Added basic tests

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala

@@ -330,7 +330,7 @@ object BaseCounter extends ToolCommand {
         val blockStart = block.getReferenceStart
         val blockEnd = blockStart + block.getLength - 1
         if (start <= blockEnd && end >= blockStart) {
-          (if (end < blockEnd) end else blockEnd) - (if (start > blockStart) start else blockStart)
+          (if (end < blockEnd) end else blockEnd) - (if (start > blockStart) start else blockStart) + 1
         } else 0
       }.sum
   }

public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BaseCounterTest.scala

+package nl.lumc.sasc.biopet.tools
+
+import htsjdk.samtools.util.OverlapDetector
+import htsjdk.samtools.{SAMReadGroupRecord, SAMSequenceRecord, SAMLineParser, SAMFileHeader}
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+import picard.annotation.Gene
+
+/**
+  * Created by pjvan_thof on 1/29/16.
+  */
+class BaseCounterTest extends TestNGSuite with Matchers {
+
+  import BaseCounter._
+
+  @Test
+  def testCountsClass(): Unit = {
+    val counts = new Counts
+    counts.antiSenseBases shouldBe 0
+    counts.antiSenseReads shouldBe 0
+    counts.senseBases shouldBe 0
+    counts.senseReads shouldBe 0
+    counts.totalBases shouldBe 0
+    counts.totalReads shouldBe 0
+
+    counts.antiSenseBases = 1
+    counts.senseBases = 2
+    counts.totalBases shouldBe 3
+
+    counts.antiSenseReads = 1
+    counts.senseReads = 2
+    counts.totalReads shouldBe 3
+  }
+
+  @Test
+  def testBamRecordBasesOverlapBlocks(): Unit = {
+    val read = BaseCounterTest.lineParser.parseLine("r02\t0\tchrQ\t50\t60\t4M2D4M\t*\t0\t0\tTACGTACGTA\tEEFFGGHHII\tRG:Z:001")
+    bamRecordBasesOverlap(read, 40, 70) shouldBe 8
+    bamRecordBasesOverlap(read, 50, 59) shouldBe 8
+    bamRecordBasesOverlap(read, 50, 55) shouldBe 4
+    bamRecordBasesOverlap(read, 55, 60) shouldBe 4
+    bamRecordBasesOverlap(read, 10, 20) shouldBe 0
+    bamRecordBasesOverlap(read, 40, 49) shouldBe 0
+    bamRecordBasesOverlap(read, 40, 50) shouldBe 1
+    bamRecordBasesOverlap(read, 40, 51) shouldBe 2
+    bamRecordBasesOverlap(read, 58, 70) shouldBe 2
+    bamRecordBasesOverlap(read, 59, 70) shouldBe 1
+    bamRecordBasesOverlap(read, 60, 70) shouldBe 0
+  }
+
+    @Test
+  def testBamRecordBasesOverlap(): Unit = {
+    val read = BaseCounterTest.lineParser.parseLine("r02\t0\tchrQ\t50\t60\t10M\t*\t0\t0\tTACGTACGTA\tEEFFGGHHII\tRG:Z:001")
+    bamRecordBasesOverlap(read, 40, 70) shouldBe 10
+    bamRecordBasesOverlap(read, 50, 59) shouldBe 10
+    bamRecordBasesOverlap(read, 50, 55) shouldBe 6
+    bamRecordBasesOverlap(read, 55, 60) shouldBe 5
+    bamRecordBasesOverlap(read, 10, 20) shouldBe 0
+    bamRecordBasesOverlap(read, 40, 49) shouldBe 0
+    bamRecordBasesOverlap(read, 40, 50) shouldBe 1
+    bamRecordBasesOverlap(read, 40, 51) shouldBe 2
+    bamRecordBasesOverlap(read, 58, 70) shouldBe 2
+    bamRecordBasesOverlap(read, 59, 70) shouldBe 1
+    bamRecordBasesOverlap(read, 60, 70) shouldBe 0
+
+    val counts = new Counts
+    bamRecordBasesOverlap(read, 40, 70, counts, true)
+    counts.senseBases shouldBe 10
+    counts.antiSenseBases shouldBe 0
+    counts.senseReads shouldBe 1
+    counts.antiSenseReads shouldBe 0
+
+    bamRecordBasesOverlap(read, 50, 54, counts, false)
+    counts.senseBases shouldBe 10
+    counts.antiSenseBases shouldBe 5
+    counts.senseReads shouldBe 1
+    counts.antiSenseReads shouldBe 1
+  }
+}
+
+object BaseCounterTest {
+  val lineParser = {
+    val header = new SAMFileHeader
+    header.addSequence(new SAMSequenceRecord("chrQ", 10000))
+    header.addSequence(new SAMSequenceRecord("chrR", 10000))
+    header.addReadGroup(new SAMReadGroupRecord("001"))
+
+    new SAMLineParser(header)
+  }
+
+  val genes = List()
+}
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