Class/Object

org.bdgenomics.adam.rdd.read

AlignmentRecordRDD

Related Docs: object AlignmentRecordRDD | package read

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sealed abstract class AlignmentRecordRDD extends AvroRecordGroupGenomicDataset[AlignmentRecord, AlignmentRecord, AlignmentRecordRDD]

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  1. AlignmentRecordRDD
  2. AvroRecordGroupGenomicDataset
  3. GenomicDatasetWithLineage
  4. AvroGenomicDataset
  5. GenomicDataset
  6. Logging
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Abstract Value Members

  1. abstract val dataset: Dataset[AlignmentRecord]

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    These data as a Spark SQL Dataset.

    These data as a Spark SQL Dataset.

    Definition Classes
    GenomicDataset
  2. abstract val optPartitionMap: Option[Array[Option[(ReferenceRegion, ReferenceRegion)]]]

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    Attributes
    protected
    Definition Classes
    GenomicDataset
  3. abstract val processingSteps: Seq[ProcessingStep]

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    The processing steps that have been applied to this GenomicDataset.

    The processing steps that have been applied to this GenomicDataset.

    Definition Classes
    GenomicDatasetWithLineage
  4. abstract val rdd: RDD[AlignmentRecord]

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    The RDD of genomic data that we are wrapping.

    The RDD of genomic data that we are wrapping.

    Definition Classes
    GenomicDataset
  5. abstract val recordGroups: RecordGroupDictionary

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    A dictionary describing the record groups attached to this GenomicDataset.

    A dictionary describing the record groups attached to this GenomicDataset.

    Definition Classes
    AvroRecordGroupGenomicDataset
  6. abstract def replaceProcessingSteps(newProcessingSteps: Seq[ProcessingStep]): AlignmentRecordRDD

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    Replaces the processing steps attached to this RDD.

    Replaces the processing steps attached to this RDD.

    newProcessingSteps

    The new processing steps to attach to this RDD.

    returns

    Returns a new GenomicDataset with new processing lineage attached.

    Definition Classes
    GenomicDatasetWithLineage
  7. abstract def replaceRecordGroups(newRecordGroups: RecordGroupDictionary): AlignmentRecordRDD

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    Replaces the record groups attached to this RDD.

    Replaces the record groups attached to this RDD.

    newRecordGroups

    The new record group dictionary to attach.

    returns

    Returns a new GenomicDataset with new record groups attached.

    Definition Classes
    AvroRecordGroupGenomicDataset
  8. abstract def replaceSequences(newSequences: SequenceDictionary): AlignmentRecordRDD

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    Replaces the sequence dictionary attached to a GenomicDataset.

    Replaces the sequence dictionary attached to a GenomicDataset.

    newSequences

    The new sequence dictionary to attach.

    returns

    Returns a new GenomicDataset with the sequences replaced.

    Definition Classes
    GenomicDataset
  9. abstract val sequences: SequenceDictionary

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    The sequence dictionary describing the reference assembly this dataset is aligned to.

    The sequence dictionary describing the reference assembly this dataset is aligned to.

    Definition Classes
    GenomicDataset

Concrete Value Members

  1. final def !=(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  2. final def ##(): Int

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    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  4. def addProcessingStep(newProcessingStep: ProcessingStep): AlignmentRecordRDD

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    Merges a new processing record with the extant computational lineage.

    Merges a new processing record with the extant computational lineage.

    returns

    Returns a new GenomicDataset with new record groups merged in.

    Definition Classes
    GenomicDatasetWithLineage
  5. def addRecordGroup(recordGroupToAdd: RecordGroup): AlignmentRecordRDD

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    Adds a single record group to the extant record groups.

    Adds a single record group to the extant record groups.

    recordGroupToAdd

    The record group to append to the extant record groups.

    returns

    Returns a new GenomicDataset with the new record group added.

    Definition Classes
    AvroRecordGroupGenomicDataset
  6. def addRecordGroups(recordGroupsToAdd: RecordGroupDictionary): AlignmentRecordRDD

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    Merges a new set of record groups with the extant record groups.

    Merges a new set of record groups with the extant record groups.

    recordGroupsToAdd

    The record group dictionary to append to the extant record groups.

    returns

    Returns a new GenomicDataset with new record groups merged in.

    Definition Classes
    AvroRecordGroupGenomicDataset
  7. def addSequence(sequenceToAdd: SequenceRecord): AlignmentRecordRDD

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    Appends metadata for a single sequence to the current RDD.

    Appends metadata for a single sequence to the current RDD.

    sequenceToAdd

    The sequence to add.

    returns

    Returns a new GenomicDataset with this sequence appended.

    Definition Classes
    GenomicDataset
  8. def addSequences(sequencesToAdd: SequenceDictionary): AlignmentRecordRDD

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    Appends sequence metadata to the current RDD.

    Appends sequence metadata to the current RDD.

    sequencesToAdd

    The new sequences to append.

    returns

    Returns a new GenomicDataset with the sequences appended.

    Definition Classes
    GenomicDataset
  9. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any
  10. def binQualityScores(bins: Seq[QualityScoreBin]): AlignmentRecordRDD

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    Rewrites the quality scores of reads to place all quality scores in bins.

    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.

    bins

    The bins to use.

    returns

    Reads whose quality scores are binned.

  11. def broadcast()(implicit tTag: ClassTag[AlignmentRecord]): GenomicBroadcast[AlignmentRecord, AlignmentRecord, AlignmentRecordRDD]

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    Definition Classes
    GenomicDataset
  12. def broadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X], txTag: ClassTag[(AlignmentRecord, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(AlignmentRecord, Y)]): GenericGenomicDataset[(AlignmentRecord, X), (AlignmentRecord, Y)]

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    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.

    genomicRdd

    The right RDD in the join.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainst

  13. def broadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X], txTag: ClassTag[(AlignmentRecord, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(AlignmentRecord, Y)]): GenericGenomicDataset[(AlignmentRecord, X), (AlignmentRecord, Y)]

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    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.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainst

  14. def broadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(AlignmentRecord, X), (AlignmentRecord, Y)]

    Permalink

    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. Python/Java friendly version.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
  15. def broadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(AlignmentRecord, X), (AlignmentRecord, Y)]

    Permalink

    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. SparkR friendly version.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
  16. def broadcastRegionJoinAgainst[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](broadcast: GenomicBroadcast[X, Y, Z])(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(Y, AlignmentRecord)]): GenericGenomicDataset[(X, AlignmentRecord), (Y, AlignmentRecord)]

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    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.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
    Note

    This function differs from other region joins as it treats the calling RDD as the right side of the join, and not the left.

    See also

    broadcastRegionJoin

  17. def broadcastRegionJoinAgainstAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](broadcast: GenomicBroadcast[X, Y, Z])(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X], syuTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Y], AlignmentRecord)]): GenericGenomicDataset[(Iterable[X], AlignmentRecord), (Seq[Y], AlignmentRecord)]

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    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.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
    Note

    This function differs from other region joins as it treats the calling RDD as the right side of the join, and not the left.

    See also

    broadcastRegionJoinAndGroupByRight

  18. def broadcastRegionJoinAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[AlignmentRecord], X)], iuyTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[AlignmentRecord], Y)]): GenericGenomicDataset[(Iterable[AlignmentRecord], X), (Seq[AlignmentRecord], Y)]

    Permalink

    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.

    genomicRdd

    The right RDD in the join.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainstAndGroupByRight

  19. def broadcastRegionJoinAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[AlignmentRecord], X)], iuyTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[AlignmentRecord], Y)]): GenericGenomicDataset[(Iterable[AlignmentRecord], X), (Seq[AlignmentRecord], Y)]

    Permalink

    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.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainstAndGroupByRight

  20. def broadcastRegionJoinAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Iterable[AlignmentRecord], X), (Seq[AlignmentRecord], Y)]

    Permalink

    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. PySpark/Java friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainstAndGroupByRight

  21. def broadcastRegionJoinAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Iterable[AlignmentRecord], X), (Seq[AlignmentRecord], Y)]

    Permalink

    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. SparkR friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainstAndGroupByRight

  22. def buildTree(rdd: RDD[(ReferenceRegion, AlignmentRecord)])(implicit tTag: ClassTag[AlignmentRecord]): IntervalArray[ReferenceRegion, AlignmentRecord]

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    Attributes
    protected
    Definition Classes
    AlignmentRecordRDDGenomicDataset
  23. def cache(): AlignmentRecordRDD

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    Caches underlying RDD in memory.

    Caches underlying RDD in memory.

    returns

    Cached GenomicDataset.

    Definition Classes
    GenomicDataset
  24. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  25. def computeMismatchingPositions(referenceFile: ReferenceFile, overwriteExistingTags: Boolean = false, validationStringency: ValidationStringency = ValidationStringency.LENIENT): AlignmentRecordRDD

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    Computes the mismatching positions field (SAM "MD" tag).

    Computes the mismatching positions field (SAM "MD" tag).

    referenceFile

    A reference file that can be broadcast to all nodes.

    overwriteExistingTags

    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.

    validationStringency

    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

    Returns a new AlignmentRecordRDD where all reads have the mismatchingPositions field populated.

  26. def convertToSam(isSorted: Boolean = false): (RDD[SAMRecordWritable], SAMFileHeader)

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    Converts an RDD of ADAM read records into SAM records.

    Converts an RDD of ADAM read records into SAM records.

    returns

    Returns a SAM/BAM formatted RDD of reads, as well as the file header.

  27. def countKmers(kmerLength: Int): RDD[(String, Long)]

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    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.

    kmerLength

    The value of _k_ to use for cutting _k_-mers.

    returns

    Returns an RDD containing k-mer/count pairs.

  28. def countKmers(kmerLength: Integer): JavaRDD[(String, Long)]

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    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.

    Java friendly variant.

    kmerLength

    The value of _k_ to use for cutting _k_-mers.

    returns

    Returns an RDD containing k-mer/count pairs.

  29. def countKmersAsDataset(kmerLength: Integer): Dataset[(String, Long)]

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    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.

    kmerLength

    The value of _k_ to use for cutting _k_-mers.

    returns

    Returns a Dataset containing k-mer/count pairs.

  30. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  31. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  32. def filterByOverlappingRegion(query: ReferenceRegion): AlignmentRecordRDD

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    Runs a filter that selects data in the underlying RDD that overlaps a single genomic region.

    Runs a filter that selects data in the underlying RDD that overlaps a single genomic region.

    query

    The region to query for.

    returns

    Returns a new GenomicDataset containing only data that overlaps the query region.

    Definition Classes
    GenomicDataset
  33. def filterByOverlappingRegions(querys: Iterable[ReferenceRegion]): AlignmentRecordRDD

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    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. Java friendly version.

    querys

    The regions to query for.

    returns

    Returns a new GenomicRDD containing only data that overlaps the querys region.

    Definition Classes
    GenomicDataset
  34. def filterByOverlappingRegions(querys: Iterable[ReferenceRegion]): AlignmentRecordRDD

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    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.

    querys

    The regions to query for.

    returns

    Returns a new GenomicDataset containing only data that overlaps the querys region.

    Definition Classes
    GenomicDataset
  35. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  36. def flagStat(): (FlagStatMetrics, FlagStatMetrics)

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    Runs a quality control pass akin to the Samtools FlagStat tool.

    Runs a quality control pass akin to the Samtools FlagStat tool.

    returns

    Returns a tuple of (failedQualityMetrics, passedQualityMetrics)

  37. def flattenRddByRegions(): RDD[(ReferenceRegion, AlignmentRecord)]

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    Attributes
    protected
    Definition Classes
    GenomicDataset
  38. def fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X], otoxTag: ClassTag[(Option[AlignmentRecord], Option[X])], ouoyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[AlignmentRecord], Option[Y])]): GenericGenomicDataset[(Option[AlignmentRecord], Option[X]), (Option[AlignmentRecord], Option[Y])]

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    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.

    genomicRdd

    The right RDD in the join.

    returns

    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.

    Definition Classes
    GenomicDataset
  39. def fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X], otoxTag: ClassTag[(Option[AlignmentRecord], Option[X])], ouoyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[AlignmentRecord], Option[Y])]): GenericGenomicDataset[(Option[AlignmentRecord], Option[X]), (Option[AlignmentRecord], Option[Y])]

    Permalink

    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.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic 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.

    Definition Classes
    GenomicDataset
  40. def fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Option[AlignmentRecord], Option[X]), (Option[AlignmentRecord], Option[Y])]

    Permalink

    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. PySpark/Java friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic 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.

    Definition Classes
    GenomicDataset
  41. def fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Option[AlignmentRecord], Option[X]), (Option[AlignmentRecord], Option[Y])]

    Permalink

    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. SparkR friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic 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.

    Definition Classes
    GenomicDataset
  42. final def getClass(): Class[_]

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    Definition Classes
    AnyRef → Any
  43. def getReferenceRegions(elem: AlignmentRecord): Seq[ReferenceRegion]

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    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.

    elem

    Read to produce regions for.

    returns

    The seq of reference regions this read covers.

    Attributes
    protected
    Definition Classes
    AlignmentRecordRDDGenomicDataset
  44. def hashCode(): Int

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    Definition Classes
    AnyRef → Any
  45. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any
  46. def isSorted: Boolean

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    Definition Classes
    GenomicDataset
  47. def isTraceEnabled(): Boolean

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    Attributes
    protected
    Definition Classes
    Logging
  48. lazy val jrdd: JavaRDD[AlignmentRecord]

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    The underlying RDD of genomic data, as a JavaRDD.

    The underlying RDD of genomic data, as a JavaRDD.

    Definition Classes
    GenomicDataset
  49. def leftNormalizeIndels(): AlignmentRecordRDD

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    Left normalizes the INDELs in reads containing INDELs.

    Left normalizes the INDELs in reads containing INDELs.

    returns

    Returns a new RDD where the reads that contained INDELs have their INDELs left normalized.

  50. def leftOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X], toxTag: ClassTag[(AlignmentRecord, Option[X])], uoyTag: scala.reflect.api.JavaUniverse.TypeTag[(AlignmentRecord, Option[Y])]): GenericGenomicDataset[(AlignmentRecord, Option[X]), (AlignmentRecord, Option[Y])]

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    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.

    genomicRdd

    The right RDD in the join.

    returns

    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.

    Definition Classes
    GenomicDataset
  51. def leftOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X], toxTag: ClassTag[(AlignmentRecord, Option[X])], uoyTag: scala.reflect.api.JavaUniverse.TypeTag[(AlignmentRecord, Option[Y])]): GenericGenomicDataset[(AlignmentRecord, Option[X]), (AlignmentRecord, Option[Y])]

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    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.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic 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.

    Definition Classes
    GenomicDataset
  52. def leftOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(AlignmentRecord, Option[X]), (AlignmentRecord, Option[Y])]

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    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. PySpark/Java friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic 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.

    Definition Classes
    GenomicDataset
  53. def leftOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(AlignmentRecord, Option[X]), (AlignmentRecord, Option[Y])]

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    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. SparkR friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic 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.

    Definition Classes
    GenomicDataset
  54. def leftOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X], toxTag: ClassTag[(AlignmentRecord, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(AlignmentRecord, Seq[Y])]): GenericGenomicDataset[(AlignmentRecord, Iterable[X]), (AlignmentRecord, Seq[Y])]

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    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.

    genomicRdd

    The right RDD in the join.

    returns

    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.

    Definition Classes
    GenomicDataset
  55. def leftOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X], toxTag: ClassTag[(AlignmentRecord, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(AlignmentRecord, Seq[Y])]): GenericGenomicDataset[(AlignmentRecord, Iterable[X]), (AlignmentRecord, Seq[Y])]

    Permalink

    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.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic 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.

    Definition Classes
    GenomicDataset
  56. def leftOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(AlignmentRecord, Iterable[X]), (AlignmentRecord, Seq[Y])]

    Permalink

    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. PySpark/Java friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic 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.

    Definition Classes
    GenomicDataset
  57. def leftOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(AlignmentRecord, Iterable[X]), (AlignmentRecord, Seq[Y])]

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    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. SparkR friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic 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.

    Definition Classes
    GenomicDataset
  58. def log: Logger

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    Attributes
    protected
    Definition Classes
    Logging
  59. def logDebug(msg: ⇒ String, throwable: Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  60. def logDebug(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  61. def logError(msg: ⇒ String, throwable: Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  62. def logError(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  63. def logInfo(msg: ⇒ String, throwable: Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  64. def logInfo(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  65. def logName: String

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    Attributes
    protected
    Definition Classes
    Logging
  66. def logTrace(msg: ⇒ String, throwable: Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  67. def logTrace(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  68. def logWarning(msg: ⇒ String, throwable: Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  69. def logWarning(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  70. def markDuplicates(): AlignmentRecordRDD

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    Marks reads as possible fragment duplicates.

    Marks reads as possible fragment duplicates.

    returns

    A new RDD where reads have the duplicate read flag set. Duplicate reads are NOT filtered out.

  71. final def ne(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  72. final def notify(): Unit

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    Definition Classes
    AnyRef
  73. final def notifyAll(): Unit

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    Definition Classes
    AnyRef
  74. def persist(sl: StorageLevel): AlignmentRecordRDD

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    Persists underlying RDD in memory or disk.

    Persists underlying RDD in memory or disk.

    sl

    new StorageLevel

    returns

    Persisted GenomicDataset.

    Definition Classes
    GenomicDataset
  75. def pipe[X, Y <: Product, Z <: GenomicDataset[X, Y, Z], W <: InFormatter[AlignmentRecord, AlignmentRecord, AlignmentRecordRDD, W]](cmd: List[String], files: List[String], environment: Map[String, String], flankSize: Integer, tFormatter: Class[W], xFormatter: OutFormatter[X], convFn: Function2[AlignmentRecordRDD, RDD[X], Z]): Z

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    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.

    X

    The type of the record created by the piped command.

    Y

    A GenomicDataset containing X's.

    cmd

    Command to run.

    files

    Files to make locally available to the commands being run. Default is empty.

    environment

    A map containing environment variable/value pairs to set in the environment for the newly created process. Default is empty.

    flankSize

    Number of bases to flank each command invocation by.

    tFormatter

    Class of formatter for data going into pipe command.

    xFormatter

    Formatter for data coming out of the pipe command.

    convFn

    The conversion function used to build the final RDD.

    returns

    Returns a new GenomicDataset of type Y.

    Definition Classes
    GenomicDataset
  76. def pipe[X, Y <: Product, Z <: GenomicDataset[X, Y, Z], W <: InFormatter[AlignmentRecord, AlignmentRecord, AlignmentRecordRDD, W]](cmd: Seq[Any], files: Seq[Any], environment: Map[Any, Any], flankSize: Double, tFormatter: Class[W], xFormatter: OutFormatter[X], convFn: Function2[AlignmentRecordRDD, RDD[X], Z]): Z

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    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.

    X

    The type of the record created by the piped command.

    Y

    A GenomicDataset containing X's.

    cmd

    Command to run.

    files

    Files to make locally available to the commands being run. Default is empty.

    environment

    A map containing environment variable/value pairs to set in the environment for the newly created process. Default is empty.

    flankSize

    Number of bases to flank each command invocation by.

    tFormatter

    Class of formatter for data going into pipe command.

    xFormatter

    Formatter for data coming out of the pipe command.

    convFn

    The conversion function used to build the final RDD.

    returns

    Returns a new GenomicDataset of type Y.

    Definition Classes
    GenomicDataset
  77. def pipe[X, Y <: Product, Z <: GenomicDataset[X, Y, Z], W <: InFormatter[AlignmentRecord, AlignmentRecord, AlignmentRecordRDD, W]](cmd: Seq[String], files: Seq[String] = Seq.empty, environment: Map[String, String] = Map.empty, flankSize: Int = 0, optTimeout: Option[Int] = None)(implicit tFormatterCompanion: InFormatterCompanion[AlignmentRecord, AlignmentRecord, AlignmentRecordRDD, W], xFormatter: OutFormatter[X], convFn: (AlignmentRecordRDD, RDD[X]) ⇒ Z, tManifest: ClassTag[AlignmentRecord], xManifest: ClassTag[X]): Z

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    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 GenomicDataset. The implicit InFormatterCompanion yields an InFormatter which is used to format the input to the pipe, and the implicit OutFormatter is used to parse the output from the pipe.

    X

    The type of the record created by the piped command.

    Y

    A GenomicDataset containing X's.

    cmd

    Command to run.

    files

    Files to make locally available to the commands being run. Default is empty.

    environment

    A map containing environment variable/value pairs to set in the environment for the newly created process. Default is empty.

    flankSize

    Number of bases to flank each command invocation by.

    optTimeout

    An optional parameter specifying how long to let a single partition run for, in seconds. If the partition times out, the partial results will be returned, and no exception will be logged. The partition will log that the command timed out.

    returns

    Returns a new GenomicDataset of type Y.

