Merge branch 'fix-BIOPET-489' into 'develop'

Fix biopet 489



See merge request !509

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

@@ -136,7 +136,7 @@ class BamMetrics(val root: Configurable) extends QScript
         ampBedToInterval.isIntermediate = true
         add(ampBedToInterval)
 
-        val chsMetrics = CalculateHsMetrics(this, inputBam,
+        val chsMetrics = CollectHsMetrics(this, inputBam,
           List(ampIntervals), ampIntervals :: roiIntervals.map(_.intervals), outputDir)
         add(chsMetrics)
         addSummarizable(chsMetrics, "hs_metrics")

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

@@ -75,7 +75,7 @@ class BamMetricsTest extends TestNGSuite with Matchers {
     bammetrics.functions.count(_.isInstanceOf[CollectRnaSeqMetrics]) shouldBe (if (rna) 1 else 0)
     bammetrics.functions.count(_.isInstanceOf[CollectWgsMetrics]) shouldBe (if (wgs) 1 else 0)
     bammetrics.functions.count(_.isInstanceOf[CollectMultipleMetrics]) shouldBe 1
-    bammetrics.functions.count(_.isInstanceOf[CalculateHsMetrics]) shouldBe (if (amplicon) 1 else 0)
+    bammetrics.functions.count(_.isInstanceOf[CollectHsMetrics]) shouldBe (if (amplicon) 1 else 0)
     bammetrics.functions.count(_.isInstanceOf[CollectTargetedPcrMetrics]) shouldBe (if (amplicon) 1 else 0)
     bammetrics.functions.count(_.isInstanceOf[BamStats]) shouldBe 1
   }

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala → biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectHsMetrics.scala

@@ -22,8 +22,8 @@ import nl.lumc.sasc.biopet.core.summary.Summarizable
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
 
 /** Extension for picard CalculateHsMetrics */
-class CalculateHsMetrics(val root: Configurable) extends Picard with Summarizable with Reference {
-  javaMainClass = new picard.analysis.directed.CalculateHsMetrics().getClass.getName
+class CollectHsMetrics(val root: Configurable) extends Picard with Summarizable with Reference {
+  javaMainClass = new picard.analysis.directed.CollectHsMetrics().getClass.getName
 
   @Input(doc = "The input SAM or BAM files to analyze.  Must be coordinate sorted.", required = true)
   var input: File = _
@@ -72,14 +72,14 @@ class CalculateHsMetrics(val root: Configurable) extends Picard with Summarizabl
   def summaryStats: Any = Picard.getMetrics(output).getOrElse(Map())
 }
 
-object CalculateHsMetrics {
+object CollectHsMetrics {
   /** Returns default CalculateHsMetrics */
   def apply(root: Configurable,
             input: File,
             baitIntervals: List[File],
             targetIntervals: List[File],
-            outputDir: File): CalculateHsMetrics = {
-    val calculateHsMetrics = new CalculateHsMetrics(root)
+            outputDir: File): CollectHsMetrics = {
+    val calculateHsMetrics = new CollectHsMetrics(root)
     calculateHsMetrics.input = input
     calculateHsMetrics.baitIntervals = baitIntervals
     calculateHsMetrics.targetIntervals = targetIntervals

biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala

@@ -16,11 +16,10 @@ package nl.lumc.sasc.biopet.extensions.tools
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.summary.{ Summarizable, SummaryQScript }
+import nl.lumc.sasc.biopet.core.summary.{ Summarizable }
 import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFunction }
-import nl.lumc.sasc.biopet.tools.vcfstats.VcfStats
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.utils.{ ConfigUtils, tryToParseNumber }
+import nl.lumc.sasc.biopet.utils.{ ConfigUtils }
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 import scala.io.Source
@@ -31,7 +30,7 @@ import scala.io.Source
  * Created by pjvan_thof on 1/10/15.
  */
 class VcfStats(val root: Configurable) extends ToolCommandFunction with Summarizable with Reference {
-  def toolObject = VcfStats
+  def toolObject = nl.lumc.sasc.biopet.tools.vcfstats.VcfStats
 
   mainFunction = false
 

gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Impute2Vcf.scala

@@ -39,14 +39,16 @@ class Impute2Vcf(val root: Configurable) extends QScript with BiopetQScript with
   val phenotypeFile: File = config("phenotype_file")
 
   val inputGens: List[GensInput] = config("input_gens", default = Nil).asList.map {
-    case value: Map[String, Any] =>
-      GensInput(new File(value("genotypes").toString),
-        value.get("info").map(x => new File(x.toString)),
-        value("contig").toString)
-    case value: util.LinkedHashMap[String, _] =>
-      GensInput(new File(value.get("genotypes").toString),
-        value.toMap.get("info").map(x => new File(x.toString)),
-        value.get("contig").toString)
+    case value: Map[_, _] =>
+      val map = value.map(x => x._1.toString -> x._2)
+      GensInput(new File(map("genotypes").toString),
+        map.get("info").map(x => new File(x.toString)),
+        map("contig").toString)
+    case value: util.LinkedHashMap[_, _] =>
+      val map = value.map(x => x._1.toString -> x._2)
+      GensInput(new File(map("genotypes").toString),
+        map.get("info").map(x => new File(x.toString)),
+        map("contig").toString)
     case _ => throw new IllegalArgumentException
   } ++ (specsFile match {
     case Some(file) => Impute2Vcf.imputeSpecsToGensInput(file, config("validate_specs", default = true))