case class DatasetBoundCoverageDataset extends CoverageDataset with DatasetBoundGenomicDataset[Coverage, Coverage, CoverageDataset] with Product with Serializable
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- DatasetBoundGenomicDataset
- CoverageDataset
- MultisampleGenomicDataset
- GenomicDataset
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def
addSample(sampleToAdd: Sample): CoverageDataset
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]): CoverageDataset
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
-
def
addSequence(sequenceToAdd: SequenceRecord): CoverageDataset
Appends metadata for a single sequence to the current genomic dataset.
Appends metadata for a single sequence to the current genomic dataset.
- sequenceToAdd
The sequence to add.
- returns
Returns a new GenomicDataset with this sequence appended.
- Definition Classes
- GenomicDataset
-
def
addSequences(sequencesToAdd: SequenceDictionary): CoverageDataset
Appends sequence metadata to the current genomic dataset.
Appends sequence metadata to the current genomic dataset.
- sequencesToAdd
The new sequences to append.
- returns
Returns a new GenomicDataset with the sequences appended.
- Definition Classes
- GenomicDataset
-
def
aggregatedCoverage(bpPerBin: Int = 1): CoverageDataset
(Scala-specific) Gets coverage overlapping specified ReferenceRegion.
(Scala-specific) Gets coverage overlapping specified ReferenceRegion.
For large ReferenceRegions, base pairs per bin (bpPerBin) can be specified to bin together ReferenceRegions of equal size. The coverage of each bin is the mean coverage over all base pairs in that bin.
- bpPerBin
base pairs per bin, number of bases to combine to one bin.
- returns
Genomic dataset of Coverage Records.
- Definition Classes
- CoverageDataset
-
def
aggregatedCoverage(bpPerBin: Integer): CoverageDataset
(Java-specific) Gets coverage overlapping specified ReferenceRegion.
(Java-specific) Gets coverage overlapping specified ReferenceRegion.
For large ReferenceRegions, base pairs per bin (bpPerBin) can be specified to bin together ReferenceRegions of equal size. The coverage of each bin is the mean coverage over all base pairs in that bin.
- bpPerBin
base pairs per bin, number of bases to combine to one bin.
- returns
Genomic dataset of Coverage Records.
- Definition Classes
- CoverageDataset
-
final
def
asInstanceOf[T0]: T0
- Definition Classes
- Any
-
def
broadcast()(implicit tTag: ClassTag[Coverage]): GenomicBroadcast[Coverage, Coverage, CoverageDataset]
- Definition Classes
- GenomicDataset
-
def
broadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Coverage], xTag: ClassTag[X], txTag: ClassTag[(Coverage, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(Coverage, Y)]): GenericGenomicDataset[(Coverage, X), (Coverage, 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[Coverage], xTag: ClassTag[X], txTag: ClassTag[(Coverage, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(Coverage, Y)]): GenericGenomicDataset[(Coverage, X), (Coverage, 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[(Coverage, X), (Coverage, 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[(Coverage, X), (Coverage, 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[Coverage], xTag: ClassTag[X], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(Y, Coverage)]): GenericGenomicDataset[(X, Coverage), (Y, Coverage)]
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[Coverage], xTag: ClassTag[X], syuTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Y], Coverage)]): GenericGenomicDataset[(Iterable[X], Coverage), (Seq[Y], Coverage)]
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[Coverage], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[Coverage], X)], iuyTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Coverage], Y)]): GenericGenomicDataset[(Iterable[Coverage], X), (Seq[Coverage], 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[Coverage], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[Coverage], X)], iuyTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Coverage], Y)]): GenericGenomicDataset[(Iterable[Coverage], X), (Seq[Coverage], 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[Coverage], X), (Seq[Coverage], 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[Coverage], X), (Seq[Coverage], 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, Coverage)])(implicit tTag: ClassTag[Coverage]): IntervalArray[ReferenceRegion, Coverage]
- Attributes
- protected
- Definition Classes
- CoverageDataset → GenomicDataset
-
def
cache(): CoverageDataset
Caches underlying RDD in memory.
Caches underlying RDD in memory.
- returns
Cached GenomicDataset.
- Definition Classes
- DatasetBoundGenomicDataset → GenomicDataset
-
def
clone(): AnyRef
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- protected[java.lang]
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- @native() @throws( ... )
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def
collapse(): CoverageDataset
Merges adjacent ReferenceRegions with the same coverage value.
