case class RDDBoundSliceDataset extends SliceDataset with Product with Serializable
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def
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final
def
==(arg0: Any): Boolean
- Definition Classes
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-
def
addReference(referenceToAdd: SequenceRecord): SliceDataset
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): SliceDataset
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): SliceDataset
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]): SliceDataset
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[Slice]): GenomicBroadcast[Slice, Slice, SliceDataset]
- Definition Classes
- GenomicDataset
-
def
broadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Slice], xTag: ClassTag[X], txTag: ClassTag[(Slice, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(Slice, Y)]): GenericGenomicDataset[(Slice, X), (Slice, 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[Slice], xTag: ClassTag[X], txTag: ClassTag[(Slice, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(Slice, Y)]): GenericGenomicDataset[(Slice, X), (Slice, 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[(Slice, X), (Slice, 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[(Slice, X), (Slice, 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[Slice], xTag: ClassTag[X], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(Y, Slice)]): GenericGenomicDataset[(X, Slice), (Y, Slice)]
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[Slice], xTag: ClassTag[X], syuTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Y], Slice)]): GenericGenomicDataset[(Iterable[X], Slice), (Seq[Y], Slice)]
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[Slice], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[Slice], X)], iuyTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Slice], Y)]): GenericGenomicDataset[(Iterable[Slice], X), (Seq[Slice], 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[Slice], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[Slice], X)], iuyTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Slice], Y)]): GenericGenomicDataset[(Iterable[Slice], X), (Seq[Slice], 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[Slice], X), (Seq[Slice], 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[Slice], X), (Seq[Slice], 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, Slice)])(implicit tTag: ClassTag[Slice]): IntervalArray[ReferenceRegion, Slice]
- Attributes
- protected
- Definition Classes
- SliceDataset → GenomicDataset
-
def
cache(): SliceDataset
Caches underlying RDD in memory.
-
def
clone(): AnyRef
- Attributes
- protected[lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( ... ) @native() @HotSpotIntrinsicCandidate()
-
def
countKmers(kmerLength: Integer): JavaRDD[(String, Long)]
(Java-specific) Cuts slices after flanking into _k_-mers, and then counts the number of occurrences of each _k_-mer.
(Java-specific) Cuts slices after flanking into _k_-mers, and then counts the number of occurrences of each _k_-mer.
- kmerLength
The value of _k_ to use for cutting _k_-mers.
- returns
Returns a JavaRDD containing k-mer/count pairs.
- Definition Classes
- SliceDataset
-
def
countKmers(kmerLength: Int): RDD[(String, Long)]
(Scala-specific) Cuts slices after flanking into _k_-mers, and then counts the number of occurrences of each _k_-mer.
(Scala-specific) Cuts slices after flanking into _k_-mers, and then counts the number of occurrences of each _k_-mer.
- kmerLength
The value of _k_ to use for cutting _k_-mers.
- returns
Returns an RDD containing k-mer/count pairs.
- Definition Classes
- SliceDataset
-
def
createReferences(): SliceDataset
Replace the references for this SliceDataset with those created from the slices in this SliceDataset.
Replace the references for this SliceDataset with those created from the slices in this SliceDataset.
- returns
Returns a new SliceDataset with the references replaced.
- Definition Classes
- SliceDataset
-
lazy val
dataset: Dataset[Slice]
A SQL Dataset of slices.
A SQL Dataset of slices.
- Definition Classes
- RDDBoundSliceDataset → GenomicDataset
-
def
debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
def
debug(msg: ⇒ Any, t: ⇒ Throwable): Unit
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- protected
- Definition Classes
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def
debug(msg: ⇒ Any): Unit
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final
def
eq(arg0: AnyRef): Boolean
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def
error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
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def
error(msg: ⇒ Any, t: ⇒ Throwable): Unit
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def
error(msg: ⇒ Any): Unit
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def
extract(region: ReferenceRegion): String
Extract the specified region from this genomic dataset of slices as a string, merging slices if necessary.
Extract the specified region from this genomic dataset of slices as a string, merging slices if necessary.
- region
Region to extract.
- returns
Return the specified region from this genomic dataset of slices as a string, merging slices if necessary.
- Definition Classes
- SliceDataset
-
def
extractRegions(regions: Iterable[ReferenceRegion]): RDD[(ReferenceRegion, String)]
Extract the specified regions from this genomic dataset of slices as an RDD of (ReferenceRegion, String) tuples, merging slices if necessary.
Extract the specified regions from this genomic dataset of slices as an RDD of (ReferenceRegion, String) tuples, merging slices if necessary.
- regions
Zero or more regions to extract.
- returns
Return the specified regions from this genomic dataset of slices as an RDD of (ReferenceRegion, String) tuples, merging slices if necessary.
- Definition Classes
- SliceDataset
-
def
filterByOverlappingRegion(query: ReferenceRegion): SliceDataset
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]): SliceDataset
(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
filterByOverlappingRegions(querys: Iterable[ReferenceRegion]): SliceDataset
(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
- GenomicDataset
-
def
filterToSample(sampleId: String): SliceDataset
Filter this SliceDataset by sample to those that match the specified sample.
Filter this SliceDataset by sample to those that match the specified sample.
- sampleId
Sample to filter by. return SliceDataset filtered by sample.
- Definition Classes
- SliceDataset
-
def
filterToSamples(sampleIds: Seq[String]): SliceDataset
(Scala-specific) Filter this SliceDataset by sample to those that match the specified samples.
(Scala-specific) Filter this SliceDataset by sample to those that match the specified samples.
- sampleIds
Sequence of samples to filter by. return SliceDataset filtered by one or more samples.
- Definition Classes
- SliceDataset
-
def
filterToSamples(sampleIds: List[String]): SliceDataset
(Java-specific) Filter this SliceDataset by sample to those that match the specified samples.
(Java-specific) Filter this SliceDataset by sample to those that match the specified samples.
- sampleIds
List of samples to filter by. return SliceDataset filtered by one or more samples.
- Definition Classes
- SliceDataset
-
def
flankAdjacent(flankLength: Int): SliceDataset
(Scala-specific) For all adjacent slices in this genomic dataset, we extend the slices so that the adjacent slices now overlap by _n_ bases, where _n_ is the flank length.
(Scala-specific) For all adjacent slices in this genomic dataset, we extend the slices so that the adjacent slices now overlap by _n_ bases, where _n_ is the flank length.
- flankLength
The length to extend adjacent slices by.
- returns
Returns this genomic dataset, with all adjacent slices extended with flanking sequence.
- Definition Classes
- SliceDataset
-
def
flankAdjacent(flankLength: Integer): SliceDataset
(Java-specific) For all adjacent slices in this genomic dataset, we extend the slices so that the adjacent slices now overlap by _n_ bases, where _n_ is the flank length.
(Java-specific) For all adjacent slices in this genomic dataset, we extend the slices so that the adjacent slices now overlap by _n_ bases, where _n_ is the flank length.
- flankLength
The length to extend adjacent slices by.
- returns
Returns this genomic dataset, with all adjacent slices extended with flanking sequence.
- Definition Classes
- SliceDataset
-
def
flattenRddByRegions(): RDD[(ReferenceRegion, Slice)]
- Attributes
- protected
- Definition Classes
- GenomicDataset
-
def
fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Slice], xTag: ClassTag[X], otoxTag: ClassTag[(Option[Slice], Option[X])], ouoyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Slice], Option[Y])]): GenericGenomicDataset[(Option[Slice], Option[X]), (Option[Slice], 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[Slice], xTag: ClassTag[X], otoxTag: ClassTag[(Option[Slice], Option[X])], ouoyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Slice], Option[Y])]): GenericGenomicDataset[(Option[Slice], Option[X]), (Option[Slice], 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[Slice], Option[X]), (Option[Slice], 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[Slice], Option[X]), (Option[Slice], 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() @HotSpotIntrinsicCandidate()
-
def
getReferenceRegions(slice: Slice): Seq[ReferenceRegion]
- slice
Slice to extract a region from.
- returns
Returns a reference region that covers the entirety of the slice.
- Attributes
- protected
- Definition Classes
- SliceDataset → 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
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def
info(msg: ⇒ Any): Unit
- Attributes
- protected
- Definition Classes
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def
isDebugEnabled: Boolean
- Attributes
- protected
- Definition Classes
- Logging
-
def
isErrorEnabled: Boolean
- Attributes
- protected
- Definition Classes
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-
def
isInfoEnabled: Boolean
- Attributes
- protected
- Definition Classes
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final
def
isInstanceOf[T0]: Boolean
- Definition Classes
- Any
-
def
isSorted: Boolean
- Definition Classes
- GenomicDataset
-
def
isTraceEnabled: Boolean
- Attributes
- protected
- Definition Classes
- Logging
-
def
isWarnEnabled: Boolean
- Attributes
- protected
- Definition Classes
- Logging
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lazy val
jrdd: JavaRDD[Slice]
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[Slice], xTag: ClassTag[X], toxTag: ClassTag[(Slice, Option[X])], uoyTag: scala.reflect.api.JavaUniverse.TypeTag[(Slice, Option[Y])]): GenericGenomicDataset[(Slice, Option[X]), (Slice, 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[Slice], xTag: ClassTag[X], toxTag: ClassTag[(Slice, Option[X])], uoyTag: scala.reflect.api.JavaUniverse.TypeTag[(Slice, Option[Y])]): GenericGenomicDataset[(Slice, Option[X]), (Slice, 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[(Slice, Option[X]), (Slice, 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[(Slice, Option[X]), (Slice, 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[Slice], xTag: ClassTag[X], toxTag: ClassTag[(Slice, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(Slice, Seq[Y])]): GenericGenomicDataset[(Slice, Iterable[X]), (Slice, 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[Slice], xTag: ClassTag[X], toxTag: ClassTag[(Slice, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(Slice, Seq[Y])]): GenericGenomicDataset[(Slice, Iterable[X]), (Slice, 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[(Slice, Iterable[X]), (Slice, 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[(Slice, Iterable[X]), (Slice, 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
-
def
merge(): SequenceDataset
Merge slices into sequences.
Merge slices into sequences.
- returns
Returns a SequenceDataset containing merged slices.
- Definition Classes
- SliceDataset
-
final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
final
def
notify(): Unit
- Definition Classes
- AnyRef
- Annotations
- @native() @HotSpotIntrinsicCandidate()
-
final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
- Annotations
- @native() @HotSpotIntrinsicCandidate()
-
val
optPartitionMap: Option[Array[Option[(ReferenceRegion, ReferenceRegion)]]]
- Definition Classes
- RDDBoundSliceDataset → GenomicDataset
-
def
persist(sl: StorageLevel): SliceDataset
Persists underlying RDD in memory or disk.
Persists underlying RDD in memory or disk.
- sl
new StorageLevel
- returns
Persisted GenomicDataset.
- Definition Classes
- GenomicDataset
-
def
pipe[X, Y <: Product, Z <: GenomicDataset[X, Y, Z], W <: InFormatter[Slice, Slice, SliceDataset, W]](cmd: List[String], files: List[String], environment: Map[String, String], flankSize: Integer, tFormatter: Class[W], xFormatter: OutFormatter[X], convFn: Function2[SliceDataset, 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[Slice, Slice, SliceDataset, W]](cmd: Seq[Any], files: Seq[Any], environment: Map[Any, Any], flankSize: Double, tFormatter: Class[W], xFormatter: OutFormatter[X], convFn: Function2[SliceDataset, 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[Slice, Slice, SliceDataset, 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[Slice, Slice, SliceDataset, W], xFormatter: OutFormatter[X], convFn: (SliceDataset, RDD[X]) ⇒ Z, tManifest: ClassTag[Slice], 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: (Slice) ⇒ Slice
- Attributes
- protected
- Definition Classes
- SliceDataset → GenomicDataset
-
val
rdd: RDD[Slice]
The RDD of genomic data that we are wrapping.
The RDD of genomic data that we are wrapping.
- Definition Classes
- RDDBoundSliceDataset → 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
- RDDBoundSliceDataset → GenomicDataset
-
def
replaceRdd(newRdd: RDD[Slice], newPartitionMap: Option[Array[Option[(ReferenceRegion, ReferenceRegion)]]] = None): SliceDataset
- newRdd
The RDD to replace the underlying RDD with.
