Value Members
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final
def
!=(arg0: AnyRef): Boolean
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final
def
!=(arg0: Any): Boolean
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final
def
##(): Int
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final
def
==(arg0: AnyRef): Boolean
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final
def
==(arg0: Any): Boolean
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final
def
asInstanceOf[T0]: T0
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def
clone(): AnyRef
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def
computeVariants(args: Arguments, sc: SparkContext): (RDD[CalledAllele], SequenceDictionary, Vector[String])
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def
debug(msg: ⇒ Any, t: ⇒ Throwable): Unit
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def
debug(msg: ⇒ Any): Unit
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val
description: String
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def
discoverGermlineVariants(partitionedReads: PartitionedReads, sampleName: SampleName, kmerSize: Int, assemblyWindowRange: Int, minOccurrence: Int, minAreaVaf: Float, reference: ReferenceBroadcast, minMeanKmerQuality: Int, minAltReads: Int = 2, minPhredScaledLikelihood: Int = 0, shortcutAssembly: Boolean = false): RDD[CalledAllele]
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final
def
eq(arg0: AnyRef): Boolean
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def
equals(arg0: Any): Boolean
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def
error(msg: ⇒ Any, t: ⇒ Throwable): Unit
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def
error(msg: ⇒ Any): Unit
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def
finalize(): Unit
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final
def
getClass(): Class[_]
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def
hashCode(): Int
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def
info(msg: ⇒ Any, t: ⇒ Throwable): Unit
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def
info(msg: ⇒ Any): Unit
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def
isDebugEnabled: Boolean
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def
isErrorEnabled: Boolean
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def
isInfoEnabled: Boolean
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final
def
isInstanceOf[T0]: Boolean
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def
isTraceEnabled: Boolean
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def
isWarnEnabled: Boolean
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def
logger: Logger
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def
loggerName: String
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val
name: String
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final
def
ne(arg0: AnyRef): Boolean
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final
def
notify(): Unit
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final
def
notifyAll(): Unit
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def
run(args: Arguments, sc: SparkContext): Unit
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def
run(args: Arguments): Unit
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def
run(args: String*): Unit
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def
run(args: Array[String]): Unit
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def
setDefaultConf(key: String, value: String): Unit
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final
def
synchronized[T0](arg0: ⇒ T0): T0
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def
toString(): String
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def
trace(msg: ⇒ Any, t: ⇒ Throwable): Unit
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def
trace(msg: ⇒ Any): Unit
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final
def
wait(): Unit
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final
def
wait(arg0: Long, arg1: Int): Unit
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final
def
wait(arg0: Long): Unit
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def
warn(msg: ⇒ Any, t: ⇒ Throwable): Unit
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def
warn(msg: ⇒ Any): Unit
Inherited from Logging
Inherited from Serializable
Inherited from Serializable
Inherited from AnyRef
Inherited from Any