Trait

com.fulcrumgenomics.bam

PileupEntry

Related Doc: package bam

Permalink

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
  1. Alphabetic
  2. By Inheritance
Inherited
  1. PileupEntry
  2. AnyRef
  3. Any
Implicitly
  1. by any2stringadd
  2. by StringFormat
  3. by Ensuring
  4. by ArrowAssoc
  1. Hide All
  2. Show All
Visibility
  1. Public
  2. All

Abstract Value Members

  1. abstract val offset: Int

    Permalink

    The zero-based offset within the com.fulcrumgenomics.bam.api.SamRecord that is represented.

    The zero-based offset within the com.fulcrumgenomics.bam.api.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

    Permalink

    The SamRecord that the pileup entry represents.

Concrete Value Members

  1. final def !=(arg0: Any): Boolean

    Permalink
    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

    Permalink
    Definition Classes
    AnyRef → Any

  3. def +(other: String): String

    Permalink
    Implicit information
    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)

    Permalink
    Implicit information
    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

    Permalink
    Definition Classes
    AnyRef → Any

  6. final def asInstanceOf[T0]: T0

    Permalink
    Definition Classes
    Any

  7. def clone(): AnyRef

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

  8. def ensuring(cond: (PileupEntry) ⇒ Boolean, msg: ⇒ Any): PileupEntry

    Permalink
    Implicit information
    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

    Permalink
    Implicit information
    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

    Permalink
    Implicit information
    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

    Permalink
    Implicit information
    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

    Permalink
    Definition Classes
    AnyRef

  13. def equals(arg0: Any): Boolean

    Permalink
    Definition Classes
    AnyRef → Any

  14. def finalize(): Unit

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

  15. def formatted(fmtstr: String): String

    Permalink
    Implicit information
    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[_]

    Permalink
    Definition Classes
    AnyRef → Any

  17. def hashCode(): Int

    Permalink
    Definition Classes
    AnyRef → Any

  18. final def isInstanceOf[T0]: Boolean

    Permalink
    Definition Classes
    Any

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

    Permalink
    Definition Classes
    AnyRef

  20. final def notify(): Unit

    Permalink
    Definition Classes
    AnyRef

  21. final def notifyAll(): Unit

    Permalink
    Definition Classes
    AnyRef

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

    Permalink
    Definition Classes
    AnyRef

  23. def toString(): String

    Permalink
    Definition Classes
    AnyRef → Any

  24. final def wait(): Unit

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  27. def →[B](y: B): (PileupEntry, B)

    Permalink
    Implicit information
    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]

Ungrouped