rename sortReadsBy methods

adam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformAlignments.scala

@@ -346,9 +346,9 @@ class TransformAlignments(protected val args: TransformAlignmentsArgs) extends B
 
       // are we sorting lexicographically or using legacy SAM sort order?
       val sortedDs = if (args.sortLexicographically) {
-        ds.sortReadsByReferencePosition()
+        ds.sortByReferencePosition()
       } else {
-        ds.sortReadsByReferencePositionAndIndex()
+        ds.sortByReferencePositionAndIndex()
       }
 
       // unpersist the cached rdd, if caching was requested

adam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformFragments.scala

@@ -132,9 +132,9 @@ class TransformFragments(protected val args: TransformFragmentsArgs) extends BDG
 
       // prep to save
       val finalRdd = if (args.sortReads) {
-        readRdd.sortReadsByReferencePosition()
+        readRdd.sortByReferencePosition()
       } else if (args.sortLexicographically) {
-        readRdd.sortReadsByReferencePositionAndIndex()
+        readRdd.sortByReferencePositionAndIndex()
       } else {
         readRdd
       }

adam-core/src/main/scala/org/bdgenomics/adam/instrumentation/Timers.scala

@@ -26,7 +26,6 @@ object Timers extends Metrics {
 
   // Load methods
   val LoadAlignments = timer("Load Alignments")
-  val LoadContigFragments = timer("Load Contig Fragments")
   val LoadCoverage = timer("Load Coverage")
   val LoadFeatures = timer("Load Features")
   val LoadFragments = timer("Load Fragments")
@@ -110,9 +109,9 @@ object Timers extends Metrics {
   val SweepReadOverReferenceForQuality = timer("Sweep Read Over Reference For Quality")
   val FinalizingRealignments = timer("Finalizing Realignments")
 
-  // Sort Reads
-  val SortReads = timer("Sort Reads")
-  val SortByIndex = timer("Sort Reads By Index")
+  // Sort Alignments
+  val SortAlignments = timer("Sort Alignments")
+  val SortAlignmentsByIndex = timer("Sort Alignments By Index")
 
   // File Saving
   val SAMSave = timer("SAM Save")

adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDataset.scala

@@ -970,29 +970,29 @@ sealed abstract class AlignmentRecordDataset extends AvroReadGroupGenomicDataset
   }
 
   /**
-   * Sorts our read data by read name.
+   * Sorts our alignments by read name.
    *
-   * @return Returns a new RDD containing sorted reads.
+   * @return Returns a new genomic dataset containing sorted alignments.
    */
-  def sortReadsByReadName(): AlignmentRecordDataset = SortReads.time {
-    info("Sorting reads by read name")
+  def sortByReadName(): AlignmentRecordDataset = SortAlignments.time {
+    info("Sorting alignments by read name")
 
     transformDataset(_.orderBy("readName", "readInFragment"))
   }
 
   /**
-   * Sorts our read data by reference positions, with references ordered by name.
+   * Sorts our alignments by reference position, with references ordered by name.
    *
-   * Sorts reads by the location where they are aligned. Unaligned reads are
+   * Sorts alignments by the location where the reads are aligned. Unaligned reads are
    * put at the end and sorted by read name. References are ordered
    * lexicographically.
    *
-   * @return Returns a new genomic dataset containing sorted reads.
+   * @return Returns a new genomic dataset containing sorted alignments.
    *
-   * @see sortReadsByReferencePositionAndIndex
+   * @see sortByReferencePositionAndIndex
    */
-  def sortReadsByReferencePosition(): AlignmentRecordDataset = SortReads.time {
-    info("Sorting reads by reference position")
+  def sortByReferencePosition(): AlignmentRecordDataset = SortAlignments.time {
+    info("Sorting alignments by reference position")
 
     // NOTE: In order to keep unmapped reads from swamping a single partition
     // we sort the unmapped reads by read name. We prefix with tildes ("~";
@@ -1008,18 +1008,18 @@ sealed abstract class AlignmentRecordDataset extends AvroReadGroupGenomicDataset
   }
 
   /**
-   * Sorts our read data by reference positions, with references ordered by index.
+   * Sorts our alignments by reference position, with references ordered by index.
    *
-   * Sorts reads by the location where they are aligned. Unaligned reads are
+   * Sorts alignments by the location where the reads are aligned. Unaligned reads are
    * put at the end and sorted by read name. References are ordered by index
    * that they are ordered in the SequenceDictionary.
    *
-   * @return Returns a new genomic dataset containing sorted reads.
+   * @return Returns a new genomic dataset containing sorted alignments.
    *
-   * @see sortReadsByReferencePosition
+   * @see sortByReferencePosition
    */
-  def sortReadsByReferencePositionAndIndex(): AlignmentRecordDataset = SortByIndex.time {
-    info("Sorting reads by reference index, using %s.".format(sequences))
+  def sortByReferencePositionAndIndex(): AlignmentRecordDataset = SortAlignmentsByIndex.time {
+    info("Sorting alignments by reference index, using %s.".format(sequences))
 
     import scala.math.Ordering.{ Int => ImplicitIntOrdering, _ }
 

adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDatasetSuite.scala

@@ -177,7 +177,7 @@ class AlignmentRecordDatasetSuite extends ADAMFunSuite {
     val sd = new SequenceDictionary(contigNames.map(v => SequenceRecord(v, 1000000L)).toVector)
 
     val sortedReads = AlignmentRecordDataset(rdd, sd, ReadGroupDictionary.empty, Seq.empty)
-      .sortReadsByReferencePosition()
+      .sortByReferencePosition()
       .rdd
       .collect()
       .zipWithIndex
@@ -193,7 +193,7 @@ class AlignmentRecordDatasetSuite extends ADAMFunSuite {
   sparkTest("unmapped reads go at the end when sorting") {
     val inputPath = testFile("reads13.sam")
     val reads = sc.loadAlignments(inputPath)
-    val sortedReads = reads.sortReadsByReferencePosition()
+    val sortedReads = reads.sortByReferencePosition()
       .rdd
       .collect()
     assert(!sortedReads.last.getReadMapped)
@@ -286,7 +286,7 @@ class AlignmentRecordDatasetSuite extends ADAMFunSuite {
 
     val rdd = sc.parallelize(reads)
     val sortedReads = AlignmentRecordDataset(rdd, sd, ReadGroupDictionary.empty, Seq.empty)
-      .sortReadsByReferencePositionAndIndex()
+      .sortByReferencePositionAndIndex()
       .rdd
       .collect()
       .zipWithIndex
@@ -536,7 +536,7 @@ class AlignmentRecordDatasetSuite extends ADAMFunSuite {
     val reads = ardd.rdd
 
     val actualSortedPath = tmpFile("sorted.sam")
-    ardd.sortReadsByReferencePosition()
+    ardd.sortByReferencePosition()
       .saveAsSam(actualSortedPath,
         isSorted = true,
         asSingleFile = true)
@@ -560,7 +560,7 @@ class AlignmentRecordDatasetSuite extends ADAMFunSuite {
   sparkTest("writing ordered sam from unordered sam") {
     val unsortedPath = testFile("unordered.sam")
     val ardd = sc.loadBam(unsortedPath)
-    val reads = ardd.sortReadsByReferencePosition
+    val reads = ardd.sortByReferencePosition
 
     val actualSortedPath = tmpFile("ordered.sam")
     reads.saveAsSam(actualSortedPath,
@@ -1838,7 +1838,7 @@ class AlignmentRecordDatasetSuite extends ADAMFunSuite {
     val reads = ardd.rdd
 
     val actualSortedPath = tmpFile("readname_sorted.sam")
-    ardd.sortReadsByReadName()
+    ardd.sortByReadName()
       .saveAsSam(actualSortedPath,
         asType = None,
         asSingleFile = true,

adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/RealignIndelsSuite.scala

@@ -56,7 +56,7 @@ class RealignIndelsSuite extends ADAMFunSuite {
       .realignIndels(consensusModel = cg,
         maxReadsPerTarget = maxCoverage,
         optReferenceFile = optRefFile)
-      .sortReadsByReferencePosition()
+      .sortByReferencePosition()
       .rdd
   }