org.bdgenomics.adam.rdd

# variation

#### package variation

Visibility

1. Public
2. All

### Type Members

1. #### class ADAMHeaderlessVCFOutputFormat[K] extends KeyIgnoringVCFOutputFormat[K] with Serializable

   Wrapper for Hadoop-BAM to work around requirement for no-args constructor.

2. #### class ADAMVCFOutputFormat[K] extends KeyIgnoringVCFOutputFormat[K] with Serializable

   Wrapper for Hadoop-BAM to work around requirement for no-args constructor.

3. #### case class DatabaseVariantAnnotationRDD(rdd: RDD[DatabaseVariantAnnotation], sequences: SequenceDictionary) extends AvroGenomicRDD[DatabaseVariantAnnotation, DatabaseVariantAnnotationRDD] with Product with Serializable

   An RDD containing variant annotations against a given reference genome.

   An RDD containing variant annotations against a given reference genome.

   rdd

     Variant annotations.

   sequences

     A dictionary describing the reference genome.

4. #### case class GenotypeRDD(rdd: RDD[Genotype], sequences: SequenceDictionary, samples: Seq[Sample]) extends MultisampleAvroGenomicRDD[Genotype, GenotypeRDD] with Product with Serializable

   An RDD containing genotypes called in a set of samples against a given reference genome.

   An RDD containing genotypes called in a set of samples against a given reference genome.

   rdd

     Called genotypes.

   sequences

     A dictionary describing the reference genome.

   samples

     The samples called.

5. #### case class VCFInFormatter(sequences: SequenceDictionary, samples: Seq[String]) extends InFormatter[VariantContext, VariantContextRDD, VCFInFormatter] with Product with Serializable

6. #### case class VCFOutFormatter() extends OutFormatter[VariantContext] with Product with Serializable

7. #### case class VariantContextRDD(rdd: RDD[VariantContext], sequences: SequenceDictionary, samples: Seq[Sample]) extends MultisampleGenomicRDD[VariantContext, VariantContextRDD] with Logging with Product with Serializable

   An RDD containing VariantContexts attached to a reference and samples.

   An RDD containing VariantContexts attached to a reference and samples.

   rdd

     The underlying RDD of VariantContexts.

   sequences

     The genome sequence these variants were called against.

   samples

     The genotyped samples in this RDD of VariantContexts.

8. #### case class VariantRDD(rdd: RDD[Variant], sequences: SequenceDictionary) extends AvroGenomicRDD[Variant, VariantRDD] with Product with Serializable

   An RDD containing variants called against a given reference genome.

   An RDD containing variants called against a given reference genome.

   rdd

     Variants.

   sequences

     A dictionary describing the reference genome.

### Value Members

1. #### object VCFInFormatter extends InFormatterCompanion[VariantContext, VariantContextRDD, VCFInFormatter] with Serializable

### Ungrouped