org.bdgenomics.adam.rdd.read

MDTagging

case class MDTagging(reads: RDD[AlignmentRecord], referenceFile: ReferenceFile, partitionSize: Long = 1000000, overwriteExistingTags: Boolean = false, validationStringency: ValidationStringency = ValidationStringency.STRICT) extends Logging with Product with Serializable

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Serializable, Serializable, Product, Equals, Logging, AnyRef, Any
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  1. MDTagging
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. Logging
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Instance Constructors

  1. new MDTagging(reads: RDD[AlignmentRecord], referenceFile: ReferenceFile, partitionSize: Long = 1000000, overwriteExistingTags: Boolean = false, validationStringency: ValidationStringency = ValidationStringency.STRICT)

Value Members

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

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

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

    Definition Classes
    AnyRef → Any
  4. def addMDTagsBroadcast(): RDD[AlignmentRecord]

  5. final def asInstanceOf[T0]: T0

    Definition Classes
    Any
  6. def clone(): AnyRef

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  7. final def eq(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef
  8. def finalize(): Unit

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  9. final def getClass(): Class[_]

    Definition Classes
    AnyRef → Any
  10. val incorrectMDTags: Accumulator[Long]

  11. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any
  12. def isTraceEnabled(): Boolean

    Attributes
    protected
    Definition Classes
    Logging
  13. def log: Logger

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

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

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

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

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

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

    Attributes
    protected
    Definition Classes
    Logging
  20. def logName: String

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

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

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

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

    Attributes
    protected
    Definition Classes
    Logging
  25. def maybeMDTagRead(read: AlignmentRecord, refSeq: String): AlignmentRecord

  26. val mdTagsAdded: Accumulator[Long]

  27. val mdTagsExtant: Accumulator[Long]

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

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

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

    Definition Classes
    AnyRef
  31. val numUnmappedReads: Accumulator[Long]

  32. val overwriteExistingTags: Boolean

  33. val partitionSize: Long

  34. val reads: RDD[AlignmentRecord]

  35. val referenceFile: ReferenceFile

  36. val sc: SparkContext

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

    Definition Classes
    AnyRef
  38. val taggedReads: RDD[AlignmentRecord]

  39. val validationStringency: ValidationStringency

  40. final def wait(): Unit

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

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from Logging

Inherited from AnyRef

Inherited from Any

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