Merges adjacent ReferenceRegions with the same coverage value. This reduces the loss of coverage information while reducing the number of records in the RDD. For example, adjacent records Coverage("chr1", 1, 10, 3.0) and Coverage("chr1", 10, 20, 3.0) would be merged into one record Coverage("chr1", 1, 20, 3.0).
- returns
merged tuples of adjacent ReferenceRegions and coverage.
- Definition Classes
- CoverageDataset
- Note
Data must be sorted before collapse is called.
-
def
coverage(bpPerBin: Int = 1): CoverageDataset
(Scala-specific) Gets coverage overlapping specified ReferenceRegion.
(Scala-specific) Gets coverage overlapping specified ReferenceRegion.
For large ReferenceRegions, base pairs per bin (bpPerBin) can be specified to bin together ReferenceRegions of equal size. The coverage of each bin is coverage of the first base pair in that bin.
- bpPerBin
base pairs per bin, number of bases to combine to one bin.
- returns
Genomic dataset of Coverage Records.
- Definition Classes
- CoverageDataset
-
def
coverage(bpPerBin: Integer): CoverageDataset
(Java-specific) Gets coverage overlapping specified ReferenceRegion.
(Java-specific) Gets coverage overlapping specified ReferenceRegion.
For large ReferenceRegions, base pairs per bin (bpPerBin) can be specified to bin together ReferenceRegions of equal size. The coverage of each bin is coverage of the first base pair in that bin.
- bpPerBin
base pairs per bin, number of bases to combine to one bin.
- returns
Genomic dataset of Coverage Records.
- Definition Classes
- CoverageDataset
-
val
dataset: Dataset[Coverage]
These data as a Spark SQL Dataset.
These data as a Spark SQL Dataset.
- Definition Classes
- DatasetBoundCoverageDataset → GenomicDataset
-
def
debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
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def
debug(msg: ⇒ Any, t: ⇒ Throwable): Unit
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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
filterByOverlappingRegion(query: ReferenceRegion): CoverageDataset
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]): CoverageDataset
(Scala-specific) Runs a filter that selects data in the underlying RDD that overlaps several genomic regions.
(Scala-specific) Runs a filter that selects data in the underlying RDD that overlaps several genomic regions.
- querys
The regions to query for.
- returns
Returns a new GenomicDataset containing only data that overlaps the querys region.
- Definition Classes
- DatasetBoundGenomicDataset → GenomicDataset
-
def
filterByOverlappingRegions(querys: Iterable[ReferenceRegion]): CoverageDataset
(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
finalize(): Unit
- Attributes
- protected[java.lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( classOf[java.lang.Throwable] )
-
def
flatten(): CoverageDataset
Gets flattened genomic dataset of coverage, with coverage mapped to a ReferenceRegion at each base pair.
Gets flattened genomic dataset of coverage, with coverage mapped to a ReferenceRegion at each base pair.
- returns
CoverageDataset of flattened Coverage records.
- Definition Classes
- CoverageDataset
-
def
flattenRddByRegions(): RDD[(ReferenceRegion, Coverage)]
- Attributes
- protected
- Definition Classes
- GenomicDataset
-
def
fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Coverage], xTag: ClassTag[X], otoxTag: ClassTag[(Option[Coverage], Option[X])], ouoyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Coverage], Option[Y])]): GenericGenomicDataset[(Option[Coverage], Option[X]), (Option[Coverage], 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[Coverage], xTag: ClassTag[X], otoxTag: ClassTag[(Option[Coverage], Option[X])], ouoyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Coverage], Option[Y])]): GenericGenomicDataset[(Option[Coverage], Option[X]), (Option[Coverage], 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[Coverage], Option[X]), (Option[Coverage], 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[Coverage], Option[X]), (Option[Coverage], Option[Y])]
(R-specific) Performs a sort-merge full outer join between this genomic dataset and another genomic dataset.
(R-specific) Performs a sort-merge full outer join between this genomic dataset and another genomic dataset.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a full outer join, if a value from either genomic dataset does not overlap any values in the other genomic dataset, it will be paired with a
None
in the product of the join.- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, and values that did not overlap will be paired with a
None
.
- Definition Classes
- GenomicDataset
-
final
def
getClass(): Class[_]
- Definition Classes
- AnyRef → Any
- Annotations
- @native()
-
def
getReferenceRegions(elem: Coverage): Seq[ReferenceRegion]
Gets sequence of ReferenceRegions from Coverage element.
Gets sequence of ReferenceRegions from Coverage element. Since coverage maps directly to a single genomic region, this method will always return a Seq of exactly one ReferenceRegion.
