From 6011d8c3bed4d0b2278c12b618b2962cd0632183 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 6 Jul 2016 08:11:58 +0200
Subject: [PATCH] Style changes
---
.../sasc/biopet/tools/bamstats/BamStats.scala | 16 ++++++++--------
.../sasc/biopet/tools/bamstats/Histogram.scala | 6 +++---
.../lumc/sasc/biopet/tools/bamstats/Stats.scala | 1 -
3 files changed, 11 insertions(+), 12 deletions(-)
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 f8ed110e7..bf8acd07e 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 7f4107d69..64be87680 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 7dee85fd0..07b145926 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.
*/
--
GitLab