[ADAM-513] Remove ReferenceMappable trait.

bigdatagenomics · Feb 25, 2015 · c404316 · c404316
1 parent 94f4841
commit c404316
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Showing 14 changed files with 76 additions and 626 deletions.
diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAMMain.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAMMain.scala
@@ -65,7 +65,6 @@ object ADAMMain extends Logging {
           PrintADAM,
           PrintGenes,
           FlagStat,
-          VizReads,
           PrintTags,
           ListDict,
           SummarizeGenotypes,

diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/CalculateDepth.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/CalculateDepth.scala
@@ -28,7 +28,6 @@ import org.bdgenomics.adam.projections.Projection
 import org.bdgenomics.adam.projections.AlignmentRecordField._
 import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.adam.rdd.BroadcastRegionJoin
-import org.bdgenomics.adam.rich.ReferenceMappingContext._
 import org.bdgenomics.formats.avro.AlignmentRecord
 import scala.io._
 
@@ -90,8 +89,8 @@ class CalculateDepth(protected val args: CalculateDepthArgs) extends ADAMSparkCo
     val variantNames = vcf.collect().toMap
 
     val joinedRDD: RDD[(ReferenceRegion, AlignmentRecord)] =
-      if (args.cartesian) BroadcastRegionJoin.cartesianFilter(variantPositions, mappedRDD)
-      else BroadcastRegionJoin.partitionAndJoin(sc, variantPositions, mappedRDD)
+      if (args.cartesian) BroadcastRegionJoin.cartesianFilter(variantPositions.keyBy(v => v), mappedRDD.keyBy(ReferenceRegion(_).get))
+      else BroadcastRegionJoin.partitionAndJoin(sc, variantPositions.keyBy(v => v), mappedRDD.keyBy(ReferenceRegion(_).get))
 
     val depths: RDD[(ReferenceRegion, Int)] =
       joinedRDD.map { case (region, record) => (region, 1) }.reduceByKey(_ + _).sortByKey()

diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/VizReads.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/VizReads.scala
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceMapping.scala b/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceMapping.scala
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/models/TrackedLayout.scala b/adam-core/src/main/scala/org/bdgenomics/adam/models/TrackedLayout.scala