna: Boolean) = {
+    val map = ConfigUtils.mergeMaps(Map("output_dir" -> BamMetricsTest.outputDir, "rna_metrcis" -> rna
+    ), Map(BamMetricsTest.executables.toSeq: _*)) ++
+      (if (amplicon) Map("amplicon_bed" -> "amplicon.bed") else Map()) ++
+      Map("regions_of_interest" -> (1 to rois).map("roi_" + _ + ".bed").toList)
+    val bammetrics: BamMetrics = initPipeline(map)
+
+    bammetrics.inputBam = new File("input.bam")
+    bammetrics.sampleId = Some("1")
+    bammetrics.libId = Some("1")
+    bammetrics.script()
+
+    var regions: Int = rois + (if (amplicon) 1 else 0)
+
+    bammetrics.functions.count(_.isInstanceOf[CollectRnaSeqMetrics]) shouldBe (if (rna) 1 else 0)
+    bammetrics.functions.count(_.isInstanceOf[CollectWgsMetrics]) shouldBe 1
+    bammetrics.functions.count(_.isInstanceOf[CollectMultipleMetrics]) shouldBe 1
+    bammetrics.functions.count(_.isInstanceOf[CalculateHsMetrics]) shouldBe (if (amplicon) 1 else 0)
+    bammetrics.functions.count(_.isInstanceOf[CollectTargetedPcrMetrics]) shouldBe (if (amplicon) 1 else 0)
+    bammetrics.functions.count(_.isInstanceOf[BiopetFlagstat]) shouldBe (1 + (regions * 2))
+    bammetrics.functions.count(_.isInstanceOf[SamtoolsFlagstat]) shouldBe (1 + (regions * 2))
+    bammetrics.functions.count(_.isInstanceOf[BedtoolsIntersect]) shouldBe (regions * 2)
+
+    bammetrics.functions.count(_.isInstanceOf[BedtoolsCoverage]) shouldBe regions
+    bammetrics.functions.count(_.isInstanceOf[CoverageStats]) shouldBe regions
+  }
+
+  // remove temporary run directory all tests in the class have been run
+  @AfterClass
+  def removeTempOutputDir() = {
+    FileUtils.deleteDirectory(BamMetricsTest.outputDir)
+  }
+}
+
+object BamMetricsTest {
+  val outputDir = Files.createTempDir()
+
+  val executables = Map(
+    "refFlat" -> "bla.refFlat",
+    "reference" -> "reference.fa",
+    "samtools" -> Map("exe" -> "test"),
+    "bedtools" -> Map("exe" -> "test")
+  )
+}

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

@@ -36,4 +36,9 @@ trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetC
     val finalCmd = executable + cmd.substring(cmd.indexOf(" "))
     return cmd
   }
+
+  override def setupRetry(): Unit = {
+    super.setupRetry()
+    javaMemoryLimit = memoryLimit
+  }
 }

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

@@ -115,7 +115,7 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
       }).foldRight(jobsMap)((a, b) => ConfigUtils.mergeMaps(a, b))
 
     val writer = new PrintWriter(out)
-    writer.println(ConfigUtils.mapToJson(combinedMap).spaces4)
+    writer.println(ConfigUtils.mapToJson(combinedMap).nospaces)
     writer.close()
   }
 

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

@@ -37,7 +37,7 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "Fastq file", shortName = "FQ")
   var fastqfile: File = null
 
-  @Output(doc = "Output", shortName = "out")
+  @Output(doc = "Output", shortName = "out", required = true)
   var output: File = null
 
   executable = config("exe", default = "fastqc")
@@ -54,6 +54,7 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
 
   /** Sets contaminants and adapters when not yet set */
   override def beforeGraph {
+    this.jobOutputFile = new File(output.getParentFile, ".fastqc.out")
     this.preProcesExecutable
 
     val fastqcDir = new File(executable).getParent

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

@@ -113,10 +113,10 @@ object Star {
    * @return Return Star
    *
    */
-  def apply(configurable: Configurable, R1: File, R2: File, outputDir: File, isIntermediate: Boolean = false, deps: List[File] = Nil): Star = {
+  def apply(configurable: Configurable, R1: File, R2: Option[File], outputDir: File, isIntermediate: Boolean = false, deps: List[File] = Nil): Star = {
     val star = new Star(configurable)
     star.R1 = R1
-    if (R2 != null) star.R2 = R2
+    R2.foreach(R2 => star.R2 = R2)
     star.outputDir = outputDir
     star.isIntermediate = isIntermediate
     star.deps = deps
@@ -136,11 +136,11 @@ object Star {
    */
   def _2pass(configurable: Configurable,
              R1: File,
-             R2: File,
+             R2: Option[File],
              outputDir: File,
              isIntermediate: Boolean = false,
              deps: List[File] = Nil): (File, List[Star]) = {
-    val starCommand_pass1 = Star(configurable, R1, if (R2 != null) R2 else null, new File(outputDir, "aln-pass1"))
+    val starCommand_pass1 = Star(configurable, R1, R2, new File(outputDir, "aln-pass1"))
     starCommand_pass1.isIntermediate = isIntermediate
     starCommand_pass1.deps = deps
     starCommand_pass1.beforeGraph
@@ -152,7 +152,7 @@ object Star {
     starCommand_reindex.isIntermediate = isIntermediate
     starCommand_reindex.beforeGraph
 
-    val starCommand_pass2 = Star(configurable, R1, if (R2 != null) R2 else null, new File(outputDir, "aln-pass2"))
+    val starCommand_pass2 = Star(configurable, R1, R2, new File(outputDir, "aln-pass2"))
     starCommand_pass2.genomeDir = starCommand_reindex.outputDir
     starCommand_pass2.isIntermediate = isIntermediate
     starCommand_pass2.deps = deps

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala

@@ -55,12 +55,12 @@ class BedtoolsIntersect(val root: Configurable) extends Bedtools {
 object BedtoolsIntersect {
   /** Returns default bedtools intersect */
   def apply(root: Configurable, input: File, intersect: File, output: File,
-            minOverlap: Double = 0, count: Boolean = false): BedtoolsIntersect = {
+            minOverlap: Option[Double] = None, count: Boolean = false): BedtoolsIntersect = {
     val bedtoolsIntersect = new BedtoolsIntersect(root)
     bedtoolsIntersect.input = input
     bedtoolsIntersect.intersectFile = intersect
     bedtoolsIntersect.output = output
-    if (minOverlap > 0) bedtoolsIntersect.minOverlap = Option(minOverlap)
+    bedtoolsIntersect.minOverlap = minOverlap
     bedtoolsIntersect.count = count
     return bedtoolsIntersect
   }

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

@@ -21,7 +21,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 
 /** Extension for picard AddOrReplaceReadGroups */
 class AddOrReplaceReadGroups(val root: Configurable) extends Picard {
-  javaMainClass = "picard.sam.AddOrReplaceReadGroups"
+  javaMainClass = new picard.sam.AddOrReplaceReadGroups().getClass.getName
 
   @Input(doc = "The input SAM or BAM files to analyze.", required = true)
   var input: File = _

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.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.{ Output, Input }
+
+/**
+ * Created by pjvan_thof on 4/15/15.
+ */
+class BedToIntervalList(val root: Configurable) extends Picard {
+  javaMainClass = new picard.util.BedToIntervalList().getClass.getName
+
+  @Input(doc = "Input bed file", required = true)
+  var input: File = null
+
+  @Input(doc = "Reference dict file", required = true)
+  var dict: File = new File(config("reference").asString.stripSuffix(".fa").stripSuffix(".fasta") + ".dict")
+
+  @Output(doc = "Output interval list", required = true)
+  var output: File = null
+
+  override def commandLine = super.commandLine +
+    required("SEQUENCE_DICTIONARY=", dict, spaceSeparated = false) +
+    required("INPUT=", input, spaceSeparated = false) +
+    required("OUTPUT=", output, spaceSeparated = false)
+}
+
+object BedToIntervalList {
+  def apply(root: Configurable, input: File, output: File): BedToIntervalList = {
+    val bi = new BedToIntervalList(root)
+    bi.input = input
+    bi.output = output
+    bi
+  }
+}
\ No newline at end of file

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

@@ -17,20 +17,21 @@ package nl.lumc.sasc.biopet.extensions.picard
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.summary.Summarizable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 
 /** Extension for picard CalculateHsMetrics */
-class CalculateHsMetrics(val root: Configurable) extends Picard {
-  javaMainClass = "picard.analysis.directed.CalculateHsMetrics"
+class CalculateHsMetrics(val root: Configurable) extends Picard with Summarizable {
+  javaMainClass = new picard.analysis.directed.CalculateHsMetrics().getClass.getName
 
   @Input(doc = "The input SAM or BAM files to analyze.  Must be coordinate sorted.", required = true)
   var input: File = _
 
   @Input(doc = "BAIT_INTERVALS", required = true)
-  var baitIntervals: File = _
+  var baitIntervals: List[File] = _
 
   @Input(doc = "TARGET_INTERVALS", required = true)
-  var targetIntervals: File = _
+  var targetIntervals: List[File] = Nil
 
   @Output(doc = "The output file to write statistics to", required = true)
   var output: File = _
@@ -53,21 +54,31 @@ class CalculateHsMetrics(val root: Configurable) extends Picard {
     required("OUTPUT=", output, spaceSeparated = false) +
     optional("REFERENCE_SEQUENCE=", reference, spaceSeparated = false) +
     repeat("METRIC_ACCUMULATION_LEVEL=", metricAccumulationLevel, spaceSeparated = false) +
-    required("BAIT_INTERVALS=", baitIntervals, spaceSeparated = false) +
-    required("TARGET_INTERVALS=", targetIntervals, spaceSeparated = false) +
+    repeat("BAIT_INTERVALS=", baitIntervals, spaceSeparated = false) +
+    repeat("TARGET_INTERVALS=", targetIntervals, spaceSeparated = false) +
     optional("PER_TARGET_COVERAGE=", perTargetCoverage, spaceSeparated = false) +
     optional("BAIT_SET_NAME=", baitSetName, spaceSeparated = false)
+
+  /** Returns files for summary */
+  def summaryFiles: Map[String, File] = Map()
+
+  /** Returns stats for summary */
+  def summaryStats: Map[String, Any] = Picard.getMetrics(output).getOrElse(Map())
 }
 
 object CalculateHsMetrics {
   /** Returns default CalculateHsMetrics */
-  def apply(root: Configurable, input: File, baitIntervals: File, targetIntervals: 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
   }
 }
\ No newline at end of file

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

@@ -22,7 +22,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 
 /** Extension for picard CollectAlignmentSummaryMetrics */
 class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with Summarizable {
-  javaMainClass = "picard.analysis.CollectAlignmentSummaryMetrics"
+  javaMainClass = new picard.analysis.CollectAlignmentSummaryMetrics().getClass.getName
 
   @Input(doc = "The input SAM or BAM files to analyze.  Must be coordinate sorted.", required = true)
   var input: File = _
@@ -66,19 +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) match {
-    case None => Map()
-    case Some((header, content)) =>
-      (for (category <- 0 until content.size) yield {
-        content(category)(0).toString -> (