- elem
The Coverage to get an underlying region for.
- returns
Sequence of ReferenceRegions extracted from Coverage.
- Attributes
- protected
- Definition Classes
- CoverageDataset → GenomicDataset
-
def
info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
- Attributes
- protected
- Definition Classes
- Logging
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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
- Logging
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def
isDebugEnabled: Boolean
- Attributes
- protected
- Definition Classes
- Logging
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def
isErrorEnabled: Boolean
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- protected
- Definition Classes
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def
isInfoEnabled: Boolean
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- protected
- Definition Classes
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final
def
isInstanceOf[T0]: Boolean
- Definition Classes
- Any
-
val
isPartitioned: Boolean
- Definition Classes
- DatasetBoundCoverageDataset → DatasetBoundGenomicDataset
-
def
isSorted: Boolean
- Definition Classes
- GenomicDataset
-
def
isTraceEnabled: Boolean
- Attributes
- protected
- Definition Classes
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def
isWarnEnabled: Boolean
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lazy val
jrdd: JavaRDD[Coverage]
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[Coverage], xTag: ClassTag[X], toxTag: ClassTag[(Coverage, Option[X])], uoyTag: scala.reflect.api.JavaUniverse.TypeTag[(Coverage, Option[Y])]): GenericGenomicDataset[(Coverage, Option[X]), (Coverage, 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[Coverage], xTag: ClassTag[X], toxTag: ClassTag[(Coverage, Option[X])], uoyTag: scala.reflect.api.JavaUniverse.TypeTag[(Coverage, Option[Y])]): GenericGenomicDataset[(Coverage, Option[X]), (Coverage, 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[(Coverage, Option[X]), (Coverage, 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[(Coverage, Option[X]), (Coverage, 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[Coverage], xTag: ClassTag[X], toxTag: ClassTag[(Coverage, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(Coverage, Seq[Y])]): GenericGenomicDataset[(Coverage, Iterable[X]), (Coverage, 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[Coverage], xTag: ClassTag[X], toxTag: ClassTag[(Coverage, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(Coverage, Seq[Y])]): GenericGenomicDataset[(Coverage, Iterable[X]), (Coverage, 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[(Coverage, Iterable[X]), (Coverage, 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[(Coverage, Iterable[X]), (Coverage, Seq[Y])]
(R-specific) Performs a sort-merge left outer join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value.
(R-specific) Performs a sort-merge left outer join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a left outer join, all values in the right genomic dataset that do not overlap a value from the left genomic dataset are dropped. If a value from the left genomic dataset does not overlap any values in the right genomic dataset, it will be paired with an empty Iterable in the product of the join.
- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the left genomic dataset that did not overlap a key in the right genomic dataset.
- Definition Classes
- GenomicDataset
-
def
logger: Logger
- Attributes
- protected
- Definition Classes
- Logging
-
def
loggerName: String
- Attributes
- protected
- Definition Classes
- Logging
-
final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
final
def
notify(): Unit
- Definition Classes
- AnyRef
- Annotations
- @native()
-
final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
- Annotations
- @native()
-
val
optLookbackPartitions: Option[Int]
- Definition Classes
- DatasetBoundCoverageDataset → DatasetBoundGenomicDataset
-
val
optPartitionBinSize: Option[Int]
- Definition Classes
- DatasetBoundCoverageDataset → DatasetBoundGenomicDataset
-
lazy val
optPartitionMap: None.type
- Attributes
- protected
- Definition Classes
- DatasetBoundCoverageDataset → GenomicDataset
-
def
persist(sl: StorageLevel): CoverageDataset
Persists underlying RDD in memory or disk.
Persists underlying RDD in memory or disk.
- sl
new StorageLevel
- returns
Persisted GenomicDataset.
- Definition Classes
- DatasetBoundGenomicDataset → GenomicDataset
-
def
pipe[X, Y <: Product, Z <: GenomicDataset[X, Y, Z], W <: InFormatter[Coverage, Coverage, CoverageDataset, W]](cmd: List[String], files: List[String], environment: Map[String, String], flankSize: Integer, tFormatter: Class[W], xFormatter: OutFormatter[X], convFn: Function2[CoverageDataset, 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[Coverage, Coverage, CoverageDataset, W]](cmd: Seq[Any], files: Seq[Any], environment: Map[Any, Any], flankSize: Double, tFormatter: Class[W], xFormatter: OutFormatter[X], convFn: Function2[CoverageDataset, 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[Coverage, Coverage, CoverageDataset, 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[Coverage, Coverage, CoverageDataset, W], xFormatter: OutFormatter[X], convFn: (CoverageDataset, RDD[X]) ⇒ Z, tManifest: ClassTag[Coverage], 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: (Coverage) ⇒ Coverage
- Attributes
- protected
- Definition Classes
- CoverageDataset → GenomicDataset
-
lazy val
rdd: RDD[Coverage]
The RDD of genomic data that we are wrapping.
