sealed abstract class FragmentDataset extends AvroReadGroupGenomicDataset[Fragment, Fragment, FragmentDataset]
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- FragmentDataset
- AvroReadGroupGenomicDataset
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- GenomicDataset
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abstract
val
dataset: Dataset[Fragment]
These data as a Spark SQL Dataset.
These data as a Spark SQL Dataset.
- Definition Classes
- GenomicDataset
-
abstract
val
optPartitionMap: Option[Array[Option[(ReferenceRegion, ReferenceRegion)]]]
- Attributes
- protected
- Definition Classes
- GenomicDataset
-
abstract
val
processingSteps: Seq[ProcessingStep]
The processing steps that have been applied to this GenomicDataset.
The processing steps that have been applied to this GenomicDataset.
- Definition Classes
- GenomicDatasetWithLineage
-
abstract
val
rdd: RDD[Fragment]
The RDD of genomic data that we are wrapping.
The RDD of genomic data that we are wrapping.
- Definition Classes
- GenomicDataset
-
abstract
val
readGroups: ReadGroupDictionary
A dictionary describing the read groups attached to this GenomicDataset.
A dictionary describing the read groups attached to this GenomicDataset.
- Definition Classes
- AvroReadGroupGenomicDataset
-
abstract
def
replaceProcessingSteps(newProcessingSteps: Seq[ProcessingStep]): FragmentDataset
Replaces the processing steps attached to this genomic dataset.
Replaces the processing steps attached to this genomic dataset.
- newProcessingSteps
The new processing steps to attach to this genomic dataset.
- returns
Returns a new GenomicDataset with new processing lineage attached.
- Definition Classes
- GenomicDatasetWithLineage
-
abstract
def
replaceReadGroups(newReadGroups: ReadGroupDictionary): FragmentDataset
Replaces the read groups attached to this genomic dataset.
Replaces the read groups attached to this genomic dataset.
- newReadGroups
The new read group dictionary to attach.
- returns
Returns a new GenomicDataset with new read groups attached.
- Definition Classes
- AvroReadGroupGenomicDataset
-
abstract
def
replaceSequences(newSequences: SequenceDictionary): FragmentDataset
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
- GenomicDataset
-
abstract
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
- GenomicDataset
Concrete Value Members
-
final
def
!=(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
final
def
##(): Int
- Definition Classes
- AnyRef → Any
-
final
def
==(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
def
addProcessingStep(newProcessingStep: ProcessingStep): FragmentDataset
Merges a new processing record with the extant computational lineage.
Merges a new processing record with the extant computational lineage.
- returns
Returns a new GenomicDataset with new read groups merged in.
- Definition Classes
- GenomicDatasetWithLineage
-
def
addReadGroup(readGroupToAdd: ReadGroup): FragmentDataset
Adds a single read group to the extant read groups.
Adds a single read group to the extant read groups.
- readGroupToAdd
The read group to append to the extant read groups.
- returns
Returns a new GenomicDataset with the new read group added.
- Definition Classes
- AvroReadGroupGenomicDataset
-
def
addReadGroups(readGroupsToAdd: ReadGroupDictionary): FragmentDataset
Merges a new set of read groups with the extant read groups.
Merges a new set of read groups with the extant read groups.
- readGroupsToAdd
The read group dictionary to append to the extant read groups.
- returns
Returns a new GenomicDataset with new read groups merged in.
- Definition Classes
- AvroReadGroupGenomicDataset
-
def
addSequence(sequenceToAdd: SequenceRecord): FragmentDataset
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): FragmentDataset
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
-
final
def
asInstanceOf[T0]: T0
- Definition Classes
- Any
-
def
binQualityScores(bins: Seq[QualityScoreBin]): FragmentDataset
(Scala-specific) Rewrites the quality scores of fragments to place all quality scores in bins.
(Scala-specific) Rewrites the quality scores of fragments to place all quality scores in bins.
Quality score binning maps all quality scores to a limited number of discrete values, thus reducing the entropy of the quality score distribution, and reducing the amount of space that fragments consume on disk.
- bins
The bins to use.
- returns
Fragments whose quality scores are binned.
-
def
binQualityScores(bins: List[QualityScoreBin]): FragmentDataset
(Java-specific) Rewrites the quality scores of fragments to place all quality scores in bins.
(Java-specific) Rewrites the quality scores of fragments to place all quality scores in bins.
Quality score binning maps all quality scores to a limited number of discrete values, thus reducing the entropy of the quality score distribution, and reducing the amount of space that fragments consume on disk.
- bins
The bins to use.
- returns
Fragments whose quality scores are binned.
-
def
broadcast()(implicit tTag: ClassTag[Fragment]): GenomicBroadcast[Fragment, Fragment, FragmentDataset]
- Definition Classes
- GenomicDataset
-
def
broadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Fragment], xTag: ClassTag[X], txTag: ClassTag[(Fragment, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(Fragment, Y)]): GenericGenomicDataset[(Fragment, X), (Fragment, 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[Fragment], xTag: ClassTag[X], txTag: ClassTag[(Fragment, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(Fragment, Y)]): GenericGenomicDataset[(Fragment, X), (Fragment, 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[(Fragment, X), (Fragment, 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[(Fragment, X), (Fragment, 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[Fragment], xTag: ClassTag[X], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(Y, Fragment)]): GenericGenomicDataset[(X, Fragment), (Y, Fragment)]
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[Fragment], xTag: ClassTag[X], syuTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Y], Fragment)]): GenericGenomicDataset[(Iterable[X], Fragment), (Seq[Y], Fragment)]
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[Fragment], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[Fragment], X)], iuyTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Fragment], Y)]): GenericGenomicDataset[(Iterable[Fragment], X), (Seq[Fragment], 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[Fragment], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[Fragment], X)], iuyTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Fragment], Y)]): GenericGenomicDataset[(Iterable[Fragment], X), (Seq[Fragment], 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[Fragment], X), (Seq[Fragment], 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[Fragment], X), (Seq[Fragment], 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, Fragment)])(implicit tTag: ClassTag[Fragment]): IntervalArray[ReferenceRegion, Fragment]
- Attributes
- protected
- Definition Classes
- FragmentDataset → GenomicDataset
-
def
cache(): FragmentDataset
Caches underlying RDD in memory.
-
def
clone(): AnyRef
- Attributes
- protected[java.lang]
- Definition Classes
- AnyRef
- Annotations
- @native() @throws( ... )
-
def
debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
- Attributes
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- Definition Classes
- Logging
-
def
debug(msg: ⇒ Any, t: ⇒ Throwable): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
def
debug(msg: ⇒ Any): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
def
equals(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
def
error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
- Attributes
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- Logging
-
def
error(msg: ⇒ Any, t: ⇒ Throwable): Unit
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-
def
error(msg: ⇒ Any): Unit
- Attributes
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- Logging
-
def
filterByOverlappingRegion(query: ReferenceRegion): FragmentDataset
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]): FragmentDataset
(Java-specific) Runs a filter that selects data in the underlying RDD that overlaps several genomic regions.
(Java-specific) Runs a filter that selects data in the underlying RDD that overlaps several genomic regions.
- querys
The regions to query for.
- returns
Returns a new GenomicDataset containing only data that overlaps the querys region.
- Definition Classes
- GenomicDataset
-
def
filterByOverlappingRegions(querys: Iterable[ReferenceRegion]): FragmentDataset
(Scala-specific) Runs a filter that selects data in the underlying RDD that overlaps several genomic regions.
(Scala-specific) Runs a filter that selects data in the underlying RDD that overlaps several genomic regions.
- querys
The regions to query for.
- returns
Returns a new GenomicDataset containing only data that overlaps the querys region.
- Definition Classes
- GenomicDataset
-
def
finalize(): Unit
- Attributes
- protected[java.lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( classOf[java.lang.Throwable] )
-
def
flattenRddByRegions(): RDD[(ReferenceRegion, Fragment)]
- Attributes
- protected
- Definition Classes
- GenomicDataset
-
def
fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Fragment], xTag: ClassTag[X], otoxTag: ClassTag[(Option[Fragment], Option[X])], ouoyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Fragment], Option[Y])]): GenericGenomicDataset[(Option[Fragment], Option[X]), (Option[Fragment], 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[Fragment], xTag: ClassTag[X], otoxTag: ClassTag[(Option[Fragment], Option[X])], ouoyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Fragment], Option[Y])]): GenericGenomicDataset[(Option[Fragment], Option[X]), (Option[Fragment], 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[Fragment], Option[X]), (Option[Fragment], 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[Fragment], Option[X]), (Option[Fragment], 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: Fragment): Seq[ReferenceRegion]
Returns the regions that this fragment covers.
Returns the regions that this fragment covers.
Since a fragment may be chimeric or multi-mapped, we do not try to compute the hull of the underlying element.
- elem
The Fragment to get the region from.
- returns
Returns all regions covered by this fragment.
- Attributes
- protected
- Definition Classes
- FragmentDataset → GenomicDataset
-
def
hashCode(): Int
- Definition Classes
- AnyRef → Any
- Annotations
- @native()
-
def
info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
def
info(msg: ⇒ Any, t: ⇒ Throwable): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
def
info(msg: ⇒ Any): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
def
isDebugEnabled: Boolean
- Attributes
- protected
- Definition Classes
- Logging
-
def
isErrorEnabled: Boolean
- Attributes
- protected
- Definition Classes
- Logging
-
def
isInfoEnabled: Boolean
- Attributes
- protected
- Definition Classes
- Logging
-
final
def
isInstanceOf[T0]: Boolean
- Definition Classes
- Any
-
def
isSorted: Boolean
- Definition Classes
- GenomicDataset
-
def
isTraceEnabled: Boolean
- Attributes
- protected
- Definition Classes
- Logging
-
def
isWarnEnabled: Boolean
- Attributes
- protected
- Definition Classes
- Logging
-
lazy val
jrdd: JavaRDD[Fragment]
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[Fragment], xTag: ClassTag[X], toxTag: ClassTag[(Fragment, Option[X])], uoyTag: scala.reflect.api.JavaUniverse.TypeTag[(Fragment, Option[Y])]): GenericGenomicDataset[(Fragment, Option[X]), (Fragment, 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[Fragment], xTag: ClassTag[X], toxTag: ClassTag[(Fragment, Option[X])], uoyTag: scala.reflect.api.JavaUniverse.TypeTag[(Fragment, Option[Y])]): GenericGenomicDataset[(Fragment, Option[X]), (Fragment, 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[(Fragment, Option[X]), (Fragment, 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[(Fragment, Option[X]), (Fragment, 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[Fragment], xTag: ClassTag[X], toxTag: ClassTag[(Fragment, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(Fragment, Seq[Y])]): GenericGenomicDataset[(Fragment, Iterable[X]), (Fragment, 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[Fragment], xTag: ClassTag[X], toxTag: ClassTag[(Fragment, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(Fragment, Seq[Y])]): GenericGenomicDataset[(Fragment, Iterable[X]), (Fragment, 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[(Fragment, Iterable[X]), (Fragment, 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[(Fragment, Iterable[X]), (Fragment, Seq[Y])]
(R-specific) Performs a sort-merge left outer join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value.
(R-specific) Performs a sort-merge left outer join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value.
In a sort-merge join, both genomic datasets are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a left outer join, all values in the right genomic dataset that do not overlap a value from the left genomic dataset are dropped. If a value from the left genomic dataset does not overlap any values in the right genomic dataset, it will be paired with an empty Iterable in the product of the join.
- genomicDataset
The right genomic dataset in the join.
- flankSize
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
- returns
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the left genomic dataset that did not overlap a key in the right genomic dataset.
- Definition Classes
- GenomicDataset
-
def
logger: Logger
- Attributes
- protected
- Definition Classes
- Logging
-
def
loggerName: String
- Attributes
- protected
- Definition Classes
- Logging
-
def
markDuplicates(): FragmentDataset
Marks reads as possible fragment duplicates.
Marks reads as possible fragment duplicates.
- returns
A new genomic dataset where reads have the duplicate read flag set. Duplicate reads are NOT filtered out.
-
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()
-
def
persist(sl: StorageLevel): FragmentDataset
Persists underlying RDD in memory or disk.
Persists underlying RDD in memory or disk.
- sl
new StorageLevel
- returns
Persisted GenomicDataset.
- Definition Classes
- GenomicDataset
-
def
pipe[X, Y <: Product, Z <: GenomicDataset[X, Y, Z], W <: InFormatter[Fragment, Fragment, FragmentDataset, W]](cmd: List[String], files: List[String], environment: Map[String, String], flankSize: Integer, tFormatter: Class[W], xFormatter: OutFormatter[X], convFn: Function2[FragmentDataset, 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[Fragment, Fragment, FragmentDataset, W]](cmd: Seq[Any], files: Seq[Any], environment: Map[Any, Any], flankSize: Double, tFormatter: Class[W], xFormatter: OutFormatter[X], convFn: Function2[FragmentDataset, 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[Fragment, Fragment, FragmentDataset, 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[Fragment, Fragment, FragmentDataset, W], xFormatter: OutFormatter[X], convFn: (FragmentDataset, RDD[X]) ⇒ Z, tManifest: ClassTag[Fragment], 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: (Fragment) ⇒ Fragment
- Attributes
- protected
- Definition Classes
- FragmentDataset → GenomicDataset
-
def
replaceRdd(newRdd: RDD[Fragment], newPartitionMap: Option[Array[Option[(ReferenceRegion, ReferenceRegion)]]] = None): FragmentDataset
Replaces the underlying RDD with a new RDD.
Replaces the underlying RDD with a new RDD.
- newRdd
The RDD to replace our underlying RDD with.
- returns
Returns a new FragmentDataset where the underlying RDD has been swapped out.
- Attributes
- protected
- Definition Classes
- FragmentDataset → GenomicDataset
-
def
rightOuterBroadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Fragment], xTag: ClassTag[X], otxTag: ClassTag[(Option[Fragment], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Fragment], Y)]): GenericGenomicDataset[(Option[Fragment], X), (Option[Fragment], 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[Fragment], xTag: ClassTag[X], otxTag: ClassTag[(Option[Fragment], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Fragment], Y)]): GenericGenomicDataset[(Option[Fragment], X), (Option[Fragment], 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[Fragment], X), (Option[Fragment], 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[Fragment], X), (Option[Fragment], 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[Fragment], xTag: ClassTag[X], oyuTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Y], Fragment)]): GenericGenomicDataset[(Option[X], Fragment), (Option[Y], Fragment)]
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[Fragment], xTag: ClassTag[X], syuTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Y], Fragment)]): GenericGenomicDataset[(Iterable[X], Fragment), (Seq[Y], Fragment)]
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[Fragment], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[Fragment], X)], iuyTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Fragment], Y)]): GenericGenomicDataset[(Iterable[Fragment], X), (Seq[Fragment], 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[Fragment], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[Fragment], X)], iuyTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Fragment], Y)]): GenericGenomicDataset[(Iterable[Fragment], X), (Seq[Fragment], 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[Fragment], X), (Seq[Fragment], 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[Fragment], X), (Seq[Fragment], 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[Fragment], xTag: ClassTag[X], otxTag: ClassTag[(Option[Fragment], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Fragment], Y)]): GenericGenomicDataset[(Option[Fragment], X), (Option[Fragment], 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[Fragment], xTag: ClassTag[X], otxTag: ClassTag[(Option[Fragment], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Fragment], Y)]): GenericGenomicDataset[(Option[Fragment], X), (Option[Fragment], 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[Fragment], X), (Option[Fragment], 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[Fragment], X), (Option[Fragment], 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[Fragment], xTag: ClassTag[X], otixTag: ClassTag[(Option[Fragment], Iterable[X])], otsyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Fragment], Seq[Y])]): GenericGenomicDataset[(Option[Fragment], Iterable[X]), (Option[Fragment], 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[Fragment], xTag: ClassTag[X], otixTag: ClassTag[(Option[Fragment], Iterable[X])], ousyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Fragment], Seq[Y])]): GenericGenomicDataset[(Option[Fragment], Iterable[X]), (Option[Fragment], 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[Fragment], Iterable[X]), (Option[Fragment], 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[Fragment], Iterable[X]), (Option[Fragment], 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
-
def
save(filePath: String): Unit
Saves Fragments to Parquet.
Saves Fragments to Parquet.
- filePath
Path to save fragments at.
-
def
saveAsParquet(pathName: String): Unit
Saves this genomic dataset to disk as a Parquet file.
Saves this genomic dataset to disk as a Parquet file.
- pathName
Path to save the file at.
- Definition Classes
- AvroGenomicDataset
-
def
saveAsParquet(pathName: String, blockSize: Integer, pageSize: Integer, compressionCodec: CompressionCodecName, disableDictionaryEncoding: Boolean): Unit
(Java-specific) Saves this genomic dataset to disk as a Parquet file.
(Java-specific) Saves this genomic dataset to disk as a Parquet file.
- pathName
Path to save the file at.
- blockSize
The size in bytes of blocks to write.
- pageSize
The size in bytes of pages to write.
- compressionCodec
The compression codec to apply to pages.
- disableDictionaryEncoding
If false, dictionary encoding is used. If true, delta encoding is used.
- Definition Classes
- AvroGenomicDataset
-
def
saveAsParquet(pathName: String, blockSize: Int = 128 * 1024 * 1024, pageSize: Int = 1 * 1024 * 1024, compressionCodec: CompressionCodecName = CompressionCodecName.GZIP, disableDictionaryEncoding: Boolean = false): Unit
Saves this genomic dataset to disk as a Parquet file.
