Added test to Stats class

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala

@@ -4,7 +4,7 @@ import java.io.File
 import java.util.concurrent.TimeoutException
 
 import htsjdk.samtools.reference.FastaSequenceFile
-import htsjdk.samtools.{SAMSequenceDictionary, SamReaderFactory}
+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 }
@@ -13,6 +13,7 @@ import scala.collection.JavaConversions._
 import scala.concurrent.ExecutionContext.Implicits.global
 import scala.concurrent.duration._
 import scala.concurrent.{ Await, Future }
+import scala.language.postfixOps
 
 /**
  * This tool will collect stats from a bamfile
@@ -76,14 +77,14 @@ object BamStats extends ToolCommand {
   }
 
   /**
-    * This is the main running function of [[BamStats]]. This will start the thereads and collect and write the results.
-    *
-    * @param outputDir All output files will be placed here
-    * @param bamFile Input bam file
-    * @param referenceDict Dict for scattering
-    * @param binSize stats binsize
-    * @param threadBinSize Thread binsize
-    */
+   * This is the main running function of [[BamStats]]. This will start the thereads and collect and write the results.
+   *
+   * @param outputDir All output files will be placed here
+   * @param bamFile Input bam file
+   * @param referenceDict Dict for scattering
+   * @param binSize stats binsize
+   * @param threadBinSize Thread binsize
+   */
   def init(outputDir: File, bamFile: File, referenceDict: SAMSequenceDictionary, binSize: Int, threadBinSize: Int): Unit = {
     val contigsFutures = BedRecordList.fromDict(referenceDict).allRecords.map { contig =>
       Future { processContig(contig, bamFile, binSize, threadBinSize) }
@@ -105,28 +106,28 @@ object BamStats extends ToolCommand {
   }
 
   /**
-    * This will start the subjobs for each contig and collect [[Stats]] on contig level
-    *
-    * @param region Region to check, mostly yhis is the complete contig
-    * @param bamFile Input bam file
-    * @param binSize stats binsize
-    * @param threadBinSize Thread binsize
-    * @return Output stats
-    */
+   * This will start the subjobs for each contig and collect [[Stats]] on contig level
+   *
+   * @param region Region to check, mostly yhis is the complete contig
+   * @param bamFile Input bam file
+   * @param binSize stats binsize
+   * @param threadBinSize Thread binsize
+   * @return Output stats
+   */
   def processContig(region: BedRecord, bamFile: File, binSize: Int, threadBinSize: Int): Stats = {
     val scattersFutures = region
       .scatter(binSize)
       .grouped((region.length.toDouble / threadBinSize).ceil.toInt)
-      .map( scatters => Future { processThread(scatters, bamFile) })
+      .map(scatters => Future { processThread(scatters, bamFile) })
     waitOnFutures(scattersFutures.toList, Some(region.chr))
   }
 
   /**
-    * This method will wait when all futures are complete and collect a single [[Stats]] instance
-    * @param futures List of futures to monitor
-    * @param msg Optional message for logging
-    * @return Output stats
-    */
+   * This method will wait when all futures are complete and collect a single [[Stats]] instance
+   * @param futures List of futures to monitor
+   * @param msg Optional message for logging
+   * @return Output stats
+   */
   def waitOnFutures(futures: List[Future[Stats]], msg: Option[String] = None): Stats = {
     msg.foreach(m => logger.info(s"Start monitoring jobs for '$m', ${futures.size} jobs"))
     futures.foreach(_.onFailure { case t => throw new RuntimeException(t) })
@@ -148,12 +149,12 @@ object BamStats extends ToolCommand {
   }
 
   /**
-    * This method will process 1 thread bin
-    *
-    * @param scatters bins to check
-    * @param bamFile Input bamfile
-    * @return Output stats
-    */
+   * This method will process 1 thread bin
+   *
+   * @param scatters bins to check
+   * @param bamFile Input bamfile
+   * @return Output stats
+   */
   def processThread(scatters: List[BedRecord], bamFile: File): Stats = {
     val totalStats = Stats()
     val sortedScatters = scatters.sortBy(_.start)
@@ -201,10 +202,10 @@ object BamStats extends ToolCommand {
   }
 
