class AnnotateBamWithUmis extends FgBioTool with LazyLogging
- Annotations
- @ClpAnnotation()
Linear Supertypes
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Inherited
- AnnotateBamWithUmis
- LazyLogging
- FgBioTool
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Implicitly
- by any2stringadd
- by StringFormat
- by Ensuring
- by ArrowAssoc
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Visibility
- Public
- All
Instance Constructors
- new AnnotateBamWithUmis(input: FgBioDef.PathToBam, fastq: FgBioDef.PathToFastq, output: FgBioDef.PathToBam, attribute: String = "RX", failFast: Boolean = false)
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 AnnotateBamWithUmis to any2stringadd[AnnotateBamWithUmis] performed by method any2stringadd in scala.Predef.
- Definition Classes
- any2stringadd
-
def
->[B](y: B): (AnnotateBamWithUmis, B)
- Implicit
- This member is added by an implicit conversion from AnnotateBamWithUmis to ArrowAssoc[AnnotateBamWithUmis] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc
- Annotations
- @inline()
-
final
def
==(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
final
def
asInstanceOf[T0]: T0
- Definition Classes
- Any
- val attribute: String
-
def
clone(): AnyRef
- Attributes
- protected[java.lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
def
ensuring(cond: (AnnotateBamWithUmis) ⇒ Boolean, msg: ⇒ Any): AnnotateBamWithUmis
- Implicit
- This member is added by an implicit conversion from AnnotateBamWithUmis to Ensuring[AnnotateBamWithUmis] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: (AnnotateBamWithUmis) ⇒ Boolean): AnnotateBamWithUmis
- Implicit
- This member is added by an implicit conversion from AnnotateBamWithUmis to Ensuring[AnnotateBamWithUmis] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean, msg: ⇒ Any): AnnotateBamWithUmis
- Implicit
- This member is added by an implicit conversion from AnnotateBamWithUmis to Ensuring[AnnotateBamWithUmis] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean): AnnotateBamWithUmis
- Implicit
- This member is added by an implicit conversion from AnnotateBamWithUmis to Ensuring[AnnotateBamWithUmis] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
def
equals(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
def
execute(): Unit
Main method that does the work of reading input files, matching up reads and writing the output file.
Main method that does the work of reading input files, matching up reads and writing the output file.
- Definition Classes
- AnnotateBamWithUmis → 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
- val failFast: Boolean
- val fastq: FgBioDef.PathToFastq
-
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 AnnotateBamWithUmis to StringFormat[AnnotateBamWithUmis] 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 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
- AnyRef
-
final
def
notify(): Unit
- Definition Classes
- AnyRef
-
final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
- val output: FgBioDef.PathToBam
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final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
- AnyRef
-
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
- AnyRef
- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long, arg1: Int): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
def
→[B](y: B): (AnnotateBamWithUmis, B)
- Implicit
- This member is added by an implicit conversion from AnnotateBamWithUmis to ArrowAssoc[AnnotateBamWithUmis] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc