org.bdgenomics.utils.intervalrdd

IntervalRDD

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

Linear Supertypes
RDD[(K, V)], Logging, Serializable, Serializable, AnyRef, Any
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  1. IntervalRDD
  2. RDD
  3. Logging
  4. Serializable
  5. Serializable
  6. AnyRef
  7. Any
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Instance Constructors

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

Value Members

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

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

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

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

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

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

    Definition Classes
    Any
  7. def cache(): IntervalRDD.this.type

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

    Definition Classes
    RDD
  9. def checkpoint(): Unit

    Definition Classes
    RDD
  10. def clearDependencies(): Unit

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

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

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

    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

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

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

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

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

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

    Definition Classes
    IntervalRDD → RDD
  17. def context: SparkContext

    Definition Classes
    RDD
  18. def count(): Long

    The number of elements in the RDD.

    The number of elements in the RDD.

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

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

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

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

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

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

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

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

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

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

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

    Performs filtering given a predicate

    Performs filtering given a predicate

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

  31. def finalize(): Unit

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

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

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

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

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

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

    Definition Classes
    RDD
  38. def getCheckpointFile: Option[String]

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

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

    Attributes
    protected
    Definition Classes
    RDD
  41. final def getNumPartitions: Int

    Definition Classes
    RDD
    Annotations
    @Since( "1.6.0" )
  42. def getPartitions: Array[Partition]

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

    Attributes
    protected
    Definition Classes
    RDD
  44. def getStorageLevel: StorageLevel

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

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

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

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

    Definition Classes
    RDD
  49. def hashCode(): Int

    Definition Classes
    AnyRef → Any
  50. val id: Int

    Definition Classes
    RDD
  51. def intersection(other: RDD[(K, V)], numPartitions: Int): RDD[(K, V)]

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

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

    Definition Classes
    RDD
  54. def isCheckpointed: Boolean

    Definition Classes
    RDD
  55. def isEmpty(): Boolean

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

    Definition Classes
    Any
  57. def isTraceEnabled(): Boolean

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

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

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

    Definition Classes
    RDD
  61. def log: Logger

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

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

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

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

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

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

    Attributes
    protected
    Definition Classes
    Logging
  68. def logName: String

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

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

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

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

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

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

    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]

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

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

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

    Maps each value, preserving the index.

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

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

    Definition Classes
    RDD
  80. def multiput(elems: RDD[(K, V)]): IntervalRDD[K, V]

    Unconditionally updates the specified keys to have the specified value.

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

  81. def multiput(elem: (K, V)): IntervalRDD[K, V]

    Unconditionally updates the specified keys to have the specified value.

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

  82. def multiput(elems: Array[(K, V)]): IntervalRDD[K, V]

    Unconditionally updates the specified keys to have the specified value.

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

  83. var name: String

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

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

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

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

    Attributes
    protected[org.apache.spark]
    Definition Classes
    RDD
  88. val partitioner: Option[Partitioner]

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

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

    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
  91. def persist(): IntervalRDD.this.type

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

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

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

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

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

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

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

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

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

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

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

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

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

    Definition Classes
    RDD
  105. def sparkContext: SparkContext

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

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

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

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

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

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

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

    Definition Classes
    RDD
  113. def toDebugString: String

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

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

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

  117. def toString(): String

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

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

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

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

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

    Unpersists the interval partitions using

    Unpersists the interval partitions using

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

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

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

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

    Definition Classes
    RDD
  127. 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]

    Definition Classes
    RDD
  128. 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]

    Definition Classes
    RDD
  129. 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]

    Definition Classes
    RDD
  130. 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]

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

    Definition Classes
    RDD
  132. 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]

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

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

    Definition Classes
    RDD

Deprecated Value Members

  1. def filterWith[A](constructA: (Int) ⇒ A)(p: ((K, V), A) ⇒ Boolean): RDD[(K, V)]

    Definition Classes
    RDD
    Annotations
    @deprecated
    Deprecated

    (Since version 1.0.0) use mapPartitionsWithIndex and filter

  2. def flatMapWith[A, U](constructA: (Int) ⇒ A, preservesPartitioning: Boolean)(f: ((K, V), A) ⇒ Seq[U])(implicit arg0: ClassTag[U]): RDD[U]

    Definition Classes
    RDD
    Annotations
    @deprecated
    Deprecated

    (Since version 1.0.0) use mapPartitionsWithIndex and flatMap

  3. def foreachWith[A](constructA: (Int) ⇒ A)(f: ((K, V), A) ⇒ Unit): Unit

    Definition Classes
    RDD
    Annotations
    @deprecated
    Deprecated

    (Since version 1.0.0) use mapPartitionsWithIndex and foreach

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

    Definition Classes
    RDD
    Annotations
    @DeveloperApi() @deprecated
    Deprecated

    (Since version 1.2.0) use TaskContext.get

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

    Definition Classes
    RDD
    Annotations
    @deprecated
    Deprecated

    (Since version 0.7.0) use mapPartitionsWithIndex

  6. def mapWith[A, U](constructA: (Int) ⇒ A, preservesPartitioning: Boolean)(f: ((K, V), A) ⇒ U)(implicit arg0: ClassTag[U]): RDD[U]

    Definition Classes
    RDD
    Annotations
    @deprecated
    Deprecated

    (Since version 1.0.0) use mapPartitionsWithIndex

  7. def toArray(): Array[(K, V)]

    Definition Classes
    RDD
    Annotations
    @deprecated
    Deprecated

    (Since version 1.0.0) use collect

Inherited from RDD[(K, V)]

Inherited from Logging

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

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