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: AnyRef): Boolean

    Definition Classes
    AnyRef
  2. final def !=(arg0: Any): Boolean

    Definition Classes
    Any
  3. final def ##(): Int

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

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

    Definition Classes
    Any
  6. def alignmentQuality: Option[QualityScore]

  7. final def asInstanceOf[T0]: T0

    Definition Classes
    Any
  8. def clone(): AnyRef

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  9. def ensureAligned: Boolean

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

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

    Definition Classes
    AnyRef → Any
  12. def finalize(): Unit

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

    Definition Classes
    AnyRef → Any
  14. def hashCode(): Int

    Definition Classes
    AnyRef → Any
  15. def isAligned: Boolean

  16. def isCanonicalRecord: Boolean

  17. def isDuplicate: Boolean

  18. def isFirstOfPair: Boolean

  19. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any
  20. def isNegativeRead: Boolean

  21. def isPaired: Boolean

  22. def isPrimaryAlignment: Boolean

  23. def isSecondOfPair: Boolean

  24. def isTraceEnabled(): Boolean

    Attributes
    protected
    Definition Classes
    Logging
  25. def log: Logger

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

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

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

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

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

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

    Attributes
    protected
    Definition Classes
    Logging
  32. def logName: String

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

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

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

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

    Attributes
    protected
    Definition Classes
    Logging
  37. def mismatches: MdTag

  38. def mismatchesOption: Option[MdTag]

  39. def name: String

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

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

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

    Definition Classes
    AnyRef
  43. def passedQualityChecks: Boolean

  44. lazy val readGroup: String

  45. val record: RichAlignmentRecord

  46. lazy val residues: IndexedSeq[Residue]

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

    Definition Classes
    AnyRef
  48. def toString(): String

    Definition Classes
    AnyRef → Any
  49. final def wait(): Unit

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

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

    Definition Classes
    AnyRef
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    @throws( ... )

Inherited from Logging

Inherited from AnyRef

Inherited from Any

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