class PickIlluminaIndices extends FgBioTool
Program for picking sets of indices of arbitrary length that meet certain constraints and attempt to maximize the edit distance between all members of the set picked.
- Annotations
- @ClpAnnotation()
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Inherited
- PickIlluminaIndices
- FgBioTool
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- Any
Implicitly
- by any2stringadd
- by StringFormat
- by Ensuring
- by ArrowAssoc
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Visibility
- Public
- All
Instance Constructors
- new PickIlluminaIndices(length: Int = 8, indices: Int, editDistance: Int = 3, output: FgBioDef.FilePath, allowReverses: Boolean = false, allowReverseComplements: Boolean = false, allowPalindromes: Boolean = false, maxHomopolymer: Int = 2, minGc: Double = 0, maxGc: Double = 0.7, threads: Int = 4, viennaRnaDir: Option[FgBioDef.DirPath] = None, minDeltaG: Double = 10, adapters: Seq[String] = IlluminaAdapters.DualIndexed.both, avoidSequence: Seq[String] = ...)
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 PickIlluminaIndices to any2stringadd[PickIlluminaIndices] performed by method any2stringadd in scala.Predef.
- Definition Classes
- any2stringadd
-
def
->[B](y: B): (PickIlluminaIndices, B)
- Implicit
- This member is added by an implicit conversion from PickIlluminaIndices to ArrowAssoc[PickIlluminaIndices] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc
- Annotations
- @inline()
-
final
def
==(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
- val adapters: Seq[String]
- val allowPalindromes: Boolean
- val allowReverseComplements: Boolean
- val allowReverses: Boolean
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final
def
asInstanceOf[T0]: T0
- Definition Classes
- Any
- val avoidSequence: Seq[String]
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def
clone(): AnyRef
- Attributes
- protected[java.lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
- val editDistance: Int
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def
ensuring(cond: (PickIlluminaIndices) ⇒ Boolean, msg: ⇒ Any): PickIlluminaIndices
- Implicit
- This member is added by an implicit conversion from PickIlluminaIndices to Ensuring[PickIlluminaIndices] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: (PickIlluminaIndices) ⇒ Boolean): PickIlluminaIndices
- Implicit
- This member is added by an implicit conversion from PickIlluminaIndices to Ensuring[PickIlluminaIndices] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean, msg: ⇒ Any): PickIlluminaIndices
- Implicit
- This member is added by an implicit conversion from PickIlluminaIndices to Ensuring[PickIlluminaIndices] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean): PickIlluminaIndices
- Implicit
- This member is added by an implicit conversion from PickIlluminaIndices to Ensuring[PickIlluminaIndices] 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
-
def
execute(): Unit
- Definition Classes
- PickIlluminaIndices → 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
-
def
fail(exit: Int): Nothing
Fail with just an exit code.
Fail with just an exit code.
- Definition Classes
- FgBioTool
-
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 PickIlluminaIndices to StringFormat[PickIlluminaIndices] performed by method StringFormat in scala.Predef.
- Definition Classes
- StringFormat
- Annotations
- @inline()
-
final
def
getClass(): Class[_]
- Definition Classes
- AnyRef → Any
-
def
hashCode(): Int
- Definition Classes
- AnyRef → Any
- val indices: Int
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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
-
final
def
isInstanceOf[T0]: Boolean
- Definition Classes
- Any
- val length: Int
- val maxGc: Double
- val maxHomopolymer: Int
- val minDeltaG: Double
- val minGc: Double
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final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
final
def
notify(): Unit
- Definition Classes
- AnyRef
-
final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
- val output: FgBioDef.FilePath
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final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
- AnyRef
- val threads: Int
-
def
toString(): String
- Definition Classes
- AnyRef → Any
-
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
- val viennaRnaDir: Option[FgBioDef.DirPath]
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final
def
wait(): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long, arg1: Int): Unit
- Definition Classes
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- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
def
→[B](y: B): (PickIlluminaIndices, B)
- Implicit
- This member is added by an implicit conversion from PickIlluminaIndices to ArrowAssoc[PickIlluminaIndices] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc