Merge 6ba1351 into 12c56fd

bigdatagenomics · Aug 29, 2017 · 8fd70f1 · 8fd70f1
2 parents 12c56fd + 6ba1351
commit 8fd70f1
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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
@@ -490,4 +490,7 @@ sealed abstract class NucleotideContigFragmentRDD extends AvroGenomicRDD[Nucleot
       (p._1, p._2: java.lang.Long)
     }).toJavaRDD()
   }
+
+  override def toString = "%s with %d reference sequences"
+    .format(getClass.getSimpleName, sequences.size)
 }
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/CoverageRDD.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/CoverageRDD.scala
@@ -405,5 +405,8 @@ abstract class CoverageRDD extends GenomicDataset[Coverage, Coverage, CoverageRD
       positions.map(n => Coverage(r.contigName, n, n + 1, r.count))
     })
   }
+
+  override def toString = "%s with %d reference sequences"
+    .format(getClass.getSimpleName, sequences.size)
 }
 
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
@@ -575,4 +575,7 @@ sealed abstract class FeatureRDD extends AvroGenomicRDD[Feature, FeatureProduct,
 
     replaceRdd(rdd.sortBy(f => f, ascending, numPartitions))
   }
+
+  override def toString = "%s with %d reference sequences"
+    .format(getClass.getSimpleName, sequences.size)
 }
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
@@ -371,4 +371,7 @@ sealed abstract class FragmentRDD extends AvroRecordGroupGenomicRDD[Fragment, Fr
       .flatMap(r => ReferenceRegion.opt(r))
       .toSeq
   }
+
+  override def toString = "%s with %d reference sequences, %d read groups, and %d processing steps"
+    .format(getClass.getSimpleName, sequences.size, recordGroups.size, processingSteps.size)
 }
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
@@ -1478,4 +1478,7 @@ sealed abstract class AlignmentRecordRDD extends AvroRecordGroupGenomicRDD[Align
     AlignmentRecordRDD.validateBins(bins)
     BinQualities(this, bins)
   }
+
+  override def toString = "%s with %d reference sequences, %d read groups, and %d processing steps"
+    .format(getClass.getSimpleName, sequences.size, recordGroups.size, processingSteps.size)
 }
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
@@ -324,4 +324,7 @@ sealed abstract class GenotypeRDD extends MultisampleAvroGenomicRDD[Genotype, Ge
   protected def getReferenceRegions(elem: Genotype): Seq[ReferenceRegion] = {
     Seq(ReferenceRegion(elem))
   }
+
+  override def toString = "%s with %d reference sequences and %d samples"
+    .format(getClass.getSimpleName, sequences.size, samples.size)
 }
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/variant/VariantContextRDD.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/variant/VariantContextRDD.scala
@@ -355,4 +355,7 @@ case class VariantContextRDD(rdd: RDD[VariantContext],
   protected def getReferenceRegions(elem: VariantContext): Seq[ReferenceRegion] = {
     Seq(ReferenceRegion(elem.position))
   }
+
+  override def toString = "%s with %d reference sequences and %d samples"
+    .format(getClass.getSimpleName, sequences.size, samples.size)
 }
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
@@ -300,4 +300,7 @@ sealed abstract class VariantRDD extends AvroGenomicRDD[Variant, VariantProduct,
   protected def getReferenceRegions(elem: Variant): Seq[ReferenceRegion] = {
     Seq(ReferenceRegion(elem))
   }
+
+  override def toString = "%s with %d reference sequences"
+    .format(getClass.getSimpleName, sequences.size)
 }