Merge a957395 into beec466

adam-apis/src/main/scala/org/bdgenomics/adam/apis/java/JavaAlignmentRecordRDD.scala

@@ -19,7 +19,7 @@ package org.bdgenomics.adam.apis.java
 
 import org.apache.spark.api.java.JavaRDD
 import org.bdgenomics.adam.rdd.ADAMContext._
-import org.bdgenomics.adam.rdd.read.ADAMAlignmentRecordContext._
+import org.bdgenomics.adam.rdd.read.AlignmentRecordContext._
 import org.bdgenomics.formats.avro._
 import parquet.hadoop.metadata.CompressionCodecName
 

adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAM2Vcf.scala

@@ -19,7 +19,7 @@ package org.bdgenomics.adam.cli
 
 import org.bdgenomics.formats.avro.Genotype
 import org.bdgenomics.adam.rdd.ADAMContext._
-import org.bdgenomics.adam.rdd.variation.ADAMVariationContext._
+import org.bdgenomics.adam.rdd.variation.VariationContext._
 import org.kohsuke.args4j.{ Option => Args4jOption, Argument }
 import org.apache.spark.rdd.RDD
 import org.apache.spark.{ Logging, SparkContext }

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

@@ -22,7 +22,7 @@ import org.apache.hadoop.mapreduce.Job
 import org.apache.spark.{ SparkContext, Logging }
 import org.apache.spark.rdd.RDD
 import org.bdgenomics.adam.rdd.ADAMContext._
-import org.bdgenomics.adam.rdd.read.ADAMAlignmentRecordContext._
+import org.bdgenomics.adam.rdd.read.AlignmentRecordContext._
 import org.bdgenomics.adam.util.ParquetLogger
 import org.bdgenomics.formats.avro.AlignmentRecord
 import org.kohsuke.args4j.{ Argument, Option => Args4jOption }

adam-cli/src/main/scala/org/bdgenomics/adam/cli/Fasta2ADAM.scala

@@ -21,8 +21,8 @@ import org.apache.hadoop.mapreduce.Job
 import org.apache.spark.{ Logging, SparkContext }
 import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.adam.rdd.ADAMContext
-import org.bdgenomics.adam.rdd.contig.ADAMNucleotideContigFragmentContext._
-import org.bdgenomics.adam.rdd.contig.ADAMNucleotideContigFragmentContext
+import org.bdgenomics.adam.rdd.contig.NucleotideContigFragmentContext._
+import org.bdgenomics.adam.rdd.contig.NucleotideContigFragmentContext
 import org.bdgenomics.formats.avro.AlignmentRecord
 import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
 
@@ -53,7 +53,7 @@ class Fasta2ADAM(protected val args: Fasta2ADAMArgs) extends ADAMSparkCommand[Fa
 
   def run(sc: SparkContext, job: Job) {
     log.info("Loading FASTA data from disk.")
-    val adamFasta = new ADAMNucleotideContigFragmentContext(sc).adamSequenceLoad(args.fastaFile, args.fragmentLength)
+    val adamFasta = new NucleotideContigFragmentContext(sc).adamSequenceLoad(args.fastaFile, args.fragmentLength)
     if (args.verbose) {
       println("FASTA contains:")
       println(adamFasta.adamGetSequenceDictionary())

adam-cli/src/main/scala/org/bdgenomics/adam/cli/Features2ADAM.scala

@@ -22,7 +22,7 @@ import org.apache.spark.SparkContext
 import org.apache.spark.rdd.RDD
 import org.bdgenomics.adam.models.BaseFeature
 import org.bdgenomics.adam.rdd.ADAMContext._
-import org.bdgenomics.adam.rdd.features.ADAMFeaturesContext._
+import org.bdgenomics.adam.rdd.features.FeaturesContext._
 import org.bdgenomics.formats.avro.Feature
 import org.kohsuke.args4j.Argument
 

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

@@ -22,7 +22,7 @@ import org.apache.spark.SparkContext
 import org.apache.spark.rdd.RDD
 import org.bdgenomics.adam.projections.{ Projection, AlignmentRecordField }
 import org.bdgenomics.adam.rdd.ADAMContext._
-import org.bdgenomics.adam.rdd.read.ADAMAlignmentRecordContext._
+import org.bdgenomics.adam.rdd.read.AlignmentRecordContext._
 import org.bdgenomics.formats.avro.AlignmentRecord
 import org.kohsuke.args4j.Argument
 

