Merge pull request #1 from fnothaft/fix-oc-npe

Use option to avoid NPE in test.
bigdatagenomics · Oct 31, 2014 · 4186c74 · 4186c74
2 parents f0bc0f0 + 7eb8883
commit 4186c74
Showing 1 changed file with 4 additions and 5 deletions.
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/RealignIndelsSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/RealignIndelsSuite.scala
@@ -260,13 +260,12 @@ class RealignIndelsSuite extends SparkFunSuite {
  val readName = realn.getReadName()
  val op = realn.getOldPosition()
  val oc = realn.getOldCigar()
- if (op != null && op > 0) {
+
+ Option(op).filter(_ >= 0).foreach(oPos => {
  val s = artificial_reads.collect().filter(x => (x.getReadName() == readName))
- assert(oc != null)
- assert(s.filter(x => (x.getStart() == op)).length > 0)
+ assert(s.filter(x => (x.getStart() == oPos)).length > 0)
  assert(s.filter(x => (x.getCigar() == oc)).length > 0)
- }
+ })
  })
  }
-
 }