diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala index f8ed110e7d129dfa78d71a954fad72654aa54eda..bf8acd07e51a0ab78f9d0c6484c927a6933ea4ee 100644 --- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala +++ b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala @@ -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) => diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Histogram.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Histogram.scala index 7f4107d69c41f0b8004a3ce68857a24612942fc9..64be8768003449b7db21477d89f5b6f11a0c5015 100644 --- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Histogram.scala +++ b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Histogram.scala @@ -1,14 +1,14 @@ 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() diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Stats.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Stats.scala index 7dee85fd0c7ca73feec5b63a4cc93451a004c917..07b1459269d90a807559e1fe3ff448b6146ca3b0 100644 --- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Stats.scala +++ b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Stats.scala @@ -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. */