org.bdgenomics.adam.rdd.variant
ParquetUnboundVariantDataset
Related Doc:
package variant
Adds a VCF header line describing an 'R' array format field.
Adds a VCF header line describing an 'R' array format field.
This adds a format field that is an array whose length is equal to the total number of alleles (including the reference allele) for the genotype we are annotating.
The identifier for the field.
A description of the data stored in this format field.
The type of the data stored in this format field.
A new genomic dataset with the new header line added.
Adds a VCF header line describing an 'R' array info field.
Adds a VCF header line describing an 'R' array info field.
This adds a info field that is an array whose length is equal to the total number of alleles (including the reference allele) for the genotype we are annotating.
The identifier for the field.
A description of the data stored in this info field.
The type of the data stored in this info field.
A new genomic dataset with the new header line added.
Adds a VCF header line describing an 'A' array format field.
Adds a VCF header line describing an 'A' array format field.
This adds a format field that is an array whose length is equal to the number of alternate alleles for the genotype we are annotating.
The identifier for the field.
A description of the data stored in this format field.
The type of the data stored in this format field.
A new genomic dataset with the new header line added.
Adds a VCF header line describing an 'A' array info field.
Adds a VCF header line describing an 'A' array info field.
This adds a info field that is an array whose length is equal to the number of alternate alleles for the genotype we are annotating.
The identifier for the field.
A description of the data stored in this info field.
The type of the data stored in this info field.
A new genomic dataset with the new header line added.
Adds a VCF header line describing a variant/genotype filter.
Adds a VCF header line describing a variant/genotype filter.
The identifier for the filter.
A description of the filter.
A new genomic dataset with the new header line added.
(Java-specific) Adds a VCF header line describing an array format field, with fixed count.
(Java-specific) Adds a VCF header line describing an array format field, with fixed count.
The identifier for the field.
The number of elements in the array.
The type of the data stored in this format field.
A description of the data stored in this format field.
A new genomic dataset with the new header line added.
(Scala-specific) Adds a VCF header line describing an array format field, with fixed count.
(Scala-specific) Adds a VCF header line describing an array format field, with fixed count.
The identifier for the field.
The number of elements in the array.
A description of the data stored in this format field.
The type of the data stored in this format field.
A new genomic dataset with the new header line added.
(Java-specific) Adds a VCF header line describing an array info field, with fixed count.
(Java-specific) Adds a VCF header line describing an array info field, with fixed count.
The identifier for the field.
The number of elements in the array.
The type of the data stored in this info field.
A description of the data stored in this info field.
A new genomic dataset with the new header line added.
(Scala-specific) Adds a VCF header line describing an array info field, with fixed count.
(Scala-specific) Adds a VCF header line describing an array info field, with fixed count.
The identifier for the field.
The number of elements in the array.
A description of the data stored in this info field.
The type of the data stored in this info field.
A new genomic dataset with the new header line added.
Adds a VCF header line describing an 'G' array format field.
Adds a VCF header line describing an 'G' array format field.
This adds a format field that is an array whose length is equal to the number of genotypes for the genotype we are annotating.
The identifier for the field.
A description of the data stored in this format field.
The type of the data stored in this format field.
A new genomic dataset with the new header line added.
Appends a new header line to the existing lines.
Appends a new header line to the existing lines.
A header line to add.
A new genomic dataset with the new header line added.
Appends new header lines to the existing lines.
Appends new header lines to the existing lines.
Zero or more header lines to add.
A new genomic dataset with the new header lines added.
Adds a VCF header line describing a scalar format field.
Adds a VCF header line describing a scalar format field.
The identifier for the field.
A description of the data stored in this format field.
The type of the data stored in this format field.
A new genomic dataset with the new header line added.
Adds a VCF header line describing a scalar info field.
Adds a VCF header line describing a scalar info field.
The identifier for the field.
A description of the data stored in this info field.
The type of the data stored in this info field.
A new genomic dataset with the new header line added.
Appends metadata for a single sequence to the current genomic dataset.
Appends metadata for a single sequence to the current genomic dataset.
The sequence to add.
Returns a new GenomicDataset with this sequence appended.
Appends sequence metadata to the current genomic dataset.
Appends sequence metadata to the current genomic dataset.
The new sequences to append.
Returns a new GenomicDataset with the sequences appended.
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.
The right genomic dataset in the join.
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
broadcastRegionJoinAgainst
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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
broadcastRegionJoinAgainst
(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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
(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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
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.
The data on the left side of the join.
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
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.
broadcastRegionJoin
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.
The data on the left side of the join.
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
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.
broadcastRegionJoinAndGroupByRight
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.
The right genomic dataset in the join.
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
broadcastRegionJoinAgainstAndGroupByRight
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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
broadcastRegionJoinAgainstAndGroupByRight
(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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
broadcastRegionJoinAgainstAndGroupByRight
(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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
broadcastRegionJoinAgainstAndGroupByRight
Caches underlying RDD in memory.
These data as a Spark SQL Dataset.
These data as a Spark SQL Dataset.
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.
The region to query for.
Returns a new GenomicDataset containing only data that overlaps the query region.
(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.
The regions to query for.
Returns a new GenomicDataset containing only data that overlaps the querys region.
(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.
The regions to query for.
Returns a new GenomicDataset containing only data that overlaps the querys region.
Filter this VariantDataset by quality (VCF column 6 "QUAL").
Filter this VariantDataset by quality (VCF column 6 "QUAL"). Variants split for multi-allelic sites will also be filtered out.
Minimum quality to filter by, inclusive.
VariantDataset filtered by quality.
Filter this VariantDataset by total read depth (VCF INFO reserved key AD, Number=R,
split for multi-allelic sites into single integer values for the reference allele
(filterByReferenceReadDepth) and the alternate allele (this method)).
Filter this VariantDataset by total read depth (VCF INFO reserved key AD, Number=R,
split for multi-allelic sites into single integer values for the reference allele
(filterByReferenceReadDepth) and the alternate allele (this method)).
Minimum total read depth to filter by, inclusive.
VariantDataset filtered by total read depth.
Filter this VariantDataset by reference total read depth (VCF INFO reserved key AD, Number=R,
split for multi-allelic sites into single integer values for the alternate allele
(filterByReadDepth) and the reference allele (this method)).
Filter this VariantDataset by reference total read depth (VCF INFO reserved key AD, Number=R,
split for multi-allelic sites into single integer values for the alternate allele
(filterByReadDepth) and the reference allele (this method)).
Minimum reference total read depth to filter by, inclusive.
VariantDataset filtered by reference total read depth.
Filter insertions and deletions (indels) from this VariantDataset.
Filter insertions and deletions (indels) from this VariantDataset.
VariantDataset filtered to remove insertions and deletions (indels).
Filter multiple nucleotide variants (MNPs) from this VariantDataset.
Filter multiple nucleotide variants (MNPs) from this VariantDataset.
VariantDataset filtered to remove multiple nucleotide variants (MNPs).
Filter single nucleotide variants (SNPs) from this VariantDataset.
Filter single nucleotide variants (SNPs) from this VariantDataset.
VariantDataset filtered to remove single nucleotide variants (SNPs).
Filter this VariantDataset to filters passed (VCF column 7 "FILTER" value PASS).
Filter this VariantDataset to filters passed (VCF column 7 "FILTER" value PASS).
VariantDataset filtered to filters passed.
Filter this VariantDataset to include only insertions and deletions (indels).
Filter this VariantDataset to include only insertions and deletions (indels).
VariantDataset filtered to include only insertions and deletions (indels).
Filter this VariantDataset to include only multiple nucleotide variants (MNPs).
Filter this VariantDataset to include only multiple nucleotide variants (MNPs).
VariantDataset filtered to include only multiple nucleotide variants (MNPs).
Filter this VariantDataset to include only single nucleotide variants (SNPs).
Filter this VariantDataset to include only single nucleotide variants (SNPs).
VariantDataset filtered to include only single nucleotide variants (SNPs).
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.
The right genomic dataset in the join.
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.
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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
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.
(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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
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.
(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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
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.
The variant to get a reference region for.
Returns the singular region this variant covers.
The underlying RDD of genomic data, as a JavaRDD.
The underlying RDD of genomic data, as a JavaRDD.
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.
The right genomic dataset in the join.
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.
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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
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.
(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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
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.
(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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
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.
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.
The right genomic dataset in the join.
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.
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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
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.
(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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
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.
(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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
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.
Persists underlying RDD in memory or disk.
Persists underlying RDD in memory or disk.
new StorageLevel
Persisted GenomicDataset.
(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.
The type of the record created by the piped command.
A GenomicDataset containing X's.
Command to run.
Files to make locally available to the commands being run. Default is empty.
A map containing environment variable/value pairs to set in the environment for the newly created process. Default is empty.
Number of bases to flank each command invocation by.
Class of formatter for data going into pipe command.
Formatter for data coming out of the pipe command.
The conversion function used to build the final genomic dataset.
Returns a new GenomicDataset of type Y.
(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.
The type of the record created by the piped command.
A GenomicDataset containing X's.
Command to run.
Files to make locally available to the commands being run. Default is empty.
A map containing environment variable/value pairs to set in the environment for the newly created process. Default is empty.
Number of bases to flank each command invocation by.
Class of formatter for data going into pipe command.
Formatter for data coming out of the pipe command.
The conversion function used to build the final genomic dataset.
Returns a new GenomicDataset of type Y.
(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.
The type of the record created by the piped command.
A GenomicDataset containing X's.
Command to run.
Files to make locally available to the commands being run. Default is empty.
A map containing environment variable/value pairs to set in the environment for the newly created process. Default is empty.
Number of bases to flank each command invocation by.
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 a new GenomicDataset of type Y.
The RDD of genomic data that we are wrapping.
The RDD of genomic data that we are wrapping.
Replaces the header lines attached to this genomic dataset.
Replaces the header lines attached to this genomic dataset.
The new header lines to attach to this genomic dataset.
A new genomic dataset with the header lines replaced.
An RDD to replace the underlying RDD with.
Returns a new VariantDataset with the underlying RDD replaced.
Replaces the sequence dictionary attached to a GenomicDataset.
Replaces the sequence dictionary attached to a GenomicDataset.
The new sequence dictionary to attach.
Returns a new GenomicDataset with the sequences replaced.
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.
The right genomic dataset in the join.
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.
rightOuterBroadcastRegionJoin
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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
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.
rightOuterBroadcastRegionJoin
(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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
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.
(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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
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.
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.
The data on the left side of the join.
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
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.
rightOuterBroadcastRegionJoin
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.
The data on the left side of the join.
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
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.
rightOuterBroadcastRegionJoinAndGroupByRight
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.
The right genomic dataset in the join.
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.
rightOuterBroadcastRegionJoinAgainstAndGroupByRight
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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
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.
rightOuterBroadcastRegionJoinAgainstAndGroupByRight
(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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
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.
rightOuterBroadcastRegionJoinAgainstAndGroupByRight
(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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
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.
rightOuterBroadcastRegionJoinAgainstAndGroupByRight
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.
The right genomic dataset in the join.
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.
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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
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.
(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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
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.
(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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
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.
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.
The right genomic dataset in the join.
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.
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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
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.
(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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
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.
(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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
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.
Saves this genomic dataset to disk as a Parquet file.
Saves this genomic dataset to disk as a Parquet file.
Path to save the file at.
(Java-specific) Saves this genomic dataset to disk as a Parquet file.
(Java-specific) Saves this genomic dataset to disk as a Parquet file.
Path to save the file at.
The size in bytes of blocks to write.
The size in bytes of pages to write.
The compression codec to apply to pages.
If false, dictionary encoding is used. If true, delta encoding is used.
Saves this genomic dataset to disk as a Parquet file.
Saves this genomic dataset to disk as a Parquet file.
Path to save the file at.
Size per block.
Size per page.
Name of the compression codec to use.
Whether or not to disable bit-packing. Default is false.
Saves a genomic dataset to Parquet.
Saves a genomic dataset to Parquet.
The output format configuration to use when saving the data.
Saves this RDD to disk in range binned partitioned Parquet format.
Saves this RDD to disk in range binned partitioned Parquet format.
The path to save the partitioned Parquet file to.
Name of the compression codec to use.
Size of partitions used when writing Parquet, in base pairs (bp). Defaults to 1,000,000 bp.
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.
The type of the specific record we are saving.
Path to save records to.
SparkContext used for identifying underlying file system.
Schema of records we are saving.
Seq of records we are saving.
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.
Save the partition map to disk.
