class CallMolecularConsensusReads extends FgBioTool with LazyLogging
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- @ClpAnnotation()
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- CallMolecularConsensusReads
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Instance Constructors
- new CallMolecularConsensusReads(input: FgBioDef.PathToBam, output: FgBioDef.PathToBam, rejects: Option[FgBioDef.PathToBam] = None, tag: String = DefaultTag, readNamePrefix: Option[String] = None, readGroupId: String = "A", errorRatePreUmi: PhredScore = DefaultErrorRatePreUmi, errorRatePostUmi: PhredScore = DefaultErrorRatePostUmi, minInputBaseQuality: PhredScore = DefaultMinInputBaseQuality, minConsensusBaseQuality: PhredScore = 2.toByte, minReads: Int, maxReads: Option[Int] = None, outputPerBaseTags: Boolean = DefaultProducePerBaseTags, sortOrder: Option[SamOrder] = Some(SamOrder.Queryname), debug: Boolean = false)
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 CallMolecularConsensusReads to any2stringadd[CallMolecularConsensusReads] performed by method any2stringadd in scala.Predef.
- Definition Classes
- any2stringadd
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def
->[B](y: B): (CallMolecularConsensusReads, B)
- Implicit
- This member is added by an implicit conversion from CallMolecularConsensusReads to ArrowAssoc[CallMolecularConsensusReads] 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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- val debug: Boolean
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def
ensuring(cond: (CallMolecularConsensusReads) ⇒ Boolean, msg: ⇒ Any): CallMolecularConsensusReads
- Implicit
- This member is added by an implicit conversion from CallMolecularConsensusReads to Ensuring[CallMolecularConsensusReads] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: (CallMolecularConsensusReads) ⇒ Boolean): CallMolecularConsensusReads
- Implicit
- This member is added by an implicit conversion from CallMolecularConsensusReads to Ensuring[CallMolecularConsensusReads] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean, msg: ⇒ Any): CallMolecularConsensusReads
- Implicit
- This member is added by an implicit conversion from CallMolecularConsensusReads to Ensuring[CallMolecularConsensusReads] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean): CallMolecularConsensusReads
- Implicit
- This member is added by an implicit conversion from CallMolecularConsensusReads to Ensuring[CallMolecularConsensusReads] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
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final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
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def
equals(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
- val errorRatePostUmi: PhredScore
- val errorRatePreUmi: PhredScore
-
def
execute(): Unit
Main method that does the work of reading input files, creating the consensus reads, and writing the output file.
Main method that does the work of reading input files, creating the consensus reads, and writing the output file.
- Definition Classes
- CallMolecularConsensusReads → 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
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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 CallMolecularConsensusReads to StringFormat[CallMolecularConsensusReads] performed by method StringFormat in scala.Predef.
- Definition Classes
- StringFormat
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- @inline()
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final
def
getClass(): Class[_]
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def
hashCode(): Int
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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 maxReads: Option[Int]
- val minConsensusBaseQuality: PhredScore
- val minInputBaseQuality: PhredScore
- val minReads: Int
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final
def
ne(arg0: AnyRef): Boolean
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final
def
notify(): Unit
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final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
- val output: FgBioDef.PathToBam
- val outputPerBaseTags: Boolean
- val readGroupId: String
- val readNamePrefix: Option[String]
- val rejects: Option[FgBioDef.PathToBam]
- val sortOrder: Option[SamOrder]
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final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
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- val tag: String
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def
toString(): String
- Definition Classes
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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): (CallMolecularConsensusReads, B)
- Implicit
- This member is added by an implicit conversion from CallMolecularConsensusReads to ArrowAssoc[CallMolecularConsensusReads] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc