[ADAM-1196] Add support for open ReferenceRegions.

Resolves #1196.

adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala

@@ -72,6 +72,44 @@ object ReferenceRegion {
   implicit def orderingForPositions = RegionOrdering
   implicit def orderingForOptionalPositions = OptionalRegionOrdering
 
+  /**
+   * Creates a reference region that starts at the beginning of a contig.
+   *
+   * @param referenceName The name of the reference contig that this region is
+   *   on.
+   * @param end The end position for this region.
+   * @return Returns a reference region that goes from the start of a contig to
+   *   a user provided end point.
+   */
+  def fromStart(referenceName: String,
+                end: Long): ReferenceRegion = {
+    ReferenceRegion(referenceName, 0L, end)
+  }
+
+  /**
+   * Creates a reference region that has an open end point.
+   *
+   * @param referenceName The name of the reference contig that this region is
+   *   on.
+   * @param start The start position for this region.
+   * @return Returns a reference region that goes from a user provided starting
+   *   point to the end of a contig.
+   */
+  def toEnd(referenceName: String,
+            start: Long): ReferenceRegion = {
+    ReferenceRegion(referenceName, start, Long.MaxValue)
+  }
+
+  /**
+   * Creates a reference region that covers the entirety of a contig.
+   *
+   * @param referenceName The name of the reference contig to cover.
+   * @return Returns a reference region that covers the entirety of a contig.
+   */
+  def all(referenceName: String): ReferenceRegion = {
+    ReferenceRegion(referenceName, 0L, Long.MaxValue)
+  }
+
   /**
    * Generates a reference region from read data. Returns None if the read is not mapped;
    * else, returns the inclusive region from the start to the end of the read alignment.

adam-core/src/test/scala/org/bdgenomics/adam/models/ReferenceRegionSuite.scala

@@ -285,4 +285,27 @@ class ReferenceRegionSuite extends FunSuite {
     assert(padded.start === 0L)
     assert(padded.end === 5L)
   }
+
+  test("can build an open ended reference region") {
+    val openEnded = ReferenceRegion.toEnd("myCtg", 45L)
+
+    assert(!openEnded.overlaps(ReferenceRegion("myCtg", 44L, 45L)))
+    assert(openEnded.overlaps(ReferenceRegion("myCtg", 44L, 46L)))
+    assert(openEnded.overlaps(ReferenceRegion("myCtg", Long.MaxValue - 1L, Long.MaxValue)))
+  }
+
+  test("can build a reference region with an open start position") {
+    val openStart = ReferenceRegion.fromStart("myCtg", 45L)
+
+    assert(openStart.overlaps(ReferenceRegion("myCtg", 0L, 1L)))
+    assert(openStart.overlaps(ReferenceRegion("myCtg", 44L, 46L)))
+    assert(!openStart.overlaps(ReferenceRegion("myCtg", 45L, 46L)))
+  }
+
+  test("can build a reference region that covers the entirety of a contig") {
+    val all = ReferenceRegion.all("myCtg")
+
+    assert(all.overlaps(ReferenceRegion("myCtg", 0L, 1L)))
+    assert(all.overlaps(ReferenceRegion("myCtg", Long.MaxValue - 1L, Long.MaxValue)))
+  }
 }