Commit 6011d8c3 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Style changes

parent 8d49ccbf
......@@ -2,22 +2,22 @@ package nl.lumc.sasc.biopet.tools.bamstats
import java.io.File
import htsjdk.samtools.{CigarOperator, SAMSequenceDictionary, SamReaderFactory}
import htsjdk.samtools.{ CigarOperator, SAMSequenceDictionary, SamReaderFactory }
import htsjdk.samtools.reference.FastaSequenceFile
import nl.lumc.sasc.biopet.utils.BamUtils.SamDictCheck
import nl.lumc.sasc.biopet.utils.intervals.{BedRecord, BedRecordList}
import nl.lumc.sasc.biopet.utils.{BamUtils, ToolCommand}
import nl.lumc.sasc.biopet.utils.intervals.{ BedRecord, BedRecordList }
import nl.lumc.sasc.biopet.utils.{ BamUtils, ToolCommand }
import scala.concurrent.ExecutionContext.Implicits.global
import scala.concurrent.{Await, Future}
import scala.concurrent.{ Await, Future }
import scala.concurrent.blocking
import scala.util.{Failure, Success}
import scala.util.{ Failure, Success }
import scala.concurrent.duration.Duration
import scala.collection.JavaConversions._
/**
* Created by pjvanthof on 25/05/16.
*/
* Created by pjvanthof on 25/05/16.
*/
object BamStats extends ToolCommand {
case class Args(outputDir: File = null,
bamFile: File = null,
......@@ -26,7 +26,7 @@ object BamStats extends ToolCommand {
threadBinSize: Int = 10000000) extends AbstractArgs
class OptParser extends AbstractOptParser {
opt[File]('R', "reference") valueName "<file>" action { (x, c) =>
opt[File]('R', "reference") valueName "<file>" action { (x, c) =>
c.copy(referenceFasta = Some(x))
}
opt[File]('o', "outputDir") required () valueName "<directory>" action { (x, c) =>
......
package nl.lumc.sasc.biopet.tools.bamstats
import java.io.{File, PrintWriter}
import java.io.{ File, PrintWriter }
import scala.collection.generic.Sorted
import scala.collection.mutable
import scala.math.ScalaNumber
/**
* Created by pjvanthof on 05/07/16.
*/
* Created by pjvanthof on 05/07/16.
*/
case class Histogram() {
protected[Histogram] val histrogram: mutable.Map[Int, Long] = mutable.Map()
......
......@@ -3,7 +3,6 @@ package nl.lumc.sasc.biopet.tools.bamstats
import scala.collection.mutable
import scala.concurrent.blocking
/**
* Created by pjvanthof on 05/07/16.
*/
......
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