org.bdgenomics.adam.rdd.variant
The underlying RDD of VariantContexts.
The genome sequence these variants were called against.
The genotyped samples in this RDD of VariantContexts.
The VCF header lines that cover all INFO/FORMAT fields needed to represent this RDD of VariantContexts.
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 RDD 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 RDD with the new header lines added.
Adds a single sample to the current RDD.
Adds a single sample to the current RDD.
A single sample to add.
Returns a new RDD with this sample added.
Adds samples to the current RDD.
Adds samples to the current RDD.
Zero or more samples to add.
Returns a new RDD with samples added.
Appends metadata for a single sequence to the current RDD.
Appends metadata for a single sequence to the current RDD.
The sequence to add.
Returns a new GenomicRDD with this sequence appended.
Appends sequence metadata to the current RDD.
Appends sequence metadata to the current RDD.
The new sequences to append.
Returns a new GenomicRDD with the sequences appended.
Performs a broadcast inner join between this RDD and another RDD.
Performs a broadcast inner join between this RDD and another RDD.
In a broadcast join, the left RDD (this RDD) 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 RDD are dropped.
The right RDD in the join.
Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.
broadcastRegionJoinAgainst
Performs a broadcast inner join between this RDD and another RDD.
Performs a broadcast inner join between this RDD and another RDD.
In a broadcast join, the left RDD (this RDD) 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 RDD are dropped.
The right RDD 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 RDD containing all pairs of keys that overlapped in the genomic coordinate space.
broadcastRegionJoinAgainst
Performs a broadcast inner join between this RDD and data that has been broadcast.
Performs a broadcast inner join between this RDD 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 RDD 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 RDD containing all pairs of keys that overlapped in the genomic coordinate space.
This function differs from other region joins as it treats the calling RDD as the right side of the join, and not the left.
broadcastRegionJoin
Performs a broadcast inner join between this RDD and another RDD.
Performs a broadcast inner join between this RDD and another RDD.
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 RDD 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 RDD containing all pairs of keys that overlapped in the genomic coordinate space.
This function differs from other region joins as it treats the calling RDD as the right side of the join, and not the left.
broadcastRegionJoinAndGroupByRight
Performs a broadcast inner join between this RDD and another RDD.
Performs a broadcast inner join between this RDD and another RDD.
In a broadcast join, the left RDD (this RDD) 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 RDD are dropped.
The right RDD in the join.
Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.
broadcastRegionJoinAgainstAndGroupByRight
Performs a broadcast inner join between this RDD and another RDD.
Performs a broadcast inner join between this RDD and another RDD.
In a broadcast join, the left RDD (this RDD) 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 RDD are dropped.
The right RDD 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 RDD containing all pairs of keys that overlapped in the genomic coordinate space.
broadcastRegionJoinAgainstAndGroupByRight
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 GenomicRDD containing only data that overlaps the query region.
Runs a filter that selects data in the underlying RDD that overlaps several genomic regions.
Runs a filter that selects data in the underlying RDD that overlaps several genomic regions.
The regions to query for.
Returns a new GenomicRDD containing only data that overlaps the querys region.
Performs a sort-merge full outer join between this RDD and another RDD.
Performs a sort-merge full outer join between this RDD and another RDD.
In a sort-merge join, both RDDs 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
RDD does not overlap any values in the other RDD, it will be paired with
a None in the product of the join.
The right RDD in the join.
Returns a new genomic RDD 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 RDD and another RDD.
Performs a sort-merge full outer join between this RDD and another RDD.
In a sort-merge join, both RDDs 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
RDD does not overlap any values in the other RDD, it will be paired with
a None in the product of the join.
The right RDD 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 RDD 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 context to get a reference region for.
Returns a seq containing the position key from the variant context.
The VCF header lines that cover all INFO/FORMAT fields needed to represent this RDD of VariantContexts.
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 RDD and another RDD.
Performs a sort-merge left outer join between this RDD and another RDD.
In a sort-merge join, both RDDs 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 RDD that do not overlap a value from the left RDD are dropped.
If a value from the left RDD does not overlap any values in the right
RDD, it will be paired with a None in the product of the join.
The right RDD in the join.
Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the left RDD that did not overlap a key in the right RDD.
Performs a sort-merge left outer join between this RDD and another RDD.
