sealed trait PileupEntry extends AnyRef

Base trait for pileup entries that exposes the com.fulcrumgenomics.bam.api.SamRecord and the 0-based offset into the record's bases and qualities that is relevant to the pileup.

Linear Supertypes
AnyRef, Any
Known Subclasses
BaseEntry, DeletionEntry, InsertionEntry
Ordering
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Inherited
  1. PileupEntry
  2. AnyRef
  3. Any
Implicitly
  1. by any2stringadd
  2. by StringFormat
  3. by Ensuring
  4. by ArrowAssoc
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Visibility
  1. Public
  2. All

Abstract Value Members

  1. abstract val offset: Int

    The zero-based offset within the SamRecord that is represented.

    The zero-based offset within the SamRecord that is represented. For matches and mismatches this is the offset of the base in question. For deletions it is the base prior to the deleted sequence. For insertions it is the first inserted base in the read.

  2. abstract val rec: SamRecord

    The SamRecord that the pileup entry represents.

Concrete 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 PileupEntry to any2stringadd[PileupEntry] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ->[B](y: B): (PileupEntry, B)
    Implicit
    This member is added by an implicit conversion from PileupEntry to ArrowAssoc[PileupEntry] 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. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  8. def ensuring(cond: (PileupEntry) ⇒ Boolean, msg: ⇒ Any): PileupEntry
    Implicit
    This member is added by an implicit conversion from PileupEntry to Ensuring[PileupEntry] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  9. def ensuring(cond: (PileupEntry) ⇒ Boolean): PileupEntry
    Implicit
    This member is added by an implicit conversion from PileupEntry to Ensuring[PileupEntry] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  10. def ensuring(cond: Boolean, msg: ⇒ Any): PileupEntry
    Implicit
    This member is added by an implicit conversion from PileupEntry to Ensuring[PileupEntry] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  11. def ensuring(cond: Boolean): PileupEntry
    Implicit
    This member is added by an implicit conversion from PileupEntry to Ensuring[PileupEntry] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  12. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  13. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  14. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  15. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from PileupEntry to StringFormat[PileupEntry] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  16. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  17. def hashCode(): Int
    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. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  23. def toString(): String
    Definition Classes
    AnyRef → Any
  24. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  25. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  26. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  27. def →[B](y: B): (PileupEntry, B)
    Implicit
    This member is added by an implicit conversion from PileupEntry to ArrowAssoc[PileupEntry] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Inherited from AnyRef

Inherited from Any

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

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

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

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

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