   /**
-    * This method will only count the unmapped fragments
-    * @param bamFile Input bamfile
-    * @return Output stats
-    */
+   * This method will only count the unmapped fragments
+   * @param bamFile Input bamfile
+   * @return Output stats
+   */
   def processUnmappedReads(bamFile: File): Stats = {
     val stats = Stats()
     val samReader = SamReaderFactory.makeDefault().open(bamFile)

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Histogram.scala

@@ -34,6 +34,13 @@ class Counts[T](_counts: Map[T, Long] = Map[T, Long]())(implicit ord: Ordering[T
     counts.keys.toList.sorted.foreach(x => writer.println(s"$x\t${counts(x)}"))
     writer.close()
   }
+
+  override def equals(other: Any): Boolean = {
+    other match {
+      case c: Counts[T] => this.counts == c.counts
+      case _            => false
+    }
+  }
 }
 
 class Histogram[T](_counts: Map[T, Long] = Map[T, Long]())(implicit ord: Numeric[T]) extends Counts[T](_counts) {

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Stats.scala

@@ -3,18 +3,16 @@ package nl.lumc.sasc.biopet.tools.bamstats
 /**
  * Created by pjvanthof on 05/07/16.
  */
-case class Stats() {
-
-  var totalReads = 0L
-  var unmapped = 0L
-  var secondary = 0L
-  val mappingQualityHistogram = new Histogram[Int]()
-  val insertSizeHistogram = new Histogram[Int]()
-  val clippingHistogram = new Histogram[Int]()
-  val leftClippingHistogram = new Histogram[Int]()
-  val rightClippingHistogram = new Histogram[Int]()
-  val _5_ClippingHistogram = new Histogram[Int]()
-  val _3_ClippingHistogram = new Histogram[Int]()
+case class Stats(var totalReads: Long = 0L,
+                 var unmapped: Long = 0L,
+                 var secondary: Long = 0L,
+                 mappingQualityHistogram: Histogram[Int] = new Histogram[Int](),
+                 insertSizeHistogram: Histogram[Int] = new Histogram[Int](),
+                 clippingHistogram: Histogram[Int] = new Histogram[Int](),
+                 leftClippingHistogram: Histogram[Int] = new Histogram[Int](),
+                 rightClippingHistogram: Histogram[Int] = new Histogram[Int](),
+                 _5_ClippingHistogram: Histogram[Int] = new Histogram[Int](),
+                 _3_ClippingHistogram: Histogram[Int] = new Histogram[Int]()) {
 
   /** This will add an other [[Stats]] inside `this` */
   def +=(other: Stats): Stats = {

biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/CountsTest.scala

@@ -9,12 +9,12 @@ import org.testng.annotations.Test
 import scala.io.Source
 
 /**
-  * Created by pjvan_thof on 19-7-16.
-  */
+ * Created by pjvan_thof on 19-7-16.
+ */
 class CountsTest extends TestNGSuite with Matchers {
   @Test
-  def testValues: Unit = {
-    val data:  Map[String, Long] = Map("1" -> 1, "2" -> 2, "3" -> 3)
+  def testValues(): Unit = {
+    val data: Map[String, Long] = Map("1" -> 1, "2" -> 2, "3" -> 3)
     val c1 = new Counts[String](data)
     c1.countsMap shouldBe data
     c1.get("1") shouldBe Some(1)
@@ -37,14 +37,36 @@ class CountsTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testEmpty: Unit = {
+  def testEmpty(): Unit = {
     val c1 = new Counts[Int]()
     c1.countsMap.isEmpty shouldBe true
   }
 
