Class/Object

org.bdgenomics.utils.interval.rdd

IntervalRDD

Related Docs: object IntervalRDD | package rdd

Permalink

class IntervalRDD[K <: Interval[K], V] extends RDD[(K, V)]

Linear Supertypes
RDD[(K, V)], Logging, Serializable, Serializable, AnyRef, Any
Ordering
  1. Alphabetic
  2. By Inheritance
Inherited
  1. IntervalRDD
  2. RDD
  3. Logging
  4. Serializable
  5. Serializable
  6. AnyRef
  7. Any
  1. Hide All
  2. Show All
Visibility
  1. Public
  2. All

Instance Constructors

  1. new IntervalRDD(partitionsRDD: RDD[IntervalPartition[K, V]])(implicit arg0: ClassTag[K], arg1: ClassTag[V])

    Permalink

Value Members

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

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

    Permalink
    Definition Classes
    AnyRef → Any
  3. def ++(other: RDD[(K, V)]): RDD[(K, V)]

    Permalink
    Definition Classes
    RDD
  4. final def ==(arg0: Any): Boolean

    Permalink
    Definition Classes
    AnyRef → Any
  5. def aggregate[U](zeroValue: U)(seqOp: (U, (K, V)) ⇒ U, combOp: (U, U) ⇒ U)(implicit arg0: ClassTag[U]): U

    Permalink
    Definition Classes
    RDD
  6. final def asInstanceOf[T0]: T0

    Permalink
    Definition Classes
    Any
  7. def barrier(): RDDBarrier[(K, V)]

    Permalink
    Definition Classes
    RDD
    Annotations
    @Experimental() @Since( "2.4.0" )
  8. def cache(): IntervalRDD.this.type

    Permalink
    Definition Classes
    RDD
  9. def cartesian[U](other: RDD[U])(implicit arg0: ClassTag[U]): RDD[((K, V), U)]

    Permalink
    Definition Classes
    RDD
  10. def checkpoint(): Unit

    Permalink
    Definition Classes
    RDD
  11. def clearDependencies(): Unit

    Permalink
    Attributes
    protected
    Definition Classes
    RDD
  12. def clone(): AnyRef

    Permalink
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  13. def coalesce(numPartitions: Int, shuffle: Boolean, partitionCoalescer: Option[PartitionCoalescer])(implicit ord: Ordering[(K, V)]): RDD[(K, V)]

    Permalink
    Definition Classes
    RDD
  14. def collect(interval: K): List[V]

    Permalink

    Gets the values corresponding to the specified key, if any Assume that we're only getting data that exists (if it doesn't exist, would have been handled by upper LazyMaterialization layer

    Gets the values corresponding to the specified key, if any Assume that we're only getting data that exists (if it doesn't exist, would have been handled by upper LazyMaterialization layer

    interval

    Interval to collect overlapping data from

    returns

    List of V records overlapping interval

  15. def collect(): Array[(K, V)]

    Permalink

    Collects all elements in RDD into an array of (K, V) pairs.

    Collects all elements in RDD into an array of (K, V) pairs.

    returns

    Array of (K, V) pairs

    Definition Classes
    IntervalRDD → RDD
  16. def collect[U](f: PartialFunction[(K, V), U])(implicit arg0: ClassTag[U]): RDD[U]

    Permalink
    Definition Classes
    RDD
  17. def compute(part: Partition, context: TaskContext): Iterator[(K, V)]

    Permalink

    Provides the RDD[(K, V)] equivalent output.

    Provides the RDD[(K, V)] equivalent output.

    part

    Partition

    context

    TaskContext

    returns

    Iterator of (K, V) pairs

    Definition Classes
    IntervalRDD → RDD
  18. def context: SparkContext

    Permalink
    Definition Classes
    RDD
  19. def count(): Long

    Permalink

    The number of elements in the RDD.

    The number of elements in the RDD.

    Definition Classes
    IntervalRDD → RDD
  20. def countApprox(timeout: Long, confidence: Double): PartialResult[BoundedDouble]

    Permalink
    Definition Classes
    RDD
  21. def countApproxDistinct(relativeSD: Double): Long

    Permalink
    Definition Classes
    RDD
  22. def countApproxDistinct(p: Int, sp: Int): Long

    Permalink
    Definition Classes
    RDD
  23. def countByValue()(implicit ord: Ordering[(K, V)]): Map[(K, V), Long]

    Permalink
    Definition Classes
    RDD
  24. def countByValueApprox(timeout: Long, confidence: Double)(implicit ord: Ordering[(K, V)]): PartialResult[Map[(K, V), BoundedDouble]]

