case class DatasetBoundFeatureDataset extends FeatureDataset with DatasetBoundGenomicDataset[Feature, Feature, FeatureDataset] with Product with Serializable
- Alphabetic
- By Inheritance
- DatasetBoundFeatureDataset
- Serializable
- Serializable
- Product
- Equals
- DatasetBoundGenomicDataset
- FeatureDataset
- MultisampleGenomicDataset
- AvroGenomicDataset
- GenomicDataset
- Logging
- AnyRef
- Any
- Hide All
- Show All
- Public
- All
Value Members
-
final
def
!=(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
final
def
##(): Int
- Definition Classes
- AnyRef → Any
-
final
def
==(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
def
addReference(referenceToAdd: SequenceRecord): FeatureDataset
Appends metadata for a single reference sequence to the current genomic dataset.
Appends metadata for a single reference sequence to the current genomic dataset.
- referenceToAdd
The reference sequence to add.
- returns
Returns a new GenomicDataset with this reference sequence appended.
- Definition Classes
- GenomicDataset
-
def
addReferences(referencesToAdd: SequenceDictionary): FeatureDataset
Appends reference sequence metadata to the current genomic dataset.
Appends reference sequence metadata to the current genomic dataset.
- referencesToAdd
The new reference sequences to append.
- returns
Returns a new GenomicDataset with the reference sequences appended.
- Definition Classes
- GenomicDataset
-
def
addSample(sampleToAdd: Sample): FeatureDataset
Adds a single sample to the current genomic dataset.
Adds a single sample to the current genomic dataset.
- sampleToAdd
A single sample to add.
- returns
Returns a new genomic dataset with this sample added.
- Definition Classes
- MultisampleGenomicDataset
-
def
addSamples(samplesToAdd: Iterable[Sample]): FeatureDataset
Adds samples to the current genomic dataset.
Adds samples to the current genomic dataset.
- samplesToAdd
Zero or more samples to add.
- returns
Returns a new genomic dataset with samples added.
- Definition Classes
- MultisampleGenomicDataset
-
final
def
asInstanceOf[T0]: T0
- Definition Classes
- Any
-
def
broadcast()(implicit tTag: ClassTag[Feature]): GenomicBroadcast[Feature, Feature, FeatureDataset]
- Definition Classes
- GenomicDataset
-
def
broadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Feature], xTag: ClassTag[X], txTag: ClassTag[(Feature, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(Feature, Y)]): GenericGenomicDataset[(Feature, X), (Feature, Y)]
Performs a broadcast inner join between this genomic dataset and another genomic dataset.
Performs a broadcast inner join between this genomic dataset and another genomic dataset.
In a broadcast join, the left genomic dataset (this genomic dataset) is collected to the driver, and broadcast to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other genomic dataset are dropped.
- genomicDataset
The right genomic dataset in the join.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
- Definition Classes
- GenomicDataset
- See also
broadcastRegionJoinAgainst
-
def
broadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[Feature], xTag: ClassTag[X], txTag: ClassTag[(Feature, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(Feature, Y)]): GenericGenomicDataset[(Feature, X), (Feature, Y)]
Performs a broadcast inner join between this genomic dataset and another genomic dataset.
Performs a broadcast inner join between this genomic dataset and another genomic dataset.
In a broadcast join, the left genomic dataset (this genomic dataset) is collected to the driver, and broadcast to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other genomic dataset are dropped.
- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
- Definition Classes
- GenomicDataset
- See also
broadcastRegionJoinAgainst
-
def
broadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Feature, X), (Feature, Y)]
(Java-specific) Performs a broadcast inner join between this genomic dataset and another genomic dataset.
(Java-specific) Performs a broadcast inner join between this genomic dataset and another genomic dataset.
In a broadcast join, the left genomic dataset (this genomic dataset) is collected to the driver, and broadcast to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other genomic dataset are dropped.
- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
- Definition Classes
- GenomicDataset
-
def
broadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Feature, X), (Feature, Y)]
(R-specific) Performs a broadcast inner join between this genomic dataset and another genomic dataset.
(R-specific) Performs a broadcast inner join between this genomic dataset and another genomic dataset.
In a broadcast join, the left genomic dataset (this genomic dataset) is collected to the driver, and broadcast to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other genomic dataset are dropped.
- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
- Definition Classes
- GenomicDataset
-
def
broadcastRegionJoinAgainst[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](broadcast: GenomicBroadcast[X, Y, Z])(implicit tTag: ClassTag[Feature], xTag: ClassTag[X], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(Y, Feature)]): GenericGenomicDataset[(X, Feature), (Y, Feature)]
Performs a broadcast inner join between this genomic dataset and data that has been broadcast.
Performs a broadcast inner join between this genomic dataset and data that has been broadcast.
In a broadcast join, the left side of the join (broadcastTree) is broadcast to to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other genomic dataset are dropped. As compared to broadcastRegionJoin, this function allows the broadcast object to be reused across multiple joins.
- broadcast
The data on the left side of the join.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
- Definition Classes
- GenomicDataset
- Note
This function differs from other region joins as it treats the calling genomic dataset as the right side of the join, and not the left.
- See also
broadcastRegionJoin
-
def
broadcastRegionJoinAgainstAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](broadcast: GenomicBroadcast[X, Y, Z])(implicit tTag: ClassTag[Feature], xTag: ClassTag[X], syuTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Y], Feature)]): GenericGenomicDataset[(Iterable[X], Feature), (Seq[Y], Feature)]
Performs a broadcast inner join between this genomic dataset and another genomic dataset.
Performs a broadcast inner join between this genomic dataset and another genomic dataset.
In a broadcast join, the left side of the join (broadcastTree) is broadcast to to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other genomic dataset are dropped. As compared to broadcastRegionJoin, this function allows the broadcast object to be reused across multiple joins.
- broadcast
The data on the left side of the join.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
- Definition Classes
- GenomicDataset
- Note
This function differs from other region joins as it treats the calling genomic dataset as the right side of the join, and not the left.
- See also
broadcastRegionJoinAndGroupByRight
-
def
broadcastRegionJoinAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Feature], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[Feature], X)], iuyTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Feature], Y)]): GenericGenomicDataset[(Iterable[Feature], X), (Seq[Feature], Y)]
Performs a broadcast inner join between this genomic dataset and another genomic dataset.
Performs a broadcast inner join between this genomic dataset and another genomic dataset.
In a broadcast join, the left genomic dataset (this genomic dataset) is collected to the driver, and broadcast to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other genomic dataset are dropped.
- genomicDataset
The right genomic dataset in the join.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
- Definition Classes
- GenomicDataset
- See also
broadcastRegionJoinAgainstAndGroupByRight
-
def
broadcastRegionJoinAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[Feature], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[Feature], X)], iuyTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Feature], Y)]): GenericGenomicDataset[(Iterable[Feature], X), (Seq[Feature], Y)]
Performs a broadcast inner join between this genomic dataset and another genomic dataset.
Performs a broadcast inner join between this genomic dataset and another genomic dataset.
In a broadcast join, the left genomic dataset (this genomic dataset) is collected to the driver, and broadcast to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other genomic dataset are dropped.
- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
- Definition Classes
- GenomicDataset
- See also
broadcastRegionJoinAgainstAndGroupByRight
-
def
broadcastRegionJoinAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Iterable[Feature], X), (Seq[Feature], Y)]
(Java-specific) Performs a broadcast inner join between this genomic dataset and another genomic dataset.
(Java-specific) Performs a broadcast inner join between this genomic dataset and another genomic dataset.
In a broadcast join, the left genomic dataset (this genomic dataset) is collected to the driver, and broadcast to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other genomic dataset are dropped.
- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
- Definition Classes
- GenomicDataset
- See also
broadcastRegionJoinAgainstAndGroupByRight
-
def
broadcastRegionJoinAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Iterable[Feature], X), (Seq[Feature], Y)]
(R-specific) Performs a broadcast inner join between this genomic dataset and another genomic dataset.
(R-specific) Performs a broadcast inner join between this genomic dataset and another genomic dataset.
In a broadcast join, the left genomic dataset (this genomic dataset) is collected to the driver, and broadcast to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other genomic dataset are dropped.
- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
- Definition Classes
- GenomicDataset
- See also
broadcastRegionJoinAgainstAndGroupByRight
-
def
buildTree(rdd: RDD[(ReferenceRegion, Feature)])(implicit tTag: ClassTag[Feature]): IntervalArray[ReferenceRegion, Feature]
- Attributes
- protected
- Definition Classes
- FeatureDataset → GenomicDataset
-
def
cache(): FeatureDataset
Caches underlying RDD in memory.
Caches underlying RDD in memory.
- returns
Cached GenomicDataset.
- Definition Classes
- DatasetBoundGenomicDataset → GenomicDataset
-
def
clone(): AnyRef
- Attributes
- protected[lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( ... ) @native()
-
val
dataset: Dataset[Feature]
These data as a Spark SQL Dataset.
These data as a Spark SQL Dataset.
- Definition Classes
- DatasetBoundFeatureDataset → GenomicDataset
-
def
debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
def
debug(msg: ⇒ Any, t: ⇒ Throwable): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
def
debug(msg: ⇒ Any): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
def
error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
def
error(msg: ⇒ Any, t: ⇒ Throwable): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
def
error(msg: ⇒ Any): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
def
filterByAttribute(key: String, value: String): FeatureDataset
Filter this FeatureDataset by attribute to those that match the specified attribute key and value.
