From 5b3d289824df255b0ae3875fb3033e646a77b9a4 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 6 Jul 2016 08:29:52 +0200
Subject: [PATCH] Remove unused imports
---
.../nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala | 11 ++++-------
.../lumc/sasc/biopet/tools/bamstats/Histogram.scala | 5 +++--
.../nl/lumc/sasc/biopet/tools/bamstats/Stats.scala | 3 ---
3 files changed, 7 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 bf8acd07e..385a6b5ce 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
@@ -2,18 +2,15 @@ package nl.lumc.sasc.biopet.tools.bamstats
import java.io.File
-import htsjdk.samtools.{ CigarOperator, SAMSequenceDictionary, SamReaderFactory }
import htsjdk.samtools.reference.FastaSequenceFile
+import htsjdk.samtools.{ SAMSequenceDictionary, SamReaderFactory }
import nl.lumc.sasc.biopet.utils.BamUtils.SamDictCheck
+import nl.lumc.sasc.biopet.utils.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.blocking
-import scala.util.{ Failure, Success }
-import scala.concurrent.duration.Duration
import scala.collection.JavaConversions._
+import scala.concurrent.ExecutionContext.Implicits.global
+import scala.concurrent.Future
/**
* Created by pjvanthof on 25/05/16.
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 64be87680..6a97e2303 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
@@ -2,9 +2,7 @@ package nl.lumc.sasc.biopet.tools.bamstats
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.
@@ -12,15 +10,18 @@ import scala.math.ScalaNumber
case class Histogram() {
protected[Histogram] val histrogram: mutable.Map[Int, Long] = mutable.Map()
+ /** This will add an other histogram to `this` */
def +=(other: Histogram): Histogram = {
other.histrogram.foreach(x => this.histrogram += x._1 -> (this.histrogram.getOrElse(x._1, 0L) + x._2))
this
}
+ /** With this a value can be added to the histogram */
def add(value: Int): Unit = {
histrogram += value -> (histrogram.getOrElse(value, 0L) + 1)
}
+ /** Write histogram to a tsv/count file */
def writeToTsv(file: File): Unit = {
val writer = new PrintWriter(file)
writer.println("value\tcount")
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 aa3a58963..cc3e72f89 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
@@ -1,8 +1,5 @@
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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