Merge branch 'fix-xhmm' into 'develop'

fix biopet-495



See merge request !496

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/DepthOfCoverage.scala

@@ -18,31 +18,31 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
   @Output(fullName = "out", shortName = "o", doc = "File name base to which coverage metric should be written")
   var out: File = _
 
+  @Output
   private var _summaryFile: File = _
+  @Output
   private var _statisticsFile: File = _
+  @Output
   private var _intervalSummaryFile: File = _
+  @Output
   private var _intervalStatisticsFile: File = _
+  @Output
   private var _geneSummaryFile: File = _
+  @Output
   private var _geneStatisticsFile: File = _
+  @Output
   private var _cumulativeCoverageCountsFile: File = _
+  @Output
   private var _cumulativeCoverageProportionsFile: File = _
 
-  @Output
-  var summaryFile = _summaryFile
-  @Output
-  var statisticsFile = _statisticsFile
-  @Output
-  var intervalSummaryFile = _intervalSummaryFile
-  @Output
-  var intervalStatisticsFile = _intervalStatisticsFile
-  @Output
-  var geneSummaryFile = _geneSummaryFile
-  @Output
-  var geneStatisticsFile = _geneStatisticsFile
-  @Output
-  var culumativeCoverageCountsFile = _cumulativeCoverageCountsFile
-  @Output
-  var cumulativeCoverageProportionsFile = _cumulativeCoverageProportionsFile
+  def summaryFile = new File(out + ".sample_summary")
+  def statisticsFile = new File(out + ".sample_statistics")
+  def intervalSummaryFile = new File(out + ".sample_interval_summary")
+  def intervalStatisticsFile = new File(out + ".sample_interval_statistics")
+  def geneSummaryFile = new File(out + ".sample_gene_summary")
+  def geneStatisticsFile = new File(out + ".sample_gene_statistics")
+  def cumulativeCoverageCountsFile = new File(out + ".sample_cumulative_coverage_counts")
+  def cumulativeCoverageProportionsFile = new File(out + ".sample_cumulative_coverage_proportions")
 
   @Input(required = false)
   var calculateCoverageOverGenes: Option[File] = config("calculate_coverage_over_genes", namespace = "depth_of_coverage", default = None)
@@ -92,14 +92,14 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
     if (out == null) {
       throw new IllegalStateException("You must set the <out> variable")
     }
-    _summaryFile = new File(out + ".sample_summary")
-    _statisticsFile = new File(out + ".sample_statistics")
-    _intervalSummaryFile = new File(out + ".sample_interval_summary")
-    _intervalStatisticsFile = new File(out + ".sample_interval_statistics")
-    _geneSummaryFile = new File(out + ".sample_gene_summary")
-    _geneStatisticsFile = new File(out + ".sample_gene_statistics")
-    _cumulativeCoverageCountsFile = new File(out + ".sample_cumulative_coverage_counts")
-    _cumulativeCoverageProportionsFile = new File(out + ".sample_cumulative_coverage_proportions")
+    _summaryFile = summaryFile
+    _statisticsFile = statisticsFile
+    _intervalSummaryFile = intervalSummaryFile
+    _intervalStatisticsFile = intervalStatisticsFile
+    _geneSummaryFile = geneSummaryFile
+    _geneStatisticsFile = geneStatisticsFile
+    _cumulativeCoverageCountsFile = cumulativeCoverageCountsFile
+    _cumulativeCoverageProportionsFile = cumulativeCoverageProportionsFile
   }
 
   override def cmdLine = {

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmDiscover.scala

@@ -22,10 +22,10 @@ class XhmmDiscover(val root: Configurable) extends Xhmm with Summarizable {
   @Input
   var r: File = _
 
+  @Output
   private var _outputXcnvAuxFile: File = _
 
-  @Output
-  var outputXcnvAuxFile = _outputXcnvAuxFile
+  def outputXcnvAuxFile = new File(outputXcnv.getAbsolutePath + ".aux")
 
   var xhmmAnalysisName: String = _
 
@@ -34,7 +34,7 @@ class XhmmDiscover(val root: Configurable) extends Xhmm with Summarizable {
     if (outputXcnv == null) {
       throw new IllegalStateException("Must set output file")
     }
-    _outputXcnvAuxFile = new File(outputXcnv.getAbsolutePath + ".aux")
+    _outputXcnvAuxFile = outputXcnvAuxFile
   }
 
   def cmdLine = {

kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala

@@ -36,7 +36,7 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
 
   def biopetScript() = {
     val depths = inputBams.map { keyValuePair =>
-      DepthOfCoverage(this, List(keyValuePair._2), swapExt(xhmmDir, ".bam", ".dcov"), List(targets))
+      DepthOfCoverage(this, List(keyValuePair._2), swapExt(xhmmDir, keyValuePair._2, ".bam", ".dcov"), List(targets))
     }.toList
     addAll(depths)