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 bf8acd07e51a0ab78f9d0c6484c927a6933ea4ee..385a6b5ce4822be725fed45b20a4cfefdfab10d7 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 64be8768003449b7db21477d89f5b6f11a0c5015..6a97e23032ecb300f44fb949f1fc5b8c929e6dbc 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 aa3a58963412ef376681c3a43560d5339ceca65f..cc3e72f898d3969cc1214fc680d891add5d00680 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. */