Filter this FeatureDataset by attribute to those that match the specified attribute key and value.
- key
Attribute key to filter by.
- value
Attribute value to filter by.
- returns
FeatureDataset filtered by the specified attribute.
- Definition Classes
- DatasetBoundFeatureDataset → FeatureDataset
-
def
filterByOverlappingRegion(query: ReferenceRegion): FeatureDataset
Runs a filter that selects data in the underlying RDD that overlaps a single genomic region.
Runs a filter that selects data in the underlying RDD that overlaps a single genomic region.
- query
The region to query for.
- returns
Returns a new GenomicDataset containing only data that overlaps the query region.
- Definition Classes
- GenomicDataset
-
def
filterByOverlappingRegions(querys: Iterable[ReferenceRegion]): FeatureDataset
(Scala-specific) Runs a filter that selects data in the underlying RDD that overlaps several genomic regions.
(Scala-specific) Runs a filter that selects data in the underlying RDD that overlaps several genomic regions.
- querys
The regions to query for.
- returns
Returns a new GenomicDataset containing only data that overlaps the querys region.
- Definition Classes
- DatasetBoundGenomicDataset → GenomicDataset
-
def
filterByOverlappingRegions(querys: Iterable[ReferenceRegion]): FeatureDataset
(Java-specific) Runs a filter that selects data in the underlying RDD that overlaps several genomic regions.
(Java-specific) Runs a filter that selects data in the underlying RDD that overlaps several genomic regions.
- querys
The regions to query for.
- returns
Returns a new GenomicDataset containing only data that overlaps the querys region.
- Definition Classes
- GenomicDataset
-
def
filterByScore(minimumScore: Double): FeatureDataset
Filter this FeatureDataset by score.
Filter this FeatureDataset by score.
- minimumScore
Minimum score to filter by, inclusive.
- returns
FeatureDataset filtered by the specified minimum score.
- Definition Classes
- DatasetBoundFeatureDataset → FeatureDataset
-
def
filterToExon(exonId: String): FeatureDataset
Filter this FeatureDataset by exon to those that match the specified exon.
Filter this FeatureDataset by exon to those that match the specified exon.
- exonId
Exon to filter by.
- returns
FeatureDataset filtered by the specified exon.
- Definition Classes
- DatasetBoundFeatureDataset → FeatureDataset
-
def
filterToExons(exonIds: Seq[String]): FeatureDataset
(Scala-specific) Filter this FeatureDataset by exon to those that match the specified exons.
(Scala-specific) Filter this FeatureDataset by exon to those that match the specified exons.
- exonIds
Sequence of exons to filter by.
- returns
FeatureDataset filtered by the specified exons.
- Definition Classes
- DatasetBoundFeatureDataset → FeatureDataset
-
def
filterToExons(exonIds: List[String]): FeatureDataset
(Java-specific) Filter this FeatureDataset by exon to those that match the specified exons.
(Java-specific) Filter this FeatureDataset by exon to those that match the specified exons.
- exonIds
List of exons to filter by.
- returns
FeatureDataset filtered by the specified exons.
- Definition Classes
- FeatureDataset
-
def
filterToFeatureType(featureType: String): FeatureDataset
Filter this FeatureDataset by feature type to those that match the specified feature type.
Filter this FeatureDataset by feature type to those that match the specified feature type.
- featureType
Feature type to filter by.
- returns
FeatureDataset filtered by the specified feature type.
- Definition Classes
- DatasetBoundFeatureDataset → FeatureDataset
-
def
filterToFeatureTypes(featureTypes: Seq[String]): FeatureDataset
(Scala-specific) Filter this FeatureDataset by feature type to those that match the specified feature types.
(Scala-specific) Filter this FeatureDataset by feature type to those that match the specified feature types.
- returns
FeatureDataset filtered by the specified feature types.
- Definition Classes
- DatasetBoundFeatureDataset → FeatureDataset
-
def
filterToFeatureTypes(featureTypes: List[String]): FeatureDataset
(Java-specific) Filter this FeatureDataset by feature type to those that match the specified feature types.
(Java-specific) Filter this FeatureDataset by feature type to those that match the specified feature types.
- returns
FeatureDataset filtered by the specified feature types.
- Definition Classes
- FeatureDataset
-
def
filterToGene(geneId: String): FeatureDataset
Filter this FeatureDataset by gene to those that match the specified gene.
Filter this FeatureDataset by gene to those that match the specified gene.
- geneId
Gene to filter by.
- returns
FeatureDataset filtered by the specified gene.
- Definition Classes
- DatasetBoundFeatureDataset → FeatureDataset
-
def
filterToGenes(geneIds: Seq[String]): FeatureDataset
(Scala-specific) Filter this FeatureDataset by gene to those that match the specified genes.
(Scala-specific) Filter this FeatureDataset by gene to those that match the specified genes.
- geneIds
Sequence of genes to filter by.
- returns
FeatureDataset filtered by the specified genes.
- Definition Classes
- DatasetBoundFeatureDataset → FeatureDataset
-
def
filterToGenes(geneIds: List[String]): FeatureDataset
(Java-specific) Filter this FeatureDataset by gene to those that match the specified genes.
(Java-specific) Filter this FeatureDataset by gene to those that match the specified genes.
- geneIds
List of genes to filter by.
- returns
FeatureDataset filtered by the specified genes.
- Definition Classes
- FeatureDataset
-
def
filterToParent(parentId: String): FeatureDataset
Filter this FeatureDataset by parent to those that match the specified parent.
Filter this FeatureDataset by parent to those that match the specified parent.
- parentId
Parent to filter by.
- returns
FeatureDataset filtered by the specified parent.
- Definition Classes
- DatasetBoundFeatureDataset → FeatureDataset
-
def
filterToParents(parentIds: Seq[String]): FeatureDataset
(Scala-specific) Filter this FeatureDataset by parent to those that match the specified parents.
(Scala-specific) Filter this FeatureDataset by parent to those that match the specified parents.
- parentIds
Sequence of parents to filter by.
- returns
FeatureDataset filtered by the specified parents.
- Definition Classes
- DatasetBoundFeatureDataset → FeatureDataset
-
def
filterToParents(parentIds: List[String]): FeatureDataset
(Java-specific) Filter this FeatureDataset by parent to those that match the specified parents.
(Java-specific) Filter this FeatureDataset by parent to those that match the specified parents.
- parentIds
List of parents to filter by.
- returns
FeatureDataset filtered by the specified parents.
- Definition Classes
- FeatureDataset
-
def
filterToProtein(proteinId: String): FeatureDataset
Filter this FeatureDataset by protein to those that match the specified protein.
Filter this FeatureDataset by protein to those that match the specified protein.
- proteinId
Protein to filter by.
- returns
FeatureDataset filtered by the specified protein.
- Definition Classes
- DatasetBoundFeatureDataset → FeatureDataset
-
def
filterToProteins(proteinIds: Seq[String]): FeatureDataset
(Scala-specific) Filter this FeatureDataset by protein to those that match the specified proteins.
(Scala-specific) Filter this FeatureDataset by protein to those that match the specified proteins.
- proteinIds
Sequence of proteins to filter by.
- returns
FeatureDataset filtered by the specified proteins.
- Definition Classes
- DatasetBoundFeatureDataset → FeatureDataset
-
def
filterToProteins(proteinIds: List[String]): FeatureDataset
(Java-specific) Filter this FeatureDataset by protein to those that match the specified proteins.
(Java-specific) Filter this FeatureDataset by protein to those that match the specified proteins.
- proteinIds
List of proteins to filter by.
- returns
FeatureDataset filtered by the specified proteins.
- Definition Classes
- FeatureDataset
-
def
filterToReferenceName(referenceName: String): FeatureDataset
Filter this FeatureDataset by reference name to those that match the specified reference name.
Filter this FeatureDataset by reference name to those that match the specified reference name.
- referenceName
Reference name to filter by.
- returns
FeatureDataset filtered by the specified reference name.
- Definition Classes
- DatasetBoundFeatureDataset → FeatureDataset
-
def
filterToTranscript(transcriptId: String): FeatureDataset
Filter this FeatureDataset by transcript to those that match the specified transcript.
Filter this FeatureDataset by transcript to those that match the specified transcript.
- transcriptId
Transcript to filter by.
- returns
FeatureDataset filtered by the specified transcript.
- Definition Classes
- DatasetBoundFeatureDataset → FeatureDataset
-
def
filterToTranscripts(transcriptIds: Seq[String]): FeatureDataset
(Scala-specific) Filter this FeatureDataset by transcript to those that match the specified transcripts.
(Scala-specific) Filter this FeatureDataset by transcript to those that match the specified transcripts.
- transcriptIds
Sequence of transcripts to filter by.
- returns
FeatureDataset filtered by the specified transcripts.
- Definition Classes
- DatasetBoundFeatureDataset → FeatureDataset
-
def
filterToTranscripts(transcriptIds: List[String]): FeatureDataset
(Java-specific) Filter this FeatureDataset by transcript to those that match the specified transcripts.
(Java-specific) Filter this FeatureDataset by transcript to those that match the specified transcripts.
- transcriptIds
List of transcripts to filter by.
- returns
FeatureDataset filtered by the specified transcripts.
- Definition Classes
- FeatureDataset
-
def
finalize(): Unit
- Attributes
- protected[lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( classOf[java.lang.Throwable] )
-
def
flattenRddByRegions(): RDD[(ReferenceRegion, Feature)]
- Attributes
- protected
- Definition Classes
- GenomicDataset
-
def
fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Feature], xTag: ClassTag[X], otoxTag: ClassTag[(Option[Feature], Option[X])], ouoyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Feature], Option[Y])]): GenericGenomicDataset[(Option[Feature], Option[X]), (Option[Feature], Option[Y])]
Performs a sort-merge full outer join between this genomic dataset and another genomic dataset.
Performs a sort-merge full outer join between this genomic dataset and another genomic dataset.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a full outer join, if a value from either genomic dataset does not overlap any values in the other genomic dataset, it will be paired with a
None
in the product of the join.- genomicDataset
The right genomic dataset in the join.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, and values that did not overlap will be paired with a
None
.
- Definition Classes
- GenomicDataset
-
def
fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[Feature], xTag: ClassTag[X], otoxTag: ClassTag[(Option[Feature], Option[X])], ouoyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Feature], Option[Y])]): GenericGenomicDataset[(Option[Feature], Option[X]), (Option[Feature], Option[Y])]
Performs a sort-merge full outer join between this genomic dataset and another genomic dataset.
Performs a sort-merge full outer join between this genomic dataset and another genomic dataset.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a full outer join, if a value from either genomic dataset does not overlap any values in the other genomic dataset, it will be paired with a
None
in the product of the join.- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, and values that did not overlap will be paired with a
None
.
- Definition Classes
- GenomicDataset
-
def
fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Option[Feature], Option[X]), (Option[Feature], Option[Y])]
(Python-specific) Performs a sort-merge full outer join between this genomic dataset and another genomic dataset.
(Python-specific) Performs a sort-merge full outer join between this genomic dataset and another genomic dataset.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a full outer join, if a value from either genomic dataset does not overlap any values in the other genomic dataset, it will be paired with a
None
in the product of the join.- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, and values that did not overlap will be paired with a
None
.
- Definition Classes
- GenomicDataset
-
def
fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Option[Feature], Option[X]), (Option[Feature], Option[Y])]
(R-specific) Performs a sort-merge full outer join between this genomic dataset and another genomic dataset.
(R-specific) Performs a sort-merge full outer join between this genomic dataset and another genomic dataset.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a full outer join, if a value from either genomic dataset does not overlap any values in the other genomic dataset, it will be paired with a
None
in the product of the join.- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, and values that did not overlap will be paired with a
None
.
- Definition Classes
- GenomicDataset
-
final
def
getClass(): Class[_]
- Definition Classes
- AnyRef → Any
- Annotations
- @native()
-
def
getReferenceRegions(elem: Feature): Seq[ReferenceRegion]
- elem
The Feature to get an underlying region for.
- returns
Since a feature maps directly to a single genomic region, this method will always return a Seq of exactly one ReferenceRegion.
- Attributes
- protected
- Definition Classes
- FeatureDataset → GenomicDataset
-
def
info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
def
info(msg: ⇒ Any, t: ⇒ Throwable): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
def
info(msg: ⇒ Any): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
def
isDebugEnabled: Boolean
- Attributes
- protected
- Definition Classes
- Logging
-
def
isErrorEnabled: Boolean
- Attributes
- protected
- Definition Classes
- Logging
-
def
isInfoEnabled: Boolean
- Attributes
- protected
- Definition Classes
- Logging
-
final
def
isInstanceOf[T0]: Boolean
- Definition Classes
- Any
-
val
isPartitioned: Boolean
- Definition Classes
- DatasetBoundFeatureDataset → DatasetBoundGenomicDataset
-
def
isSorted: Boolean
- Definition Classes
- GenomicDataset
-
def
isTraceEnabled: Boolean
- Attributes
- protected
- Definition Classes
- Logging
-
def
isWarnEnabled: Boolean
- Attributes
- protected
- Definition Classes
- Logging
-
lazy val
jrdd: JavaRDD[Feature]
The underlying RDD of genomic data, as a JavaRDD.
The underlying RDD of genomic data, as a JavaRDD.
- Definition Classes
- GenomicDataset
-
def
leftOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Feature], xTag: ClassTag[X], toxTag: ClassTag[(Feature, Option[X])], uoyTag: scala.reflect.api.JavaUniverse.TypeTag[(Feature, Option[Y])]): GenericGenomicDataset[(Feature, Option[X]), (Feature, Option[Y])]
Performs a sort-merge left outer join between this genomic dataset and another genomic dataset.
Performs a sort-merge left outer join between this genomic dataset and another genomic dataset.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a left outer join, all values in the right genomic dataset that do not overlap a value from the left genomic dataset are dropped. If a value from the left genomic dataset does not overlap any values in the right genomic dataset, it will be paired with a
None
in the product of the join.- genomicDataset
The right genomic dataset in the join.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the left genomic dataset that did not overlap a key in the right genomic dataset.
- Definition Classes
- GenomicDataset
-
def
leftOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[Feature], xTag: ClassTag[X], toxTag: ClassTag[(Feature, Option[X])], uoyTag: scala.reflect.api.JavaUniverse.TypeTag[(Feature, Option[Y])]): GenericGenomicDataset[(Feature, Option[X]), (Feature, Option[Y])]
Performs a sort-merge left outer join between this genomic dataset and another genomic dataset.
Performs a sort-merge left outer join between this genomic dataset and another genomic dataset.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a left outer join, all values in the right genomic dataset that do not overlap a value from the left genomic dataset are dropped. If a value from the left genomic dataset does not overlap any values in the right genomic dataset, it will be paired with a
None
in the product of the join.- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the left genomic dataset that did not overlap a key in the right genomic dataset.
- Definition Classes
- GenomicDataset
-
def
leftOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Feature, Option[X]), (Feature, Option[Y])]
(Java-specific) Performs a sort-merge left outer join between this genomic dataset and another genomic dataset.
(Java-specific) Performs a sort-merge left outer join between this genomic dataset and another genomic dataset.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a left outer join, all values in the right genomic dataset that do not overlap a value from the left genomic dataset are dropped. If a value from the left genomic dataset does not overlap any values in the right genomic dataset, it will be paired with a
None
in the product of the join.- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the left genomic dataset that did not overlap a key in the right genomic dataset.
- Definition Classes
- GenomicDataset
-
def
leftOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Feature, Option[X]), (Feature, Option[Y])]
(R-specific) Performs a sort-merge left outer join between this genomic dataset and another genomic dataset.
(R-specific) Performs a sort-merge left outer join between this genomic dataset and another genomic dataset.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a left outer join, all values in the right genomic dataset that do not overlap a value from the left genomic dataset are dropped. If a value from the left genomic dataset does not overlap any values in the right genomic dataset, it will be paired with a
None
in the product of the join.- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the left genomic dataset that did not overlap a key in the right genomic dataset.
- Definition Classes
- GenomicDataset
-
def
leftOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Feature], xTag: ClassTag[X], toxTag: ClassTag[(Feature, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(Feature, Seq[Y])]): GenericGenomicDataset[(Feature, Iterable[X]), (Feature, Seq[Y])]
Performs a sort-merge left outer join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value.
Performs a sort-merge left outer join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a left outer join, all values in the right genomic dataset that do not overlap a value from the left genomic dataset are dropped. If a value from the left genomic dataset does not overlap any values in the right genomic dataset, it will be paired with an empty Iterable in the product of the join.
- genomicDataset
The right genomic dataset in the join.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the left genomic dataset that did not overlap a key in the right genomic dataset.
- Definition Classes
- GenomicDataset
-
def
leftOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[Feature], xTag: ClassTag[X], toxTag: ClassTag[(Feature, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(Feature, Seq[Y])]): GenericGenomicDataset[(Feature, Iterable[X]), (Feature, Seq[Y])]
Performs a sort-merge left outer join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value.
Performs a sort-merge left outer join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a left outer join, all values in the right genomic dataset that do not overlap a value from the left genomic dataset are dropped. If a value from the left genomic dataset does not overlap any values in the right genomic dataset, it will be paired with an empty Iterable in the product of the join.
- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the left genomic dataset that did not overlap a key in the right genomic dataset.
- Definition Classes
- GenomicDataset
-
def
leftOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Feature, Iterable[X]), (Feature, Seq[Y])]
(Java-specific) Performs a sort-merge left outer join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value.
(Java-specific) Performs a sort-merge left outer join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a left outer join, all values in the right genomic dataset that do not overlap a value from the left genomic dataset are dropped. If a value from the left genomic dataset does not overlap any values in the right genomic dataset, it will be paired with an empty Iterable in the product of the join.
- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the left genomic dataset that did not overlap a key in the right genomic dataset.
- Definition Classes
- GenomicDataset
-
def
leftOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Feature, Iterable[X]), (Feature, Seq[Y])]
(R-specific) Performs a sort-merge left outer join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value.
(R-specific) Performs a sort-merge left outer join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a left outer join, all values in the right genomic dataset that do not overlap a value from the left genomic dataset are dropped. If a value from the left genomic dataset does not overlap any values in the right genomic dataset, it will be paired with an empty Iterable in the product of the join.
- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the left genomic dataset that did not overlap a key in the right genomic dataset.
- Definition Classes
- GenomicDataset
-
def
logger: Logger
- Attributes
- protected
- Definition Classes
- Logging
-
def
loggerName: String
- Attributes
- protected
- Definition Classes
- Logging
-
final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
final
def
notify(): Unit
- Definition Classes
- AnyRef
- Annotations
- @native()
-
final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
- Annotations
- @native()
-
val
optLookbackPartitions: Option[Int]
- Definition Classes
- DatasetBoundFeatureDataset → DatasetBoundGenomicDataset
-
val
optPartitionBinSize: Option[Int]
- Definition Classes
- DatasetBoundFeatureDataset → DatasetBoundGenomicDataset
-
lazy val
optPartitionMap: None.type
- Attributes
- protected
- Definition Classes
- DatasetBoundFeatureDataset → GenomicDataset
-
def
persist(sl: StorageLevel): FeatureDataset
Persists underlying RDD in memory or disk.
Persists underlying RDD in memory or disk.
- sl
new StorageLevel
- returns
Persisted GenomicDataset.
- Definition Classes
- DatasetBoundGenomicDataset → GenomicDataset
-
def
pipe[X, Y <: Product, Z <: GenomicDataset[X, Y, Z], W <: InFormatter[Feature, Feature, FeatureDataset, W]](cmd: List[String], files: List[String], environment: Map[String, String], flankSize: Integer, tFormatter: Class[W], xFormatter: OutFormatter[X], convFn: Function2[FeatureDataset, RDD[X], Z]): Z
(Java/Python-specific) Pipes genomic data to a subprocess that runs in parallel using Spark.
(Java/Python-specific) Pipes genomic data to a subprocess that runs in parallel using Spark.
- X
The type of the record created by the piped command.
- Y
A GenomicDataset containing X's.
- cmd
Command to run.
- files
Files to make locally available to the commands being run. Default is empty.
- environment
A map containing environment variable/value pairs to set in the environment for the newly created process. Default is empty.
- flankSize
Number of bases to flank each command invocation by.
- tFormatter
Class of formatter for data going into pipe command.
- xFormatter
Formatter for data coming out of the pipe command.
- convFn
The conversion function used to build the final genomic dataset.
- returns
Returns a new GenomicDataset of type Y.
- Definition Classes
- GenomicDataset
-
def
pipe[X, Y <: Product, Z <: GenomicDataset[X, Y, Z], W <: InFormatter[Feature, Feature, FeatureDataset, W]](cmd: Seq[Any], files: Seq[Any], environment: Map[Any, Any], flankSize: Double, tFormatter: Class[W], xFormatter: OutFormatter[X], convFn: Function2[FeatureDataset, RDD[X], Z]): Z
(R-specific) Pipes genomic data to a subprocess that runs in parallel using Spark.
(R-specific) Pipes genomic data to a subprocess that runs in parallel using Spark.
- X
The type of the record created by the piped command.
- Y
A GenomicDataset containing X's.
- cmd
Command to run.
- files
Files to make locally available to the commands being run. Default is empty.
- environment
A map containing environment variable/value pairs to set in the environment for the newly created process. Default is empty.
- flankSize
Number of bases to flank each command invocation by.
- tFormatter
Class of formatter for data going into pipe command.
- xFormatter
Formatter for data coming out of the pipe command.
- convFn
The conversion function used to build the final genomic dataset.
- returns
Returns a new GenomicDataset of type Y.
- Definition Classes
- GenomicDataset
-
def
pipe[X, Y <: Product, Z <: GenomicDataset[X, Y, Z], W <: InFormatter[Feature, Feature, FeatureDataset, W]](cmd: Seq[String], files: Seq[String] = Seq.empty, environment: Map[String, String] = Map.empty, flankSize: Int = 0, optTimeout: Option[Int] = None)(implicit tFormatterCompanion: InFormatterCompanion[Feature, Feature, FeatureDataset, W], xFormatter: OutFormatter[X], convFn: (FeatureDataset, RDD[X]) ⇒ Z, tManifest: ClassTag[Feature], xManifest: ClassTag[X]): Z
(Scala-specific) Pipes genomic data to a subprocess that runs in parallel using Spark.
(Scala-specific) Pipes genomic data to a subprocess that runs in parallel using Spark.
Files are substituted in to the command with a $x syntax. E.g., to invoke a command that uses the first file from the files Seq, use $0. To access the path to the directory where the files are copied, use $root.
Pipes require the presence of an InFormatterCompanion and an OutFormatter as implicit values. The InFormatterCompanion should be a singleton whose apply method builds an InFormatter given a specific type of GenomicDataset. The implicit InFormatterCompanion yields an InFormatter which is used to format the input to the pipe, and the implicit OutFormatter is used to parse the output from the pipe.
- X
The type of the record created by the piped command.
- Y
A GenomicDataset containing X's.
- cmd
Command to run.
- files
Files to make locally available to the commands being run. Default is empty.
- environment
A map containing environment variable/value pairs to set in the environment for the newly created process. Default is empty.
- flankSize
Number of bases to flank each command invocation by.
- optTimeout
An optional parameter specifying how long to let a single partition run for, in seconds. If the partition times out, the partial results will be returned, and no exception will be logged. The partition will log that the command timed out.
- returns
Returns a new GenomicDataset of type Y.
- Definition Classes
- GenomicDataset
-
val
productFn: (Feature) ⇒ Feature
- Attributes
- protected
- Definition Classes
- FeatureDataset → GenomicDataset
-
lazy val
rdd: RDD[Feature]
The RDD of genomic data that we are wrapping.
The RDD of genomic data that we are wrapping.
- Definition Classes
- DatasetBoundFeatureDataset → GenomicDataset
-
val
references: SequenceDictionary
The sequence dictionary describing the reference assembly this dataset is aligned to.
The sequence dictionary describing the reference assembly this dataset is aligned to.
- Definition Classes
- DatasetBoundFeatureDataset → GenomicDataset
-
def
replaceRdd(newRdd: RDD[Feature], newPartitionMap: Option[Array[Option[(ReferenceRegion, ReferenceRegion)]]] = None): FeatureDataset
- newRdd
The RDD to replace the underlying RDD with.
- returns
Returns a new FeatureDataset with the underlying RDD replaced.
- Attributes
- protected
- Definition Classes
- FeatureDataset → GenomicDataset
-
def
replaceReferences(newReferences: SequenceDictionary): FeatureDataset
Replaces the reference sequence dictionary attached to a GenomicDataset.
Replaces the reference sequence dictionary attached to a GenomicDataset.
- newReferences
The new reference sequence dictionary to attach.
- returns
Returns a new GenomicDataset with the reference sequences replaced.
- Definition Classes
- DatasetBoundFeatureDataset → GenomicDataset
-
def
replaceSamples(newSamples: Iterable[Sample]): FeatureDataset
Replaces the sample metadata attached to the genomic dataset.
Replaces the sample metadata attached to the genomic dataset.
- newSamples
The new sample metadata to attach.
- returns
A GenomicDataset with new sample metadata.
- Definition Classes
- DatasetBoundFeatureDataset → MultisampleGenomicDataset
-
def
rightOuterBroadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Feature], xTag: ClassTag[X], otxTag: ClassTag[(Option[Feature], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Feature], Y)]): GenericGenomicDataset[(Option[Feature], X), (Option[Feature], Y)]
Performs a broadcast right outer join between this genomic dataset and another genomic dataset.
Performs a broadcast right outer join between this genomic dataset and another genomic dataset.
In a broadcast join, the left genomic dataset (this genomic dataset) is collected to the driver, and broadcast to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is a right outer join, all values in the left genomic dataset that do not overlap a value from the right genomic dataset are dropped. If a value from the right genomic dataset does not overlap any values in the left genomic dataset, it will be paired with a
None
in the product of the join.- genomicDataset
The right genomic dataset in the join.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right genomic dataset that did not overlap a key in the left genomic dataset.
- Definition Classes
- GenomicDataset
- See also
rightOuterBroadcastRegionJoin
-
def
rightOuterBroadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[Feature], xTag: ClassTag[X], otxTag: ClassTag[(Option[Feature], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Feature], Y)]): GenericGenomicDataset[(Option[Feature], X), (Option[Feature], Y)]
Performs a broadcast right outer join between this genomic dataset and another genomic dataset.
Performs a broadcast right outer join between this genomic dataset and another genomic dataset.
In a broadcast join, the left genomic dataset (this genomic dataset) is collected to the driver, and broadcast to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is a right outer join, all values in the left genomic dataset that do not overlap a value from the right genomic dataset are dropped. If a value from the right genomic dataset does not overlap any values in the left genomic dataset, it will be paired with a
None
in the product of the join.- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right genomic dataset that did not overlap a key in the left genomic dataset.
- Definition Classes
- GenomicDataset
- See also
rightOuterBroadcastRegionJoin
-
def
rightOuterBroadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Option[Feature], X), (Option[Feature], Y)]
(Java-specific) Performs a broadcast right outer join between this genomic dataset and another genomic dataset.
(Java-specific) Performs a broadcast right outer join between this genomic dataset and another genomic dataset.
In a broadcast join, the left genomic dataset (this genomic dataset) is collected to the driver, and broadcast to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is a right outer join, all values in the left genomic dataset that do not overlap a value from the right genomic dataset are dropped. If a value from the right genomic dataset does not overlap any values in the left genomic dataset, it will be paired with a
None
in the product of the join.- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right genomic dataset that did not overlap a key in the left genomic dataset.
- Definition Classes
- GenomicDataset
-
def
rightOuterBroadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Option[Feature], X), (Option[Feature], Y)]
(R-specific) Performs a broadcast right outer join between this genomic dataset and another genomic dataset.
(R-specific) Performs a broadcast right outer join between this genomic dataset and another genomic dataset.
In a broadcast join, the left genomic dataset (this genomic dataset) is collected to the driver, and broadcast to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is a right outer join, all values in the left genomic dataset that do not overlap a value from the right genomic dataset are dropped. If a value from the right genomic dataset does not overlap any values in the left genomic dataset, it will be paired with a
None
in the product of the join.- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right genomic dataset that did not overlap a key in the left genomic dataset.
- Definition Classes
- GenomicDataset
-
def
rightOuterBroadcastRegionJoinAgainst[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](broadcast: GenomicBroadcast[X, Y, Z])(implicit tTag: ClassTag[Feature], xTag: ClassTag[X], oyuTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Y], Feature)]): GenericGenomicDataset[(Option[X], Feature), (Option[Y], Feature)]
Performs a broadcast right outer join between this genomic dataset and data that has been broadcast.
Performs a broadcast right outer join between this genomic dataset and data that has been broadcast.
In a broadcast join, the left side of the join (broadcastTree) is broadcast to to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is a right outer join, all values in the left table that do not overlap a value from the right genomic dataset are dropped. If a value from the right genomic dataset does not overlap any values in the left table, it will be paired with a
None
in the product of the join. As compared to broadcastRegionJoin, this function allows the broadcast object to be reused across multiple joins.- broadcast
The data on the left side of the join.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
- Definition Classes
- GenomicDataset
- Note
This function differs from other region joins as it treats the calling genomic dataset as the right side of the join, and not the left.
- See also
rightOuterBroadcastRegionJoin
-
def
rightOuterBroadcastRegionJoinAgainstAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](broadcast: GenomicBroadcast[X, Y, Z])(implicit tTag: ClassTag[Feature], xTag: ClassTag[X], syuTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Y], Feature)]): GenericGenomicDataset[(Iterable[X], Feature), (Seq[Y], Feature)]
Performs a broadcast right outer join between this genomic dataset and another genomic dataset.
Performs a broadcast right outer join between this genomic dataset and another genomic dataset.
In a broadcast join, the left side of the join (broadcastTree) is broadcast to to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is a right outer join, all values in the left table that do not overlap a value from the right genomic dataset are dropped. If a value from the right genomic dataset does not overlap any values in the left table, it will be paired with a
None
in the product of the join. As compared to broadcastRegionJoin, this function allows the broadcast object to be reused across multiple joins.- broadcast
The data on the left side of the join.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
- Definition Classes
- GenomicDataset
- Note
This function differs from other region joins as it treats the calling genomic dataset as the right side of the join, and not the left.
- See also
rightOuterBroadcastRegionJoinAndGroupByRight
-
def
rightOuterBroadcastRegionJoinAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Feature], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[Feature], X)], iuyTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Feature], Y)]): GenericGenomicDataset[(Iterable[Feature], X), (Seq[Feature], Y)]
Performs a broadcast right outer join between this genomic dataset and another genomic dataset.
Performs a broadcast right outer join between this genomic dataset and another genomic dataset.
In a broadcast join, the left side of the join (broadcastTree) is broadcast to to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is a right outer join, all values in the left genomic dataset that do not overlap a value from the right genomic dataset are dropped. If a value from the right genomic dataset does not overlap any values in the left genomic dataset, it will be paired with a
None
in the product of the join.- genomicDataset
The right genomic dataset in the join.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right genomic dataset that did not overlap a key in the left genomic dataset.
- Definition Classes
- GenomicDataset
- See also
rightOuterBroadcastRegionJoinAgainstAndGroupByRight
-
def
rightOuterBroadcastRegionJoinAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[Feature], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[Feature], X)], iuyTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Feature], Y)]): GenericGenomicDataset[(Iterable[Feature], X), (Seq[Feature], Y)]
Performs a broadcast right outer join between this genomic dataset and another genomic dataset.
Performs a broadcast right outer join between this genomic dataset and another genomic dataset.
In a broadcast join, the left side of the join (broadcastTree) is broadcast to to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is a right outer join, all values in the left genomic dataset that do not overlap a value from the right genomic dataset are dropped. If a value from the right genomic dataset does not overlap any values in the left genomic dataset, it will be paired with a
None
in the product of the join.- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right genomic dataset that did not overlap a key in the left genomic dataset.
- Definition Classes
- GenomicDataset
- See also
rightOuterBroadcastRegionJoinAgainstAndGroupByRight
-
def
rightOuterBroadcastRegionJoinAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Iterable[Feature], X), (Seq[Feature], Y)]
(Java-specific) Performs a broadcast right outer join between this genomic dataset and another genomic dataset.
(Java-specific) Performs a broadcast right outer join between this genomic dataset and another genomic dataset.
In a broadcast join, the left side of the join (broadcastTree) is broadcast to to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is a right outer join, all values in the left genomic dataset that do not overlap a value from the right genomic dataset are dropped. If a value from the right genomic dataset does not overlap any values in the left genomic dataset, it will be paired with a
None
in the product of the join.- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right genomic dataset that did not overlap a key in the left genomic dataset.
- Definition Classes
- GenomicDataset
- See also
rightOuterBroadcastRegionJoinAgainstAndGroupByRight
-
def
rightOuterBroadcastRegionJoinAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Iterable[Feature], X), (Seq[Feature], Y)]
(R-specific) Performs a broadcast right outer join between this genomic dataset and another genomic dataset.
(R-specific) Performs a broadcast right outer join between this genomic dataset and another genomic dataset.
In a broadcast join, the left side of the join (broadcastTree) is broadcast to to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is a right outer join, all values in the left genomic dataset that do not overlap a value from the right genomic dataset are dropped. If a value from the right genomic dataset does not overlap any values in the left genomic dataset, it will be paired with a
None
in the product of the join.- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right genomic dataset that did not overlap a key in the left genomic dataset.
- Definition Classes
- GenomicDataset
- See also
rightOuterBroadcastRegionJoinAgainstAndGroupByRight
-
def
rightOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Feature], xTag: ClassTag[X], otxTag: ClassTag[(Option[Feature], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Feature], Y)]): GenericGenomicDataset[(Option[Feature], X), (Option[Feature], Y)]
Performs a sort-merge right outer join between this genomic dataset and another genomic dataset.
Performs a sort-merge right outer join between this genomic dataset and another genomic dataset.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a right outer join, all values in the left genomic dataset that do not overlap a value from the right genomic dataset are dropped. If a value from the right genomic dataset does not overlap any values in the left genomic dataset, it will be paired with a
None
in the product of the join.- genomicDataset
The right genomic dataset in the join.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right genomic dataset that did not overlap a key in the left genomic dataset.
- Definition Classes
- GenomicDataset
-
def
rightOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[Feature], xTag: ClassTag[X], otxTag: ClassTag[(Option[Feature], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Feature], Y)]): GenericGenomicDataset[(Option[Feature], X), (Option[Feature], Y)]
Performs a sort-merge right outer join between this genomic dataset and another genomic dataset.
Performs a sort-merge right outer join between this genomic dataset and another genomic dataset.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a right outer join, all values in the left genomic dataset that do not overlap a value from the right genomic dataset are dropped. If a value from the right genomic dataset does not overlap any values in the left genomic dataset, it will be paired with a
None
in the product of the join.- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right genomic dataset that did not overlap a key in the left genomic dataset.
- Definition Classes
- GenomicDataset
-
def
rightOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Option[Feature], X), (Option[Feature], Y)]
(Java-specific) Performs a sort-merge right outer join between this genomic dataset and another genomic dataset.
(Java-specific) Performs a sort-merge right outer join between this genomic dataset and another genomic dataset.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a right outer join, all values in the left genomic dataset that do not overlap a value from the right genomic dataset are dropped. If a value from the right genomic dataset does not overlap any values in the left genomic dataset, it will be paired with a
None
in the product of the join.- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right genomic dataset that did not overlap a key in the left genomic dataset.
- Definition Classes
- GenomicDataset
-
def
rightOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Option[Feature], X), (Option[Feature], Y)]
(R-specific) Performs a sort-merge right outer join between this genomic dataset and another genomic dataset.
(R-specific) Performs a sort-merge right outer join between this genomic dataset and another genomic dataset.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a right outer join, all values in the left genomic dataset that do not overlap a value from the right genomic dataset are dropped. If a value from the right genomic dataset does not overlap any values in the left genomic dataset, it will be paired with a
None
in the product of the join.- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right genomic dataset that did not overlap a key in the left genomic dataset.
- Definition Classes
- GenomicDataset
-
def
rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Feature], xTag: ClassTag[X], otixTag: ClassTag[(Option[Feature], Iterable[X])], otsyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Feature], Seq[Y])]): GenericGenomicDataset[(Option[Feature], Iterable[X]), (Option[Feature], Seq[Y])]
Performs a sort-merge right outer join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value, if not null.
Performs a sort-merge right outer join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value, if not null.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. In the same operation, we group all values by the left item in the genomic dataset. Since this is a right outer join, all values from the right genomic dataset who did not overlap a value from the left genomic dataset are placed into a length-1 Iterable with a
None
key.- genomicDataset
The right genomic dataset in the join.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, grouped together by the value they overlapped in the left genomic dataset, and all values from the right genomic dataset that did not overlap an item in the left genomic dataset.
- Definition Classes
- GenomicDataset
-
def
rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[Feature], xTag: ClassTag[X], otixTag: ClassTag[(Option[Feature], Iterable[X])], ousyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Feature], Seq[Y])]): GenericGenomicDataset[(Option[Feature], Iterable[X]), (Option[Feature], Seq[Y])]
Performs a sort-merge right outer join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value, if not null.
Performs a sort-merge right outer join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value, if not null.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. In the same operation, we group all values by the left item in the genomic dataset. Since this is a right outer join, all values from the right genomic dataset who did not overlap a value from the left genomic dataset are placed into a length-1 Iterable with a
None
key.- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, grouped together by the value they overlapped in the left genomic dataset, and all values from the right genomic dataset that did not overlap an item in the left genomic dataset.
- Definition Classes
- GenomicDataset
-
def
rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Option[Feature], Iterable[X]), (Option[Feature], Seq[Y])]
(Java-specific) Performs a sort-merge right outer join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value, if not null.
(Java-specific) Performs a sort-merge right outer join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value, if not null.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. In the same operation, we group all values by the left item in the genomic dataset. Since this is a right outer join, all values from the right genomic dataset who did not overlap a value from the left genomic dataset are placed into a length-1 Iterable with a
None
key.- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, grouped together by the value they overlapped in the left genomic dataset, and all values from the right genomic dataset that did not overlap an item in the left genomic dataset.
- Definition Classes
- GenomicDataset
-
def
rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Option[Feature], Iterable[X]), (Option[Feature], Seq[Y])]
(R-specific) Performs a sort-merge right outer join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value, if not null.
(R-specific) Performs a sort-merge right outer join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value, if not null.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. In the same operation, we group all values by the left item in the genomic dataset. Since this is a right outer join, all values from the right genomic dataset who did not overlap a value from the left genomic dataset are placed into a length-1 Iterable with a
None
key.- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, grouped together by the value they overlapped in the left genomic dataset, and all values from the right genomic dataset that did not overlap an item in the left genomic dataset.
- Definition Classes
- GenomicDataset
-
val
samples: Seq[Sample]
The samples who have data contained in this GenomicDataset.
The samples who have data contained in this GenomicDataset.
- Definition Classes
- DatasetBoundFeatureDataset → MultisampleGenomicDataset
-
def
save(filePath: String, asSingleFile: Boolean, disableFastConcat: Boolean): Unit
Java friendly save function.
Java friendly save function. Automatically detects the output format.
Writes files ending in .bed as BED6/12, .gff3 as GFF3, .gtf/.gff as GTF/GFF2, .narrow[pP]eak as NarrowPeak, and .interval_list as IntervalList. If none of these match, we fall back to Parquet. These files are written as sharded text files.
- filePath
The location to write the output.
- asSingleFile
If false, writes file to disk as shards with one shard per partition. If true, we save the file to disk as a single file by merging the shards.
- disableFastConcat
If asSingleFile is true, disables the use of the fast file concatenation engine.
- Definition Classes
- FeatureDataset
-
def
saveAsBed(fileName: String, asSingleFile: Boolean = false, disableFastConcat: Boolean = false): Unit
Save this FeatureDataset in bedtools2 BED format, where score is formatted as double floating point values with missing values.
Save this FeatureDataset in bedtools2 BED format, where score is formatted as double floating point values with missing values.
- fileName
The path to save BED formatted text file(s) to.
- asSingleFile
By default (false), writes file to disk as shards with one shard per partition. If true, we save the file to disk as a single file by merging the shards.
- disableFastConcat
If asSingleFile is true, disables the use of the parallel file merging engine.
- Definition Classes
- FeatureDataset
-
def
saveAsGff3(fileName: String, asSingleFile: Boolean = false, disableFastConcat: Boolean = false): Unit
Save this FeatureDataset in GFF3 format.
Save this FeatureDataset in GFF3 format.
- fileName
The path to save GFF3 formatted text file(s) to.
- asSingleFile
By default (false), writes file to disk as shards with one shard per partition. If true, we save the file to disk as a single file by merging the shards.
- disableFastConcat
If asSingleFile is true, disables the use of the parallel file merging engine.
- Definition Classes
- FeatureDataset
-
def
saveAsGtf(fileName: String, asSingleFile: Boolean = false, disableFastConcat: Boolean = false): Unit
Save this FeatureDataset in GTF format.
Save this FeatureDataset in GTF format.
- fileName
The path to save GTF formatted text file(s) to.
- asSingleFile
By default (false), writes file to disk as shards with one shard per partition. If true, we save the file to disk as a single file by merging the shards.
- disableFastConcat
If asSingleFile is true, disables the use of the parallel file merging engine.
- Definition Classes
- FeatureDataset
-
def
saveAsIntervalList(fileName: String, asSingleFile: Boolean = false, disableFastConcat: Boolean = false): Unit
Save this FeatureDataset in interval list format.
Save this FeatureDataset in interval list format.
- fileName
The path to save interval list formatted text file(s) to.
- asSingleFile
By default (false), writes file to disk as shards with one shard per partition. If true, we save the file to disk as a single file by merging the shards.
- disableFastConcat
If asSingleFile is true, disables the use of the parallel file merging engine.
- Definition Classes
- FeatureDataset
-
def
saveAsNarrowPeak(fileName: String, asSingleFile: Boolean = false, disableFastConcat: Boolean = false): Unit
Save this FeatureDataset in NarrowPeak format.
Save this FeatureDataset in NarrowPeak format.
- fileName
The path to save NarrowPeak formatted text file(s) to.
- asSingleFile
By default (false), writes file to disk as shards with one shard per partition. If true, we save the file to disk as a single file by merging the shards.
- disableFastConcat
If asSingleFile is true, disables the use of the parallel file merging engine.
- Definition Classes
- FeatureDataset
-
def
saveAsParquet(filePath: String, blockSize: Int = 128 * 1024 * 1024, pageSize: Int = 1 * 1024 * 1024, compressionCodec: CompressionCodecName = CompressionCodecName.GZIP, disableDictionaryEncoding: Boolean = false): Unit
Saves this genomic dataset to disk as a Parquet file.
Saves this genomic dataset to disk as a Parquet file.
- blockSize
Size per block.
- pageSize
Size per page.
- compressionCodec
Name of the compression codec to use.
- disableDictionaryEncoding
Whether or not to disable bit-packing. Default is false.
- Definition Classes
- DatasetBoundFeatureDataset → AvroGenomicDataset → GenomicDataset
-
def
saveAsParquet(pathName: String): Unit
Saves this genomic dataset to disk as a Parquet file.
Saves this genomic dataset to disk as a Parquet file.
- pathName
Path to save the file at.
- Definition Classes
- AvroGenomicDataset
-
def
saveAsParquet(pathName: String, blockSize: Integer, pageSize: Integer, compressionCodec: CompressionCodecName, disableDictionaryEncoding: Boolean): Unit
(Java-specific) Saves this genomic dataset to disk as a Parquet file.
(Java-specific) Saves this genomic dataset to disk as a Parquet file.
- pathName
Path to save the file at.
- blockSize
The size in bytes of blocks to write.
- pageSize
The size in bytes of pages to write.
- compressionCodec
The compression codec to apply to pages.
- disableDictionaryEncoding
If false, dictionary encoding is used. If true, delta encoding is used.
- Definition Classes
- AvroGenomicDataset
-
def
saveAsParquet(args: SaveArgs): Unit
Saves a genomic dataset to Parquet.
Saves a genomic dataset to Parquet.
- args
The output format configuration to use when saving the data.
- Definition Classes
- GenomicDataset
-
def
saveAsPartitionedParquet(pathName: String, compressionCodec: CompressionCodecName = CompressionCodecName.GZIP, partitionSize: Int = 1000000): Unit
Saves this RDD to disk in range binned partitioned Parquet format.
Saves this RDD to disk in range binned partitioned Parquet format.
- pathName
The path to save the partitioned Parquet file to.
- compressionCodec
Name of the compression codec to use.
- partitionSize
Size of partitions used when writing Parquet, in base pairs (bp). Defaults to 1,000,000 bp.
- Definition Classes
- GenomicDataset
-
def
saveAsUcscBed(fileName: String, asSingleFile: Boolean = false, disableFastConcat: Boolean = false, minimumScore: Double, maximumScore: Double, missingValue: Int = 0): Unit
Save this FeatureDataset in UCSC BED format, where score is formatted as integer values between 0 and 1000, with missing value as specified.
Save this FeatureDataset in UCSC BED format, where score is formatted as integer values between 0 and 1000, with missing value as specified.
- fileName
The path to save BED formatted text file(s) to.
- asSingleFile
By default (false), writes file to disk as shards with one shard per partition. If true, we save the file to disk as a single file by merging the shards.
- disableFastConcat
If asSingleFile is true, disables the use of the parallel file merging engine.
- minimumScore
Minimum score, interpolated to 0.
- maximumScore
Maximum score, interpolated to 1000.
- missingValue
Value to use if score is not specified. Defaults to 0.
- Definition Classes
- FeatureDataset
-
def
saveAvro[U <: SpecificRecordBase](pathName: String, sc: SparkContext, schema: Schema, avro: Seq[U])(implicit tUag: ClassTag[U]): Unit
Saves Avro data to a Hadoop file system.
Saves Avro data to a Hadoop file system.
This method uses a SparkContext to identify our underlying file system, which we then save to.
Frustratingly enough, although all records generated by the Avro IDL compiler have a static SCHEMA$ field, this field does not belong to the SpecificRecordBase abstract class, or the SpecificRecord interface. As such, we must force the user to pass in the schema.
- U
The type of the specific record we are saving.
- pathName
Path to save records to.
- sc
SparkContext used for identifying underlying file system.
- schema
Schema of records we are saving.
- avro
Seq of records we are saving.
- Attributes
- protected
- Definition Classes
- GenomicDataset
-
def
saveMetadata(pathName: String): Unit
Saves metadata for a FeatureDataset, including partition map, sequences, and samples.
Saves metadata for a FeatureDataset, including partition map, sequences, and samples.
- pathName
The path name to save meta data for this FeatureDataset.
- Attributes
- protected
- Definition Classes
- FeatureDataset → AvroGenomicDataset → GenomicDataset
-
def
savePartitionMap(pathName: String): Unit
Save the partition map to disk.
Save the partition map to disk. This is done by adding the partition map to the schema.
- pathName
The filepath where we will save the partition map.
- Attributes
- protected
- Definition Classes
- AvroGenomicDataset
-
def
saveRddAsParquet(pathName: String, blockSize: Int = 128 * 1024 * 1024, pageSize: Int = 1 * 1024 * 1024, compressionCodec: CompressionCodecName = CompressionCodecName.GZIP, disableDictionaryEncoding: Boolean = false, optSchema: Option[Schema] = None): Unit
Saves a genomic dataset of Avro data to Parquet.
Saves a genomic dataset of Avro data to Parquet.
- pathName
The path to save the file to.
- blockSize
The size in bytes of blocks to write. Defaults to 128 * 1024 * 1024.
- pageSize
The size in bytes of pages to write. Defaults to 1 * 1024 * 1024.
- compressionCodec
The compression codec to apply to pages. Defaults to CompressionCodecName.GZIP.
- disableDictionaryEncoding
If false, dictionary encoding is used. If true, delta encoding is used. Defaults to false.
- optSchema
The optional schema to set. Defaults to None.
- Attributes
- protected
- Definition Classes
- AvroGenomicDataset
-
def
saveRddAsParquet(args: SaveArgs): Unit
- Attributes
- protected
- Definition Classes
- AvroGenomicDataset
-
def
saveReferences(pathName: String): Unit
Save the reference sequence dictionary to disk.
Save the reference sequence dictionary to disk.
- pathName
The path to save the reference sequence dictionary to.
- Attributes
- protected
- Definition Classes
- GenomicDataset
-
def
saveSamples(pathName: String): Unit
Save the samples to disk.
Save the samples to disk.
- pathName
The path to save samples to.
- Attributes
- protected
- Definition Classes
- MultisampleGenomicDataset
-
def
shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Feature], xTag: ClassTag[X], txTag: ClassTag[(Feature, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(Feature, Y)]): GenericGenomicDataset[(Feature, X), (Feature, Y)]
Performs a sort-merge inner join between this genomic dataset and another genomic dataset.
Performs a sort-merge inner join between this genomic dataset and another genomic dataset.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other genomic dataset are dropped.
- genomicDataset
The right genomic dataset in the join.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
- Definition Classes
- GenomicDataset
-
def
shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[Feature], xTag: ClassTag[X], txTag: ClassTag[(Feature, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(Feature, Y)]): GenericGenomicDataset[(Feature, X), (Feature, Y)]
Performs a sort-merge inner join between this genomic dataset and another genomic dataset.
Performs a sort-merge inner join between this genomic dataset and another genomic dataset.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other genomic dataset are dropped.
- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
- Definition Classes
- GenomicDataset
-
def
shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Feature, X), (Feature, Y)]
(Java-specific) Performs a sort-merge inner join between this genomic dataset and another genomic dataset.
(Java-specific) Performs a sort-merge inner join between this genomic dataset and another genomic dataset.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other genomic dataset are dropped.
- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
- Definition Classes
- GenomicDataset
-
def
shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Feature, X), (Feature, Y)]
(R-specific) Performs a sort-merge inner join between this genomic dataset and another genomic dataset.
(R-specific) Performs a sort-merge inner join between this genomic dataset and another genomic dataset.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other genomic dataset are dropped.
- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
- Definition Classes
- GenomicDataset
-
def
shuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Feature], xTag: ClassTag[X], tixTag: ClassTag[(Feature, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(Feature, Seq[Y])]): GenericGenomicDataset[(Feature, Iterable[X]), (Feature, Seq[Y])]
Performs a sort-merge inner join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value.
Performs a sort-merge inner join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other genomic dataset are dropped. In the same operation, we group all values by the left item in the genomic dataset.
- genomicDataset
The right genomic dataset in the join.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, grouped together by the value they overlapped in the left genomic dataset.
- Definition Classes
- GenomicDataset
-
def
shuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[Feature], xTag: ClassTag[X], tixTag: ClassTag[(Feature, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(Feature, Seq[Y])]): GenericGenomicDataset[(Feature, Iterable[X]), (Feature, Seq[Y])]
Performs a sort-merge inner join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value.
Performs a sort-merge inner join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other genomic dataset are dropped. In the same operation, we group all values by the left item in the genomic dataset.
- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, grouped together by the value they overlapped in the left genomic dataset.
- Definition Classes
- GenomicDataset
-
def
shuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Feature, Iterable[X]), (Feature, Seq[Y])]
(Java-specific) Performs a sort-merge inner join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value.
(Java-specific) Performs a sort-merge inner join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. In the same operation, we group all values by the left item in the genomic dataset.
- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, grouped together by the value they overlapped in the left genomic dataset.
- Definition Classes
- GenomicDataset
-
def
shuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Feature, Iterable[X]), (Feature, Seq[Y])]
(R-specific) Performs a sort-merge inner join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value.
(R-specific) Performs a sort-merge inner join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. In the same operation, we group all values by the left item in the genomic dataset.
- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, grouped together by the value they overlapped in the left genomic dataset.
- Definition Classes
- GenomicDataset
-
def
sort(partitions: Int = rdd.partitions.length, stringency: ValidationStringency = ValidationStringency.STRICT)(implicit tTag: ClassTag[Feature]): FeatureDataset
Sorts our genome aligned data by reference positions, with references ordered by index.
Sorts our genome aligned data by reference positions, with references ordered by index.
- partitions
The number of partitions for the new genomic dataset.
- stringency
The level of ValidationStringency to enforce.
- returns
Returns a new genomic dataset containing sorted data.
- Definition Classes
- GenomicDataset
- Note
Uses ValidationStringency to handle unaligned or where objects align to multiple positions.
- See also
sortLexicographically
-
def
sort(): FeatureDataset
Sorts our genome aligned data by reference positions, with references ordered by index.
Sorts our genome aligned data by reference positions, with references ordered by index.
- returns
Returns a new genomic dataset containing sorted data.
- Definition Classes
- GenomicDataset
- See also
sortLexicographically
-
def
sortByReference(ascending: Boolean = true, numPartitions: Int = rdd.partitions.length): FeatureDataset
Sorts the RDD by the reference ordering.
Sorts the RDD by the reference ordering.
- ascending
Whether to sort in ascending order or not.
- numPartitions
The number of partitions to have after sorting. Defaults to the partition count of the underlying RDD.
- Definition Classes
- FeatureDataset
-
def
sortLexicographically(partitions: Int = rdd.partitions.length, storePartitionMap: Boolean = false, storageLevel: StorageLevel = StorageLevel.MEMORY_ONLY, stringency: ValidationStringency = ValidationStringency.STRICT)(implicit tTag: ClassTag[Feature]): FeatureDataset
Sorts our genome aligned data by reference positions, with references ordered lexicographically.
Sorts our genome aligned data by reference positions, with references ordered lexicographically.
- partitions
The number of partitions for the new genomic dataset.
- storePartitionMap
A Boolean flag to determine whether to store the partition bounds from the resulting genomic dataset.
- storageLevel
The level at which to persist the resulting genomic dataset.
- stringency
The level of ValidationStringency to enforce.
- returns
Returns a new genomic dataset containing sorted data.
- Definition Classes
- GenomicDataset
- Note
Uses ValidationStringency to handle data that is unaligned or where objects align to multiple positions.
- See also
sort
-
def
sortLexicographically(): FeatureDataset
Sorts our genome aligned data by reference positions, with references ordered lexicographically.
Sorts our genome aligned data by reference positions, with references ordered lexicographically.
- returns
Returns a new genomic dataset containing sorted data.
- Definition Classes
- GenomicDataset
- See also
sort
-
lazy val
spark: SparkSession
- Definition Classes
- GenomicDataset
- Annotations
- @transient()
-
final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
- AnyRef
-
def
toCoverage(): CoverageDataset
Converts the FeatureDataset to a CoverageDataset.
Converts the FeatureDataset to a CoverageDataset.
- returns
Genomic dataset containing Coverage records.
- Definition Classes
- DatasetBoundFeatureDataset → FeatureDataset
-
def
toDF(): DataFrame
- returns
These data as a Spark SQL DataFrame.
- Definition Classes
- GenomicDataset
-
def
toString(): String
- Definition Classes
- MultisampleGenomicDataset → GenomicDataset → AnyRef → Any
-
def
trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
def
trace(msg: ⇒ Any, t: ⇒ Throwable): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
def
trace(msg: ⇒ Any): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
def
transform(tFn: Function[JavaRDD[Feature], JavaRDD[Feature]]): FeatureDataset
(Java-specific) Applies a function that transforms the underlying RDD into a new RDD.
(Java-specific) Applies a function that transforms the underlying RDD into a new RDD.
- tFn
A function that transforms the underlying RDD.
- returns
A new genomic dataset where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.
- Definition Classes
- GenomicDataset
-
def
transform(tFn: (RDD[Feature]) ⇒ RDD[Feature]): FeatureDataset
(Scala-specific) Applies a function that transforms the underlying RDD into a new RDD.
(Scala-specific) Applies a function that transforms the underlying RDD into a new RDD.
- tFn
A function that transforms the underlying RDD.
- returns
A new genomic dataset where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.
- Definition Classes
- GenomicDataset
-
def
transformDataFrame(tFn: Function[DataFrame, DataFrame]): FeatureDataset
(Java-specific) Applies a function that transforms the underlying DataFrame into a new DataFrame using the Spark SQL API.
(Java-specific) Applies a function that transforms the underlying DataFrame into a new DataFrame using the Spark SQL API.
- tFn
A function that transforms the underlying DataFrame as a DataFrame.
- returns
A new genomic dataset where the DataFrame of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.
- Definition Classes
- GenomicDataset
-
def
transformDataFrame(tFn: (DataFrame) ⇒ DataFrame)(implicit uTag: scala.reflect.api.JavaUniverse.TypeTag[Feature]): FeatureDataset
(Scala-specific) Applies a function that transforms the underlying DataFrame into a new DataFrame using the Spark SQL API.
(Scala-specific) Applies a function that transforms the underlying DataFrame into a new DataFrame using the Spark SQL API.
- tFn
A function that transforms the underlying data as a DataFrame.
- returns
A new genomic dataset where the DataFrame of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.
- Definition Classes
- GenomicDataset
-
def
transformDataset(tFn: Function[Dataset[Feature], Dataset[Feature]]): FeatureDataset
(Java-specific) Applies a function that transforms the underlying Dataset into a new Dataset using the Spark SQL API.
(Java-specific) Applies a function that transforms the underlying Dataset into a new Dataset using the Spark SQL API.
- tFn
A function that transforms the underlying Dataset as a Dataset.
- returns
A new genomic dataset where the Dataset of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.
- Definition Classes
- DatasetBoundFeatureDataset → FeatureDataset → GenomicDataset
-
def
transformDataset(tFn: (Dataset[Feature]) ⇒ Dataset[Feature]): FeatureDataset
(Scala-specific) Applies a function that transforms the underlying Dataset into a new Dataset using the Spark SQL API.
(Scala-specific) Applies a function that transforms the underlying Dataset into a new Dataset using the Spark SQL API.
- tFn
A function that transforms the underlying Dataset as a Dataset.
- returns
A new genomic dataset where the Dataset of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.
- Definition Classes
- DatasetBoundFeatureDataset → FeatureDataset → GenomicDataset
-
def
transmute[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[JavaRDD[Feature], JavaRDD[X]], convFn: Function2[FeatureDataset, RDD[X], Z]): Z
(Java-specific) Applies a function that transmutes the underlying RDD into a new RDD of a different type.
(Java-specific) Applies a function that transmutes the underlying RDD into a new RDD of a different type.
- tFn
A function that transforms the underlying RDD.
- convFn
The conversion function used to build the final RDD.
- returns
A new genomid dataset where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.
- Definition Classes
- GenomicDataset
-
def
transmute[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: (RDD[Feature]) ⇒ RDD[X])(implicit convFn: (FeatureDataset, RDD[X]) ⇒ Z): Z
(Scala-specific) Applies a function that transmutes the underlying RDD into a new RDD of a different type.
(Scala-specific) Applies a function that transmutes the underlying RDD into a new RDD of a different type.
- tFn
A function that transforms the underlying RDD.
- returns
A new genomic dataset where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.
- Definition Classes
- GenomicDataset
-
def
transmuteDataFrame[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[DataFrame, DataFrame], convFn: GenomicDatasetConversion[Feature, Feature, FeatureDataset, X, Y, Z]): Z
(Java-specific) Applies a function that transmutes the underlying DataFrame into a new DataFrame of a different type.
(Java-specific) Applies a function that transmutes the underlying DataFrame into a new DataFrame of a different type.
- tFn
A function that transforms the underlying DataFrame.
- returns
A new genomic dataset where the DataFrame of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.
- Definition Classes
- GenomicDataset
-
def
transmuteDataFrame[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: (DataFrame) ⇒ DataFrame)(implicit yTag: scala.reflect.api.JavaUniverse.TypeTag[Y], convFn: (FeatureDataset, Dataset[Y]) ⇒ Z): Z
(Java-specific) Applies a function that transmutes the underlying DataFrame into a new DataFrame of a different type.
(Java-specific) Applies a function that transmutes the underlying DataFrame into a new DataFrame of a different type.
- tFn
A function that transforms the underlying DataFrame.
- returns
A new genomic dataset where the DataFrame of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.
- Definition Classes
- GenomicDataset
-
def
transmuteDataset[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[Dataset[Feature], Dataset[Y]], convFn: GenomicDatasetConversion[Feature, Feature, FeatureDataset, X, Y, Z]): Z
(Java-specific) Applies a function that transmutes the underlying Dataset into a new Dataset of a different type.
(Java-specific) Applies a function that transmutes the underlying Dataset into a new Dataset of a different type.
- tFn
A function that transforms the underlying Dataset.
- returns
A new genomic dataset where the Dataset of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.
- Definition Classes
- GenomicDataset
-
def
transmuteDataset[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: (Dataset[Feature]) ⇒ Dataset[Y])(implicit yTag: scala.reflect.api.JavaUniverse.TypeTag[Y], convFn: (FeatureDataset, Dataset[Y]) ⇒ Z): Z
(Scala-specific) Applies a function that transmutes the underlying Dataset into a new Dataset of a different type.
(Scala-specific) Applies a function that transmutes the underlying Dataset into a new Dataset of a different type.
- tFn
A function that transforms the underlying Dataset.
- returns
A new genomic dataset where the Dataset of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.
- Definition Classes
- GenomicDataset
-
val
uTag: scala.reflect.api.JavaUniverse.TypeTag[Feature]
- Definition Classes
- FeatureDataset → GenomicDataset
-
def
union(datasets: FeatureDataset*): FeatureDataset
(Scala-specific) Unions together multiple genomic datasets.
(Scala-specific) Unions together multiple genomic datasets.
- datasets
Genomic datasets to union with this genomic dataset.
- Definition Classes
- FeatureDataset → GenomicDataset
-
def
union(datasets: List[FeatureDataset]): FeatureDataset
(Java-specific) Unions together multiple genomic datasets.
(Java-specific) Unions together multiple genomic datasets.
- datasets
Genomic datasets to union with this genomic dataset.
- Definition Classes
- GenomicDataset
-
def
unpersist(): FeatureDataset
Unpersists underlying RDD from memory or disk.
Unpersists underlying RDD from memory or disk.
- returns
Uncached GenomicDataset.
- Definition Classes
- DatasetBoundGenomicDataset → GenomicDataset
-
val
unproductFn: (Feature) ⇒ Feature
- Attributes
- protected
- Definition Classes
- FeatureDataset → GenomicDataset
-
final
def
wait(): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long, arg1: Int): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... ) @native()
-
def
warn(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
def
warn(msg: ⇒ Any, t: ⇒ Throwable): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
def
warn(msg: ⇒ Any): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
def
writePartitionedParquetFlag(pathName: String, partitionSize: Int): Unit
Save partition size into the partitioned Parquet flag file.
Save partition size into the partitioned Parquet flag file.
- pathName
Path to save the file at.
- partitionSize
Partition bin size, in base pairs, used in Hive-style partitioning.
- Definition Classes
- AvroGenomicDataset → GenomicDataset
-
def
writeTextRdd[T](rdd: RDD[T], outputPath: String, asSingleFile: Boolean, disableFastConcat: Boolean, optHeaderPath: Option[String] = None): Unit
Writes an RDD to disk as text and optionally merges.
Writes an RDD to disk as text and optionally merges.
- rdd
RDD to save.
- outputPath
Output path to save text files to.
- asSingleFile
If true, combines all partition shards.
- disableFastConcat
If asSingleFile is true, disables the use of the parallel file merging engine.
- optHeaderPath
If provided, the header file to include.
- Attributes
- protected
- Definition Classes
- GenomicDataset