[ADAM-780] Make DecadentRead package private.

This change changes the DecadentRead class and object from public to package
private (org.bdgenomics.adam). Additionally, we mark both items as deprecated
in favor of the RichAlignmentRecord. Resolves #780.

adam-core/src/main/scala/org/bdgenomics/adam/rich/DecadentRead.scala

@@ -26,7 +26,8 @@ import org.bdgenomics.adam.rich.RichAlignmentRecord._
 import org.bdgenomics.adam.util.{ MdTag, QualityScore }
 import org.bdgenomics.formats.avro.AlignmentRecord
 
-object DecadentRead extends Logging with Serializable {
+@deprecated("Use RichAlignmentRecord wherever possible in new development.", since = "0.18.0")
+private[adam] object DecadentRead extends Logging with Serializable {
   type Residue = DecadentRead#Residue
 
   // Constructors
@@ -72,7 +73,8 @@ object DecadentRead extends Logging with Serializable {
   implicit def decay(rdd: RDD[DecadentRead]): RDD[AlignmentRecord] = rdd.map(_.record)
 }
 
-class DecadentRead(val record: RichAlignmentRecord) extends Logging {
+@deprecated("Use RichAlignmentRecord wherever possible in new development.", since = "0.18.0")
+private[adam] class DecadentRead(val record: RichAlignmentRecord) extends Logging {
   // Can't be a primary alignment unless it has been aligned
   require(!record.getPrimaryAlignment || record.getReadMapped, "Unaligned read can't be a primary alignment")