The RDD of genomic data that we are wrapping.
- Definition Classes
- DatasetBoundCoverageDataset → GenomicDataset
-
def
replaceRdd(newRdd: RDD[Coverage], newPartitionMap: Option[Array[Option[(ReferenceRegion, ReferenceRegion)]]] = None): CoverageDataset
- newRdd
The RDD to replace the underlying RDD with.
- returns
Returns a new CoverageDataset with the underlying RDD replaced.
- Attributes
- protected
- Definition Classes
- CoverageDataset → GenomicDataset
-
def
replaceSamples(newSamples: Iterable[Sample]): CoverageDataset
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
- DatasetBoundCoverageDataset → MultisampleGenomicDataset
-
def
replaceSequences(newSequences: SequenceDictionary): CoverageDataset
Replaces the sequence dictionary attached to a GenomicDataset.
Replaces the sequence dictionary attached to a GenomicDataset.
- newSequences
The new sequence dictionary to attach.
- returns
Returns a new GenomicDataset with the sequences replaced.
- Definition Classes
- DatasetBoundCoverageDataset → GenomicDataset
-
def
rightOuterBroadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Coverage], xTag: ClassTag[X], otxTag: ClassTag[(Option[Coverage], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Coverage], Y)]): GenericGenomicDataset[(Option[Coverage], X), (Option[Coverage], 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[Coverage], xTag: ClassTag[X], otxTag: ClassTag[(Option[Coverage], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Coverage], Y)]): GenericGenomicDataset[(Option[Coverage], X), (Option[Coverage], 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[Coverage], X), (Option[Coverage], 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[Coverage], X), (Option[Coverage], 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[Coverage], xTag: ClassTag[X], oyuTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Y], Coverage)]): GenericGenomicDataset[(Option[X], Coverage), (Option[Y], Coverage)]
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[Coverage], xTag: ClassTag[X], syuTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Y], Coverage)]): GenericGenomicDataset[(Iterable[X], Coverage), (Seq[Y], Coverage)]
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[Coverage], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[Coverage], X)], iuyTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Coverage], Y)]): GenericGenomicDataset[(Iterable[Coverage], X), (Seq[Coverage], 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[Coverage], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[Coverage], X)], iuyTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Coverage], Y)]): GenericGenomicDataset[(Iterable[Coverage], X), (Seq[Coverage], 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[Coverage], X), (Seq[Coverage], 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[Coverage], X), (Seq[Coverage], 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[Coverage], xTag: ClassTag[X], otxTag: ClassTag[(Option[Coverage], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Coverage], Y)]): GenericGenomicDataset[(Option[Coverage], X), (Option[Coverage], 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[Coverage], xTag: ClassTag[X], otxTag: ClassTag[(Option[Coverage], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Coverage], Y)]): GenericGenomicDataset[(Option[Coverage], X), (Option[Coverage], 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[Coverage], X), (Option[Coverage], 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[Coverage], X), (Option[Coverage], 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[Coverage], xTag: ClassTag[X], otixTag: ClassTag[(Option[Coverage], Iterable[X])], otsyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Coverage], Seq[Y])]): GenericGenomicDataset[(Option[Coverage], Iterable[X]), (Option[Coverage], 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[Coverage], xTag: ClassTag[X], otixTag: ClassTag[(Option[Coverage], Iterable[X])], ousyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Coverage], Seq[Y])]): GenericGenomicDataset[(Option[Coverage], Iterable[X]), (Option[Coverage], 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[Coverage], Iterable[X]), (Option[Coverage], 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[Coverage], Iterable[X]), (Option[Coverage], 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
- DatasetBoundCoverageDataset → MultisampleGenomicDataset
-
def
save(filePath: String, asSingleFile: Boolean, disableFastConcat: Boolean): Unit
Saves coverage as feature file.
Saves coverage as feature file.
- filePath
The location to write the output.
- asSingleFile
If false, writes file to disk as shards with one shard per partition. If true, we save the file to disk as a single file by merging the shards.
