fixed missing extends typoe tin DataBoundAlignmentRecordRDD

bigdatagenomics · Feb 17, 2018 · 5c29dde · 5c29dde
1 parent 211072b
commit 5c29dde
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Showing 7 changed files with 32 additions and 33 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
@@ -2560,6 +2560,7 @@ abstract class AvroGenomicRDD[T <% IndexedRecord: Manifest, U <: Product, V <: A
         "\' and (end > " + r.start + " and start < " + r.end + "))")
         .mkString(" or ")
     }
+
   }
 
   /**

diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentRDD.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentRDD.scala
@@ -136,12 +136,10 @@ case class ParquetUnboundNucleotideContigFragmentRDD private[rdd] (
 }
 
 case class DatasetBoundNucleotideContigFragmentRDD private[rdd] (
-    dataset: Dataset[NucleotideContigFragmentProduct],
-    sequences: SequenceDictionary,
-    partitionedBinSize: Option[Int] = None) extends NucleotideContigFragmentRDD 
-     with DatasetBoundGenomicDataset[NucleotideContigFragment, 
-                                     NucleotideContigFragmentProduct, 
-                                     NucleotideContigFragmentRDD] {
+  dataset: Dataset[NucleotideContigFragmentProduct],
+  sequences: SequenceDictionary,
+  partitionedBinSize: Option[Int] = None) extends NucleotideContigFragmentRDD
+    with DatasetBoundGenomicDataset[NucleotideContigFragment, NucleotideContigFragmentProduct, NucleotideContigFragmentRDD] {
   lazy val rdd: RDD[NucleotideContigFragment] = dataset.rdd.map(_.toAvro)
 
   protected lazy val optPartitionMap = None

diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/FeatureRDD.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/FeatureRDD.scala
@@ -275,10 +275,10 @@ case class ParquetUnboundFeatureRDD private[rdd] (
 }
 
 case class DatasetBoundFeatureRDD private[rdd] (
-    dataset: Dataset[FeatureProduct],
-    sequences: SequenceDictionary,
-    partitionedBinSize: Option[Int] = None) extends FeatureRDD 
-      with DatasetBoundGenomicDataset[Feature, FeatureProduct, FeatureRDD] {
+  dataset: Dataset[FeatureProduct],
+  sequences: SequenceDictionary,
+  partitionedBinSize: Option[Int] = None) extends FeatureRDD
+    with DatasetBoundGenomicDataset[Feature, FeatureProduct, FeatureRDD] {
 
   lazy val rdd = dataset.rdd.map(_.toAvro)
   protected lazy val optPartitionMap = None

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
@@ -184,12 +184,12 @@ case class ParquetUnboundFragmentRDD private[rdd] (
 }
 
 case class DatasetBoundFragmentRDD private[rdd] (
-    dataset: Dataset[FragmentProduct],
-    sequences: SequenceDictionary,
-    recordGroups: RecordGroupDictionary,
-    @transient val processingSteps: Seq[ProcessingStep],
-    partitionedBinSize: Option[Int] = None) extends FragmentRDD 
-      with DatasetBoundGenomicDataset[Fragment, FragmentProduct, FragmentRDD] {
+  dataset: Dataset[FragmentProduct],
+  sequences: SequenceDictionary,
+  recordGroups: RecordGroupDictionary,
+  @transient val processingSteps: Seq[ProcessingStep],
+  partitionedBinSize: Option[Int] = None) extends FragmentRDD
+    with DatasetBoundGenomicDataset[Fragment, FragmentProduct, FragmentRDD] {
 
   lazy val rdd = dataset.rdd.map(_.toAvro)
 

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
@@ -234,12 +234,12 @@ case class ParquetUnboundAlignmentRecordRDD private[rdd] (
 }
 
 case class DatasetBoundAlignmentRecordRDD private[rdd] (
-    dataset: Dataset[AlignmentRecordProduct],
-    sequences: SequenceDictionary,
-    recordGroups: RecordGroupDictionary,
-    @transient val processingSteps: Seq[ProcessingStep],
-    partitionedBinSize: Option[Int] = None) extends 
-      with DatasetBoundGenomicDataset[AlignmentRecord, AlignmentRecordProduct, AlignmentRecordRDD] {
+  dataset: Dataset[AlignmentRecordProduct],
+  sequences: SequenceDictionary,
+  recordGroups: RecordGroupDictionary,
+  @transient val processingSteps: Seq[ProcessingStep],
+  partitionedBinSize: Option[Int] = None) extends AlignmentRecordRDD
+    with DatasetBoundGenomicDataset[AlignmentRecord, AlignmentRecordProduct, AlignmentRecordRDD] {
 
   lazy val rdd = dataset.rdd.map(_.toAvro)
 

diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/variant/GenotypeRDD.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/variant/GenotypeRDD.scala
@@ -142,12 +142,12 @@ case class ParquetUnboundGenotypeRDD private[rdd] (
 }
 
 case class DatasetBoundGenotypeRDD private[rdd] (
-    dataset: Dataset[GenotypeProduct],
-    sequences: SequenceDictionary,
-    @transient samples: Seq[Sample],
-    @transient headerLines: Seq[VCFHeaderLine] = DefaultHeaderLines.allHeaderLines,
-    partitionedBinSize: Option[Int] = None) extends GenotypeRDD 
-      with DatasetBoundGenomicDataset[Genotype, GenotypeProduct, GenotypeRDD] {
+  dataset: Dataset[GenotypeProduct],
+  sequences: SequenceDictionary,
+  @transient samples: Seq[Sample],
+  @transient headerLines: Seq[VCFHeaderLine] = DefaultHeaderLines.allHeaderLines,
+  partitionedBinSize: Option[Int] = None) extends GenotypeRDD
+    with DatasetBoundGenomicDataset[Genotype, GenotypeProduct, GenotypeRDD] {
 
   protected lazy val optPartitionMap = None
 

diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/variant/VariantRDD.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/variant/VariantRDD.scala
@@ -133,11 +133,11 @@ case class ParquetUnboundVariantRDD private[rdd] (
 }
 
 case class DatasetBoundVariantRDD private[rdd] (
-    dataset: Dataset[VariantProduct],
-    sequences: SequenceDictionary,
-    @transient headerLines: Seq[VCFHeaderLine] = DefaultHeaderLines.allHeaderLines,
-    partitionedBinSize: Option[Int] = None) extends VariantRDD 
-      with DatasetBoundGenomicDataset[Variant, VariantProduct, VariantRDD] {
+  dataset: Dataset[VariantProduct],
+  sequences: SequenceDictionary,
+  @transient headerLines: Seq[VCFHeaderLine] = DefaultHeaderLines.allHeaderLines,
+  partitionedBinSize: Option[Int] = None) extends VariantRDD
+    with DatasetBoundGenomicDataset[Variant, VariantProduct, VariantRDD] {
 
   protected lazy val optPartitionMap = None