variant

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 VCFOutFormatter() extends OutFormatter[VariantContext] with Product with Serializable

   OutFormatter that reads streaming VCF.

5. case class VariantAnnotationRDD(rdd: RDD[VariantAnnotation], sequences: SequenceDictionary, headerLines: Seq[VCFHeaderLine] = ...) extends AvroGenomicRDD[VariantAnnotation, VariantAnnotationRDD] with Product with Serializable

   An RDD containing variant annotations against a given reference genome.

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.