Merge pull request #168 from biopet/fix-BIOPET-757

Adding a tool to merge jobreports

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/jobreport/MergeQueueJobReports.scala

+package nl.lumc.sasc.biopet.core.jobreport
+
+import java.io.{File, PrintStream}
+
+import nl.lumc.sasc.biopet.utils.{AbstractOptParser, ToolCommand}
+import org.broadinstitute.gatk.utils.report.GATKReport
+
+import scala.collection.JavaConversions._
+
+/**
+  * Created by pjvanthof on 25/07/2017.
+  */
+object MergeQueueJobReports extends ToolCommand {
+  case class Args(inputFiles: List[File] = Nil, outputfile: File = null)
+
+  class OptParser extends AbstractOptParser[Args](commandName) {
+    opt[File]('I', "inputFile") unbounded () required () valueName "<file>" action { (x, c) =>
+      c.copy(inputFiles = x :: c.inputFiles)
+    } text "Output directory of the pipeline"
+    opt[File]('o', "outputFile") unbounded () required () maxOccurs 1 valueName "<file>" action {
+      (x, c) =>
+        c.copy(outputfile = x)
+    } text "Output directory of this tool"
+  }
+
+  def main(args: Array[String]): Unit = {
+    logger.info("Start")
+
+    val argsParser = new OptParser
+    val cmdArgs
+      : Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
+
+    val newReport = new GATKReport
+    val reports = cmdArgs.inputFiles.map(new GATKReport(_))
+    val tableNames = reports.flatMap(_.getTables.map(_.getTableName)).distinct
+
+    for (name <- tableNames; report <- reports if report.hasTable(name)) {
+      val table = report.getTable(name)
+      if (newReport.hasTable(name)) newReport.getTable(name).concat(table)
+      else newReport.addTable(table)
+    }
+
+    val writer = new PrintStream(cmdArgs.outputfile)
+    newReport.print(writer)
+    writer.close()
+
+    logger.info("Done")
+  }
+
+}

biopet-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutableMain.scala

@@ -14,6 +14,7 @@
   */
 package nl.lumc.sasc.biopet
 
+import nl.lumc.sasc.biopet.core.jobreport.MergeQueueJobReports
 import nl.lumc.sasc.biopet.core.pipelinestatus.PipelineStatus
 import nl.lumc.sasc.biopet.utils.{BiopetExecutable, MainCommand}
 
@@ -46,7 +47,8 @@ object BiopetExecutableMain extends BiopetExecutable {
     nl.lumc.sasc.biopet.pipelines.generateindexes.ValidateAnnotations
   )
 
-  def tools: List[MainCommand] = PipelineStatus :: BiopetToolsExecutable.tools
+  def tools: List[MainCommand] =
+    MergeQueueJobReports :: PipelineStatus :: BiopetToolsExecutable.tools
 
   def templates: List[MainCommand] = List(
     nl.lumc.sasc.biopet.pipelines.mapping.template.MultiSampleMapping,