Added sambamba to multisamplemapping

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala

@@ -41,7 +41,7 @@ class SambambaMarkdup(val parent: Configurable) extends Sambamba {
   override def defaultCoreMemory = 4.0
 
   /** Returns command to execute */
-  def cmdLine = required(executable) +
+  def cmdLine: String = required(executable) +
     required("markdup") +
     conditional(removeDuplicates, "--remove-duplicates") +
     optional("-t", nCoresRequest) +
@@ -55,10 +55,11 @@ class SambambaMarkdup(val parent: Configurable) extends Sambamba {
 }
 
 object SambambaMarkdup {
-  def apply(root: Configurable, input: File, output: File): SambambaMarkdup = {
+  def apply(root: Configurable, input: File, output: File, isIntermediate: Boolean = false): SambambaMarkdup = {
     val markdup = new SambambaMarkdup(root)
     markdup.input = input
     markdup.output = output
+    markdup.isIntermediate = isIntermediate
     markdup
   }
 

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala

@@ -21,7 +21,6 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /** Extension for sambemba merge  */
 class SambambaMerge(val parent: Configurable) extends Sambamba {
-  override def defaultThreads = 4
 
   @Input(doc = "Bam File[s]")
   var input: List[File] = Nil
@@ -39,7 +38,7 @@ class SambambaMerge(val parent: Configurable) extends Sambamba {
   override def defaultCoreMemory = 4.0
 
   /** Returns command to execute */
-  def cmdLine = required(executable) +
+  def cmdLine: String = required(executable) +
     required("merge") +
     optional("-t", nCoresRequest) +
     optional("-l", compressionLevel) +
@@ -47,5 +46,5 @@ class SambambaMerge(val parent: Configurable) extends Sambamba {
     conditional(header, "--header") +
     conditional(showProgress, "--show-progress") +
     required(output) +
-    repeat("", input)
+    repeat(input)
 }

mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala

@@ -19,7 +19,7 @@ import java.io.File
 import htsjdk.samtools.SamReaderFactory
 import htsjdk.samtools.reference.FastaSequenceFile
 import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
-import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, MultiSampleQScript }
+import nl.lumc.sasc.biopet.core.{ MultiSampleQScript, PipelineCommand, Reference }
 import nl.lumc.sasc.biopet.extensions.Ln
 import nl.lumc.sasc.biopet.extensions.picard._
 import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
@@ -28,8 +28,8 @@ import nl.lumc.sasc.biopet.pipelines.gears.GearsSingle
 import nl.lumc.sasc.biopet.utils.Logging
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
-
 import MultisampleMapping.MergeStrategy
+import nl.lumc.sasc.biopet.extensions.sambamba.{ SambambaMarkdup, SambambaMerge }
 
 import scala.collection.JavaConversions._
 
@@ -247,7 +247,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript
 
       mergeStrategy match {
         case MergeStrategy.None =>
-        case (MergeStrategy.MergeSam | MergeStrategy.MarkDuplicates) if libraries.flatMap(_._2.bamFile).size == 1 =>
+        case (MergeStrategy.MergeSam) if libraries.flatMap(_._2.bamFile).size == 1 =>
           add(Ln.linkBamFile(qscript, libraries.flatMap(_._2.bamFile).head, bamFile.get): _*)
         case (MergeStrategy.PreProcessMergeSam | MergeStrategy.PreProcessMarkDuplicates) if libraries.flatMap(_._2.preProcessBam).size == 1 =>
           add(Ln.linkBamFile(qscript, libraries.flatMap(_._2.preProcessBam).head, bamFile.get): _*)
@@ -259,6 +259,17 @@ trait MultisampleMappingTrait extends MultiSampleQScript
           add(MarkDuplicates(qscript, libraries.flatMap(_._2.bamFile).toList, bamFile.get, isIntermediate = !keepMergedFiles))
         case MergeStrategy.PreProcessMarkDuplicates =>
           add(MarkDuplicates(qscript, libraries.flatMap(_._2.preProcessBam).toList, bamFile.get, isIntermediate = !keepMergedFiles))
+        case MergeStrategy.PreProcessSambambaMarkdup =>
+          val mergedBam = new File(sampleDir, "merged.bam")
+          if (libraries.flatMap(_._2.bamFile).size == 1) {
+            add(Ln.linkBamFile(qscript, libraries.flatMap(_._2.preProcessBam).head, mergedBam): _*)
+          } else {
+            val merge = new SambambaMerge(qscript)
+            merge.input = libraries.flatMap(_._2.preProcessBam).toList
+            merge.output = mergedBam
+            add(merge)
+          }
+          add(SambambaMarkdup(qscript, mergedBam, bamFile.get, isIntermediate = !keepMergedFiles))
         case _ => throw new IllegalStateException("This should not be possible, unimplemented MergeStrategy?")
       }
 
@@ -301,7 +312,7 @@ class MultisampleMapping(val parent: Configurable) extends QScript with Multisam
 object MultisampleMapping extends PipelineCommand {
 
   object MergeStrategy extends Enumeration {
-    val None, MergeSam, MarkDuplicates, PreProcessMergeSam, PreProcessMarkDuplicates = Value
+    val None, MergeSam, MarkDuplicates, PreProcessMergeSam, PreProcessMarkDuplicates, PreProcessSambambaMarkdup = Value
   }
 
   /** When file is not absolute an error is raise att the end of the script of a pipeline */