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
7. AnyRef
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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 Product

### Inherited from Equals

### Inherited from Logging

### Inherited from AnyRef

### Inherited from Any

### Ungrouped