Rename AvroReadGroupGenomicRDD to AvroRecordGroupGenomicRDD.

bigdatagenomics · Jul 12, 2017 · 79d26d5 · 79d26d5
1 parent 15e40b2
commit 79d26d5
Show file tree

Hide file tree

Showing 3 changed files with 7 additions and 7 deletions.
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicRDD.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicRDD.scala
@@ -1389,12 +1389,12 @@ trait GenomicDataset[T, U <: Product, V <: GenomicDataset[T, U, V]] extends Geno
  * An abstract class describing a GenomicRDD where:
  *
  * * The data are Avro IndexedRecords.
- * * The data are associated to read groups (i.e., they are reads or fragments).
+ * * The data are associated to record groups (i.e., they are reads or fragments).
  */
-abstract class AvroReadGroupGenomicRDD[T <% IndexedRecord: Manifest, U <: Product, V <: AvroReadGroupGenomicRDD[T, U, V]] extends AvroGenomicRDD[T, U, V] {
+abstract class AvroRecordGroupGenomicRDD[T <% IndexedRecord: Manifest, U <: Product, V <: AvroRecordGroupGenomicRDD[T, U, V]] extends AvroGenomicRDD[T, U, V] {
 
   /**
-   * A dictionary describing the read groups attached to this GenomicRDD.
+   * A dictionary describing the record groups attached to this GenomicRDD.
    */
   val recordGroups: RecordGroupDictionary
 

diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/fragment/FragmentRDD.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/fragment/FragmentRDD.scala
@@ -30,7 +30,7 @@ import org.bdgenomics.adam.models.{
   SequenceDictionary
 }
 import org.bdgenomics.adam.rdd.ADAMContext._
-import org.bdgenomics.adam.rdd.{ AvroReadGroupGenomicRDD, JavaSaveArgs }
+import org.bdgenomics.adam.rdd.{ AvroRecordGroupGenomicRDD, JavaSaveArgs }
 import org.bdgenomics.adam.rdd.read.{
   AlignmentRecordRDD,
   BinQualities,
@@ -225,7 +225,7 @@ case class RDDBoundFragmentRDD private[rdd] (
   }
 }
 
-sealed abstract class FragmentRDD extends AvroReadGroupGenomicRDD[Fragment, FragmentProduct, FragmentRDD] {
+sealed abstract class FragmentRDD extends AvroRecordGroupGenomicRDD[Fragment, FragmentProduct, FragmentRDD] {
 
   protected def buildTree(rdd: RDD[(ReferenceRegion, Fragment)])(
     implicit tTag: ClassTag[Fragment]): IntervalArray[ReferenceRegion, Fragment] = {

diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDD.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDD.scala
@@ -42,7 +42,7 @@ import org.bdgenomics.adam.instrumentation.Timers._
 import org.bdgenomics.adam.models._
 import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.adam.rdd.{
-  AvroReadGroupGenomicRDD,
+  AvroRecordGroupGenomicRDD,
   ADAMSaveAnyArgs,
   FileMerger,
   JavaSaveArgs,
@@ -279,7 +279,7 @@ case class RDDBoundAlignmentRecordRDD private[rdd] (
 private case class AlignmentWindow(contigName: String, start: Long, end: Long) {
 }
 
-sealed abstract class AlignmentRecordRDD extends AvroReadGroupGenomicRDD[AlignmentRecord, AlignmentRecordProduct, AlignmentRecordRDD] {
+sealed abstract class AlignmentRecordRDD extends AvroRecordGroupGenomicRDD[AlignmentRecord, AlignmentRecordProduct, AlignmentRecordRDD] {
 
   /**
    * Applies a function that transforms the underlying RDD into a new RDD using