    Permalink
    Definition Classes
    RDD
  25. final def dependencies: Seq[Dependency[_]]

    Permalink
    Definition Classes
    RDD
  26. def distinct(): RDD[(K, V)]

    Permalink
    Definition Classes
    RDD
  27. def distinct(numPartitions: Int)(implicit ord: Ordering[(K, V)]): RDD[(K, V)]

    Permalink
    Definition Classes
    RDD
  28. final def eq(arg0: AnyRef): Boolean

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

    Permalink
    Definition Classes
    AnyRef → Any
  30. def filter(pred: ((K, V)) ⇒ Boolean): IntervalRDD[K, V]

    Permalink

    Performs filtering given a predicate.

    Performs filtering given a predicate.

    pred

    Predicate to filter (K,V) pairs by

    returns

    new IntervalRDD with filtered predicate

    Definition Classes
    IntervalRDD → RDD
  31. def filterByInterval(r: K): IntervalRDD[K, V]

    Permalink

    Filters IntervalRDD by interval and returns new IntervalRDD.

    Filters IntervalRDD by interval and returns new IntervalRDD.

    r

    Interval to filter by

    returns

    filtered IntervalRDD

  32. def finalize(): Unit

    Permalink
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  33. def first(): (K, V)

    Permalink

    Gets first element in the RDD.

    Gets first element in the RDD.

    returns

    first (K,V) pair

    Definition Classes
    IntervalRDD → RDD
  34. def firstParent[U](implicit arg0: ClassTag[U]): RDD[U]

    Permalink
    Attributes
    protected[org.apache.spark]
    Definition Classes
    RDD
  35. def flatMap[U](f: ((K, V)) ⇒ TraversableOnce[U])(implicit arg0: ClassTag[U]): RDD[U]

    Permalink
    Definition Classes
    RDD
  36. def fold(zeroValue: (K, V))(op: ((K, V), (K, V)) ⇒ (K, V)): (K, V)

    Permalink
    Definition Classes
    RDD
  37. def foreach(f: ((K, V)) ⇒ Unit): Unit

    Permalink
    Definition Classes
    RDD
  38. def foreachPartition(f: (Iterator[(K, V)]) ⇒ Unit): Unit

    Permalink
    Definition Classes
    RDD
  39. def getCheckpointFile: Option[String]

    Permalink
    Definition Classes
    RDD
  40. final def getClass(): Class[_]

    Permalink
    Definition Classes
    AnyRef → Any
  41. def getDependencies: Seq[Dependency[_]]

    Permalink
    Attributes
    protected
    Definition Classes
    RDD
  42. final def getNumPartitions: Int

    Permalink
    Definition Classes
    RDD
    Annotations
    @Since( "1.6.0" )
  43. def getOutputDeterministicLevel: apache.spark.rdd.DeterministicLevel.Value

    Permalink
    Attributes
    protected
    Definition Classes
    RDD
    Annotations
    @DeveloperApi()
  44. def getPartitions: Array[Partition]

    Permalink
    Attributes
    protected
    Definition Classes
    IntervalRDD → RDD
  45. def getPreferredLocations(split: Partition): Seq[String]

    Permalink
    Attributes
    protected
    Definition Classes
    RDD
  46. def getStorageLevel: StorageLevel

    Permalink
    Definition Classes
    RDD
  47. def glom(): RDD[Array[(K, V)]]

    Permalink
    Definition Classes
    RDD
  48. def groupBy[K](f: ((K, V)) ⇒ K, p: Partitioner)(implicit kt: ClassTag[K], ord: Ordering[K]): RDD[(K, Iterable[(K, V)])]

    Permalink
    Definition Classes
    RDD
  49. def groupBy[K](f: ((K, V)) ⇒ K, numPartitions: Int)(implicit kt: ClassTag[K]): RDD[(K, Iterable[(K, V)])]

    Permalink
    Definition Classes
    RDD
  50. def groupBy[K](f: ((K, V)) ⇒ K)(implicit kt: ClassTag[K]): RDD[(K, Iterable[(K, V)])]

    Permalink
    Definition Classes
    RDD
  51. def hashCode(): Int

    Permalink
    Definition Classes
    AnyRef → Any
  52. val id: Int

    Permalink
    Definition Classes
    RDD
  53. def initializeLogIfNecessary(isInterpreter: Boolean, silent: Boolean): Boolean

    Permalink
    Attributes
    protected
    Definition Classes
    Logging
  54. def initializeLogIfNecessary(isInterpreter: Boolean): Unit

