From 7a3e8399e2e43d48333f59c5e3537bb3c9d5cf96 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 19 Jul 2016 16:47:17 +0200
Subject: [PATCH] Added unit testing to count / histogram
---
.../biopet/tools/bamstats/Histogram.scala | 12 +++-
.../sasc/biopet/tools/bamstats/Stats.scala | 14 ++---
.../biopet/tools/bamstats/CountsTest.scala | 59 +++++++++++++++++++
.../biopet/tools/bamstats/HistogramTest.scala | 59 +++++++++++++++++++
4 files changed, 134 insertions(+), 10 deletions(-)
create mode 100644 biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/CountsTest.scala
create mode 100644 biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/HistogramTest.scala
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 fa68fa455..67f9bd6cf 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
@@ -7,8 +7,14 @@ import scala.collection.mutable
/**
* Created by pjvanthof on 05/07/16.
*/
-class Counts[T](implicit ord: Ordering[T]) {
- protected[Counts] val counts: mutable.Map[T, Long] = mutable.Map()
+class Counts[T](_counts: Map[T, Long] = Map[T, Long]())(implicit ord: Ordering[T]) {
+ protected[Counts] val counts: mutable.Map[T, Long] = mutable.Map() ++ _counts
+
+ /** Returns histogram as map */
+ def countsMap = counts.toMap
+
+ /** Returns value if it does exist */
+ def get(key: T) = counts.get(key)
/** This will add an other histogram to `this` */
def +=(other: Counts[T]): Counts[T] = {
@@ -30,6 +36,6 @@ class Counts[T](implicit ord: Ordering[T]) {
}
}
-class Histogram[T](implicit ord: Numeric[T]) extends Counts[T] {
+class Histogram[T](_counts: Map[T, Long] = Map[T, Long]())(implicit ord: Numeric[T]) extends Counts[T](_counts) {
}
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 14bb97525..bf446e2dd 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
@@ -8,13 +8,13 @@ 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]
+ 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]()
/** This will add an other [[Stats]] inside `this` */
def +=(other: Stats): Stats = {
diff --git a/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/CountsTest.scala b/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/CountsTest.scala
new file mode 100644
index 000000000..286abc245
--- /dev/null
+++ b/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/CountsTest.scala
@@ -0,0 +1,59 @@
+package nl.lumc.sasc.biopet.tools.bamstats
+
+import java.io.File
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import scala.io.Source
+
+/**
+ * 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)
+ val c1 = new Counts[String](data)
+ c1.countsMap shouldBe data
+ c1.get("1") shouldBe Some(1)
+ c1.get("2") shouldBe Some(2)
+ c1.get("3") shouldBe Some(3)
+ c1.get("4") shouldBe None
+
+ c1.add("1")
+ c1.get("1") shouldBe Some(2)
+ c1.add("4")
+ c1.get("4") shouldBe Some(1)
+
+ val c2 = new Counts[String](data)
+ c1 += c2
+
+ c1.get("1") shouldBe Some(3)
+ c1.get("2") shouldBe Some(4)
+ c1.get("3") shouldBe Some(6)
+ c1.get("4") shouldBe Some(1)
+ }
+
+ @Test
+ 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)
+ val c1 = new Counts[Int](data)
+
+ val tsvFile = File.createTempFile("counts.", ".tsv")
+ tsvFile.deleteOnExit()
+
+ c1.writeToTsv(tsvFile)
+
+ val reader = Source.fromFile(tsvFile)
+ reader.getLines().toList shouldBe List("value\tcount", "1\t1", "2\t2", "3\t3")
+ reader.close()
+ }
+}
diff --git a/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/HistogramTest.scala b/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/HistogramTest.scala
new file mode 100644
index 000000000..9944821b5
--- /dev/null
+++ b/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/HistogramTest.scala
@@ -0,0 +1,59 @@
+package nl.lumc.sasc.biopet.tools.bamstats
+
+import java.io.File
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import scala.io.Source
+
+/**
+ * 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 c1 = new Histogram[Int](data)
+ c1.countsMap shouldBe data
+ c1.get(1) shouldBe Some(1)
+ c1.get(2) shouldBe Some(2)
+ c1.get(3) shouldBe Some(3)
+ c1.get(4) shouldBe None
+
+ c1.add(1)
+ c1.get(1) shouldBe Some(2)
+ c1.add(4)
+ c1.get(4) shouldBe Some(1)
+
+ val c2 = new Counts[Int](data)
+ c1 += c2
+
+ c1.get(1) shouldBe Some(3)
+ c1.get(2) shouldBe Some(4)
+ c1.get(3) shouldBe Some(6)
+ c1.get(4) shouldBe Some(1)
+ }
+
+ @Test
+ def testEmpty: Unit = {
+ val c1 = new Histogram[Int]()
+ c1.countsMap.isEmpty shouldBe true
+ }
+
+ @Test
+ def testTsv: Unit = {
+ val data: Map[Int, Long] = Map(1 -> 1, 2 -> 2, 3 -> 3)
+ val c1 = new Histogram[Int](data)
+
+ val tsvFile = File.createTempFile("counts.", ".tsv")
+ tsvFile.deleteOnExit()
+
+ c1.writeToTsv(tsvFile)
+
+ val reader = Source.fromFile(tsvFile)
+ reader.getLines().toList shouldBe List("value\tcount", "1\t1", "2\t2", "3\t3")
+ reader.close()
+ }
+}
--
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