- newPartitionMap
New partition map, if any.
- returns
Returns a new SliceDataset with the underlying RDD replaced.
- Attributes
- protected
- Definition Classes
- SliceDataset → GenomicDataset
-
def
replaceReferences(newReferences: SequenceDictionary): SliceDataset
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
- RDDBoundSliceDataset → GenomicDataset
-
def
replaceSamples(newSamples: Iterable[Sample]): SliceDataset
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
- RDDBoundSliceDataset → MultisampleGenomicDataset
-
def
rightOuterBroadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Slice], xTag: ClassTag[X], otxTag: ClassTag[(Option[Slice], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Slice], Y)]): GenericGenomicDataset[(Option[Slice], X), (Option[Slice], 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[Slice], xTag: ClassTag[X], otxTag: ClassTag[(Option[Slice], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Slice], Y)]): GenericGenomicDataset[(Option[Slice], X), (Option[Slice], 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[Slice], X), (Option[Slice], 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[Slice], X), (Option[Slice], 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[Slice], xTag: ClassTag[X], oyuTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Y], Slice)]): GenericGenomicDataset[(Option[X], Slice), (Option[Y], Slice)]
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[Slice], xTag: ClassTag[X], syuTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Y], Slice)]): GenericGenomicDataset[(Iterable[X], Slice), (Seq[Y], Slice)]
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[Slice], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[Slice], X)], iuyTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Slice], Y)]): GenericGenomicDataset[(Iterable[Slice], X), (Seq[Slice], 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[Slice], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[Slice], X)], iuyTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Slice], Y)]): GenericGenomicDataset[(Iterable[Slice], X), (Seq[Slice], 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[Slice], X), (Seq[Slice], 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[Slice], X), (Seq[Slice], 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[Slice], xTag: ClassTag[X], otxTag: ClassTag[(Option[Slice], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Slice], Y)]): GenericGenomicDataset[(Option[Slice], X), (Option[Slice], 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[Slice], xTag: ClassTag[X], otxTag: ClassTag[(Option[Slice], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Slice], Y)]): GenericGenomicDataset[(Option[Slice], X), (Option[Slice], 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[Slice], X), (Option[Slice], 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[Slice], X), (Option[Slice], 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[Slice], xTag: ClassTag[X], otixTag: ClassTag[(Option[Slice], Iterable[X])], otsyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Slice], Seq[Y])]): GenericGenomicDataset[(Option[Slice], Iterable[X]), (Option[Slice], 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[Slice], xTag: ClassTag[X], otixTag: ClassTag[(Option[Slice], Iterable[X])], ousyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Slice], Seq[Y])]): GenericGenomicDataset[(Option[Slice], Iterable[X]), (Option[Slice], 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[Slice], Iterable[X]), (Option[Slice], 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[Slice], Iterable[X]), (Option[Slice], 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
- RDDBoundSliceDataset → MultisampleGenomicDataset
-
def
save(filePath: String, asSingleFile: Boolean, disableFastConcat: Boolean): Unit
Save slices as Parquet or FASTA.
Save slices as Parquet or FASTA.
If filename ends in .fa or .fasta, saves as FASTA. If not, saves slices to Parquet. Defaults to 60 character line length, if saving to FASTA.
- filePath
Path to save files to.
- asSingleFile
If true, saves output as a single file.
- disableFastConcat
If asSingleFile is true, disables the use of the parallel file merging engine.
- Definition Classes
- SliceDataset
-
def
saveAsFasta(filePath: String, asSingleFile: Boolean = false, disableFastConcat: Boolean = false, lineWidth: Int = 60): Unit
Save slices in FASTA format.
Save slices in FASTA format.
The coordinate fields for this slice are appended to the description field for the FASTA description line:
>description start-slice:strand
- filePath
Path to save files to.
- asSingleFile
If true, saves output as a single file.
- disableFastConcat
If asSingleFile is true, disables the use of the parallel file merging engine.
- lineWidth
Hard wrap FASTA formatted slice at line width, default 60.
- Definition Classes
- SliceDataset
-
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(pathName: 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.
- pathName
Path to save the file at.
- 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
- AvroGenomicDataset → GenomicDataset
-
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
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
Called in saveAsParquet after saving genomic dataset to Parquet to save metadata.
Called in saveAsParquet after saving genomic dataset to Parquet to save metadata.
Writes any necessary metadata to disk. If not overridden, writes the sequence dictionary to disk as Avro.
- pathName
The filepath to the file where we will save the Metadata.
- Attributes
- protected
- Definition Classes
- SliceDataset → 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[Slice], xTag: ClassTag[X], txTag: ClassTag[(Slice, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(Slice, Y)]): GenericGenomicDataset[(Slice, X), (Slice, 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[Slice], xTag: ClassTag[X], txTag: ClassTag[(Slice, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(Slice, Y)]): GenericGenomicDataset[(Slice, X), (Slice, 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[(Slice, X), (Slice, 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[(Slice, X), (Slice, 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[Slice], xTag: ClassTag[X], tixTag: ClassTag[(Slice, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(Slice, Seq[Y])]): GenericGenomicDataset[(Slice, Iterable[X]), (Slice, 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[Slice], xTag: ClassTag[X], tixTag: ClassTag[(Slice, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(Slice, Seq[Y])]): GenericGenomicDataset[(Slice, Iterable[X]), (Slice, 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[(Slice, Iterable[X]), (Slice, 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[(Slice, Iterable[X]), (Slice, 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[Slice]): SliceDataset
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(): SliceDataset
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
sortLexicographically(partitions: Int = rdd.partitions.length, storePartitionMap: Boolean = false, storageLevel: StorageLevel = StorageLevel.MEMORY_ONLY, stringency: ValidationStringency = ValidationStringency.STRICT)(implicit tTag: ClassTag[Slice]): SliceDataset
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(): SliceDataset
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
toDF(): DataFrame
- returns
These data as a Spark SQL DataFrame.
- Definition Classes
- GenomicDataset
-
def
toReads: ReadDataset
Convert this genomic dataset of slices into reads.
Convert this genomic dataset of slices into reads.
- returns
Returns a new ReadDataset converted from this genomic dataset of slices.
- Definition Classes
- SliceDataset
-
def
toSequences: SequenceDataset
Convert this genomic dataset of slices into sequences.
Convert this genomic dataset of slices into sequences.
- returns
Returns a new SequenceDataset converted from this genomic dataset of slices.
- Definition Classes
- SliceDataset
-
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[Slice], JavaRDD[Slice]]): SliceDataset
(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[Slice]) ⇒ RDD[Slice]): SliceDataset
(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]): SliceDataset
(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[Slice]): SliceDataset
(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[Slice], Dataset[Slice]]): SliceDataset
(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
- SliceDataset → GenomicDataset
-
def
transformDataset(tFn: (Dataset[Slice]) ⇒ Dataset[Slice]): SliceDataset
(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
- SliceDataset → GenomicDataset
-
def
transmute[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[JavaRDD[Slice], JavaRDD[X]], convFn: Function2[SliceDataset, 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[Slice]) ⇒ RDD[X])(implicit convFn: (SliceDataset, 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[Slice, Slice, SliceDataset, 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: (SliceDataset, 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[Slice], Dataset[Y]], convFn: GenomicDatasetConversion[Slice, Slice, SliceDataset, 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[Slice]) ⇒ Dataset[Y])(implicit yTag: scala.reflect.api.JavaUniverse.TypeTag[Y], convFn: (SliceDataset, 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[Slice]
- Definition Classes
- SliceDataset → GenomicDataset
-
def
union(datasets: SliceDataset*): SliceDataset
(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
- SliceDataset → GenomicDataset
-
def
union(datasets: List[SliceDataset]): SliceDataset
(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(): SliceDataset
Unpersists underlying RDD from memory or disk.
Unpersists underlying RDD from memory or disk.
- returns
Uncached GenomicDataset.
- Definition Classes
- GenomicDataset
-
val
unproductFn: (Slice) ⇒ Slice
- Attributes
- protected
- Definition Classes
- SliceDataset → GenomicDataset
-
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()
-
final
def
wait(): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
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
Deprecated Value Members
-
def
finalize(): Unit
- Attributes
- protected[lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( classOf[java.lang.Throwable] ) @Deprecated
- Deprecated