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

@@ -25,7 +25,7 @@ import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
 import org.bdgenomics.adam.predicates.GenotypeRecordPASSPredicate
 import org.bdgenomics.adam.projections.GenotypeField
 import org.bdgenomics.adam.rdd.ADAMContext._
-import org.bdgenomics.adam.rdd.variation.ADAMVariationContext._
+import org.bdgenomics.adam.rdd.variation.VariationContext._
 import org.bdgenomics.adam.rdd.variation.ConcordanceTable
 import org.bdgenomics.formats.avro.Genotype
 

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

@@ -20,7 +20,7 @@ package org.bdgenomics.adam.cli
 import org.apache.hadoop.mapreduce.Job
 import org.apache.spark.rdd.RDD
 import org.bdgenomics.adam.models._
-import org.bdgenomics.adam.rdd.features.ADAMFeaturesContext._
+import org.bdgenomics.adam.rdd.features.FeaturesContext._
 import org.bdgenomics.adam.models.GeneContext._
 import org.bdgenomics.adam.rdd.features.GeneFeatureRDD._
 import org.bdgenomics.formats.avro.Feature

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

@@ -23,7 +23,7 @@ import org.apache.spark.rdd.RDD
 import org.bdgenomics.adam.projections.AlignmentRecordField._
 import org.bdgenomics.adam.projections.Projection
 import org.bdgenomics.adam.rdd.ADAMContext._
-import org.bdgenomics.adam.rdd.read.ADAMAlignmentRecordContext._
+import org.bdgenomics.adam.rdd.read.AlignmentRecordContext._
 import org.bdgenomics.formats.avro.AlignmentRecord
 import org.kohsuke.args4j.{ Argument, Option }
 

adam-cli/src/main/scala/org/bdgenomics/adam/cli/Reads2Ref.scala

@@ -22,8 +22,8 @@ import org.apache.spark.SparkContext
 import org.apache.spark.rdd.RDD
 import org.bdgenomics.adam.predicates.UniqueMappedReadPredicate
 import org.bdgenomics.adam.rdd.ADAMContext._
-import org.bdgenomics.adam.rdd.pileup.ADAMPileupContext._
-import org.bdgenomics.adam.rdd.read.ADAMAlignmentRecordContext._
+import org.bdgenomics.adam.rdd.pileup.PileupContext._
+import org.bdgenomics.adam.rdd.read.AlignmentRecordContext._
 import org.bdgenomics.formats.avro.{ AlignmentRecord, Pileup }
 import org.kohsuke.args4j.{ Option => option, Argument }
 

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

@@ -22,8 +22,8 @@ import org.apache.spark.{ SparkContext, Logging }
 import org.apache.spark.rdd.RDD
 import org.bdgenomics.adam.models.SnpTable
 import org.bdgenomics.adam.rdd.ADAMContext._
-import org.bdgenomics.adam.rdd.read.ADAMAlignmentRecordContext._
-import org.bdgenomics.adam.rdd.variation.ADAMVariationContext._
+import org.bdgenomics.adam.rdd.read.AlignmentRecordContext._
+import org.bdgenomics.adam.rdd.variation.VariationContext._
 import org.bdgenomics.adam.rich.RichVariant
 import org.bdgenomics.formats.avro.AlignmentRecord
 import org.kohsuke.args4j.{ Argument, Option => Args4jOption }

adam-cli/src/main/scala/org/bdgenomics/adam/cli/Vcf2ADAM.scala

@@ -19,7 +19,7 @@ package org.bdgenomics.adam.cli
 
 import org.bdgenomics.adam.models.{ SequenceDictionary, VariantContext }
 import org.bdgenomics.adam.rdd.ADAMContext._
-import org.bdgenomics.adam.rdd.variation.ADAMVariationContext._
+import org.bdgenomics.adam.rdd.variation.VariationContext._
 import org.apache.hadoop.mapreduce.Job
 import org.apache.spark.{ Logging, SparkContext }
 import org.apache.spark.rdd.RDD

adam-cli/src/main/scala/org/bdgenomics/adam/cli/VcfAnnotation2ADAM.scala

@@ -36,7 +36,7 @@ package org.bdgenomics.adam.cli
 import org.apache.hadoop.mapreduce.Job
 import org.apache.spark.{ Logging, SparkContext }
 import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
-import org.bdgenomics.adam.rdd.variation.ADAMVariationContext._
+import org.bdgenomics.adam.rdd.variation.VariationContext._
 import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.formats.avro._
 import org.apache.spark.rdd.RDD

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

@@ -24,7 +24,7 @@ import org.bdgenomics.adam.models.{ OrderedTrackedLayout, ReferenceRegion }
 import org.bdgenomics.adam.projections.AlignmentRecordField._
 import org.bdgenomics.adam.projections.Projection
 import org.bdgenomics.adam.rdd.ADAMContext._
-import org.bdgenomics.adam.rdd.read.ADAMAlignmentRecordContext._
+import org.bdgenomics.adam.rdd.read.AlignmentRecordContext._
 import org.bdgenomics.adam.rich.ReferenceMappingContext.AlignmentRecordReferenceMapping
 import org.bdgenomics.formats.avro.AlignmentRecord
 import org.fusesource.scalate.TemplateEngine

adam-core/src/main/scala/org/bdgenomics/adam/algorithms/consensus/ConsensusGeneratorFromKnowns.scala

@@ -22,7 +22,7 @@ import org.apache.spark.rdd.RDD
 import org.bdgenomics.adam.models._
 import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.adam.rdd.read.realignment.IndelRealignmentTarget
-import org.bdgenomics.adam.rdd.variation.ADAMVariationContext._
+import org.bdgenomics.adam.rdd.variation.VariationContext._
 import org.bdgenomics.adam.rich.RichAlignmentRecord
 
 class ConsensusGeneratorFromKnowns(file: String, sc: SparkContext) extends ConsensusGenerator {

adam-core/src/main/scala/org/bdgenomics/adam/models/IndelTable.scala

@@ -20,7 +20,7 @@ package org.bdgenomics.adam.models
 import org.apache.spark.{ Logging, SparkContext }
 import org.apache.spark.SparkContext._
 import org.apache.spark.rdd.RDD
-import org.bdgenomics.adam.rdd.variation.ADAMVariationContext._
+import org.bdgenomics.adam.rdd.variation.VariationContext._
 import org.bdgenomics.formats.avro.Variant
 
 class IndelTable(private val table: Map[String, Iterable[Consensus]]) extends Serializable with Logging {

adam-core/src/main/scala/org/bdgenomics/adam/models/VariantContext.scala

@@ -23,7 +23,7 @@ import org.bdgenomics.adam.rich.RichVariant._
 
 /**
  * Note: VariantContext inherits its name from the Picard VariantContext, and is not related to the SparkContext object.
- * If you're looking for the latter, see [[org.bdgenomics.adam.rdd.variation.ADAMVariationContext]]
+ * If you're looking for the latter, see [[org.bdgenomics.adam.rdd.variation.VariationContext]]
  */
 
 object VariantContext {

adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala

@@ -33,7 +33,7 @@ import org.bdgenomics.adam.instrumentation.ADAMMetricsListener
 import org.bdgenomics.adam.models._
 import org.bdgenomics.adam.predicates.ADAMPredicate
 import org.bdgenomics.adam.projections.{ AlignmentRecordField, NucleotideContigFragmentField, Projection }
-import org.bdgenomics.adam.rdd.read.ADAMAlignmentRecordContext
+import org.bdgenomics.adam.rdd.read.AlignmentRecordContext
 import org.bdgenomics.adam.rich.RichAlignmentRecord
 import org.bdgenomics.adam.util.HadoopUtil
 import org.bdgenomics.formats.avro.{ AlignmentRecord, NucleotideContigFragment, Pileup }
@@ -195,7 +195,7 @@ class ADAMContext(val sc: SparkContext) extends Serializable with Logging {
       if (projection.isDefined) {
         log.warn("Projection is ignored when loading a BAM file")
       }
-      val reads = ADAMAlignmentRecordContext.adamBamLoad(sc, filePath).asInstanceOf[RDD[T]]
+      val reads = AlignmentRecordContext.adamBamLoad(sc, filePath).asInstanceOf[RDD[T]]
       if (predicate.isDefined) {
         val predicateClass = predicate.get
         val filter = predicateClass.newInstance()
@@ -208,7 +208,7 @@ class ADAMContext(val sc: SparkContext) extends Serializable with Logging {
       if (projection.isDefined) {
         log.warn("Projection is ignored when loading an interleaved FASTQ file")
       }
-      val reads = ADAMAlignmentRecordContext.adamInterleavedFastqLoad(sc, filePath).asInstanceOf[RDD[T]]
+      val reads = AlignmentRecordContext.adamInterleavedFastqLoad(sc, filePath).asInstanceOf[RDD[T]]
       if (predicate.isDefined) {
         val predicateClass = predicate.get
         val filter = predicateClass.newInstance()
@@ -221,7 +221,7 @@ class ADAMContext(val sc: SparkContext) extends Serializable with Logging {
       if (projection.isDefined) {
         log.warn("Projection is ignored when loading a FASTQ file")
       }
-      val reads = ADAMAlignmentRecordContext.adamUnpairedFastqLoad(sc, filePath).asInstanceOf[RDD[T]]
+      val reads = AlignmentRecordContext.adamUnpairedFastqLoad(sc, filePath).asInstanceOf[RDD[T]]
       if (predicate.isDefined) {
         val predicateClass = predicate.get
         val filter = predicateClass.newInstance()