- disableFastConcat
If asSingleFile is true, disables the use of the fast file concatenation engine.
- Definition Classes
- CoverageDataset
- See also
FeatureDataset.save Coverage is saved as a feature where coverage is stored in the score column and sampleId is stored in attributes, if available.
-
def
saveAsParquet(filePath: String, blockSize: Int = 128 * 1024 * 1024, pageSize: Int = 1 * 1024 * 1024, compressionCodec: CompressionCodecName = CompressionCodecName.GZIP, disableDictionaryEncoding: Boolean = false): Unit
Saves a genomic dataset to Parquet.
Saves a genomic dataset to Parquet.
- 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
- CoverageDataset → 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
Writes any necessary metadata to disk.
Writes any necessary metadata to disk. If not overridden, writes the sequence dictionary to disk as Avro.
- pathName
The path to save metadata 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
saveSequences(pathName: String): Unit
Save the sequence dictionary to disk.
Save the sequence dictionary to disk.
- pathName
The path to save the sequence dictionary to.
- Attributes
- protected
- Definition Classes
- GenomicDataset
-
val
sequences: 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
- DatasetBoundCoverageDataset → GenomicDataset
-
def
shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Coverage], xTag: ClassTag[X], txTag: ClassTag[(Coverage, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(Coverage, Y)]): GenericGenomicDataset[(Coverage, X), (Coverage, 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[Coverage], xTag: ClassTag[X], txTag: ClassTag[(Coverage, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(Coverage, Y)]): GenericGenomicDataset[(Coverage, X), (Coverage, 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[(Coverage, X), (Coverage, 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[(Coverage, X), (Coverage, 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[Coverage], xTag: ClassTag[X], tixTag: ClassTag[(Coverage, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(Coverage, Seq[Y])]): GenericGenomicDataset[(Coverage, Iterable[X]), (Coverage, 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[Coverage], xTag: ClassTag[X], tixTag: ClassTag[(Coverage, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(Coverage, Seq[Y])]): GenericGenomicDataset[(Coverage, Iterable[X]), (Coverage, 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[(Coverage, Iterable[X]), (Coverage, 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[(Coverage, Iterable[X]), (Coverage, 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[Coverage]): CoverageDataset
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(): CoverageDataset
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[Coverage]): CoverageDataset
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(): CoverageDataset
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
toFeatures(): FeatureDataset
Converts CoverageDataset to FeatureDataset.
Converts CoverageDataset to FeatureDataset.
- returns
Returns a FeatureDataset from CoverageDataset.
- Definition Classes
- DatasetBoundCoverageDataset → CoverageDataset
-
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[Coverage], JavaRDD[Coverage]]): CoverageDataset
(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[Coverage]) ⇒ RDD[Coverage]): CoverageDataset
(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]): CoverageDataset
(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[Coverage]): CoverageDataset
(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[Coverage], Dataset[Coverage]]): CoverageDataset
(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
- CoverageDataset → GenomicDataset
-
def
transformDataset(tFn: (Dataset[Coverage]) ⇒ Dataset[Coverage]): CoverageDataset
(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
- CoverageDataset → GenomicDataset
-
def
transmute[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[JavaRDD[Coverage], JavaRDD[X]], convFn: Function2[CoverageDataset, 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[Coverage]) ⇒ RDD[X])(implicit convFn: (CoverageDataset, 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[Coverage, Coverage, CoverageDataset, 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: (CoverageDataset, 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[Coverage], Dataset[Y]], convFn: GenomicDatasetConversion[Coverage, Coverage, CoverageDataset, 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[Coverage]) ⇒ Dataset[Y])(implicit yTag: scala.reflect.api.JavaUniverse.TypeTag[Y], convFn: (CoverageDataset, 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[Coverage]
- Definition Classes
- CoverageDataset → GenomicDataset
-
def
union(datasets: CoverageDataset*): CoverageDataset
(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
- CoverageDataset → GenomicDataset
-
def
union(datasets: List[CoverageDataset]): CoverageDataset
(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(): CoverageDataset
Unpersists underlying RDD from memory or disk.
Unpersists underlying RDD from memory or disk.
- returns
Uncached GenomicDataset.
- Definition Classes
- DatasetBoundGenomicDataset → GenomicDataset
-
val
unproductFn: (Coverage) ⇒ Coverage
- Attributes
- protected
- Definition Classes
- CoverageDataset → GenomicDataset
-
final
def
wait(): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long, arg1: Int): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long): Unit
- Definition Classes
- AnyRef
- Annotations
- @native() @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
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