org.bdgenomics.adam.rdd.read

IncorrectMDTagException

case class IncorrectMDTagException(read: AlignmentRecord, mdTag: String) extends Exception with Product with Serializable

A class describing an exception where a read's MD tag was recomputed and did not match the MD tag originally attached to the read.

read

The read whose MD tag was recomputed, with original MD tag.

mdTag

The recomputed MD tag.

Linear Supertypes
Serializable, Product, Equals, Exception, Throwable, Serializable, AnyRef, Any
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Inherited
  1. IncorrectMDTagException
  2. Serializable
  3. Product
  4. Equals
  5. Exception
  6. Throwable
  7. Serializable
  8. AnyRef
  9. Any
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Instance Constructors

  1. new IncorrectMDTagException(read: AlignmentRecord, mdTag: String)

    read

    The read whose MD tag was recomputed, with original MD tag.

    mdTag

    The recomputed MD tag.

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. final def addSuppressed(arg0: Throwable): Unit

    Definition Classes
    Throwable

  7. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  8. def clone(): AnyRef

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

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

    Definition Classes
    AnyRef

  10. def fillInStackTrace(): Throwable

    Definition Classes
    Throwable

  11. def finalize(): Unit

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

  12. def getCause(): Throwable

    Definition Classes
    Throwable

  13. final def getClass(): Class[_]

    Definition Classes
    AnyRef → Any

  14. def getLocalizedMessage(): String

    Definition Classes
    Throwable

  15. def getMessage(): String

    Definition Classes
    IncorrectMDTagException → Throwable

  16. def getStackTrace(): Array[StackTraceElement]

    Definition Classes
    Throwable

  17. final def getSuppressed(): Array[Throwable]

    Definition Classes
    Throwable

  18. def initCause(arg0: Throwable): Throwable

    Definition Classes
    Throwable

  19. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  20. val mdTag: String

    The recomputed MD tag.

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

    Definition Classes
    AnyRef

  22. final def notify(): Unit

    Definition Classes
    AnyRef

  23. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  24. def printStackTrace(arg0: PrintWriter): Unit

    Definition Classes
    Throwable

  25. def printStackTrace(arg0: PrintStream): Unit

    Definition Classes
    Throwable

  26. def printStackTrace(): Unit

    Definition Classes
    Throwable

  27. val read: AlignmentRecord

    The read whose MD tag was recomputed, with original MD tag.

  28. def setStackTrace(arg0: Array[StackTraceElement]): Unit

    Definition Classes
    Throwable

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

    Definition Classes
    AnyRef

  30. def toString(): String

    Definition Classes
    Throwable → AnyRef → Any

  31. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from Exception

Inherited from Throwable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

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