Performs a sort-merge left outer join between this RDD and another RDD.
In a sort-merge join, both RDDs 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 RDD that do not overlap a value from the left RDD are dropped.
If a value from the left RDD does not overlap any values in the right
RDD, it will be paired with a None in the product of the join.
The right RDD 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 RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the left RDD that did not overlap a key in the right RDD.
Performs a sort-merge left outer join between this RDD and another RDD, followed by a groupBy on the left value.
Performs a sort-merge left outer join between this RDD and another RDD, followed by a groupBy on the left value.
In a sort-merge join, both RDDs 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 RDD that do not overlap a value from the left RDD are dropped. If a value from the left RDD does not overlap any values in the right RDD, it will be paired with an empty Iterable in the product of the join.
The right RDD in the join.
Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the left RDD that did not overlap a key in the right RDD.
Performs a sort-merge left outer join between this RDD and another RDD, followed by a groupBy on the left value.
Performs a sort-merge left outer join between this RDD and another RDD, followed by a groupBy on the left value.
In a sort-merge join, both RDDs 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 RDD that do not overlap a value from the left RDD are dropped. If a value from the left RDD does not overlap any values in the right RDD, it will be paired with an empty Iterable in the product of the join.
The right RDD 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 RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the left RDD that did not overlap a key in the right RDD.
Pipes genomic data to a subprocess that runs in parallel using Spark.
Pipes genomic data to a subprocess that runs in parallel using Spark.
Java/PySpark friendly variant.
The type of the record created by the piped command.
A GenomicRDD containing X's.
The InFormatter to use for formatting the data being piped to the command.
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 RDD.
Returns a new GenomicRDD of type Y.
Pipes genomic data to a subprocess that runs in parallel using Spark.
Pipes genomic data to a subprocess that runs in parallel using Spark.
SparkR friendly variant.
The type of the record created by the piped command.
A GenomicRDD containing X's.
The InFormatter to use for formatting the data being piped to the command.
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 RDD.
Returns a new GenomicRDD of type Y.
Pipes genomic data to a subprocess that runs in parallel using Spark.
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 GenomicRDD. 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 GenomicRDD containing X's.
The InFormatter to use for formatting the data being piped to the command.
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.
Returns a new GenomicRDD of type Y.
The underlying RDD of VariantContexts.
The underlying RDD of VariantContexts.
Replaces the header lines attached to this RDD.
Replaces the header lines attached to this RDD.
The new header lines to attach to this RDD.
A new RDD with the header lines replaced.
The RDD of VariantContexts to replace the underlying RDD.
Returns a new VariantContextRDD where the underlying RDD has been replaced.
Replaces the sample metadata attached to the RDD.
Replaces the sample metadata attached to the RDD.
The new sample metadata to attach.
A GenomicRDD with new sample metadata.
Replaces the sequence dictionary attached to a GenomicRDD.
Replaces the sequence dictionary attached to a GenomicRDD.
The new sequence dictionary to attach.
Returns a new GenomicRDD with the sequences replaced.
Performs a broadcast right outer join between this RDD and another RDD.
Performs a broadcast right outer join between this RDD and another RDD.
In a broadcast join, the left RDD (this RDD) 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 RDD that do not overlap a
value from the right RDD are dropped. If a value from the right RDD does
not overlap any values in the left RDD, it will be paired with a None
in the product of the join.
The right RDD in the join.
Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right RDD that did not overlap a key in the left RDD.
rightOuterBroadcastRegionJoin
Performs a broadcast right outer join between this RDD and another RDD.
Performs a broadcast right outer join between this RDD and another RDD.
In a broadcast join, the left RDD (this RDD) 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 RDD that do not overlap a
value from the right RDD are dropped. If a value from the right RDD does
not overlap any values in the left RDD, it will be paired with a None
in the product of the join.
The right RDD 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 RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right RDD that did not overlap a key in the left RDD.
rightOuterBroadcastRegionJoin
Performs a broadcast right outer join between this RDD and data that has been broadcast.
Performs a broadcast right outer join between this RDD 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 RDD are dropped. If a value from the right RDD 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 RDD containing all pairs of keys that overlapped in the genomic coordinate space.
This function differs from other region joins as it treats the calling RDD as the right side of the join, and not the left.
rightOuterBroadcastRegionJoin
Performs a broadcast right outer join between this RDD and another RDD.
