org.bdgenomics.adam.rich

# DecadentRead

#### class DecadentRead extends Logging

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### Instance Constructors

1. #### new DecadentRead(record: RichAlignmentRecord)

### Type Members

1. #### class Residue extends AnyRef

   In biochemistry and molecular biology, a "residue" refers to a specific monomer within a polymeric chain, such as DNA.

### 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 alignmentQuality: Option[QualityScore]

5. #### final def asInstanceOf[T0]: T0

   Definition Classes
     Any

6. #### def clone(): AnyRef

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

7. #### def ensureAligned: Boolean

8. #### final def eq(arg0: AnyRef): Boolean

   Definition Classes
     AnyRef

9. #### def equals(arg0: Any): Boolean

   Definition Classes
     AnyRef → Any

10. #### def finalize(): Unit

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

11. #### final def getClass(): Class[_]

    Definition Classes
      AnyRef → Any

12. #### def hashCode(): Int

    Definition Classes
      AnyRef → Any

13. #### def isAligned: Boolean

14. #### def isCanonicalRecord: Boolean

15. #### def isDuplicate: Boolean

16. #### def isFirstOfPair: Boolean

17. #### final def isInstanceOf[T0]: Boolean

    Definition Classes
      Any

18. #### def isNegativeRead: Boolean

19. #### def isPaired: Boolean

20. #### def isPrimaryAlignment: Boolean

21. #### def isSecondOfPair: Boolean

22. #### def isTraceEnabled(): Boolean

    Attributes
      protected
    Definition Classes
      Logging

23. #### def log: Logger

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

25. #### def logDebug(msg: ⇒ String): Unit

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

27. #### def logError(msg: ⇒ String): Unit

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

29. #### def logInfo(msg: ⇒ String): Unit

    Attributes
      protected
    Definition Classes
      Logging

30. #### def logName: String

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

32. #### def logTrace(msg: ⇒ String): Unit

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

34. #### def logWarning(msg: ⇒ String): Unit

    Attributes
      protected
    Definition Classes
      Logging

35. #### def mismatches: MdTag

36. #### def mismatchesOption: Option[MdTag]

37. #### def name: String

38. #### final def ne(arg0: AnyRef): Boolean

    Definition Classes
      AnyRef

39. #### final def notify(): Unit

    Definition Classes
      AnyRef

40. #### final def notifyAll(): Unit

    Definition Classes
      AnyRef

41. #### def passedQualityChecks: Boolean

42. #### lazy val readGroup: String

43. #### val record: RichAlignmentRecord

44. #### lazy val residues: IndexedSeq[Residue]

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

    Definition Classes
      AnyRef

46. #### def toString(): String

    Definition Classes
      AnyRef → Any

47. #### final def wait(): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

49. #### final def wait(arg0: Long): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

### Inherited from Logging

### Inherited from AnyRef

### Inherited from Any

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