AlignmentDataset
Related Docs:
object AlignmentDataset
| package read
These data as a Spark SQL Dataset.
These data as a Spark SQL Dataset.
The processing steps that have been applied to this GenomicDataset.
The processing steps that have been applied to this GenomicDataset.
The RDD of genomic data that we are wrapping.
The RDD of genomic data that we are wrapping.
A dictionary describing the read groups attached to this GenomicDataset.
A dictionary describing the read groups attached to this GenomicDataset.
Replaces the processing steps attached to this genomic dataset.
Replaces the processing steps attached to this genomic dataset.
The new processing steps to attach to this genomic dataset.
Returns a new GenomicDataset with new processing lineage attached.
Replaces the read groups attached to this genomic dataset.
Replaces the read groups attached to this genomic dataset.
The new read group dictionary to attach.
Returns a new GenomicDataset with new read groups attached.
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.
The sequence dictionary describing the reference assembly this dataset is aligned to.
The sequence dictionary describing the reference assembly this dataset is aligned to.
Merges a new processing record with the extant computational lineage.
Merges a new processing record with the extant computational lineage.
Returns a new GenomicDataset with new read groups merged in.
Adds a single read group to the extant read groups.
Adds a single read group to the extant read groups.
The read group to append to the extant read groups.
Returns a new GenomicDataset with the new read group added.
Merges a new set of read groups with the extant read groups.
Merges a new set of read groups with the extant read groups.
The read group dictionary to append to the extant read groups.
Returns a new GenomicDataset with new read groups merged in.
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.
(Scala-specific) Rewrites the quality scores of reads to place all quality scores in bins.
(Scala-specific) Rewrites the quality scores of reads to place all quality scores in bins.
Quality score binning maps all quality scores to a limited number of discrete values, thus reducing the entropy of the quality score distribution, and reducing the amount of space that reads consume on disk.
The bins to use.
Reads whose quality scores are binned.
(Java-specific) Rewrites the quality scores of reads to place all quality scores in bins.
(Java-specific) Rewrites the quality scores of reads to place all quality scores in bins.
Quality score binning maps all quality scores to a limited number of discrete values, thus reducing the entropy of the quality score distribution, and reducing the amount of space that reads consume on disk.
The bins to use.
Reads whose quality scores are binned.
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.
(Scala-specific) Computes the mismatching positions field (SAM "MD" tag).
(Scala-specific) Computes the mismatching positions field (SAM "MD" tag).
A reference file that can be broadcast to all nodes.
If true, overwrites the MD tags on reads where it is already populated. If false, we only tag reads that are currently missing an MD tag. Default is false.
If we are recalculating existing tags and we find that the MD tag that was previously on the read doesn't match our new tag, LENIENT will log a warning message, STRICT will throw an exception, and SILENT will ignore. Default is LENIENT.
Returns a new AlignmentDataset where all reads have the mismatchingPositions field populated.
(Java-specific) Computes the mismatching positions field (SAM "MD" tag).
(Java-specific) Computes the mismatching positions field (SAM "MD" tag).
A reference file that can be broadcast to all nodes.
If true, overwrites the MD tags on reads where it is already populated. If false, we only tag reads that are currently missing an MD tag.
If we are recalculating existing tags and we find that the MD tag that was previously on the read doesn't match our new tag, LENIENT will log a warning message, STRICT will throw an exception, and SILENT will ignore.
Returns a new AlignmentDataset where all reads have the mismatchingPositions field populated.
Converts this genomic dataset of Alignments to HTSJDK SAMRecords.
Converts this genomic dataset of Alignments to HTSJDK SAMRecords.
Sort order.
Return a tuple of SAMFileHeader and an RDD of HTSJDK SAMRecords.
Converts this genomic dataset of Alignments to HTSJDK SAMRecords.
Converts this genomic dataset of Alignments to HTSJDK SAMRecords.
True if sorted.
Return a tuple of SAMFileHeader and an RDD of HTSJDK SAMRecords.
Cuts reads into _k_-mers, and then counts the number of occurrences of each _k_-mer.
Cuts reads into _k_-mers, and then counts the number of occurrences of each _k_-mer.
The value of _k_ to use for cutting _k_-mers.
Returns an RDD containing k-mer/count pairs.
Cuts reads into _k_-mers, and then counts the number of occurrences of each _k_-mer.
Cuts reads into _k_-mers, and then counts the number of occurrences of each _k_-mer.
The value of _k_ to use for cutting _k_-mers.
Returns a Dataset containing k-mer/count pairs.
Filter this AlignmentDataset by mapping quality.
Filter this AlignmentDataset by mapping quality.
Minimum mapping quality to filter by, inclusive.
AlignmentDataset filtered by mapping quality.
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 duplicate reads from this AlignmentDataset.
Filter duplicate reads from this AlignmentDataset.
AlignmentDataset filtered to remove duplicate reads.
Filter this AlignmentDataset to include only primary alignments.
Filter this AlignmentDataset to include only primary alignments.
AlignmentDataset filtered to include only primary alignments.
Filter this AlignmentDataset by read group to those that match the specified read group.
Filter this AlignmentDataset by read group to those that match the specified read group.
Read group to filter by.
AlignmentDataset filtered by read group.
(Scala-specific) Filter this AlignmentDataset by read group to those that match the specified read groups.
(Scala-specific) Filter this AlignmentDataset by read group to those that match the specified read groups.
Sequence of read groups to filter by.
AlignmentDataset filtered by one or more read groups.
(Java-specific) Filter this AlignmentDataset by read group to those that match the specified read groups.
(Java-specific) Filter this AlignmentDataset by read group to those that match the specified read groups.
List of read groups to filter by.
AlignmentDataset filtered by one or more read groups.
Filter this AlignmentDataset by sample to those that match the specified sample.
Filter this AlignmentDataset by sample to those that match the specified sample.
Sample to filter by.
AlignmentDataset filtered by the specified sample.
(Scala-specific) Filter this AlignmentDataset by sample to those that match the specified samples.
(Scala-specific) Filter this AlignmentDataset by sample to those that match the specified samples.
Sequence of samples to filter by.
AlignmentDataset filtered by the specified samples.
(Java-specific) Filter this AlignmentDataset by sample to those that match the specified samples.
(Java-specific) Filter this AlignmentDataset by sample to those that match the specified samples.
List of samples to filter by.
AlignmentDataset filtered by the specified samples.
Filter unaligned reads from this AlignmentDataset.
Filter unaligned reads from this AlignmentDataset.
AlignmentDataset filtered to remove unaligned reads.
Filter unpaired reads from this AlignmentDataset.
Filter unpaired reads from this AlignmentDataset.
AlignmentDataset filtered to remove unpaired reads.
Runs a quality control pass akin to the Samtools FlagStat tool.
Runs a quality control pass akin to the Samtools FlagStat tool.
Returns a tuple of (failedQualityMetrics, passedQualityMetrics)
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.
Returns all reference regions that overlap this read.
Returns all reference regions that overlap this read.
If a read is unaligned, it covers no reference region. If a read is aligned we expect it to cover a single region. A chimeric read would cover multiple regions, but we store chimeric reads in a way similar to BAM, where the split alignments are stored in multiple separate reads.
Read to produce regions for.
The seq of reference regions this read covers.
The underlying RDD of genomic data, as a JavaRDD.
The underlying RDD of genomic data, as a JavaRDD.
Left normalizes the INDELs in reads containing INDELs.
Left normalizes the INDELs in reads containing INDELs.
Returns a new genomic dataset where the reads that contained INDELs have their INDELs left normalized.
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.
Marks reads as possible fragment duplicates.
Marks reads as possible fragment duplicates.
A new genomic dataset where reads have the duplicate read flag set. Duplicate reads are NOT filtered out.
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.
(Scala-specific) Realigns indels using a consensus-based heuristic.
(Scala-specific) Realigns indels using a consensus-based heuristic.
The model to use for generating consensus sequences to realign against.
If the input data is sorted, setting this parameter to true avoids a second sort. Defaults to false.
The size of the largest indel to use for realignment. Defaults to 500.
The maximum number of consensus sequences to realign against per target region. Defaults to 30.
Log-odds threshold to use when realigning; realignments are only finalized if the log-odds threshold is exceeded. Defaults to 5.0.
The maximum width of a single target region for realignment. Defaults to 3000.
Maximum number of reads per target. Defaults to 20000.
If true, unclips reads prior to realignment. Else, omits clipped bases during realignment. Defaults to false.
An optional reference. If not provided, reference will be inferred from MD tags. Defaults to None.
Returns a genomic dataset of mapped reads which have been realigned.
(Java-specific) Realigns indels using a consensus-based heuristic with the specified reference.
(Java-specific) Realigns indels using a consensus-based heuristic with the specified reference.
The model to use for generating consensus sequences to realign against.
If the input data is sorted, setting this parameter to true avoids a second sort.
The size of the largest indel to use for realignment.
The maximum number of consensus sequences to realign against per target region.
Log-odds threshold to use when realigning; realignments are only finalized if the log-odds threshold is exceeded.
The maximum width of a single target region for realignment.
Maximum number of reads per target.
If true, unclips reads prior to realignment. Else, omits clipped bases during realignment.
Reference file.