adam-core/src/main/scala/org/bdgenomics/adam/rdd/contig/ADAMNucleotideContigFragmentContext.scala → adam-core/src/main/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentContext.scala

@@ -25,15 +25,15 @@ import org.bdgenomics.adam.converters.FastaConverter
 import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.formats.avro.NucleotideContigFragment
 
-object ADAMNucleotideContigFragmentContext {
+object NucleotideContigFragmentContext {
   // Add ADAM Spark context methods
-  implicit def sparkContextToADAMContext(sc: SparkContext): ADAMNucleotideContigFragmentContext = new ADAMNucleotideContigFragmentContext(sc)
+  implicit def sparkContextToADAMContext(sc: SparkContext): NucleotideContigFragmentContext = new NucleotideContigFragmentContext(sc)
 
   // Add methods specific to the ADAMNucleotideContig RDDs
-  implicit def rddToContigFragmentRDD(rdd: RDD[NucleotideContigFragment]) = new ADAMNucleotideContigFragmentRDDFunctions(rdd)
+  implicit def rddToContigFragmentRDD(rdd: RDD[NucleotideContigFragment]) = new NucleotideContigFragmentRDDFunctions(rdd)
 }
 
-class ADAMNucleotideContigFragmentContext(val sc: SparkContext) extends Serializable with Logging {
+class NucleotideContigFragmentContext(val sc: SparkContext) extends Serializable with Logging {
 
   def adamSequenceLoad(filePath: String, fragmentLength: Long): RDD[NucleotideContigFragment] = {
     if (filePath.endsWith(".fasta") || filePath.endsWith(".fa")) {

adam-core/src/main/scala/org/bdgenomics/adam/rdd/contig/ADAMNucleotideContigFragmentRDDFunctions.scala → adam-core/src/main/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentRDDFunctions.scala

@@ -37,7 +37,7 @@ import parquet.hadoop.util.ContextUtil
 import scala.math.max
 import scala.Some
 
-class ADAMNucleotideContigFragmentRDDFunctions(rdd: RDD[NucleotideContigFragment]) extends ADAMSequenceDictionaryRDDAggregator[NucleotideContigFragment](rdd) {
+class NucleotideContigFragmentRDDFunctions(rdd: RDD[NucleotideContigFragment]) extends ADAMSequenceDictionaryRDDAggregator[NucleotideContigFragment](rdd) {
 
   /**
    * Rewrites the contig IDs of a FASTA reference set to match the contig IDs present in a

adam-core/src/main/scala/org/bdgenomics/adam/rdd/features/ADAMFeaturesContext.scala → adam-core/src/main/scala/org/bdgenomics/adam/rdd/features/FeaturesContext.scala

@@ -21,11 +21,11 @@ import org.apache.spark.{ SparkContext, Logging }
 import org.apache.spark.rdd.RDD
 import org.bdgenomics.formats.avro.Feature
 
-object ADAMFeaturesContext {
-  implicit def sparkContextToADAMFeaturesContext(sc: SparkContext): ADAMFeaturesContext = new ADAMFeaturesContext(sc)
+object FeaturesContext {
+  implicit def sparkContextToADAMFeaturesContext(sc: SparkContext): FeaturesContext = new FeaturesContext(sc)
 }
 
-class ADAMFeaturesContext(sc: SparkContext) extends Serializable with Logging {
+class FeaturesContext(sc: SparkContext) extends Serializable with Logging {
 
   def adamGTFFeatureLoad(filePath: String): RDD[Feature] = {
     sc.textFile(filePath).flatMap(new GTFParser().parse)

adam-core/src/main/scala/org/bdgenomics/adam/rdd/pileup/ADAMPileupContext.scala → adam-core/src/main/scala/org/bdgenomics/adam/rdd/pileup/PileupContext.scala