Save the partition map to disk. This is done by adding the partition map to the schema.
The filepath where we will save the partition map.
Saves a genomic dataset of Avro data to Parquet.
Saves a genomic dataset of Avro data to Parquet.
The path to save the file to.
The size in bytes of blocks to write. Defaults to 128 * 1024 * 1024.
The size in bytes of pages to write. Defaults to 1 * 1024 * 1024.
The compression codec to apply to pages. Defaults to CompressionCodecName.GZIP.
If false, dictionary encoding is used. If true, delta encoding is used. Defaults to false.
The optional schema to set. Defaults to None.
Save the sequence dictionary to disk.
Save the sequence dictionary to disk.
The path to save the sequence dictionary to.
Save the VCF headers to disk.
Save the VCF headers to disk.
The filepath to the file where we will save the VCF headers.
The sequence dictionary describing the reference assembly this dataset is aligned to.
The sequence dictionary describing the reference assembly this dataset is aligned to.
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.
The right genomic dataset in the join.
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
(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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
(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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
Returns a new genomic dataset containing all pairs of keys that overlapped in the genomic coordinate space.
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.
The right genomic dataset in the join.
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.
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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
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.
(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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
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.
(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.
The right genomic dataset in the join.
Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.
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.
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.
The number of partitions for the new genomic dataset.
The level of ValidationStringency to enforce.
Returns a new genomic dataset containing sorted data.
Uses ValidationStringency to handle unaligned or where objects align to multiple positions.
sortLexicographically
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 a new genomic dataset containing sorted data.
sortLexicographically
Sorts our genome aligned data by reference positions, with references ordered lexicographically.
Sorts our genome aligned data by reference positions, with references ordered lexicographically.
The number of partitions for the new genomic dataset.
A Boolean flag to determine whether to store the partition bounds from the resulting genomic dataset.
The level at which to persist the resulting genomic dataset.
The level of ValidationStringency to enforce.
Returns a new genomic dataset containing sorted data.
Uses ValidationStringency to handle data that is unaligned or where objects align to multiple positions.
sort
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 a new genomic dataset containing sorted data.
sort
These data as a Spark SQL DataFrame.
Returns this VariantDataset as a VariantContextDataset.
(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.
A function that transforms the underlying RDD.
A new genomic dataset where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.
(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.
A function that transforms the underlying RDD.
A new genomic dataset where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.
(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.
A function that transforms the underlying DataFrame as a DataFrame.
A new genomic dataset where the DataFrame of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.
(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.
A function that transforms the underlying data as a DataFrame.
A new genomic dataset where the DataFrame of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.
(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.
A function that transforms the underlying Dataset as a Dataset.
A new genomic dataset where the Dataset of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.
(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.
A function that transforms the underlying Dataset as a Dataset.
A new genomic dataset where the Dataset of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.
(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.
A function that transforms the underlying RDD.
The conversion function used to build the final RDD.
A new genomid dataset where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.
(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.
A function that transforms the underlying RDD.
A new genomic dataset where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.
(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.
A function that transforms the underlying DataFrame.
A new genomic dataset where the DataFrame of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.
(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.
A function that transforms the underlying DataFrame.
A new genomic dataset where the DataFrame of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.
(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.
A function that transforms the underlying Dataset.
A new genomic dataset where the Dataset of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.
(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.
A function that transforms the underlying Dataset.
A new genomic dataset where the Dataset of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.
(Scala-specific) Unions together multiple genomic datasets.
(Scala-specific) Unions together multiple genomic datasets.
(Java-specific) Unions together multiple genomic datasets.
(Java-specific) Unions together multiple genomic datasets.
Genomic datasets to union with this genomic dataset.
Unpersists underlying RDD from memory or disk.
Unpersists underlying RDD from memory or disk.
Uncached GenomicDataset.
Save partition size into the partitioned Parquet flag file.
Save partition size into the partitioned Parquet flag file.
Path to save the file at.
Partition bin size, in base pairs, used in Hive-style partitioning.
Writes an RDD to disk as text and optionally merges.
Writes an RDD to disk as text and optionally merges.
RDD to save.
Output path to save text files to.
If true, combines all partition shards.
If asSingleFile is true, disables the use of the parallel file merging engine.
If provided, the header file to include.