Returns a genomic dataset of mapped reads which have been realigned.
(Java-specific) Realigns indels using a consensus-based heuristic.
(Java-specific) Realigns indels using a consensus-based heuristic.
The model to use for generating consensus sequences to realign against.
If the input data is sorted, setting this parameter to true avoids a second sort.
The size of the largest indel to use for realignment.
The maximum number of consensus sequences to realign against per target region.
Log-odds threshold to use when realigning; realignments are only finalized if the log-odds threshold is exceeded.
The maximum width of a single target region for realignment.
Maximum number of reads per target.
If true, unclips reads prior to realignment. Else, omits clipped bases during realignment.
Returns a genomic dataset of mapped reads which have been realigned.
(Java-specific) Realigns indels using a consensus-based heuristic with the specified reference and default parameters.
(Java-specific) Realigns indels using a consensus-based heuristic with the specified reference and default parameters.
Reference file.
Returns a genomic dataset of mapped reads which have been realigned.
(Java-specific) Realigns indels using a consensus-based heuristic with default parameters.
(Java-specific) Realigns indels using a consensus-based heuristic with default parameters.
Returns a genomic dataset of mapped reads which have been realigned.
(Scala-specific) Reassembles read pairs from two sets of unpaired reads.
(Scala-specific) Reassembles read pairs from two sets of unpaired reads. The assumption is that the two sets were _originally_ paired together.
The rdd containing the second read from the pairs.
How stringently to validate the reads.
Returns a genomic dataset with the pair information recomputed.
The RDD that this is called on should be the RDD with the first read from the pair.
(Java-specific) Reassembles read pairs from two sets of unpaired reads.
(Java-specific) Reassembles read pairs from two sets of unpaired reads. The assumption is that the two sets were _originally_ paired together.
The rdd containing the second read from the pairs.
How stringently to validate the reads.
Returns a genomic dataset with the pair information recomputed.
The RDD that this is called on should be the RDD with the first read from the pair.
(Scala-specific) Runs base quality score recalibration on a set of reads.
(Scala-specific) Runs base quality score recalibration on a set of reads. Uses a table of known SNPs to mask true variation during the recalibration process.
A table of known SNPs to mask valid variants.
The minimum quality score to recalibrate.
An optional storage level to set for the output of the first stage of BQSR. Defaults to StorageLevel.MEMORY_ONLY.
An optional fraction of reads to sample when generating the covariate table.
An optional seed to provide if downsampling reads.
Returns a genomic dataset of recalibrated reads.
(Java-specific) Runs base quality score recalibration on a set of reads.
(Java-specific) Runs base quality score recalibration on a set of reads. Uses a table of known SNPs to mask true variation during the recalibration process.
A table of known SNPs to mask valid variants.
The minimum quality score to recalibrate.
Storage level to set for the output of the first stage of BQSR. Set to null to omit.
Fraction of reads to sample when generating the covariate table.
Seed to provide if downsampling reads.
Returns a genomic dataset of recalibrated reads.
(Java-specific) Runs base quality score recalibration on a set of reads.
(Java-specific) Runs base quality score recalibration on a set of reads. Uses a table of known SNPs to mask true variation during the recalibration process.
A table of known SNPs to mask valid variants.
The minimum quality score to recalibrate.
An optional storage level to set for the output of the first stage of BQSR. Set to null to omit.
Returns a genomic dataset of recalibrated reads.
Replaces the underlying RDD and SequenceDictionary and emits a new object.
Replaces the underlying RDD and SequenceDictionary and emits a new object.
New RDD to replace current RDD.
New sequence dictionary to replace current dictionary.
Returns a new AlignmentDataset.
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, with the type identified by the extension.
Saves this genomic dataset to disk, with the type identified by the extension.
Path to save the file at.
Whether the file is sorted or not.
Returns true if saving succeeded.
Saves Alignments as a directory of Parquet files or as SAM/BAM.
Saves Alignments as a directory of Parquet files or as SAM/BAM.
This method infers the output format from the file extension. Filenames ending in .sam/.bam are saved as SAM/BAM, and all other files are saved as Parquet.
Save configuration arguments.
If the output is sorted, this will modify the SAM/BAM header.
Returns true if saving succeeded.
Saves reads in FASTQ format.
Saves reads in FASTQ format.
Path to save files at.
Optional second path for saving files. If set, two files will be saved.
If true, writes out reads with the base quality scores from the original quality scores (SAM "OQ") field. If false, writes out reads with the quality scores from the qualityScores field. Default is false.
Whether to sort the FASTQ files by read name or not. Defaults to false. Sorting the output will recover pair order, if desired.
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.
Iff strict, throw an exception if any read in this genomic dataset is not accompanied by its mate.