@@ -21,11 +21,11 @@ import org.apache.spark.rdd.RDD
 import org.bdgenomics.adam.models._
 import org.bdgenomics.formats.avro.Pileup
 
-object ADAMPileupContext {
+object PileupContext {
 
   // Add methods specific to the Pileup RDDs
-  implicit def rddToADAMPileupRDD(rdd: RDD[Pileup]) = new ADAMPileupRDDFunctions(rdd)
+  implicit def rddToPileupRDD(rdd: RDD[Pileup]) = new PileupRDDFunctions(rdd)
 
   // Add methods specific to the Rod RDDs
-  implicit def rddToRodRDD(rdd: RDD[Rod]) = new ADAMRodRDDFunctions(rdd)
+  implicit def rddToRodRDD(rdd: RDD[Rod]) = new RodRDDFunctions(rdd)
 }

adam-core/src/main/scala/org/bdgenomics/adam/rdd/pileup/ADAMPileupRDDFunctions.scala → adam-core/src/main/scala/org/bdgenomics/adam/rdd/pileup/PileupRDDFunctions.scala

@@ -22,7 +22,7 @@ import org.apache.spark.rdd.RDD
 import org.bdgenomics.adam.models._
 import org.bdgenomics.formats.avro._
 
-class ADAMPileupRDDFunctions(rdd: RDD[Pileup]) extends Serializable with Logging {
+class PileupRDDFunctions(rdd: RDD[Pileup]) extends Serializable with Logging {
 
   /**
    * Converts ungrouped pileup bases into reference grouped bases.
@@ -37,14 +37,14 @@ class ADAMPileupRDDFunctions(rdd: RDD[Pileup]) extends Serializable with Logging
   }
 }
 
-class ADAMRodRDDFunctions(rdd: RDD[Rod]) extends Serializable with Logging {
+class RodRDDFunctions(rdd: RDD[Rod]) extends Serializable with Logging {
   /**
    * Given an RDD of rods, splits the rods up by the specific sample they correspond to.
    * Returns a flat RDD.
    *
    * @return Rods split up by samples and _not_ grouped together.
    */
-  def adamSplitRodsBySamples(): RDD[Rod] = {
+  def splitRodsBySamples(): RDD[Rod] = {
     rdd.flatMap(_.splitBySamples())
   }
 
@@ -54,7 +54,7 @@ class ADAMRodRDDFunctions(rdd: RDD[Rod]) extends Serializable with Logging {
    *
    * @return Rods split up by samples and grouped together by position.
    */
-  def adamDivideRodsBySamples(): RDD[(ReferencePosition, List[Rod])] = {
+  def divideRodsBySamples(): RDD[(ReferencePosition, List[Rod])] = {
     rdd.keyBy(_.position).map(r => (r._1, r._2.splitBySamples()))
   }
 
@@ -68,7 +68,7 @@ class ADAMRodRDDFunctions(rdd: RDD[Rod]) extends Serializable with Logging {
    *
    * @return Average coverage across mapped loci.
    */
-  def adamRodCoverage(): Double = {
+  def rodCoverage(): Double = {
     val totalBases: Long = rdd.map(_.pileups.length.toLong).reduce(_ + _)
 
     // coverage is the total count of bases, over the total number of loci

adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/ADAMAlignmentRecordContext.scala → adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordContext.scala

@@ -42,12 +42,12 @@ import org.seqdoop.hadoop_bam.{
 import org.seqdoop.hadoop_bam.util.SAMHeaderReader
 import parquet.hadoop.util.ContextUtil
 
-object ADAMAlignmentRecordContext extends Serializable with Logging {
+object AlignmentRecordContext extends Serializable with Logging {
   // Add ADAM Spark context methods
-  implicit def adamContextToADAMContext(ac: ADAMContext): ADAMAlignmentRecordContext = new ADAMAlignmentRecordContext(ac.sc)
+  implicit def adamContextToADAMContext(ac: ADAMContext): AlignmentRecordContext = new AlignmentRecordContext(ac.sc)
 
   // Add methods specific to Read RDDs
-  implicit def rddToADAMRecordRDD(rdd: RDD[AlignmentRecord]) = new ADAMAlignmentRecordRDDFunctions(rdd)
+  implicit def rddToADAMRecordRDD(rdd: RDD[AlignmentRecord]) = new AlignmentRecordRDDFunctions(rdd)
 
   private[rdd] def adamBamLoad(sc: SparkContext,
                                filePath: String): RDD[AlignmentRecord] = {
@@ -90,14 +90,14 @@ object ADAMAlignmentRecordContext extends Serializable with Logging {
   }
 }
 
