[ADAM-582] Eliminate .get on option in FragmentCoverter.

Resolves #582. In the FragmentConverter, we had code that called .get on an
optional ReferenceRegion. If a NucleotideContigFragment didn't have a contig
associated with it, then we would call .get on the empty option, which would
throw an error. This commit changes that code to call map on the
Option[ReferenceRegion], and then changes the usage of that method so that it
is called in a flatMap. Additionally, I've added a test to cover this case.

adam-core/src/main/scala/org/bdgenomics/adam/converters/FragmentConverter.scala

@@ -35,11 +35,11 @@ private object FragmentCollector extends Serializable {
  * @return Returns key value pair where the key is the contig metadata and the
  * value is a Fragment Collector object.
  */
- def apply(fragment: NucleotideContigFragment): (Contig, FragmentCollector) = {
- (
- fragment.getContig,
- FragmentCollector(Seq((ReferenceRegion(fragment).get, fragment.getFragmentSequence)))
- )
+ def apply(fragment: NucleotideContigFragment): Option[(Contig, FragmentCollector)] = {
+ ReferenceRegion(fragment).map(rr => {
+ (fragment.getContig,
+  FragmentCollector(Seq((rr, fragment.getFragmentSequence))))
+ })
  }
 }
 
@@ -153,7 +153,7 @@ private[adam] object FragmentConverter extends Serializable {
  * @return Returns an RDD of reads that represent aligned contigs.
  */
  def convertRdd(rdd: RDD[NucleotideContigFragment]): RDD[AlignmentRecord] = {
- rdd.map(FragmentCollector(_))
+ rdd.flatMap(FragmentCollector(_))
  .reduceByKey(mergeFragments)
  .flatMap(convertFragment)
  }

adam-core/src/test/scala/org/bdgenomics/adam/converters/FragmentConverterSuite.scala

@@ -24,11 +24,13 @@ import org.bdgenomics.formats.avro._
 class FragmentConverterSuite extends ADAMFunSuite {
 
  test("build a fragment collector and convert to a read") {
- val (builtContig, builtFragment) = FragmentCollector(NucleotideContigFragment.newBuilder()
+ val fcOpt = FragmentCollector(NucleotideContigFragment.newBuilder()
  .setContig(Contig.newBuilder().setContigName("ctg").build())
  .setFragmentSequence("ACACACAC")
  .setFragmentStartPosition(0L)
  .build())
+ assert(fcOpt.isDefined)
+ val (builtContig, builtFragment) = fcOpt.get
 
  assert(builtContig.getContigName === "ctg")
  assert(builtFragment.fragments.length === 1)
@@ -46,6 +48,11 @@ class FragmentConverterSuite extends ADAMFunSuite {
  assert(convertedRead.getEnd === 8L)
  }
 
+ test("if a fragment isn't associated with a contig, don't get a fragment collector") {
+ val fcOpt = FragmentCollector(NucleotideContigFragment.newBuilder().build())
+ assert(fcOpt.isEmpty)
+ }
+
  sparkTest("convert an rdd of discontinuous fragments, all from the same contig") {
  val rdd = sc.parallelize(Seq(NucleotideContigFragment.newBuilder()
  .setContig(Contig.newBuilder().setContigName("ctg").build())