    Permalink
    Attributes
    protected
    Definition Classes
    Logging
  55. def intersection(other: RDD[(K, V)], numPartitions: Int): RDD[(K, V)]

    Permalink
    Definition Classes
    RDD
  56. def intersection(other: RDD[(K, V)], partitioner: Partitioner)(implicit ord: Ordering[(K, V)]): RDD[(K, V)]

    Permalink
    Definition Classes
    RDD
  57. def intersection(other: RDD[(K, V)]): RDD[(K, V)]

    Permalink
    Definition Classes
    RDD
  58. lazy val isBarrier_: Boolean

    Permalink
    Attributes
    protected
    Definition Classes
    RDD
  59. def isCheckpointed: Boolean

    Permalink
    Definition Classes
    RDD
  60. def isEmpty(): Boolean

    Permalink
    Definition Classes
    RDD
  61. final def isInstanceOf[T0]: Boolean

    Permalink
    Definition Classes
    Any
  62. def isTraceEnabled(): Boolean

    Permalink
    Attributes
    protected
    Definition Classes
    Logging
  63. final def iterator(split: Partition, context: TaskContext): Iterator[(K, V)]

    Permalink
    Definition Classes
    RDD
  64. def keyBy[K](f: ((K, V)) ⇒ K): RDD[(K, (K, V))]

    Permalink
    Definition Classes
    RDD
  65. def localCheckpoint(): IntervalRDD.this.type

    Permalink
    Definition Classes
    RDD
  66. def log: Logger

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

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

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

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

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

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

    Permalink
    Attributes
    protected
    Definition Classes
    Logging
  73. def logName: String

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

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

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

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

    Permalink
    Attributes
    protected
    Definition Classes
    Logging
  78. def map[U](f: ((K, V)) ⇒ U)(implicit arg0: ClassTag[U]): RDD[U]

    Permalink
    Definition Classes
    RDD
  79. def mapIntervalPartitions[K2 <: Interval[K2], V2](f: (IntervalPartition[K, V]) ⇒ IntervalPartition[K2, V2])(implicit arg0: ClassTag[K2], arg1: ClassTag[V2]): IntervalRDD[K2, V2]

    Permalink

    Maps interval partitions in partitionsRDD.

    Maps interval partitions in partitionsRDD.

    K2

    key type extending Interval

    V2

    data type

    f

    mapping function for interval partitions

    returns

    new IntervalRDD of type [K2, V2]

  80. def mapPartitions[U](f: (Iterator[(K, V)]) ⇒ Iterator[U], preservesPartitioning: Boolean)(implicit arg0: ClassTag[U]): RDD[U]

    Permalink
    Definition Classes
    RDD
  81. def mapPartitionsWithIndex[U](f: (Int, Iterator[(K, V)]) ⇒ Iterator[U], preservesPartitioning: Boolean)(implicit arg0: ClassTag[U]): RDD[U]

    Permalink
    Definition Classes
    RDD
  82. def mapValues[V2](f: (V) ⇒ V2)(implicit arg0: ClassTag[V2]): IntervalRDD[K, V2]

    Permalink

    Maps each value, preserving the index.

    Maps each value, preserving the index.

    returns

    new IntervalRDD with values V2

  83. def max()(implicit ord: Ordering[(K, V)]): (K, V)

    Permalink
    Definition Classes
    RDD
  84. def min()(implicit ord: Ordering[(K, V)]): (K, V)

    Permalink
    Definition Classes
    RDD
  85. def multiput(elems: Array[(K, V)], isSorted: Boolean = false): IntervalRDD[K, V]

    Permalink

    Unconditionally updates the specified keys to have the specified value.

    Unconditionally updates the specified keys to have the specified value. Returns a new IntervalRDD.

    elems

    Array of (K,V) pairs

    returns

    IntervalRDD with inserted elems

  86. def multiputRDD(elems: RDD[(K, V)], sorted: Boolean = false): IntervalRDD[K, V]

    Permalink

    Unconditionally updates the specified keys to have the specified value.

    Unconditionally updates the specified keys to have the specified value. Returns a new IntervalRDD.

    elems

    RDD of (K,V) pairs

    sorted

    Boolean that determines whether elems is sorted

    returns

    IntervalRDD with inserted elems

  87. var name: String

    Permalink
    Definition Classes
    RDD
  88. final def ne(arg0: AnyRef): Boolean

    Permalink
    Definition Classes
    AnyRef
  89. final def notify(): Unit

    Permalink
    Definition Classes
    AnyRef
  90. final def notifyAll(): Unit

    Permalink
    Definition Classes
    AnyRef
  91. def parent[U](j: Int)(implicit arg0: ClassTag[U]): RDD[U]

    Permalink
    Attributes
    protected[org.apache.spark]
    Definition Classes
    RDD
  92. def partitionBy(partitioner: Partitioner): IntervalRDD[K, V]

    Permalink

    Repartitions underlying data in IntervalRDD.

