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
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    @throws( ... )

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

    Definition Classes
    AnyRef
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    @throws( ... )

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

    Definition Classes
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    @throws( ... )

Inherited from Logging

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