class ClipBam extends FgBioTool with LazyLogging
- Annotations
- @ClpAnnotation()
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- ClipBam
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- FgBioTool
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Instance Constructors
- new ClipBam(input: FgBioDef.PathToBam, output: FgBioDef.PathToBam, metrics: Option[FgBioDef.FilePath] = None, ref: FgBioDef.PathToFasta, softClip: Boolean = false, clippingMode: Option[ClippingMode] = None, autoClipAttributes: Boolean = false, upgradeClipping: Boolean = false, readOneFivePrime: Int = 0, readOneThreePrime: Int = 0, readTwoFivePrime: Int = 0, readTwoThreePrime: Int = 0, clipOverlappingReads: Boolean = false)
Value Members
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final
def
!=(arg0: Any): Boolean
- Definition Classes
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final
def
##(): Int
- Definition Classes
- AnyRef → Any
- def +(other: String): String
- def ->[B](y: B): (ClipBam, B)
-
final
def
==(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
final
def
asInstanceOf[T0]: T0
- Definition Classes
- Any
- val autoClipAttributes: Boolean
-
def
clipOverlappingReads(f: SamRecord, r: SamRecord): (Int, Int)
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
- val clipOverlappingReads: Boolean
- val clippingMode: Option[ClippingMode]
-
def
clone(): AnyRef
- Attributes
- protected[java.lang]
- Definition Classes
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- Annotations
- @native() @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
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final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
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def
equals(arg0: Any): Boolean
- Definition Classes
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- 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]
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- @throws( classOf[java.lang.Throwable] )
- def formatted(fmtstr: String): String
-
final
def
getClass(): Class[_]
- Definition Classes
- AnyRef → Any
- Annotations
- @native()
-
def
hashCode(): Int
- Definition Classes
- AnyRef → Any
- Annotations
- @native()
- 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
- val metrics: Option[FgBioDef.FilePath]
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final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
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final
def
notify(): Unit
- Definition Classes
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- Annotations
- @native()
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final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
- Annotations
- @native()
- val output: FgBioDef.PathToBam
- val readOneFivePrime: Int
- val readOneThreePrime: Int
- val readTwoFivePrime: Int
- val readTwoThreePrime: Int
- val ref: FgBioDef.PathToFasta
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final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
- AnyRef
-
def
toString(): String
- Definition Classes
- AnyRef → Any
- val upgradeClipping: Boolean
-
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
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- @throws( ... )
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final
def
wait(arg0: Long, arg1: Int): Unit
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- @throws( ... )
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final
def
wait(arg0: Long): Unit
- Definition Classes
- AnyRef
- Annotations
- @native() @throws( ... )
- def →[B](y: B): (ClipBam, B)