org.bdgenomics.adam.rdd

# variant

#### package variant

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 GenotypeRDD(rdd: RDD[Genotype], sequences: SequenceDictionary, samples: Seq[Sample], headerLines: Seq[VCFHeaderLine] = ...) extends MultisampleAvroGenomicRDD[Genotype, GenotypeRDD] with Product with Serializable

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

4. #### case class VCFInFormatter extends InFormatter[VariantContext, VariantContextRDD, VCFInFormatter] with Product with Serializable

5. #### case class VCFOutFormatter(headerLines: Seq[VCFHeaderLine]) extends OutFormatter[VariantContext] with Product with Serializable

   OutFormatter that reads streaming VCF.

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

   An RDD containing VariantContexts attached to a reference and samples.

7. #### case class VariantRDD(rdd: RDD[Variant], sequences: SequenceDictionary, headerLines: Seq[VCFHeaderLine] = ...) extends AvroGenomicRDD[Variant, VariantRDD] with Product with Serializable

   An RDD containing variants called against a given reference genome.

### Value Members

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

   InFormatter companion that builds a VCFInFormatter to write VCF to a pipe.

### Ungrouped