-class ADAMAlignmentRecordContext(val sc: SparkContext) extends Serializable with Logging {
+class AlignmentRecordContext(val sc: SparkContext) extends Serializable with Logging {
 
   def adamFastqLoad(firstPairPath: String,
                     secondPairPath: String,
                     fixPairs: Boolean = false): RDD[AlignmentRecord] = {
     // load rdds
-    val firstPairRdd = ADAMAlignmentRecordContext.adamUnpairedFastqLoad(sc, firstPairPath)
-    val secondPairRdd = ADAMAlignmentRecordContext.adamUnpairedFastqLoad(sc, secondPairPath)
+    val firstPairRdd = AlignmentRecordContext.adamUnpairedFastqLoad(sc, firstPairPath)
+    val secondPairRdd = AlignmentRecordContext.adamUnpairedFastqLoad(sc, secondPairPath)
 
     // cache rdds
     firstPairRdd.cache()

adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/ADAMAlignmentRecordRDDFunctions.scala → adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDFunctions.scala

@@ -31,15 +31,15 @@ import org.bdgenomics.adam.converters.AlignmentRecordConverter
 import org.bdgenomics.adam.models._
 import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.adam.rdd.ADAMSequenceDictionaryRDDAggregator
-import org.bdgenomics.adam.rdd.read.ADAMAlignmentRecordContext._
+import org.bdgenomics.adam.rdd.read.AlignmentRecordContext._
 import org.bdgenomics.adam.rdd.read.correction.{ ErrorCorrection, TrimReads }
 import org.bdgenomics.adam.rdd.read.realignment.RealignIndels
 import org.bdgenomics.adam.rdd.read.recalibration.BaseQualityRecalibration
 import org.bdgenomics.adam.rich.RichAlignmentRecord
 import org.bdgenomics.adam.util.MapTools
 import org.bdgenomics.formats.avro._
 
-class ADAMAlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord]) extends ADAMSequenceDictionaryRDDAggregator[AlignmentRecord](rdd) {
+class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord]) extends ADAMSequenceDictionaryRDDAggregator[AlignmentRecord](rdd) {
 
   /**
    * Calculates the subset of the RDD whose AlignmentRecords overlap the corresponding

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

@@ -20,7 +20,7 @@ package org.bdgenomics.adam.rdd.read
 import org.apache.spark.rdd.RDD
 import org.bdgenomics.adam.models.{ ReferencePositionPair, ReferencePositionWithOrientation, SingleReadBucket }
 import org.bdgenomics.adam.rdd.ADAMContext._
-import org.bdgenomics.adam.rdd.read.ADAMAlignmentRecordContext._
+import org.bdgenomics.adam.rdd.read.AlignmentRecordContext._
 import org.bdgenomics.formats.avro.AlignmentRecord
 
 private[rdd] object MarkDuplicates extends Serializable {

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

@@ -27,16 +27,16 @@ import org.bdgenomics.adam.metrics.filters.GeneratorFilter
 import org.bdgenomics.adam.models.ReadBucket
 import org.bdgenomics.adam.projections.{ FieldValue, Projection }
 import org.bdgenomics.adam.rdd.ADAMContext._
-import org.bdgenomics.adam.rdd.read.ADAMAlignmentRecordContext._
-import org.bdgenomics.adam.rdd.read.ADAMAlignmentRecordContext
+import org.bdgenomics.adam.rdd.read.AlignmentRecordContext._
+import org.bdgenomics.adam.rdd.read.AlignmentRecordContext
 import org.bdgenomics.formats.avro.AlignmentRecord
 import scala.reflect.ClassTag
 
 class ComparisonTraversalEngine(schema: Seq[FieldValue], input1: RDD[AlignmentRecord], input2: RDD[AlignmentRecord])(implicit sc: SparkContext) {
   def this(schema: Seq[FieldValue], input1Paths: Seq[Path], input2Paths: Seq[Path])(implicit sc: SparkContext) =
     this(schema,
-      new ADAMAlignmentRecordContext(sc).loadADAMFromPaths(input1Paths),
-      new ADAMAlignmentRecordContext(sc).loadADAMFromPaths(input2Paths))(sc)
+      new AlignmentRecordContext(sc).loadADAMFromPaths(input1Paths),
+      new AlignmentRecordContext(sc).loadADAMFromPaths(input2Paths))(sc)
 
   lazy val projection = Projection(schema: _*)