Saves this genomic dataset to disk as a Parquet file.
- pathName
Path to save the file at.
- blockSize
Size per block.
- pageSize
Size per page.
- compressionCodec
Name of the compression codec to use.
- disableDictionaryEncoding
Whether or not to disable bit-packing. Default is false.
- Definition Classes
- AvroGenomicDataset → GenomicDataset
-
def
saveAsParquet(args: SaveArgs): Unit
Saves a genomic dataset to Parquet.
Saves a genomic dataset to Parquet.
- args
The output format configuration to use when saving the data.
- Definition Classes
- GenomicDataset
-
def
saveAsPartitionedParquet(pathName: String, compressionCodec: CompressionCodecName = CompressionCodecName.GZIP, partitionSize: Int = 1000000): Unit
Saves this RDD to disk in range binned partitioned Parquet format.
Saves this RDD to disk in range binned partitioned Parquet format.
- pathName
The path to save the partitioned Parquet file to.
- compressionCodec
Name of the compression codec to use.
- partitionSize
Size of partitions used when writing Parquet, in base pairs (bp). Defaults to 1,000,000 bp.
- Definition Classes
- GenomicDataset
-
def
saveAvro[U <: SpecificRecordBase](pathName: String, sc: SparkContext, schema: Schema, avro: Seq[U])(implicit tUag: ClassTag[U]): Unit
Saves Avro data to a Hadoop file system.
Saves Avro data to a Hadoop file system.
This method uses a SparkContext to identify our underlying file system, which we then save to.
Frustratingly enough, although all records generated by the Avro IDL compiler have a static SCHEMA$ field, this field does not belong to the SpecificRecordBase abstract class, or the SpecificRecord interface. As such, we must force the user to pass in the schema.
- U
The type of the specific record we are saving.
- pathName
Path to save records to.
- sc
SparkContext used for identifying underlying file system.
- schema
Schema of records we are saving.
- avro
Seq of records we are saving.
- Attributes
- protected
- Definition Classes
- GenomicDataset
-
def
saveMetadata(pathName: String): Unit
Called in saveAsParquet after saving genomic dataset to Parquet to save metadata.
Called in saveAsParquet after saving genomic dataset to Parquet to save metadata.
Writes any necessary metadata to disk. If not overridden, writes the sequence dictionary to disk as Avro.
- pathName
The filepath to the file where we will save the Metadata.
- Attributes
- protected
- Definition Classes
- AvroReadGroupGenomicDataset → AvroGenomicDataset → GenomicDataset
-
def
savePartitionMap(pathName: String): Unit
Save the partition map to disk.
Save the partition map to disk. This is done by adding the partition map to the schema.
- pathName
The filepath where we will save the partition map.
- Attributes
- protected
- Definition Classes
- AvroGenomicDataset
-
def
saveProcessingSteps(pathName: String): Unit
Save the processing steps to disk.
Save the processing steps to disk.
- pathName
The path to save processing steps to.
- Attributes
- protected
- Definition Classes
- AvroReadGroupGenomicDataset
-
def
saveRddAsParquet(pathName: String, blockSize: Int = 128 * 1024 * 1024, pageSize: Int = 1 * 1024 * 1024, compressionCodec: CompressionCodecName = CompressionCodecName.GZIP, disableDictionaryEncoding: Boolean = false, optSchema: Option[Schema] = None): Unit
Saves a genomic dataset of Avro data to Parquet.
Saves a genomic dataset of Avro data to Parquet.
- pathName
The path to save the file to.
- blockSize
The size in bytes of blocks to write. Defaults to 128 * 1024 * 1024.
- pageSize
The size in bytes of pages to write. Defaults to 1 * 1024 * 1024.
- compressionCodec
The compression codec to apply to pages. Defaults to CompressionCodecName.GZIP.
- disableDictionaryEncoding
If false, dictionary encoding is used. If true, delta encoding is used. Defaults to false.
- optSchema
The optional schema to set. Defaults to None.
- Attributes
- protected
- Definition Classes
- AvroGenomicDataset
-
def
saveRddAsParquet(args: SaveArgs): Unit
- Attributes
- protected
- Definition Classes
- AvroGenomicDataset
-
def
saveReadGroups(pathName: String): Unit
Save the read groups to disk.
