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.

   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] = DefaultHeaderLines.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 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] = DefaultHeaderLines.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] = DefaultHeaderLines.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.

### 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