convert MergeSamFiles to biopet function

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.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.{ Input, Output, Argument }
+
+class MergeSamFiles(val root: Configurable) extends Picard {
+  javaMainClass = "picard.sam.MergeSamFiles"
+
+  @Input(doc = "The input SAM or BAM files to analyze.", required = true)
+  var input: List[File] = Nil
+
+  @Output(doc = "The output file to bam file to", required = true)
+  var output: File = _
+
+  @Argument(doc = "Sort order of output file Required. Possible values: {unsorted, queryname, coordinate} ", required = true)
+  var sortOrder: String = _
+
+  @Argument(doc = "ASSUME_SORTED", required = false)
+  var assumeSorted: Boolean = config("assumesorted", default = false)
+  
+  @Argument(doc = "MERGE_SEQUENCE_DICTIONARIES", required = false)
+  var mergeSequenceDictionaries: Boolean = config("merge_sequence_dictionaries", default = false)
+  
+  @Argument(doc = "USE_THREADING", required = false)
+  var useThreading: Boolean = config("use_threading", default = false)
+  
+  @Argument(doc = "COMMENT", required = false)
+  var comment: String = config("comment")
+  
+  override def commandLine = super.commandLine +
+    required("INPUT=", input, spaceSeparated = false) +
+    required("OUTPUT=", output, spaceSeparated = false) +
+    required("SORT_ORDER=", sortOrder, spaceSeparated = false) +
+    conditional(assumeSorted, "ASSUME_SORTED=TRUE") +
+    conditional(mergeSequenceDictionaries, "MERGE_SEQUENCE_DICTIONARIES=TRUE") +
+    optional("COMMENT=", comment, spaceSeparated = false)
+}
+
+object MergeSamFiles {
+  def apply(root: Configurable, input: List[File], outputDir: String, sortOrder: String = null): MergeSamFiles = {
+    val mergeSamFiles = new MergeSamFiles(root)
+    mergeSamFiles.input = input
+    mergeSamFiles.output = new File(outputDir, input.head.getName.stripSuffix(".bam").stripSuffix(".sam") + ".merge.bam")
+    if (sortOrder == null) mergeSamFiles.sortOrder = "coordinate"
+    else mergeSamFiles.sortOrder = sortOrder
+    return mergeSamFiles
+  }
+}
\ No newline at end of file

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

@@ -6,12 +6,12 @@ import java.util.Date
 import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import nl.lumc.sasc.biopet.core.apps.FastqSplitter
 import nl.lumc.sasc.biopet.extensions.aligners.{ Bwa, Star }
-import nl.lumc.sasc.biopet.extensions.picard.{MarkDuplicates, SortSam}
+import nl.lumc.sasc.biopet.extensions.picard.{MarkDuplicates, SortSam, MergeSamFiles}
 import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
 import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
 import org.broadinstitute.gatk.queue.QScript
 import org.broadinstitute.gatk.utils.commandline.{ Input, Argument, ClassType }
-import org.broadinstitute.gatk.queue.extensions.picard.{ MergeSamFiles, AddOrReplaceReadGroups }
+import org.broadinstitute.gatk.queue.extensions.picard.{ AddOrReplaceReadGroups }
 import scala.math._
 
 class Mapping(val root: Configurable) extends QScript with BiopetQScript {
@@ -218,7 +218,11 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
     if (!skipMarkduplicates) {
       bamFile = new File(outputDir + outputName + ".dedup.bam")
       add(MarkDuplicates(this, bamFiles, bamFile))
-    } else if (skipMarkduplicates && chunking) bamFile = addMergeBam(bamFiles, new File(outputDir + outputName + ".bam"), outputDir)
+    } else if (skipMarkduplicates && chunking) {
+      val mergeSamFile = MergeSamFiles(this, bamFiles, outputDir)
+      add(mergeSamFile)
+      bamFile = mergeSamFile.output
+    }
     
     if (!skipMetrics) addAll(BamMetrics.apply(this, bamFile, outputDir + "metrics/").functions)
     
@@ -239,21 +243,21 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
 //    return sortSam.output
 //  }
 
-  def addMergeBam(inputSam: List[File], outputFile: File, dir: String): File = {
-    val mergeSam = new MergeSamFiles
-    mergeSam.input = inputSam
-    mergeSam.createIndex = true
-    mergeSam.output = outputFile
-    mergeSam.memoryLimit = 2
-    mergeSam.nCoresRequest = 2
-    mergeSam.assumeSorted = true
-    mergeSam.USE_THREADING = true
-    mergeSam.jobResourceRequests :+= "h_vmem=4G"
-    if (!skipMarkduplicates) mergeSam.isIntermediate = true
-    add(mergeSam)
-
-    return mergeSam.output
-  }
+//  def addMergeBam(inputSam: List[File], outputFile: File, dir: String): File = {
+//    val mergeSam = new MergeSamFiles
+//    mergeSam.input = inputSam
+//    mergeSam.createIndex = true
+//    mergeSam.output = outputFile
+//    mergeSam.memoryLimit = 2
+//    mergeSam.nCoresRequest = 2
+//    mergeSam.assumeSorted = true
+//    mergeSam.USE_THREADING = true
+//    mergeSam.jobResourceRequests :+= "h_vmem=4G"
+//    if (!skipMarkduplicates) mergeSam.isIntermediate = true
+//    add(mergeSam)
+//
+//    return mergeSam.output
+//  }
 
   def addAddOrReplaceReadGroups(inputSam: List[File], outputFile: File, dir: String): File = {
     val addOrReplaceReadGroups = new AddOrReplaceReadGroups