class CallDuplexConsensusReads extends FgBioTool with LazyLogging
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- @ClpAnnotation()
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- CallDuplexConsensusReads
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- FgBioTool
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Implicitly
- by any2stringadd
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Instance Constructors
- new CallDuplexConsensusReads(input: FgBioDef.PathToBam, output: FgBioDef.PathToBam, readNamePrefix: Option[String] = None, readGroupId: String = "A", errorRatePreUmi: PhredScore = DefaultErrorRatePreUmi, errorRatePostUmi: PhredScore = DefaultErrorRatePostUmi, minInputBaseQuality: PhredScore = DefaultMinInputBaseQuality, trim: Boolean = false, sortOrder: Option[SamOrder] = Some(SamOrder.Queryname), minReads: Seq[Int] = Seq(1))
Value Members
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final
def
!=(arg0: Any): Boolean
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final
def
##(): Int
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def
+(other: String): String
- Implicit
- This member is added by an implicit conversion from CallDuplexConsensusReads to any2stringadd[CallDuplexConsensusReads] performed by method any2stringadd in scala.Predef.
- Definition Classes
- any2stringadd
-
def
->[B](y: B): (CallDuplexConsensusReads, B)
- Implicit
- This member is added by an implicit conversion from CallDuplexConsensusReads to ArrowAssoc[CallDuplexConsensusReads] performed by method ArrowAssoc in scala.Predef.
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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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- @throws( ... )
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def
ensuring(cond: (CallDuplexConsensusReads) ⇒ Boolean, msg: ⇒ Any): CallDuplexConsensusReads
- Implicit
- This member is added by an implicit conversion from CallDuplexConsensusReads to Ensuring[CallDuplexConsensusReads] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: (CallDuplexConsensusReads) ⇒ Boolean): CallDuplexConsensusReads
- Implicit
- This member is added by an implicit conversion from CallDuplexConsensusReads to Ensuring[CallDuplexConsensusReads] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean, msg: ⇒ Any): CallDuplexConsensusReads
- Implicit
- This member is added by an implicit conversion from CallDuplexConsensusReads to Ensuring[CallDuplexConsensusReads] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean): CallDuplexConsensusReads
- Implicit
- This member is added by an implicit conversion from CallDuplexConsensusReads to Ensuring[CallDuplexConsensusReads] 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
- val errorRatePostUmi: PhredScore
- val errorRatePreUmi: PhredScore
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def
execute(): Unit
- Definition Classes
- CallDuplexConsensusReads → FgBioTool
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def
fail(exit: Int, message: String): Nothing
Fail with a specific error code and message.
Fail with a specific error code and message.
- Definition Classes
- FgBioTool
-
def
fail(message: String): Nothing
Fail with the default exit code and a message.
Fail with the default exit code and a message.
- Definition Classes
- FgBioTool
-
def
fail(exit: Int): Nothing
Fail with just an exit code.
Fail with just an exit code.
- Definition Classes
- FgBioTool
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def
finalize(): Unit
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def
formatted(fmtstr: String): String
- Implicit
- This member is added by an implicit conversion from CallDuplexConsensusReads to StringFormat[CallDuplexConsensusReads] 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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- val input: FgBioDef.PathToBam
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def
invalid(message: String): Nothing
Generates a new validation exception with the given message.
Generates a new validation exception with the given message.
- Definition Classes
- FgBioTool
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final
def
isInstanceOf[T0]: Boolean
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lazy val
logger: Logger
- Attributes
- protected
- Definition Classes
- LazyLogging
- val minInputBaseQuality: PhredScore
- val minReads: Seq[Int]
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final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
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final
def
notify(): Unit
- Definition Classes
- AnyRef
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final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
- val output: FgBioDef.PathToBam
- val readGroupId: String
- val readNamePrefix: Option[String]
- val sortOrder: Option[SamOrder]
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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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- val trim: Boolean
-
def
validate(test: Boolean, message: ⇒ String): Unit
Generates a validation exception if the test value is false.
Generates a validation exception if the test value is false.
- Definition Classes
- FgBioTool
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final
def
wait(): Unit
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final
def
wait(arg0: Long, arg1: Int): Unit
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final
def
wait(arg0: Long): Unit
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def
→[B](y: B): (CallDuplexConsensusReads, B)
- Implicit
- This member is added by an implicit conversion from CallDuplexConsensusReads to ArrowAssoc[CallDuplexConsensusReads] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc