org.bdgenomics.adam.rdd.read

AlignmentRecordRDD

case class AlignmentRecordRDD(rdd: RDD[AlignmentRecord], sequences: SequenceDictionary, recordGroups: RecordGroupDictionary) extends AvroReadGroupGenomicRDD[AlignmentRecord, AlignmentRecordRDD] with Product with Serializable

Linear Supertypes
Product, Equals, AvroReadGroupGenomicRDD[AlignmentRecord, AlignmentRecordRDD], AvroGenomicRDD[AlignmentRecord, AlignmentRecordRDD], GenomicRDD[AlignmentRecord, AlignmentRecordRDD], ADAMRDDFunctions[AlignmentRecord], Logging, Serializable, Serializable, AnyRef, Any
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  1. AlignmentRecordRDD
  2. Product
  3. Equals
  4. AvroReadGroupGenomicRDD
  5. AvroGenomicRDD
  6. GenomicRDD
  7. ADAMRDDFunctions
  8. Logging
  9. Serializable
  10. Serializable
  11. AnyRef
  12. Any
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Instance Constructors

  1. new AlignmentRecordRDD(rdd: RDD[AlignmentRecord], sequences: SequenceDictionary, recordGroups: RecordGroupDictionary)

Value Members

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

    Definition Classes
    AnyRef
  2. final def !=(arg0: Any): Boolean

    Definition Classes
    Any
  3. final def ##(): Int

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

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

    Definition Classes
    Any
  6. final def asInstanceOf[T0]: T0

    Definition Classes
    Any
  7. def broadcastRegionJoin[X, Y <: GenomicRDD[X, Y], Z <: GenomicRDD[(AlignmentRecord, X), Z]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X]): GenomicRDD[(AlignmentRecord, X), Z]

    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
    GenomicRDD
  8. def broadcastRegionJoinAndGroupByRight[X, Y <: GenomicRDD[X, Y], Z <: GenomicRDD[(Iterable[AlignmentRecord], X), Z]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X]): GenomicRDD[(Iterable[AlignmentRecord], X), Z]

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

    Attributes
    protected
    Definition Classes
    AlignmentRecordRDDGenomicRDD
  10. def clone(): AnyRef

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

    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.

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

    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.

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

    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.

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

    Definition Classes
    AnyRef
  15. def filterByOverlappingRegion(query: ReferenceRegion): AlignmentRecordRDD

    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 GenomicRDD containing only data that overlaps the query region.

    Definition Classes
    GenomicRDD
  16. def filterByOverlappingRegions(querys: List[ReferenceRegion]): AlignmentRecordRDD

    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 GenomicRDD containing only data that overlaps the querys region.

    Definition Classes
    GenomicRDD
  17. def finalize(): Unit

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

    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)

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

    Attributes
    protected
    Definition Classes
    GenomicRDD
  20. def fullOuterShuffleRegionJoin[X, Y <: GenomicRDD[X, Y], Z <: GenomicRDD[(Option[AlignmentRecord], Option[X]), Z]](genomicRdd: GenomicRDD[X, Y], optPartitions: Option[Int] = None)(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X]): GenomicRDD[(Option[AlignmentRecord], Option[X]), Z]

    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
    GenomicRDD
  21. final def getClass(): Class[_]

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

    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
    AlignmentRecordRDDGenomicRDD
  23. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any
  24. def isTraceEnabled(): Boolean

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

    The underlying RDD of genomic data, as a JavaRDD.

    The underlying RDD of genomic data, as a JavaRDD.

    Definition Classes
    GenomicRDD
  26. def leftOuterShuffleRegionJoin[X, Y <: GenomicRDD[X, Y], Z <: GenomicRDD[(AlignmentRecord, Option[X]), Z]](genomicRdd: GenomicRDD[X, Y], optPartitions: Option[Int] = None)(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X]): GenomicRDD[(AlignmentRecord, Option[X]), Z]

    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
    GenomicRDD
  27. def log: Logger

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

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

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

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

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

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

    Attributes
    protected
    Definition Classes
    Logging
  34. def logName: String

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

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

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

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

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

    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.

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

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

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

    Definition Classes
    AnyRef
  43. def pipe[X, Y <: GenomicRDD[X, Y], V <: InFormatter[AlignmentRecord, AlignmentRecordRDD, V]](cmd: String, files: Seq[String] = Seq.empty, environment: Map[String, String] = Map.empty, flankSize: Int = 0)(implicit tFormatterCompanion: InFormatterCompanion[AlignmentRecord, AlignmentRecordRDD, V], xFormatter: OutFormatter[X], convFn: (AlignmentRecordRDD, RDD[X]) ⇒ Y, tManifest: ClassTag[AlignmentRecord], xManifest: ClassTag[X]): Y

    Pipes genomic data to a subprocess that runs in parallel using Spark.

    Pipes genomic data to a subprocess that runs in parallel using Spark.

    Files are substituted in to the command with a $x syntax. E.g., to invoke a command that uses the first file from the files Seq, use $0.

    Pipes require the presence of an InFormatterCompanion and an OutFormatter as implicit values. The InFormatterCompanion should be a singleton whose apply method builds an InFormatter given a specific type of GenomicRDD. The implicit InFormatterCompanion yields an InFormatter which is used to format the input to the pipe, and the implicit OutFormatter is used to parse the output from the pipe.

    X

    The type of the record created by the piped command.

    Y

    A GenomicRDD containing X's.

    V

    The InFormatter to use for formatting the data being piped to the command.

    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.

    returns

    Returns a new GenomicRDD of type Y.

    Definition Classes
    GenomicRDD
  44. val rdd: RDD[AlignmentRecord]

    The RDD of genomic data that we are wrapping.

    The RDD of genomic data that we are wrapping.

    Definition Classes
    AlignmentRecordRDDGenomicRDD → ADAMRDDFunctions
  45. def realignIndels(consensusModel: ConsensusGenerator = new ConsensusGeneratorFromReads, isSorted: Boolean = false, maxIndelSize: Int = 500, maxConsensusNumber: Int = 30, lodThreshold: Double = 5.0, maxTargetSize: Int = 3000): AlignmentRecordRDD

    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.

    returns

    Returns an RDD of mapped reads which have been realigned.

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

    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.

  47. def recalibateBaseQualities(knownSnps: Broadcast[SnpTable], minAcceptableQuality: Int = 5, optStorageLevel: Option[StorageLevel] = Some(StorageLevel.MEMORY_ONLY)): AlignmentRecordRDD

    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.

    returns

    Returns an RDD of recalibrated reads.

  48. val recordGroups: RecordGroupDictionary

    A dictionary describing the read groups attached to this GenomicRDD.

    A dictionary describing the read groups attached to this GenomicRDD.

    Definition Classes
    AlignmentRecordRDDAvroReadGroupGenomicRDD
  49. def replaceRdd(newRdd: RDD[AlignmentRecord]): AlignmentRecordRDD

    Attributes
    protected
    Definition Classes
    AlignmentRecordRDDGenomicRDD
  50. def replaceRddAndSequences(newRdd: RDD[AlignmentRecord], newSequences: SequenceDictionary): AlignmentRecordRDD

    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
  51. def rightOuterBroadcastRegionJoin[X, Y <: GenomicRDD[X, Y], Z <: GenomicRDD[(Option[AlignmentRecord], X), Z]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X]): GenomicRDD[(Option[AlignmentRecord], X), Z]

    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
    GenomicRDD
  52. def rightOuterBroadcastRegionJoinAndGroupByRight[X, Y <: GenomicRDD[X, Y], Z <: GenomicRDD[(Iterable[AlignmentRecord], X), Z]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X]): GenomicRDD[(Iterable[AlignmentRecord], X), Z]

    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
    GenomicRDD
  53. def rightOuterShuffleRegionJoin[X, Y <: GenomicRDD[X, Y], Z <: GenomicRDD[(Option[AlignmentRecord], X), Z]](genomicRdd: GenomicRDD[X, Y], optPartitions: Option[Int] = None)(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X]): GenomicRDD[(Option[AlignmentRecord], X), Z]

    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
    GenomicRDD
  54. def rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: GenomicRDD[X, Y], Z <: GenomicRDD[(Option[AlignmentRecord], Iterable[X]), Z]](genomicRdd: GenomicRDD[X, Y], optPartitions: Option[Int] = None)(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X]): GenomicRDD[(Option[AlignmentRecord], Iterable[X]), Z]

    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
    GenomicRDD
  55. def save(filePath: String, isSorted: Boolean): Boolean

    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.

