Merge branch 'fix-seqstat-arraysize' into 'develop'

Seqstat: length array was too short for keeping the readlengths.

the array was too short

See merge request !349

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

@@ -130,7 +130,7 @@ object SeqStat extends ToolCommand {
       baseStats ++= mutable.ArrayBuffer.fill(record.length - baseStats.length)(BaseStat())
     }
 
-    if (readStats.lengths.length < record.length) {
+    if (readStats.lengths.length <= record.length) {
       readStats.lengths ++= mutable.ArrayBuffer.fill(record.length - readStats.lengths.length + 1)(0)
     }
 

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

@@ -109,6 +109,21 @@ class SeqStatTest extends TestNGSuite with MockitoSugar with Matchers {
 
   }
 
+  @Test(dataProvider = "mockReaderProvider", groups = Array("check_readstats"), singleThreaded = true, dependsOnGroups = Array("report"))
+  def testReadStatsObject(fqMock: FastqReader) = {
+    when(fqMock.getFile) thenReturn new File("/tmp/test.fq")
+    when(fqMock.iterator) thenReturn recordsOver("1", "2", "3", "4", "5")
+    val seqstat = SeqStat
+
+    // the histogram should store the lenght==0 value also, for example sequence length 5 is size 6.
+    // please note that we already loaded the dataset twice in seqstat. (seqstat.Seqstat is called 2 times in previous steps)
+    seqstat.readStats.lengths(5) shouldBe 10
+    seqstat.readStats.lengths.length shouldBe 6
+
+    seqstat.readStats.nucs.sum shouldBe 50
+    seqstat.readStats.withN shouldBe 10
+  }
+
   @Test def testArgsMinimum() = {
     val args = Array(
       "-i", resourcePath("/paired01a.fq"))