An optional persistance level to set. If this level is set, then reads will be cached (at the given persistance) level between passes.
(Java-specific) Saves reads in FASTQ format.
(Java-specific) Saves reads in FASTQ format.
Path to save files at.
If true, writes out reads with the base quality scores from the original quality scores (SAM "OQ") field. If false, writes out reads with the quality scores from the qualityScores field. Default is false.
Whether to sort the FASTQ files by read name or not. Defaults to false. Sorting the output will recover pair order, if desired.
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.
If asSingleFile is true, disables the use of the parallel file merging engine.
Iff strict, throw an exception if any read in this genomic dataset is not accompanied by its mate.
Saves these Alignments to two FASTQ files.
Saves these Alignments to two FASTQ files.
The files are one for the first mate in each pair, and the other for the second mate in the pair.
Path at which to save a FASTQ file containing the first mate of each pair.
Path at which to save a FASTQ file containing the second mate of each pair.
If true, writes out reads with the base quality scores from the original quality scores (SAM "OQ") field. If false, writes out reads with the quality scores from the qualityScores field. Default is false.
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.
Iff strict, throw an exception if any read in this genomic dataset is not accompanied by its mate.
An optional persistance level to set. If this level is set, then reads will be cached (at the given persistance) level between passes.
(Java-specific) Saves these Alignments to two FASTQ files.
(Java-specific) Saves these Alignments to two FASTQ files.
The files are one for the first mate in each pair, and the other for the second mate in the pair.
Path at which to save a FASTQ file containing the first mate of each pair.
Path at which to save a FASTQ file containing the second mate of each pair.
If true, writes out reads with the base quality scores from the original quality scores (SAM "OQ") field. If false, writes out reads with the quality scores from the qualityScores field. Default is false.
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.
If asSingleFile is true, disables the use of the parallel file merging engine.
Iff strict, throw an exception if any read in this genomic dataset is not accompanied by its mate.
The persistence level to cache reads at between passes.
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 this genomic dataset to disk as a SAM/BAM/CRAM file.
Saves this genomic dataset to disk as a SAM/BAM/CRAM file.
Path to save the file at.
The SAMFormat to save as. If left null, we will infer the format from the file extension.
If true, saves output as a single file.
If the output is sorted, this will modify the header.
Saves this genomic dataset of ADAM read data into the SAM/BAM format.
Saves this genomic dataset of ADAM read data into the SAM/BAM format.
Path to save files to.
Selects whether to save as SAM, BAM, or CRAM. The default value is None, which means the file type is inferred from the extension.
If true, saves output as a single file.
If the output is sorted, this will modify the 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.
Converts this genomic dataset into the SAM spec string it represents.
Converts this genomic dataset into the SAM spec string it represents.
This method converts a genomic dataset of Alignments back to an RDD of SAMRecordWritables and a SAMFileHeader, and then maps this RDD into a string on the driver that represents this file in SAM.
A string on the driver representing this genomic dataset of reads in SAM format.
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.
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.
Save the processing steps to disk.
Save the processing steps to disk.
The path to save processing steps to.
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 read groups to disk.
Save the read groups to disk.
The path to save read groups to.
Save the sequence dictionary to disk.
Save the sequence dictionary to disk.
The path to save the sequence dictionary 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 alignments by read name.
Sorts our alignments by read name.
Returns a new genomic dataset containing sorted alignments.
Sorts our alignments by reference position, with references ordered by name.
Sorts our alignments by reference position, with references ordered by name.
Sorts alignments by the location where the reads are aligned. Unaligned reads are put at the end and sorted by read name. References are ordered lexicographically.
Returns a new genomic dataset containing sorted alignments.
sortByReferencePositionAndIndex
Sorts our alignments by reference position, with references ordered by index.
Sorts our alignments by reference position, with references ordered by index.
Sorts alignments by the location where the reads are aligned. Unaligned reads are put at the end and sorted by read name. References are ordered by index that they are ordered in the SequenceDictionary.
Returns a new genomic dataset containing sorted alignments.
sortByReferencePosition
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
Converts this dataset of alignments into a corresponding CoverageDataset.
Converts this dataset of alignments into a corresponding CoverageDataset.
CoverageDataset containing mapped genomic dataset of Coverage.
These data as a Spark SQL DataFrame.
Convert this set of reads into fragments.
Convert this set of reads into fragments.
Returns a FragmentDataset where all reads have been grouped together by the original sequence fragment they come from.
Convert this genomic dataset of alignments to reads.
Convert this genomic dataset of alignments to reads.
Return this genomic dataset of alignments converted to a ReadDataset.
(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.
Genomic datasets to union with this genomic dataset.
(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.