class ClipBam extends FgBioTool with LazyLogging
- Annotations
- @ClpAnnotation()
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Inherited
- ClipBam
- LazyLogging
- FgBioTool
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Implicitly
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Visibility
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Instance Constructors
- new ClipBam(input: FgBioDef.PathToBam, output: FgBioDef.PathToBam, ref: FgBioDef.PathToFasta, softClip: Boolean = false, autoClipAttributes: Boolean = false, readOneFivePrime: Int = 0, readOneThreePrime: Int = 0, readTwoFivePrime: Int = 0, readTwoThreePrime: Int = 0, overlappingReads: Boolean = false)
Value Members
-
final
def
!=(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
final
def
##(): Int
- Definition Classes
- AnyRef → Any
- def +(other: String): String
- def ->[B](y: B): (ClipBam, B)
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final
def
==(arg0: Any): Boolean
- Definition Classes
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-
final
def
asInstanceOf[T0]: T0
- Definition Classes
- Any
- val autoClipAttributes: Boolean
-
def
clone(): AnyRef
- Attributes
- protected[java.lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
- def ensuring(cond: (ClipBam) ⇒ Boolean, msg: ⇒ Any): ClipBam
- def ensuring(cond: (ClipBam) ⇒ Boolean): ClipBam
- def ensuring(cond: Boolean, msg: ⇒ Any): ClipBam
- def ensuring(cond: Boolean): ClipBam
-
final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
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-
def
equals(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
- def execute(): Unit
-
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
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- Annotations
- @throws( classOf[java.lang.Throwable] )
- def formatted(fmtstr: String): String
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final
def
getClass(): Class[_]
- Definition Classes
- AnyRef → Any
-
def
hashCode(): Int
- Definition Classes
- AnyRef → Any
- 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
-
final
def
isInstanceOf[T0]: Boolean
- Definition Classes
- Any
-
lazy val
logger: Logger
- Attributes
- protected
- Definition Classes
- LazyLogging
-
final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
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final
def
notify(): Unit
- Definition Classes
- AnyRef
-
final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
- val output: FgBioDef.PathToBam
- val overlappingReads: Boolean
- val readOneFivePrime: Int
- val readOneThreePrime: Int
- val readTwoFivePrime: Int
- val readTwoThreePrime: Int
- val ref: FgBioDef.PathToFasta
- val softClip: Boolean
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final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
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-
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
-
final
def
wait(): Unit
- Definition Classes
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- Annotations
- @throws( ... )
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final
def
wait(arg0: Long, arg1: Int): Unit
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- @throws( ... )
-
final
def
wait(arg0: Long): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
- def →[B](y: B): (ClipBam, B)