    Definition Classes
    GenomicDataset
  78. val productFn: (AlignmentRecord) ⇒ AlignmentRecord

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    Attributes
    protected
    Definition Classes
    AlignmentRecordRDDGenomicDataset
  79. def realignIndels(consensusModel: ConsensusGenerator = new ConsensusGeneratorFromReads, isSorted: Boolean = false, maxIndelSize: Int = 500, maxConsensusNumber: Int = 30, lodThreshold: Double = 5.0, maxTargetSize: Int = 3000, maxReadsPerTarget: Int = 20000, optReferenceFile: Option[ReferenceFile] = None, unclipReads: Boolean = false): AlignmentRecordRDD

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    Realigns indels using a concensus-based heuristic.

    Realigns indels using a concensus-based heuristic.

    consensusModel

    The model to use for generating consensus sequences to realign against.

    isSorted

    If the input data is sorted, setting this parameter to true avoids a second sort.

    maxIndelSize

    The size of the largest indel to use for realignment.

    maxConsensusNumber

    The maximum number of consensus sequences to realign against per target region.

    lodThreshold

    Log-odds threshold to use when realigning; realignments are only finalized if the log-odds threshold is exceeded.

    maxTargetSize

    The maximum width of a single target region for realignment.

    optReferenceFile

    An optional reference. If not provided, reference will be inferred from MD tags.

    unclipReads

    If true, unclips reads prior to realignment. Else, omits clipped bases during realignment.

    returns

    Returns an RDD of mapped reads which have been realigned.

  80. def realignIndels(consensusModel: ConsensusGenerator, isSorted: Boolean, maxIndelSize: Integer, maxConsensusNumber: Integer, lodThreshold: Double, maxTargetSize: Integer): AlignmentRecordRDD

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    Realigns indels using a consensus-based heuristic.

    Realigns indels using a consensus-based heuristic.

    Java friendly variant.

    consensusModel

    The model to use for generating consensus sequences to realign against.

    isSorted

    If the input data is sorted, setting this parameter to true avoids a second sort.

    maxIndelSize

    The size of the largest indel to use for realignment.

    maxConsensusNumber

    The maximum number of consensus sequences to realign against per target region.

    lodThreshold

    Log-odds threshold to use when realigning; realignments are only finalized if the log-odds threshold is exceeded.

    maxTargetSize

    The maximum width of a single target region for realignment.

    returns

    Returns an RDD of mapped reads which have been realigned.

  81. def reassembleReadPairs(secondPairRdd: RDD[AlignmentRecord], validationStringency: ValidationStringency = ValidationStringency.LENIENT): AlignmentRecordRDD

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    Reassembles read pairs from two sets of unpaired reads.

    Reassembles read pairs from two sets of unpaired reads. The assumption is that the two sets were _originally_ paired together.

    secondPairRdd

    The rdd containing the second read from the pairs.

    validationStringency

    How stringently to validate the reads.

    returns

    Returns an RDD with the pair information recomputed.

    Note

    The RDD that this is called on should be the RDD with the first read from the pair.

  82. def reassembleReadPairs(secondPairRdd: JavaRDD[AlignmentRecord], validationStringency: ValidationStringency): AlignmentRecordRDD

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    Reassembles read pairs from two sets of unpaired reads.

    Reassembles read pairs from two sets of unpaired reads. The assumption is that the two sets were _originally_ paired together. Java friendly variant.

    secondPairRdd

    The rdd containing the second read from the pairs.

    validationStringency

    How stringently to validate the reads.

    returns

    Returns an RDD with the pair information recomputed.

    Note

    The RDD that this is called on should be the RDD with the first read from the pair.

  83. def recalibrateBaseQualities(knownSnps: Broadcast[SnpTable], minAcceptableQuality: Int = 5, optStorageLevel: Option[StorageLevel] = Some(StorageLevel.MEMORY_ONLY), optSamplingFraction: Option[Double] = None, optSamplingSeed: Option[Long] = None): AlignmentRecordRDD

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    Runs base quality score recalibration on a set of reads.

    Runs base quality score recalibration on a set of reads. Uses a table of known SNPs to mask true variation during the recalibration process.

    knownSnps

    A table of known SNPs to mask valid variants.

    minAcceptableQuality

    The minimum quality score to recalibrate.

    optStorageLevel

    An optional storage level to set for the output of the first stage of BQSR. Defaults to StorageLevel.MEMORY_ONLY.

    optSamplingFraction

    An optional fraction of reads to sample when generating the covariate table.

    optSamplingSeed

    An optional seed to provide if downsampling reads.

    returns

    Returns an RDD of recalibrated reads.

  84. def recalibrateBaseQualities(knownSnps: VariantRDD, minAcceptableQuality: Integer, storageLevel: StorageLevel): AlignmentRecordRDD

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    Runs base quality score recalibration on a set of reads.

    Runs base quality score recalibration on a set of reads. Uses a table of known SNPs to mask true variation during the recalibration process.

    Java friendly variant.

    knownSnps

    A table of known SNPs to mask valid variants.

    minAcceptableQuality

    The minimum quality score to recalibrate.

    storageLevel

    An optional storage level to set for the output of the first stage of BQSR. Set to null to omit.

    returns

    Returns an RDD of recalibrated reads.

  85. def replaceRdd(newRdd: RDD[AlignmentRecord], newPartitionMap: Option[Array[Option[(ReferenceRegion, ReferenceRegion)]]] = None): AlignmentRecordRDD

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    Attributes
    protected
    Definition Classes
    AlignmentRecordRDDGenomicDataset
  86. def replaceRddAndSequences(newRdd: RDD[AlignmentRecord], newSequences: SequenceDictionary, partitionMap: Option[Array[Option[(ReferenceRegion, ReferenceRegion)]]] = None): AlignmentRecordRDD

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    Replaces the underlying RDD and SequenceDictionary and emits a new object.

    Replaces the underlying RDD and SequenceDictionary and emits a new object.

    newRdd

    New RDD to replace current RDD.

    newSequences

    New sequence dictionary to replace current dictionary.

    returns

    Returns a new AlignmentRecordRDD.

    Attributes
    protected
  87. def rightOuterBroadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X], otxTag: ClassTag[(Option[AlignmentRecord], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[AlignmentRecord], Y)]): GenericGenomicDataset[(Option[AlignmentRecord], X), (Option[AlignmentRecord], Y)]

    Permalink

    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.

    genomicRdd

    The right RDD in the join.

    returns

    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.

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoin

  88. def rightOuterBroadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X], otxTag: ClassTag[(Option[AlignmentRecord], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[AlignmentRecord], Y)]): GenericGenomicDataset[(Option[AlignmentRecord], X), (Option[AlignmentRecord], Y)]

    Permalink

    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.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic 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.

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoin

  89. def rightOuterBroadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Option[AlignmentRecord], X), (Option[AlignmentRecord], Y)]

    Permalink

    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. PySpark/Java friendly version.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic 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.

    Definition Classes
    GenomicDataset
  90. def rightOuterBroadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Option[AlignmentRecord], X), (Option[AlignmentRecord], Y)]

    Permalink

    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. SparkR friendly version.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic 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.

