package variant
Ordering
- Alphabetic
Visibility
- Public
- All
Type Members
-
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.
- case class DatasetBoundGenotypeDataset extends GenotypeDataset with DatasetBoundGenomicDataset[Genotype, Genotype, GenotypeDataset] with Product with Serializable
- case class DatasetBoundVariantContextDataset extends VariantContextDataset with DatasetBoundGenomicDataset[VariantContext, VariantContext, VariantContextDataset] with Product with Serializable
- case class DatasetBoundVariantDataset extends VariantDataset with DatasetBoundGenomicDataset[Variant, Variant, VariantDataset] with Product with Serializable
- sealed abstract class GenotypeDataset extends MultisampleAvroGenomicDataset[Genotype, Genotype, GenotypeDataset] with VCFSupportingGenomicDataset[Genotype, Genotype, GenotypeDataset]
- case class ParquetUnboundGenotypeDataset extends GenotypeDataset with Product with Serializable
- case class ParquetUnboundVariantDataset extends VariantDataset with Product with Serializable
- case class RDDBoundGenotypeDataset extends GenotypeDataset with Product with Serializable
- case class RDDBoundVariantContextDataset extends VariantContextDataset with Product with Serializable
- case class RDDBoundVariantDataset extends VariantDataset with Product with Serializable
- case class VCFInFormatter extends InFormatter[VariantContext, VariantContext, VariantContextDataset, VCFInFormatter] with Product with Serializable
-
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.
-
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.
- sealed abstract class VariantDataset extends AvroGenomicDataset[Variant, Variant, VariantDataset] with VCFSupportingGenomicDataset[Variant, Variant, VariantDataset]
Value Members
- object GenotypeDataset extends Serializable
-
object
VCFInFormatter extends InFormatterCompanion[VariantContext, VariantContext, VariantContextDataset, VCFInFormatter] with Serializable
InFormatter companion that builds a VCFInFormatter to write VCF to a pipe.
- object VariantContextDataset extends Serializable
- object VariantDataset extends Serializable