Fixed subtract bug and tests

bigdatagenomics · Sep 27, 2017 · 9bc5aad · 9bc5aad
1 parent b2c243f
commit 9bc5aad
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Showing 2 changed files with 3 additions and 8 deletions.
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala b/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala
@@ -698,15 +698,10 @@ case class ReferenceRegion(
  start,
  other.start,
  newRegionStrand))
- } else if (end > other.end) {
- Iterable(ReferenceRegion(referenceName,
- start,
- other.end,
- newRegionStrand))
  } else {
  Iterable.empty[ReferenceRegion]
  }
- val second = if (other.start > start && end > other.end) {
+ val second = if (end > other.end) {
  Iterable(ReferenceRegion(referenceName,
  other.end,
  end,

diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/models/ReferenceRegionSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/models/ReferenceRegionSuite.scala
@@ -264,13 +264,13 @@ class ReferenceRegionSuite extends FunSuite {
  // right end unstranded
  assert(ReferenceRegion("chr0", 10, 100, Strand.FORWARD).subtract(ReferenceRegion("chr0", 90, 150, Strand.REVERSE), false) === List(ReferenceRegion("chr0", 10, 90)))
  // left end unstranded
- assert(ReferenceRegion("chr0", 90, 150, Strand.REVERSE).subtract(ReferenceRegion("chr0", 10, 100, Strand.FORWARD), false) === List(ReferenceRegion("chr0", 90, 100)))
+ assert(ReferenceRegion("chr0", 90, 150, Strand.REVERSE).subtract(ReferenceRegion("chr0", 10, 100, Strand.FORWARD), false) === List(ReferenceRegion("chr0", 100, 150)))
  // contained unstranded
  assert(ReferenceRegion("chr0", 2, 150, Strand.REVERSE).subtract(ReferenceRegion("chr0", 10, 100, Strand.FORWARD), false) === List(ReferenceRegion("chr0", 2, 10), ReferenceRegion("chr0", 100, 150)))
  // right end stranded
  assert(ReferenceRegion("chr0", 10, 100, Strand.FORWARD).subtract(ReferenceRegion("chr0", 90, 150, Strand.FORWARD), true) === List(ReferenceRegion("chr0", 10, 90, Strand.FORWARD)))
  // left end stranded
- assert(ReferenceRegion("chr0", 90, 150, Strand.FORWARD).subtract(ReferenceRegion("chr0", 10, 100, Strand.FORWARD), true) === List(ReferenceRegion("chr0", 90, 100, Strand.FORWARD)))
+ assert(ReferenceRegion("chr0", 90, 150, Strand.FORWARD).subtract(ReferenceRegion("chr0", 10, 100, Strand.FORWARD), true) === List(ReferenceRegion("chr0", 100, 150, Strand.FORWARD)))
  // contained stranded
  assert(ReferenceRegion("chr0", 2, 150, Strand.FORWARD).subtract(ReferenceRegion("chr0", 10, 100, Strand.FORWARD), true) === List(ReferenceRegion("chr0", 2, 10, Strand.FORWARD), ReferenceRegion("chr0", 100, 150, Strand.FORWARD)))