Save the read groups to disk.
- pathName
The path to save read groups to.
- Attributes
- protected
- Definition Classes
- AvroReadGroupGenomicDataset
-
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
-
def
shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Fragment], xTag: ClassTag[X], txTag: ClassTag[(Fragment, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(Fragment, Y)]): GenericGenomicDataset[(Fragment, X), (Fragment, 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[Fragment], xTag: ClassTag[X], txTag: ClassTag[(Fragment, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(Fragment, Y)]): GenericGenomicDataset[(Fragment, X), (Fragment, 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[(Fragment, X), (Fragment, 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[(Fragment, X), (Fragment, 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[Fragment], xTag: ClassTag[X], tixTag: ClassTag[(Fragment, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(Fragment, Seq[Y])]): GenericGenomicDataset[(Fragment, Iterable[X]), (Fragment, 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[Fragment], xTag: ClassTag[X], tixTag: ClassTag[(Fragment, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(Fragment, Seq[Y])]): GenericGenomicDataset[(Fragment, Iterable[X]), (Fragment, 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[(Fragment, Iterable[X]), (Fragment, 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[(Fragment, Iterable[X]), (Fragment, 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[Fragment]): FragmentDataset
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(): FragmentDataset
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[Fragment]): FragmentDataset
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(): FragmentDataset
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
toAlignments(): AlignmentDataset
Splits up the reads in a Fragment back into alignments.
Splits up the reads in a Fragment back into alignments.
- returns
Returns this genomic dataset converted to alignments.
-
def
toDF(): DataFrame
- returns
These data as a Spark SQL DataFrame.
- Definition Classes
- GenomicDataset
-
def
toString(): String
- Definition Classes
- AvroReadGroupGenomicDataset → 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[Fragment], JavaRDD[Fragment]]): FragmentDataset
(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[Fragment]) ⇒ RDD[Fragment]): FragmentDataset
(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]): FragmentDataset
(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[Fragment]): FragmentDataset
(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[Fragment], Dataset[Fragment]]): FragmentDataset
(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
- FragmentDataset → GenomicDataset
-
def
transformDataset(tFn: (Dataset[Fragment]) ⇒ Dataset[Fragment]): FragmentDataset
(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
- FragmentDataset → GenomicDataset
-
def
transmute[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[JavaRDD[Fragment], JavaRDD[X]], convFn: Function2[FragmentDataset, 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[Fragment]) ⇒ RDD[X])(implicit convFn: (FragmentDataset, 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[Fragment, Fragment, FragmentDataset, 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: (FragmentDataset, 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[Fragment], Dataset[Y]], convFn: GenomicDatasetConversion[Fragment, Fragment, FragmentDataset, 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[Fragment]) ⇒ Dataset[Y])(implicit yTag: scala.reflect.api.JavaUniverse.TypeTag[Y], convFn: (FragmentDataset, 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[Fragment]
- Definition Classes
- FragmentDataset → GenomicDataset
-
def
union(datasets: FragmentDataset*): FragmentDataset
(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
- FragmentDataset → GenomicDataset
-
def
union(datasets: List[FragmentDataset]): FragmentDataset
(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(): FragmentDataset
Unpersists underlying RDD from memory or disk.
Unpersists underlying RDD from memory or disk.
- returns
Uncached GenomicDataset.
- Definition Classes
- GenomicDataset
-
val
unproductFn: (Fragment) ⇒ Fragment
- Attributes
- protected
- Definition Classes
- FragmentDataset → 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
writePartitionedParquetFlag(pathName: String, partitionSize: Int): Unit
Save partition size into the partitioned Parquet flag file.
Save partition size into the partitioned Parquet flag file.
- pathName
Path to save the file at.
- partitionSize
Partition bin size, in base pairs, used in Hive-style partitioning.
- Definition Classes
- AvroGenomicDataset → GenomicDataset
-
def
writeTextRdd[T](rdd: RDD[T], outputPath: String, asSingleFile: Boolean, disableFastConcat: Boolean, optHeaderPath: Option[String] = None): Unit
Writes an RDD to disk as text and optionally merges.
Writes an RDD to disk as text and optionally merges.
- rdd
RDD to save.
- outputPath
Output path to save text files to.
- asSingleFile
If true, combines all partition shards.
- disableFastConcat
If asSingleFile is true, disables the use of the parallel file merging engine.
- optHeaderPath
If provided, the header file to include.
- Attributes
- protected
- Definition Classes
- GenomicDataset