variant

Type Members

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

   

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

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

   K

   The key type. Keys are not written.

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

   

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

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

   K

   The key type. Keys are not written.

3. case class GenotypeRDD(rdd: RDD[Genotype], sequences: SequenceDictionary, samples: Seq[Sample], headerLines: Seq[VCFHeaderLine] = SupportedHeaderLines.allHeaderLines) 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.

   headerLines

   The VCF header lines that cover all INFO/FORMAT fields needed to represent this RDD of Genotypes.

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] = SupportedHeaderLines.allHeaderLines) extends AvroGenomicRDD[VariantAnnotation, VariantAnnotationRDD] 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.

   headerLines

   The VCF header lines that cover all INFO/FORMAT fields needed to represent this RDD of DatabaseVariantAnnotationss.

6. case class VariantContextRDD(rdd: RDD[VariantContext], sequences: SequenceDictionary, samples: Seq[Sample], headerLines: Seq[VCFHeaderLine] = SupportedHeaderLines.allHeaderLines) 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.

   headerLines

   The VCF header lines that cover all INFO/FORMAT fields needed to represent this RDD of VariantContexts.

7. case class VariantRDD(rdd: RDD[Variant], sequences: SequenceDictionary, headerLines: Seq[VCFHeaderLine] = SupportedHeaderLines.allHeaderLines) 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.

   headerLines

   The VCF header lines that cover all INFO/FORMAT fields needed to represent this RDD of Variants.