Remove copy class

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/gather/BQSRGather.scala

-package nl.lumc.sasc.biopet.extensions.gatk.broad.gather
-
-import java.io.{ File, FileNotFoundException, PrintStream }
-import java.util
-
-import org.apache.commons.collections.CollectionUtils
-import org.apache.log4j.Logger
-import org.broadinstitute.gatk.engine.recalibration.RecalibrationReport
-import org.broadinstitute.gatk.utils.commandline.Gatherer
-import org.broadinstitute.gatk.utils.exceptions.{ ReviewedGATKException, UserException }
-import org.broadinstitute.gatk.utils.report.GATKReport
-
-import scala.collection.JavaConversions._
-
-/**
- * Created by pjvanthof on 26/04/16.
- */
-class BQSRGatherer extends Gatherer {
-  private val logger: Logger = Logger.getLogger(classOf[BQSRGatherer])
-  private val EMPTY_INPUT_LIST: String = "list of inputs files is empty or there is no usable data in any input file"
-  private val MISSING_OUTPUT_FILE: String = "missing output file name"
-  private val MISSING_READ_GROUPS: String = "Missing read group(s)"
-
-  def gather(inputs: util.List[File], output: File) {
-    val outputFile: PrintStream = try {
-      new PrintStream(output)
-    } catch {
-      case e: FileNotFoundException => {
-        throw new UserException.MissingArgument("output", MISSING_OUTPUT_FILE)
-      }
-    }
-    val report: GATKReport = gatherReport(inputs)
-    report.print(outputFile)
-  }
-
-  def gatherReport(inputs: util.List[File]): GATKReport = {
-    val allReadGroups: util.SortedSet[String] = new util.TreeSet[String]
-    val inputReadGroups: util.LinkedHashMap[File, util.Set[String]] = new util.LinkedHashMap[File, util.Set[String]]
-    for (input <- inputs) {
-      val readGroups: util.Set[String] = RecalibrationReport.getReadGroups(input)
-      inputReadGroups.put(input, readGroups)
-      allReadGroups.addAll(readGroups)
-    }
-    import scala.collection.JavaConversions._
-    for (entry <- inputReadGroups.entrySet) {
-      val input: File = entry.getKey
-      val readGroups: util.Set[String] = entry.getValue
-      if (allReadGroups.size != readGroups.size) {
-        logger.info(MISSING_READ_GROUPS + ": " + input.getAbsolutePath)
-        import scala.collection.JavaConversions._
-        for (readGroup <- CollectionUtils.subtract(allReadGroups, readGroups)) {
-          logger.info("  " + readGroup)
-        }
-      }
-    }
-    var generalReport: RecalibrationReport = null
-    import scala.collection.JavaConversions._
-    for (input <- inputs if !new RecalibrationReport(input, allReadGroups).isEmpty) {
-      val inputReport: RecalibrationReport = new RecalibrationReport(input, allReadGroups)
-      if (generalReport == null) generalReport = inputReport
-      else generalReport.combine(inputReport)
-    }
-    if (generalReport == null) throw new ReviewedGATKException(EMPTY_INPUT_LIST)
-    generalReport.calculateQuantizedQualities
-    return generalReport.createGATKReport
-  }
-}