class FilterConsensusReads extends FgBioTool with LazyLogging
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- @ClpAnnotation()
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- FilterConsensusReads
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Instance Constructors
- new FilterConsensusReads(input: FgBioDef.PathToBam, output: FgBioDef.PathToBam, ref: FgBioDef.PathToFasta, reversePerBaseTags: Boolean = false, minReads: Seq[Int], maxReadErrorRate: Seq[Double] = Seq(0.025), maxBaseErrorRate: Seq[Double] = Seq(0.1), minBaseQuality: PhredScore, maxNoCallFraction: Double = 0.2, minMeanBaseQuality: Option[PhredScore] = None, requireSingleStrandAgreement: Boolean = false)
Type Members
- case class FilterResult (keepRead: Boolean, maskedBases: Int) extends Product with Serializable
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 FilterConsensusReads to any2stringadd[FilterConsensusReads] performed by method any2stringadd in scala.Predef.
- Definition Classes
- any2stringadd
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def
->[B](y: B): (FilterConsensusReads, B)
- Implicit
- This member is added by an implicit conversion from FilterConsensusReads to ArrowAssoc[FilterConsensusReads] performed by method ArrowAssoc in scala.Predef.
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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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def
ensuring(cond: (FilterConsensusReads) ⇒ Boolean, msg: ⇒ Any): FilterConsensusReads
- Implicit
- This member is added by an implicit conversion from FilterConsensusReads to Ensuring[FilterConsensusReads] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: (FilterConsensusReads) ⇒ Boolean): FilterConsensusReads
- Implicit
- This member is added by an implicit conversion from FilterConsensusReads to Ensuring[FilterConsensusReads] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean, msg: ⇒ Any): FilterConsensusReads
- Implicit
- This member is added by an implicit conversion from FilterConsensusReads to Ensuring[FilterConsensusReads] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean): FilterConsensusReads
- Implicit
- This member is added by an implicit conversion from FilterConsensusReads to Ensuring[FilterConsensusReads] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
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final
def
eq(arg0: AnyRef): Boolean
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def
equals(arg0: Any): Boolean
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def
execute(): Unit
- Definition Classes
- FilterConsensusReads → FgBioTool
-
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
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def
fail(exit: Int): Nothing
Fail with just an exit code.
Fail with just an exit code.
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- 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 FilterConsensusReads to StringFormat[FilterConsensusReads] performed by method StringFormat in scala.Predef.
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- StringFormat
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- @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
-
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 maxBaseErrorRate: Seq[Double]
- val maxNoCallFraction: Double
- val maxReadErrorRate: Seq[Double]
- val minBaseQuality: PhredScore
- val minMeanBaseQuality: Option[PhredScore]
- val minReads: Seq[Int]
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final
def
ne(arg0: AnyRef): Boolean
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final
def
notify(): Unit
- Definition Classes
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final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
- val output: FgBioDef.PathToBam
- val ref: FgBioDef.PathToFasta
- val requireSingleStrandAgreement: Boolean
- val reversePerBaseTags: Boolean
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final
def
synchronized[T0](arg0: ⇒ T0): T0
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def
toString(): String
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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): (FilterConsensusReads, B)
- Implicit
- This member is added by an implicit conversion from FilterConsensusReads to ArrowAssoc[FilterConsensusReads] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc