class MakeTwoSampleMixtureVcf extends FgBioTool
Creates a VCF by mixing two germline samples at a given proportion.
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- @ClpAnnotation()
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- MakeTwoSampleMixtureVcf
- FgBioTool
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- by any2stringadd
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Instance Constructors
- new MakeTwoSampleMixtureVcf(input: FgBioDef.PathToVcf, output: FgBioDef.PathToVcf, tumor: String, normal: String, tumorFraction: Double = 0.5, tumorOnly: Boolean = false, noCallIsHomRef: Boolean = true, intervals: Option[FgBioDef.PathToIntervals] = None)
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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 MakeTwoSampleMixtureVcf to any2stringadd[MakeTwoSampleMixtureVcf] performed by method any2stringadd in scala.Predef.
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- any2stringadd
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def
->[B](y: B): (MakeTwoSampleMixtureVcf, B)
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- This member is added by an implicit conversion from MakeTwoSampleMixtureVcf to ArrowAssoc[MakeTwoSampleMixtureVcf] 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: (MakeTwoSampleMixtureVcf) ⇒ Boolean, msg: ⇒ Any): MakeTwoSampleMixtureVcf
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- This member is added by an implicit conversion from MakeTwoSampleMixtureVcf to Ensuring[MakeTwoSampleMixtureVcf] performed by method Ensuring in scala.Predef.
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- Ensuring
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def
ensuring(cond: (MakeTwoSampleMixtureVcf) ⇒ Boolean): MakeTwoSampleMixtureVcf
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- This member is added by an implicit conversion from MakeTwoSampleMixtureVcf to Ensuring[MakeTwoSampleMixtureVcf] performed by method Ensuring in scala.Predef.
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- Ensuring
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def
ensuring(cond: Boolean, msg: ⇒ Any): MakeTwoSampleMixtureVcf
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- This member is added by an implicit conversion from MakeTwoSampleMixtureVcf to Ensuring[MakeTwoSampleMixtureVcf] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
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def
ensuring(cond: Boolean): MakeTwoSampleMixtureVcf
- Implicit
- This member is added by an implicit conversion from MakeTwoSampleMixtureVcf to Ensuring[MakeTwoSampleMixtureVcf] performed by method Ensuring in scala.Predef.
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- 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
- MakeTwoSampleMixtureVcf → 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.
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- 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.
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- 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
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- This member is added by an implicit conversion from MakeTwoSampleMixtureVcf to StringFormat[MakeTwoSampleMixtureVcf] 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[_]
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def
hashCode(): Int
- Definition Classes
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- val input: FgBioDef.PathToVcf
- val intervals: Option[FgBioDef.PathToIntervals]
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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.
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- FgBioTool
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final
def
isInstanceOf[T0]: Boolean
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def
iterator(in: VCFFileReader, intervals: Option[FgBioDef.PathToIntervals]): Iterator[VariantContext]
Generates an iterator over the whole file, or over the intervals if provided.
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final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
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- val noCallIsHomRef: Boolean
- val normal: String
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final
def
notify(): Unit
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final
def
notifyAll(): Unit
- Definition Classes
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- val output: FgBioDef.PathToVcf
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final
def
synchronized[T0](arg0: ⇒ T0): T0
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def
toString(): String
- Definition Classes
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- val tumor: String
- val tumorFraction: Double
- val tumorOnly: Boolean
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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.
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- 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): (MakeTwoSampleMixtureVcf, B)
- Implicit
- This member is added by an implicit conversion from MakeTwoSampleMixtureVcf to ArrowAssoc[MakeTwoSampleMixtureVcf] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc