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.
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Abstract Value Members
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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.
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abstract
val
rec: SamRecord
The SamRecord that the pileup entry represents.
Concrete Value Members
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final
def
!=(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
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final
def
##(): Int
- Definition Classes
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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
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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
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- @inline()
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final
def
==(arg0: Any): Boolean
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final
def
asInstanceOf[T0]: T0
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def
clone(): AnyRef
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- protected[java.lang]
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- AnyRef
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- @throws( ... )
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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
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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
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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
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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
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final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
def
equals(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
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def
finalize(): Unit
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- protected[java.lang]
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- @throws( classOf[java.lang.Throwable] )
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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()
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final
def
getClass(): Class[_]
- Definition Classes
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def
hashCode(): Int
- Definition Classes
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final
def
isInstanceOf[T0]: Boolean
- Definition Classes
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final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
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final
def
notify(): Unit
- Definition Classes
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final
def
notifyAll(): Unit
- Definition Classes
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final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
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def
toString(): String
- Definition Classes
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final
def
wait(): Unit
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- @throws( ... )
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final
def
wait(arg0: Long, arg1: Int): Unit
- Definition Classes
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- @throws( ... )
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final
def
wait(arg0: Long): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
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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