[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-cli/src/main/scala/org/bdgenomics/adam/cli/Transform.scala

@@ -158,6 +158,12 @@ class Transform(protected val args: TransformArgs) extends BDGSparkCommand[Trans
  }
 
  def run(sc: SparkContext) {
+ // warn if aligned read predicate or projection flags are used improperly
+ if ((args.useAlignedReadPredicate || args.limitProjection) &&
+ (args.forceLoadBam || args.forceLoadFastq || args.forceLoadIFastq)) {
+ log.warn("-aligned_read_predicate and -limit_projection only apply to Parquet files, but a non-Parquet force load flag was passed.")
+ }
+
  val rdd =
  if (args.forceLoadBam) {
  sc.loadBam(args.inputPath)

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")