    Definition Classes
    GenomicDataset
  91. def rightOuterBroadcastRegionJoinAgainst[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](broadcast: GenomicBroadcast[X, Y, Z])(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X], oyuTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Y], AlignmentRecord)]): GenericGenomicDataset[(Option[X], AlignmentRecord), (Option[Y], AlignmentRecord)]

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    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.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
    Note

    This function differs from other region joins as it treats the calling RDD as the right side of the join, and not the left.

    See also

    rightOuterBroadcastRegionJoin

  92. def rightOuterBroadcastRegionJoinAgainstAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](broadcast: GenomicBroadcast[X, Y, Z])(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X], syuTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Y], AlignmentRecord)]): GenericGenomicDataset[(Iterable[X], AlignmentRecord), (Seq[Y], AlignmentRecord)]

    Permalink

    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.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
    Note

    This function differs from other region joins as it treats the calling RDD as the right side of the join, and not the left.

    See also

    rightOuterBroadcastRegionJoinAndGroupByRight

  93. def rightOuterBroadcastRegionJoinAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[AlignmentRecord], X)], iuyTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[AlignmentRecord], Y)]): GenericGenomicDataset[(Iterable[AlignmentRecord], X), (Seq[AlignmentRecord], Y)]

    Permalink

    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.

    genomicRdd

    The right RDD in the join.

    returns

    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.

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

  94. def rightOuterBroadcastRegionJoinAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[AlignmentRecord], X)], iuyTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[AlignmentRecord], Y)]): GenericGenomicDataset[(Iterable[AlignmentRecord], X), (Seq[AlignmentRecord], Y)]

    Permalink

    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.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic 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.

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

  95. def rightOuterBroadcastRegionJoinAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Iterable[AlignmentRecord], X), (Seq[AlignmentRecord], Y)]

    Permalink

    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. PySpark/Java friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic 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.

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

  96. def rightOuterBroadcastRegionJoinAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Iterable[AlignmentRecord], X), (Seq[AlignmentRecord], Y)]

    Permalink

    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. SparkR friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic 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.

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

  97. def rightOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X], otxTag: ClassTag[(Option[AlignmentRecord], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[AlignmentRecord], Y)]): GenericGenomicDataset[(Option[AlignmentRecord], X), (Option[AlignmentRecord], Y)]

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    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.

    genomicRdd

    The right RDD in the join.

    returns

    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.

    Definition Classes
    GenomicDataset
  98. def rightOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X], otxTag: ClassTag[(Option[AlignmentRecord], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[AlignmentRecord], Y)]): GenericGenomicDataset[(Option[AlignmentRecord], X), (Option[AlignmentRecord], Y)]

    Permalink

    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.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic 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.

    Definition Classes
    GenomicDataset
  99. def rightOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Option[AlignmentRecord], X), (Option[AlignmentRecord], Y)]

    Permalink

    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. PySpark/Java friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic 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.

    Definition Classes
    GenomicDataset
  100. def rightOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Option[AlignmentRecord], X), (Option[AlignmentRecord], Y)]

    Permalink

    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. SparkR friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic 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.

    Definition Classes
    GenomicDataset
  101. def rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X], otixTag: ClassTag[(Option[AlignmentRecord], Iterable[X])], otsyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[AlignmentRecord], Seq[Y])]): GenericGenomicDataset[(Option[AlignmentRecord], Iterable[X]), (Option[AlignmentRecord], Seq[Y])]

    Permalink

    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.

    genomicRdd

    The right RDD in the join.

    returns

    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.

    Definition Classes
    GenomicDataset
  102. def rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X], otixTag: ClassTag[(Option[AlignmentRecord], Iterable[X])], ousyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[AlignmentRecord], Seq[Y])]): GenericGenomicDataset[(Option[AlignmentRecord], Iterable[X]), (Option[AlignmentRecord], Seq[Y])]

    Permalink

    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.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic 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.

    Definition Classes
    GenomicDataset
  103. def rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Option[AlignmentRecord], Iterable[X]), (Option[AlignmentRecord], Seq[Y])]

    Permalink

    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. PySpark/Java friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic 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.

    Definition Classes
    GenomicDataset
  104. def rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Option[AlignmentRecord], Iterable[X]), (Option[AlignmentRecord], Seq[Y])]

    Permalink

    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. SparkR friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic 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.

    Definition Classes
    GenomicDataset
  105. def save(filePath: String, isSorted: Boolean): Boolean

    Permalink

    Saves this RDD to disk, with the type identified by the extension.

    Saves this RDD to disk, with the type identified by the extension.

    filePath

    Path to save the file at.

    isSorted

    Whether the file is sorted or not.

    returns

    Returns true if saving succeeded.

  106. def save(args: ADAMSaveAnyArgs, isSorted: Boolean = false): Boolean

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    Saves AlignmentRecords as a directory of Parquet files or as SAM/BAM.

    Saves AlignmentRecords 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.

    args

    Save configuration arguments.

    isSorted

    If the output is sorted, this will modify the SAM/BAM header.

    returns

    Returns true if saving succeeded.

  107. def saveAsFastq(fileName: String, fileName2Opt: Option[String] = None, outputOriginalBaseQualities: Boolean = false, sort: Boolean = false, asSingleFile: Boolean = false, disableFastConcat: Boolean = false, validationStringency: ValidationStringency = ValidationStringency.LENIENT, persistLevel: Option[StorageLevel] = None): Unit

    Permalink

    Saves reads in FASTQ format.

    Saves reads in FASTQ format.

    fileName

    Path to save files at.

    fileName2Opt

    Optional second path for saving files. If set, two files will be saved.

    outputOriginalBaseQualities

    If true, writes out reads with the base qualities from the original qualities (SAM "OQ") field. If false, writes out reads with the base qualities from the qual field. Default is false.

    sort

    Whether to sort the FASTQ files by read name or not. Defaults to false. Sorting the output will recover pair order, if desired.

    asSingleFile

    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.

    disableFastConcat

    If asSingleFile is true, disables the use of the parallel file merging engine.

    validationStringency

    Iff strict, throw an exception if any read in this RDD is not accompanied by its mate.

    persistLevel

    An optional persistance level to set. If this level is set, then reads will be cached (at the given persistance) level between passes.

  108. def saveAsFastq(fileName: String, outputOriginalBaseQualities: Boolean, sort: Boolean, asSingleFile: Boolean, disableFastConcat: Boolean, validationStringency: ValidationStringency): Unit

    Permalink

    Saves reads in FASTQ format.

    Saves reads in FASTQ format.

    Java friendly variant.

    fileName

    Path to save files at.

    outputOriginalBaseQualities

    If true, writes out reads with the base qualities from the original qualities (SAM "OQ") field. If false, writes out reads with the base qualities from the qual field. Default is false.

    sort

    Whether to sort the FASTQ files by read name or not. Defaults to false. Sorting the output will recover pair order, if desired.

    asSingleFile

    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.

    disableFastConcat

    If asSingleFile is true, disables the use of the parallel file merging engine.

    validationStringency

    Iff strict, throw an exception if any read in this RDD is not accompanied by its mate.

  109. def saveAsPairedFastq(fileName1: String, fileName2: String, outputOriginalBaseQualities: Boolean = false, asSingleFile: Boolean = false, disableFastConcat: Boolean = false, validationStringency: ValidationStringency = ValidationStringency.LENIENT, persistLevel: Option[StorageLevel] = None): Unit

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    Saves these AlignmentRecords to two FASTQ files.

    Saves these AlignmentRecords 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.

    fileName1

    Path at which to save a FASTQ file containing the first mate of each pair.

    fileName2

    Path at which to save a FASTQ file containing the second mate of each pair.

    outputOriginalBaseQualities

    If true, writes out reads with the base qualities from the original qualities (SAM "OQ") field. If false, writes out reads with the base qualities from the qual field. Default is false.

    asSingleFile

    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.

    disableFastConcat

    If asSingleFile is true, disables the use of the parallel file merging engine.

    validationStringency

    Iff strict, throw an exception if any read in this RDD is not accompanied by its mate.

    persistLevel

    An optional persistance level to set. If this level is set, then reads will be cached (at the given persistance) level between passes.

  110. def saveAsPairedFastq(fileName1: String, fileName2: String, outputOriginalBaseQualities: Boolean, asSingleFile: Boolean, disableFastConcat: Boolean, validationStringency: ValidationStringency, persistLevel: StorageLevel): Unit

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    Saves these AlignmentRecords to two FASTQ files.

    Saves these AlignmentRecords 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. Java friendly variant.

    fileName1

    Path at which to save a FASTQ file containing the first mate of each pair.

    fileName2

    Path at which to save a FASTQ file containing the second mate of each pair.

    outputOriginalBaseQualities

    If true, writes out reads with the base qualities from the original qualities (SAM "OQ") field. If false, writes out reads with the base qualities from the qual field. Default is false.

    asSingleFile

    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.

    disableFastConcat

    If asSingleFile is true, disables the use of the parallel file merging engine.

    validationStringency

    Iff strict, throw an exception if any read in this RDD is not accompanied by its mate.

    persistLevel

    The persistence level to cache reads at between passes.

  111. def saveAsParquet(filePath: String): Unit

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    Saves this RDD to disk as a Parquet file.

    Saves this RDD to disk as a Parquet file.

    filePath

    Path to save the file at.

    Definition Classes
    AvroGenomicDataset
  112. def saveAsParquet(filePath: String, blockSize: Integer, pageSize: Integer, compressCodec: CompressionCodecName, disableDictionaryEncoding: Boolean): Unit

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    Saves this RDD to disk as a Parquet file.

    Saves this RDD to disk as a Parquet file.

    filePath

    Path to save the file at.

    blockSize

    Size per block.

    pageSize

    Size per page.

    compressCodec

    Name of the compression codec to use.

    disableDictionaryEncoding

    Whether or not to disable bit-packing.

    Definition Classes
    AvroGenomicDataset
  113. def saveAsParquet(filePath: String, blockSize: Int = 128 * 1024 * 1024, pageSize: Int = 1 * 1024 * 1024, compressCodec: CompressionCodecName = CompressionCodecName.GZIP, disableDictionaryEncoding: Boolean = false): Unit

    Permalink

    Saves this RDD to disk as a Parquet file.

    Saves this RDD to disk as a Parquet file.

    filePath

    Path to save the file at.

    blockSize

    Size per block.

    pageSize

    Size per page.

    compressCodec

    Name of the compression codec to use.

    disableDictionaryEncoding

    Whether or not to disable bit-packing. Default is false.

    Definition Classes
    AvroGenomicDatasetGenomicDataset
  114. def saveAsParquet(args: SaveArgs): Unit

    Permalink

    Saves an RDD to Parquet.

    Saves an RDD to Parquet.

    args

    The output format configuration to use when saving the data.

    Definition Classes
    GenomicDataset
  115. def saveAsPartitionedParquet(filePath: String, compressCodec: CompressionCodecName = CompressionCodecName.GZIP, partitionSize: Int = 1000000): Unit

    Permalink

    Saves this RDD to disk in range binned partitioned Parquet + Avro format

    Saves this RDD to disk in range binned partitioned Parquet + Avro format

    filePath

    Path to save the file at.

    compressCodec

    Name of the compression codec to use.

    partitionSize

    size of partitions used when writing parquet, in base pairs. Defaults to 1000000.

    Definition Classes
    AvroGenomicDataset
  116. def saveAsSam(filePath: String, asType: SAMFormat, asSingleFile: Boolean, isSorted: Boolean): Unit

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    Saves this RDD to disk as a SAM/BAM/CRAM file.

    Saves this RDD to disk as a SAM/BAM/CRAM file.

    filePath

    Path to save the file at.

    asType

    The SAMFormat to save as. If left null, we will infer the format from the file extension.

    asSingleFile

    If true, saves output as a single file.

    isSorted

    If the output is sorted, this will modify the header.

  117. def saveAsSam(filePath: String, asType: Option[SAMFormat] = None, asSingleFile: Boolean = false, isSorted: Boolean = false, deferMerging: Boolean = false, disableFastConcat: Boolean = false): Unit

    Permalink

    Saves an RDD of ADAM read data into the SAM/BAM format.

    Saves an RDD of ADAM read data into the SAM/BAM format.

    filePath

    Path to save files to.

    asType

    Selects whether to save as SAM, BAM, or CRAM. The default value is None, which means the file type is inferred from the extension.

    asSingleFile

    If true, saves output as a single file.

    isSorted

    If the output is sorted, this will modify the header.

    deferMerging

    If true and asSingleFile is true, we will save the output shards as a headerless file, but we will not merge the shards.

    disableFastConcat

    If asSingleFile is true and deferMerging is false, disables the use of the parallel file merging engine.

  118. def saveAsSamString(): String

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    Converts an RDD into the SAM spec string it represents.

    Converts an RDD into the SAM spec string it represents.

    This method converts an RDD of AlignmentRecords 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.

    returns

    A string on the driver representing this RDD of reads in SAM format.

  119. def saveAvro[U <: SpecificRecordBase](pathName: String, sc: SparkContext, schema: Schema, avro: Seq[U])(implicit tUag: ClassTag[U]): Unit

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    Saves Avro data to a Hadoop file system.

    Saves Avro data to a Hadoop file system.

    This method uses a SparkContext to identify our underlying file system, which we then save to.

    Frustratingly enough, although all records generated by the Avro IDL compiler have a static SCHEMA$ field, this field does not belong to the SpecificRecordBase abstract class, or the SpecificRecord interface. As such, we must force the user to pass in the schema.

    U

    The type of the specific record we are saving.

    pathName

    Path to save records to.

    sc

    SparkContext used for identifying underlying file system.

    schema

    Schema of records we are saving.

    avro

    Seq of records we are saving.

    Attributes
    protected
    Definition Classes
    GenomicDataset
  120. def saveMetadata(filePath: String): Unit

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    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.

    filePath

    The filepath to the file where we will save the Metadata.

    Attributes
    protected
    Definition Classes
    AvroRecordGroupGenomicDatasetAvroGenomicDataset
  121. def savePartitionMap(filePath: String): Unit

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    Save the partition map to disk.

    Save the partition map to disk. This is done by adding the partition map to the schema.

    filePath

    The filepath where we will save the partition map.

    Attributes
    protected
    Definition Classes
    AvroGenomicDataset
  122. def saveProcessingSteps(filePath: String): Unit

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    Save the processing steps to disk.

    Save the processing steps to disk.

    filePath

    The filepath to the directory within which we will save the processing step descriptions..

    Attributes
    protected
    Definition Classes
    AvroRecordGroupGenomicDataset
  123. def saveRddAsParquet(pathName: String, blockSize: Int = 128 * 1024 * 1024, pageSize: Int = 1 * 1024 * 1024, compressCodec: CompressionCodecName = CompressionCodecName.GZIP, disableDictionaryEncoding: Boolean = false, optSchema: Option[Schema] = None): Unit

    Permalink

    Saves an RDD of Avro data to Parquet.

    Saves an RDD of Avro data to Parquet.

    pathName

    The path to save the file to.

    blockSize

    The size in bytes of blocks to write. Defaults to 128 * 1024 * 1024.

    pageSize

    The size in bytes of pages to write. Defaults to 1 * 1024 * 1024.

    compressCodec

    The compression codec to apply to pages. Defaults to CompressionCodecName.GZIP.

    disableDictionaryEncoding

    If false, dictionary encoding is used. If true, delta encoding is used. Defaults to false.

    optSchema

    The optional schema to set. Defaults to None.

    Attributes
    protected
    Definition Classes
    AvroGenomicDataset
  124. def saveRddAsParquet(args: SaveArgs): Unit

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    Attributes
    protected
    Definition Classes
    AvroGenomicDataset
  125. def saveRecordGroups(filePath: String): Unit

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    Save the record groups to disk.

    Save the record groups to disk.

    filePath

    The filepath to the file where we will save the record groups.

    Attributes
    protected
    Definition Classes
    AvroRecordGroupGenomicDataset
  126. def saveSequences(filePath: String): Unit

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    Save the sequence dictionary to disk.

    Save the sequence dictionary to disk.

    filePath

    The filepath where we will save the sequence dictionary.

    Attributes
    protected
    Definition Classes
    GenomicDataset
  127. def shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X], txTag: ClassTag[(AlignmentRecord, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(AlignmentRecord, Y)]): GenericGenomicDataset[(AlignmentRecord, X), (AlignmentRecord, Y)]

    Permalink

    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.

    genomicRdd

    The right RDD in the join.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
  128. def shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X], txTag: ClassTag[(AlignmentRecord, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(AlignmentRecord, Y)]): GenericGenomicDataset[(AlignmentRecord, X), (AlignmentRecord, Y)]

    Permalink

    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.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
  129. def shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(AlignmentRecord, X), (AlignmentRecord, Y)]

    Permalink

    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. PySpark/Java friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
  130. def shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(AlignmentRecord, X), (AlignmentRecord, Y)]

    Permalink

    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. SparkR friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
  131. def shuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X], tixTag: ClassTag[(AlignmentRecord, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(AlignmentRecord, Seq[Y])]): GenericGenomicDataset[(AlignmentRecord, Iterable[X]), (AlignmentRecord, Seq[Y])]

    Permalink

    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.

    genomicRdd

    The right RDD in the join.

    returns

    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..

    Definition Classes
    GenomicDataset
  132. def shuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X], tixTag: ClassTag[(AlignmentRecord, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(AlignmentRecord, Seq[Y])]): GenericGenomicDataset[(AlignmentRecord, Iterable[X]), (AlignmentRecord, Seq[Y])]

    Permalink

    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.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, grouped together by the value they overlapped in the left RDD..

    Definition Classes
    GenomicDataset
  133. def shuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(AlignmentRecord, Iterable[X]), (AlignmentRecord, Seq[Y])]

    Permalink

    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. In the same operation, we group all values by the left item in the RDD. PySpark/Java friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, grouped together by the value they overlapped in the left RDD.

    Definition Classes
    GenomicDataset
  134. def shuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(AlignmentRecord, Iterable[X]), (AlignmentRecord, Seq[Y])]

    Permalink

    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. In the same operation, we group all values by the left item in the RDD. SparkR friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, grouped together by the value they overlapped in the left RDD.

    Definition Classes
    GenomicDataset
  135. def sort(partitions: Int = rdd.partitions.length, stringency: ValidationStringency = ValidationStringency.STRICT)(implicit tTag: ClassTag[AlignmentRecord]): AlignmentRecordRDD

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    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.

    partitions

    The number of partitions for the new RDD.

    stringency

    The level of ValidationStringency to enforce.

    returns

    Returns a new RDD containing sorted data.

    Definition Classes
    GenomicDataset
    Note

    Uses ValidationStringency to handle unaligned or where objects align to multiple positions.

    See also

    sortLexicographically

  136. def sort(): AlignmentRecordRDD

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    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

    Returns a new RDD containing sorted data.

    Definition Classes
    GenomicDataset
    See also

    sortLexicographically

  137. def sortLexicographically(partitions: Int = rdd.partitions.length, storePartitionMap: Boolean = false, storageLevel: StorageLevel = StorageLevel.MEMORY_ONLY, stringency: ValidationStringency = ValidationStringency.STRICT)(implicit tTag: ClassTag[AlignmentRecord]): AlignmentRecordRDD

    Permalink

    Sorts our genome aligned data by reference positions, with contigs ordered lexicographically.

    Sorts our genome aligned data by reference positions, with contigs ordered lexicographically.

    partitions

    The number of partitions for the new RDD.

    storePartitionMap

    A Boolean flag to determine whether to store the partition bounds from the resulting RDD.

    storageLevel

    The level at which to persist the resulting RDD.

    stringency

    The level of ValidationStringency to enforce.

    returns

    Returns a new RDD containing sorted data.

    Definition Classes
    GenomicDataset
    Note

    Uses ValidationStringency to handle data that is unaligned or where objects align to multiple positions.

    See also

    sort

  138. def sortLexicographically(): AlignmentRecordRDD

    Permalink

    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

    Returns a new RDD containing sorted data.

    Definition Classes
    GenomicDataset
    See also

    sort

  139. def sortReadsByReferencePosition(): AlignmentRecordRDD

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    Sorts our read data by reference positions, with contigs ordered by name.

    Sorts our read data by reference positions, with contigs ordered by name.

    Sorts reads by the location where they are aligned. Unaligned reads are put at the end and sorted by read name. Contigs are ordered lexicographically.

    returns

    Returns a new RDD containing sorted reads.

    See also

    sortReadsByReferencePositionAndIndex

  140. def sortReadsByReferencePositionAndIndex(): AlignmentRecordRDD

    Permalink

    Sorts our read data by reference positions, with contigs ordered by index.

    Sorts our read data by reference positions, with contigs ordered by index.

    Sorts reads by the location where they are aligned. Unaligned reads are put at the end and sorted by read name. Contigs are ordered by index that they are ordered in the SequenceDictionary.

    returns

    Returns a new RDD containing sorted reads.

    See also

    sortReadsByReferencePosition

  141. final def synchronized[T0](arg0: ⇒ T0): T0

    Permalink
    Definition Classes
    AnyRef
  142. def toCoverage(): CoverageRDD

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    Converts this set of reads into a corresponding CoverageRDD.

