Use MergeSamFiles for all merges

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala

@@ -28,7 +28,7 @@ import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.config._
 import nl.lumc.sasc.biopet.core.summary._
 import nl.lumc.sasc.biopet.extensions.{ HtseqCount, Ln }
-import nl.lumc.sasc.biopet.extensions.picard.{ CollectRnaSeqMetrics, GatherBamFiles, MergeSamFiles, SortSam }
+import nl.lumc.sasc.biopet.extensions.picard.{ CollectRnaSeqMetrics, SortSam, MergeSamFiles }
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
 import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
 import nl.lumc.sasc.biopet.pipelines.gentrap.extensions.{ CustomVarScan, Pdflatex, RawBaseCounter }
@@ -511,7 +511,7 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
           case Some(r2j) => List(f1Job.output, r2j.output)
           case None      => List(f1Job.output)
         }
-        val combineJob = makeCombineJob(perStrandFiles, createFile(".plus_strand.bam"), gather = true)
+        val combineJob = makeCombineJob(perStrandFiles, createFile(".plus_strand.bam"))
 
         Option(StrandSeparationJobSet(f1Job, r2Job, combineJob))
 
@@ -552,7 +552,7 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
           case Some(r1j) => List(f2Job.output, r1j.output)
           case None      => List(f2Job.output)
         }
-        val combineJob = makeCombineJob(perStrandFiles, createFile(".minus_strand.bam"), gather = true)
+        val combineJob = makeCombineJob(perStrandFiles, createFile(".minus_strand.bam"))
 
         Option(StrandSeparationJobSet(f2Job, r1Job, combineJob))
 
@@ -648,11 +648,11 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
         job
       }
 
-    /** Super type of Ln and MergeSamFile */
+    /** Super type of Ln and MergeSamFiles */
     private type CombineFileFunction = QFunction { def output: File }
 
     /** Ln or MergeSamFile job, depending on how many inputs are supplied */
-    private def makeCombineJob(inFiles: List[File], outFile: File, gather: Boolean = false,
+    private def makeCombineJob(inFiles: List[File], outFile: File,
                                mergeSortOrder: String = "coordinate"): CombineFileFunction = {
       require(inFiles.nonEmpty, "At least one input files for combine job")
       if (inFiles.size == 1) {
@@ -660,11 +660,6 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
         job.input = inFiles.head
         job.output = outFile
         job
-      } else if (gather) {
-        val job = new GatherBamFiles(qscript)
-        job.input = inFiles
-        job.output = outFile
-        job
       } else {
         val job = new MergeSamFiles(qscript)
         job.input = inFiles