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

    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.

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

    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.

    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.

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

    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.

    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.

  59. def saveAsParquet(filePath: String): Unit

    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
    AvroGenomicRDD
  60. def saveAsParquet(filePath: String, blockSize: Integer, pageSize: Integer, compressCodec: CompressionCodecName, disableDictionaryEncoding: Boolean): Unit

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

    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
    AvroGenomicRDD
  62. def saveAsParquet(args: SaveArgs): Unit

    Saves RDD as a directory of Parquet files.

    Saves RDD as a directory of Parquet files.

    The RDD is written as a directory of Parquet files, with Parquet configuration described by the input param args. The provided sequence dictionary is written at args.outputPath/_seqdict.avro as Avro binary.

    args

    Save configuration arguments.

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

    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.

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

    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.

  65. def saveAsSamString(): String

    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.

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

    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.

    filename

    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
    ADAMRDDFunctions
  67. def saveMetadata(filePath: String): Unit

    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.

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

    Saves an RDD of Avro data to Parquet.

    Saves an RDD of Avro data to Parquet.

    filePath

    The path to save the file to.

    blockSize

    The size in bytes of blocks to write.

    pageSize

    The size in bytes of pages to write.

    compressCodec

    The compression codec to apply to pages.

    disableDictionaryEncoding

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

    schema

    The schema to set.

    Attributes
    protected
    Definition Classes
    ADAMRDDFunctions
  69. def saveRddAsParquet(args: SaveArgs): Unit

    Attributes
    protected
    Definition Classes
    ADAMRDDFunctions
  70. val sequences: SequenceDictionary

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

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

    Definition Classes
    AlignmentRecordRDDGenomicRDD
  71. def shuffleRegionJoin[X, Y <: GenomicRDD[X, Y], Z <: GenomicRDD[(AlignmentRecord, X), Z]](genomicRdd: GenomicRDD[X, Y], optPartitions: Option[Int] = None)(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X]): GenomicRDD[(AlignmentRecord, X), Z]

    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
    GenomicRDD
  72. def shuffleRegionJoinAndGroupByLeft[X, Y <: GenomicRDD[X, Y], Z <: GenomicRDD[(AlignmentRecord, Iterable[X]), Z]](genomicRdd: GenomicRDD[X, Y], optPartitions: Option[Int] = None)(implicit tTag: ClassTag[AlignmentRecord], xTag: ClassTag[X]): GenomicRDD[(AlignmentRecord, Iterable[X]), Z]

    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
    GenomicRDD
  73. def sort(): AlignmentRecordRDD

    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
    GenomicRDD
    Note

    Does not support data that is unaligned or where objects align to multiple positions.

    See also

    sortLexicographically

  74. def sortLexicographically(): AlignmentRecordRDD

    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
    GenomicRDD
    Note

    Does not support data that is unaligned or where objects align to multiple positions.

    See also

    sort

  75. def sortReadsByReferencePosition(): AlignmentRecordRDD

    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

  76. def sortReadsByReferencePositionAndIndex(): AlignmentRecordRDD

    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

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

    Definition Classes
    AnyRef
  78. def toCoverage(collapse: Boolean = true): CoverageRDD

    Converts this set of reads into a corresponding CoverageRDD.

    Converts this set of reads into a corresponding CoverageRDD.

    collapse

    Determines whether to merge adjacent coverage elements with the same score a single coverage.

    returns

    CoverageRDD containing mapped RDD of Coverage.

  79. def toFragments: FragmentRDD

    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.

  80. def transform(tFn: (RDD[AlignmentRecord]) ⇒ RDD[AlignmentRecord]): AlignmentRecordRDD

    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) is copied without modification.

    Definition Classes
    GenomicRDD
  81. final def wait(): Unit

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

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Product

Inherited from Equals

Inherited from AvroReadGroupGenomicRDD[AlignmentRecord, AlignmentRecordRDD]

Inherited from AvroGenomicRDD[AlignmentRecord, AlignmentRecordRDD]

Inherited from GenomicRDD[AlignmentRecord, AlignmentRecordRDD]

Inherited from ADAMRDDFunctions[AlignmentRecord]

Inherited from Logging

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

Ungrouped