ADAM_2.12: Core 0.29.0 API < Back
 

# Packages

-  package root
  Definition Classes
    root
-  package org
  Definition Classes
    root
-  package bdgenomics
  Definition Classes
    org
-  package adam
  Definition Classes
    bdgenomics
-  package rdd
  Definition Classes
    adam
-  package feature
  Definition Classes
    rdd
-  package fragment
  Definition Classes
    rdd
-  package read
  Definition Classes
    rdd
-  package sequence
  Definition Classes
    rdd
-  package variant
  Definition Classes
    rdd
- ADAMVCFOutputFormat
- DatasetBoundGenotypeDataset
- DatasetBoundVariantContextDataset
- DatasetBoundVariantDataset
- GenotypeDataset
- ParquetUnboundGenotypeDataset
- ParquetUnboundVariantDataset
- RDDBoundGenotypeDataset
- RDDBoundVariantContextDataset
- RDDBoundVariantDataset
- VCFInFormatter
- VCFOutFormatter
- VariantContextDataset
- VariantDataset

p

org.bdgenomics.adam.rdd

# variant 

#### package variant

 
Ordering

1. Alphabetic

Visibility

1. Public
2. All

### Type Members

1.  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.

2.  case class DatasetBoundGenotypeDataset extends GenotypeDataset with DatasetBoundGenomicDataset[Genotype, Genotype, GenotypeDataset] with Product with Serializable
3.  case class DatasetBoundVariantContextDataset extends VariantContextDataset with DatasetBoundGenomicDataset[VariantContext, VariantContext, VariantContextDataset] with Product with Serializable
4.  case class DatasetBoundVariantDataset extends VariantDataset with DatasetBoundGenomicDataset[Variant, Variant, VariantDataset] with Product with Serializable
5.  sealed abstract class GenotypeDataset extends MultisampleAvroGenomicDataset[Genotype, Genotype, GenotypeDataset] with VCFSupportingGenomicDataset[Genotype, Genotype, GenotypeDataset]
6.  case class ParquetUnboundGenotypeDataset extends GenotypeDataset with Product with Serializable
7.  case class ParquetUnboundVariantDataset extends VariantDataset with Product with Serializable
8.  case class RDDBoundGenotypeDataset extends GenotypeDataset with Product with Serializable
9.  case class RDDBoundVariantContextDataset extends VariantContextDataset with Product with Serializable
10.  case class RDDBoundVariantDataset extends VariantDataset with Product with Serializable
11.  case class VCFInFormatter extends InFormatter[VariantContext, VariantContext, VariantContextDataset, VCFInFormatter] with Product with Serializable
12.  case class VCFOutFormatter(conf: Configuration, stringency: ValidationStringency, optHeaderLines: Option[CollectionAccumulator[VCFHeaderLine]]) extends OutFormatter[VariantContext] with Logging with Product with Serializable

    OutFormatter that reads streaming VCF.

    OutFormatter that reads streaming VCF.

    conf

      Hadoop configuration.

    stringency

      Validation stringency.

    optHeaderLines

      Optional accumulator for VCF header lines.

13.  sealed abstract class VariantContextDataset extends MultisampleGenomicDataset[VariantContext, VariantContext, VariantContextDataset] with GenomicDataset[VariantContext, VariantContext, VariantContextDataset] with Logging with VCFSupportingGenomicDataset[VariantContext, VariantContext, VariantContextDataset]

    An genomic dataset containing VariantContexts attached to a reference and samples.

14.  sealed abstract class VariantDataset extends AvroGenomicDataset[Variant, Variant, VariantDataset] with VCFSupportingGenomicDataset[Variant, Variant, VariantDataset]

### Value Members

1.  object GenotypeDataset extends Serializable
2.  object VCFInFormatter extends InFormatterCompanion[VariantContext, VariantContext, VariantContextDataset, VCFInFormatter] with Serializable

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

3.  object VariantContextDataset extends Serializable
4.  object VariantDataset extends Serializable

### Ungrouped