Performs a broadcast right outer join between this RDD and another RDD.
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 RDD are dropped. If a value from the right RDD 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 RDD containing all pairs of keys that overlapped in the genomic coordinate space.
This function differs from other region joins as it treats the calling RDD as the right side of the join, and not the left.
rightOuterBroadcastRegionJoinAndGroupByRight
Performs a broadcast right outer join between this RDD and another RDD.
Performs a broadcast right outer join between this RDD and another RDD.
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 RDD that do not overlap a
value from the right RDD are dropped. If a value from the right RDD does
not overlap any values in the left RDD, it will be paired with a None
in the product of the join.
The right RDD in the join.
Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right RDD that did not overlap a key in the left RDD.
rightOuterBroadcastRegionJoinAgainstAndGroupByRight
Performs a broadcast right outer join between this RDD and another RDD.
Performs a broadcast right outer join between this RDD and another RDD.
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 RDD that do not overlap a
value from the right RDD are dropped. If a value from the right RDD does
not overlap any values in the left RDD, it will be paired with a None
in the product of the join.
The right RDD 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 RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right RDD that did not overlap a key in the left RDD.
rightOuterBroadcastRegionJoinAgainstAndGroupByRight
Performs a sort-merge right outer join between this RDD and another RDD.
Performs a sort-merge right outer join between this RDD and another RDD.
In a sort-merge join, both RDDs 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 RDD that do not overlap a value from the right RDD are dropped.
If a value from the right RDD does not overlap any values in the left
RDD, it will be paired with a None in the product of the join.
The right RDD in the join.
Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right RDD that did not overlap a key in the left RDD.
Performs a sort-merge right outer join between this RDD and another RDD.
Performs a sort-merge right outer join between this RDD and another RDD.
In a sort-merge join, both RDDs 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 RDD that do not overlap a value from the right RDD are dropped.
If a value from the right RDD does not overlap any values in the left
RDD, it will be paired with a None in the product of the join.
The right RDD 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 RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right RDD that did not overlap a key in the left RDD.
Performs a sort-merge right outer join between this RDD and another RDD, followed by a groupBy on the left value, if not null.
Performs a sort-merge right outer join between this RDD and another RDD, followed by a groupBy on the left value, if not null.
In a sort-merge join, both RDDs 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 RDD. Since this is a right outer join, all values from the
right RDD who did not overlap a value from the left RDD are placed into
a length-1 Iterable with a None key.
The right RDD in the join.
Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, grouped together by the value they overlapped in the left RDD, and all values from the right RDD that did not overlap an item in the left RDD.
Performs a sort-merge right outer join between this RDD and another RDD, followed by a groupBy on the left value, if not null.
Performs a sort-merge right outer join between this RDD and another RDD, followed by a groupBy on the left value, if not null.
In a sort-merge join, both RDDs 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 RDD. Since this is a right outer join, all values from the
right RDD who did not overlap a value from the left RDD are placed into
a length-1 Iterable with a None key.
The right RDD 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 RDD containing all pairs of keys that overlapped in the genomic coordinate space, grouped together by the value they overlapped in the left RDD, and all values from the right RDD that did not overlap an item in the left RDD.
The genotyped samples in this RDD of VariantContexts.
The genotyped samples in this RDD of VariantContexts.
Converts an RDD of ADAM VariantContexts to HTSJDK VariantContexts and saves to disk as VCF.
Converts an RDD of ADAM VariantContexts to HTSJDK VariantContexts and saves to disk as VCF.
File paths that end in .gz or .bgz will be saved as block GZIP compressed VCFs.
The file path to save to.
If true, saves the output as a single file by merging the sharded output after completing the write to HDFS. If false, the output of this call will be written as shards, where each shard has a valid VCF header.
If true and asSingleFile is true, we will save the output shards as a headerless file, but we will not merge the shards.
If asSingleFile is true and deferMerging is false, disables the use of the parallel file merging engine.
The validation stringency to use when writing the VCF.
Converts an RDD of ADAM VariantContexts to HTSJDK VariantContexts and saves as a single file to disk as VCF.
Converts an RDD of ADAM VariantContexts to HTSJDK VariantContexts and saves as a single file to disk as VCF. Uses lenient validation stringency.
File paths that end in .gz or .bgz will be saved as block GZIP compressed VCFs.
The file path to save to.
Converts an RDD of ADAM VariantContexts to HTSJDK VariantContexts and saves to disk as VCF.
Converts an RDD of ADAM VariantContexts to HTSJDK VariantContexts and saves to disk as VCF.
File paths that end in .gz or .bgz will be saved as block GZIP compressed VCFs.
Arguments defining where to save the file.
The validation stringency to use when writing the VCF. Defaults to LENIENT.
The genome sequence these variants were called against.
The genome sequence these variants were called against.
Performs a sort-merge inner join between this RDD and another RDD.
Performs a sort-merge inner join between this RDD and another RDD.
In a sort-merge join, both RDDs 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 RDD are dropped.
The right RDD in the join.
Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.
Performs a sort-merge inner join between this RDD and another RDD.
Performs a sort-merge inner join between this RDD and another RDD.
In a sort-merge join, both RDDs 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 RDD are dropped.
The right RDD 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 RDD containing all pairs of keys that overlapped in the genomic coordinate space.
Performs a sort-merge inner join between this RDD and another RDD, followed by a groupBy on the left value.
Performs a sort-merge inner join between this RDD and another RDD, followed by a groupBy on the left value.
In a sort-merge join, both RDDs 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 RDD are dropped. In the same operation, we group all values by the left item in the RDD.
The right RDD in the join.
Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, grouped together by the value they overlapped in the left RDD..
Performs a sort-merge inner join between this RDD and another RDD, followed by a groupBy on the left value.
Performs a sort-merge inner join between this RDD and another RDD, followed by a groupBy on the left value.
In a sort-merge join, both RDDs 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 RDD are dropped. In the same operation, we group all values by the left item in the RDD.
The right RDD 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 RDD containing all pairs of keys that overlapped in the genomic coordinate space, grouped together by the value they overlapped in the left RDD..
Sorts our genome aligned data by reference positions, with contigs ordered by index.
Sorts our genome aligned data by reference positions, with contigs ordered by index.
The number of partitions for the new RDD.
The level of ValidationStringency to enforce.
Returns a new RDD 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 contigs ordered by index.
Sorts our genome aligned data by reference positions, with contigs ordered by index.
Returns a new RDD containing sorted data.
sortLexicographically
Sorts our genome aligned data by reference positions, with contigs ordered lexicographically.
Sorts our genome aligned data by reference positions, with contigs ordered lexicographically.
The number of partitions for the new RDD.
A Boolean flag to determine whether to store the partition bounds from the resulting RDD.
The level at which to persist the resulting RDD.
The level of ValidationStringency to enforce.
Returns a new RDD 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 contigs ordered lexicographically.
Sorts our genome aligned data by reference positions, with contigs ordered lexicographically.
Returns a new RDD containing sorted data.
sort
Returns a GenotypeRDD containing the Genotypes in this RDD.
Returns the Variants in this RDD.
Applies a function that transforms the underlying RDD into a new RDD.
Applies a function that transforms the underlying RDD into a new RDD.
A function that transforms the underlying RDD.
A new RDD where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) is copied without modification.
Applies a function that transforms the underlying RDD into a new RDD.
Applies a function that transforms the underlying RDD into a new RDD.
A function that transforms the underlying RDD.
A new RDD where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) is copied without modification.
Applies a function that transmutes the underlying RDD into a new RDD of a different type.
Applies a function that transmutes the underlying RDD into a new RDD of a different type. Java friendly version.
A function that transforms the underlying RDD.
The conversion function used to build the final RDD.
A new RDD where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) is copied without modification.
Applies a function that transmutes the underlying RDD into a new RDD of a different type.
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 RDD where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) is copied without modification.
Unions together multiple genomic RDDs.
Unions together multiple genomic RDDs.
RDDs to union with this RDD.
Unions together multiple genomic RDDs.
Unions together multiple genomic RDDs.
RDDs to union with this RDD.
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.
An RDD containing VariantContexts attached to a reference and samples.
The underlying RDD of VariantContexts.
The genome sequence these variants were called against.
The genotyped samples in this RDD of VariantContexts.
The VCF header lines that cover all INFO/FORMAT fields needed to represent this RDD of VariantContexts.