Merge pull request #1 from fnothaft/issues/1122-remove-pairing-rdd

[ADAM-1122] Remove Coverage and PairingRDD. Resolves #1122.
bigdatagenomics · Aug 23, 2016 · b13eee5 · b13eee5
2 parents a5ced0f + 1859fce
commit b13eee5
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Showing 5 changed files with 1 addition and 626 deletions.
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/Coverage.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/Coverage.scala
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/PairingRDD.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/PairingRDD.scala
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/serialization/ADAMKryoRegistrator.scala b/adam-core/src/main/scala/org/bdgenomics/adam/serialization/ADAMKryoRegistrator.scala
@@ -50,7 +50,7 @@ import org.bdgenomics.adam.models._
 import org.bdgenomics.adam.rdd.read.realignment._
 import org.bdgenomics.adam.rdd.read.recalibration.{ CovariateKey, CovariateSpace, CycleCovariate, DinucCovariate, Observation, ObservationAccumulator }
 import org.bdgenomics.adam.rdd.read.{ DuplicateMetrics, FlagStatMetrics }
-import org.bdgenomics.adam.rdd.{ GenomeBins, OrientedPoint }
+import org.bdgenomics.adam.rdd.GenomeBins
 import org.bdgenomics.adam.rich.{ DecadentRead, ReferenceSequenceContext, RichAlignmentRecord, RichVariant }
 import org.bdgenomics.adam.util.{ MdTag, QualityScore, ReferenceContigMap, TwoBitFile, TwoBitFileSerializer }
 import org.bdgenomics.formats.avro._
@@ -274,9 +274,6 @@ class ADAMKryoRegistrator extends KryoRegistrator {
  kryo.register(classOf[util.HashMap[_, _]])
  kryo.register(classOf[util.HashSet[_]])
 
- kryo.register(classOf[Array[OrientedPoint]])
- kryo.register(classOf[OrientedPoint])
-
  kryo.register(scala.math.Numeric.LongIsIntegral.getClass)
  kryo.register(Map.empty.getClass)