org.bdgenomics.adam.rdd.contig
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
Counts the k-mers contained in a FASTA contig.
Counts the k-mers contained in a FASTA contig.
Java friendly variant.
The length of k-mers to count.
Returns an RDD containing k-mer/count pairs.
Counts the k-mers contained in a FASTA contig.
Counts the k-mers contained in a FASTA contig.
The length of k-mers to count.
Returns an RDD containing k-mer/count pairs.
A SQL Dataset of contig fragments.
A SQL Dataset of contig fragments.
From a set of contigs, returns the base sequence that corresponds to a region of the reference.
From a set of contigs, returns the base sequence that corresponds to a region of the reference.
Reference region over which to get sequence.
String of bases corresponding to reference sequence.
Throws exception if query region is not found.
From a set of contigs, returns a list of sequences based on reference regions provided
From a set of contigs, returns a list of sequences based on reference regions provided
List of Reference regions over which to get sequences
RDD[(ReferenceRegion, String)] of region -> sequence pairs.
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.
For all adjacent records in the RDD, we extend the records so that the adjacent records now overlap by _n_ bases, where _n_ is the flank length.
For all adjacent records in the RDD, we extend the records so that the adjacent records now overlap by _n_ bases, where _n_ is the flank length.
The length to extend adjacent records by.
Returns the RDD, with all adjacent fragments extended with flanking sequence.
For all adjacent records in the RDD, we extend the records so that the adjacent records now overlap by _n_ bases, where _n_ is the flank length.
For all adjacent records in the RDD, we extend the records so that the adjacent records now overlap by _n_ bases, where _n_ is the flank length.
Java friendly variant.
The length to extend adjacent records by.
Returns the RDD, with all adjacent fragments extended with flanking sequence.
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.
Fragment to extract a region from.
If a fragment is aligned to a reference location, returns a single reference region. If the fragment start position and name is not defined, returns no regions.
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.
Merge fragments by contig name.
Merge fragments by contig name.
Returns a NucleotideContigFragmentRDD containing a single fragment per contig.
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.
Underlying RDD
Underlying RDD
Replaces the underlying RDD with a new RDD.
Replaces the underlying RDD with a new RDD.
The RDD to use for the new NucleotideContigFragmentRDD.
Returns a new NucleotideContigFragmentRDD where the underlying RDD has been replaced.
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.
Save nucleotide contig fragments as Parquet or FASTA.
Save nucleotide contig fragments as Parquet or FASTA.
If filename ends in .fa or .fasta, saves as Fasta. If not, saves fragments to Parquet. Defaults to 60 character line length, if saving to FASTA.
file name
If false, writes file to disk as shards with one shard per partition. If true, we save the file to disk as a single file by merging the shards.
Save nucleotide contig fragments in FASTA format.
Save nucleotide contig fragments in FASTA format.
file name
hard wrap FASTA formatted sequence at line width, default 60
By default (false), writes file to disk as shards with one shard per partition. If true, we save the file to disk as a single file by merging the shards.
If asSingleFile is true, disables the use of the parallel file merging engine.
Saves this RDD to disk as a Parquet file.
Saves this RDD to disk as a Parquet file.
Path to save the file at.
Saves this RDD to disk as a Parquet file.
Saves this RDD 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.
Saves this RDD to disk as a Parquet file.
Saves this RDD 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 RDD as a directory of Parquet files.
Saves RDD as a directory of Parquet files.
The RDD is written as a directory of Parquet files, with Parquet configuration described by the input param args. The provided sequence dictionary is written at args.outputPath/_seqdict.avro as Avro binary.
Save configuration arguments.
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 RDD to Parquet to save metadata.
Called in saveAsParquet after saving RDD to Parquet to save metadata.
Writes any necessary metadata to disk. If not overridden, writes the sequence dictionary to disk as Avro.
The filepath to the file where we will save the Metadata.
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 an RDD of Avro data to Parquet.
Saves an RDD 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 filepath where we will save the sequence dictionary.
Sequence dictionary computed from rdd
Sequence dictionary computed from rdd
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
This data as a Spark SQL DataFrame.
Converts an RDD of nucleotide contig fragments into reads.
Converts an RDD of nucleotide contig fragments into reads. Adjacent contig fragments are combined.
Returns an RDD of reads.
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 transforms the underlying DataFrame into a new DataFrame using the Spark SQL API.
Applies a function that transforms the underlying DataFrame into a new DataFrame using the Spark SQL API. Java-friendly variant.
A function that transforms the underlying RDD as a DataFrame.
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 DataFrame into a new DataFrame using the Spark SQL API.
Applies a function that transforms the underlying DataFrame into a new DataFrame using the Spark SQL API.
A function that transforms the underlying RDD as a DataFrame.
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 using the Spark SQL API.
Applies a function that transforms the underlying RDD into a new RDD using the Spark SQL API.
A function that transforms the underlying RDD as a Dataset.
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.
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 variant.
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 variant.
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 variant.
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.
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.
A wrapper class for RDD[NucleotideContigFragment].