case class BaseEntry(rec: SAMRecord, offset: Int) extends PileupEntry with Product with Serializable

Pileup entry representing a match or mismatch.

Linear Supertypes
Serializable, Serializable, Product, Equals, PileupEntry, AnyRef, Any
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Inherited
  1. BaseEntry
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. PileupEntry
  7. AnyRef
  8. Any
Implicitly
  1. by any2stringadd
  2. by StringFormat
  3. by Ensuring
  4. by ArrowAssoc
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new BaseEntry(rec: SAMRecord, offset: Int)

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. def +(other: String): String
    Implicit
    This member is added by an implicit conversion from BaseEntry to any2stringadd[BaseEntry] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ->[B](y: B): (BaseEntry, B)
    Implicit
    This member is added by an implicit conversion from BaseEntry to ArrowAssoc[BaseEntry] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()
  5. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  6. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  7. val base: Byte
  8. def baseInReadOrientation: Byte

    Returns the base as it was read on the sequencer.

  9. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  10. def ensuring(cond: (BaseEntry) ⇒ Boolean, msg: ⇒ Any): BaseEntry
    Implicit
    This member is added by an implicit conversion from BaseEntry to Ensuring[BaseEntry] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  11. def ensuring(cond: (BaseEntry) ⇒ Boolean): BaseEntry
    Implicit
    This member is added by an implicit conversion from BaseEntry to Ensuring[BaseEntry] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  12. def ensuring(cond: Boolean, msg: ⇒ Any): BaseEntry
    Implicit
    This member is added by an implicit conversion from BaseEntry to Ensuring[BaseEntry] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  13. def ensuring(cond: Boolean): BaseEntry
    Implicit
    This member is added by an implicit conversion from BaseEntry to Ensuring[BaseEntry] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  14. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  15. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  16. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from BaseEntry to StringFormat[BaseEntry] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  17. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  18. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  19. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  20. final def notify(): Unit
    Definition Classes
    AnyRef
  21. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  22. val offset: Int
    Definition Classes
    BaseEntry → PileupEntry
  23. def positionInRead: Int

    Returns the 1-based position within the read in the read's current orientation.

  24. def positionInReadInReadOrder: Int

    Returns the 1-based position within the read in the order the read was sequenced.

    Returns the 1-based position within the read in the order the read was sequenced. This can be thought of as the offset from the 5' end plus one.

  25. val qual: Byte
  26. val rec: SAMRecord
    Definition Classes
    BaseEntry → PileupEntry
  27. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  28. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  29. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  30. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  31. def →[B](y: B): (BaseEntry, B)
    Implicit
    This member is added by an implicit conversion from BaseEntry to ArrowAssoc[BaseEntry] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from PileupEntry

Inherited from AnyRef

Inherited from Any

Inherited by implicit conversion any2stringadd from BaseEntry to any2stringadd[BaseEntry]

Inherited by implicit conversion StringFormat from BaseEntry to StringFormat[BaseEntry]

Inherited by implicit conversion Ensuring from BaseEntry to Ensuring[BaseEntry]

Inherited by implicit conversion ArrowAssoc from BaseEntry to ArrowAssoc[BaseEntry]

Ungrouped