class ClipOverlappingReads extends ClipBam
- Annotations
- @deprecated @ClpAnnotation()
- Deprecated
(Since version fgbio 0.2.0) Use ClipBam instead
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- ClipOverlappingReads
- ClipBam
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- FgBioTool
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- by StringFormat
- by Ensuring
- by ArrowAssoc
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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
clipOverlappingReads(f: SamRecord, r: SamRecord): Unit
Clips overlapping reads, where both ends of the read pair are mapped to the same chromosome, and in FR orientation.
Clips overlapping reads, where both ends of the read pair are mapped to the same chromosome, and in FR orientation.
- Attributes
- protected
- Definition Classes
- ClipBam
-
var
clipOverlappingReads: 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
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