    Converts this set of reads into a corresponding CoverageRDD.

    returns

    CoverageRDD containing mapped RDD of Coverage.

  143. def toDF(): DataFrame

    Permalink

    returns

    This data as a Spark SQL DataFrame.

    Definition Classes
    GenomicDataset
  144. def toFragments(): FragmentRDD

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    Convert this set of reads into fragments.

    Convert this set of reads into fragments.

    returns

    Returns a FragmentRDD where all reads have been grouped together by the original sequence fragment they come from.

  145. def toString(): String

    Permalink
    Definition Classes
    AvroRecordGroupGenomicDatasetGenomicDataset → AnyRef → Any
  146. def transform(tFn: Function[JavaRDD[AlignmentRecord], JavaRDD[AlignmentRecord]]): AlignmentRecordRDD

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    Applies a function that transforms the underlying RDD into a new RDD.

    Applies a function that transforms the underlying RDD into a new RDD.

    tFn

    A function that transforms the underlying RDD.

    returns

    A new RDD where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.

    Definition Classes
    GenomicDataset
  147. def transform(tFn: (RDD[AlignmentRecord]) ⇒ RDD[AlignmentRecord]): AlignmentRecordRDD

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    Applies a function that transforms the underlying RDD into a new RDD.

    Applies a function that transforms the underlying RDD into a new RDD.

    tFn

    A function that transforms the underlying RDD.

    returns

    A new RDD where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.

    Definition Classes
    GenomicDataset
  148. def transformDataFrame(tFn: Function[DataFrame, DataFrame]): AlignmentRecordRDD

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    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.

    tFn

    A function that transforms the underlying RDD as a DataFrame.

    returns

    A new RDD where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.

    Definition Classes
    GenomicDataset
  149. def transformDataFrame(tFn: (DataFrame) ⇒ DataFrame)(implicit uTag: scala.reflect.api.JavaUniverse.TypeTag[AlignmentRecord]): AlignmentRecordRDD

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    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.

    tFn

    A function that transforms the underlying RDD as a DataFrame.

    returns

    A new RDD where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.

    Definition Classes
    GenomicDataset
  150. def transformDataset(tFn: (Dataset[AlignmentRecord]) ⇒ Dataset[AlignmentRecord]): AlignmentRecordRDD

    Permalink

    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.

    tFn

    A function that transforms the underlying RDD as a Dataset.

    returns

    A new RDD where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) is copied without modification.

    Definition Classes
    AlignmentRecordRDDGenomicDataset
  151. def transmute[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[JavaRDD[AlignmentRecord], JavaRDD[X]], convFn: Function2[AlignmentRecordRDD, RDD[X], Z]): Z

    Permalink

    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.

    tFn

    A function that transforms the underlying RDD.

    convFn

    The conversion function used to build the final RDD.

    returns

    A new RDD where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.

    Definition Classes
    GenomicDataset
  152. def transmute[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: (RDD[AlignmentRecord]) ⇒ RDD[X])(implicit convFn: (AlignmentRecordRDD, RDD[X]) ⇒ Z): Z

    Permalink

    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.

    tFn

    A function that transforms the underlying RDD.

    returns

    A new RDD where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.

    Definition Classes
    GenomicDataset
  153. def transmuteDataFrame[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[DataFrame, DataFrame], convFn: GenomicDatasetConversion[AlignmentRecord, AlignmentRecord, AlignmentRecordRDD, X, Y, Z]): Z

    Permalink

    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.

    tFn

    A function that transforms the underlying RDD.

    returns

    A new RDD where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.

    Definition Classes
    GenomicDataset
  154. def transmuteDataFrame[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: (DataFrame) ⇒ DataFrame)(implicit yTag: scala.reflect.api.JavaUniverse.TypeTag[Y], convFn: (AlignmentRecordRDD, Dataset[Y]) ⇒ Z): Z

    Permalink

    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.

    tFn

    A function that transforms the underlying RDD.

    returns

    A new RDD where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.

    Definition Classes
    GenomicDataset
  155. def transmuteDataset[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[Dataset[AlignmentRecord], Dataset[Y]], convFn: GenomicDatasetConversion[AlignmentRecord, AlignmentRecord, AlignmentRecordRDD, X, Y, Z]): Z

    Permalink

    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.

    tFn

    A function that transforms the underlying RDD.

    returns

    A new RDD where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.

    Definition Classes
    GenomicDataset
  156. def transmuteDataset[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: (Dataset[AlignmentRecord]) ⇒ Dataset[Y])(implicit yTag: scala.reflect.api.JavaUniverse.TypeTag[Y], convFn: (AlignmentRecordRDD, Dataset[Y]) ⇒ Z): Z

    Permalink

    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.

    tFn

    A function that transforms the underlying RDD.

    returns

    A new RDD where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.

    Definition Classes
    GenomicDataset
  157. val uTag: scala.reflect.api.JavaUniverse.TypeTag[AlignmentRecord]

    Permalink
    Definition Classes
    AlignmentRecordRDDGenomicDataset
  158. def union(rdds: AlignmentRecordRDD*): AlignmentRecordRDD

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    Unions together multiple genomic RDDs.

    Unions together multiple genomic RDDs.

    rdds

    RDDs to union with this RDD.

    Definition Classes
    AlignmentRecordRDDGenomicDataset
  159. def union(rdds: List[AlignmentRecordRDD]): AlignmentRecordRDD

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    Unions together multiple genomic RDDs.

    Unions together multiple genomic RDDs.

    rdds

    RDDs to union with this RDD.

    Definition Classes
    GenomicDataset
  160. def unpersist(): AlignmentRecordRDD

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    Unpersists underlying RDD from memory or disk.

    Unpersists underlying RDD from memory or disk.

    returns

    Uncached GenomicDataset.

    Definition Classes
    GenomicDataset
  161. val unproductFn: (AlignmentRecord) ⇒ AlignmentRecord

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    Attributes
    protected
    Definition Classes
    AlignmentRecordRDDGenomicDataset
  162. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  163. final def wait(arg0: Long, arg1: Int): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  164. final def wait(arg0: Long): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  165. def writeTextRdd[T](rdd: RDD[T], outputPath: String, asSingleFile: Boolean, disableFastConcat: Boolean, optHeaderPath: Option[String] = None): Unit

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    Writes an RDD to disk as text and optionally merges.

    Writes an RDD to disk as text and optionally merges.

    rdd

    RDD to save.

    outputPath

    Output path to save text files to.

    asSingleFile

    If true, combines all partition shards.

    disableFastConcat

    If asSingleFile is true, disables the use of the parallel file merging engine.

    optHeaderPath

    If provided, the header file to include.

    Attributes
    protected
    Definition Classes
    GenomicDataset

Inherited from AvroGenomicDataset[AlignmentRecord, AlignmentRecord, AlignmentRecordRDD]

Inherited from GenomicDataset[AlignmentRecord, AlignmentRecord, AlignmentRecordRDD]

Inherited from Logging

Inherited from AnyRef

Inherited from Any

Ungrouped