    Repartitions underlying data in IntervalRDD.

    partitioner

    new Partitioner to partition data by

    returns

    repartitioned IntervalRDD

  93. val partitioner: Option[Partitioner]

    Permalink
    Definition Classes
    IntervalRDD → RDD
  94. final def partitions: Array[Partition]

    Permalink
    Definition Classes
    RDD
  95. def persist(newLevel: StorageLevel): IntervalRDD.this.type

    Permalink

    Persists the interval partitions using targetStorageLevel, which defaults to MEMORY_ONLY.

    Persists the interval partitions using targetStorageLevel, which defaults to MEMORY_ONLY.

    Definition Classes
    IntervalRDD → RDD
  96. def persist(): IntervalRDD.this.type

    Permalink
    Definition Classes
    RDD
  97. def pipe(command: Seq[String], env: Map[String, String], printPipeContext: ((String) ⇒ Unit) ⇒ Unit, printRDDElement: ((K, V), (String) ⇒ Unit) ⇒ Unit, separateWorkingDir: Boolean, bufferSize: Int, encoding: String): RDD[String]

    Permalink
    Definition Classes
    RDD
  98. def pipe(command: String, env: Map[String, String]): RDD[String]

    Permalink
    Definition Classes
    RDD
  99. def pipe(command: String): RDD[String]

    Permalink
    Definition Classes
    RDD
  100. final def preferredLocations(split: Partition): Seq[String]

    Permalink
    Definition Classes
    RDD
  101. def put(elem: (K, V)): IntervalRDD[K, V]

    Permalink

    Unconditionally updates the specified keys to have the specified value.

    Unconditionally updates the specified keys to have the specified value. Returns a new IntervalRDD.

    elem

    (K,V) pair

    returns

    IntervalRDD with inserted elem

  102. def randomSplit(weights: Array[Double], seed: Long): Array[RDD[(K, V)]]

    Permalink
    Definition Classes
    RDD
  103. def reduce(f: ((K, V), (K, V)) ⇒ (K, V)): (K, V)

    Permalink
    Definition Classes
    RDD
  104. def repartition(numPartitions: Int)(implicit ord: Ordering[(K, V)]): RDD[(K, V)]

    Permalink
    Definition Classes
    RDD
  105. def sample(withReplacement: Boolean, fraction: Double, seed: Long): RDD[(K, V)]

    Permalink
    Definition Classes
    RDD
  106. def saveAsObjectFile(path: String): Unit

    Permalink
    Definition Classes
    RDD
  107. def saveAsTextFile(path: String, codec: Class[_ <: CompressionCodec]): Unit

    Permalink
    Definition Classes
    RDD
  108. def saveAsTextFile(path: String): Unit

    Permalink
    Definition Classes
    RDD
  109. def setName(_name: String): IntervalRDD.this.type

    Permalink

    Resets RDD name

    Resets RDD name

    _name

    RDD name

    Definition Classes
    IntervalRDD → RDD
  110. def sortBy[K](f: ((K, V)) ⇒ K, ascending: Boolean, numPartitions: Int)(implicit ord: Ordering[K], ctag: ClassTag[K]): RDD[(K, V)]

    Permalink
    Definition Classes
    RDD
  111. def sparkContext: SparkContext

    Permalink
    Definition Classes
    RDD
  112. def subtract(other: RDD[(K, V)], p: Partitioner)(implicit ord: Ordering[(K, V)]): RDD[(K, V)]

    Permalink
    Definition Classes
    RDD
  113. def subtract(other: RDD[(K, V)], numPartitions: Int): RDD[(K, V)]

    Permalink
    Definition Classes
    RDD
  114. def subtract(other: RDD[(K, V)]): RDD[(K, V)]

    Permalink
    Definition Classes
    RDD
  115. final def synchronized[T0](arg0: ⇒ T0): T0

    Permalink
    Definition Classes
    AnyRef
  116. def take(num: Int): Array[(K, V)]

    Permalink
    Definition Classes
    RDD
  117. def takeOrdered(num: Int)(implicit ord: Ordering[(K, V)]): Array[(K, V)]

    Permalink
    Definition Classes
    RDD
  118. def takeSample(withReplacement: Boolean, num: Int, seed: Long): Array[(K, V)]

    Permalink
    Definition Classes
    RDD
  119. def toDebugString: String

    Permalink
    Definition Classes
    RDD
  120. def toJavaRDD(): JavaRDD[(K, V)]

    Permalink
    Definition Classes
    RDD
  121. def toLocalIterator: Iterator[(K, V)]

    Permalink
    Definition Classes
    RDD
  122. def toRDD: RDD[(K, V)]

    Permalink

    Converts to normal RDD of (K, V) pairs

    Converts to normal RDD of (K, V) pairs

    returns

    RDD of (K, V) pairs

  123. def toString(): String

    Permalink
    Definition Classes
    RDD → AnyRef → Any
  124. def top(num: Int)(implicit ord: Ordering[(K, V)]): Array[(K, V)]

    Permalink
    Definition Classes
    RDD
  125. def treeAggregate[U](zeroValue: U)(seqOp: (U, (K, V)) ⇒ U, combOp: (U, U) ⇒ U, depth: Int)(implicit arg0: ClassTag[U]): U

    Permalink
    Definition Classes
    RDD
  126. def treeReduce(f: ((K, V), (K, V)) ⇒ (K, V), depth: Int): (K, V)

    Permalink
    Definition Classes
    RDD
  127. def union(other: RDD[(K, V)]): RDD[(K, V)]

    Permalink
    Definition Classes
    RDD
  128. def unpersist(blocking: Boolean = true): IntervalRDD.this.type

    Permalink

    Unpersists the interval partitions using

    Unpersists the interval partitions using

    Definition Classes
    IntervalRDD → RDD
  129. final def wait(): Unit

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

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

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  132. def zip[U](other: RDD[U])(implicit arg0: ClassTag[U]): RDD[((K, V), U)]

    Permalink
    Definition Classes
    RDD
  133. def zipPartitions[B, C, D, V](rdd2: RDD[B], rdd3: RDD[C], rdd4: RDD[D])(f: (Iterator[(K, V)], Iterator[B], Iterator[C], Iterator[D]) ⇒ Iterator[V])(implicit arg0: ClassTag[B], arg1: ClassTag[C], arg2: ClassTag[D], arg3: ClassTag[V]): RDD[V]

    Permalink
    Definition Classes
    RDD
  134. def zipPartitions[B, C, D, V](rdd2: RDD[B], rdd3: RDD[C], rdd4: RDD[D], preservesPartitioning: Boolean)(f: (Iterator[(K, V)], Iterator[B], Iterator[C], Iterator[D]) ⇒ Iterator[V])(implicit arg0: ClassTag[B], arg1: ClassTag[C], arg2: ClassTag[D], arg3: ClassTag[V]): RDD[V]

    Permalink
    Definition Classes
    RDD
  135. def zipPartitions[B, C, V](rdd2: RDD[B], rdd3: RDD[C])(f: (Iterator[(K, V)], Iterator[B], Iterator[C]) ⇒ Iterator[V])(implicit arg0: ClassTag[B], arg1: ClassTag[C], arg2: ClassTag[V]): RDD[V]

    Permalink
    Definition Classes
    RDD
  136. def zipPartitions[B, C, V](rdd2: RDD[B], rdd3: RDD[C], preservesPartitioning: Boolean)(f: (Iterator[(K, V)], Iterator[B], Iterator[C]) ⇒ Iterator[V])(implicit arg0: ClassTag[B], arg1: ClassTag[C], arg2: ClassTag[V]): RDD[V]

    Permalink
    Definition Classes
    RDD
  137. def zipPartitions[B, V](rdd2: RDD[B])(f: (Iterator[(K, V)], Iterator[B]) ⇒ Iterator[V])(implicit arg0: ClassTag[B], arg1: ClassTag[V]): RDD[V]

    Permalink
    Definition Classes
    RDD
  138. def zipPartitions[B, V](rdd2: RDD[B], preservesPartitioning: Boolean)(f: (Iterator[(K, V)], Iterator[B]) ⇒ Iterator[V])(implicit arg0: ClassTag[B], arg1: ClassTag[V]): RDD[V]

    Permalink
    Definition Classes
    RDD
  139. def zipWithIndex(): RDD[((K, V), Long)]

    Permalink
    Definition Classes
    RDD
  140. def zipWithUniqueId(): RDD[((K, V), Long)]

    Permalink
    Definition Classes
    RDD

Inherited from RDD[(K, V)]

Inherited from Logging

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

Ungrouped