   @Test
-  def testTsv: Unit = {
-    val data:  Map[Int, Long] = Map(1 -> 1, 2 -> 2, 3 -> 3)
+  def testEqual(): Unit = {
+    val c1 = new Counts[Int]()
+    val c2 = new Counts[Int]()
+
+    c1 should not be "be a string"
+
+    c1 shouldBe c1
+    c2 shouldBe c2
+    c1 shouldBe c2
+
+    c1.add(1)
+    c1 shouldBe c1
+    c2 shouldBe c2
+    c1 should not be c2
+
+    c2.add(1)
+    c1 shouldBe c1
+    c2 shouldBe c2
+    c1 shouldBe c2
+  }
+
+  @Test
+  def testTsv(): Unit = {
+    val data: Map[Int, Long] = Map(1 -> 1, 2 -> 2, 3 -> 3)
     val c1 = new Counts[Int](data)
 
     val tsvFile = File.createTempFile("counts.", ".tsv")

biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/HistogramTest.scala

@@ -9,12 +9,12 @@ import org.testng.annotations.Test
 import scala.io.Source
 
 /**
-  * Created by pjvan_thof on 19-7-16.
-  */
+ * Created by pjvan_thof on 19-7-16.
+ */
 class HistogramTest extends TestNGSuite with Matchers {
   @Test
   def testValues: Unit = {
-    val data:  Map[Int, Long] = Map(1 -> 1, 2 -> 2, 3 -> 3)
+    val data: Map[Int, Long] = Map(1 -> 1, 2 -> 2, 3 -> 3)
     val c1 = new Histogram[Int](data)
     c1.countsMap shouldBe data
     c1.get(1) shouldBe Some(1)
@@ -44,7 +44,7 @@ class HistogramTest extends TestNGSuite with Matchers {
 
   @Test
   def testTsv: Unit = {
-    val data:  Map[Int, Long] = Map(1 -> 1, 2 -> 2, 3 -> 3)
+    val data: Map[Int, Long] = Map(1 -> 1, 2 -> 2, 3 -> 3)
     val c1 = new Histogram[Int](data)
 
     val tsvFile = File.createTempFile("counts.", ".tsv")

biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/StatsTest.scala

+package nl.lumc.sasc.biopet.tools.bamstats
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+  * Created by pjvan_thof on 19-7-16.
+  */
+class StatsTest extends TestNGSuite with Matchers {
+  @Test
+  def testEqual(): Unit = {
+    val s1 = new Stats()
+    val s2 = new Stats()
+
+    s1 shouldBe s2
+
+    s1.totalReads += 1
+    s1 should not be s2
+
+    s2.totalReads += 1
+    s1 shouldBe s2
+
+    s1.mappingQualityHistogram.add(1)
+    s1 should not be s2
+
+    s2.mappingQualityHistogram.add(1)
+    s1 shouldBe s2
+  }
+
+  @Test
+  def testEmpty(): Unit = {
+    val stats = new Stats()
+
+    stats.totalReads shouldBe 0
+    stats.unmapped shouldBe 0
+    stats.secondary shouldBe 0
+
+    stats.clippingHistogram.countsMap shouldBe empty
+    stats.insertSizeHistogram.countsMap shouldBe empty
+    stats.mappingQualityHistogram.countsMap shouldBe empty
+    stats.leftClippingHistogram.countsMap shouldBe empty
+    stats.rightClippingHistogram.countsMap shouldBe empty
+    stats._5_ClippingHistogram.countsMap shouldBe empty
+    stats._3_ClippingHistogram.countsMap shouldBe empty
+  }
+
+  @Test
+  def testPlus: Unit = {
+    val s1 = new Stats()
+    val s2 = new Stats()
+
+    s2.totalReads += 1
+    s2._3_ClippingHistogram.add(1)
+
+    s1.totalReads shouldBe 0
+    s1._3_ClippingHistogram.get(1) shouldBe None
+    s1 += s2
+    s1.totalReads shouldBe 1
+    s1._3_ClippingHistogram.get(1) shouldBe Some(1)
+  }
+}