case class DuplexConsensusRead(id: String, bases: Array[Byte], quals: Array[Byte], errors: Array[Short], abConsensus: VanillaConsensusRead, baConsensus: VanillaConsensusRead) extends SimpleRead with Product with Serializable
Stores information about a consensus read. Bases, arrays, and the two single strand consensus reads must all be the same length.
- bases
the base calls of the consensus read
- quals
the calculated phred-scaled quality scores of the bases
- errors
the total number of raw read errors vs. the final consensus sequence at each base
- abConsensus
the AB consensus read from which the duplex was constructed
- baConsensus
the AB consensus read from which the duplex was constructed
Linear Supertypes
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Implicitly
- by any2stringadd
- by StringFormat
- by Ensuring
- by ArrowAssoc
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Instance Constructors
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new
DuplexConsensusRead(id: String, bases: Array[Byte], quals: Array[Byte], errors: Array[Short], abConsensus: VanillaConsensusRead, baConsensus: VanillaConsensusRead)
- bases
the base calls of the consensus read
- quals
the calculated phred-scaled quality scores of the bases
- errors
the total number of raw read errors vs. the final consensus sequence at each base
- abConsensus
the AB consensus read from which the duplex was constructed
- baConsensus
the AB consensus read from which the duplex was constructed
Value Members
-
final
def
!=(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
final
def
##(): Int
- Definition Classes
- AnyRef → Any
-
def
+(other: String): String
- Implicit
- This member is added by an implicit conversion from DuplexConsensusRead to any2stringadd[DuplexConsensusRead] performed by method any2stringadd in scala.Predef.
- Definition Classes
- any2stringadd
-
def
->[B](y: B): (DuplexConsensusRead, B)
- Implicit
- This member is added by an implicit conversion from DuplexConsensusRead to ArrowAssoc[DuplexConsensusRead] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc
- Annotations
- @inline()
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final
def
==(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
- val abConsensus: VanillaConsensusRead
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final
def
asInstanceOf[T0]: T0
- Definition Classes
- Any
- val baConsensus: VanillaConsensusRead
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def
baseString: String
Returns the consensus read a String - mostly useful for testing.
Returns the consensus read a String - mostly useful for testing.
- Definition Classes
- SimpleRead
-
val
bases: Array[Byte]
- Definition Classes
- DuplexConsensusRead → SimpleRead
-
def
clone(): AnyRef
- Attributes
- protected[java.lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
def
ensuring(cond: (DuplexConsensusRead) ⇒ Boolean, msg: ⇒ Any): DuplexConsensusRead
- Implicit
- This member is added by an implicit conversion from DuplexConsensusRead to Ensuring[DuplexConsensusRead] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: (DuplexConsensusRead) ⇒ Boolean): DuplexConsensusRead
- Implicit
- This member is added by an implicit conversion from DuplexConsensusRead to Ensuring[DuplexConsensusRead] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean, msg: ⇒ Any): DuplexConsensusRead
- Implicit
- This member is added by an implicit conversion from DuplexConsensusRead to Ensuring[DuplexConsensusRead] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean): DuplexConsensusRead
- Implicit
- This member is added by an implicit conversion from DuplexConsensusRead to Ensuring[DuplexConsensusRead] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
- val errors: Array[Short]
-
def
finalize(): Unit
- Attributes
- protected[java.lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( classOf[java.lang.Throwable] )
-
def
formatted(fmtstr: String): String
- Implicit
- This member is added by an implicit conversion from DuplexConsensusRead to StringFormat[DuplexConsensusRead] performed by method StringFormat in scala.Predef.
- Definition Classes
- StringFormat
- Annotations
- @inline()
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final
def
getClass(): Class[_]
- Definition Classes
- AnyRef → Any
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val
id: String
- Definition Classes
- DuplexConsensusRead → SimpleRead
-
final
def
isInstanceOf[T0]: Boolean
- Definition Classes
- Any
-
def
length: Int
Gets the length of the consensus read.
Gets the length of the consensus read.
- Definition Classes
- SimpleRead
-
final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
final
def
notify(): Unit
- Definition Classes
- AnyRef
-
final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
-
val
quals: Array[Byte]
- Definition Classes
- DuplexConsensusRead → SimpleRead
-
final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
- AnyRef
-
final
def
wait(): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long, arg1: Int): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
def
→[B](y: B): (DuplexConsensusRead, B)
- Implicit
- This member is added by an implicit conversion from DuplexConsensusRead to ArrowAssoc[DuplexConsensusRead] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc