org.bdgenomics.utils.intervalrdd

IntervalRDD

class IntervalRDD[K <: Interval, 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, partitionCoalescer: Option[PartitionCoalescer])(implicit ord: Ordering[(K, V)]): RDD[(K, V)]

    Definition Classes
    RDD

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

    Definition Classes
    IntervalRDD → RDD

  14. def collect[U](f: PartialFunction[(K, V), U])(implicit arg0: ClassTag[U]): RDD[U]

    Definition Classes
    RDD

  15. 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

  16. def context: SparkContext

    Definition Classes
    RDD

  17. def count(): Long

    The number of elements in the RDD.

    The number of elements in the RDD.

    Definition Classes
    IntervalRDD → RDD

  18. def countApprox(timeout: Long, confidence: Double): PartialResult[BoundedDouble]

    Definition Classes
    RDD

  19. def countApproxDistinct(relativeSD: Double): Long

    Definition Classes
    RDD

  20. def countApproxDistinct(p: Int, sp: Int): Long

    Definition Classes
    RDD

  21. def countByValue()(implicit ord: Ordering[(K, V)]): Map[(K, V), Long]

    Definition Classes
    RDD

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

    Definition Classes
    RDD

  23. final def dependencies: Seq[Dependency[_]]

    Definition Classes
    RDD

  24. def distinct(): RDD[(K, V)]

    Definition Classes
    RDD

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

    Definition Classes
    RDD

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

    Definition Classes
    AnyRef

  27. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  28. def filter(pred: ((K, V)) ⇒ Boolean): IntervalRDD[K, V]

    Performs filtering given a predicate

    Performs filtering given a predicate

    Definition Classes
    IntervalRDD → RDD

  29. def filterByInterval(r: K): IntervalRDD[K, V]

  30. def finalize(): Unit

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

  31. def first(): (K, V)

    Definition Classes
    RDD

  32. def firstParent[U](implicit arg0: ClassTag[U]): RDD[U]

    Attributes
    protected[org.apache.spark]
    Definition Classes
    RDD

  33. def flatMap[U](f: ((K, V)) ⇒ TraversableOnce[U])(implicit arg0: ClassTag[U]): RDD[U]

    Definition Classes
    RDD

  34. def fold(zeroValue: (K, V))(op: ((K, V), (K, V)) ⇒ (K, V)): (K, V)

    Definition Classes
    RDD

  35. def foreach(f: ((K, V)) ⇒ Unit): Unit

    Definition Classes
    RDD

  36. def foreachPartition(f: (Iterator[(K, V)]) ⇒ Unit): Unit

    Definition Classes
    RDD

  37. def get(interval: K): List[(K, 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

  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 initializeLogIfNecessary(isInterpreter: Boolean): Unit

    Attributes
    protected
    Definition Classes
    Logging

  52. def intersection(other: RDD[(K, V)], numPartitions: Int): RDD[(K, V)]

    Definition Classes
    RDD

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

    Definition Classes
    RDD

  54. def intersection(other: RDD[(K, V)]): RDD[(K, V)]

    Definition Classes
    RDD

  55. def isCheckpointed: Boolean

    Definition Classes
    RDD

  56. def isEmpty(): Boolean

    Definition Classes
    RDD

  57. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  58. def isTraceEnabled(): Boolean

    Attributes
    protected
    Definition Classes
    Logging

  59. final def iterator(split: Partition, context: TaskContext): Iterator[(K, V)]

    Definition Classes
    RDD

  60. def keyBy[K](f: ((K, V)) ⇒ K): RDD[(K, (K, V))]

    Definition Classes
    RDD

  61. def localCheckpoint(): IntervalRDD.this.type

    Definition Classes
    RDD

  62. def log: Logger

    Attributes
    protected
    Definition Classes
    Logging

  63. def logDebug(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
    protected
    Definition Classes
    Logging

  64. def logDebug(msg: ⇒ String): Unit

    Attributes
    protected
    Definition Classes
    Logging

  65. def logError(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
    protected
    Definition Classes
    Logging

  66. def logError(msg: ⇒ String): Unit

    Attributes
    protected
    Definition Classes
    Logging

  67. def logInfo(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
    protected
    Definition Classes
    Logging

  68. def logInfo(msg: ⇒ String): Unit

    Attributes
    protected
    Definition Classes
    Logging

  69. def logName: String

    Attributes
    protected
    Definition Classes
    Logging

  70. def logTrace(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
    protected
    Definition Classes
    Logging

  71. def logTrace(msg: ⇒ String): Unit

    Attributes
    protected
    Definition Classes
    Logging

  72. def logWarning(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
    protected
    Definition Classes
    Logging

  73. def logWarning(msg: ⇒ String): Unit

    Attributes
    protected
    Definition Classes
    Logging

  74. def map[U](f: ((K, V)) ⇒ U)(implicit arg0: ClassTag[U]): RDD[U]

    Definition Classes
    RDD

  75. def mapIntervalPartitions[K2 <: Interval, 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]

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

    Definition Classes
    RDD

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

    Definition Classes
    RDD

  78. def mapValues[V2](f: (V) ⇒ V2)(implicit arg0: ClassTag[V2]): IntervalRDD[K, V2]

    Maps each value, preserving the index.

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

    Definition Classes
    RDD

  80. def min()(implicit ord: Ordering[(K, V)]): (K, V)

    Definition Classes
    RDD

  81. 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

  82. 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

  83. 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

  84. var name: String

    Definition Classes
    RDD

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

    Definition Classes
    AnyRef

  86. final def notify(): Unit

    Definition Classes
    AnyRef

  87. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  88. def parent[U](j: Int)(implicit arg0: ClassTag[U]): RDD[U]

    Attributes
    protected[org.apache.spark]
    Definition Classes
    RDD

  89. val partitioner: Option[Partitioner]

    Definition Classes
    IntervalRDD → RDD

  90. final def partitions: Array[Partition]

    Definition Classes
    RDD

  91. 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

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

    Definition Classes
    RDD

  93. 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]

    Definition Classes
    RDD

  94. def pipe(command: String, env: Map[String, String]): RDD[String]

    Definition Classes
    RDD

  95. def pipe(command: String): RDD[String]

    Definition Classes
    RDD

  96. final def preferredLocations(split: Partition): Seq[String]

    Definition Classes
    RDD

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

    Definition Classes
    RDD

  98. def reduce(f: ((K, V), (K, V)) ⇒ (K, V)): (K, V)

    Definition Classes
    RDD

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

    Definition Classes
    RDD

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

    Definition Classes
    RDD

  101. def saveAsObjectFile(path: String): Unit

    Definition Classes
    RDD

  102. def saveAsTextFile(path: String, codec: Class[_ <: CompressionCodec]): Unit

    Definition Classes
    RDD

  103. def saveAsTextFile(path: String): Unit

    Definition Classes
    RDD

  104. def setName(_name: String): IntervalRDD.this.type

    Definition Classes
    IntervalRDD → RDD

  105. def sortBy[K](f: ((K, V)) ⇒ K, ascending: Boolean, numPartitions: Int)(implicit ord: Ordering[K], ctag: ClassTag[K]): RDD[(K, V)]

    Definition Classes
    RDD

  106. def sparkContext: SparkContext

    Definition Classes
    RDD

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

    Definition Classes
    RDD

  108. def subtract(other: RDD[(K, V)], numPartitions: Int): RDD[(K, V)]

    Definition Classes
    RDD

  109. def subtract(other: RDD[(K, V)]): RDD[(K, V)]

    Definition Classes
    RDD

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

    Definition Classes
    AnyRef

  111. def take(num: Int): Array[(K, V)]

    Definition Classes
    RDD

  112. def takeOrdered(num: Int)(implicit ord: Ordering[(K, V)]): Array[(K, V)]

    Definition Classes
    RDD

  113. def takeSample(withReplacement: Boolean, num: Int, seed: Long): Array[(K, V)]

    Definition Classes
    RDD

  114. def toDebugString: String

    Definition Classes
    RDD

  115. def toJavaRDD(): JavaRDD[(K, V)]

    Definition Classes
    RDD

  116. def toLocalIterator: Iterator[(K, V)]

    Definition Classes
    RDD

  117. def toRDD: RDD[(K, V)]

  118. def toString(): String

    Definition Classes
    RDD → AnyRef → Any

  119. def top(num: Int)(implicit ord: Ordering[(K, V)]): Array[(K, V)]

    Definition Classes
    RDD

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

    Definition Classes
    RDD

  121. def treeReduce(f: ((K, V), (K, V)) ⇒ (K, V), depth: Int): (K, V)

    Definition Classes
    RDD

  122. def union(other: RDD[(K, V)]): RDD[(K, V)]

    Definition Classes
    RDD

  123. def unpersist(blocking: Boolean = true): IntervalRDD.this.type

    Unpersists the interval partitions using

    Unpersists the interval partitions using

    Definition Classes
    IntervalRDD → RDD

  124. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  125. final def wait(arg0: Long, arg1: Int): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  126. final def wait(arg0: Long): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  127. def zip[U](other: RDD[U])(implicit arg0: ClassTag[U]): RDD[((K, V), U)]

    Definition Classes
    RDD

  128. 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

  129. 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

  130. 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

  131. 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

  132. 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

  133. 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

  134. def zipWithIndex(): RDD[((K, V), Long)]

    Definition Classes
    RDD

  135. def zipWithUniqueId(): RDD[((K, V), Long)]

    Definition Classes
    RDD

Inherited from RDD[(K, V)]

Inherited from Logging

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

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