class ClipOverlappingReads extends ClipBam
- Annotations
- @deprecated @ClpAnnotation()
- Deprecated
(Since version fgbio 0.2.0) Use ClipBam instead
Linear Supertypes
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Inherited
- ClipOverlappingReads
- ClipBam
- LazyLogging
- FgBioTool
- AnyRef
- Any
Implicitly
- by any2stringadd
- by StringFormat
- by Ensuring
- by ArrowAssoc
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Visibility
- Public
- All
Instance Constructors
- new ClipOverlappingReads(input: FgBioDef.PathToBam, output: FgBioDef.PathToBam, ref: FgBioDef.PathToFasta, softClip: Boolean = false, autoClipAttributes: 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 ClipOverlappingReads to any2stringadd[ClipOverlappingReads] performed by method any2stringadd in scala.Predef.
- Definition Classes
- any2stringadd
-
def
->[B](y: B): (ClipOverlappingReads, B)
- Implicit
- This member is added by an implicit conversion from ClipOverlappingReads to ArrowAssoc[ClipOverlappingReads] 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
autoClipAttributes: Boolean
- Definition Classes
- ClipBam
-
def
clone(): AnyRef
- Attributes
- protected[java.lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
def
ensuring(cond: (ClipOverlappingReads) ⇒ Boolean, msg: ⇒ Any): ClipOverlappingReads
- Implicit
- This member is added by an implicit conversion from ClipOverlappingReads to Ensuring[ClipOverlappingReads] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: (ClipOverlappingReads) ⇒ Boolean): ClipOverlappingReads
- Implicit
- This member is added by an implicit conversion from ClipOverlappingReads to Ensuring[ClipOverlappingReads] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean, msg: ⇒ Any): ClipOverlappingReads
- Implicit
- This member is added by an implicit conversion from ClipOverlappingReads to Ensuring[ClipOverlappingReads] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean): ClipOverlappingReads
- Implicit
- This member is added by an implicit conversion from ClipOverlappingReads to Ensuring[ClipOverlappingReads] 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
-
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 ClipOverlappingReads to StringFormat[ClipOverlappingReads] 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
- Definition Classes
- ClipBam
-
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
- Definition Classes
- ClipBam
-
val
overlappingReads: Boolean
- Definition Classes
- ClipBam
-
val
readOneFivePrime: Int
- Definition Classes
- ClipBam
-
val
readOneThreePrime: Int
- Definition Classes
- ClipBam
-
val
readTwoFivePrime: Int
- Definition Classes
- ClipBam
-
val
readTwoThreePrime: Int
- Definition Classes
- ClipBam
-
val
ref: FgBioDef.PathToFasta
- Definition Classes
- ClipBam
-
val
softClip: Boolean
- Definition Classes
- ClipBam
-
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): (ClipOverlappingReads, B)
- Implicit
- This member is added by an implicit conversion from ClipOverlappingReads to ArrowAssoc[ClipOverlappingReads] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc